--- /dev/null
- -D Git_EXECUTABLE="${Git_EXECUTABLE}"
- -D Git_VERSION="${Git_VERSION}"
+set(LIBGROMACS_SOURCES)
+
+add_subdirectory(legacyheaders)
+add_subdirectory(gmxlib)
+add_subdirectory(mdlib)
+add_subdirectory(gmxpreprocess)
+add_subdirectory(analysisdata)
+add_subdirectory(fatalerror)
+add_subdirectory(options)
+add_subdirectory(selection)
+add_subdirectory(trajectoryanalysis)
+add_subdirectory(utility)
+
+file(GLOB LIBGROMACS_HEADERS *.h)
+install(FILES ${LIBGROMACS_HEADERS} DESTINATION ${INCL_INSTALL_DIR}/gromacs
+ COMPONENT development)
+
+# only fiddle with assembly kernels if we're not doing OpenMM build
+if(NOT GMX_OPENMM)
+if(GMX_ASM_USEASM-NASM)
+ enable_language(ASM-NASM)
+ # if NASM is used, we need a special build command for windows...
+ FOREACH(SRC ${GMX_SSEKERNEL_ASM_SRC})
+ GET_FILENAME_COMPONENT(FILE_BASE ${SRC} NAME_WE)
+ SET(OBJ ${CMAKE_CURRENT_BINARY_DIR}/${FILE_BASE}${CMAKE_C_OUTPUT_EXTENSION})
+
+ ADD_CUSTOM_COMMAND(OUTPUT ${OBJ}
+ MAIN_DEPENDENCY ${SRC}
+ COMMAND ${CMAKE_ASM-NASM_COMPILER} -f ${CMAKE_ASM-NASM_OBJECT_FORMAT} -o ${OBJ} ${SRC})
+
+ SET(ALL_ASM_OBJS ${ALL_ASM_OBJS} ${OBJ})
+ ENDFOREACH(SRC ${GMX_SSEKERNEL_ASM_SRC})
+ set(GMX_SSEKERNEL_ASM_SRC ${ALL_ASM_OBJS})
+else(GMX_ASM_USEASM-NASM)
+ enable_language(ASM-ATT)
+ SET(CMAKE_ASM-ATT_COMPILER ${CMAKE_C_COMPILER})
+ if(GMX_IA32_ASM)
+ set_source_files_properties(${GMX_SSEKERNEL_ASM_SRC} PROPERTIES COMPILE_FLAGS "-c -m32")
+ else()
+ set_source_files_properties(${GMX_SSEKERNEL_ASM_SRC} PROPERTIES COMPILE_FLAGS "-c -m64")
+ endif()
+endif(GMX_ASM_USEASM-NASM)
+endif(NOT GMX_OPENMM)
+
+list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${GMX_SSEKERNEL_ASM_SRC} ${MDLIB_SOURCES})
+
+# add target that generates version.c every time a make is run
+# only do this if we generate the version
+if (USE_VERSION_H)
+ add_custom_target(gmx_version ALL
+ COMMAND ${CMAKE_COMMAND}
++ -D GIT_EXECUTABLE="${GIT_EXECUTABLE}"
++ -D GIT_VERSION="${GIT_VERSION}"
+ -D PROJECT_VERSION="${PROJECT_VERSION}"
+ -D PROJECT_SOURCE_DIR="${PROJECT_SOURCE_DIR}"
+ -D VERSION_C_CMAKEIN="${CMAKE_CURRENT_SOURCE_DIR}/version.c.cmakein"
+ -D VERSION_C_OUT="${CMAKE_CURRENT_BINARY_DIR}/version.c"
+ -P ${CMAKE_SOURCE_DIR}/cmake/gmxGenerateVersionInfo.cmake
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/src/gmxlib
+ DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/version.c.cmakein
+ COMMENT "Generating version information")
+ list(APPEND LIBGROMACS_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/version.c) # auto-generated
+ set_source_files_properties(${CMAKE_CURRENT_BINARY_DIR}/version.c
+ PROPERTIES GENERATED true)
+endif (USE_VERSION_H)
+
+add_library(libgromacs ${LIBGROMACS_SOURCES})
+if (USE_VERSION_H)
+ add_dependencies(libgromacs gmx_version)
+endif (USE_VERSION_H)
+target_link_libraries(libgromacs
+ ${GMX_EXTRA_LIBRARIES} ${FFT_LIBRARIES} ${XML_LIBRARIES}
+ ${THREAD_LIB})
+set_target_properties(libgromacs PROPERTIES
+ OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
+ SOVERSION ${SOVERSION}
+ INSTALL_NAME_DIR "${LIB_INSTALL_DIR}")
+
+install(TARGETS libgromacs DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgromacs.pc.cmakein
+ ${CMAKE_CURRENT_BINARY_DIR}/libgromacs.pc @ONLY)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgromacs.pc
+ DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+ RENAME "libgromacs${GMX_LIBS_SUFFIX}.pc"
+ COMPONENT development)
--- /dev/null
- "no", "umbrella", "constraint", "constant_force", NULL
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * GROningen Mixture of Alchemy and Childrens' Stories
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "typedefs.h"
+#include "names.h"
+
+/* note: these arrays should correspond to enums in include/types/enums.h */
+
+const char *epbc_names[epbcNR+1]=
+{
+ "xyz", "no", "xy", "screw", NULL
+};
+
+const char *ens_names[ensNR+1]=
+{
+ "Grid","Simple", NULL
+};
+
+const char *ei_names[eiNR+1]=
+{
+ "md", "steep", "cg", "bd", "sd", "nm", "l-bfgs", "tpi", "tpic", "sd1", "md-vv", "md-vv-avek",NULL
+};
+
+const char *bool_names[BOOL_NR+1]=
+{
+ "FALSE","TRUE", NULL
+};
+
+const char *yesno_names[BOOL_NR+1]=
+{
+ "no","yes", NULL
+};
+
+const char *ptype_str[eptNR+1] = {
+ "Atom", "Nucleus", "Shell", "Bond", "VSite", NULL
+};
+
+const char *eel_names[eelNR+1] = {
+ "Cut-off", "Reaction-Field", "Generalized-Reaction-Field",
+ "PME", "Ewald", "PPPM", "Poisson", "Switch", "Shift", "User",
+ "Generalized-Born", "Reaction-Field-nec", "Encad-shift",
+ "PME-User", "PME-Switch", "PME-User-Switch",
+ "Reaction-Field-zero", NULL
+};
+
+const char *eewg_names[eewgNR+1] = {
+ "3d", "3dc", NULL
+};
+
+const char *evdw_names[evdwNR+1] = {
+ "Cut-off", "Switch", "Shift", "User", "Encad-shift", NULL
+};
+
+const char *econstr_names[econtNR+1] = {
+ "Lincs", "Shake", NULL
+};
+
+const char *egrp_nm[egNR+1] = {
+ "Coul-SR","LJ-SR","Buck-SR", "Coul-LR", "LJ-LR", "Buck-LR",
+ "Coul-14", "LJ-14", NULL
+};
+
+const char *etcoupl_names[etcNR+1] = {
+ "No", "Berendsen", "Nose-Hoover", "yes", "Andersen", "Andersen-interval", "V-rescale", NULL
+}; /* yes is alias for berendsen */
+
+const char *epcoupl_names[epcNR+1] = {
+ "No", "Berendsen", "Parrinello-Rahman", "Isotropic", "MTTK", NULL
+}; /* isotropic is alias for berendsen */
+
+const char *epcoupltype_names[epctNR+1] = {
+ "Isotropic", "Semiisotropic", "Anisotropic", "Surface-Tension", NULL
+};
+
+const char *erefscaling_names[erscNR+1] = {
+ "No", "All", "COM", NULL
+};
+
+const char *edisre_names[edrNR+1] = {
+ "No", "Simple", "Ensemble", NULL
+};
+
+const char *edisreweighting_names[edrwNR+1] = {
+ "Conservative", "Equal", NULL
+};
+
+const char *enbf_names[eNBF_NR+1] = {
+ "", "LJ", "Buckingham", NULL
+};
+
+const char *ecomb_names[eCOMB_NR+1] = {
+ "", "Geometric", "Arithmetic", "GeomSigEps", NULL
+};
+
+const char *gtypes[egcNR+1] = {
+ "T-Coupling", "Energy Mon.", "Acceleration", "Freeze",
+ "User1", "User2", "VCM", "XTC", "Or. Res. Fit", "QMMM", NULL
+};
+
+const char *efep_names[efepNR+1] = {
+ "no", "yes", NULL
+};
+
+const char *separate_dhdl_file_names[sepdhdlfileNR+1] = {
+ "yes", "no", NULL
+};
+
+const char *dhdl_derivatives_names[dhdlderivativesNR+1] = {
+ "yes", "no", NULL
+};
+
+const char *esol_names[esolNR+1] = {
+ "No", "SPC", "TIP4p", NULL
+};
+
+const char *enlist_names[enlistNR+1] = {
+ "Atom-Atom", "SPC-Atom", "SPC-SPC", "TIP4p-Atom", "TIP4p-TIP4p", "CG-CG", NULL
+};
+
+const char *edispc_names[edispcNR+1] = {
+ "No", "EnerPres", "Ener", "AllEnerPres", "AllEner", NULL
+};
+
+const char *ecm_names[ecmNR+1] = {
+ "Linear", "Angular", "None", NULL
+};
+
+const char *eann_names[eannNR+1] = {
+ "No", "Single", "Periodic", NULL
+};
+
+const char *eis_names[eisNR+1] = {
+ "No", "GBSA", NULL
+};
+
+const char *egb_names[egbNR+1] = {
+ "Still", "HCT", "OBC", NULL
+};
+
+const char *esa_names[esaNR+1] = {
+ "Ace-approximation", "None", "Still", NULL
+};
+
+const char *ewt_names[ewtNR+1] = {
+ "9-3", "10-4", "table", "12-6", NULL
+};
+
+const char *epull_names[epullNR+1] = {
- "distance", "direction", "cylinder", "position", "direction_periodic", NULL
++ "no", "umbrella", "constraint", "constant-force", NULL
+};
+
+const char *epullg_names[epullgNR+1] = {
++ "distance", "direction", "cylinder", "position", "direction-periodic", NULL
+};
+
+const char *erotg_names[erotgNR+1] = {
+ "iso", "iso-pf", "pm", "pm-pf", "rm", "rm-pf", "rm2", "rm2-pf", "flex", "flex-t", "flex2", "flex2-t", NULL
+};
+
+const char *erotg_fitnames[erotgFitNR+1] = {
+ "rmsd", "norm", "potential", NULL
+};
+
+const char *eQMmethod_names[eQMmethodNR+1] = {
+ "AM1", "PM3", "RHF",
+ "UHF", "DFT", "B3LYP", "MP2", "CASSCF","B3LYPLAN",
+ "DIRECT", NULL
+};
+
+const char *eQMbasis_names[eQMbasisNR+1] = {
+ "STO3G", "STO-3G", "3-21G",
+ "3-21G*", "3-21+G*", "6-21G",
+ "6-31G", "6-31G*", "6-31+G*",
+ "6-311G", NULL
+};
+
+const char *eQMMMscheme_names[eQMMMschemeNR+1] = {
+ "normal", "ONIOM", NULL
+};
+
+const char *eMultentOpt_names[eMultentOptNR+1] = {
+ "multiple_entries", "no", "use_last", NULL
+};
+
--- /dev/null
- if (nr > cr->mpb->ibuf_alloc) {
- cr->mpb->ibuf_alloc = nr;
- srenew(cr->mpb->ibuf,cr->mpb->ibuf_alloc);
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * GROningen Mixture of Alchemy and Childrens' Stories
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <string.h>
+#include "gmx_fatal.h"
+#include "main.h"
+#include "smalloc.h"
+#include "network.h"
+#include "copyrite.h"
+#include "statutil.h"
+#include "ctype.h"
+#include "macros.h"
+
+#ifdef GMX_LIB_MPI
+#include <mpi.h>
+#endif
+
+#ifdef GMX_THREADS
+#include "tmpi.h"
+#endif
+
+
+/* The source code in this file should be thread-safe.
+ Please keep it that way. */
+
+gmx_bool gmx_mpi_initialized(void)
+{
+ int n;
+#ifndef GMX_MPI
+ return 0;
+#else
+ MPI_Initialized(&n);
+
+ return n;
+#endif
+}
+
+int gmx_setup(int *argc,char **argv,int *nnodes)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_setup");
+ return 0;
+#else
+ char buf[256];
+ int resultlen; /* actual length of node name */
+ int i,flag;
+ int mpi_num_nodes;
+ int mpi_my_rank;
+ char mpi_hostname[MPI_MAX_PROCESSOR_NAME];
+
+ /* Call the MPI routines */
+#ifdef GMX_LIB_MPI
+#ifdef GMX_FAHCORE
+ (void) fah_MPI_Init(argc,&argv);
+#else
+ (void) MPI_Init(argc,&argv);
+#endif
+#endif
+ (void) MPI_Comm_size( MPI_COMM_WORLD, &mpi_num_nodes );
+ (void) MPI_Comm_rank( MPI_COMM_WORLD, &mpi_my_rank );
+ (void) MPI_Get_processor_name( mpi_hostname, &resultlen );
+
+#ifdef GMX_LIB_MPI
+ fprintf(stderr,"NNODES=%d, MYRANK=%d, HOSTNAME=%s\n",
+ mpi_num_nodes,mpi_my_rank,mpi_hostname);
+#endif
+
+ *nnodes=mpi_num_nodes;
+
+ return mpi_my_rank;
+#endif
+}
+
+int gmx_node_num(void)
+{
+#ifndef GMX_MPI
+ return 1;
+#else
+ int i;
+ (void) MPI_Comm_size(MPI_COMM_WORLD, &i);
+ return i;
+#endif
+}
+
+int gmx_node_rank(void)
+{
+#ifndef GMX_MPI
+ return 0;
+#else
+ int i;
+ (void) MPI_Comm_rank(MPI_COMM_WORLD, &i);
+ return i;
+#endif
+}
+
+void gmx_setup_nodecomm(FILE *fplog,t_commrec *cr)
+{
+ gmx_nodecomm_t *nc;
+ int n,rank,resultlen,hostnum,i,j,ng,ni;
+#ifdef GMX_MPI
+ char mpi_hostname[MPI_MAX_PROCESSOR_NAME],num[MPI_MAX_PROCESSOR_NAME];
+#endif
+
+ /* Many MPI implementations do not optimize MPI_Allreduce
+ * (and probably also other global communication calls)
+ * for multi-core nodes connected by a network.
+ * We can optimize such communication by using one MPI call
+ * within each node and one between the nodes.
+ * For MVAPICH2 and Intel MPI this reduces the time for
+ * the global_stat communication by 25%
+ * for 2x2-core 3 GHz Woodcrest connected by mixed DDR/SDR Infiniband.
+ * B. Hess, November 2007
+ */
+
+ nc = &cr->nc;
+
+ nc->bUse = FALSE;
+#ifndef GMX_THREADS
+ if (getenv("GMX_NO_NODECOMM") == NULL) {
+#ifdef GMX_MPI
+ MPI_Comm_size(cr->mpi_comm_mygroup,&n);
+ MPI_Comm_rank(cr->mpi_comm_mygroup,&rank);
+ MPI_Get_processor_name(mpi_hostname,&resultlen);
+ /* This procedure can only differentiate nodes with host names
+ * that end on unique numbers.
+ */
+ i = 0;
+ j = 0;
+ /* Only parse the host name up to the first dot */
+ while(i < resultlen && mpi_hostname[i] != '.') {
+ if (isdigit(mpi_hostname[i])) {
+ num[j++] = mpi_hostname[i];
+ }
+ i++;
+ }
+ num[j] = '\0';
+ if (j == 0) {
+ hostnum = 0;
+ } else {
+ /* Use only the last 9 decimals, so we don't overflow an int */
+ hostnum = strtol(num + max(0,j-9), NULL, 10);
+ }
+
+ if (debug) {
+ fprintf(debug,
+ "In gmx_setup_nodecomm: splitting communicator of size %d\n",
+ n);
+ fprintf(debug,"In gmx_setup_nodecomm: hostname '%s', hostnum %d\n",
+ mpi_hostname,hostnum);
+ }
+
+ /* The intra-node communicator, split on node number */
+ MPI_Comm_split(cr->mpi_comm_mygroup,hostnum,rank,&nc->comm_intra);
+ MPI_Comm_rank(nc->comm_intra,&nc->rank_intra);
+ if (debug) {
+ fprintf(debug,"In gmx_setup_nodecomm: node rank %d rank_intra %d\n",
+ rank,nc->rank_intra);
+ }
+ /* The inter-node communicator, split on rank_intra.
+ * We actually only need the one for rank=0,
+ * but it is easier to create them all.
+ */
+ MPI_Comm_split(cr->mpi_comm_mygroup,nc->rank_intra,rank,&nc->comm_inter);
+ /* Check if this really created two step communication */
+ MPI_Comm_size(nc->comm_inter,&ng);
+ MPI_Comm_size(nc->comm_intra,&ni);
+ if (debug) {
+ fprintf(debug,"In gmx_setup_nodecomm: groups %d, my group size %d\n",
+ ng,ni);
+ }
+ if ((ng > 1 && ng < n) || (ni > 1 && ni < n)) {
+ nc->bUse = TRUE;
+ if (fplog)
+ fprintf(fplog,"Using two step summing over %d groups of on average %.1f processes\n\n",ng,(real)n/(real)ng);
+ if (nc->rank_intra > 0)
+ MPI_Comm_free(&nc->comm_inter);
+ } else {
+ /* One group or all processes in a separate group, use normal summing */
+ MPI_Comm_free(&nc->comm_inter);
+ MPI_Comm_free(&nc->comm_intra);
+ }
+#endif
+ }
+#endif
+}
+
+void gmx_barrier(const t_commrec *cr)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_barrier");
+#else
+ MPI_Barrier(cr->mpi_comm_mygroup);
+#endif
+}
+
+void gmx_abort(int noderank,int nnodes,int errorno)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_abort");
+#else
+#ifdef GMX_THREADS
+ fprintf(stderr,"Halting program %s\n",ShortProgram());
+ thanx(stderr);
+ exit(1);
+#else
+ if (nnodes > 1)
+ {
+ fprintf(stderr,"Halting parallel program %s on CPU %d out of %d\n",
+ ShortProgram(),noderank,nnodes);
+ }
+ else
+ {
+ fprintf(stderr,"Halting program %s\n",ShortProgram());
+ }
+
+ thanx(stderr);
+ MPI_Abort(MPI_COMM_WORLD,errorno);
+ exit(1);
+#endif
+#endif
+}
+
+void gmx_bcast(int nbytes,void *b,const t_commrec *cr)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_bast");
+#else
+ MPI_Bcast(b,nbytes,MPI_BYTE,MASTERRANK(cr),cr->mpi_comm_mygroup);
+#endif
+}
+
+void gmx_bcast_sim(int nbytes,void *b,const t_commrec *cr)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_bast");
+#else
+ MPI_Bcast(b,nbytes,MPI_BYTE,MASTERRANK(cr),cr->mpi_comm_mysim);
+#endif
+}
+
+void gmx_sumd(int nr,double r[],const t_commrec *cr)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_sumd");
+#else
+#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
+ if (cr->nc.bUse) {
+ if (cr->nc.rank_intra == 0)
+ {
+ /* Use two step summing. */
+ MPI_Reduce(MPI_IN_PLACE,r,nr,MPI_DOUBLE,MPI_SUM,0,
+ cr->nc.comm_intra);
+ /* Sum the roots of the internal (intra) buffers. */
+ MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_DOUBLE,MPI_SUM,
+ cr->nc.comm_inter);
+ }
+ else
+ {
+ /* This is here because of the silly MPI specification
+ that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
+ MPI_Reduce(r,NULL,nr,MPI_DOUBLE,MPI_SUM,0,cr->nc.comm_intra);
+ }
+ MPI_Bcast(r,nr,MPI_DOUBLE,0,cr->nc.comm_intra);
+ }
+ else
+ {
+ MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_DOUBLE,MPI_SUM,
+ cr->mpi_comm_mygroup);
+ }
+#else
+ int i;
+
+ if (nr > cr->mpb->dbuf_alloc) {
+ cr->mpb->dbuf_alloc = nr;
+ srenew(cr->mpb->dbuf,cr->mpb->dbuf_alloc);
+ }
+ if (cr->nc.bUse) {
+ /* Use two step summing */
+ MPI_Allreduce(r,cr->mpb->dbuf,nr,MPI_DOUBLE,MPI_SUM,cr->nc.comm_intra);
+ if (cr->nc.rank_intra == 0) {
+ /* Sum with the buffers reversed */
+ MPI_Allreduce(cr->mpb->dbuf,r,nr,MPI_DOUBLE,MPI_SUM,
+ cr->nc.comm_inter);
+ }
+ MPI_Bcast(r,nr,MPI_DOUBLE,0,cr->nc.comm_intra);
+ } else {
+ MPI_Allreduce(r,cr->mpb->dbuf,nr,MPI_DOUBLE,MPI_SUM,
+ cr->mpi_comm_mygroup);
+ for(i=0; i<nr; i++)
+ r[i] = cr->mpb->dbuf[i];
+ }
+#endif
+#endif
+}
+
+void gmx_sumf(int nr,float r[],const t_commrec *cr)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_sumf");
+#else
+#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
+ if (cr->nc.bUse) {
+ /* Use two step summing. */
+ if (cr->nc.rank_intra == 0)
+ {
+ MPI_Reduce(MPI_IN_PLACE,r,nr,MPI_FLOAT,MPI_SUM,0,
+ cr->nc.comm_intra);
+ /* Sum the roots of the internal (intra) buffers */
+ MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_FLOAT,MPI_SUM,
+ cr->nc.comm_inter);
+ }
+ else
+ {
+ /* This is here because of the silly MPI specification
+ that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
+ MPI_Reduce(r,NULL,nr,MPI_FLOAT,MPI_SUM,0,cr->nc.comm_intra);
+ }
+ MPI_Bcast(r,nr,MPI_FLOAT,0,cr->nc.comm_intra);
+ }
+ else
+ {
+ MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_FLOAT,MPI_SUM,cr->mpi_comm_mygroup);
+ }
+#else
+ int i;
+
+ if (nr > cr->mpb->fbuf_alloc) {
+ cr->mpb->fbuf_alloc = nr;
+ srenew(cr->mpb->fbuf,cr->mpb->fbuf_alloc);
+ }
+ if (cr->nc.bUse) {
+ /* Use two step summing */
+ MPI_Allreduce(r,cr->mpb->fbuf,nr,MPI_FLOAT,MPI_SUM,cr->nc.comm_intra);
+ if (cr->nc.rank_intra == 0) {
+ /* Sum with the buffers reversed */
+ MPI_Allreduce(cr->mpb->fbuf,r,nr,MPI_FLOAT,MPI_SUM,
+ cr->nc.comm_inter);
+ }
+ MPI_Bcast(r,nr,MPI_FLOAT,0,cr->nc.comm_intra);
+ } else {
+ MPI_Allreduce(r,cr->mpb->fbuf,nr,MPI_FLOAT,MPI_SUM,
+ cr->mpi_comm_mygroup);
+ for(i=0; i<nr; i++)
+ r[i] = cr->mpb->fbuf[i];
+ }
+#endif
+#endif
+}
+
+void gmx_sumi(int nr,int r[],const t_commrec *cr)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_sumi");
+#else
+#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
+ if (cr->nc.bUse) {
+ /* Use two step summing */
+ if (cr->nc.rank_intra == 0)
+ {
+ MPI_Reduce(MPI_IN_PLACE,r,nr,MPI_INT,MPI_SUM,0,cr->nc.comm_intra);
+ /* Sum with the buffers reversed */
+ MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_INT,MPI_SUM,cr->nc.comm_inter);
+ }
+ else
+ {
+ /* This is here because of the silly MPI specification
+ that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
+ MPI_Reduce(r,NULL,nr,MPI_INT,MPI_SUM,0,cr->nc.comm_intra);
+ }
+ MPI_Bcast(r,nr,MPI_INT,0,cr->nc.comm_intra);
+ }
+ else
+ {
+ MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_INT,MPI_SUM,cr->mpi_comm_mygroup);
+ }
+#else
+ int i;
+
+ if (nr > cr->mpb->ibuf_alloc) {
+ cr->mpb->ibuf_alloc = nr;
+ srenew(cr->mpb->ibuf,cr->mpb->ibuf_alloc);
+ }
+ if (cr->nc.bUse) {
+ /* Use two step summing */
+ MPI_Allreduce(r,cr->mpb->ibuf,nr,MPI_INT,MPI_SUM,cr->nc.comm_intra);
+ if (cr->nc.rank_intra == 0) {
+ /* Sum with the buffers reversed */
+ MPI_Allreduce(cr->mpb->ibuf,r,nr,MPI_INT,MPI_SUM,cr->nc.comm_inter);
+ }
+ MPI_Bcast(r,nr,MPI_INT,0,cr->nc.comm_intra);
+ } else {
+ MPI_Allreduce(r,cr->mpb->ibuf,nr,MPI_INT,MPI_SUM,cr->mpi_comm_mygroup);
+ for(i=0; i<nr; i++)
+ r[i] = cr->mpb->ibuf[i];
+ }
+#endif
+#endif
+}
+
+void gmx_sumli(int nr,gmx_large_int_t r[],const t_commrec *cr)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_sumli");
+#else
+#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
+ if (cr->nc.bUse) {
+ /* Use two step summing */
+ if (cr->nc.rank_intra == 0)
+ {
+ MPI_Reduce(MPI_IN_PLACE,r,nr,GMX_MPI_LARGE_INT,MPI_SUM,0,
+ cr->nc.comm_intra);
+ /* Sum with the buffers reversed */
+ MPI_Allreduce(MPI_IN_PLACE,r,nr,GMX_MPI_LARGE_INT,MPI_SUM,
+ cr->nc.comm_inter);
+ }
+ else
+ {
+ /* This is here because of the silly MPI specification
+ that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
+ MPI_Reduce(r,NULL,nr,GMX_MPI_LARGE_INT,MPI_SUM,0,cr->nc.comm_intra);
+ }
+ MPI_Bcast(r,nr,GMX_MPI_LARGE_INT,0,cr->nc.comm_intra);
+ }
+ else
+ {
+ MPI_Allreduce(MPI_IN_PLACE,r,nr,GMX_MPI_LARGE_INT,MPI_SUM,cr->mpi_comm_mygroup);
+ }
+#else
+ int i;
+
- MPI_Allreduce(r,cr->mpb->ibuf,nr,GMX_MPI_LARGE_INT,MPI_SUM,
++ if (nr > cr->mpb->libuf_alloc) {
++ cr->mpb->libuf_alloc = nr;
++ srenew(cr->mpb->libuf,cr->mpb->libuf_alloc);
+ }
+ if (cr->nc.bUse) {
+ /* Use two step summing */
- MPI_Allreduce(cr->mpb->ibuf,r,nr,GMX_MPI_LARGE_INT,MPI_SUM,
++ MPI_Allreduce(r,cr->mpb->libuf,nr,GMX_MPI_LARGE_INT,MPI_SUM,
+ cr->nc.comm_intra);
+ if (cr->nc.rank_intra == 0) {
+ /* Sum with the buffers reversed */
- MPI_Allreduce(r,cr->mpb->ibuf,nr,GMX_MPI_LARGE_INT,MPI_SUM,
++ MPI_Allreduce(cr->mpb->libuf,r,nr,GMX_MPI_LARGE_INT,MPI_SUM,
+ cr->nc.comm_inter);
+ }
+ MPI_Bcast(r,nr,GMX_MPI_LARGE_INT,0,cr->nc.comm_intra);
+ } else {
- r[i] = cr->mpb->ibuf[i];
++ MPI_Allreduce(r,cr->mpb->libuf,nr,GMX_MPI_LARGE_INT,MPI_SUM,
+ cr->mpi_comm_mygroup);
+ for(i=0; i<nr; i++)
- if (nr > ms->mpb->ibuf_alloc) {
- ms->mpb->ibuf_alloc = nr;
- srenew(ms->mpb->ibuf,ms->mpb->ibuf_alloc);
++ r[i] = cr->mpb->libuf[i];
+ }
+#endif
+#endif
+}
+
+
+
+#ifdef GMX_MPI
+void gmx_sumd_comm(int nr,double r[],MPI_Comm mpi_comm)
+{
+#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
+ MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_DOUBLE,MPI_SUM,mpi_comm);
+#else
+ /* this function is only used in code that is not performance critical,
+ (during setup, when comm_rec is not the appropriate communication
+ structure), so this isn't as bad as it looks. */
+ double *buf;
+ int i;
+
+ snew(buf, nr);
+ MPI_Allreduce(r,buf,nr,MPI_DOUBLE,MPI_SUM,mpi_comm);
+ for(i=0; i<nr; i++)
+ r[i] = buf[i];
+ sfree(buf);
+#endif
+}
+#endif
+
+#ifdef GMX_MPI
+void gmx_sumf_comm(int nr,float r[],MPI_Comm mpi_comm)
+{
+#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
+ MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_FLOAT,MPI_SUM,mpi_comm);
+#else
+ /* this function is only used in code that is not performance critical,
+ (during setup, when comm_rec is not the appropriate communication
+ structure), so this isn't as bad as it looks. */
+ float *buf;
+ int i;
+
+ snew(buf, nr);
+ MPI_Allreduce(r,buf,nr,MPI_FLOAT,MPI_SUM,mpi_comm);
+ for(i=0; i<nr; i++)
+ r[i] = buf[i];
+ sfree(buf);
+#endif
+}
+#endif
+
+void gmx_sumd_sim(int nr,double r[],const gmx_multisim_t *ms)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_sumd_sim");
+#else
+ gmx_sumd_comm(nr,r,ms->mpi_comm_masters);
+#endif
+}
+
+void gmx_sumf_sim(int nr,float r[],const gmx_multisim_t *ms)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_sumf_sim");
+#else
+ gmx_sumf_comm(nr,r,ms->mpi_comm_masters);
+#endif
+}
+
+void gmx_sumi_sim(int nr,int r[], const gmx_multisim_t *ms)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_sumi_sim");
+#else
+#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
+ MPI_Allreduce(MPI_IN_PLACE,r,nr,MPI_INT,MPI_SUM,ms->mpi_comm_masters);
+#else
+ /* this is thread-unsafe, but it will do for now: */
+ int i;
+
+ if (nr > ms->mpb->ibuf_alloc) {
+ ms->mpb->ibuf_alloc = nr;
+ srenew(ms->mpb->ibuf,ms->mpb->ibuf_alloc);
+ }
+ MPI_Allreduce(r,ms->mpb->ibuf,nr,MPI_INT,MPI_SUM,ms->mpi_comm_masters);
+ for(i=0; i<nr; i++)
+ r[i] = ms->mpb->ibuf[i];
+#endif
+#endif
+}
+
+void gmx_sumli_sim(int nr,gmx_large_int_t r[], const gmx_multisim_t *ms)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_sumli_sim");
+#else
+#if defined(MPI_IN_PLACE_EXISTS) || defined(GMX_THREADS)
+ MPI_Allreduce(MPI_IN_PLACE,r,nr,GMX_MPI_LARGE_INT,MPI_SUM,
+ ms->mpi_comm_masters);
+#else
+ /* this is thread-unsafe, but it will do for now: */
+ int i;
+
- MPI_Allreduce(r,ms->mpb->ibuf,nr,GMX_MPI_LARGE_INT,MPI_SUM,
++ if (nr > ms->mpb->libuf_alloc) {
++ ms->mpb->libuf_alloc = nr;
++ srenew(ms->mpb->libuf,ms->mpb->libuf_alloc);
+ }
- r[i] = ms->mpb->ibuf[i];
++ MPI_Allreduce(r,ms->mpb->libuf,nr,GMX_MPI_LARGE_INT,MPI_SUM,
+ ms->mpi_comm_masters);
+ for(i=0; i<nr; i++)
++ r[i] = ms->mpb->libuf[i];
+#endif
+#endif
+}
+
+
+void gmx_finalize(void)
+{
+#ifndef GMX_MPI
+ gmx_call("gmx_finalize");
+#else
+ int ret;
+
+ /* just as a check; we don't want to finalize twice */
+ int finalized;
+ MPI_Finalized(&finalized);
+ if (finalized)
+ return;
+
+ /* We sync the processes here to try to avoid problems
+ * with buggy MPI implementations that could cause
+ * unfinished processes to terminate.
+ */
+ MPI_Barrier(MPI_COMM_WORLD);
+
+ /*
+ if (DOMAINDECOMP(cr)) {
+ if (cr->npmenodes > 0 || cr->dd->bCartesian)
+ MPI_Comm_free(&cr->mpi_comm_mygroup);
+ if (cr->dd->bCartesian)
+ MPI_Comm_free(&cr->mpi_comm_mysim);
+ }
+ */
+
+ /* Apparently certain mpich implementations cause problems
+ * with MPI_Finalize. In that case comment out MPI_Finalize.
+ */
+ if (debug)
+ fprintf(debug,"Will call MPI_Finalize now\n");
+
+ ret = MPI_Finalize();
+ if (debug)
+ fprintf(debug,"Return code from MPI_Finalize = %d\n",ret);
+#endif
+}
+
--- /dev/null
- fprintf(out,"ref_t%s",bMDPformat ? " = " : ":");
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * GROningen Mixture of Alchemy and Childrens' Stories
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+/* This file is completely threadsafe - please keep it that way! */
+#ifdef GMX_THREADS
+#include <thread_mpi.h>
+#endif
+
+
+#include <stdio.h>
+#include "smalloc.h"
+#include "typedefs.h"
+#include "names.h"
+#include "txtdump.h"
+#include "string2.h"
+#include "vec.h"
+
+
+int pr_indent(FILE *fp,int n)
+{
+ int i;
+
+ for (i=0; i<n; i++) (void) fprintf(fp," ");
+ return n;
+}
+
+int available(FILE *fp,void *p,int indent,const char *title)
+{
+ if (!p) {
+ if (indent > 0)
+ pr_indent(fp,indent);
+ (void) fprintf(fp,"%s: not available\n",title);
+ }
+ return (p!=NULL);
+}
+
+int pr_title(FILE *fp,int indent,const char *title)
+{
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s:\n",title);
+ return (indent+INDENT);
+}
+
+int pr_title_n(FILE *fp,int indent,const char *title,int n)
+{
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s (%d):\n",title,n);
+ return (indent+INDENT);
+}
+
+int pr_title_nxn(FILE *fp,int indent,const char *title,int n1,int n2)
+{
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s (%dx%d):\n",title,n1,n2);
+ return (indent+INDENT);
+}
+
+void pr_ivec(FILE *fp,int indent,const char *title,int vec[],int n, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp,vec,indent,title))
+ {
+ indent=pr_title_n(fp,indent,title,n);
+ for (i=0; i<n; i++)
+ {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s[%d]=%d\n",title,bShowNumbers?i:-1,vec[i]);
+ }
+ }
+}
+
+void pr_ivec_block(FILE *fp,int indent,const char *title,int vec[],int n, gmx_bool bShowNumbers)
+{
+ int i,j;
+
+ if (available(fp,vec,indent,title))
+ {
+ indent=pr_title_n(fp,indent,title,n);
+ i = 0;
+ while (i < n)
+ {
+ j = i+1;
+ while (j < n && vec[j] == vec[j-1]+1)
+ {
+ j++;
+ }
+ /* Print consecutive groups of 3 or more as blocks */
+ if (j - i < 3)
+ {
+ while(i < j)
+ {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s[%d]=%d\n",
+ title,bShowNumbers?i:-1,vec[i]);
+ i++;
+ }
+ }
+ else
+ {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s[%d,...,%d] = {%d,...,%d}\n",
+ title,
+ bShowNumbers?i:-1,
+ bShowNumbers?j-1:-1,
+ vec[i],vec[j-1]);
+ i = j;
+ }
+ }
+ }
+}
+
+void pr_bvec(FILE *fp,int indent,const char *title,gmx_bool vec[],int n, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp,vec,indent,title))
+ {
+ indent=pr_title_n(fp,indent,title,n);
+ for (i=0; i<n; i++)
+ {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s[%d]=%s\n",title,bShowNumbers?i:-1,
+ BOOL(vec[i]));
+ }
+ }
+}
+
+void pr_ivecs(FILE *fp,int indent,const char *title,ivec vec[],int n, gmx_bool bShowNumbers)
+{
+ int i,j;
+
+ if (available(fp,vec,indent,title))
+ {
+ indent=pr_title_nxn(fp,indent,title,n,DIM);
+ for (i=0; i<n; i++)
+ {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s[%d]={",title,bShowNumbers?i:-1);
+ for (j=0; j<DIM; j++)
+ {
+ if (j!=0) (void) fprintf(fp,", ");
+ fprintf(fp,"%d",vec[i][j]);
+ }
+ (void) fprintf(fp,"}\n");
+ }
+ }
+}
+
+void pr_rvec(FILE *fp,int indent,const char *title,real vec[],int n, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp,vec,indent,title))
+ {
+ indent=pr_title_n(fp,indent,title,n);
+ for (i=0; i<n; i++)
+ {
+ pr_indent(fp,indent);
+ fprintf(fp,"%s[%d]=%12.5e\n",title,bShowNumbers?i:-1,vec[i]);
+ }
+ }
+}
+
+void pr_dvec(FILE *fp,int indent,const char *title,double vec[],int n, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp,vec,indent,title))
+ {
+ indent=pr_title_n(fp,indent,title,n);
+ for (i=0; i<n; i++)
+ {
+ pr_indent(fp,indent);
+ fprintf(fp,"%s[%d]=%12.5e\n",title,bShowNumbers?i:-1,vec[i]);
+ }
+ }
+}
+
+
+/*
+void pr_mat(FILE *fp,int indent,char *title,matrix m)
+{
+ int i,j;
+
+ if (available(fp,m,indent,title)) {
+ indent=pr_title_n(fp,indent,title,n);
+ for(i=0; i<n; i++) {
+ pr_indent(fp,indent);
+ fprintf(fp,"%s[%d]=%12.5e %12.5e %12.5e\n",
+ title,bShowNumbers?i:-1,m[i][XX],m[i][YY],m[i][ZZ]);
+ }
+ }
+}
+*/
+
+void pr_rvecs_len(FILE *fp,int indent,const char *title,rvec vec[],int n)
+{
+ int i,j;
+
+ if (available(fp,vec,indent,title)) {
+ indent=pr_title_nxn(fp,indent,title,n,DIM);
+ for (i=0; i<n; i++) {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s[%5d]={",title,i);
+ for (j=0; j<DIM; j++) {
+ if (j != 0)
+ (void) fprintf(fp,", ");
+ (void) fprintf(fp,"%12.5e",vec[i][j]);
+ }
+ (void) fprintf(fp,"} len=%12.5e\n",norm(vec[i]));
+ }
+ }
+}
+
+void pr_rvecs(FILE *fp,int indent,const char *title,rvec vec[],int n)
+{
+ const char *fshort = "%12.5e";
+ const char *flong = "%15.8e";
+ const char *format;
+ int i,j;
+
+ if (getenv("LONGFORMAT") != NULL)
+ format = flong;
+ else
+ format = fshort;
+
+ if (available(fp,vec,indent,title)) {
+ indent=pr_title_nxn(fp,indent,title,n,DIM);
+ for (i=0; i<n; i++) {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s[%5d]={",title,i);
+ for (j=0; j<DIM; j++) {
+ if (j != 0)
+ (void) fprintf(fp,", ");
+ (void) fprintf(fp,format,vec[i][j]);
+ }
+ (void) fprintf(fp,"}\n");
+ }
+ }
+}
+
+
+void pr_reals(FILE *fp,int indent,const char *title,real *vec,int n)
+{
+ int i;
+
+ if (available(fp,vec,indent,title)) {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s:\t",title);
+ for(i=0; i<n; i++)
+ fprintf(fp," %10g",vec[i]);
+ (void) fprintf(fp,"\n");
+ }
+}
+
+void pr_doubles(FILE *fp,int indent,const char *title,double *vec,int n)
+{
+ int i;
+
+ if (available(fp,vec,indent,title)) {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s:\t",title);
+ for(i=0; i<n; i++)
+ fprintf(fp," %10g",vec[i]);
+ (void) fprintf(fp,"\n");
+ }
+}
+
+static void pr_int(FILE *fp,int indent,const char *title,int i)
+{
+ pr_indent(fp,indent);
+ fprintf(fp,"%-20s = %d\n",title,i);
+}
+
+static void pr_gmx_large_int(FILE *fp,int indent,const char *title,gmx_large_int_t i)
+{
+ char buf[STEPSTRSIZE];
+
+ pr_indent(fp,indent);
+ fprintf(fp,"%-20s = %s\n",title,gmx_step_str(i,buf));
+}
+
+static void pr_real(FILE *fp,int indent,const char *title,real r)
+{
+ pr_indent(fp,indent);
+ fprintf(fp,"%-20s = %g\n",title,r);
+}
+
+static void pr_double(FILE *fp,int indent,const char *title,double d)
+{
+ pr_indent(fp,indent);
+ fprintf(fp,"%-20s = %g\n",title,d);
+}
+
+static void pr_str(FILE *fp,int indent,const char *title,const char *s)
+{
+ pr_indent(fp,indent);
+ fprintf(fp,"%-20s = %s\n",title,s);
+}
+
+void pr_qm_opts(FILE *fp,int indent,const char *title,t_grpopts *opts)
+{
+ int i,m,j;
+
+ fprintf(fp,"%s:\n",title);
+
+ pr_int(fp,indent,"ngQM",opts->ngQM);
+ if (opts->ngQM > 0) {
+ pr_ivec(fp,indent,"QMmethod",opts->QMmethod,opts->ngQM,FALSE);
+ pr_ivec(fp,indent,"QMbasis",opts->QMbasis,opts->ngQM,FALSE);
+ pr_ivec(fp,indent,"QMcharge",opts->QMcharge,opts->ngQM,FALSE);
+ pr_ivec(fp,indent,"QMmult",opts->QMmult,opts->ngQM,FALSE);
+ pr_bvec(fp,indent,"bSH",opts->bSH,opts->ngQM,FALSE);
+ pr_ivec(fp,indent,"CASorbitals",opts->CASorbitals,opts->ngQM,FALSE);
+ pr_ivec(fp,indent,"CASelectrons",opts->CASelectrons,opts->ngQM,FALSE);
+ pr_rvec(fp,indent,"SAon",opts->SAon,opts->ngQM,FALSE);
+ pr_rvec(fp,indent,"SAon",opts->SAon,opts->ngQM,FALSE);
+ pr_ivec(fp,indent,"SAsteps",opts->SAsteps,opts->ngQM,FALSE);
+ pr_bvec(fp,indent,"bOPT",opts->bOPT,opts->ngQM,FALSE);
+ pr_bvec(fp,indent,"bTS",opts->bTS,opts->ngQM,FALSE);
+ }
+}
+
+static void pr_grp_opts(FILE *out,int indent,const char *title,t_grpopts *opts,
+ gmx_bool bMDPformat)
+{
+ int i,m,j;
+
+ if (!bMDPformat)
+ fprintf(out,"%s:\n",title);
+
+ pr_indent(out,indent);
+ fprintf(out,"nrdf%s",bMDPformat ? " = " : ":");
+ for(i=0; (i<opts->ngtc); i++)
+ fprintf(out," %10g",opts->nrdf[i]);
+ fprintf(out,"\n");
+
+ pr_indent(out,indent);
- fprintf(out,"tau_t%s",bMDPformat ? " = " : ":");
++ fprintf(out,"ref-t%s",bMDPformat ? " = " : ":");
+ for(i=0; (i<opts->ngtc); i++)
+ fprintf(out," %10g",opts->ref_t[i]);
+ fprintf(out,"\n");
+
+ pr_indent(out,indent);
- fprintf(out,"ann_npoints%s",bMDPformat ? " = " : ":");
++ fprintf(out,"tau-t%s",bMDPformat ? " = " : ":");
+ for(i=0; (i<opts->ngtc); i++)
+ fprintf(out," %10g",opts->tau_t[i]);
+ fprintf(out,"\n");
+
+ /* Pretty-print the simulated annealing info */
+ fprintf(out,"anneal%s",bMDPformat ? " = " : ":");
+ for(i=0; (i<opts->ngtc); i++)
+ fprintf(out," %10s",EANNEAL(opts->annealing[i]));
+ fprintf(out,"\n");
+
- fprintf(out,"energygrp_flags[%3d]:",i);
++ fprintf(out,"ann-npoints%s",bMDPformat ? " = " : ":");
+ for(i=0; (i<opts->ngtc); i++)
+ fprintf(out," %10d",opts->anneal_npoints[i]);
+ fprintf(out,"\n");
+
+ for(i=0; (i<opts->ngtc); i++) {
+ if(opts->anneal_npoints[i]>0) {
+ fprintf(out,"ann. times [%d]:\t",i);
+ for(j=0; (j<opts->anneal_npoints[i]); j++)
+ fprintf(out," %10.1f",opts->anneal_time[i][j]);
+ fprintf(out,"\n");
+ fprintf(out,"ann. temps [%d]:\t",i);
+ for(j=0; (j<opts->anneal_npoints[i]); j++)
+ fprintf(out," %10.1f",opts->anneal_temp[i][j]);
+ fprintf(out,"\n");
+ }
+ }
+
+ pr_indent(out,indent);
+ fprintf(out,"acc:\t");
+ for(i=0; (i<opts->ngacc); i++)
+ for(m=0; (m<DIM); m++)
+ fprintf(out," %10g",opts->acc[i][m]);
+ fprintf(out,"\n");
+
+ pr_indent(out,indent);
+ fprintf(out,"nfreeze:");
+ for(i=0; (i<opts->ngfrz); i++)
+ for(m=0; (m<DIM); m++)
+ fprintf(out," %10s",opts->nFreeze[i][m] ? "Y" : "N");
+ fprintf(out,"\n");
+
+
+ for(i=0; (i<opts->ngener); i++) {
+ pr_indent(out,indent);
- fprintf(fp,"pull_group %d:\n",g);
++ fprintf(out,"energygrp-flags[%3d]:",i);
+ for(m=0; (m<opts->ngener); m++)
+ fprintf(out," %d",opts->egp_flags[opts->ngener*i+m]);
+ fprintf(out,"\n");
+ }
+
+ fflush(out);
+}
+
+static void pr_matrix(FILE *fp,int indent,const char *title,rvec *m,
+ gmx_bool bMDPformat)
+{
+ if (bMDPformat)
+ fprintf(fp,"%-10s = %g %g %g %g %g %g\n",title,
+ m[XX][XX],m[YY][YY],m[ZZ][ZZ],m[XX][YY],m[XX][ZZ],m[YY][ZZ]);
+ else
+ pr_rvecs(fp,indent,title,m,DIM);
+}
+
+static void pr_cosine(FILE *fp,int indent,const char *title,t_cosines *cos,
+ gmx_bool bMDPformat)
+{
+ int j;
+
+ if (bMDPformat) {
+ fprintf(fp,"%s = %d\n",title,cos->n);
+ }
+ else {
+ indent=pr_title(fp,indent,title);
+ (void) pr_indent(fp,indent);
+ fprintf(fp,"n = %d\n",cos->n);
+ if (cos->n > 0) {
+ (void) pr_indent(fp,indent+2);
+ fprintf(fp,"a =");
+ for(j=0; (j<cos->n); j++)
+ fprintf(fp," %e",cos->a[j]);
+ fprintf(fp,"\n");
+ (void) pr_indent(fp,indent+2);
+ fprintf(fp,"phi =");
+ for(j=0; (j<cos->n); j++)
+ fprintf(fp," %e",cos->phi[j]);
+ fprintf(fp,"\n");
+ }
+ }
+}
+
+#define PS(t,s) pr_str(fp,indent,t,s)
+#define PI(t,s) pr_int(fp,indent,t,s)
+#define PSTEP(t,s) pr_gmx_large_int(fp,indent,t,s)
+#define PR(t,s) pr_real(fp,indent,t,s)
+#define PD(t,s) pr_double(fp,indent,t,s)
+
+static void pr_pullgrp(FILE *fp,int indent,int g,t_pullgrp *pg)
+{
+ pr_indent(fp,indent);
- PS("pull_geometry",EPULLGEOM(pull->eGeom));
- pr_ivec(fp,indent,"pull_dim",pull->dim,DIM,TRUE);
- PR("pull_r1",pull->cyl_r1);
- PR("pull_r0",pull->cyl_r0);
- PR("pull_constr_tol",pull->constr_tol);
- PI("pull_nstxout",pull->nstxout);
- PI("pull_nstfout",pull->nstfout);
- PI("pull_ngrp",pull->ngrp);
++ fprintf(fp,"pull-group %d:\n",g);
+ indent += 2;
+ pr_ivec_block(fp,indent,"atom",pg->ind,pg->nat,TRUE);
+ pr_rvec(fp,indent,"weight",pg->weight,pg->nweight,TRUE);
+ PI("pbcatom",pg->pbcatom);
+ pr_rvec(fp,indent,"vec",pg->vec,DIM,TRUE);
+ pr_rvec(fp,indent,"init",pg->init,DIM,TRUE);
+ PR("rate",pg->rate);
+ PR("k",pg->k);
+ PR("kB",pg->kB);
+}
+
+static void pr_pull(FILE *fp,int indent,t_pull *pull)
+{
+ int g;
+
- PSTEP("init_step",ir->init_step);
- PS("ns_type",ENS(ir->ns_type));
++ PS("pull-geometry",EPULLGEOM(pull->eGeom));
++ pr_ivec(fp,indent,"pull-dim",pull->dim,DIM,TRUE);
++ PR("pull-r1",pull->cyl_r1);
++ PR("pull-r0",pull->cyl_r0);
++ PR("pull-constr-tol",pull->constr_tol);
++ PI("pull-nstxout",pull->nstxout);
++ PI("pull-nstfout",pull->nstfout);
++ PI("pull-ngrp",pull->ngrp);
+ for(g=0; g<pull->ngrp+1; g++)
+ pr_pullgrp(fp,indent,g,&pull->grp[g]);
+}
+
+static void pr_rotgrp(FILE *fp,int indent,int g,t_rotgrp *rotg)
+{
+ pr_indent(fp,indent);
+ fprintf(fp,"rotation_group %d:\n",g);
+ indent += 2;
+ PS("type",EROTGEOM(rotg->eType));
+ PS("massw",BOOL(rotg->bMassW));
+ pr_ivec_block(fp,indent,"atom",rotg->ind,rotg->nat,TRUE);
+ pr_rvecs(fp,indent,"x_ref",rotg->x_ref,rotg->nat);
+ pr_rvec(fp,indent,"vec",rotg->vec,DIM,TRUE);
+ pr_rvec(fp,indent,"pivot",rotg->pivot,DIM,TRUE);
+ PR("rate",rotg->rate);
+ PR("k",rotg->k);
+ PR("slab_dist",rotg->slab_dist);
+ PR("min_gaussian",rotg->min_gaussian);
+ PR("epsilon",rotg->eps);
+ PS("fit_method",EROTFIT(rotg->eFittype));
+ PI("potfitangle_nstep",rotg->PotAngle_nstep);
+ PR("potfitangle_step",rotg->PotAngle_step);
+}
+
+static void pr_rot(FILE *fp,int indent,t_rot *rot)
+{
+ int g;
+
+ PI("rot_nstrout",rot->nstrout);
+ PI("rot_nstsout",rot->nstsout);
+ PI("rot_ngrp",rot->ngrp);
+ for(g=0; g<rot->ngrp; g++)
+ pr_rotgrp(fp,indent,g,&rot->grp[g]);
+}
+
+void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
+ gmx_bool bMDPformat)
+{
+ const char *infbuf="inf";
+ int i;
+
+ if (available(fp,ir,indent,title)) {
+ if (!bMDPformat)
+ indent=pr_title(fp,indent,title);
+ PS("integrator",EI(ir->eI));
+ PSTEP("nsteps",ir->nsteps);
- PS("comm_mode",ECOM(ir->comm_mode));
++ PSTEP("init-step",ir->init_step);
++ PS("ns-type",ENS(ir->ns_type));
+ PI("nstlist",ir->nstlist);
+ PI("ndelta",ir->ndelta);
+ PI("nstcomm",ir->nstcomm);
- PR("init_t",ir->init_t);
- PR("delta_t",ir->delta_t);
++ PS("comm-mode",ECOM(ir->comm_mode));
+ PI("nstlog",ir->nstlog);
+ PI("nstxout",ir->nstxout);
+ PI("nstvout",ir->nstvout);
+ PI("nstfout",ir->nstfout);
+ PI("nstcalcenergy",ir->nstcalcenergy);
+ PI("nstenergy",ir->nstenergy);
+ PI("nstxtcout",ir->nstxtcout);
- PI("pme_order",ir->pme_order);
- PR("ewald_rtol",ir->ewald_rtol);
- PR("ewald_geometry",ir->ewald_geometry);
- PR("epsilon_surface",ir->epsilon_surface);
- PS("optimize_fft",BOOL(ir->bOptFFT));
++ PR("init-t",ir->init_t);
++ PR("delta-t",ir->delta_t);
+
+ PR("xtcprec",ir->xtcprec);
+ PI("nkx",ir->nkx);
+ PI("nky",ir->nky);
+ PI("nkz",ir->nkz);
- PR("tau_p",ir->tau_p);
- pr_matrix(fp,indent,"ref_p",ir->ref_p,bMDPformat);
++ PI("pme-order",ir->pme_order);
++ PR("ewald-rtol",ir->ewald_rtol);
++ PR("ewald-geometry",ir->ewald_geometry);
++ PR("epsilon-surface",ir->epsilon_surface);
++ PS("optimize-fft",BOOL(ir->bOptFFT));
+ PS("ePBC",EPBC(ir->ePBC));
+ PS("bPeriodicMols",BOOL(ir->bPeriodicMols));
+ PS("bContinuation",BOOL(ir->bContinuation));
+ PS("bShakeSOR",BOOL(ir->bShakeSOR));
+ PS("etc",ETCOUPLTYPE(ir->etc));
+ PI("nsttcouple",ir->nsttcouple);
+ PS("epc",EPCOUPLTYPE(ir->epc));
+ PS("epctype",EPCOUPLTYPETYPE(ir->epct));
+ PI("nstpcouple",ir->nstpcouple);
- PS("refcoord_scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
++ PR("tau-p",ir->tau_p);
++ pr_matrix(fp,indent,"ref-p",ir->ref_p,bMDPformat);
+ pr_matrix(fp,indent,"compress",ir->compress,bMDPformat);
- fprintf(fp,"posres_com = %g %g %g\n",ir->posres_com[XX],
++ PS("refcoord-scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
+ if (bMDPformat)
- pr_rvec(fp,indent,"posres_com",ir->posres_com,DIM,TRUE);
++ fprintf(fp,"posres-com = %g %g %g\n",ir->posres_com[XX],
+ ir->posres_com[YY],ir->posres_com[ZZ]);
+ else
- fprintf(fp,"posres_comB = %g %g %g\n",ir->posres_comB[XX],
++ pr_rvec(fp,indent,"posres-com",ir->posres_com,DIM,TRUE);
+ if (bMDPformat)
- pr_rvec(fp,indent,"posres_comB",ir->posres_comB,DIM,TRUE);
- PI("andersen_seed",ir->andersen_seed);
++ fprintf(fp,"posres-comB = %g %g %g\n",ir->posres_comB[XX],
+ ir->posres_comB[YY],ir->posres_comB[ZZ]);
+ else
- PR("rcoulomb_switch",ir->rcoulomb_switch);
++ pr_rvec(fp,indent,"posres-comB",ir->posres_comB,DIM,TRUE);
++ PI("andersen-seed",ir->andersen_seed);
+ PR("rlist",ir->rlist);
+ PR("rlistlong",ir->rlistlong);
+ PR("rtpi",ir->rtpi);
+ PS("coulombtype",EELTYPE(ir->coulombtype));
- PR("rvdw_switch",ir->rvdw_switch);
++ PR("rcoulomb-switch",ir->rcoulomb_switch);
+ PR("rcoulomb",ir->rcoulomb);
+ PS("vdwtype",EVDWTYPE(ir->vdwtype));
- PR("epsilon_r",ir->epsilon_r);
++ PR("rvdw-switch",ir->rvdw_switch);
+ PR("rvdw",ir->rvdw);
+ if (ir->epsilon_r != 0)
- PS("epsilon_r",infbuf);
++ PR("epsilon-r",ir->epsilon_r);
+ else
- PR("epsilon_rf",ir->epsilon_rf);
++ PS("epsilon-r",infbuf);
+ if (ir->epsilon_rf != 0)
- PS("epsilon_rf",infbuf);
++ PR("epsilon-rf",ir->epsilon_rf);
+ else
- PS("implicit_solvent",EIMPLICITSOL(ir->implicit_solvent));
- PS("gb_algorithm",EGBALGORITHM(ir->gb_algorithm));
- PR("gb_epsilon_solvent",ir->gb_epsilon_solvent);
++ PS("epsilon-rf",infbuf);
+ PR("tabext",ir->tabext);
- PR("gb_saltconc",ir->gb_saltconc);
- PR("gb_obc_alpha",ir->gb_obc_alpha);
- PR("gb_obc_beta",ir->gb_obc_beta);
- PR("gb_obc_gamma",ir->gb_obc_gamma);
- PR("gb_dielectric_offset",ir->gb_dielectric_offset);
- PS("sa_algorithm",ESAALGORITHM(ir->gb_algorithm));
- PR("sa_surface_tension",ir->sa_surface_tension);
++ PS("implicit-solvent",EIMPLICITSOL(ir->implicit_solvent));
++ PS("gb-algorithm",EGBALGORITHM(ir->gb_algorithm));
++ PR("gb-epsilon-solvent",ir->gb_epsilon_solvent);
+ PI("nstgbradii",ir->nstgbradii);
+ PR("rgbradii",ir->rgbradii);
- PS("free_energy",EFEPTYPE(ir->efep));
- PR("init_lambda",ir->init_lambda);
- PR("delta_lambda",ir->delta_lambda);
++ PR("gb-saltconc",ir->gb_saltconc);
++ PR("gb-obc-alpha",ir->gb_obc_alpha);
++ PR("gb-obc-beta",ir->gb_obc_beta);
++ PR("gb-obc-gamma",ir->gb_obc_gamma);
++ PR("gb-dielectric-offset",ir->gb_dielectric_offset);
++ PS("sa-algorithm",ESAALGORITHM(ir->gb_algorithm));
++ PR("sa-surface-tension",ir->sa_surface_tension);
+
+ PS("DispCorr",EDISPCORR(ir->eDispCorr));
- PI("n_foreign_lambda",ir->n_flambda);
++ PS("free-energy",EFEPTYPE(ir->efep));
++ PR("init-lambda",ir->init_lambda);
++ PR("delta-lambda",ir->delta_lambda);
+ if (!bMDPformat)
+ {
- fprintf(fp,"foreign_lambda%s",bMDPformat ? " = " : ":");
++ PI("n-foreign-lambda",ir->n_flambda);
+ }
+ if (ir->n_flambda > 0)
+ {
+ pr_indent(fp,indent);
- PR("sc_alpha",ir->sc_alpha);
- PI("sc_power",ir->sc_power);
- PR("sc_sigma",ir->sc_sigma);
- PR("sc_sigma_min",ir->sc_sigma_min);
++ fprintf(fp,"foreign-lambda%s",bMDPformat ? " = " : ":");
+ for(i=0; i<ir->n_flambda; i++)
+ {
+ fprintf(fp," %10g",ir->flambda[i]);
+ }
+ fprintf(fp,"\n");
+ }
- PS("separate_dhdl_file", SEPDHDLFILETYPE(ir->separate_dhdl_file));
- PS("dhdl_derivatives", DHDLDERIVATIVESTYPE(ir->dhdl_derivatives));
- PI("dh_hist_size", ir->dh_hist_size);
- PD("dh_hist_spacing", ir->dh_hist_spacing);
++ PR("sc-alpha",ir->sc_alpha);
++ PI("sc-power",ir->sc_power);
++ PR("sc-sigma",ir->sc_sigma);
++ PR("sc-sigma-min",ir->sc_sigma_min);
+ PI("nstdhdl", ir->nstdhdl);
- PS("wall_type",EWALLTYPE(ir->wall_type));
- PI("wall_atomtype[0]",ir->wall_atomtype[0]);
- PI("wall_atomtype[1]",ir->wall_atomtype[1]);
- PR("wall_density[0]",ir->wall_density[0]);
- PR("wall_density[1]",ir->wall_density[1]);
- PR("wall_ewald_zfac",ir->wall_ewald_zfac);
++ PS("separate-dhdl-file", SEPDHDLFILETYPE(ir->separate_dhdl_file));
++ PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(ir->dhdl_derivatives));
++ PI("dh-hist-size", ir->dh_hist_size);
++ PD("dh-hist-spacing", ir->dh_hist_spacing);
+
+ PI("nwall",ir->nwall);
- PS("disre_weighting",EDISREWEIGHTING(ir->eDisreWeighting));
- PS("disre_mixed",BOOL(ir->bDisreMixed));
- PR("dr_fc",ir->dr_fc);
- PR("dr_tau",ir->dr_tau);
++ PS("wall-type",EWALLTYPE(ir->wall_type));
++ PI("wall-atomtype[0]",ir->wall_atomtype[0]);
++ PI("wall-atomtype[1]",ir->wall_atomtype[1]);
++ PR("wall-density[0]",ir->wall_density[0]);
++ PR("wall-density[1]",ir->wall_density[1]);
++ PR("wall-ewald-zfac",ir->wall_ewald_zfac);
+
+ PS("pull",EPULLTYPE(ir->ePull));
+ if (ir->ePull != epullNO)
+ pr_pull(fp,indent,ir->pull);
+
+ PS("rotation",BOOL(ir->bRot));
+ if (ir->bRot)
+ pr_rot(fp,indent,ir->rot);
+
+ PS("disre",EDISRETYPE(ir->eDisre));
- PR("orires_fc",ir->orires_fc);
- PR("orires_tau",ir->orires_tau);
++ PS("disre-weighting",EDISREWEIGHTING(ir->eDisreWeighting));
++ PS("disre-mixed",BOOL(ir->bDisreMixed));
++ PR("dr-fc",ir->dr_fc);
++ PR("dr-tau",ir->dr_tau);
+ PR("nstdisreout",ir->nstdisreout);
- PR("em_stepsize",ir->em_stepsize);
- PR("em_tol",ir->em_tol);
++ PR("orires-fc",ir->orires_fc);
++ PR("orires-tau",ir->orires_tau);
+ PR("nstorireout",ir->nstorireout);
+
+ PR("dihre-fc",ir->dihre_fc);
+
- PR("fc_stepsize",ir->fc_stepsize);
++ PR("em-stepsize",ir->em_stepsize);
++ PR("em-tol",ir->em_tol);
+ PI("niter",ir->niter);
- PR("shake_tol",ir->shake_tol);
- PI("lincs_order",ir->nProjOrder);
- PR("lincs_warnangle",ir->LincsWarnAngle);
- PI("lincs_iter",ir->nLincsIter);
- PR("bd_fric",ir->bd_fric);
- PI("ld_seed",ir->ld_seed);
- PR("cos_accel",ir->cos_accel);
++ PR("fc-stepsize",ir->fc_stepsize);
+ PI("nstcgsteep",ir->nstcgsteep);
+ PI("nbfgscorr",ir->nbfgscorr);
+
+ PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
- pr_qm_opts(fp,indent,"qm_opts",&(ir->opts));
++ PR("shake-tol",ir->shake_tol);
++ PI("lincs-order",ir->nProjOrder);
++ PR("lincs-warnangle",ir->LincsWarnAngle);
++ PI("lincs-iter",ir->nLincsIter);
++ PR("bd-fric",ir->bd_fric);
++ PI("ld-seed",ir->ld_seed);
++ PR("cos-accel",ir->cos_accel);
+ pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
+ PI("userint1",ir->userint1);
+ PI("userint2",ir->userint2);
+ PI("userint3",ir->userint3);
+ PI("userint4",ir->userint4);
+ PR("userreal1",ir->userreal1);
+ PR("userreal2",ir->userreal2);
+ PR("userreal3",ir->userreal3);
+ PR("userreal4",ir->userreal4);
+ pr_grp_opts(fp,indent,"grpopts",&(ir->opts),bMDPformat);
+ pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]),bMDPformat);
+ pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]),bMDPformat);
+ pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]),bMDPformat);
+ pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]),bMDPformat);
+ pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]),bMDPformat);
+ pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]),bMDPformat);
+ PS("bQMMM",BOOL(ir->bQMMM));
+ PI("QMconstraints",ir->QMconstraints);
+ PI("QMMMscheme",ir->QMMMscheme);
+ PR("scalefactor",ir->scalefactor);
++ pr_qm_opts(fp,indent,"qm-opts",&(ir->opts));
+ }
+}
+#undef PS
+#undef PR
+#undef PI
+
+static void pr_harm(FILE *fp,t_iparams *iparams,const char *r,const char *kr)
+{
+ fprintf(fp,"%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
+ r,iparams->harmonic.rA,kr,iparams->harmonic.krA,
+ r,iparams->harmonic.rB,kr,iparams->harmonic.krB);
+}
+
+void pr_iparams(FILE *fp,t_functype ftype,t_iparams *iparams)
+{
+ int i;
+ real VA[4],VB[4],*rbcA,*rbcB;
+
+ switch (ftype) {
+ case F_ANGLES:
+ case F_G96ANGLES:
+ pr_harm(fp,iparams,"th","ct");
+ break;
+ case F_CROSS_BOND_BONDS:
+ fprintf(fp,"r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
+ iparams->cross_bb.r1e,iparams->cross_bb.r2e,
+ iparams->cross_bb.krr);
+ break;
+ case F_CROSS_BOND_ANGLES:
+ fprintf(fp,"r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
+ iparams->cross_ba.r1e,iparams->cross_ba.r2e,
+ iparams->cross_ba.r3e,iparams->cross_ba.krt);
+ break;
+ case F_UREY_BRADLEY:
+ fprintf(fp,"theta=%15.8e, ktheta=%15.8e, r13=%15.8e, kUB=%15.8e\n",
+ iparams->u_b.theta,iparams->u_b.ktheta,iparams->u_b.r13,iparams->u_b.kUB);
+ break;
+ case F_QUARTIC_ANGLES:
+ fprintf(fp,"theta=%15.8e",iparams->qangle.theta);
+ for(i=0; i<5; i++)
+ fprintf(fp,", c%c=%15.8e",'0'+i,iparams->qangle.c[i]);
+ fprintf(fp,"\n");
+ break;
+ case F_BHAM:
+ fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
+ iparams->bham.a,iparams->bham.b,iparams->bham.c);
+ break;
+ case F_BONDS:
+ case F_G96BONDS:
+ case F_HARMONIC:
+ pr_harm(fp,iparams,"b0","cb");
+ break;
+ case F_IDIHS:
+ pr_harm(fp,iparams,"xi","cx");
+ break;
+ case F_MORSE:
+ fprintf(fp,"b0=%15.8e, cb=%15.8e, beta=%15.8e\n",
+ iparams->morse.b0,iparams->morse.cb,iparams->morse.beta);
+ break;
+ case F_CUBICBONDS:
+ fprintf(fp,"b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
+ iparams->cubic.b0,iparams->cubic.kb,iparams->cubic.kcub);
+ break;
+ case F_CONNBONDS:
+ fprintf(fp,"\n");
+ break;
+ case F_FENEBONDS:
+ fprintf(fp,"bm=%15.8e, kb=%15.8e\n",iparams->fene.bm,iparams->fene.kb);
+ break;
+ case F_RESTRBONDS:
+ fprintf(fp,"lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, up2B=%15.8e, kB=%15.8e,\n",
+ iparams->restraint.lowA,iparams->restraint.up1A,
+ iparams->restraint.up2A,iparams->restraint.kA,
+ iparams->restraint.lowB,iparams->restraint.up1B,
+ iparams->restraint.up2B,iparams->restraint.kB);
+ break;
+ case F_TABBONDS:
+ case F_TABBONDSNC:
+ case F_TABANGLES:
+ case F_TABDIHS:
+ fprintf(fp,"tab=%d, kA=%15.8e, kB=%15.8e\n",
+ iparams->tab.table,iparams->tab.kA,iparams->tab.kB);
+ break;
+ case F_POLARIZATION:
+ fprintf(fp,"alpha=%15.8e\n",iparams->polarize.alpha);
+ break;
+ case F_THOLE_POL:
+ fprintf(fp,"a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
+ iparams->thole.a,iparams->thole.alpha1,iparams->thole.alpha2,
+ iparams->thole.rfac);
+ break;
+ case F_WATER_POL:
+ fprintf(fp,"al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
+ iparams->wpol.al_x,iparams->wpol.al_y,iparams->wpol.al_z,
+ iparams->wpol.rOH,iparams->wpol.rHH,iparams->wpol.rOD);
+ break;
+ case F_LJ:
+ fprintf(fp,"c6=%15.8e, c12=%15.8e\n",iparams->lj.c6,iparams->lj.c12);
+ break;
+ case F_LJ14:
+ fprintf(fp,"c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
+ iparams->lj14.c6A,iparams->lj14.c12A,
+ iparams->lj14.c6B,iparams->lj14.c12B);
+ break;
+ case F_LJC14_Q:
+ fprintf(fp,"fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
+ iparams->ljc14.fqq,
+ iparams->ljc14.qi,iparams->ljc14.qj,
+ iparams->ljc14.c6,iparams->ljc14.c12);
+ break;
+ case F_LJC_PAIRS_NB:
+ fprintf(fp,"qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
+ iparams->ljcnb.qi,iparams->ljcnb.qj,
+ iparams->ljcnb.c6,iparams->ljcnb.c12);
+ break;
+ case F_PDIHS:
+ case F_PIDIHS:
+ case F_ANGRES:
+ case F_ANGRESZ:
+ fprintf(fp,"phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
+ iparams->pdihs.phiA,iparams->pdihs.cpA,
+ iparams->pdihs.phiB,iparams->pdihs.cpB,
+ iparams->pdihs.mult);
+ break;
+ case F_DISRES:
+ fprintf(fp,"label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
+ iparams->disres.label,iparams->disres.type,
+ iparams->disres.low,iparams->disres.up1,
+ iparams->disres.up2,iparams->disres.kfac);
+ break;
+ case F_ORIRES:
+ fprintf(fp,"ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
+ iparams->orires.ex,iparams->orires.label,iparams->orires.power,
+ iparams->orires.c,iparams->orires.obs,iparams->orires.kfac);
+ break;
+ case F_DIHRES:
+ fprintf(fp,"label=%d, power=%4d phi=%15.8e, dphi=%15.8e, kfac=%15.8e)\n",
+ iparams->dihres.label,iparams->dihres.power,
+ iparams->dihres.phi,iparams->dihres.dphi,iparams->dihres.kfac);
+ break;
+ case F_POSRES:
+ fprintf(fp,"pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)\n",
+ iparams->posres.pos0A[XX],iparams->posres.pos0A[YY],
+ iparams->posres.pos0A[ZZ],iparams->posres.fcA[XX],
+ iparams->posres.fcA[YY],iparams->posres.fcA[ZZ],
+ iparams->posres.pos0B[XX],iparams->posres.pos0B[YY],
+ iparams->posres.pos0B[ZZ],iparams->posres.fcB[XX],
+ iparams->posres.fcB[YY],iparams->posres.fcB[ZZ]);
+ break;
+ case F_RBDIHS:
+ for (i=0; i<NR_RBDIHS; i++)
+ fprintf(fp,"%srbcA[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcA[i]);
+ fprintf(fp,"\n");
+ for (i=0; i<NR_RBDIHS; i++)
+ fprintf(fp,"%srbcB[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcB[i]);
+ fprintf(fp,"\n");
+ break;
+ case F_FOURDIHS:
+ /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get the
+ * OPLS potential constants back.
+ */
+ rbcA = iparams->rbdihs.rbcA;
+ rbcB = iparams->rbdihs.rbcB;
+
+ VA[3] = -0.25*rbcA[4];
+ VA[2] = -0.5*rbcA[3];
+ VA[1] = 4.0*VA[3]-rbcA[2];
+ VA[0] = 3.0*VA[2]-2.0*rbcA[1];
+
+ VB[3] = -0.25*rbcB[4];
+ VB[2] = -0.5*rbcB[3];
+ VB[1] = 4.0*VB[3]-rbcB[2];
+ VB[0] = 3.0*VB[2]-2.0*rbcB[1];
+
+ for (i=0; i<NR_FOURDIHS; i++)
+ fprintf(fp,"%sFourA[%d]=%15.8e",i==0?"":", ",i,VA[i]);
+ fprintf(fp,"\n");
+ for (i=0; i<NR_FOURDIHS; i++)
+ fprintf(fp,"%sFourB[%d]=%15.8e",i==0?"":", ",i,VB[i]);
+ fprintf(fp,"\n");
+ break;
+
+ case F_CONSTR:
+ case F_CONSTRNC:
+ fprintf(fp,"dA=%15.8e, dB=%15.8e\n",iparams->constr.dA,iparams->constr.dB);
+ break;
+ case F_SETTLE:
+ fprintf(fp,"doh=%15.8e, dhh=%15.8e\n",iparams->settle.doh,
+ iparams->settle.dhh);
+ break;
+ case F_VSITE2:
+ fprintf(fp,"a=%15.8e\n",iparams->vsite.a);
+ break;
+ case F_VSITE3:
+ case F_VSITE3FD:
+ case F_VSITE3FAD:
+ fprintf(fp,"a=%15.8e, b=%15.8e\n",iparams->vsite.a,iparams->vsite.b);
+ break;
+ case F_VSITE3OUT:
+ case F_VSITE4FD:
+ case F_VSITE4FDN:
+ fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
+ iparams->vsite.a,iparams->vsite.b,iparams->vsite.c);
+ break;
+ case F_VSITEN:
+ fprintf(fp,"n=%2d, a=%15.8e\n",iparams->vsiten.n,iparams->vsiten.a);
+ break;
+ case F_GB12:
+ case F_GB13:
+ case F_GB14:
+ fprintf(fp, "sar=%15.8e, st=%15.8e, pi=%15.8e, gbr=%15.8e, bmlt=%15.8e\n",iparams->gb.sar,iparams->gb.st,iparams->gb.pi,iparams->gb.gbr,iparams->gb.bmlt);
+ break;
+ case F_CMAP:
+ fprintf(fp, "cmapA=%1d, cmapB=%1d\n",iparams->cmap.cmapA, iparams->cmap.cmapB);
+ break;
+ default:
+ gmx_fatal(FARGS,"unknown function type %d (%s) in %s line %d",
+ ftype,interaction_function[ftype].name,__FILE__,__LINE__);
+ }
+}
+
+void pr_ilist(FILE *fp,int indent,const char *title,
+ t_functype *functype,t_ilist *ilist, gmx_bool bShowNumbers)
+{
+ int i,j,k,type,ftype;
+ t_iatom *iatoms;
+
+ if (available(fp,ilist,indent,title) && ilist->nr > 0)
+ {
+ indent=pr_title(fp,indent,title);
+ (void) pr_indent(fp,indent);
+ fprintf(fp,"nr: %d\n",ilist->nr);
+ if (ilist->nr > 0) {
+ (void) pr_indent(fp,indent);
+ fprintf(fp,"iatoms:\n");
+ iatoms=ilist->iatoms;
+ for (i=j=0; i<ilist->nr;) {
+#ifndef DEBUG
+ (void) pr_indent(fp,indent+INDENT);
+ type=*(iatoms++);
+ ftype=functype[type];
+ (void) fprintf(fp,"%d type=%d (%s)",
+ bShowNumbers?j:-1,bShowNumbers?type:-1,
+ interaction_function[ftype].name);
+ j++;
+ for (k=0; k<interaction_function[ftype].nratoms; k++)
+ (void) fprintf(fp," %u",*(iatoms++));
+ (void) fprintf(fp,"\n");
+ i+=1+interaction_function[ftype].nratoms;
+#else
+ fprintf(fp,"%5d%5d\n",i,iatoms[i]);
+ i++;
+#endif
+ }
+ }
+ }
+}
+
+static void pr_cmap(FILE *fp, int indent, const char *title,
+ gmx_cmap_t *cmap_grid, gmx_bool bShowNumbers)
+{
+ int i,j,nelem;
+ real dx,idx;
+
+ dx = 360.0 / cmap_grid->grid_spacing;
+ nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
+
+ if(available(fp,cmap_grid,indent,title))
+ {
+ fprintf(fp,"%s\n",title);
+
+ for(i=0;i<cmap_grid->ngrid;i++)
+ {
+ idx = -180.0;
+ fprintf(fp,"%8s %8s %8s %8s\n","V","dVdx","dVdy","d2dV");
+
+ fprintf(fp,"grid[%3d]={\n",bShowNumbers?i:-1);
+
+ for(j=0;j<nelem;j++)
+ {
+ if( (j%cmap_grid->grid_spacing)==0)
+ {
+ fprintf(fp,"%8.1f\n",idx);
+ idx+=dx;
+ }
+
+ fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4]);
+ fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+1]);
+ fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+2]);
+ fprintf(fp,"%8.3f\n",cmap_grid->cmapdata[i].cmap[j*4+3]);
+ }
+ fprintf(fp,"\n");
+ }
+ }
+
+}
+
+void pr_ffparams(FILE *fp,int indent,const char *title,
+ gmx_ffparams_t *ffparams,
+ gmx_bool bShowNumbers)
+{
+ int i,j;
+
+ indent=pr_title(fp,indent,title);
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"atnr=%d\n",ffparams->atnr);
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"ntypes=%d\n",ffparams->ntypes);
+ for (i=0; i<ffparams->ntypes; i++) {
+ (void) pr_indent(fp,indent+INDENT);
+ (void) fprintf(fp,"functype[%d]=%s, ",
+ bShowNumbers?i:-1,
+ interaction_function[ffparams->functype[i]].name);
+ pr_iparams(fp,ffparams->functype[i],&ffparams->iparams[i]);
+ }
+ (void) pr_double(fp,indent,"reppow",ffparams->reppow);
+ (void) pr_real(fp,indent,"fudgeQQ",ffparams->fudgeQQ);
+ pr_cmap(fp,indent,"cmap",&ffparams->cmap_grid,bShowNumbers);
+}
+
+void pr_idef(FILE *fp,int indent,const char *title,t_idef *idef, gmx_bool bShowNumbers)
+{
+ int i,j;
+
+ if (available(fp,idef,indent,title)) {
+ indent=pr_title(fp,indent,title);
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"atnr=%d\n",idef->atnr);
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"ntypes=%d\n",idef->ntypes);
+ for (i=0; i<idef->ntypes; i++) {
+ (void) pr_indent(fp,indent+INDENT);
+ (void) fprintf(fp,"functype[%d]=%s, ",
+ bShowNumbers?i:-1,
+ interaction_function[idef->functype[i]].name);
+ pr_iparams(fp,idef->functype[i],&idef->iparams[i]);
+ }
+ (void) pr_real(fp,indent,"fudgeQQ",idef->fudgeQQ);
+
+ for(j=0; (j<F_NRE); j++)
+ pr_ilist(fp,indent,interaction_function[j].longname,
+ idef->functype,&idef->il[j],bShowNumbers);
+ }
+}
+
+static int pr_block_title(FILE *fp,int indent,const char *title,t_block *block)
+{
+ int i;
+
+ if (available(fp,block,indent,title))
+ {
+ indent=pr_title(fp,indent,title);
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"nr=%d\n",block->nr);
+ }
+ return indent;
+}
+
+static int pr_blocka_title(FILE *fp,int indent,const char *title,t_blocka *block)
+{
+ int i;
+
+ if (available(fp,block,indent,title))
+ {
+ indent=pr_title(fp,indent,title);
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"nr=%d\n",block->nr);
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"nra=%d\n",block->nra);
+ }
+ return indent;
+}
+
+static void low_pr_block(FILE *fp,int indent,const char *title,t_block *block, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp,block,indent,title))
+ {
+ indent=pr_block_title(fp,indent,title,block);
+ for (i=0; i<=block->nr; i++)
+ {
+ (void) pr_indent(fp,indent+INDENT);
+ (void) fprintf(fp,"%s->index[%d]=%u\n",
+ title,bShowNumbers?i:-1,block->index[i]);
+ }
+ }
+}
+
+static void low_pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp,block,indent,title))
+ {
+ indent=pr_blocka_title(fp,indent,title,block);
+ for (i=0; i<=block->nr; i++)
+ {
+ (void) pr_indent(fp,indent+INDENT);
+ (void) fprintf(fp,"%s->index[%d]=%u\n",
+ title,bShowNumbers?i:-1,block->index[i]);
+ }
+ for (i=0; i<block->nra; i++)
+ {
+ (void) pr_indent(fp,indent+INDENT);
+ (void) fprintf(fp,"%s->a[%d]=%u\n",
+ title,bShowNumbers?i:-1,block->a[i]);
+ }
+ }
+}
+
+void pr_block(FILE *fp,int indent,const char *title,t_block *block,gmx_bool bShowNumbers)
+{
+ int i,j,ok,size,start,end;
+
+ if (available(fp,block,indent,title))
+ {
+ indent=pr_block_title(fp,indent,title,block);
+ start=0;
+ end=start;
+ if ((ok=(block->index[start]==0))==0)
+ (void) fprintf(fp,"block->index[%d] should be 0\n",start);
+ else
+ for (i=0; i<block->nr; i++)
+ {
+ end=block->index[i+1];
+ size=pr_indent(fp,indent);
+ if (end<=start)
+ size+=fprintf(fp,"%s[%d]={}\n",title,i);
+ else
+ size+=fprintf(fp,"%s[%d]={%d..%d}\n",
+ title,bShowNumbers?i:-1,
+ bShowNumbers?start:-1,bShowNumbers?end-1:-1);
+ start=end;
+ }
+ }
+}
+
+void pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block,gmx_bool bShowNumbers)
+{
+ int i,j,ok,size,start,end;
+
+ if (available(fp,block,indent,title))
+ {
+ indent=pr_blocka_title(fp,indent,title,block);
+ start=0;
+ end=start;
+ if ((ok=(block->index[start]==0))==0)
+ (void) fprintf(fp,"block->index[%d] should be 0\n",start);
+ else
+ for (i=0; i<block->nr; i++)
+ {
+ end=block->index[i+1];
+ size=pr_indent(fp,indent);
+ if (end<=start)
+ size+=fprintf(fp,"%s[%d]={",title,i);
+ else
+ size+=fprintf(fp,"%s[%d][%d..%d]={",
+ title,bShowNumbers?i:-1,
+ bShowNumbers?start:-1,bShowNumbers?end-1:-1);
+ for (j=start; j<end; j++)
+ {
+ if (j>start) size+=fprintf(fp,", ");
+ if ((size)>(USE_WIDTH))
+ {
+ (void) fprintf(fp,"\n");
+ size=pr_indent(fp,indent+INDENT);
+ }
+ size+=fprintf(fp,"%u",block->a[j]);
+ }
+ (void) fprintf(fp,"}\n");
+ start=end;
+ }
+ if ((end!=block->nra)||(!ok))
+ {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"tables inconsistent, dumping complete tables:\n");
+ low_pr_blocka(fp,indent,title,block,bShowNumbers);
+ }
+ }
+}
+
+static void pr_strings(FILE *fp,int indent,const char *title,char ***nm,int n, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp,nm,indent,title))
+ {
+ indent=pr_title_n(fp,indent,title,n);
+ for (i=0; i<n; i++)
+ {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s[%d]={name=\"%s\"}\n",
+ title,bShowNumbers?i:-1,*(nm[i]));
+ }
+ }
+}
+
+static void pr_strings2(FILE *fp,int indent,const char *title,
+ char ***nm,char ***nmB,int n, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp,nm,indent,title))
+ {
+ indent=pr_title_n(fp,indent,title,n);
+ for (i=0; i<n; i++)
+ {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s[%d]={name=\"%s\",nameB=\"%s\"}\n",
+ title,bShowNumbers?i:-1,*(nm[i]),*(nmB[i]));
+ }
+ }
+}
+
+static void pr_resinfo(FILE *fp,int indent,const char *title,t_resinfo *resinfo,int n, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp,resinfo,indent,title))
+ {
+ indent=pr_title_n(fp,indent,title,n);
+ for (i=0; i<n; i++)
+ {
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n",
+ title,bShowNumbers?i:-1,
+ *(resinfo[i].name),resinfo[i].nr,
+ (resinfo[i].ic == '\0') ? ' ' : resinfo[i].ic);
+ }
+ }
+}
+
+static void pr_atom(FILE *fp,int indent,const char *title,t_atom *atom,int n)
+{
+ int i,j;
+
+ if (available(fp,atom,indent,title)) {
+ indent=pr_title_n(fp,indent,title,n);
+ for (i=0; i<n; i++) {
+ (void) pr_indent(fp,indent);
+ fprintf(fp,"%s[%6d]={type=%3d, typeB=%3d, ptype=%8s, m=%12.5e, "
+ "q=%12.5e, mB=%12.5e, qB=%12.5e, resind=%5d, atomnumber=%3d}\n",
+ title,i,atom[i].type,atom[i].typeB,ptype_str[atom[i].ptype],
+ atom[i].m,atom[i].q,atom[i].mB,atom[i].qB,
+ atom[i].resind,atom[i].atomnumber);
+ }
+ }
+}
+
+static void pr_grps(FILE *fp,int indent,const char *title,t_grps grps[],
+ char **grpname[], gmx_bool bShowNumbers)
+{
+ int i,j;
+
+ for(i=0; (i<egcNR); i++)
+ {
+ fprintf(fp,"%s[%-12s] nr=%d, name=[",title,gtypes[i],grps[i].nr);
+ for(j=0; (j<grps[i].nr); j++)
+ {
+ fprintf(fp," %s",*(grpname[grps[i].nm_ind[j]]));
+ }
+ fprintf(fp,"]\n");
+ }
+}
+
+static void pr_groups(FILE *fp,int indent,const char *title,
+ gmx_groups_t *groups,
+ gmx_bool bShowNumbers)
+{
+ int grpnr[egcNR];
+ int nat_max,i,g;
+
+ pr_grps(fp,indent,"grp",groups->grps,groups->grpname,bShowNumbers);
+ pr_strings(fp,indent,"grpname",groups->grpname,groups->ngrpname,bShowNumbers);
+
+ (void) pr_indent(fp,indent);
+ fprintf(fp,"groups ");
+ for(g=0; g<egcNR; g++)
+ {
+ printf(" %5.5s",gtypes[g]);
+ }
+ printf("\n");
+
+ (void) pr_indent(fp,indent);
+ fprintf(fp,"allocated ");
+ nat_max = 0;
+ for(g=0; g<egcNR; g++)
+ {
+ printf(" %5d",groups->ngrpnr[g]);
+ nat_max = max(nat_max,groups->ngrpnr[g]);
+ }
+ printf("\n");
+
+ if (nat_max == 0)
+ {
+ (void) pr_indent(fp,indent);
+ fprintf(fp,"groupnr[%5s] =","*");
+ for(g=0; g<egcNR; g++)
+ {
+ fprintf(fp," %3d ",0);
+ }
+ fprintf(fp,"\n");
+ }
+ else
+ {
+ for(i=0; i<nat_max; i++)
+ {
+ (void) pr_indent(fp,indent);
+ fprintf(fp,"groupnr[%5d] =",i);
+ for(g=0; g<egcNR; g++)
+ {
+ fprintf(fp," %3d ",
+ groups->grpnr[g] ? groups->grpnr[g][i] : 0);
+ }
+ fprintf(fp,"\n");
+ }
+ }
+}
+
+void pr_atoms(FILE *fp,int indent,const char *title,t_atoms *atoms,
+ gmx_bool bShownumbers)
+{
+ if (available(fp,atoms,indent,title))
+ {
+ indent=pr_title(fp,indent,title);
+ pr_atom(fp,indent,"atom",atoms->atom,atoms->nr);
+ pr_strings(fp,indent,"atom",atoms->atomname,atoms->nr,bShownumbers);
+ pr_strings2(fp,indent,"type",atoms->atomtype,atoms->atomtypeB,atoms->nr,bShownumbers);
+ pr_resinfo(fp,indent,"residue",atoms->resinfo,atoms->nres,bShownumbers);
+ }
+}
+
+
+void pr_atomtypes(FILE *fp,int indent,const char *title,t_atomtypes *atomtypes,
+ gmx_bool bShowNumbers)
+{
+ int i;
+ if (available(fp,atomtypes,indent,title))
+ {
+ indent=pr_title(fp,indent,title);
+ for(i=0;i<atomtypes->nr;i++) {
+ pr_indent(fp,indent);
+ fprintf(fp,
+ "atomtype[%3d]={radius=%12.5e, volume=%12.5e, gb_radius=%12.5e, surftens=%12.5e, atomnumber=%4d, S_hct=%12.5e)}\n",
+ bShowNumbers?i:-1,atomtypes->radius[i],atomtypes->vol[i],
+ atomtypes->gb_radius[i],
+ atomtypes->surftens[i],atomtypes->atomnumber[i],atomtypes->S_hct[i]);
+ }
+ }
+}
+
+static void pr_moltype(FILE *fp,int indent,const char *title,
+ gmx_moltype_t *molt,int n,
+ gmx_ffparams_t *ffparams,
+ gmx_bool bShowNumbers)
+{
+ int j;
+
+ indent = pr_title_n(fp,indent,title,n);
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"name=\"%s\"\n",*(molt->name));
+ pr_atoms(fp,indent,"atoms",&(molt->atoms),bShowNumbers);
+ pr_block(fp,indent,"cgs",&molt->cgs, bShowNumbers);
+ pr_blocka(fp,indent,"excls",&molt->excls, bShowNumbers);
+ for(j=0; (j<F_NRE); j++) {
+ pr_ilist(fp,indent,interaction_function[j].longname,
+ ffparams->functype,&molt->ilist[j],bShowNumbers);
+ }
+}
+
+static void pr_molblock(FILE *fp,int indent,const char *title,
+ gmx_molblock_t *molb,int n,
+ gmx_moltype_t *molt,
+ gmx_bool bShowNumbers)
+{
+ indent = pr_title_n(fp,indent,title,n);
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"%-20s = %d \"%s\"\n",
+ "moltype",molb->type,*(molt[molb->type].name));
+ pr_int(fp,indent,"#molecules",molb->nmol);
+ pr_int(fp,indent,"#atoms_mol",molb->natoms_mol);
+ pr_int(fp,indent,"#posres_xA",molb->nposres_xA);
+ if (molb->nposres_xA > 0) {
+ pr_rvecs(fp,indent,"posres_xA",molb->posres_xA,molb->nposres_xA);
+ }
+ pr_int(fp,indent,"#posres_xB",molb->nposres_xB);
+ if (molb->nposres_xB > 0) {
+ pr_rvecs(fp,indent,"posres_xB",molb->posres_xB,molb->nposres_xB);
+ }
+}
+
+void pr_mtop(FILE *fp,int indent,const char *title,gmx_mtop_t *mtop,
+ gmx_bool bShowNumbers)
+{
+ int mt,mb;
+
+ if (available(fp,mtop,indent,title)) {
+ indent=pr_title(fp,indent,title);
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"name=\"%s\"\n",*(mtop->name));
+ pr_int(fp,indent,"#atoms",mtop->natoms);
+ for(mb=0; mb<mtop->nmolblock; mb++) {
+ pr_molblock(fp,indent,"molblock",&mtop->molblock[mb],mb,
+ mtop->moltype,bShowNumbers);
+ }
+ pr_ffparams(fp,indent,"ffparams",&(mtop->ffparams),bShowNumbers);
+ pr_atomtypes(fp,indent,"atomtypes",&(mtop->atomtypes),bShowNumbers);
+ for(mt=0; mt<mtop->nmoltype; mt++) {
+ pr_moltype(fp,indent,"moltype",&mtop->moltype[mt],mt,
+ &mtop->ffparams,bShowNumbers);
+ }
+ pr_groups(fp,indent,"groups",&mtop->groups,bShowNumbers);
+ }
+}
+
+void pr_top(FILE *fp,int indent,const char *title,t_topology *top, gmx_bool bShowNumbers)
+{
+ if (available(fp,top,indent,title)) {
+ indent=pr_title(fp,indent,title);
+ (void) pr_indent(fp,indent);
+ (void) fprintf(fp,"name=\"%s\"\n",*(top->name));
+ pr_atoms(fp,indent,"atoms",&(top->atoms),bShowNumbers);
+ pr_atomtypes(fp,indent,"atomtypes",&(top->atomtypes),bShowNumbers);
+ pr_block(fp,indent,"cgs",&top->cgs, bShowNumbers);
+ pr_block(fp,indent,"mols",&top->mols, bShowNumbers);
+ pr_blocka(fp,indent,"excls",&top->excls, bShowNumbers);
+ pr_idef(fp,indent,"idef",&top->idef,bShowNumbers);
+ }
+}
+
+void pr_header(FILE *fp,int indent,const char *title,t_tpxheader *sh)
+{
+ char buf[22];
+
+ if (available(fp,sh,indent,title))
+ {
+ indent=pr_title(fp,indent,title);
+ pr_indent(fp,indent);
+ fprintf(fp,"bIr = %spresent\n",sh->bIr?"":"not ");
+ pr_indent(fp,indent);
+ fprintf(fp,"bBox = %spresent\n",sh->bBox?"":"not ");
+ pr_indent(fp,indent);
+ fprintf(fp,"bTop = %spresent\n",sh->bTop?"":"not ");
+ pr_indent(fp,indent);
+ fprintf(fp,"bX = %spresent\n",sh->bX?"":"not ");
+ pr_indent(fp,indent);
+ fprintf(fp,"bV = %spresent\n",sh->bV?"":"not ");
+ pr_indent(fp,indent);
+ fprintf(fp,"bF = %spresent\n",sh->bF?"":"not ");
+
+ pr_indent(fp,indent);
+ fprintf(fp,"natoms = %d\n",sh->natoms);
+ pr_indent(fp,indent);
+ fprintf(fp,"lambda = %e\n",sh->lambda);
+ }
+}
+
+void pr_commrec(FILE *fp,int indent,t_commrec *cr)
+{
+ pr_indent(fp,indent);
+ fprintf(fp,"commrec:\n");
+ indent+=2;
+ pr_indent(fp,indent);
+ fprintf(fp,"nodeid = %d\n",cr->nodeid);
+ pr_indent(fp,indent);
+ fprintf(fp,"nnodes = %d\n",cr->nnodes);
+ pr_indent(fp,indent);
+ fprintf(fp,"npmenodes = %d\n",cr->npmenodes);
+ /*
+ pr_indent(fp,indent);
+ fprintf(fp,"threadid = %d\n",cr->threadid);
+ pr_indent(fp,indent);
+ fprintf(fp,"nthreads = %d\n",cr->nthreads);
+ */
+}
--- /dev/null
- sprintf(err_buf,"tau_p must be > 0 instead of %g\n",ir->tau_p);
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <ctype.h>
+#include <stdlib.h>
+#include <limits.h>
+#include "sysstuff.h"
+#include "smalloc.h"
+#include "typedefs.h"
+#include "physics.h"
+#include "names.h"
+#include "gmx_fatal.h"
+#include "macros.h"
+#include "index.h"
+#include "symtab.h"
+#include "string2.h"
+#include "readinp.h"
+#include "warninp.h"
+#include "readir.h"
+#include "toputil.h"
+#include "index.h"
+#include "network.h"
+#include "vec.h"
+#include "pbc.h"
+#include "mtop_util.h"
+#include "chargegroup.h"
+#include "inputrec.h"
+
+#define MAXPTR 254
+#define NOGID 255
+
+/* Resource parameters
+ * Do not change any of these until you read the instruction
+ * in readinp.h. Some cpp's do not take spaces after the backslash
+ * (like the c-shell), which will give you a very weird compiler
+ * message.
+ */
+
+static char tcgrps[STRLEN],tau_t[STRLEN],ref_t[STRLEN],
+ acc[STRLEN],accgrps[STRLEN],freeze[STRLEN],frdim[STRLEN],
+ energy[STRLEN],user1[STRLEN],user2[STRLEN],vcm[STRLEN],xtc_grps[STRLEN],
+ couple_moltype[STRLEN],orirefitgrp[STRLEN],egptable[STRLEN],egpexcl[STRLEN],
+ wall_atomtype[STRLEN],wall_density[STRLEN],deform[STRLEN],QMMM[STRLEN];
+static char foreign_lambda[STRLEN];
+static char **pull_grp;
+static char **rot_grp;
+static char anneal[STRLEN],anneal_npoints[STRLEN],
+ anneal_time[STRLEN],anneal_temp[STRLEN];
+static char QMmethod[STRLEN],QMbasis[STRLEN],QMcharge[STRLEN],QMmult[STRLEN],
+ bSH[STRLEN],CASorbitals[STRLEN], CASelectrons[STRLEN],SAon[STRLEN],
+ SAoff[STRLEN],SAsteps[STRLEN],bTS[STRLEN],bOPT[STRLEN];
+static char efield_x[STRLEN],efield_xt[STRLEN],efield_y[STRLEN],
+ efield_yt[STRLEN],efield_z[STRLEN],efield_zt[STRLEN];
+
+enum {
+ egrptpALL, /* All particles have to be a member of a group. */
+ egrptpALL_GENREST, /* A rest group with name is generated for particles *
+ * that are not part of any group. */
+ egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
+ * for the rest group. */
+ egrptpONE /* Merge all selected groups into one group, *
+ * make a rest group for the remaining particles. */
+};
+
+
+void init_ir(t_inputrec *ir, t_gromppopts *opts)
+{
+ snew(opts->include,STRLEN);
+ snew(opts->define,STRLEN);
+}
+
+static void _low_check(gmx_bool b,char *s,warninp_t wi)
+{
+ if (b)
+ {
+ warning_error(wi,s);
+ }
+}
+
+static void check_nst(const char *desc_nst,int nst,
+ const char *desc_p,int *p,
+ warninp_t wi)
+{
+ char buf[STRLEN];
+
+ if (*p > 0 && *p % nst != 0)
+ {
+ /* Round up to the next multiple of nst */
+ *p = ((*p)/nst + 1)*nst;
+ sprintf(buf,"%s should be a multiple of %s, changing %s to %d\n",
+ desc_p,desc_nst,desc_p,*p);
+ warning(wi,buf);
+ }
+}
+
+static gmx_bool ir_NVE(const t_inputrec *ir)
+{
+ return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
+}
+
+static int lcd(int n1,int n2)
+{
+ int d,i;
+
+ d = 1;
+ for(i=2; (i<=n1 && i<=n2); i++)
+ {
+ if (n1 % i == 0 && n2 % i == 0)
+ {
+ d = i;
+ }
+ }
+
+ return d;
+}
+
+void check_ir(const char *mdparin,t_inputrec *ir, t_gromppopts *opts,
+ warninp_t wi)
+/* Check internal consistency */
+{
+ /* Strange macro: first one fills the err_buf, and then one can check
+ * the condition, which will print the message and increase the error
+ * counter.
+ */
+#define CHECK(b) _low_check(b,err_buf,wi)
+ char err_buf[256],warn_buf[STRLEN];
+ int ns_type=0;
+ real dt_pcoupl;
+
+ set_warning_line(wi,mdparin,-1);
+
+ /* BASIC CUT-OFF STUFF */
+ if (ir->rlist == 0 ||
+ !((EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > ir->rlist) ||
+ (EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > ir->rlist))) {
+ /* No switched potential and/or no twin-range:
+ * we can set the long-range cut-off to the maximum of the other cut-offs.
+ */
+ ir->rlistlong = max_cutoff(ir->rlist,max_cutoff(ir->rvdw,ir->rcoulomb));
+ } else if (ir->rlistlong < 0) {
+ ir->rlistlong = max_cutoff(ir->rlist,max_cutoff(ir->rvdw,ir->rcoulomb));
+ sprintf(warn_buf,"rlistlong was not set, setting it to %g (no buffer)",
+ ir->rlistlong);
+ warning(wi,warn_buf);
+ }
+ if (ir->rlistlong == 0 && ir->ePBC != epbcNONE) {
+ warning_error(wi,"Can not have an infinite cut-off with PBC");
+ }
+ if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist)) {
+ warning_error(wi,"rlistlong can not be shorter than rlist");
+ }
+ if (IR_TWINRANGE(*ir) && ir->nstlist <= 0) {
+ warning_error(wi,"Can not have nstlist<=0 with twin-range interactions");
+ }
+
+ /* GENERAL INTEGRATOR STUFF */
+ if (!(ir->eI == eiMD || EI_VV(ir->eI)))
+ {
+ ir->etc = etcNO;
+ }
+ if (!EI_DYNAMICS(ir->eI))
+ {
+ ir->epc = epcNO;
+ }
+ if (EI_DYNAMICS(ir->eI))
+ {
+ if (ir->nstcalcenergy < 0)
+ {
+ ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
+ if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
+ {
+ /* nstcalcenergy larger than nstener does not make sense.
+ * We ideally want nstcalcenergy=nstener.
+ */
+ if (ir->nstlist > 0)
+ {
+ ir->nstcalcenergy = lcd(ir->nstenergy,ir->nstlist);
+ }
+ else
+ {
+ ir->nstcalcenergy = ir->nstenergy;
+ }
+ }
+ }
+ if (ir->epc != epcNO)
+ {
+ if (ir->nstpcouple < 0)
+ {
+ ir->nstpcouple = ir_optimal_nstpcouple(ir);
+ }
+ }
+ if (IR_TWINRANGE(*ir))
+ {
+ check_nst("nstlist",ir->nstlist,
+ "nstcalcenergy",&ir->nstcalcenergy,wi);
+ if (ir->epc != epcNO)
+ {
+ check_nst("nstlist",ir->nstlist,
+ "nstpcouple",&ir->nstpcouple,wi);
+ }
+ }
+
+ if (ir->nstcalcenergy > 1)
+ {
+ /* for storing exact averages nstenergy should be
+ * a multiple of nstcalcenergy
+ */
+ check_nst("nstcalcenergy",ir->nstcalcenergy,
+ "nstenergy",&ir->nstenergy,wi);
+ if (ir->efep != efepNO)
+ {
+ /* nstdhdl should be a multiple of nstcalcenergy */
+ check_nst("nstcalcenergy",ir->nstcalcenergy,
+ "nstdhdl",&ir->nstdhdl,wi);
+ }
+ }
+ }
+
+ /* LD STUFF */
+ if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
+ ir->bContinuation && ir->ld_seed != -1) {
+ warning_note(wi,"You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
+ }
+
+ /* TPI STUFF */
+ if (EI_TPI(ir->eI)) {
+ sprintf(err_buf,"TPI only works with pbc = %s",epbc_names[epbcXYZ]);
+ CHECK(ir->ePBC != epbcXYZ);
+ sprintf(err_buf,"TPI only works with ns = %s",ens_names[ensGRID]);
+ CHECK(ir->ns_type != ensGRID);
+ sprintf(err_buf,"with TPI nstlist should be larger than zero");
+ CHECK(ir->nstlist <= 0);
+ sprintf(err_buf,"TPI does not work with full electrostatics other than PME");
+ CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
+ }
+
+ /* SHAKE / LINCS */
+ if ( (opts->nshake > 0) && (opts->bMorse) ) {
+ sprintf(warn_buf,
+ "Using morse bond-potentials while constraining bonds is useless");
+ warning(wi,warn_buf);
+ }
+
+ sprintf(err_buf,"shake_tol must be > 0 instead of %g while using shake",
+ ir->shake_tol);
+ CHECK(((ir->shake_tol <= 0.0) && (opts->nshake>0) &&
+ (ir->eConstrAlg == econtSHAKE)));
+
+ /* PBC/WALLS */
+ sprintf(err_buf,"walls only work with pbc=%s",epbc_names[epbcXY]);
+ CHECK(ir->nwall && ir->ePBC!=epbcXY);
+
+ /* VACUUM STUFF */
+ if (ir->ePBC != epbcXYZ && ir->nwall != 2) {
+ if (ir->ePBC == epbcNONE) {
+ if (ir->epc != epcNO) {
+ warning(wi,"Turning off pressure coupling for vacuum system");
+ ir->epc = epcNO;
+ }
+ } else {
+ sprintf(err_buf,"Can not have pressure coupling with pbc=%s",
+ epbc_names[ir->ePBC]);
+ CHECK(ir->epc != epcNO);
+ }
+ sprintf(err_buf,"Can not have Ewald with pbc=%s",epbc_names[ir->ePBC]);
+ CHECK(EEL_FULL(ir->coulombtype));
+
+ sprintf(err_buf,"Can not have dispersion correction with pbc=%s",
+ epbc_names[ir->ePBC]);
+ CHECK(ir->eDispCorr != edispcNO);
+ }
+
+ if (ir->rlist == 0.0) {
+ sprintf(err_buf,"can only have neighborlist cut-off zero (=infinite)\n"
+ "with coulombtype = %s or coulombtype = %s\n"
+ "without periodic boundary conditions (pbc = %s) and\n"
+ "rcoulomb and rvdw set to zero",
+ eel_names[eelCUT],eel_names[eelUSER],epbc_names[epbcNONE]);
+ CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
+ (ir->ePBC != epbcNONE) ||
+ (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
+
+ if (ir->nstlist < 0) {
+ warning_error(wi,"Can not have heuristic neighborlist updates without cut-off");
+ }
+ if (ir->nstlist > 0) {
+ warning_note(wi,"Simulating without cut-offs is usually (slightly) faster with nstlist=0, nstype=simple and particle decomposition");
+ }
+ }
+
+ /* COMM STUFF */
+ if (ir->nstcomm == 0) {
+ ir->comm_mode = ecmNO;
+ }
+ if (ir->comm_mode != ecmNO) {
+ if (ir->nstcomm < 0) {
+ warning(wi,"If you want to remove the rotation around the center of mass, you should set comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to its absolute value");
+ ir->nstcomm = abs(ir->nstcomm);
+ }
+
+ if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy) {
+ warning_note(wi,"nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
+ ir->nstcomm = ir->nstcalcenergy;
+ }
+
+ if (ir->comm_mode == ecmANGULAR) {
+ sprintf(err_buf,"Can not remove the rotation around the center of mass with periodic molecules");
+ CHECK(ir->bPeriodicMols);
+ if (ir->ePBC != epbcNONE)
+ warning(wi,"Removing the rotation around the center of mass in a periodic system (this is not a problem when you have only one molecule).");
+ }
+ }
+
+ if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR) {
+ warning_note(wi,"Tumbling and or flying ice-cubes: We are not removing rotation around center of mass in a non-periodic system. You should probably set comm_mode = ANGULAR.");
+ }
+
+ sprintf(err_buf,"Free-energy not implemented for Ewald and PPPM");
+ CHECK((ir->coulombtype==eelEWALD || ir->coulombtype==eelPPPM)
+ && (ir->efep!=efepNO));
+
+ sprintf(err_buf,"Twin-range neighbour searching (NS) with simple NS"
+ " algorithm not implemented");
+ CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
+ && (ir->ns_type == ensSIMPLE));
+
+ /* TEMPERATURE COUPLING */
+ if (ir->etc == etcYES)
+ {
+ ir->etc = etcBERENDSEN;
+ warning_note(wi,"Old option for temperature coupling given: "
+ "changing \"yes\" to \"Berendsen\"\n");
+ }
+
+ if (ir->etc == etcNOSEHOOVER)
+ {
+ if (ir->opts.nhchainlength < 1)
+ {
+ sprintf(warn_buf,"number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n",ir->opts.nhchainlength);
+ ir->opts.nhchainlength =1;
+ warning(wi,warn_buf);
+ }
+
+ if (ir->etc==etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
+ {
+ warning_note(wi,"leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
+ ir->opts.nhchainlength = 1;
+ }
+ }
+ else
+ {
+ ir->opts.nhchainlength = 0;
+ }
+
+ if (ir->etc == etcBERENDSEN)
+ {
+ sprintf(warn_buf,"The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
+ ETCOUPLTYPE(ir->etc),ETCOUPLTYPE(etcVRESCALE));
+ warning_note(wi,warn_buf);
+ }
+
+ if ((ir->etc==etcNOSEHOOVER || ir->etc==etcANDERSEN || ir->etc==etcANDERSENINTERVAL)
+ && ir->epc==epcBERENDSEN)
+ {
+ sprintf(warn_buf,"Using Berendsen pressure coupling invalidates the "
+ "true ensemble for the thermostat");
+ warning(wi,warn_buf);
+ }
+
+ /* PRESSURE COUPLING */
+ if (ir->epc == epcISOTROPIC)
+ {
+ ir->epc = epcBERENDSEN;
+ warning_note(wi,"Old option for pressure coupling given: "
+ "changing \"Isotropic\" to \"Berendsen\"\n");
+ }
+
+ if (ir->epc != epcNO)
+ {
+ dt_pcoupl = ir->nstpcouple*ir->delta_t;
+
- sprintf(warn_buf,"For proper integration of the %s barostat, tau_p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
++ sprintf(err_buf,"tau-p must be > 0 instead of %g\n",ir->tau_p);
+ CHECK(ir->tau_p <= 0);
+
+ if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc))
+ {
- sprintf(warn_buf,"epsilon_r = %g with GB implicit solvent, will use this value for inner dielectric",ir->epsilon_r);
++ sprintf(warn_buf,"For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
+ EPCOUPLTYPE(ir->epc),ir->tau_p,pcouple_min_integration_steps(ir->epc),dt_pcoupl);
+ warning(wi,warn_buf);
+ }
+
+ sprintf(err_buf,"compressibility must be > 0 when using pressure"
+ " coupling %s\n",EPCOUPLTYPE(ir->epc));
+ CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
+ ir->compress[ZZ][ZZ] < 0 ||
+ (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
+ ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
+
+ sprintf(err_buf,"pressure coupling with PPPM not implemented, use PME");
+ CHECK(ir->coulombtype == eelPPPM);
+
+ }
+ else if (ir->coulombtype == eelPPPM)
+ {
+ sprintf(warn_buf,"The pressure with PPPM is incorrect, if you need the pressure use PME");
+ warning(wi,warn_buf);
+ }
+
+ if (EI_VV(ir->eI))
+ {
+ if (ir->epc > epcNO)
+ {
+ if (ir->epc!=epcMTTK)
+ {
+ warning_error(wi,"NPT only defined for vv using Martyna-Tuckerman-Tobias-Klein equations");
+ }
+ }
+ }
+
+ /* ELECTROSTATICS */
+ /* More checks are in triple check (grompp.c) */
+ if (ir->coulombtype == eelPPPM)
+ {
+ warning_error(wi,"PPPM is not functional in the current version, we plan to implement PPPM through a small modification of the PME code");
+ }
+
+ if (ir->coulombtype == eelSWITCH) {
+ sprintf(warn_buf,"coulombtype = %s is only for testing purposes and can lead to serious artifacts, advice: use coulombtype = %s",
+ eel_names[ir->coulombtype],
+ eel_names[eelRF_ZERO]);
+ warning(wi,warn_buf);
+ }
+
+ if (ir->epsilon_r!=1 && ir->implicit_solvent==eisGBSA) {
- sprintf(warn_buf,"epsilon_r = %g and epsilon_rf = 1 with reaction field, assuming old format and exchanging epsilon_r and epsilon_rf",ir->epsilon_r);
++ sprintf(warn_buf,"epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric",ir->epsilon_r);
+ warning_note(wi,warn_buf);
+ }
+
+ if (EEL_RF(ir->coulombtype) && ir->epsilon_rf==1 && ir->epsilon_r!=1) {
- sprintf(err_buf,"epsilon_r must be >= 0 instead of %g\n",ir->epsilon_r);
++ sprintf(warn_buf,"epsilon-r = %g and epsilon-rf = 1 with reaction field, assuming old format and exchanging epsilon-r and epsilon-rf",ir->epsilon_r);
+ warning(wi,warn_buf);
+ ir->epsilon_rf = ir->epsilon_r;
+ ir->epsilon_r = 1.0;
+ }
+
+ if (getenv("GALACTIC_DYNAMICS") == NULL) {
- sprintf(err_buf,"With coulombtype = %s, epsilon_rf must be 0",
++ sprintf(err_buf,"epsilon-r must be >= 0 instead of %g\n",ir->epsilon_r);
+ CHECK(ir->epsilon_r < 0);
+ }
+
+ if (EEL_RF(ir->coulombtype)) {
+ /* reaction field (at the cut-off) */
+
+ if (ir->coulombtype == eelRF_ZERO) {
- sprintf(err_buf,"epsilon_rf must be >= epsilon_r");
++ sprintf(err_buf,"With coulombtype = %s, epsilon-rf must be 0",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->epsilon_rf != 0);
+ }
+
- sprintf(warn_buf,"Using epsilon_rf = epsilon_r with %s does not make sense",
++ sprintf(err_buf,"epsilon-rf must be >= epsilon-r");
+ CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
+ (ir->epsilon_r == 0));
+ if (ir->epsilon_rf == ir->epsilon_r) {
- warning_error(wi,"pme_order can not be smaller than 3");
++ sprintf(warn_buf,"Using epsilon-rf = epsilon-r with %s does not make sense",
+ eel_names[ir->coulombtype]);
+ warning(wi,warn_buf);
+ }
+ }
+ /* Allow rlist>rcoulomb for tabulated long range stuff. This just
+ * means the interaction is zero outside rcoulomb, but it helps to
+ * provide accurate energy conservation.
+ */
+ if (EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype)) {
+ if (EEL_SWITCHED(ir->coulombtype)) {
+ sprintf(err_buf,
+ "With coulombtype = %s rcoulomb_switch must be < rcoulomb",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
+ }
+ } else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype)) {
+ sprintf(err_buf,"With coulombtype = %s, rcoulomb must be >= rlist",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rlist > ir->rcoulomb);
+ }
+
+ if (EEL_FULL(ir->coulombtype)) {
+ if (ir->coulombtype==eelPMESWITCH || ir->coulombtype==eelPMEUSER ||
+ ir->coulombtype==eelPMEUSERSWITCH) {
+ sprintf(err_buf,"With coulombtype = %s, rcoulomb must be <= rlist",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rcoulomb > ir->rlist);
+ } else {
+ if (ir->coulombtype == eelPME) {
+ sprintf(err_buf,
+ "With coulombtype = %s, rcoulomb must be equal to rlist\n"
+ "If you want optimal energy conservation or exact integration use %s",
+ eel_names[ir->coulombtype],eel_names[eelPMESWITCH]);
+ } else {
+ sprintf(err_buf,
+ "With coulombtype = %s, rcoulomb must be equal to rlist",
+ eel_names[ir->coulombtype]);
+ }
+ CHECK(ir->rcoulomb != ir->rlist);
+ }
+ }
+
+ if (EEL_PME(ir->coulombtype)) {
+ if (ir->pme_order < 3) {
- sprintf(warn_buf,"With pbc=%s you should use ewald_geometry=%s",
++ warning_error(wi,"pme-order can not be smaller than 3");
+ }
+ }
+
+ if (ir->nwall==2 && EEL_FULL(ir->coulombtype)) {
+ if (ir->ewald_geometry == eewg3D) {
- sprintf(err_buf,"wall_ewald_zfac should be >= 2");
++ sprintf(warn_buf,"With pbc=%s you should use ewald-geometry=%s",
+ epbc_names[ir->ePBC],eewg_names[eewg3DC]);
+ warning(wi,warn_buf);
+ }
+ /* This check avoids extra pbc coding for exclusion corrections */
- sprintf(err_buf,"With vdwtype = %s rvdw_switch must be < rvdw",
++ sprintf(err_buf,"wall-ewald-zfac should be >= 2");
+ CHECK(ir->wall_ewald_zfac < 2);
+ }
+
+ if (EVDW_SWITCHED(ir->vdwtype)) {
- "setting implicit_solvent value to \"GBSA\" in input section.\n");
++ sprintf(err_buf,"With vdwtype = %s rvdw-switch must be < rvdw",
+ evdw_names[ir->vdwtype]);
+ CHECK(ir->rvdw_switch >= ir->rvdw);
+ } else if (ir->vdwtype == evdwCUT) {
+ sprintf(err_buf,"With vdwtype = %s, rvdw must be >= rlist",evdw_names[ir->vdwtype]);
+ CHECK(ir->rlist > ir->rvdw);
+ }
+ if (EEL_IS_ZERO_AT_CUTOFF(ir->coulombtype)
+ && (ir->rlistlong <= ir->rcoulomb)) {
+ sprintf(warn_buf,"For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
+ IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
+ warning_note(wi,warn_buf);
+ }
+ if (EVDW_SWITCHED(ir->vdwtype) && (ir->rlistlong <= ir->rvdw)) {
+ sprintf(warn_buf,"For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
+ IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
+ warning_note(wi,warn_buf);
+ }
+
+ if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO) {
+ warning_note(wi,"You have selected user tables with dispersion correction, the dispersion will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction between rvdw_switch and rvdw will not be double counted). Make sure that you really want dispersion correction to -C6/r^6.");
+ }
+
+ if (ir->nstlist == -1) {
+ sprintf(err_buf,
+ "nstlist=-1 only works with switched or shifted potentials,\n"
+ "suggestion: use vdw-type=%s and coulomb-type=%s",
+ evdw_names[evdwSHIFT],eel_names[eelPMESWITCH]);
+ CHECK(!(EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) &&
+ EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype)));
+
+ sprintf(err_buf,"With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
+ CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
+ }
+ sprintf(err_buf,"nstlist can not be smaller than -1");
+ CHECK(ir->nstlist < -1);
+
+ if (ir->eI == eiLBFGS && (ir->coulombtype==eelCUT || ir->vdwtype==evdwCUT)
+ && ir->rvdw != 0) {
+ warning(wi,"For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
+ }
+
+ if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0) {
+ warning(wi,"Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
+ }
+
+ /* FREE ENERGY */
+ if (ir->efep != efepNO) {
+ sprintf(err_buf,"The soft-core power is %d and can only be 1 or 2",
+ ir->sc_power);
+ CHECK(ir->sc_alpha!=0 && ir->sc_power!=1 && ir->sc_power!=2);
+ }
+
+ /* ENERGY CONSERVATION */
+ if (ir_NVE(ir))
+ {
+ if (!EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > 0)
+ {
+ sprintf(warn_buf,"You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
+ evdw_names[evdwSHIFT]);
+ warning_note(wi,warn_buf);
+ }
+ if (!EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > 0)
+ {
+ sprintf(warn_buf,"You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
+ eel_names[eelPMESWITCH],eel_names[eelRF_ZERO]);
+ warning_note(wi,warn_buf);
+ }
+ }
+
+ /* IMPLICIT SOLVENT */
+ if(ir->coulombtype==eelGB_NOTUSED)
+ {
+ ir->coulombtype=eelCUT;
+ ir->implicit_solvent=eisGBSA;
+ fprintf(stderr,"Note: Old option for generalized born electrostatics given:\n"
+ "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
- gmx_fatal(FARGS,"Expected %d elements for wall_density, found %d",ir->nwall,nstr);
++ "setting implicit-solvent value to \"GBSA\" in input section.\n");
+ }
+
+ if(ir->sa_algorithm==esaSTILL)
+ {
+ sprintf(err_buf,"Still SA algorithm not available yet, use %s or %s instead\n",esa_names[esaAPPROX],esa_names[esaNO]);
+ CHECK(ir->sa_algorithm == esaSTILL);
+ }
+
+ if(ir->implicit_solvent==eisGBSA)
+ {
+ sprintf(err_buf,"With GBSA implicit solvent, rgbradii must be equal to rlist.");
+ CHECK(ir->rgbradii != ir->rlist);
+
+ if(ir->coulombtype!=eelCUT)
+ {
+ sprintf(err_buf,"With GBSA, coulombtype must be equal to %s\n",eel_names[eelCUT]);
+ CHECK(ir->coulombtype!=eelCUT);
+ }
+ if(ir->vdwtype!=evdwCUT)
+ {
+ sprintf(err_buf,"With GBSA, vdw-type must be equal to %s\n",evdw_names[evdwCUT]);
+ CHECK(ir->vdwtype!=evdwCUT);
+ }
+ if(ir->nstgbradii<1)
+ {
+ sprintf(warn_buf,"Using GBSA with nstgbradii<1, setting nstgbradii=1");
+ warning_note(wi,warn_buf);
+ ir->nstgbradii=1;
+ }
+ if(ir->sa_algorithm==esaNO)
+ {
+ sprintf(warn_buf,"No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
+ warning_note(wi,warn_buf);
+ }
+ if(ir->sa_surface_tension<0 && ir->sa_algorithm!=esaNO)
+ {
+ sprintf(warn_buf,"Value of sa_surface_tension is < 0. Changing it to 2.05016 or 2.25936 kJ/nm^2/mol for Still and HCT/OBC respectively\n");
+ warning_note(wi,warn_buf);
+
+ if(ir->gb_algorithm==egbSTILL)
+ {
+ ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
+ }
+ else
+ {
+ ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
+ }
+ }
+ if(ir->sa_surface_tension==0 && ir->sa_algorithm!=esaNO)
+ {
+ sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
+ CHECK(ir->sa_surface_tension==0 && ir->sa_algorithm!=esaNO);
+ }
+
+ }
+}
+
+static int str_nelem(const char *str,int maxptr,char *ptr[])
+{
+ int np=0;
+ char *copy0,*copy;
+
+ copy0=strdup(str);
+ copy=copy0;
+ ltrim(copy);
+ while (*copy != '\0') {
+ if (np >= maxptr)
+ gmx_fatal(FARGS,"Too many groups on line: '%s' (max is %d)",
+ str,maxptr);
+ if (ptr)
+ ptr[np]=copy;
+ np++;
+ while ((*copy != '\0') && !isspace(*copy))
+ copy++;
+ if (*copy != '\0') {
+ *copy='\0';
+ copy++;
+ }
+ ltrim(copy);
+ }
+ if (ptr == NULL)
+ sfree(copy0);
+
+ return np;
+}
+
+static void parse_n_double(char *str,int *n,double **r)
+{
+ char *ptr[MAXPTR];
+ int i;
+
+ *n = str_nelem(str,MAXPTR,ptr);
+
+ snew(*r,*n);
+ for(i=0; i<*n; i++) {
+ (*r)[i] = strtod(ptr[i],NULL);
+ }
+}
+
+static void do_wall_params(t_inputrec *ir,
+ char *wall_atomtype, char *wall_density,
+ t_gromppopts *opts)
+{
+ int nstr,i;
+ char *names[MAXPTR];
+ double dbl;
+
+ opts->wall_atomtype[0] = NULL;
+ opts->wall_atomtype[1] = NULL;
+
+ ir->wall_atomtype[0] = -1;
+ ir->wall_atomtype[1] = -1;
+ ir->wall_density[0] = 0;
+ ir->wall_density[1] = 0;
+
+ if (ir->nwall > 0)
+ {
+ nstr = str_nelem(wall_atomtype,MAXPTR,names);
+ if (nstr != ir->nwall)
+ {
+ gmx_fatal(FARGS,"Expected %d elements for wall_atomtype, found %d",
+ ir->nwall,nstr);
+ }
+ for(i=0; i<ir->nwall; i++)
+ {
+ opts->wall_atomtype[i] = strdup(names[i]);
+ }
+
+ if (ir->wall_type == ewt93 || ir->wall_type == ewt104) {
+ nstr = str_nelem(wall_density,MAXPTR,names);
+ if (nstr != ir->nwall)
+ {
- gmx_fatal(FARGS,"wall_density[%d] = %f\n",i,dbl);
++ gmx_fatal(FARGS,"Expected %d elements for wall-density, found %d",ir->nwall,nstr);
+ }
+ for(i=0; i<ir->nwall; i++)
+ {
+ sscanf(names[i],"%lf",&dbl);
+ if (dbl <= 0)
+ {
- STEPTYPE ("init_step",ir->init_step, 0);
++ gmx_fatal(FARGS,"wall-density[%d] = %f\n",i,dbl);
+ }
+ ir->wall_density[i] = dbl;
+ }
+ }
+ }
+}
+
+static void add_wall_energrps(gmx_groups_t *groups,int nwall,t_symtab *symtab)
+{
+ int i;
+ t_grps *grps;
+ char str[STRLEN];
+
+ if (nwall > 0) {
+ srenew(groups->grpname,groups->ngrpname+nwall);
+ grps = &(groups->grps[egcENER]);
+ srenew(grps->nm_ind,grps->nr+nwall);
+ for(i=0; i<nwall; i++) {
+ sprintf(str,"wall%d",i);
+ groups->grpname[groups->ngrpname] = put_symtab(symtab,str);
+ grps->nm_ind[grps->nr++] = groups->ngrpname++;
+ }
+ }
+}
+
+void get_ir(const char *mdparin,const char *mdparout,
+ t_inputrec *ir,t_gromppopts *opts,
+ warninp_t wi)
+{
+ char *dumstr[2];
+ double dumdub[2][6];
+ t_inpfile *inp;
+ const char *tmp;
+ int i,j,m,ninp;
+ char warn_buf[STRLEN];
+
+ inp = read_inpfile(mdparin, &ninp, NULL, wi);
+
+ snew(dumstr[0],STRLEN);
+ snew(dumstr[1],STRLEN);
+
+ REM_TYPE("title");
+ REM_TYPE("cpp");
+ REM_TYPE("domain-decomposition");
+ REPL_TYPE("unconstrained-start","continuation");
+ REM_TYPE("dihre-tau");
+ REM_TYPE("nstdihreout");
+ REM_TYPE("nstcheckpoint");
+
+ CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
+ CTYPE ("Preprocessor information: use cpp syntax.");
+ CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
+ STYPE ("include", opts->include, NULL);
+ CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
+ STYPE ("define", opts->define, NULL);
+
+ CCTYPE ("RUN CONTROL PARAMETERS");
+ EETYPE("integrator", ir->eI, ei_names);
+ CTYPE ("Start time and timestep in ps");
+ RTYPE ("tinit", ir->init_t, 0.0);
+ RTYPE ("dt", ir->delta_t, 0.001);
+ STEPTYPE ("nsteps", ir->nsteps, 0);
+ CTYPE ("For exact run continuation or redoing part of a run");
- ITYPE ("simulation_part", ir->simulation_part, 1);
++ STEPTYPE ("init-step",ir->init_step, 0);
+ CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
- CTYPE ("Max number of iterations in relax_shells");
++ ITYPE ("simulation-part", ir->simulation_part, 1);
+ CTYPE ("mode for center of mass motion removal");
+ EETYPE("comm-mode", ir->comm_mode, ecm_names);
+ CTYPE ("number of steps for center of mass motion removal");
+ ITYPE ("nstcomm", ir->nstcomm, 10);
+ CTYPE ("group(s) for center of mass motion removal");
+ STYPE ("comm-grps", vcm, NULL);
+
+ CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
+ CTYPE ("Friction coefficient (amu/ps) and random seed");
+ RTYPE ("bd-fric", ir->bd_fric, 0.0);
+ ITYPE ("ld-seed", ir->ld_seed, 1993);
+
+ /* Em stuff */
+ CCTYPE ("ENERGY MINIMIZATION OPTIONS");
+ CTYPE ("Force tolerance and initial step-size");
+ RTYPE ("emtol", ir->em_tol, 10.0);
+ RTYPE ("emstep", ir->em_stepsize,0.01);
- EETYPE("periodic_molecules", ir->bPeriodicMols, yesno_names);
++ CTYPE ("Max number of iterations in relax-shells");
+ ITYPE ("niter", ir->niter, 20);
+ CTYPE ("Step size (ps^2) for minimization of flexible constraints");
+ RTYPE ("fcstep", ir->fc_stepsize, 0);
+ CTYPE ("Frequency of steepest descents steps when doing CG");
+ ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
+ ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
+
+ CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
+ RTYPE ("rtpi", ir->rtpi, 0.05);
+
+ /* Output options */
+ CCTYPE ("OUTPUT CONTROL OPTIONS");
+ CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
+ ITYPE ("nstxout", ir->nstxout, 100);
+ ITYPE ("nstvout", ir->nstvout, 100);
+ ITYPE ("nstfout", ir->nstfout, 0);
+ ir->nstcheckpoint = 1000;
+ CTYPE ("Output frequency for energies to log file and energy file");
+ ITYPE ("nstlog", ir->nstlog, 100);
+ ITYPE ("nstcalcenergy",ir->nstcalcenergy, -1);
+ ITYPE ("nstenergy", ir->nstenergy, 100);
+ CTYPE ("Output frequency and precision for .xtc file");
+ ITYPE ("nstxtcout", ir->nstxtcout, 0);
+ RTYPE ("xtc-precision",ir->xtcprec, 1000.0);
+ CTYPE ("This selects the subset of atoms for the .xtc file. You can");
+ CTYPE ("select multiple groups. By default all atoms will be written.");
+ STYPE ("xtc-grps", xtc_grps, NULL);
+ CTYPE ("Selection of energy groups");
+ STYPE ("energygrps", energy, NULL);
+
+ /* Neighbor searching */
+ CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
+ CTYPE ("nblist update frequency");
+ ITYPE ("nstlist", ir->nstlist, 10);
+ CTYPE ("ns algorithm (simple or grid)");
+ EETYPE("ns-type", ir->ns_type, ens_names);
+ /* set ndelta to the optimal value of 2 */
+ ir->ndelta = 2;
+ CTYPE ("Periodic boundary conditions: xyz, no, xy");
+ EETYPE("pbc", ir->ePBC, epbc_names);
- RTYPE ("epsilon_r", ir->epsilon_r, 1.0);
- RTYPE ("epsilon_rf", ir->epsilon_rf, 1.0);
++ EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
+ CTYPE ("nblist cut-off");
+ RTYPE ("rlist", ir->rlist, 1.0);
+ CTYPE ("long-range cut-off for switched potentials");
+ RTYPE ("rlistlong", ir->rlistlong, -1);
+
+ /* Electrostatics */
+ CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
+ CTYPE ("Method for doing electrostatics");
+ EETYPE("coulombtype", ir->coulombtype, eel_names);
+ CTYPE ("cut-off lengths");
+ RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
+ RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
+ CTYPE ("Relative dielectric constant for the medium and the reaction field");
- STYPE ("energygrp_table", egptable, NULL);
++ RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
++ RTYPE ("epsilon-rf", ir->epsilon_rf, 1.0);
+ CTYPE ("Method for doing Van der Waals");
+ EETYPE("vdw-type", ir->vdwtype, evdw_names);
+ CTYPE ("cut-off lengths");
+ RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
+ RTYPE ("rvdw", ir->rvdw, 1.0);
+ CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
+ EETYPE("DispCorr", ir->eDispCorr, edispc_names);
+ CTYPE ("Extension of the potential lookup tables beyond the cut-off");
+ RTYPE ("table-extension", ir->tabext, 1.0);
+ CTYPE ("Seperate tables between energy group pairs");
- ITYPE ("fourier_nx", ir->nkx, 0);
- ITYPE ("fourier_ny", ir->nky, 0);
- ITYPE ("fourier_nz", ir->nkz, 0);
++ STYPE ("energygrp-table", egptable, NULL);
+ CTYPE ("Spacing for the PME/PPPM FFT grid");
+ RTYPE ("fourierspacing", opts->fourierspacing,0.12);
+ CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
- ITYPE ("pme_order", ir->pme_order, 4);
- RTYPE ("ewald_rtol", ir->ewald_rtol, 0.00001);
- EETYPE("ewald_geometry", ir->ewald_geometry, eewg_names);
- RTYPE ("epsilon_surface", ir->epsilon_surface, 0.0);
- EETYPE("optimize_fft",ir->bOptFFT, yesno_names);
++ ITYPE ("fourier-nx", ir->nkx, 0);
++ ITYPE ("fourier-ny", ir->nky, 0);
++ ITYPE ("fourier-nz", ir->nkz, 0);
+ CTYPE ("EWALD/PME/PPPM parameters");
- EETYPE("implicit_solvent", ir->implicit_solvent, eis_names);
++ ITYPE ("pme-order", ir->pme_order, 4);
++ RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
++ EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
++ RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
++ EETYPE("optimize-fft",ir->bOptFFT, yesno_names);
+
+ CCTYPE("IMPLICIT SOLVENT ALGORITHM");
- EETYPE("gb_algorithm", ir->gb_algorithm, egb_names);
++ EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
+
+ CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
+ CTYPE ("Algorithm for calculating Born radii");
- RTYPE ("gb_epsilon_solvent",ir->gb_epsilon_solvent, 80.0);
++ EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
+ CTYPE ("Frequency of calculating the Born radii inside rlist");
+ ITYPE ("nstgbradii", ir->nstgbradii, 1);
+ CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
+ CTYPE ("between rlist and rgbradii is updated every nstlist steps");
+ RTYPE ("rgbradii", ir->rgbradii, 1.0);
+ CTYPE ("Dielectric coefficient of the implicit solvent");
- RTYPE ("gb_saltconc", ir->gb_saltconc, 0.0);
++ RTYPE ("gb-epsilon-solvent",ir->gb_epsilon_solvent, 80.0);
+ CTYPE ("Salt concentration in M for Generalized Born models");
- RTYPE ("gb_obc_alpha", ir->gb_obc_alpha, 1.0);
- RTYPE ("gb_obc_beta", ir->gb_obc_beta, 0.8);
- RTYPE ("gb_obc_gamma", ir->gb_obc_gamma, 4.85);
- RTYPE ("gb_dielectric_offset", ir->gb_dielectric_offset, 0.009);
- EETYPE("sa_algorithm", ir->sa_algorithm, esa_names);
++ RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
+ CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
- RTYPE ("sa_surface_tension", ir->sa_surface_tension, -1);
++ RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
++ RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
++ RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
++ RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
++ EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
+ CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
+ CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
- CTYPE ("Pressure coupling");
- EETYPE("Pcoupl", ir->epc, epcoupl_names);
- EETYPE("Pcoupltype", ir->epct, epcoupltype_names);
++ RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
+
+ /* Coupling stuff */
+ CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
+ CTYPE ("Temperature coupling");
+ EETYPE("tcoupl", ir->etc, etcoupl_names);
+ ITYPE ("nsttcouple", ir->nsttcouple, -1);
+ ITYPE("nh-chain-length", ir->opts.nhchainlength, NHCHAINLENGTH);
+ CTYPE ("Groups to couple separately");
+ STYPE ("tc-grps", tcgrps, NULL);
+ CTYPE ("Time constant (ps) and reference temperature (K)");
+ STYPE ("tau-t", tau_t, NULL);
+ STYPE ("ref-t", ref_t, NULL);
- EETYPE ("refcoord_scaling",ir->refcoord_scaling,erefscaling_names);
++ CTYPE ("pressure coupling");
++ EETYPE("pcoupl", ir->epc, epcoupl_names);
++ EETYPE("pcoupltype", ir->epct, epcoupltype_names);
+ ITYPE ("nstpcouple", ir->nstpcouple, -1);
+ CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
+ RTYPE ("tau-p", ir->tau_p, 1.0);
+ STYPE ("compressibility", dumstr[0], NULL);
+ STYPE ("ref-p", dumstr[1], NULL);
+ CTYPE ("Scaling of reference coordinates, No, All or COM");
- ITYPE ("andersen_seed", ir->andersen_seed, 815131);
++ EETYPE ("refcoord-scaling",ir->refcoord_scaling,erefscaling_names);
+
+ CTYPE ("Random seed for Andersen thermostat");
- STYPE ("annealing_npoints", anneal_npoints, NULL);
++ ITYPE ("andersen-seed", ir->andersen_seed, 815131);
+
+ /* QMMM */
+ CCTYPE ("OPTIONS FOR QMMM calculations");
+ EETYPE("QMMM", ir->bQMMM, yesno_names);
+ CTYPE ("Groups treated Quantum Mechanically");
+ STYPE ("QMMM-grps", QMMM, NULL);
+ CTYPE ("QM method");
+ STYPE("QMmethod", QMmethod, NULL);
+ CTYPE ("QMMM scheme");
+ EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
+ CTYPE ("QM basisset");
+ STYPE("QMbasis", QMbasis, NULL);
+ CTYPE ("QM charge");
+ STYPE ("QMcharge", QMcharge,NULL);
+ CTYPE ("QM multiplicity");
+ STYPE ("QMmult", QMmult,NULL);
+ CTYPE ("Surface Hopping");
+ STYPE ("SH", bSH, NULL);
+ CTYPE ("CAS space options");
+ STYPE ("CASorbitals", CASorbitals, NULL);
+ STYPE ("CASelectrons", CASelectrons, NULL);
+ STYPE ("SAon", SAon, NULL);
+ STYPE ("SAoff",SAoff,NULL);
+ STYPE ("SAsteps", SAsteps, NULL);
+ CTYPE ("Scale factor for MM charges");
+ RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
+ CTYPE ("Optimization of QM subsystem");
+ STYPE ("bOPT", bOPT, NULL);
+ STYPE ("bTS", bTS, NULL);
+
+ /* Simulated annealing */
+ CCTYPE("SIMULATED ANNEALING");
+ CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
+ STYPE ("annealing", anneal, NULL);
+ CTYPE ("Number of time points to use for specifying annealing in each group");
- STYPE ("annealing_time", anneal_time, NULL);
++ STYPE ("annealing-npoints", anneal_npoints, NULL);
+ CTYPE ("List of times at the annealing points for each group");
- STYPE ("annealing_temp", anneal_temp, NULL);
++ STYPE ("annealing-time", anneal_time, NULL);
+ CTYPE ("Temp. at each annealing point, for each group.");
- STYPE ("energygrp_excl", egpexcl, NULL);
++ STYPE ("annealing-temp", anneal_temp, NULL);
+
+ /* Startup run */
+ CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
+ EETYPE("gen-vel", opts->bGenVel, yesno_names);
+ RTYPE ("gen-temp", opts->tempi, 300.0);
+ ITYPE ("gen-seed", opts->seed, 173529);
+
+ /* Shake stuff */
+ CCTYPE ("OPTIONS FOR BONDS");
+ EETYPE("constraints", opts->nshake, constraints);
+ CTYPE ("Type of constraint algorithm");
+ EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
+ CTYPE ("Do not constrain the start configuration");
+ EETYPE("continuation", ir->bContinuation, yesno_names);
+ CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
+ EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
+ CTYPE ("Relative tolerance of shake");
+ RTYPE ("shake-tol", ir->shake_tol, 0.0001);
+ CTYPE ("Highest order in the expansion of the constraint coupling matrix");
+ ITYPE ("lincs-order", ir->nProjOrder, 4);
+ CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
+ CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
+ CTYPE ("For energy minimization with constraints it should be 4 to 8.");
+ ITYPE ("lincs-iter", ir->nLincsIter, 1);
+ CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
+ CTYPE ("rotates over more degrees than");
+ RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
+ CTYPE ("Convert harmonic bonds to morse potentials");
+ EETYPE("morse", opts->bMorse,yesno_names);
+
+ /* Energy group exclusions */
+ CCTYPE ("ENERGY GROUP EXCLUSIONS");
+ CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
- EETYPE("wall_type", ir->wall_type, ewt_names);
- RTYPE ("wall_r_linpot", ir->wall_r_linpot, -1);
- STYPE ("wall_atomtype", wall_atomtype, NULL);
- STYPE ("wall_density", wall_density, NULL);
- RTYPE ("wall_ewald_zfac", ir->wall_ewald_zfac, 3);
++ STYPE ("energygrp-excl", egpexcl, NULL);
+
+ /* Walls */
+ CCTYPE ("WALLS");
+ CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
+ ITYPE ("nwall", ir->nwall, 0);
- CTYPE("Pull type: no, umbrella, constraint or constant_force");
++ EETYPE("wall-type", ir->wall_type, ewt_names);
++ RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
++ STYPE ("wall-atomtype", wall_atomtype, NULL);
++ STYPE ("wall-density", wall_density, NULL);
++ RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
+
+ /* COM pulling */
+ CCTYPE("COM PULLING");
- STYPE ("foreign_lambda", foreign_lambda, NULL);
++ CTYPE("Pull type: no, umbrella, constraint or constant-force");
+ EETYPE("pull", ir->ePull, epull_names);
+ if (ir->ePull != epullNO) {
+ snew(ir->pull,1);
+ pull_grp = read_pullparams(&ninp,&inp,ir->pull,&opts->pull_start,wi);
+ }
+
+ /* Enforced rotation */
+ CCTYPE("ENFORCED ROTATION");
+ CTYPE("Enforced rotation: No or Yes");
+ EETYPE("rotation", ir->bRot, yesno_names);
+ if (ir->bRot) {
+ snew(ir->rot,1);
+ rot_grp = read_rotparams(&ninp,&inp,ir->rot,wi);
+ }
+
+ /* Refinement */
+ CCTYPE("NMR refinement stuff");
+ CTYPE ("Distance restraints type: No, Simple or Ensemble");
+ EETYPE("disre", ir->eDisre, edisre_names);
+ CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
+ EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
+ CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
+ EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
+ RTYPE ("disre-fc", ir->dr_fc, 1000.0);
+ RTYPE ("disre-tau", ir->dr_tau, 0.0);
+ CTYPE ("Output frequency for pair distances to energy file");
+ ITYPE ("nstdisreout", ir->nstdisreout, 100);
+ CTYPE ("Orientation restraints: No or Yes");
+ EETYPE("orire", opts->bOrire, yesno_names);
+ CTYPE ("Orientation restraints force constant and tau for time averaging");
+ RTYPE ("orire-fc", ir->orires_fc, 0.0);
+ RTYPE ("orire-tau", ir->orires_tau, 0.0);
+ STYPE ("orire-fitgrp",orirefitgrp, NULL);
+ CTYPE ("Output frequency for trace(SD) and S to energy file");
+ ITYPE ("nstorireout", ir->nstorireout, 100);
+ CTYPE ("Dihedral angle restraints: No or Yes");
+ EETYPE("dihre", opts->bDihre, yesno_names);
+ RTYPE ("dihre-fc", ir->dihre_fc, 1000.0);
+
+ /* Free energy stuff */
+ CCTYPE ("Free energy control stuff");
+ EETYPE("free-energy", ir->efep, efep_names);
+ RTYPE ("init-lambda", ir->init_lambda,0.0);
+ RTYPE ("delta-lambda",ir->delta_lambda,0.0);
- ITYPE ("dh_hist_size", ir->dh_hist_size, 0);
- RTYPE ("dh_hist_spacing", ir->dh_hist_spacing, 0.1);
++ STYPE ("foreign-lambda", foreign_lambda, NULL);
+ RTYPE ("sc-alpha",ir->sc_alpha,0.0);
+ ITYPE ("sc-power",ir->sc_power,0);
+ RTYPE ("sc-sigma",ir->sc_sigma,0.3);
+ ITYPE ("nstdhdl", ir->nstdhdl, 10);
+ EETYPE("separate-dhdl-file", ir->separate_dhdl_file,
+ separate_dhdl_file_names);
+ EETYPE("dhdl-derivatives", ir->dhdl_derivatives, dhdl_derivatives_names);
- warning(wi,"Can not couple a molecule with free_energy = no");
++ ITYPE ("dh-hist-size", ir->dh_hist_size, 0);
++ RTYPE ("dh-hist-spacing", ir->dh_hist_spacing, 0.1);
+ STYPE ("couple-moltype", couple_moltype, NULL);
+ EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
+ EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
+ EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
+
+ /* Non-equilibrium MD stuff */
+ CCTYPE("Non-equilibrium MD stuff");
+ STYPE ("acc-grps", accgrps, NULL);
+ STYPE ("accelerate", acc, NULL);
+ STYPE ("freezegrps", freeze, NULL);
+ STYPE ("freezedim", frdim, NULL);
+ RTYPE ("cos-acceleration", ir->cos_accel, 0);
+ STYPE ("deform", deform, NULL);
+
+ /* Electric fields */
+ CCTYPE("Electric fields");
+ CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
+ CTYPE ("and a phase angle (real)");
+ STYPE ("E-x", efield_x, NULL);
+ STYPE ("E-xt", efield_xt, NULL);
+ STYPE ("E-y", efield_y, NULL);
+ STYPE ("E-yt", efield_yt, NULL);
+ STYPE ("E-z", efield_z, NULL);
+ STYPE ("E-zt", efield_zt, NULL);
+
+ /* User defined thingies */
+ CCTYPE ("User defined thingies");
+ STYPE ("user1-grps", user1, NULL);
+ STYPE ("user2-grps", user2, NULL);
+ ITYPE ("userint1", ir->userint1, 0);
+ ITYPE ("userint2", ir->userint2, 0);
+ ITYPE ("userint3", ir->userint3, 0);
+ ITYPE ("userint4", ir->userint4, 0);
+ RTYPE ("userreal1", ir->userreal1, 0);
+ RTYPE ("userreal2", ir->userreal2, 0);
+ RTYPE ("userreal3", ir->userreal3, 0);
+ RTYPE ("userreal4", ir->userreal4, 0);
+#undef CTYPE
+
+ write_inpfile(mdparout,ninp,inp,FALSE,wi);
+ for (i=0; (i<ninp); i++) {
+ sfree(inp[i].name);
+ sfree(inp[i].value);
+ }
+ sfree(inp);
+
+ /* Process options if necessary */
+ for(m=0; m<2; m++) {
+ for(i=0; i<2*DIM; i++)
+ dumdub[m][i]=0.0;
+ if(ir->epc) {
+ switch (ir->epct) {
+ case epctISOTROPIC:
+ if (sscanf(dumstr[m],"%lf",&(dumdub[m][XX]))!=1) {
+ warning_error(wi,"Pressure coupling not enough values (I need 1)");
+ }
+ dumdub[m][YY]=dumdub[m][ZZ]=dumdub[m][XX];
+ break;
+ case epctSEMIISOTROPIC:
+ case epctSURFACETENSION:
+ if (sscanf(dumstr[m],"%lf%lf",
+ &(dumdub[m][XX]),&(dumdub[m][ZZ]))!=2) {
+ warning_error(wi,"Pressure coupling not enough values (I need 2)");
+ }
+ dumdub[m][YY]=dumdub[m][XX];
+ break;
+ case epctANISOTROPIC:
+ if (sscanf(dumstr[m],"%lf%lf%lf%lf%lf%lf",
+ &(dumdub[m][XX]),&(dumdub[m][YY]),&(dumdub[m][ZZ]),
+ &(dumdub[m][3]),&(dumdub[m][4]),&(dumdub[m][5]))!=6) {
+ warning_error(wi,"Pressure coupling not enough values (I need 6)");
+ }
+ break;
+ default:
+ gmx_fatal(FARGS,"Pressure coupling type %s not implemented yet",
+ epcoupltype_names[ir->epct]);
+ }
+ }
+ }
+ clear_mat(ir->ref_p);
+ clear_mat(ir->compress);
+ for(i=0; i<DIM; i++) {
+ ir->ref_p[i][i] = dumdub[1][i];
+ ir->compress[i][i] = dumdub[0][i];
+ }
+ if (ir->epct == epctANISOTROPIC) {
+ ir->ref_p[XX][YY] = dumdub[1][3];
+ ir->ref_p[XX][ZZ] = dumdub[1][4];
+ ir->ref_p[YY][ZZ] = dumdub[1][5];
+ if (ir->ref_p[XX][YY]!=0 && ir->ref_p[XX][ZZ]!=0 && ir->ref_p[YY][ZZ]!=0) {
+ warning(wi,"All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
+ }
+ ir->compress[XX][YY] = dumdub[0][3];
+ ir->compress[XX][ZZ] = dumdub[0][4];
+ ir->compress[YY][ZZ] = dumdub[0][5];
+ for(i=0; i<DIM; i++) {
+ for(m=0; m<i; m++) {
+ ir->ref_p[i][m] = ir->ref_p[m][i];
+ ir->compress[i][m] = ir->compress[m][i];
+ }
+ }
+ }
+
+ if (ir->comm_mode == ecmNO)
+ ir->nstcomm = 0;
+
+ opts->couple_moltype = NULL;
+ if (strlen(couple_moltype) > 0) {
+ if (ir->efep != efepNO) {
+ opts->couple_moltype = strdup(couple_moltype);
+ if (opts->couple_lam0 == opts->couple_lam1)
+ warning(wi,"The lambda=0 and lambda=1 states for coupling are identical");
+ if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
+ opts->couple_lam1 == ecouplamNONE)) {
+ warning(wi,"For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
+ }
+ } else {
- gmx_fatal(FARGS,"Invalid T coupling input: %d groups, %d ref_t values and "
- "%d tau_t values",ntcg,nref_t,ntau_t);
++ warning(wi,"Can not couple a molecule with free-energy = no");
+ }
+ }
+
+ do_wall_params(ir,wall_atomtype,wall_density,opts);
+
+ if (opts->bOrire && str_nelem(orirefitgrp,MAXPTR,NULL)!=1) {
+ warning_error(wi,"ERROR: Need one orientation restraint fit group\n");
+ }
+
+ clear_mat(ir->deform);
+ for(i=0; i<6; i++)
+ dumdub[0][i] = 0;
+ m = sscanf(deform,"%lf %lf %lf %lf %lf %lf",
+ &(dumdub[0][0]),&(dumdub[0][1]),&(dumdub[0][2]),
+ &(dumdub[0][3]),&(dumdub[0][4]),&(dumdub[0][5]));
+ for(i=0; i<3; i++)
+ ir->deform[i][i] = dumdub[0][i];
+ ir->deform[YY][XX] = dumdub[0][3];
+ ir->deform[ZZ][XX] = dumdub[0][4];
+ ir->deform[ZZ][YY] = dumdub[0][5];
+ if (ir->epc != epcNO) {
+ for(i=0; i<3; i++)
+ for(j=0; j<=i; j++)
+ if (ir->deform[i][j]!=0 && ir->compress[i][j]!=0) {
+ warning_error(wi,"A box element has deform set and compressibility > 0");
+ }
+ for(i=0; i<3; i++)
+ for(j=0; j<i; j++)
+ if (ir->deform[i][j]!=0) {
+ for(m=j; m<DIM; m++)
+ if (ir->compress[m][j]!=0) {
+ sprintf(warn_buf,"An off-diagonal box element has deform set while compressibility > 0 for the same component of another box vector, this might lead to spurious periodicity effects.");
+ warning(wi,warn_buf);
+ }
+ }
+ }
+
+ if (ir->efep != efepNO) {
+ parse_n_double(foreign_lambda,&ir->n_flambda,&ir->flambda);
+ if (ir->n_flambda > 0 && ir->rlist < max(ir->rvdw,ir->rcoulomb)) {
+ warning_note(wi,"For foreign lambda free energy differences it is assumed that the soft-core interactions have no effect beyond the neighborlist cut-off");
+ }
+ } else {
+ ir->n_flambda = 0;
+ }
+
+ sfree(dumstr[0]);
+ sfree(dumstr[1]);
+}
+
+static int search_QMstring(char *s,int ng,const char *gn[])
+{
+ /* same as normal search_string, but this one searches QM strings */
+ int i;
+
+ for(i=0; (i<ng); i++)
+ if (gmx_strcasecmp(s,gn[i]) == 0)
+ return i;
+
+ gmx_fatal(FARGS,"this QM method or basisset (%s) is not implemented\n!",s);
+
+ return -1;
+
+} /* search_QMstring */
+
+
+int search_string(char *s,int ng,char *gn[])
+{
+ int i;
+
+ for(i=0; (i<ng); i++)
+ {
+ if (gmx_strcasecmp(s,gn[i]) == 0)
+ {
+ return i;
+ }
+ }
+
+ gmx_fatal(FARGS,"Group %s not found in index file.\nGroup names must match either [moleculetype] names\nor custom index group names,in which case you\nmust supply an index file to the '-n' option of grompp.",s);
+
+ return -1;
+}
+
+static gmx_bool do_numbering(int natoms,gmx_groups_t *groups,int ng,char *ptrs[],
+ t_blocka *block,char *gnames[],
+ int gtype,int restnm,
+ int grptp,gmx_bool bVerbose,
+ warninp_t wi)
+{
+ unsigned short *cbuf;
+ t_grps *grps=&(groups->grps[gtype]);
+ int i,j,gid,aj,ognr,ntot=0;
+ const char *title;
+ gmx_bool bRest;
+ char warn_buf[STRLEN];
+
+ if (debug)
+ {
+ fprintf(debug,"Starting numbering %d groups of type %d\n",ng,gtype);
+ }
+
+ title = gtypes[gtype];
+
+ snew(cbuf,natoms);
+ /* Mark all id's as not set */
+ for(i=0; (i<natoms); i++)
+ {
+ cbuf[i] = NOGID;
+ }
+
+ snew(grps->nm_ind,ng+1); /* +1 for possible rest group */
+ for(i=0; (i<ng); i++)
+ {
+ /* Lookup the group name in the block structure */
+ gid = search_string(ptrs[i],block->nr,gnames);
+ if ((grptp != egrptpONE) || (i == 0))
+ {
+ grps->nm_ind[grps->nr++]=gid;
+ }
+ if (debug)
+ {
+ fprintf(debug,"Found gid %d for group %s\n",gid,ptrs[i]);
+ }
+
+ /* Now go over the atoms in the group */
+ for(j=block->index[gid]; (j<block->index[gid+1]); j++)
+ {
+
+ aj=block->a[j];
+
+ /* Range checking */
+ if ((aj < 0) || (aj >= natoms))
+ {
+ gmx_fatal(FARGS,"Invalid atom number %d in indexfile",aj);
+ }
+ /* Lookup up the old group number */
+ ognr = cbuf[aj];
+ if (ognr != NOGID)
+ {
+ gmx_fatal(FARGS,"Atom %d in multiple %s groups (%d and %d)",
+ aj+1,title,ognr+1,i+1);
+ }
+ else
+ {
+ /* Store the group number in buffer */
+ if (grptp == egrptpONE)
+ {
+ cbuf[aj] = 0;
+ }
+ else
+ {
+ cbuf[aj] = i;
+ }
+ ntot++;
+ }
+ }
+ }
+
+ /* Now check whether we have done all atoms */
+ bRest = FALSE;
+ if (ntot != natoms)
+ {
+ if (grptp == egrptpALL)
+ {
+ gmx_fatal(FARGS,"%d atoms are not part of any of the %s groups",
+ natoms-ntot,title);
+ }
+ else if (grptp == egrptpPART)
+ {
+ sprintf(warn_buf,"%d atoms are not part of any of the %s groups",
+ natoms-ntot,title);
+ warning_note(wi,warn_buf);
+ }
+ /* Assign all atoms currently unassigned to a rest group */
+ for(j=0; (j<natoms); j++)
+ {
+ if (cbuf[j] == NOGID)
+ {
+ cbuf[j] = grps->nr;
+ bRest = TRUE;
+ }
+ }
+ if (grptp != egrptpPART)
+ {
+ if (bVerbose)
+ {
+ fprintf(stderr,
+ "Making dummy/rest group for %s containing %d elements\n",
+ title,natoms-ntot);
+ }
+ /* Add group name "rest" */
+ grps->nm_ind[grps->nr] = restnm;
+
+ /* Assign the rest name to all atoms not currently assigned to a group */
+ for(j=0; (j<natoms); j++)
+ {
+ if (cbuf[j] == NOGID)
+ {
+ cbuf[j] = grps->nr;
+ }
+ }
+ grps->nr++;
+ }
+ }
+
+ if (grps->nr == 1)
+ {
+ groups->ngrpnr[gtype] = 0;
+ groups->grpnr[gtype] = NULL;
+ }
+ else
+ {
+ groups->ngrpnr[gtype] = natoms;
+ snew(groups->grpnr[gtype],natoms);
+ for(j=0; (j<natoms); j++)
+ {
+ groups->grpnr[gtype][j] = cbuf[j];
+ }
+ }
+
+ sfree(cbuf);
+
+ return (bRest && grptp == egrptpPART);
+}
+
+static void calc_nrdf(gmx_mtop_t *mtop,t_inputrec *ir,char **gnames)
+{
+ t_grpopts *opts;
+ gmx_groups_t *groups;
+ t_pull *pull;
+ int natoms,ai,aj,i,j,d,g,imin,jmin,nc;
+ t_iatom *ia;
+ int *nrdf2,*na_vcm,na_tot;
+ double *nrdf_tc,*nrdf_vcm,nrdf_uc,n_sub=0;
+ gmx_mtop_atomloop_all_t aloop;
+ t_atom *atom;
+ int mb,mol,ftype,as;
+ gmx_molblock_t *molb;
+ gmx_moltype_t *molt;
+
+ /* Calculate nrdf.
+ * First calc 3xnr-atoms for each group
+ * then subtract half a degree of freedom for each constraint
+ *
+ * Only atoms and nuclei contribute to the degrees of freedom...
+ */
+
+ opts = &ir->opts;
+
+ groups = &mtop->groups;
+ natoms = mtop->natoms;
+
+ /* Allocate one more for a possible rest group */
+ /* We need to sum degrees of freedom into doubles,
+ * since floats give too low nrdf's above 3 million atoms.
+ */
+ snew(nrdf_tc,groups->grps[egcTC].nr+1);
+ snew(nrdf_vcm,groups->grps[egcVCM].nr+1);
+ snew(na_vcm,groups->grps[egcVCM].nr+1);
+
+ for(i=0; i<groups->grps[egcTC].nr; i++)
+ nrdf_tc[i] = 0;
+ for(i=0; i<groups->grps[egcVCM].nr+1; i++)
+ nrdf_vcm[i] = 0;
+
+ snew(nrdf2,natoms);
+ aloop = gmx_mtop_atomloop_all_init(mtop);
+ while (gmx_mtop_atomloop_all_next(aloop,&i,&atom)) {
+ nrdf2[i] = 0;
+ if (atom->ptype == eptAtom || atom->ptype == eptNucleus) {
+ g = ggrpnr(groups,egcFREEZE,i);
+ /* Double count nrdf for particle i */
+ for(d=0; d<DIM; d++) {
+ if (opts->nFreeze[g][d] == 0) {
+ nrdf2[i] += 2;
+ }
+ }
+ nrdf_tc [ggrpnr(groups,egcTC ,i)] += 0.5*nrdf2[i];
+ nrdf_vcm[ggrpnr(groups,egcVCM,i)] += 0.5*nrdf2[i];
+ }
+ }
+
+ as = 0;
+ for(mb=0; mb<mtop->nmolblock; mb++) {
+ molb = &mtop->molblock[mb];
+ molt = &mtop->moltype[molb->type];
+ atom = molt->atoms.atom;
+ for(mol=0; mol<molb->nmol; mol++) {
+ for (ftype=F_CONSTR; ftype<=F_CONSTRNC; ftype++) {
+ ia = molt->ilist[ftype].iatoms;
+ for(i=0; i<molt->ilist[ftype].nr; ) {
+ /* Subtract degrees of freedom for the constraints,
+ * if the particles still have degrees of freedom left.
+ * If one of the particles is a vsite or a shell, then all
+ * constraint motion will go there, but since they do not
+ * contribute to the constraints the degrees of freedom do not
+ * change.
+ */
+ ai = as + ia[1];
+ aj = as + ia[2];
+ if (((atom[ia[1]].ptype == eptNucleus) ||
+ (atom[ia[1]].ptype == eptAtom)) &&
+ ((atom[ia[2]].ptype == eptNucleus) ||
+ (atom[ia[2]].ptype == eptAtom))) {
+ if (nrdf2[ai] > 0)
+ jmin = 1;
+ else
+ jmin = 2;
+ if (nrdf2[aj] > 0)
+ imin = 1;
+ else
+ imin = 2;
+ imin = min(imin,nrdf2[ai]);
+ jmin = min(jmin,nrdf2[aj]);
+ nrdf2[ai] -= imin;
+ nrdf2[aj] -= jmin;
+ nrdf_tc [ggrpnr(groups,egcTC ,ai)] -= 0.5*imin;
+ nrdf_tc [ggrpnr(groups,egcTC ,aj)] -= 0.5*jmin;
+ nrdf_vcm[ggrpnr(groups,egcVCM,ai)] -= 0.5*imin;
+ nrdf_vcm[ggrpnr(groups,egcVCM,aj)] -= 0.5*jmin;
+ }
+ ia += interaction_function[ftype].nratoms+1;
+ i += interaction_function[ftype].nratoms+1;
+ }
+ }
+ ia = molt->ilist[F_SETTLE].iatoms;
+ for(i=0; i<molt->ilist[F_SETTLE].nr; ) {
+ /* Subtract 1 dof from every atom in the SETTLE */
+ for(ai=as+ia[1]; ai<as+ia[1]+3; ai++) {
+ imin = min(2,nrdf2[ai]);
+ nrdf2[ai] -= imin;
+ nrdf_tc [ggrpnr(groups,egcTC ,ai)] -= 0.5*imin;
+ nrdf_vcm[ggrpnr(groups,egcVCM,ai)] -= 0.5*imin;
+ }
+ ia += 2;
+ i += 2;
+ }
+ as += molt->atoms.nr;
+ }
+ }
+
+ if (ir->ePull == epullCONSTRAINT) {
+ /* Correct nrdf for the COM constraints.
+ * We correct using the TC and VCM group of the first atom
+ * in the reference and pull group. If atoms in one pull group
+ * belong to different TC or VCM groups it is anyhow difficult
+ * to determine the optimal nrdf assignment.
+ */
+ pull = ir->pull;
+ if (pull->eGeom == epullgPOS) {
+ nc = 0;
+ for(i=0; i<DIM; i++) {
+ if (pull->dim[i])
+ nc++;
+ }
+ } else {
+ nc = 1;
+ }
+ for(i=0; i<pull->ngrp; i++) {
+ imin = 2*nc;
+ if (pull->grp[0].nat > 0) {
+ /* Subtract 1/2 dof from the reference group */
+ ai = pull->grp[0].ind[0];
+ if (nrdf_tc[ggrpnr(groups,egcTC,ai)] > 1) {
+ nrdf_tc [ggrpnr(groups,egcTC ,ai)] -= 0.5;
+ nrdf_vcm[ggrpnr(groups,egcVCM,ai)] -= 0.5;
+ imin--;
+ }
+ }
+ /* Subtract 1/2 dof from the pulled group */
+ ai = pull->grp[1+i].ind[0];
+ nrdf_tc [ggrpnr(groups,egcTC ,ai)] -= 0.5*imin;
+ nrdf_vcm[ggrpnr(groups,egcVCM,ai)] -= 0.5*imin;
+ if (nrdf_tc[ggrpnr(groups,egcTC,ai)] < 0)
+ gmx_fatal(FARGS,"Center of mass pulling constraints caused the number of degrees of freedom for temperature coupling group %s to be negative",gnames[groups->grps[egcTC].nm_ind[ggrpnr(groups,egcTC,ai)]]);
+ }
+ }
+
+ if (ir->nstcomm != 0) {
+ /* Subtract 3 from the number of degrees of freedom in each vcm group
+ * when com translation is removed and 6 when rotation is removed
+ * as well.
+ */
+ switch (ir->comm_mode) {
+ case ecmLINEAR:
+ n_sub = ndof_com(ir);
+ break;
+ case ecmANGULAR:
+ n_sub = 6;
+ break;
+ default:
+ n_sub = 0;
+ gmx_incons("Checking comm_mode");
+ }
+
+ for(i=0; i<groups->grps[egcTC].nr; i++) {
+ /* Count the number of atoms of TC group i for every VCM group */
+ for(j=0; j<groups->grps[egcVCM].nr+1; j++)
+ na_vcm[j] = 0;
+ na_tot = 0;
+ for(ai=0; ai<natoms; ai++)
+ if (ggrpnr(groups,egcTC,ai) == i) {
+ na_vcm[ggrpnr(groups,egcVCM,ai)]++;
+ na_tot++;
+ }
+ /* Correct for VCM removal according to the fraction of each VCM
+ * group present in this TC group.
+ */
+ nrdf_uc = nrdf_tc[i];
+ if (debug) {
+ fprintf(debug,"T-group[%d] nrdf_uc = %g, n_sub = %g\n",
+ i,nrdf_uc,n_sub);
+ }
+ nrdf_tc[i] = 0;
+ for(j=0; j<groups->grps[egcVCM].nr+1; j++) {
+ if (nrdf_vcm[j] > n_sub) {
+ nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
+ (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
+ }
+ if (debug) {
+ fprintf(debug," nrdf_vcm[%d] = %g, nrdf = %g\n",
+ j,nrdf_vcm[j],nrdf_tc[i]);
+ }
+ }
+ }
+ }
+ for(i=0; (i<groups->grps[egcTC].nr); i++) {
+ opts->nrdf[i] = nrdf_tc[i];
+ if (opts->nrdf[i] < 0)
+ opts->nrdf[i] = 0;
+ fprintf(stderr,
+ "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
+ gnames[groups->grps[egcTC].nm_ind[i]],opts->nrdf[i]);
+ }
+
+ sfree(nrdf2);
+ sfree(nrdf_tc);
+ sfree(nrdf_vcm);
+ sfree(na_vcm);
+}
+
+static void decode_cos(char *s,t_cosines *cosine,gmx_bool bTime)
+{
+ char *t;
+ char format[STRLEN],f1[STRLEN];
+ double a,phi;
+ int i;
+
+ t=strdup(s);
+ trim(t);
+
+ cosine->n=0;
+ cosine->a=NULL;
+ cosine->phi=NULL;
+ if (strlen(t)) {
+ sscanf(t,"%d",&(cosine->n));
+ if (cosine->n <= 0) {
+ cosine->n=0;
+ } else {
+ snew(cosine->a,cosine->n);
+ snew(cosine->phi,cosine->n);
+
+ sprintf(format,"%%*d");
+ for(i=0; (i<cosine->n); i++) {
+ strcpy(f1,format);
+ strcat(f1,"%lf%lf");
+ if (sscanf(t,f1,&a,&phi) < 2)
+ gmx_fatal(FARGS,"Invalid input for electric field shift: '%s'",t);
+ cosine->a[i]=a;
+ cosine->phi[i]=phi;
+ strcat(format,"%*lf%*lf");
+ }
+ }
+ }
+ sfree(t);
+}
+
+static gmx_bool do_egp_flag(t_inputrec *ir,gmx_groups_t *groups,
+ const char *option,const char *val,int flag)
+{
+ /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
+ * But since this is much larger than STRLEN, such a line can not be parsed.
+ * The real maximum is the number of names that fit in a string: STRLEN/2.
+ */
+#define EGP_MAX (STRLEN/2)
+ int nelem,i,j,k,nr;
+ char *names[EGP_MAX];
+ char ***gnames;
+ gmx_bool bSet;
+
+ gnames = groups->grpname;
+
+ nelem = str_nelem(val,EGP_MAX,names);
+ if (nelem % 2 != 0)
+ gmx_fatal(FARGS,"The number of groups for %s is odd",option);
+ nr = groups->grps[egcENER].nr;
+ bSet = FALSE;
+ for(i=0; i<nelem/2; i++) {
+ j = 0;
+ while ((j < nr) &&
+ gmx_strcasecmp(names[2*i],*(gnames[groups->grps[egcENER].nm_ind[j]])))
+ j++;
+ if (j == nr)
+ gmx_fatal(FARGS,"%s in %s is not an energy group\n",
+ names[2*i],option);
+ k = 0;
+ while ((k < nr) &&
+ gmx_strcasecmp(names[2*i+1],*(gnames[groups->grps[egcENER].nm_ind[k]])))
+ k++;
+ if (k==nr)
+ gmx_fatal(FARGS,"%s in %s is not an energy group\n",
+ names[2*i+1],option);
+ if ((j < nr) && (k < nr)) {
+ ir->opts.egp_flags[nr*j+k] |= flag;
+ ir->opts.egp_flags[nr*k+j] |= flag;
+ bSet = TRUE;
+ }
+ }
+
+ return bSet;
+}
+
+void do_index(const char* mdparin, const char *ndx,
+ gmx_mtop_t *mtop,
+ gmx_bool bVerbose,
+ t_inputrec *ir,rvec *v,
+ warninp_t wi)
+{
+ t_blocka *grps;
+ gmx_groups_t *groups;
+ int natoms;
+ t_symtab *symtab;
+ t_atoms atoms_all;
+ char warnbuf[STRLEN],**gnames;
+ int nr,ntcg,ntau_t,nref_t,nacc,nofg,nSA,nSA_points,nSA_time,nSA_temp;
+ real tau_min;
+ int nstcmin;
+ int nacg,nfreeze,nfrdim,nenergy,nvcm,nuser;
+ char *ptr1[MAXPTR],*ptr2[MAXPTR],*ptr3[MAXPTR];
+ int i,j,k,restnm;
+ real SAtime;
+ gmx_bool bExcl,bTable,bSetTCpar,bAnneal,bRest;
+ int nQMmethod,nQMbasis,nQMcharge,nQMmult,nbSH,nCASorb,nCASelec,
+ nSAon,nSAoff,nSAsteps,nQMg,nbOPT,nbTS;
+ char warn_buf[STRLEN];
+
+ if (bVerbose)
+ fprintf(stderr,"processing index file...\n");
+ debug_gmx();
+ if (ndx == NULL) {
+ snew(grps,1);
+ snew(grps->index,1);
+ snew(gnames,1);
+ atoms_all = gmx_mtop_global_atoms(mtop);
+ analyse(&atoms_all,grps,&gnames,FALSE,TRUE);
+ free_t_atoms(&atoms_all,FALSE);
+ } else {
+ grps = init_index(ndx,&gnames);
+ }
+
+ groups = &mtop->groups;
+ natoms = mtop->natoms;
+ symtab = &mtop->symtab;
+
+ snew(groups->grpname,grps->nr+1);
+
+ for(i=0; (i<grps->nr); i++) {
+ groups->grpname[i] = put_symtab(symtab,gnames[i]);
+ }
+ groups->grpname[i] = put_symtab(symtab,"rest");
+ restnm=i;
+ srenew(gnames,grps->nr+1);
+ gnames[restnm] = *(groups->grpname[i]);
+ groups->ngrpname = grps->nr+1;
+
+ set_warning_line(wi,mdparin,-1);
+
+ ntau_t = str_nelem(tau_t,MAXPTR,ptr1);
+ nref_t = str_nelem(ref_t,MAXPTR,ptr2);
+ ntcg = str_nelem(tcgrps,MAXPTR,ptr3);
+ if ((ntau_t != ntcg) || (nref_t != ntcg)) {
- fprintf(stderr,"bd_fric=0, so tau_t will be used as the inverse friction constant(s)\n");
++ gmx_fatal(FARGS,"Invalid T coupling input: %d groups, %d ref-t values and "
++ "%d tau-t values",ntcg,nref_t,ntau_t);
+ }
+
+ bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI==eiBD || EI_TPI(ir->eI));
+ do_numbering(natoms,groups,ntcg,ptr3,grps,gnames,egcTC,
+ restnm,bSetTCpar ? egrptpALL : egrptpALL_GENREST,bVerbose,wi);
+ nr = groups->grps[egcTC].nr;
+ ir->opts.ngtc = nr;
+ snew(ir->opts.nrdf,nr);
+ snew(ir->opts.tau_t,nr);
+ snew(ir->opts.ref_t,nr);
+ if (ir->eI==eiBD && ir->bd_fric==0) {
- gmx_fatal(FARGS,"Not enough ref_t and tau_t values!");
++ fprintf(stderr,"bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
+ }
+
+ if (bSetTCpar)
+ {
+ if (nr != nref_t)
+ {
- sprintf(warn_buf,"With integrator %s tau_t should be larger than 0",ei_names[ir->eI]);
++ gmx_fatal(FARGS,"Not enough ref-t and tau-t values!");
+ }
+
+ tau_min = 1e20;
+ for(i=0; (i<nr); i++)
+ {
+ ir->opts.tau_t[i] = strtod(ptr1[i],NULL);
+ if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
+ {
- sprintf(warn_buf,"For proper integration of the %s thermostat, tau_t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
++ sprintf(warn_buf,"With integrator %s tau-t should be larger than 0",ei_names[ir->eI]);
+ warning_error(wi,warn_buf);
+ }
+ if ((ir->etc == etcVRESCALE && ir->opts.tau_t[i] >= 0) ||
+ (ir->etc != etcVRESCALE && ir->opts.tau_t[i] > 0))
+ {
+ tau_min = min(tau_min,ir->opts.tau_t[i]);
+ }
+ }
+ if (ir->etc != etcNO && ir->nsttcouple == -1)
+ {
+ ir->nsttcouple = ir_optimal_nsttcouple(ir);
+ }
+ if (EI_VV(ir->eI))
+ {
+ if ((ir->epc==epcMTTK) && (ir->etc>etcNO))
+ {
+ int mincouple;
+ mincouple = ir->nsttcouple;
+ if (ir->nstpcouple < mincouple)
+ {
+ mincouple = ir->nstpcouple;
+ }
+ ir->nstpcouple = mincouple;
+ ir->nsttcouple = mincouple;
+ warning_note(wi,"for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple)");
+ }
+ }
+ nstcmin = tcouple_min_integration_steps(ir->etc);
+ if (nstcmin > 1)
+ {
+ if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
+ {
- gmx_fatal(FARGS,"ref_t for group %d negative",i);
++ sprintf(warn_buf,"For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
+ ETCOUPLTYPE(ir->etc),
+ tau_min,nstcmin,
+ ir->nsttcouple*ir->delta_t);
+ warning(wi,warn_buf);
+ }
+ }
+ for(i=0; (i<nr); i++)
+ {
+ ir->opts.ref_t[i] = strtod(ptr2[i],NULL);
+ if (ir->opts.ref_t[i] < 0)
+ {
- gmx_fatal(FARGS,"Found %d annealing_npoints values for %d groups\n",nSA_points,nSA);
++ gmx_fatal(FARGS,"ref-t for group %d negative",i);
+ }
+ }
+ }
+
+ /* Simulated annealing for each group. There are nr groups */
+ nSA = str_nelem(anneal,MAXPTR,ptr1);
+ if (nSA == 1 && (ptr1[0][0]=='n' || ptr1[0][0]=='N'))
+ nSA = 0;
+ if(nSA>0 && nSA != nr)
+ gmx_fatal(FARGS,"Not enough annealing values: %d (for %d groups)\n",nSA,nr);
+ else {
+ snew(ir->opts.annealing,nr);
+ snew(ir->opts.anneal_npoints,nr);
+ snew(ir->opts.anneal_time,nr);
+ snew(ir->opts.anneal_temp,nr);
+ for(i=0;i<nr;i++) {
+ ir->opts.annealing[i]=eannNO;
+ ir->opts.anneal_npoints[i]=0;
+ ir->opts.anneal_time[i]=NULL;
+ ir->opts.anneal_temp[i]=NULL;
+ }
+ if (nSA > 0) {
+ bAnneal=FALSE;
+ for(i=0;i<nr;i++) {
+ if(ptr1[i][0]=='n' || ptr1[i][0]=='N') {
+ ir->opts.annealing[i]=eannNO;
+ } else if(ptr1[i][0]=='s'|| ptr1[i][0]=='S') {
+ ir->opts.annealing[i]=eannSINGLE;
+ bAnneal=TRUE;
+ } else if(ptr1[i][0]=='p'|| ptr1[i][0]=='P') {
+ ir->opts.annealing[i]=eannPERIODIC;
+ bAnneal=TRUE;
+ }
+ }
+ if(bAnneal) {
+ /* Read the other fields too */
+ nSA_points = str_nelem(anneal_npoints,MAXPTR,ptr1);
+ if(nSA_points!=nSA)
- gmx_fatal(FARGS,"Found %d annealing_time values, wanter %d\n",nSA_time,k);
++ gmx_fatal(FARGS,"Found %d annealing-npoints values for %d groups\n",nSA_points,nSA);
+ for(k=0,i=0;i<nr;i++) {
+ ir->opts.anneal_npoints[i]=strtol(ptr1[i],NULL,10);
+ if(ir->opts.anneal_npoints[i]==1)
+ gmx_fatal(FARGS,"Please specify at least a start and an end point for annealing\n");
+ snew(ir->opts.anneal_time[i],ir->opts.anneal_npoints[i]);
+ snew(ir->opts.anneal_temp[i],ir->opts.anneal_npoints[i]);
+ k += ir->opts.anneal_npoints[i];
+ }
+
+ nSA_time = str_nelem(anneal_time,MAXPTR,ptr1);
+ if(nSA_time!=k)
- gmx_fatal(FARGS,"Found %d annealing_temp values, wanted %d\n",nSA_temp,k);
++ gmx_fatal(FARGS,"Found %d annealing-time values, wanter %d\n",nSA_time,k);
+ nSA_temp = str_nelem(anneal_temp,MAXPTR,ptr2);
+ if(nSA_temp!=k)
- bExcl = do_egp_flag(ir,groups,"energygrp_excl",egpexcl,EGP_EXCL);
++ gmx_fatal(FARGS,"Found %d annealing-temp values, wanted %d\n",nSA_temp,k);
+
+ for(i=0,k=0;i<nr;i++) {
+
+ for(j=0;j<ir->opts.anneal_npoints[i];j++) {
+ ir->opts.anneal_time[i][j]=strtod(ptr1[k],NULL);
+ ir->opts.anneal_temp[i][j]=strtod(ptr2[k],NULL);
+ if(j==0) {
+ if(ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
+ gmx_fatal(FARGS,"First time point for annealing > init_t.\n");
+ } else {
+ /* j>0 */
+ if(ir->opts.anneal_time[i][j]<ir->opts.anneal_time[i][j-1])
+ gmx_fatal(FARGS,"Annealing timepoints out of order: t=%f comes after t=%f\n",
+ ir->opts.anneal_time[i][j],ir->opts.anneal_time[i][j-1]);
+ }
+ if(ir->opts.anneal_temp[i][j]<0)
+ gmx_fatal(FARGS,"Found negative temperature in annealing: %f\n",ir->opts.anneal_temp[i][j]);
+ k++;
+ }
+ }
+ /* Print out some summary information, to make sure we got it right */
+ for(i=0,k=0;i<nr;i++) {
+ if(ir->opts.annealing[i]!=eannNO) {
+ j = groups->grps[egcTC].nm_ind[i];
+ fprintf(stderr,"Simulated annealing for group %s: %s, %d timepoints\n",
+ *(groups->grpname[j]),eann_names[ir->opts.annealing[i]],
+ ir->opts.anneal_npoints[i]);
+ fprintf(stderr,"Time (ps) Temperature (K)\n");
+ /* All terms except the last one */
+ for(j=0;j<(ir->opts.anneal_npoints[i]-1);j++)
+ fprintf(stderr,"%9.1f %5.1f\n",ir->opts.anneal_time[i][j],ir->opts.anneal_temp[i][j]);
+
+ /* Finally the last one */
+ j = ir->opts.anneal_npoints[i]-1;
+ if(ir->opts.annealing[i]==eannSINGLE)
+ fprintf(stderr,"%9.1f- %5.1f\n",ir->opts.anneal_time[i][j],ir->opts.anneal_temp[i][j]);
+ else {
+ fprintf(stderr,"%9.1f %5.1f\n",ir->opts.anneal_time[i][j],ir->opts.anneal_temp[i][j]);
+ if(fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0])>GMX_REAL_EPS)
+ warning_note(wi,"There is a temperature jump when your annealing loops back.\n");
+ }
+ }
+ }
+ }
+ }
+ }
+
+ if (ir->ePull != epullNO) {
+ make_pull_groups(ir->pull,pull_grp,grps,gnames);
+ }
+
+ if (ir->bRot) {
+ make_rotation_groups(ir->rot,rot_grp,grps,gnames);
+ }
+
+ nacc = str_nelem(acc,MAXPTR,ptr1);
+ nacg = str_nelem(accgrps,MAXPTR,ptr2);
+ if (nacg*DIM != nacc)
+ gmx_fatal(FARGS,"Invalid Acceleration input: %d groups and %d acc. values",
+ nacg,nacc);
+ do_numbering(natoms,groups,nacg,ptr2,grps,gnames,egcACC,
+ restnm,egrptpALL_GENREST,bVerbose,wi);
+ nr = groups->grps[egcACC].nr;
+ snew(ir->opts.acc,nr);
+ ir->opts.ngacc=nr;
+
+ for(i=k=0; (i<nacg); i++)
+ for(j=0; (j<DIM); j++,k++)
+ ir->opts.acc[i][j]=strtod(ptr1[k],NULL);
+ for( ;(i<nr); i++)
+ for(j=0; (j<DIM); j++)
+ ir->opts.acc[i][j]=0;
+
+ nfrdim = str_nelem(frdim,MAXPTR,ptr1);
+ nfreeze = str_nelem(freeze,MAXPTR,ptr2);
+ if (nfrdim != DIM*nfreeze)
+ gmx_fatal(FARGS,"Invalid Freezing input: %d groups and %d freeze values",
+ nfreeze,nfrdim);
+ do_numbering(natoms,groups,nfreeze,ptr2,grps,gnames,egcFREEZE,
+ restnm,egrptpALL_GENREST,bVerbose,wi);
+ nr = groups->grps[egcFREEZE].nr;
+ ir->opts.ngfrz=nr;
+ snew(ir->opts.nFreeze,nr);
+ for(i=k=0; (i<nfreeze); i++)
+ for(j=0; (j<DIM); j++,k++) {
+ ir->opts.nFreeze[i][j]=(gmx_strncasecmp(ptr1[k],"Y",1)==0);
+ if (!ir->opts.nFreeze[i][j]) {
+ if (gmx_strncasecmp(ptr1[k],"N",1) != 0) {
+ sprintf(warnbuf,"Please use Y(ES) or N(O) for freezedim only "
+ "(not %s)", ptr1[k]);
+ warning(wi,warn_buf);
+ }
+ }
+ }
+ for( ; (i<nr); i++)
+ for(j=0; (j<DIM); j++)
+ ir->opts.nFreeze[i][j]=0;
+
+ nenergy=str_nelem(energy,MAXPTR,ptr1);
+ do_numbering(natoms,groups,nenergy,ptr1,grps,gnames,egcENER,
+ restnm,egrptpALL_GENREST,bVerbose,wi);
+ add_wall_energrps(groups,ir->nwall,symtab);
+ ir->opts.ngener = groups->grps[egcENER].nr;
+ nvcm=str_nelem(vcm,MAXPTR,ptr1);
+ bRest =
+ do_numbering(natoms,groups,nvcm,ptr1,grps,gnames,egcVCM,
+ restnm,nvcm==0 ? egrptpALL_GENREST : egrptpPART,bVerbose,wi);
+ if (bRest) {
+ warning(wi,"Some atoms are not part of any center of mass motion removal group.\n"
+ "This may lead to artifacts.\n"
+ "In most cases one should use one group for the whole system.");
+ }
+
+ /* Now we have filled the freeze struct, so we can calculate NRDF */
+ calc_nrdf(mtop,ir,gnames);
+
+ if (v && NULL) {
+ real fac,ntot=0;
+
+ /* Must check per group! */
+ for(i=0; (i<ir->opts.ngtc); i++)
+ ntot += ir->opts.nrdf[i];
+ if (ntot != (DIM*natoms)) {
+ fac = sqrt(ntot/(DIM*natoms));
+ if (bVerbose)
+ fprintf(stderr,"Scaling velocities by a factor of %.3f to account for constraints\n"
+ "and removal of center of mass motion\n",fac);
+ for(i=0; (i<natoms); i++)
+ svmul(fac,v[i],v[i]);
+ }
+ }
+
+ nuser=str_nelem(user1,MAXPTR,ptr1);
+ do_numbering(natoms,groups,nuser,ptr1,grps,gnames,egcUser1,
+ restnm,egrptpALL_GENREST,bVerbose,wi);
+ nuser=str_nelem(user2,MAXPTR,ptr1);
+ do_numbering(natoms,groups,nuser,ptr1,grps,gnames,egcUser2,
+ restnm,egrptpALL_GENREST,bVerbose,wi);
+ nuser=str_nelem(xtc_grps,MAXPTR,ptr1);
+ do_numbering(natoms,groups,nuser,ptr1,grps,gnames,egcXTC,
+ restnm,egrptpONE,bVerbose,wi);
+ nofg = str_nelem(orirefitgrp,MAXPTR,ptr1);
+ do_numbering(natoms,groups,nofg,ptr1,grps,gnames,egcORFIT,
+ restnm,egrptpALL_GENREST,bVerbose,wi);
+
+ /* QMMM input processing */
+ nQMg = str_nelem(QMMM,MAXPTR,ptr1);
+ nQMmethod = str_nelem(QMmethod,MAXPTR,ptr2);
+ nQMbasis = str_nelem(QMbasis,MAXPTR,ptr3);
+ if((nQMmethod != nQMg)||(nQMbasis != nQMg)){
+ gmx_fatal(FARGS,"Invalid QMMM input: %d groups %d basissets"
+ " and %d methods\n",nQMg,nQMbasis,nQMmethod);
+ }
+ /* group rest, if any, is always MM! */
+ do_numbering(natoms,groups,nQMg,ptr1,grps,gnames,egcQMMM,
+ restnm,egrptpALL_GENREST,bVerbose,wi);
+ nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
+ ir->opts.ngQM = nQMg;
+ snew(ir->opts.QMmethod,nr);
+ snew(ir->opts.QMbasis,nr);
+ for(i=0;i<nr;i++){
+ /* input consists of strings: RHF CASSCF PM3 .. These need to be
+ * converted to the corresponding enum in names.c
+ */
+ ir->opts.QMmethod[i] = search_QMstring(ptr2[i],eQMmethodNR,
+ eQMmethod_names);
+ ir->opts.QMbasis[i] = search_QMstring(ptr3[i],eQMbasisNR,
+ eQMbasis_names);
+
+ }
+ nQMmult = str_nelem(QMmult,MAXPTR,ptr1);
+ nQMcharge = str_nelem(QMcharge,MAXPTR,ptr2);
+ nbSH = str_nelem(bSH,MAXPTR,ptr3);
+ snew(ir->opts.QMmult,nr);
+ snew(ir->opts.QMcharge,nr);
+ snew(ir->opts.bSH,nr);
+
+ for(i=0;i<nr;i++){
+ ir->opts.QMmult[i] = strtol(ptr1[i],NULL,10);
+ ir->opts.QMcharge[i] = strtol(ptr2[i],NULL,10);
+ ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i],"Y",1)==0);
+ }
+
+ nCASelec = str_nelem(CASelectrons,MAXPTR,ptr1);
+ nCASorb = str_nelem(CASorbitals,MAXPTR,ptr2);
+ snew(ir->opts.CASelectrons,nr);
+ snew(ir->opts.CASorbitals,nr);
+ for(i=0;i<nr;i++){
+ ir->opts.CASelectrons[i]= strtol(ptr1[i],NULL,10);
+ ir->opts.CASorbitals[i] = strtol(ptr2[i],NULL,10);
+ }
+ /* special optimization options */
+
+ nbOPT = str_nelem(bOPT,MAXPTR,ptr1);
+ nbTS = str_nelem(bTS,MAXPTR,ptr2);
+ snew(ir->opts.bOPT,nr);
+ snew(ir->opts.bTS,nr);
+ for(i=0;i<nr;i++){
+ ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i],"Y",1)==0);
+ ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i],"Y",1)==0);
+ }
+ nSAon = str_nelem(SAon,MAXPTR,ptr1);
+ nSAoff = str_nelem(SAoff,MAXPTR,ptr2);
+ nSAsteps = str_nelem(SAsteps,MAXPTR,ptr3);
+ snew(ir->opts.SAon,nr);
+ snew(ir->opts.SAoff,nr);
+ snew(ir->opts.SAsteps,nr);
+
+ for(i=0;i<nr;i++){
+ ir->opts.SAon[i] = strtod(ptr1[i],NULL);
+ ir->opts.SAoff[i] = strtod(ptr2[i],NULL);
+ ir->opts.SAsteps[i] = strtol(ptr3[i],NULL,10);
+ }
+ /* end of QMMM input */
+
+ if (bVerbose)
+ for(i=0; (i<egcNR); i++) {
+ fprintf(stderr,"%-16s has %d element(s):",gtypes[i],groups->grps[i].nr);
+ for(j=0; (j<groups->grps[i].nr); j++)
+ fprintf(stderr," %s",*(groups->grpname[groups->grps[i].nm_ind[j]]));
+ fprintf(stderr,"\n");
+ }
+
+ nr = groups->grps[egcENER].nr;
+ snew(ir->opts.egp_flags,nr*nr);
+
- bTable = do_egp_flag(ir,groups,"energygrp_table",egptable,EGP_TABLE);
++ bExcl = do_egp_flag(ir,groups,"energygrp-excl",egpexcl,EGP_EXCL);
+ if (bExcl && EEL_FULL(ir->coulombtype))
+ warning(wi,"Can not exclude the lattice Coulomb energy between energy groups");
+
- static gmx_bool absolute_reference(t_inputrec *ir,gmx_mtop_t *sys,ivec AbsRef)
++ bTable = do_egp_flag(ir,groups,"energygrp-table",egptable,EGP_TABLE);
+ if (bTable && !(ir->vdwtype == evdwUSER) &&
+ !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
+ !(ir->coulombtype == eelPMEUSERSWITCH))
+ gmx_fatal(FARGS,"Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
+
+ decode_cos(efield_x,&(ir->ex[XX]),FALSE);
+ decode_cos(efield_xt,&(ir->et[XX]),TRUE);
+ decode_cos(efield_y,&(ir->ex[YY]),FALSE);
+ decode_cos(efield_yt,&(ir->et[YY]),TRUE);
+ decode_cos(efield_z,&(ir->ex[ZZ]),FALSE);
+ decode_cos(efield_zt,&(ir->et[ZZ]),TRUE);
+
+ for(i=0; (i<grps->nr); i++)
+ sfree(gnames[i]);
+ sfree(gnames);
+ done_blocka(grps);
+ sfree(grps);
+
+}
+
+
+
+static void check_disre(gmx_mtop_t *mtop)
+{
+ gmx_ffparams_t *ffparams;
+ t_functype *functype;
+ t_iparams *ip;
+ int i,ndouble,ftype;
+ int label,old_label;
+
+ if (gmx_mtop_ftype_count(mtop,F_DISRES) > 0) {
+ ffparams = &mtop->ffparams;
+ functype = ffparams->functype;
+ ip = ffparams->iparams;
+ ndouble = 0;
+ old_label = -1;
+ for(i=0; i<ffparams->ntypes; i++) {
+ ftype = functype[i];
+ if (ftype == F_DISRES) {
+ label = ip[i].disres.label;
+ if (label == old_label) {
+ fprintf(stderr,"Distance restraint index %d occurs twice\n",label);
+ ndouble++;
+ }
+ old_label = label;
+ }
+ }
+ if (ndouble>0)
+ gmx_fatal(FARGS,"Found %d double distance restraint indices,\n"
+ "probably the parameters for multiple pairs in one restraint "
+ "are not identical\n",ndouble);
+ }
+}
+
- int d,g,i;
- gmx_mtop_ilistloop_t iloop;
- t_ilist *ilist;
- int nmol;
- t_iparams *pr;
-
- /* Check the COM */
- for(d=0; d<DIM; d++) {
- AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
- }
- /* Check for freeze groups */
- for(g=0; g<ir->opts.ngfrz; g++) {
- for(d=0; d<DIM; d++) {
- if (ir->opts.nFreeze[g][d] != 0) {
- AbsRef[d] = 1;
- }
++static gmx_bool absolute_reference(t_inputrec *ir,gmx_mtop_t *sys,
++ gmx_bool posres_only,
++ ivec AbsRef)
+{
- }
- /* Check for position restraints */
- iloop = gmx_mtop_ilistloop_init(sys);
- while (gmx_mtop_ilistloop_next(iloop,&ilist,&nmol)) {
- if (nmol > 0) {
- for(i=0; i<ilist[F_POSRES].nr; i+=2) {
- pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
- for(d=0; d<DIM; d++) {
- if (pr->posres.fcA[d] != 0) {
- AbsRef[d] = 1;
- }
- }
- }
++ int d,g,i;
++ gmx_mtop_ilistloop_t iloop;
++ t_ilist *ilist;
++ int nmol;
++ t_iparams *pr;
++
++ clear_ivec(AbsRef);
++
++ if (!posres_only)
++ {
++ /* Check the COM */
++ for(d=0; d<DIM; d++)
++ {
++ AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
++ }
++ /* Check for freeze groups */
++ for(g=0; g<ir->opts.ngfrz; g++)
++ {
++ for(d=0; d<DIM; d++)
++ {
++ if (ir->opts.nFreeze[g][d] != 0)
++ {
++ AbsRef[d] = 1;
++ }
++ }
++ }
+ }
- }
++
++ /* Check for position restraints */
++ iloop = gmx_mtop_ilistloop_init(sys);
++ while (gmx_mtop_ilistloop_next(iloop,&ilist,&nmol))
++ {
++ if (nmol > 0 &&
++ (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
++ {
++ for(i=0; i<ilist[F_POSRES].nr; i+=2)
++ {
++ pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
++ for(d=0; d<DIM; d++)
++ {
++ if (pr->posres.fcA[d] != 0)
++ {
++ AbsRef[d] = 1;
++ }
++ }
++ }
++ }
+ }
- return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
+
- !(absolute_reference(ir,sys,AbsRef) || ir->nsteps <= 10)) {
++ return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
+}
+
+void triple_check(const char *mdparin,t_inputrec *ir,gmx_mtop_t *sys,
+ warninp_t wi)
+{
+ char err_buf[256];
+ int i,m,g,nmol,npct;
+ gmx_bool bCharge,bAcc;
+ real gdt_max,*mgrp,mt;
+ rvec acc;
+ gmx_mtop_atomloop_block_t aloopb;
+ gmx_mtop_atomloop_all_t aloop;
+ t_atom *atom;
+ ivec AbsRef;
+ char warn_buf[STRLEN];
+
+ set_warning_line(wi,mdparin,-1);
+
+ if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
+ ir->comm_mode == ecmNO &&
-
++ !(absolute_reference(ir,sys,FALSE,AbsRef) || ir->nsteps <= 10)) {
+ warning(wi,"You are not using center of mass motion removal (mdp option comm-mode), numerical rounding errors can lead to build up of kinetic energy of the center of mass");
+ }
- sprintf(warn_buf,"The relative error with integrator %s is 0.5*delta_t/tau_t = %g, you might want to switch to integrator %s\n",
++
++ /* Check for pressure coupling with absolute position restraints */
++ if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
++ {
++ absolute_reference(ir,sys,TRUE,AbsRef);
++ {
++ for(m=0; m<DIM; m++)
++ {
++ if (AbsRef[m] && norm2(ir->compress[m]) > 0)
++ {
++ warning(wi,"You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
++ break;
++ }
++ }
++ }
++ }
++
+ bCharge = FALSE;
+ aloopb = gmx_mtop_atomloop_block_init(sys);
+ while (gmx_mtop_atomloop_block_next(aloopb,&atom,&nmol)) {
+ if (atom->q != 0 || atom->qB != 0) {
+ bCharge = TRUE;
+ }
+ }
+
+ if (!bCharge) {
+ if (EEL_FULL(ir->coulombtype)) {
+ sprintf(err_buf,
+ "You are using full electrostatics treatment %s for a system without charges.\n"
+ "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
+ EELTYPE(ir->coulombtype),EELTYPE(eelCUT));
+ warning(wi,err_buf);
+ }
+ } else {
+ if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent) {
+ sprintf(err_buf,
+ "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
+ "You might want to consider using %s electrostatics.\n",
+ EELTYPE(eelPME));
+ warning_note(wi,err_buf);
+ }
+ }
+
+ /* Generalized reaction field */
+ if (ir->opts.ngtc == 0) {
+ sprintf(err_buf,"No temperature coupling while using coulombtype %s",
+ eel_names[eelGRF]);
+ CHECK(ir->coulombtype == eelGRF);
+ }
+ else {
+ sprintf(err_buf,"When using coulombtype = %s"
+ " ref_t for temperature coupling should be > 0",
+ eel_names[eelGRF]);
+ CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
+ }
+
+ if (ir->eI == eiSD1) {
+ gdt_max = 0;
+ for(i=0; (i<ir->opts.ngtc); i++)
+ gdt_max = max(gdt_max,ir->delta_t/ir->opts.tau_t[i]);
+ if (0.5*gdt_max > 0.0015) {
- absolute_reference(ir,sys,AbsRef);
++ sprintf(warn_buf,"The relative error with integrator %s is 0.5*delta-t/tau-t = %g, you might want to switch to integrator %s\n",
+ ei_names[ir->eI],0.5*gdt_max,ei_names[eiSD2]);
+ warning_note(wi,warn_buf);
+ }
+ }
+
+ bAcc = FALSE;
+ for(i=0; (i<sys->groups.grps[egcACC].nr); i++) {
+ for(m=0; (m<DIM); m++) {
+ if (fabs(ir->opts.acc[i][m]) > 1e-6) {
+ bAcc = TRUE;
+ }
+ }
+ }
+ if (bAcc) {
+ clear_rvec(acc);
+ snew(mgrp,sys->groups.grps[egcACC].nr);
+ aloop = gmx_mtop_atomloop_all_init(sys);
+ while (gmx_mtop_atomloop_all_next(aloop,&i,&atom)) {
+ mgrp[ggrpnr(&sys->groups,egcACC,i)] += atom->m;
+ }
+ mt = 0.0;
+ for(i=0; (i<sys->groups.grps[egcACC].nr); i++) {
+ for(m=0; (m<DIM); m++)
+ acc[m] += ir->opts.acc[i][m]*mgrp[i];
+ mt += mgrp[i];
+ }
+ for(m=0; (m<DIM); m++) {
+ if (fabs(acc[m]) > 1e-6) {
+ const char *dim[DIM] = { "X", "Y", "Z" };
+ fprintf(stderr,
+ "Net Acceleration in %s direction, will %s be corrected\n",
+ dim[m],ir->nstcomm != 0 ? "" : "not");
+ if (ir->nstcomm != 0 && m < ndof_com(ir)) {
+ acc[m] /= mt;
+ for (i=0; (i<sys->groups.grps[egcACC].nr); i++)
+ ir->opts.acc[i][m] -= acc[m];
+ }
+ }
+ }
+ sfree(mgrp);
+ }
+
+ if (ir->efep != efepNO && ir->sc_alpha != 0 &&
+ !gmx_within_tol(sys->ffparams.reppow,12.0,10*GMX_DOUBLE_EPS)) {
+ gmx_fatal(FARGS,"Soft-core interactions are only supported with VdW repulsion power 12");
+ }
+
+ if (ir->ePull != epullNO) {
+ if (ir->pull->grp[0].nat == 0) {
- sprintf(warn_buf,"ERROR: shake_tol must be > 0 instead of %g\n",
++ absolute_reference(ir,sys,FALSE,AbsRef);
+ for(m=0; m<DIM; m++) {
+ if (ir->pull->dim[m] && !AbsRef[m]) {
+ warning(wi,"You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts.");
+ break;
+ }
+ }
+ }
+
+ if (ir->pull->eGeom == epullgDIRPBC) {
+ for(i=0; i<3; i++) {
+ for(m=0; m<=i; m++) {
+ if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
+ ir->deform[i][m] != 0) {
+ for(g=1; g<ir->pull->ngrp; g++) {
+ if (ir->pull->grp[g].vec[m] != 0) {
+ gmx_fatal(FARGS,"Can not have dynamic box while using pull geometry '%s' (dim %c)",EPULLGEOM(ir->pull->eGeom),'x'+m);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ check_disre(sys);
+}
+
+void double_check(t_inputrec *ir,matrix box,gmx_bool bConstr,warninp_t wi)
+{
+ real min_size;
+ gmx_bool bTWIN;
+ char warn_buf[STRLEN];
+ const char *ptr;
+
+ ptr = check_box(ir->ePBC,box);
+ if (ptr) {
+ warning_error(wi,ptr);
+ }
+
+ if (bConstr && ir->eConstrAlg == econtSHAKE) {
+ if (ir->shake_tol <= 0.0) {
- sprintf(warn_buf,"For accurate %s with LINCS constraints, lincs_order should be 8 or more.",ei_names[ir->eI]);
++ sprintf(warn_buf,"ERROR: shake-tol must be > 0 instead of %g\n",
+ ir->shake_tol);
+ warning_error(wi,warn_buf);
+ }
+
+ if (IR_TWINRANGE(*ir) && ir->nstlist > 1) {
+ sprintf(warn_buf,"With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
+ if (ir->epc == epcNO) {
+ warning(wi,warn_buf);
+ } else {
+ warning_error(wi,warn_buf);
+ }
+ }
+ }
+
+ if( (ir->eConstrAlg == econtLINCS) && bConstr) {
+ /* If we have Lincs constraints: */
+ if(ir->eI==eiMD && ir->etc==etcNO &&
+ ir->eConstrAlg==econtLINCS && ir->nLincsIter==1) {
+ sprintf(warn_buf,"For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
+ warning_note(wi,warn_buf);
+ }
+
+ if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder<8)) {
++ sprintf(warn_buf,"For accurate %s with LINCS constraints, lincs-order should be 8 or more.",ei_names[ir->eI]);
+ warning_note(wi,warn_buf);
+ }
+ if (ir->epc==epcMTTK) {
+ warning_error(wi,"MTTK not compatible with lincs -- use shake instead.");
+ }
+ }
+
+ if (ir->LincsWarnAngle > 90.0) {
+ sprintf(warn_buf,"lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
+ warning(wi,warn_buf);
+ ir->LincsWarnAngle = 90.0;
+ }
+
+ if (ir->ePBC != epbcNONE) {
+ if (ir->nstlist == 0) {
+ warning(wi,"With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
+ }
+ bTWIN = (ir->rlistlong > ir->rlist);
+ if (ir->ns_type == ensGRID) {
+ if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC,box)) {
+ sprintf(warn_buf,"ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease %s.\n",
+ bTWIN ? (ir->rcoulomb==ir->rlistlong ? "rcoulomb" : "rvdw"):"rlist");
+ warning_error(wi,warn_buf);
+ }
+ } else {
+ min_size = min(box[XX][XX],min(box[YY][YY],box[ZZ][ZZ]));
+ if (2*ir->rlistlong >= min_size) {
+ sprintf(warn_buf,"ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
+ warning_error(wi,warn_buf);
+ if (TRICLINIC(box))
+ fprintf(stderr,"Grid search might allow larger cut-off's than simple search with triclinic boxes.");
+ }
+ }
+ }
+}
+
+void check_chargegroup_radii(const gmx_mtop_t *mtop,const t_inputrec *ir,
+ rvec *x,
+ warninp_t wi)
+{
+ real rvdw1,rvdw2,rcoul1,rcoul2;
+ char warn_buf[STRLEN];
+
+ calc_chargegroup_radii(mtop,x,&rvdw1,&rvdw2,&rcoul1,&rcoul2);
+
+ if (rvdw1 > 0)
+ {
+ printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
+ rvdw1,rvdw2);
+ }
+ if (rcoul1 > 0)
+ {
+ printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
+ rcoul1,rcoul2);
+ }
+
+ if (ir->rlist > 0)
+ {
+ if (rvdw1 + rvdw2 > ir->rlist ||
+ rcoul1 + rcoul2 > ir->rlist)
+ {
+ sprintf(warn_buf,"The sum of the two largest charge group radii (%f) is larger than rlist (%f)\n",max(rvdw1+rvdw2,rcoul1+rcoul2),ir->rlist);
+ warning(wi,warn_buf);
+ }
+ else
+ {
+ /* Here we do not use the zero at cut-off macro,
+ * since user defined interactions might purposely
+ * not be zero at the cut-off.
+ */
+ if (EVDW_IS_ZERO_AT_CUTOFF(ir->vdwtype) &&
+ rvdw1 + rvdw2 > ir->rlist - ir->rvdw)
+ {
+ sprintf(warn_buf,"The sum of the two largest charge group radii (%f) is larger than rlist (%f) - rvdw (%f)\n",
+ rvdw1+rvdw2,
+ ir->rlist,ir->rvdw);
+ if (ir_NVE(ir))
+ {
+ warning(wi,warn_buf);
+ }
+ else
+ {
+ warning_note(wi,warn_buf);
+ }
+ }
+ if (EEL_IS_ZERO_AT_CUTOFF(ir->coulombtype) &&
+ rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
+ {
+ sprintf(warn_buf,"The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f)\n",
+ rcoul1+rcoul2,
+ ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
+ ir->rlistlong,ir->rcoulomb);
+ if (ir_NVE(ir))
+ {
+ warning(wi,warn_buf);
+ }
+ else
+ {
+ warning_note(wi,warn_buf);
+ }
+ }
+ }
+ }
+}
--- /dev/null
- if (EST_DISTR(est) && state_local->flags & (1<<est))
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This file is part of Gromacs Copyright (c) 1991-2008
+ * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org
+ *
+ * And Hey:
+ * Gnomes, ROck Monsters And Chili Sauce
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+#include <time.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
+#include "typedefs.h"
+#include "smalloc.h"
+#include "vec.h"
+#include "domdec.h"
+#include "domdec_network.h"
+#include "nrnb.h"
+#include "pbc.h"
+#include "chargegroup.h"
+#include "constr.h"
+#include "mdatoms.h"
+#include "names.h"
+#include "pdbio.h"
+#include "futil.h"
+#include "force.h"
+#include "pme.h"
+#include "pull.h"
+#include "pull_rotation.h"
+#include "gmx_wallcycle.h"
+#include "mdrun.h"
+#include "nsgrid.h"
+#include "shellfc.h"
+#include "mtop_util.h"
+#include "gmxfio.h"
+#include "gmx_ga2la.h"
+#include "gmx_sort.h"
+
+#ifdef GMX_LIB_MPI
+#include <mpi.h>
+#endif
+#ifdef GMX_THREADS
+#include "tmpi.h"
+#endif
+
+#define DDRANK(dd,rank) (rank)
+#define DDMASTERRANK(dd) (dd->masterrank)
+
+typedef struct gmx_domdec_master
+{
+ /* The cell boundaries */
+ real **cell_x;
+ /* The global charge group division */
+ int *ncg; /* Number of home charge groups for each node */
+ int *index; /* Index of nnodes+1 into cg */
+ int *cg; /* Global charge group index */
+ int *nat; /* Number of home atoms for each node. */
+ int *ibuf; /* Buffer for communication */
+ rvec *vbuf; /* Buffer for state scattering and gathering */
+} gmx_domdec_master_t;
+
+typedef struct
+{
+ /* The numbers of charge groups to send and receive for each cell
+ * that requires communication, the last entry contains the total
+ * number of atoms that needs to be communicated.
+ */
+ int nsend[DD_MAXIZONE+2];
+ int nrecv[DD_MAXIZONE+2];
+ /* The charge groups to send */
+ int *index;
+ int nalloc;
+ /* The atom range for non-in-place communication */
+ int cell2at0[DD_MAXIZONE];
+ int cell2at1[DD_MAXIZONE];
+} gmx_domdec_ind_t;
+
+typedef struct
+{
+ int np; /* Number of grid pulses in this dimension */
+ int np_dlb; /* For dlb, for use with edlbAUTO */
+ gmx_domdec_ind_t *ind; /* The indices to communicate, size np */
+ int np_nalloc;
+ gmx_bool bInPlace; /* Can we communicate in place? */
+} gmx_domdec_comm_dim_t;
+
+typedef struct
+{
+ gmx_bool *bCellMin; /* Temp. var.: is this cell size at the limit */
+ real *cell_f; /* State var.: cell boundaries, box relative */
+ real *old_cell_f; /* Temp. var.: old cell size */
+ real *cell_f_max0; /* State var.: max lower boundary, incl neighbors */
+ real *cell_f_min1; /* State var.: min upper boundary, incl neighbors */
+ real *bound_min; /* Temp. var.: lower limit for cell boundary */
+ real *bound_max; /* Temp. var.: upper limit for cell boundary */
+ gmx_bool bLimited; /* State var.: is DLB limited in this dim and row */
+ real *buf_ncd; /* Temp. var. */
+} gmx_domdec_root_t;
+
+#define DD_NLOAD_MAX 9
+
+/* Here floats are accurate enough, since these variables
+ * only influence the load balancing, not the actual MD results.
+ */
+typedef struct
+{
+ int nload;
+ float *load;
+ float sum;
+ float max;
+ float sum_m;
+ float cvol_min;
+ float mdf;
+ float pme;
+ int flags;
+} gmx_domdec_load_t;
+
+typedef struct
+{
+ int nsc;
+ int ind_gl;
+ int ind;
+} gmx_cgsort_t;
+
+typedef struct
+{
+ gmx_cgsort_t *sort1,*sort2;
+ int sort_nalloc;
+ gmx_cgsort_t *sort_new;
+ int sort_new_nalloc;
+ int *ibuf;
+ int ibuf_nalloc;
+} gmx_domdec_sort_t;
+
+typedef struct
+{
+ rvec *v;
+ int nalloc;
+} vec_rvec_t;
+
+/* This enum determines the order of the coordinates.
+ * ddnatHOME and ddnatZONE should be first and second,
+ * the others can be ordered as wanted.
+ */
+enum { ddnatHOME, ddnatZONE, ddnatVSITE, ddnatCON, ddnatNR };
+
+enum { edlbAUTO, edlbNO, edlbYES, edlbNR };
+const char *edlb_names[edlbNR] = { "auto", "no", "yes" };
+
+typedef struct
+{
+ int dim; /* The dimension */
+ gmx_bool dim_match;/* Tells if DD and PME dims match */
+ int nslab; /* The number of PME slabs in this dimension */
+ real *slb_dim_f; /* Cell sizes for determining the PME comm. with SLB */
+ int *pp_min; /* The minimum pp node location, size nslab */
+ int *pp_max; /* The maximum pp node location,size nslab */
+ int maxshift; /* The maximum shift for coordinate redistribution in PME */
+} gmx_ddpme_t;
+
+typedef struct
+{
+ real min0; /* The minimum bottom of this zone */
+ real max1; /* The maximum top of this zone */
+ real mch0; /* The maximum bottom communicaton height for this zone */
+ real mch1; /* The maximum top communicaton height for this zone */
+ real p1_0; /* The bottom value of the first cell in this zone */
+ real p1_1; /* The top value of the first cell in this zone */
+} gmx_ddzone_t;
+
+typedef struct gmx_domdec_comm
+{
+ /* All arrays are indexed with 0 to dd->ndim (not Cartesian indexing),
+ * unless stated otherwise.
+ */
+
+ /* The number of decomposition dimensions for PME, 0: no PME */
+ int npmedecompdim;
+ /* The number of nodes doing PME (PP/PME or only PME) */
+ int npmenodes;
+ int npmenodes_x;
+ int npmenodes_y;
+ /* The communication setup including the PME only nodes */
+ gmx_bool bCartesianPP_PME;
+ ivec ntot;
+ int cartpmedim;
+ int *pmenodes; /* size npmenodes */
+ int *ddindex2simnodeid; /* size npmenodes, only with bCartesianPP
+ * but with bCartesianPP_PME */
+ gmx_ddpme_t ddpme[2];
+
+ /* The DD particle-particle nodes only */
+ gmx_bool bCartesianPP;
+ int *ddindex2ddnodeid; /* size npmenode, only with bCartesianPP_PME */
+
+ /* The global charge groups */
+ t_block cgs_gl;
+
+ /* Should we sort the cgs */
+ int nstSortCG;
+ gmx_domdec_sort_t *sort;
+
+ /* Are there bonded and multi-body interactions between charge groups? */
+ gmx_bool bInterCGBondeds;
+ gmx_bool bInterCGMultiBody;
+
+ /* Data for the optional bonded interaction atom communication range */
+ gmx_bool bBondComm;
+ t_blocka *cglink;
+ char *bLocalCG;
+
+ /* The DLB option */
+ int eDLB;
+ /* Are we actually using DLB? */
+ gmx_bool bDynLoadBal;
+
+ /* Cell sizes for static load balancing, first index cartesian */
+ real **slb_frac;
+
+ /* The width of the communicated boundaries */
+ real cutoff_mbody;
+ real cutoff;
+ /* The minimum cell size (including triclinic correction) */
+ rvec cellsize_min;
+ /* For dlb, for use with edlbAUTO */
+ rvec cellsize_min_dlb;
+ /* The lower limit for the DD cell size with DLB */
+ real cellsize_limit;
+ /* Effectively no NB cut-off limit with DLB for systems without PBC? */
+ gmx_bool bVacDLBNoLimit;
+
+ /* tric_dir is only stored here because dd_get_ns_ranges needs it */
+ ivec tric_dir;
+ /* box0 and box_size are required with dim's without pbc and -gcom */
+ rvec box0;
+ rvec box_size;
+
+ /* The cell boundaries */
+ rvec cell_x0;
+ rvec cell_x1;
+
+ /* The old location of the cell boundaries, to check cg displacements */
+ rvec old_cell_x0;
+ rvec old_cell_x1;
+
+ /* The communication setup and charge group boundaries for the zones */
+ gmx_domdec_zones_t zones;
+
+ /* The zone limits for DD dimensions 1 and 2 (not 0), determined from
+ * cell boundaries of neighboring cells for dynamic load balancing.
+ */
+ gmx_ddzone_t zone_d1[2];
+ gmx_ddzone_t zone_d2[2][2];
+
+ /* The coordinate/force communication setup and indices */
+ gmx_domdec_comm_dim_t cd[DIM];
+ /* The maximum number of cells to communicate with in one dimension */
+ int maxpulse;
+
+ /* Which cg distribution is stored on the master node */
+ int master_cg_ddp_count;
+
+ /* The number of cg's received from the direct neighbors */
+ int zone_ncg1[DD_MAXZONE];
+
+ /* The atom counts, the range for each type t is nat[t-1] <= at < nat[t] */
+ int nat[ddnatNR];
+
+ /* Communication buffer for general use */
+ int *buf_int;
+ int nalloc_int;
+
+ /* Communication buffer for general use */
+ vec_rvec_t vbuf;
+
+ /* Communication buffers only used with multiple grid pulses */
+ int *buf_int2;
+ int nalloc_int2;
+ vec_rvec_t vbuf2;
+
+ /* Communication buffers for local redistribution */
+ int **cggl_flag;
+ int cggl_flag_nalloc[DIM*2];
+ rvec **cgcm_state;
+ int cgcm_state_nalloc[DIM*2];
+
+ /* Cell sizes for dynamic load balancing */
+ gmx_domdec_root_t **root;
+ real *cell_f_row;
+ real cell_f0[DIM];
+ real cell_f1[DIM];
+ real cell_f_max0[DIM];
+ real cell_f_min1[DIM];
+
+ /* Stuff for load communication */
+ gmx_bool bRecordLoad;
+ gmx_domdec_load_t *load;
+#ifdef GMX_MPI
+ MPI_Comm *mpi_comm_load;
+#endif
+
+ /* Maximum DLB scaling per load balancing step in percent */
+ int dlb_scale_lim;
+
+ /* Cycle counters */
+ float cycl[ddCyclNr];
+ int cycl_n[ddCyclNr];
+ float cycl_max[ddCyclNr];
+ /* Flop counter (0=no,1=yes,2=with (eFlop-1)*5% noise */
+ int eFlop;
+ double flop;
+ int flop_n;
+ /* Have often have did we have load measurements */
+ int n_load_have;
+ /* Have often have we collected the load measurements */
+ int n_load_collect;
+
+ /* Statistics */
+ double sum_nat[ddnatNR-ddnatZONE];
+ int ndecomp;
+ int nload;
+ double load_step;
+ double load_sum;
+ double load_max;
+ ivec load_lim;
+ double load_mdf;
+ double load_pme;
+
+ /* The last partition step */
+ gmx_large_int_t globalcomm_step;
+
+ /* Debugging */
+ int nstDDDump;
+ int nstDDDumpGrid;
+ int DD_debug;
+} gmx_domdec_comm_t;
+
+/* The size per charge group of the cggl_flag buffer in gmx_domdec_comm_t */
+#define DD_CGIBS 2
+
+/* The flags for the cggl_flag buffer in gmx_domdec_comm_t */
+#define DD_FLAG_NRCG 65535
+#define DD_FLAG_FW(d) (1<<(16+(d)*2))
+#define DD_FLAG_BW(d) (1<<(16+(d)*2+1))
+
+/* Zone permutation required to obtain consecutive charge groups
+ * for neighbor searching.
+ */
+static const int zone_perm[3][4] = { {0,0,0,0},{1,0,0,0},{3,0,1,2} };
+
+/* dd_zo and dd_zp3/dd_zp2 are set up such that i zones with non-zero
+ * components see only j zones with that component 0.
+ */
+
+/* The DD zone order */
+static const ivec dd_zo[DD_MAXZONE] =
+ {{0,0,0},{1,0,0},{1,1,0},{0,1,0},{0,1,1},{0,0,1},{1,0,1},{1,1,1}};
+
+/* The 3D setup */
+#define dd_z3n 8
+#define dd_zp3n 4
+static const ivec dd_zp3[dd_zp3n] = {{0,0,8},{1,3,6},{2,5,6},{3,5,7}};
+
+/* The 2D setup */
+#define dd_z2n 4
+#define dd_zp2n 2
+static const ivec dd_zp2[dd_zp2n] = {{0,0,4},{1,3,4}};
+
+/* The 1D setup */
+#define dd_z1n 2
+#define dd_zp1n 1
+static const ivec dd_zp1[dd_zp1n] = {{0,0,2}};
+
+/* Factors used to avoid problems due to rounding issues */
+#define DD_CELL_MARGIN 1.0001
+#define DD_CELL_MARGIN2 1.00005
+/* Factor to account for pressure scaling during nstlist steps */
+#define DD_PRES_SCALE_MARGIN 1.02
+
+/* Allowed performance loss before we DLB or warn */
+#define DD_PERF_LOSS 0.05
+
+#define DD_CELL_F_SIZE(dd,di) ((dd)->nc[(dd)->dim[(di)]]+1+(di)*2+1+(di))
+
+/* Use separate MPI send and receive commands
+ * when nnodes <= GMX_DD_NNODES_SENDRECV.
+ * This saves memory (and some copying for small nnodes).
+ * For high parallelization scatter and gather calls are used.
+ */
+#define GMX_DD_NNODES_SENDRECV 4
+
+
+/*
+#define dd_index(n,i) ((((i)[ZZ]*(n)[YY] + (i)[YY])*(n)[XX]) + (i)[XX])
+
+static void index2xyz(ivec nc,int ind,ivec xyz)
+{
+ xyz[XX] = ind % nc[XX];
+ xyz[YY] = (ind / nc[XX]) % nc[YY];
+ xyz[ZZ] = ind / (nc[YY]*nc[XX]);
+}
+*/
+
+/* This order is required to minimize the coordinate communication in PME
+ * which uses decomposition in the x direction.
+ */
+#define dd_index(n,i) ((((i)[XX]*(n)[YY] + (i)[YY])*(n)[ZZ]) + (i)[ZZ])
+
+static void ddindex2xyz(ivec nc,int ind,ivec xyz)
+{
+ xyz[XX] = ind / (nc[YY]*nc[ZZ]);
+ xyz[YY] = (ind / nc[ZZ]) % nc[YY];
+ xyz[ZZ] = ind % nc[ZZ];
+}
+
+static int ddcoord2ddnodeid(gmx_domdec_t *dd,ivec c)
+{
+ int ddindex;
+ int ddnodeid=-1;
+
+ ddindex = dd_index(dd->nc,c);
+ if (dd->comm->bCartesianPP_PME)
+ {
+ ddnodeid = dd->comm->ddindex2ddnodeid[ddindex];
+ }
+ else if (dd->comm->bCartesianPP)
+ {
+#ifdef GMX_MPI
+ MPI_Cart_rank(dd->mpi_comm_all,c,&ddnodeid);
+#endif
+ }
+ else
+ {
+ ddnodeid = ddindex;
+ }
+
+ return ddnodeid;
+}
+
+static gmx_bool dynamic_dd_box(gmx_ddbox_t *ddbox,t_inputrec *ir)
+{
+ return (ddbox->nboundeddim < DIM || DYNAMIC_BOX(*ir));
+}
+
+int ddglatnr(gmx_domdec_t *dd,int i)
+{
+ int atnr;
+
+ if (dd == NULL)
+ {
+ atnr = i + 1;
+ }
+ else
+ {
+ if (i >= dd->comm->nat[ddnatNR-1])
+ {
+ gmx_fatal(FARGS,"glatnr called with %d, which is larger than the local number of atoms (%d)",i,dd->comm->nat[ddnatNR-1]);
+ }
+ atnr = dd->gatindex[i] + 1;
+ }
+
+ return atnr;
+}
+
+t_block *dd_charge_groups_global(gmx_domdec_t *dd)
+{
+ return &dd->comm->cgs_gl;
+}
+
+static void vec_rvec_init(vec_rvec_t *v)
+{
+ v->nalloc = 0;
+ v->v = NULL;
+}
+
+static void vec_rvec_check_alloc(vec_rvec_t *v,int n)
+{
+ if (n > v->nalloc)
+ {
+ v->nalloc = over_alloc_dd(n);
+ srenew(v->v,v->nalloc);
+ }
+}
+
+void dd_store_state(gmx_domdec_t *dd,t_state *state)
+{
+ int i;
+
+ if (state->ddp_count != dd->ddp_count)
+ {
+ gmx_incons("The state does not the domain decomposition state");
+ }
+
+ state->ncg_gl = dd->ncg_home;
+ if (state->ncg_gl > state->cg_gl_nalloc)
+ {
+ state->cg_gl_nalloc = over_alloc_dd(state->ncg_gl);
+ srenew(state->cg_gl,state->cg_gl_nalloc);
+ }
+ for(i=0; i<state->ncg_gl; i++)
+ {
+ state->cg_gl[i] = dd->index_gl[i];
+ }
+
+ state->ddp_count_cg_gl = dd->ddp_count;
+}
+
+gmx_domdec_zones_t *domdec_zones(gmx_domdec_t *dd)
+{
+ return &dd->comm->zones;
+}
+
+void dd_get_ns_ranges(gmx_domdec_t *dd,int icg,
+ int *jcg0,int *jcg1,ivec shift0,ivec shift1)
+{
+ gmx_domdec_zones_t *zones;
+ int izone,d,dim;
+
+ zones = &dd->comm->zones;
+
+ izone = 0;
+ while (icg >= zones->izone[izone].cg1)
+ {
+ izone++;
+ }
+
+ if (izone == 0)
+ {
+ *jcg0 = icg;
+ }
+ else if (izone < zones->nizone)
+ {
+ *jcg0 = zones->izone[izone].jcg0;
+ }
+ else
+ {
+ gmx_fatal(FARGS,"DD icg %d out of range: izone (%d) >= nizone (%d)",
+ icg,izone,zones->nizone);
+ }
+
+ *jcg1 = zones->izone[izone].jcg1;
+
+ for(d=0; d<dd->ndim; d++)
+ {
+ dim = dd->dim[d];
+ shift0[dim] = zones->izone[izone].shift0[dim];
+ shift1[dim] = zones->izone[izone].shift1[dim];
+ if (dd->comm->tric_dir[dim] || (dd->bGridJump && d > 0))
+ {
+ /* A conservative approach, this can be optimized */
+ shift0[dim] -= 1;
+ shift1[dim] += 1;
+ }
+ }
+}
+
+int dd_natoms_vsite(gmx_domdec_t *dd)
+{
+ return dd->comm->nat[ddnatVSITE];
+}
+
+void dd_get_constraint_range(gmx_domdec_t *dd,int *at_start,int *at_end)
+{
+ *at_start = dd->comm->nat[ddnatCON-1];
+ *at_end = dd->comm->nat[ddnatCON];
+}
+
+void dd_move_x(gmx_domdec_t *dd,matrix box,rvec x[])
+{
+ int nzone,nat_tot,n,d,p,i,j,at0,at1,zone;
+ int *index,*cgindex;
+ gmx_domdec_comm_t *comm;
+ gmx_domdec_comm_dim_t *cd;
+ gmx_domdec_ind_t *ind;
+ rvec shift={0,0,0},*buf,*rbuf;
+ gmx_bool bPBC,bScrew;
+
+ comm = dd->comm;
+
+ cgindex = dd->cgindex;
+
+ buf = comm->vbuf.v;
+
+ nzone = 1;
+ nat_tot = dd->nat_home;
+ for(d=0; d<dd->ndim; d++)
+ {
+ bPBC = (dd->ci[dd->dim[d]] == 0);
+ bScrew = (bPBC && dd->bScrewPBC && dd->dim[d] == XX);
+ if (bPBC)
+ {
+ copy_rvec(box[dd->dim[d]],shift);
+ }
+ cd = &comm->cd[d];
+ for(p=0; p<cd->np; p++)
+ {
+ ind = &cd->ind[p];
+ index = ind->index;
+ n = 0;
+ if (!bPBC)
+ {
+ for(i=0; i<ind->nsend[nzone]; i++)
+ {
+ at0 = cgindex[index[i]];
+ at1 = cgindex[index[i]+1];
+ for(j=at0; j<at1; j++)
+ {
+ copy_rvec(x[j],buf[n]);
+ n++;
+ }
+ }
+ }
+ else if (!bScrew)
+ {
+ for(i=0; i<ind->nsend[nzone]; i++)
+ {
+ at0 = cgindex[index[i]];
+ at1 = cgindex[index[i]+1];
+ for(j=at0; j<at1; j++)
+ {
+ /* We need to shift the coordinates */
+ rvec_add(x[j],shift,buf[n]);
+ n++;
+ }
+ }
+ }
+ else
+ {
+ for(i=0; i<ind->nsend[nzone]; i++)
+ {
+ at0 = cgindex[index[i]];
+ at1 = cgindex[index[i]+1];
+ for(j=at0; j<at1; j++)
+ {
+ /* Shift x */
+ buf[n][XX] = x[j][XX] + shift[XX];
+ /* Rotate y and z.
+ * This operation requires a special shift force
+ * treatment, which is performed in calc_vir.
+ */
+ buf[n][YY] = box[YY][YY] - x[j][YY];
+ buf[n][ZZ] = box[ZZ][ZZ] - x[j][ZZ];
+ n++;
+ }
+ }
+ }
+
+ if (cd->bInPlace)
+ {
+ rbuf = x + nat_tot;
+ }
+ else
+ {
+ rbuf = comm->vbuf2.v;
+ }
+ /* Send and receive the coordinates */
+ dd_sendrecv_rvec(dd, d, dddirBackward,
+ buf, ind->nsend[nzone+1],
+ rbuf, ind->nrecv[nzone+1]);
+ if (!cd->bInPlace)
+ {
+ j = 0;
+ for(zone=0; zone<nzone; zone++)
+ {
+ for(i=ind->cell2at0[zone]; i<ind->cell2at1[zone]; i++)
+ {
+ copy_rvec(rbuf[j],x[i]);
+ j++;
+ }
+ }
+ }
+ nat_tot += ind->nrecv[nzone+1];
+ }
+ nzone += nzone;
+ }
+}
+
+void dd_move_f(gmx_domdec_t *dd,rvec f[],rvec *fshift)
+{
+ int nzone,nat_tot,n,d,p,i,j,at0,at1,zone;
+ int *index,*cgindex;
+ gmx_domdec_comm_t *comm;
+ gmx_domdec_comm_dim_t *cd;
+ gmx_domdec_ind_t *ind;
+ rvec *buf,*sbuf;
+ ivec vis;
+ int is;
+ gmx_bool bPBC,bScrew;
+
+ comm = dd->comm;
+
+ cgindex = dd->cgindex;
+
+ buf = comm->vbuf.v;
+
+ n = 0;
+ nzone = comm->zones.n/2;
+ nat_tot = dd->nat_tot;
+ for(d=dd->ndim-1; d>=0; d--)
+ {
+ bPBC = (dd->ci[dd->dim[d]] == 0);
+ bScrew = (bPBC && dd->bScrewPBC && dd->dim[d] == XX);
+ if (fshift == NULL && !bScrew)
+ {
+ bPBC = FALSE;
+ }
+ /* Determine which shift vector we need */
+ clear_ivec(vis);
+ vis[dd->dim[d]] = 1;
+ is = IVEC2IS(vis);
+
+ cd = &comm->cd[d];
+ for(p=cd->np-1; p>=0; p--) {
+ ind = &cd->ind[p];
+ nat_tot -= ind->nrecv[nzone+1];
+ if (cd->bInPlace)
+ {
+ sbuf = f + nat_tot;
+ }
+ else
+ {
+ sbuf = comm->vbuf2.v;
+ j = 0;
+ for(zone=0; zone<nzone; zone++)
+ {
+ for(i=ind->cell2at0[zone]; i<ind->cell2at1[zone]; i++)
+ {
+ copy_rvec(f[i],sbuf[j]);
+ j++;
+ }
+ }
+ }
+ /* Communicate the forces */
+ dd_sendrecv_rvec(dd, d, dddirForward,
+ sbuf, ind->nrecv[nzone+1],
+ buf, ind->nsend[nzone+1]);
+ index = ind->index;
+ /* Add the received forces */
+ n = 0;
+ if (!bPBC)
+ {
+ for(i=0; i<ind->nsend[nzone]; i++)
+ {
+ at0 = cgindex[index[i]];
+ at1 = cgindex[index[i]+1];
+ for(j=at0; j<at1; j++)
+ {
+ rvec_inc(f[j],buf[n]);
+ n++;
+ }
+ }
+ }
+ else if (!bScrew)
+ {
+ for(i=0; i<ind->nsend[nzone]; i++)
+ {
+ at0 = cgindex[index[i]];
+ at1 = cgindex[index[i]+1];
+ for(j=at0; j<at1; j++)
+ {
+ rvec_inc(f[j],buf[n]);
+ /* Add this force to the shift force */
+ rvec_inc(fshift[is],buf[n]);
+ n++;
+ }
+ }
+ }
+ else
+ {
+ for(i=0; i<ind->nsend[nzone]; i++)
+ {
+ at0 = cgindex[index[i]];
+ at1 = cgindex[index[i]+1];
+ for(j=at0; j<at1; j++)
+ {
+ /* Rotate the force */
+ f[j][XX] += buf[n][XX];
+ f[j][YY] -= buf[n][YY];
+ f[j][ZZ] -= buf[n][ZZ];
+ if (fshift)
+ {
+ /* Add this force to the shift force */
+ rvec_inc(fshift[is],buf[n]);
+ }
+ n++;
+ }
+ }
+ }
+ }
+ nzone /= 2;
+ }
+}
+
+void dd_atom_spread_real(gmx_domdec_t *dd,real v[])
+{
+ int nzone,nat_tot,n,d,p,i,j,at0,at1,zone;
+ int *index,*cgindex;
+ gmx_domdec_comm_t *comm;
+ gmx_domdec_comm_dim_t *cd;
+ gmx_domdec_ind_t *ind;
+ real *buf,*rbuf;
+
+ comm = dd->comm;
+
+ cgindex = dd->cgindex;
+
+ buf = &comm->vbuf.v[0][0];
+
+ nzone = 1;
+ nat_tot = dd->nat_home;
+ for(d=0; d<dd->ndim; d++)
+ {
+ cd = &comm->cd[d];
+ for(p=0; p<cd->np; p++)
+ {
+ ind = &cd->ind[p];
+ index = ind->index;
+ n = 0;
+ for(i=0; i<ind->nsend[nzone]; i++)
+ {
+ at0 = cgindex[index[i]];
+ at1 = cgindex[index[i]+1];
+ for(j=at0; j<at1; j++)
+ {
+ buf[n] = v[j];
+ n++;
+ }
+ }
+
+ if (cd->bInPlace)
+ {
+ rbuf = v + nat_tot;
+ }
+ else
+ {
+ rbuf = &comm->vbuf2.v[0][0];
+ }
+ /* Send and receive the coordinates */
+ dd_sendrecv_real(dd, d, dddirBackward,
+ buf, ind->nsend[nzone+1],
+ rbuf, ind->nrecv[nzone+1]);
+ if (!cd->bInPlace)
+ {
+ j = 0;
+ for(zone=0; zone<nzone; zone++)
+ {
+ for(i=ind->cell2at0[zone]; i<ind->cell2at1[zone]; i++)
+ {
+ v[i] = rbuf[j];
+ j++;
+ }
+ }
+ }
+ nat_tot += ind->nrecv[nzone+1];
+ }
+ nzone += nzone;
+ }
+}
+
+void dd_atom_sum_real(gmx_domdec_t *dd,real v[])
+{
+ int nzone,nat_tot,n,d,p,i,j,at0,at1,zone;
+ int *index,*cgindex;
+ gmx_domdec_comm_t *comm;
+ gmx_domdec_comm_dim_t *cd;
+ gmx_domdec_ind_t *ind;
+ real *buf,*sbuf;
+
+ comm = dd->comm;
+
+ cgindex = dd->cgindex;
+
+ buf = &comm->vbuf.v[0][0];
+
+ n = 0;
+ nzone = comm->zones.n/2;
+ nat_tot = dd->nat_tot;
+ for(d=dd->ndim-1; d>=0; d--)
+ {
+ cd = &comm->cd[d];
+ for(p=cd->np-1; p>=0; p--) {
+ ind = &cd->ind[p];
+ nat_tot -= ind->nrecv[nzone+1];
+ if (cd->bInPlace)
+ {
+ sbuf = v + nat_tot;
+ }
+ else
+ {
+ sbuf = &comm->vbuf2.v[0][0];
+ j = 0;
+ for(zone=0; zone<nzone; zone++)
+ {
+ for(i=ind->cell2at0[zone]; i<ind->cell2at1[zone]; i++)
+ {
+ sbuf[j] = v[i];
+ j++;
+ }
+ }
+ }
+ /* Communicate the forces */
+ dd_sendrecv_real(dd, d, dddirForward,
+ sbuf, ind->nrecv[nzone+1],
+ buf, ind->nsend[nzone+1]);
+ index = ind->index;
+ /* Add the received forces */
+ n = 0;
+ for(i=0; i<ind->nsend[nzone]; i++)
+ {
+ at0 = cgindex[index[i]];
+ at1 = cgindex[index[i]+1];
+ for(j=at0; j<at1; j++)
+ {
+ v[j] += buf[n];
+ n++;
+ }
+ }
+ }
+ nzone /= 2;
+ }
+}
+
+static void print_ddzone(FILE *fp,int d,int i,int j,gmx_ddzone_t *zone)
+{
+ fprintf(fp,"zone d0 %d d1 %d d2 %d min0 %6.3f max1 %6.3f mch0 %6.3f mch1 %6.3f p1_0 %6.3f p1_1 %6.3f\n",
+ d,i,j,
+ zone->min0,zone->max1,
+ zone->mch0,zone->mch0,
+ zone->p1_0,zone->p1_1);
+}
+
+static void dd_sendrecv_ddzone(const gmx_domdec_t *dd,
+ int ddimind,int direction,
+ gmx_ddzone_t *buf_s,int n_s,
+ gmx_ddzone_t *buf_r,int n_r)
+{
+ rvec vbuf_s[5*2],vbuf_r[5*2];
+ int i;
+
+ for(i=0; i<n_s; i++)
+ {
+ vbuf_s[i*2 ][0] = buf_s[i].min0;
+ vbuf_s[i*2 ][1] = buf_s[i].max1;
+ vbuf_s[i*2 ][2] = buf_s[i].mch0;
+ vbuf_s[i*2+1][0] = buf_s[i].mch1;
+ vbuf_s[i*2+1][1] = buf_s[i].p1_0;
+ vbuf_s[i*2+1][2] = buf_s[i].p1_1;
+ }
+
+ dd_sendrecv_rvec(dd, ddimind, direction,
+ vbuf_s, n_s*2,
+ vbuf_r, n_r*2);
+
+ for(i=0; i<n_r; i++)
+ {
+ buf_r[i].min0 = vbuf_r[i*2 ][0];
+ buf_r[i].max1 = vbuf_r[i*2 ][1];
+ buf_r[i].mch0 = vbuf_r[i*2 ][2];
+ buf_r[i].mch1 = vbuf_r[i*2+1][0];
+ buf_r[i].p1_0 = vbuf_r[i*2+1][1];
+ buf_r[i].p1_1 = vbuf_r[i*2+1][2];
+ }
+}
+
+static void dd_move_cellx(gmx_domdec_t *dd,gmx_ddbox_t *ddbox,
+ rvec cell_ns_x0,rvec cell_ns_x1)
+{
+ int d,d1,dim,dim1,pos,buf_size,i,j,k,p,npulse,npulse_min;
+ gmx_ddzone_t *zp,buf_s[5],buf_r[5],buf_e[5];
+ rvec extr_s[2],extr_r[2];
+ rvec dh;
+ real dist_d,c=0,det;
+ gmx_domdec_comm_t *comm;
+ gmx_bool bPBC,bUse;
+
+ comm = dd->comm;
+
+ for(d=1; d<dd->ndim; d++)
+ {
+ dim = dd->dim[d];
+ zp = (d == 1) ? &comm->zone_d1[0] : &comm->zone_d2[0][0];
+ zp->min0 = cell_ns_x0[dim];
+ zp->max1 = cell_ns_x1[dim];
+ zp->mch0 = cell_ns_x0[dim];
+ zp->mch1 = cell_ns_x1[dim];
+ zp->p1_0 = cell_ns_x0[dim];
+ zp->p1_1 = cell_ns_x1[dim];
+ }
+
+ for(d=dd->ndim-2; d>=0; d--)
+ {
+ dim = dd->dim[d];
+ bPBC = (dim < ddbox->npbcdim);
+
+ /* Use an rvec to store two reals */
+ extr_s[d][0] = comm->cell_f0[d+1];
+ extr_s[d][1] = comm->cell_f1[d+1];
+ extr_s[d][2] = 0;
+
+ pos = 0;
+ /* Store the extremes in the backward sending buffer,
+ * so the get updated separately from the forward communication.
+ */
+ for(d1=d; d1<dd->ndim-1; d1++)
+ {
+ /* We invert the order to be able to use the same loop for buf_e */
+ buf_s[pos].min0 = extr_s[d1][1];
+ buf_s[pos].max1 = extr_s[d1][0];
+ buf_s[pos].mch0 = 0;
+ buf_s[pos].mch1 = 0;
+ /* Store the cell corner of the dimension we communicate along */
+ buf_s[pos].p1_0 = comm->cell_x0[dim];
+ buf_s[pos].p1_1 = 0;
+ pos++;
+ }
+
+ buf_s[pos] = (dd->ndim == 2) ? comm->zone_d1[0] : comm->zone_d2[0][0];
+ pos++;
+
+ if (dd->ndim == 3 && d == 0)
+ {
+ buf_s[pos] = comm->zone_d2[0][1];
+ pos++;
+ buf_s[pos] = comm->zone_d1[0];
+ pos++;
+ }
+
+ /* We only need to communicate the extremes
+ * in the forward direction
+ */
+ npulse = comm->cd[d].np;
+ if (bPBC)
+ {
+ /* Take the minimum to avoid double communication */
+ npulse_min = min(npulse,dd->nc[dim]-1-npulse);
+ }
+ else
+ {
+ /* Without PBC we should really not communicate over
+ * the boundaries, but implementing that complicates
+ * the communication setup and therefore we simply
+ * do all communication, but ignore some data.
+ */
+ npulse_min = npulse;
+ }
+ for(p=0; p<npulse_min; p++)
+ {
+ /* Communicate the extremes forward */
+ bUse = (bPBC || dd->ci[dim] > 0);
+
+ dd_sendrecv_rvec(dd, d, dddirForward,
+ extr_s+d, dd->ndim-d-1,
+ extr_r+d, dd->ndim-d-1);
+
+ if (bUse)
+ {
+ for(d1=d; d1<dd->ndim-1; d1++)
+ {
+ extr_s[d1][0] = max(extr_s[d1][0],extr_r[d1][0]);
+ extr_s[d1][1] = min(extr_s[d1][1],extr_r[d1][1]);
+ }
+ }
+ }
+
+ buf_size = pos;
+ for(p=0; p<npulse; p++)
+ {
+ /* Communicate all the zone information backward */
+ bUse = (bPBC || dd->ci[dim] < dd->nc[dim] - 1);
+
+ dd_sendrecv_ddzone(dd, d, dddirBackward,
+ buf_s, buf_size,
+ buf_r, buf_size);
+
+ clear_rvec(dh);
+ if (p > 0)
+ {
+ for(d1=d+1; d1<dd->ndim; d1++)
+ {
+ /* Determine the decrease of maximum required
+ * communication height along d1 due to the distance along d,
+ * this avoids a lot of useless atom communication.
+ */
+ dist_d = comm->cell_x1[dim] - buf_r[0].p1_0;
+
+ if (ddbox->tric_dir[dim])
+ {
+ /* c is the off-diagonal coupling between the cell planes
+ * along directions d and d1.
+ */
+ c = ddbox->v[dim][dd->dim[d1]][dim];
+ }
+ else
+ {
+ c = 0;
+ }
+ det = (1 + c*c)*comm->cutoff*comm->cutoff - dist_d*dist_d;
+ if (det > 0)
+ {
+ dh[d1] = comm->cutoff - (c*dist_d + sqrt(det))/(1 + c*c);
+ }
+ else
+ {
+ /* A negative value signals out of range */
+ dh[d1] = -1;
+ }
+ }
+ }
+
+ /* Accumulate the extremes over all pulses */
+ for(i=0; i<buf_size; i++)
+ {
+ if (p == 0)
+ {
+ buf_e[i] = buf_r[i];
+ }
+ else
+ {
+ if (bUse)
+ {
+ buf_e[i].min0 = min(buf_e[i].min0,buf_r[i].min0);
+ buf_e[i].max1 = max(buf_e[i].max1,buf_r[i].max1);
+ }
+
+ if (dd->ndim == 3 && d == 0 && i == buf_size - 1)
+ {
+ d1 = 1;
+ }
+ else
+ {
+ d1 = d + 1;
+ }
+ if (bUse && dh[d1] >= 0)
+ {
+ buf_e[i].mch0 = max(buf_e[i].mch0,buf_r[i].mch0-dh[d1]);
+ buf_e[i].mch1 = max(buf_e[i].mch1,buf_r[i].mch1-dh[d1]);
+ }
+ }
+ /* Copy the received buffer to the send buffer,
+ * to pass the data through with the next pulse.
+ */
+ buf_s[i] = buf_r[i];
+ }
+ if (((bPBC || dd->ci[dim]+npulse < dd->nc[dim]) && p == npulse-1) ||
+ (!bPBC && dd->ci[dim]+1+p == dd->nc[dim]-1))
+ {
+ /* Store the extremes */
+ pos = 0;
+
+ for(d1=d; d1<dd->ndim-1; d1++)
+ {
+ extr_s[d1][1] = min(extr_s[d1][1],buf_e[pos].min0);
+ extr_s[d1][0] = max(extr_s[d1][0],buf_e[pos].max1);
+ pos++;
+ }
+
+ if (d == 1 || (d == 0 && dd->ndim == 3))
+ {
+ for(i=d; i<2; i++)
+ {
+ comm->zone_d2[1-d][i] = buf_e[pos];
+ pos++;
+ }
+ }
+ if (d == 0)
+ {
+ comm->zone_d1[1] = buf_e[pos];
+ pos++;
+ }
+ }
+ }
+ }
+
+ if (dd->ndim >= 2)
+ {
+ dim = dd->dim[1];
+ for(i=0; i<2; i++)
+ {
+ if (debug)
+ {
+ print_ddzone(debug,1,i,0,&comm->zone_d1[i]);
+ }
+ cell_ns_x0[dim] = min(cell_ns_x0[dim],comm->zone_d1[i].min0);
+ cell_ns_x1[dim] = max(cell_ns_x1[dim],comm->zone_d1[i].max1);
+ }
+ }
+ if (dd->ndim >= 3)
+ {
+ dim = dd->dim[2];
+ for(i=0; i<2; i++)
+ {
+ for(j=0; j<2; j++)
+ {
+ if (debug)
+ {
+ print_ddzone(debug,2,i,j,&comm->zone_d2[i][j]);
+ }
+ cell_ns_x0[dim] = min(cell_ns_x0[dim],comm->zone_d2[i][j].min0);
+ cell_ns_x1[dim] = max(cell_ns_x1[dim],comm->zone_d2[i][j].max1);
+ }
+ }
+ }
+ for(d=1; d<dd->ndim; d++)
+ {
+ comm->cell_f_max0[d] = extr_s[d-1][0];
+ comm->cell_f_min1[d] = extr_s[d-1][1];
+ if (debug)
+ {
+ fprintf(debug,"Cell fraction d %d, max0 %f, min1 %f\n",
+ d,comm->cell_f_max0[d],comm->cell_f_min1[d]);
+ }
+ }
+}
+
+static void dd_collect_cg(gmx_domdec_t *dd,
+ t_state *state_local)
+{
+ gmx_domdec_master_t *ma=NULL;
+ int buf2[2],*ibuf,i,ncg_home=0,*cg=NULL,nat_home=0;
+ t_block *cgs_gl;
+
+ if (state_local->ddp_count == dd->comm->master_cg_ddp_count)
+ {
+ /* The master has the correct distribution */
+ return;
+ }
+
+ if (state_local->ddp_count == dd->ddp_count)
+ {
+ ncg_home = dd->ncg_home;
+ cg = dd->index_gl;
+ nat_home = dd->nat_home;
+ }
+ else if (state_local->ddp_count_cg_gl == state_local->ddp_count)
+ {
+ cgs_gl = &dd->comm->cgs_gl;
+
+ ncg_home = state_local->ncg_gl;
+ cg = state_local->cg_gl;
+ nat_home = 0;
+ for(i=0; i<ncg_home; i++)
+ {
+ nat_home += cgs_gl->index[cg[i]+1] - cgs_gl->index[cg[i]];
+ }
+ }
+ else
+ {
+ gmx_incons("Attempted to collect a vector for a state for which the charge group distribution is unknown");
+ }
+
+ buf2[0] = dd->ncg_home;
+ buf2[1] = dd->nat_home;
+ if (DDMASTER(dd))
+ {
+ ma = dd->ma;
+ ibuf = ma->ibuf;
+ }
+ else
+ {
+ ibuf = NULL;
+ }
+ /* Collect the charge group and atom counts on the master */
+ dd_gather(dd,2*sizeof(int),buf2,ibuf);
+
+ if (DDMASTER(dd))
+ {
+ ma->index[0] = 0;
+ for(i=0; i<dd->nnodes; i++)
+ {
+ ma->ncg[i] = ma->ibuf[2*i];
+ ma->nat[i] = ma->ibuf[2*i+1];
+ ma->index[i+1] = ma->index[i] + ma->ncg[i];
+
+ }
+ /* Make byte counts and indices */
+ for(i=0; i<dd->nnodes; i++)
+ {
+ ma->ibuf[i] = ma->ncg[i]*sizeof(int);
+ ma->ibuf[dd->nnodes+i] = ma->index[i]*sizeof(int);
+ }
+ if (debug)
+ {
+ fprintf(debug,"Initial charge group distribution: ");
+ for(i=0; i<dd->nnodes; i++)
+ fprintf(debug," %d",ma->ncg[i]);
+ fprintf(debug,"\n");
+ }
+ }
+
+ /* Collect the charge group indices on the master */
+ dd_gatherv(dd,
+ dd->ncg_home*sizeof(int),dd->index_gl,
+ DDMASTER(dd) ? ma->ibuf : NULL,
+ DDMASTER(dd) ? ma->ibuf+dd->nnodes : NULL,
+ DDMASTER(dd) ? ma->cg : NULL);
+
+ dd->comm->master_cg_ddp_count = state_local->ddp_count;
+}
+
+static void dd_collect_vec_sendrecv(gmx_domdec_t *dd,
+ rvec *lv,rvec *v)
+{
+ gmx_domdec_master_t *ma;
+ int n,i,c,a,nalloc=0;
+ rvec *buf=NULL;
+ t_block *cgs_gl;
+
+ ma = dd->ma;
+
+ if (!DDMASTER(dd))
+ {
+#ifdef GMX_MPI
+ MPI_Send(lv,dd->nat_home*sizeof(rvec),MPI_BYTE,DDMASTERRANK(dd),
+ dd->rank,dd->mpi_comm_all);
+#endif
+ } else {
+ /* Copy the master coordinates to the global array */
+ cgs_gl = &dd->comm->cgs_gl;
+
+ n = DDMASTERRANK(dd);
+ a = 0;
+ for(i=ma->index[n]; i<ma->index[n+1]; i++)
+ {
+ for(c=cgs_gl->index[ma->cg[i]]; c<cgs_gl->index[ma->cg[i]+1]; c++)
+ {
+ copy_rvec(lv[a++],v[c]);
+ }
+ }
+
+ for(n=0; n<dd->nnodes; n++)
+ {
+ if (n != dd->rank)
+ {
+ if (ma->nat[n] > nalloc)
+ {
+ nalloc = over_alloc_dd(ma->nat[n]);
+ srenew(buf,nalloc);
+ }
+#ifdef GMX_MPI
+ MPI_Recv(buf,ma->nat[n]*sizeof(rvec),MPI_BYTE,DDRANK(dd,n),
+ n,dd->mpi_comm_all,MPI_STATUS_IGNORE);
+#endif
+ a = 0;
+ for(i=ma->index[n]; i<ma->index[n+1]; i++)
+ {
+ for(c=cgs_gl->index[ma->cg[i]]; c<cgs_gl->index[ma->cg[i]+1]; c++)
+ {
+ copy_rvec(buf[a++],v[c]);
+ }
+ }
+ }
+ }
+ sfree(buf);
+ }
+}
+
+static void get_commbuffer_counts(gmx_domdec_t *dd,
+ int **counts,int **disps)
+{
+ gmx_domdec_master_t *ma;
+ int n;
+
+ ma = dd->ma;
+
+ /* Make the rvec count and displacment arrays */
+ *counts = ma->ibuf;
+ *disps = ma->ibuf + dd->nnodes;
+ for(n=0; n<dd->nnodes; n++)
+ {
+ (*counts)[n] = ma->nat[n]*sizeof(rvec);
+ (*disps)[n] = (n == 0 ? 0 : (*disps)[n-1] + (*counts)[n-1]);
+ }
+}
+
+static void dd_collect_vec_gatherv(gmx_domdec_t *dd,
+ rvec *lv,rvec *v)
+{
+ gmx_domdec_master_t *ma;
+ int *rcounts=NULL,*disps=NULL;
+ int n,i,c,a;
+ rvec *buf=NULL;
+ t_block *cgs_gl;
+
+ ma = dd->ma;
+
+ if (DDMASTER(dd))
+ {
+ get_commbuffer_counts(dd,&rcounts,&disps);
+
+ buf = ma->vbuf;
+ }
+
+ dd_gatherv(dd,dd->nat_home*sizeof(rvec),lv,rcounts,disps,buf);
+
+ if (DDMASTER(dd))
+ {
+ cgs_gl = &dd->comm->cgs_gl;
+
+ a = 0;
+ for(n=0; n<dd->nnodes; n++)
+ {
+ for(i=ma->index[n]; i<ma->index[n+1]; i++)
+ {
+ for(c=cgs_gl->index[ma->cg[i]]; c<cgs_gl->index[ma->cg[i]+1]; c++)
+ {
+ copy_rvec(buf[a++],v[c]);
+ }
+ }
+ }
+ }
+}
+
+void dd_collect_vec(gmx_domdec_t *dd,
+ t_state *state_local,rvec *lv,rvec *v)
+{
+ gmx_domdec_master_t *ma;
+ int n,i,c,a,nalloc=0;
+ rvec *buf=NULL;
+
+ dd_collect_cg(dd,state_local);
+
+ if (dd->nnodes <= GMX_DD_NNODES_SENDRECV)
+ {
+ dd_collect_vec_sendrecv(dd,lv,v);
+ }
+ else
+ {
+ dd_collect_vec_gatherv(dd,lv,v);
+ }
+}
+
+
+void dd_collect_state(gmx_domdec_t *dd,
+ t_state *state_local,t_state *state)
+{
+ int est,i,j,nh;
+
+ nh = state->nhchainlength;
+
+ if (DDMASTER(dd))
+ {
+ state->lambda = state_local->lambda;
+ state->veta = state_local->veta;
+ state->vol0 = state_local->vol0;
+ copy_mat(state_local->box,state->box);
+ copy_mat(state_local->boxv,state->boxv);
+ copy_mat(state_local->svir_prev,state->svir_prev);
+ copy_mat(state_local->fvir_prev,state->fvir_prev);
+ copy_mat(state_local->pres_prev,state->pres_prev);
+
+
+ for(i=0; i<state_local->ngtc; i++)
+ {
+ for(j=0; j<nh; j++) {
+ state->nosehoover_xi[i*nh+j] = state_local->nosehoover_xi[i*nh+j];
+ state->nosehoover_vxi[i*nh+j] = state_local->nosehoover_vxi[i*nh+j];
+ }
+ state->therm_integral[i] = state_local->therm_integral[i];
+ }
+ for(i=0; i<state_local->nnhpres; i++)
+ {
+ for(j=0; j<nh; j++) {
+ state->nhpres_xi[i*nh+j] = state_local->nhpres_xi[i*nh+j];
+ state->nhpres_vxi[i*nh+j] = state_local->nhpres_vxi[i*nh+j];
+ }
+ }
+ }
+ for(est=0; est<estNR; est++)
+ {
- if (EST_DISTR(est) && state->flags & (1<<est))
++ if (EST_DISTR(est) && (state_local->flags & (1<<est)))
+ {
+ switch (est) {
+ case estX:
+ dd_collect_vec(dd,state_local,state_local->x,state->x);
+ break;
+ case estV:
+ dd_collect_vec(dd,state_local,state_local->v,state->v);
+ break;
+ case estSDX:
+ dd_collect_vec(dd,state_local,state_local->sd_X,state->sd_X);
+ break;
+ case estCGP:
+ dd_collect_vec(dd,state_local,state_local->cg_p,state->cg_p);
+ break;
+ case estLD_RNG:
+ if (state->nrngi == 1)
+ {
+ if (DDMASTER(dd))
+ {
+ for(i=0; i<state_local->nrng; i++)
+ {
+ state->ld_rng[i] = state_local->ld_rng[i];
+ }
+ }
+ }
+ else
+ {
+ dd_gather(dd,state_local->nrng*sizeof(state->ld_rng[0]),
+ state_local->ld_rng,state->ld_rng);
+ }
+ break;
+ case estLD_RNGI:
+ if (state->nrngi == 1)
+ {
+ if (DDMASTER(dd))
+ {
+ state->ld_rngi[0] = state_local->ld_rngi[0];
+ }
+ }
+ else
+ {
+ dd_gather(dd,sizeof(state->ld_rngi[0]),
+ state_local->ld_rngi,state->ld_rngi);
+ }
+ break;
+ case estDISRE_INITF:
+ case estDISRE_RM3TAV:
+ case estORIRE_INITF:
+ case estORIRE_DTAV:
+ break;
+ default:
+ gmx_incons("Unknown state entry encountered in dd_collect_state");
+ }
+ }
+ }
+}
+
+static void dd_realloc_fr_cg(t_forcerec *fr,int nalloc)
+{
+ if (debug)
+ {
+ fprintf(debug,"Reallocating forcerec: currently %d, required %d, allocating %d\n",fr->cg_nalloc,nalloc,over_alloc_dd(nalloc));
+ }
+ fr->cg_nalloc = over_alloc_dd(nalloc);
+ srenew(fr->cg_cm,fr->cg_nalloc);
+ srenew(fr->cginfo,fr->cg_nalloc);
+}
+
+static void dd_realloc_state(t_state *state,rvec **f,int nalloc)
+{
+ int est;
+
+ if (debug)
+ {
+ fprintf(debug,"Reallocating state: currently %d, required %d, allocating %d\n",state->nalloc,nalloc,over_alloc_dd(nalloc));
+ }
+
+ state->nalloc = over_alloc_dd(nalloc);
+
+ for(est=0; est<estNR; est++)
+ {
- if (EST_DISTR(i) && state_local->flags & (1<<i))
++ if (EST_DISTR(est) && (state->flags & (1<<est)))
+ {
+ switch(est) {
+ case estX:
+ srenew(state->x,state->nalloc);
+ break;
+ case estV:
+ srenew(state->v,state->nalloc);
+ break;
+ case estSDX:
+ srenew(state->sd_X,state->nalloc);
+ break;
+ case estCGP:
+ srenew(state->cg_p,state->nalloc);
+ break;
+ case estLD_RNG:
+ case estLD_RNGI:
+ case estDISRE_INITF:
+ case estDISRE_RM3TAV:
+ case estORIRE_INITF:
+ case estORIRE_DTAV:
+ /* No reallocation required */
+ break;
+ default:
+ gmx_incons("Unknown state entry encountered in dd_realloc_state");
+ }
+ }
+ }
+
+ if (f != NULL)
+ {
+ srenew(*f,state->nalloc);
+ }
+}
+
+static void dd_distribute_vec_sendrecv(gmx_domdec_t *dd,t_block *cgs,
+ rvec *v,rvec *lv)
+{
+ gmx_domdec_master_t *ma;
+ int n,i,c,a,nalloc=0;
+ rvec *buf=NULL;
+
+ if (DDMASTER(dd))
+ {
+ ma = dd->ma;
+
+ for(n=0; n<dd->nnodes; n++)
+ {
+ if (n != dd->rank)
+ {
+ if (ma->nat[n] > nalloc)
+ {
+ nalloc = over_alloc_dd(ma->nat[n]);
+ srenew(buf,nalloc);
+ }
+ /* Use lv as a temporary buffer */
+ a = 0;
+ for(i=ma->index[n]; i<ma->index[n+1]; i++)
+ {
+ for(c=cgs->index[ma->cg[i]]; c<cgs->index[ma->cg[i]+1]; c++)
+ {
+ copy_rvec(v[c],buf[a++]);
+ }
+ }
+ if (a != ma->nat[n])
+ {
+ gmx_fatal(FARGS,"Internal error a (%d) != nat (%d)",
+ a,ma->nat[n]);
+ }
+
+#ifdef GMX_MPI
+ MPI_Send(buf,ma->nat[n]*sizeof(rvec),MPI_BYTE,
+ DDRANK(dd,n),n,dd->mpi_comm_all);
+#endif
+ }
+ }
+ sfree(buf);
+ n = DDMASTERRANK(dd);
+ a = 0;
+ for(i=ma->index[n]; i<ma->index[n+1]; i++)
+ {
+ for(c=cgs->index[ma->cg[i]]; c<cgs->index[ma->cg[i]+1]; c++)
+ {
+ copy_rvec(v[c],lv[a++]);
+ }
+ }
+ }
+ else
+ {
+#ifdef GMX_MPI
+ MPI_Recv(lv,dd->nat_home*sizeof(rvec),MPI_BYTE,DDMASTERRANK(dd),
+ MPI_ANY_TAG,dd->mpi_comm_all,MPI_STATUS_IGNORE);
+#endif
+ }
+}
+
+static void dd_distribute_vec_scatterv(gmx_domdec_t *dd,t_block *cgs,
+ rvec *v,rvec *lv)
+{
+ gmx_domdec_master_t *ma;
+ int *scounts=NULL,*disps=NULL;
+ int n,i,c,a,nalloc=0;
+ rvec *buf=NULL;
+
+ if (DDMASTER(dd))
+ {
+ ma = dd->ma;
+
+ get_commbuffer_counts(dd,&scounts,&disps);
+
+ buf = ma->vbuf;
+ a = 0;
+ for(n=0; n<dd->nnodes; n++)
+ {
+ for(i=ma->index[n]; i<ma->index[n+1]; i++)
+ {
+ for(c=cgs->index[ma->cg[i]]; c<cgs->index[ma->cg[i]+1]; c++)
+ {
+ copy_rvec(v[c],buf[a++]);
+ }
+ }
+ }
+ }
+
+ dd_scatterv(dd,scounts,disps,buf,dd->nat_home*sizeof(rvec),lv);
+}
+
+static void dd_distribute_vec(gmx_domdec_t *dd,t_block *cgs,rvec *v,rvec *lv)
+{
+ if (dd->nnodes <= GMX_DD_NNODES_SENDRECV)
+ {
+ dd_distribute_vec_sendrecv(dd,cgs,v,lv);
+ }
+ else
+ {
+ dd_distribute_vec_scatterv(dd,cgs,v,lv);
+ }
+}
+
+static void dd_distribute_state(gmx_domdec_t *dd,t_block *cgs,
+ t_state *state,t_state *state_local,
+ rvec **f)
+{
+ int i,j,ngtch,ngtcp,nh;
+
+ nh = state->nhchainlength;
+
+ if (DDMASTER(dd))
+ {
+ state_local->lambda = state->lambda;
+ state_local->veta = state->veta;
+ state_local->vol0 = state->vol0;
+ copy_mat(state->box,state_local->box);
+ copy_mat(state->box_rel,state_local->box_rel);
+ copy_mat(state->boxv,state_local->boxv);
+ copy_mat(state->svir_prev,state_local->svir_prev);
+ copy_mat(state->fvir_prev,state_local->fvir_prev);
+ for(i=0; i<state_local->ngtc; i++)
+ {
+ for(j=0; j<nh; j++) {
+ state_local->nosehoover_xi[i*nh+j] = state->nosehoover_xi[i*nh+j];
+ state_local->nosehoover_vxi[i*nh+j] = state->nosehoover_vxi[i*nh+j];
+ }
+ state_local->therm_integral[i] = state->therm_integral[i];
+ }
+ for(i=0; i<state_local->nnhpres; i++)
+ {
+ for(j=0; j<nh; j++) {
+ state_local->nhpres_xi[i*nh+j] = state->nhpres_xi[i*nh+j];
+ state_local->nhpres_vxi[i*nh+j] = state->nhpres_vxi[i*nh+j];
+ }
+ }
+ }
+ dd_bcast(dd,sizeof(real),&state_local->lambda);
+ dd_bcast(dd,sizeof(real),&state_local->veta);
+ dd_bcast(dd,sizeof(real),&state_local->vol0);
+ dd_bcast(dd,sizeof(state_local->box),state_local->box);
+ dd_bcast(dd,sizeof(state_local->box_rel),state_local->box_rel);
+ dd_bcast(dd,sizeof(state_local->boxv),state_local->boxv);
+ dd_bcast(dd,sizeof(state_local->svir_prev),state_local->svir_prev);
+ dd_bcast(dd,sizeof(state_local->fvir_prev),state_local->fvir_prev);
+ dd_bcast(dd,((state_local->ngtc*nh)*sizeof(double)),state_local->nosehoover_xi);
+ dd_bcast(dd,((state_local->ngtc*nh)*sizeof(double)),state_local->nosehoover_vxi);
+ dd_bcast(dd,state_local->ngtc*sizeof(double),state_local->therm_integral);
+ dd_bcast(dd,((state_local->nnhpres*nh)*sizeof(double)),state_local->nhpres_xi);
+ dd_bcast(dd,((state_local->nnhpres*nh)*sizeof(double)),state_local->nhpres_vxi);
+
+ if (dd->nat_home > state_local->nalloc)
+ {
+ dd_realloc_state(state_local,f,dd->nat_home);
+ }
+ for(i=0; i<estNR; i++)
+ {
- if (EST_DISTR(est) && state->flags & (1<<est)) {
++ if (EST_DISTR(i) && (state_local->flags & (1<<i)))
+ {
+ switch (i) {
+ case estX:
+ dd_distribute_vec(dd,cgs,state->x,state_local->x);
+ break;
+ case estV:
+ dd_distribute_vec(dd,cgs,state->v,state_local->v);
+ break;
+ case estSDX:
+ dd_distribute_vec(dd,cgs,state->sd_X,state_local->sd_X);
+ break;
+ case estCGP:
+ dd_distribute_vec(dd,cgs,state->cg_p,state_local->cg_p);
+ break;
+ case estLD_RNG:
+ if (state->nrngi == 1)
+ {
+ dd_bcastc(dd,
+ state_local->nrng*sizeof(state_local->ld_rng[0]),
+ state->ld_rng,state_local->ld_rng);
+ }
+ else
+ {
+ dd_scatter(dd,
+ state_local->nrng*sizeof(state_local->ld_rng[0]),
+ state->ld_rng,state_local->ld_rng);
+ }
+ break;
+ case estLD_RNGI:
+ if (state->nrngi == 1)
+ {
+ dd_bcastc(dd,sizeof(state_local->ld_rngi[0]),
+ state->ld_rngi,state_local->ld_rngi);
+ }
+ else
+ {
+ dd_scatter(dd,sizeof(state_local->ld_rngi[0]),
+ state->ld_rngi,state_local->ld_rngi);
+ }
+ break;
+ case estDISRE_INITF:
+ case estDISRE_RM3TAV:
+ case estORIRE_INITF:
+ case estORIRE_DTAV:
+ /* Not implemented yet */
+ break;
+ default:
+ gmx_incons("Unknown state entry encountered in dd_distribute_state");
+ }
+ }
+ }
+}
+
+static char dim2char(int dim)
+{
+ char c='?';
+
+ switch (dim)
+ {
+ case XX: c = 'X'; break;
+ case YY: c = 'Y'; break;
+ case ZZ: c = 'Z'; break;
+ default: gmx_fatal(FARGS,"Unknown dim %d",dim);
+ }
+
+ return c;
+}
+
+static void write_dd_grid_pdb(const char *fn,gmx_large_int_t step,
+ gmx_domdec_t *dd,matrix box,gmx_ddbox_t *ddbox)
+{
+ rvec grid_s[2],*grid_r=NULL,cx,r;
+ char fname[STRLEN],format[STRLEN],buf[22];
+ FILE *out;
+ int a,i,d,z,y,x;
+ matrix tric;
+ real vol;
+
+ copy_rvec(dd->comm->cell_x0,grid_s[0]);
+ copy_rvec(dd->comm->cell_x1,grid_s[1]);
+
+ if (DDMASTER(dd))
+ {
+ snew(grid_r,2*dd->nnodes);
+ }
+
+ dd_gather(dd,2*sizeof(rvec),grid_s[0],DDMASTER(dd) ? grid_r[0] : NULL);
+
+ if (DDMASTER(dd))
+ {
+ for(d=0; d<DIM; d++)
+ {
+ for(i=0; i<DIM; i++)
+ {
+ if (d == i)
+ {
+ tric[d][i] = 1;
+ }
+ else
+ {
+ if (dd->nc[d] > 1 && d < ddbox->npbcdim)
+ {
+ tric[d][i] = box[i][d]/box[i][i];
+ }
+ else
+ {
+ tric[d][i] = 0;
+ }
+ }
+ }
+ }
+ sprintf(fname,"%s_%s.pdb",fn,gmx_step_str(step,buf));
+ sprintf(format,"%s%s\n",pdbformat,"%6.2f%6.2f");
+ out = gmx_fio_fopen(fname,"w");
+ gmx_write_pdb_box(out,dd->bScrewPBC ? epbcSCREW : epbcXYZ,box);
+ a = 1;
+ for(i=0; i<dd->nnodes; i++)
+ {
+ vol = dd->nnodes/(box[XX][XX]*box[YY][YY]*box[ZZ][ZZ]);
+ for(d=0; d<DIM; d++)
+ {
+ vol *= grid_r[i*2+1][d] - grid_r[i*2][d];
+ }
+ for(z=0; z<2; z++)
+ {
+ for(y=0; y<2; y++)
+ {
+ for(x=0; x<2; x++)
+ {
+ cx[XX] = grid_r[i*2+x][XX];
+ cx[YY] = grid_r[i*2+y][YY];
+ cx[ZZ] = grid_r[i*2+z][ZZ];
+ mvmul(tric,cx,r);
+ fprintf(out,format,"ATOM",a++,"CA","GLY",' ',1+i,
+ 10*r[XX],10*r[YY],10*r[ZZ],1.0,vol);
+ }
+ }
+ }
+ for(d=0; d<DIM; d++)
+ {
+ for(x=0; x<4; x++)
+ {
+ switch(d)
+ {
+ case 0: y = 1 + i*8 + 2*x; break;
+ case 1: y = 1 + i*8 + 2*x - (x % 2); break;
+ case 2: y = 1 + i*8 + x; break;
+ }
+ fprintf(out,"%6s%5d%5d\n","CONECT",y,y+(1<<d));
+ }
+ }
+ }
+ gmx_fio_fclose(out);
+ sfree(grid_r);
+ }
+}
+
+void write_dd_pdb(const char *fn,gmx_large_int_t step,const char *title,
+ gmx_mtop_t *mtop,t_commrec *cr,
+ int natoms,rvec x[],matrix box)
+{
+ char fname[STRLEN],format[STRLEN],format4[STRLEN],buf[22];
+ FILE *out;
+ int i,ii,resnr,c;
+ char *atomname,*resname;
+ real b;
+ gmx_domdec_t *dd;
+
+ dd = cr->dd;
+ if (natoms == -1)
+ {
+ natoms = dd->comm->nat[ddnatVSITE];
+ }
+
+ sprintf(fname,"%s_%s_n%d.pdb",fn,gmx_step_str(step,buf),cr->sim_nodeid);
+
+ sprintf(format,"%s%s\n",pdbformat,"%6.2f%6.2f");
+ sprintf(format4,"%s%s\n",pdbformat4,"%6.2f%6.2f");
+
+ out = gmx_fio_fopen(fname,"w");
+
+ fprintf(out,"TITLE %s\n",title);
+ gmx_write_pdb_box(out,dd->bScrewPBC ? epbcSCREW : epbcXYZ,box);
+ for(i=0; i<natoms; i++)
+ {
+ ii = dd->gatindex[i];
+ gmx_mtop_atominfo_global(mtop,ii,&atomname,&resnr,&resname);
+ if (i < dd->comm->nat[ddnatZONE])
+ {
+ c = 0;
+ while (i >= dd->cgindex[dd->comm->zones.cg_range[c+1]])
+ {
+ c++;
+ }
+ b = c;
+ }
+ else if (i < dd->comm->nat[ddnatVSITE])
+ {
+ b = dd->comm->zones.n;
+ }
+ else
+ {
+ b = dd->comm->zones.n + 1;
+ }
+ fprintf(out,strlen(atomname)<4 ? format : format4,
+ "ATOM",(ii+1)%100000,
+ atomname,resname,' ',resnr%10000,' ',
+ 10*x[i][XX],10*x[i][YY],10*x[i][ZZ],1.0,b);
+ }
+ fprintf(out,"TER\n");
+
+ gmx_fio_fclose(out);
+}
+
+real dd_cutoff_mbody(gmx_domdec_t *dd)
+{
+ gmx_domdec_comm_t *comm;
+ int di;
+ real r;
+
+ comm = dd->comm;
+
+ r = -1;
+ if (comm->bInterCGBondeds)
+ {
+ if (comm->cutoff_mbody > 0)
+ {
+ r = comm->cutoff_mbody;
+ }
+ else
+ {
+ /* cutoff_mbody=0 means we do not have DLB */
+ r = comm->cellsize_min[dd->dim[0]];
+ for(di=1; di<dd->ndim; di++)
+ {
+ r = min(r,comm->cellsize_min[dd->dim[di]]);
+ }
+ if (comm->bBondComm)
+ {
+ r = max(r,comm->cutoff_mbody);
+ }
+ else
+ {
+ r = min(r,comm->cutoff);
+ }
+ }
+ }
+
+ return r;
+}
+
+real dd_cutoff_twobody(gmx_domdec_t *dd)
+{
+ real r_mb;
+
+ r_mb = dd_cutoff_mbody(dd);
+
+ return max(dd->comm->cutoff,r_mb);
+}
+
+
+static void dd_cart_coord2pmecoord(gmx_domdec_t *dd,ivec coord,ivec coord_pme)
+{
+ int nc,ntot;
+
+ nc = dd->nc[dd->comm->cartpmedim];
+ ntot = dd->comm->ntot[dd->comm->cartpmedim];
+ copy_ivec(coord,coord_pme);
+ coord_pme[dd->comm->cartpmedim] =
+ nc + (coord[dd->comm->cartpmedim]*(ntot - nc) + (ntot - nc)/2)/nc;
+}
+
+static int low_ddindex2pmeindex(int ndd,int npme,int ddindex)
+{
+ /* Here we assign a PME node to communicate with this DD node
+ * by assuming that the major index of both is x.
+ * We add cr->npmenodes/2 to obtain an even distribution.
+ */
+ return (ddindex*npme + npme/2)/ndd;
+}
+
+static int ddindex2pmeindex(const gmx_domdec_t *dd,int ddindex)
+{
+ return low_ddindex2pmeindex(dd->nnodes,dd->comm->npmenodes,ddindex);
+}
+
+static int cr_ddindex2pmeindex(const t_commrec *cr,int ddindex)
+{
+ return low_ddindex2pmeindex(cr->dd->nnodes,cr->npmenodes,ddindex);
+}
+
+static int *dd_pmenodes(t_commrec *cr)
+{
+ int *pmenodes;
+ int n,i,p0,p1;
+
+ snew(pmenodes,cr->npmenodes);
+ n = 0;
+ for(i=0; i<cr->dd->nnodes; i++) {
+ p0 = cr_ddindex2pmeindex(cr,i);
+ p1 = cr_ddindex2pmeindex(cr,i+1);
+ if (i+1 == cr->dd->nnodes || p1 > p0) {
+ if (debug)
+ fprintf(debug,"pmenode[%d] = %d\n",n,i+1+n);
+ pmenodes[n] = i + 1 + n;
+ n++;
+ }
+ }
+
+ return pmenodes;
+}
+
+static int gmx_ddcoord2pmeindex(t_commrec *cr,int x,int y,int z)
+{
+ gmx_domdec_t *dd;
+ ivec coords,coords_pme,nc;
+ int slab;
+
+ dd = cr->dd;
+ /*
+ if (dd->comm->bCartesian) {
+ gmx_ddindex2xyz(dd->nc,ddindex,coords);
+ dd_coords2pmecoords(dd,coords,coords_pme);
+ copy_ivec(dd->ntot,nc);
+ nc[dd->cartpmedim] -= dd->nc[dd->cartpmedim];
+ coords_pme[dd->cartpmedim] -= dd->nc[dd->cartpmedim];
+
+ slab = (coords_pme[XX]*nc[YY] + coords_pme[YY])*nc[ZZ] + coords_pme[ZZ];
+ } else {
+ slab = (ddindex*cr->npmenodes + cr->npmenodes/2)/dd->nnodes;
+ }
+ */
+ coords[XX] = x;
+ coords[YY] = y;
+ coords[ZZ] = z;
+ slab = ddindex2pmeindex(dd,dd_index(dd->nc,coords));
+
+ return slab;
+}
+
+static int ddcoord2simnodeid(t_commrec *cr,int x,int y,int z)
+{
+ gmx_domdec_comm_t *comm;
+ ivec coords;
+ int ddindex,nodeid=-1;
+
+ comm = cr->dd->comm;
+
+ coords[XX] = x;
+ coords[YY] = y;
+ coords[ZZ] = z;
+ if (comm->bCartesianPP_PME)
+ {
+#ifdef GMX_MPI
+ MPI_Cart_rank(cr->mpi_comm_mysim,coords,&nodeid);
+#endif
+ }
+ else
+ {
+ ddindex = dd_index(cr->dd->nc,coords);
+ if (comm->bCartesianPP)
+ {
+ nodeid = comm->ddindex2simnodeid[ddindex];
+ }
+ else
+ {
+ if (comm->pmenodes)
+ {
+ nodeid = ddindex + gmx_ddcoord2pmeindex(cr,x,y,z);
+ }
+ else
+ {
+ nodeid = ddindex;
+ }
+ }
+ }
+
+ return nodeid;
+}
+
+static int dd_simnode2pmenode(t_commrec *cr,int sim_nodeid)
+{
+ gmx_domdec_t *dd;
+ gmx_domdec_comm_t *comm;
+ ivec coord,coord_pme;
+ int i;
+ int pmenode=-1;
+
+ dd = cr->dd;
+ comm = dd->comm;
+
+ /* This assumes a uniform x domain decomposition grid cell size */
+ if (comm->bCartesianPP_PME)
+ {
+#ifdef GMX_MPI
+ MPI_Cart_coords(cr->mpi_comm_mysim,sim_nodeid,DIM,coord);
+ if (coord[comm->cartpmedim] < dd->nc[comm->cartpmedim])
+ {
+ /* This is a PP node */
+ dd_cart_coord2pmecoord(dd,coord,coord_pme);
+ MPI_Cart_rank(cr->mpi_comm_mysim,coord_pme,&pmenode);
+ }
+#endif
+ }
+ else if (comm->bCartesianPP)
+ {
+ if (sim_nodeid < dd->nnodes)
+ {
+ pmenode = dd->nnodes + ddindex2pmeindex(dd,sim_nodeid);
+ }
+ }
+ else
+ {
+ /* This assumes DD cells with identical x coordinates
+ * are numbered sequentially.
+ */
+ if (dd->comm->pmenodes == NULL)
+ {
+ if (sim_nodeid < dd->nnodes)
+ {
+ /* The DD index equals the nodeid */
+ pmenode = dd->nnodes + ddindex2pmeindex(dd,sim_nodeid);
+ }
+ }
+ else
+ {
+ i = 0;
+ while (sim_nodeid > dd->comm->pmenodes[i])
+ {
+ i++;
+ }
+ if (sim_nodeid < dd->comm->pmenodes[i])
+ {
+ pmenode = dd->comm->pmenodes[i];
+ }
+ }
+ }
+
+ return pmenode;
+}
+
+gmx_bool gmx_pmeonlynode(t_commrec *cr,int sim_nodeid)
+{
+ gmx_bool bPMEOnlyNode;
+
+ if (DOMAINDECOMP(cr))
+ {
+ bPMEOnlyNode = (dd_simnode2pmenode(cr,sim_nodeid) == -1);
+ }
+ else
+ {
+ bPMEOnlyNode = FALSE;
+ }
+
+ return bPMEOnlyNode;
+}
+
+void get_pme_ddnodes(t_commrec *cr,int pmenodeid,
+ int *nmy_ddnodes,int **my_ddnodes,int *node_peer)
+{
+ gmx_domdec_t *dd;
+ int x,y,z;
+ ivec coord,coord_pme;
+
+ dd = cr->dd;
+
+ snew(*my_ddnodes,(dd->nnodes+cr->npmenodes-1)/cr->npmenodes);
+
+ *nmy_ddnodes = 0;
+ for(x=0; x<dd->nc[XX]; x++)
+ {
+ for(y=0; y<dd->nc[YY]; y++)
+ {
+ for(z=0; z<dd->nc[ZZ]; z++)
+ {
+ if (dd->comm->bCartesianPP_PME)
+ {
+ coord[XX] = x;
+ coord[YY] = y;
+ coord[ZZ] = z;
+ dd_cart_coord2pmecoord(dd,coord,coord_pme);
+ if (dd->ci[XX] == coord_pme[XX] &&
+ dd->ci[YY] == coord_pme[YY] &&
+ dd->ci[ZZ] == coord_pme[ZZ])
+ (*my_ddnodes)[(*nmy_ddnodes)++] = ddcoord2simnodeid(cr,x,y,z);
+ }
+ else
+ {
+ /* The slab corresponds to the nodeid in the PME group */
+ if (gmx_ddcoord2pmeindex(cr,x,y,z) == pmenodeid)
+ {
+ (*my_ddnodes)[(*nmy_ddnodes)++] = ddcoord2simnodeid(cr,x,y,z);
+ }
+ }
+ }
+ }
+ }
+
+ /* The last PP-only node is the peer node */
+ *node_peer = (*my_ddnodes)[*nmy_ddnodes-1];
+
+ if (debug)
+ {
+ fprintf(debug,"Receive coordinates from PP nodes:");
+ for(x=0; x<*nmy_ddnodes; x++)
+ {
+ fprintf(debug," %d",(*my_ddnodes)[x]);
+ }
+ fprintf(debug,"\n");
+ }
+}
+
+static gmx_bool receive_vir_ener(t_commrec *cr)
+{
+ gmx_domdec_comm_t *comm;
+ int pmenode,coords[DIM],rank;
+ gmx_bool bReceive;
+
+ bReceive = TRUE;
+ if (cr->npmenodes < cr->dd->nnodes)
+ {
+ comm = cr->dd->comm;
+ if (comm->bCartesianPP_PME)
+ {
+ pmenode = dd_simnode2pmenode(cr,cr->sim_nodeid);
+#ifdef GMX_MPI
+ MPI_Cart_coords(cr->mpi_comm_mysim,cr->sim_nodeid,DIM,coords);
+ coords[comm->cartpmedim]++;
+ if (coords[comm->cartpmedim] < cr->dd->nc[comm->cartpmedim])
+ {
+ MPI_Cart_rank(cr->mpi_comm_mysim,coords,&rank);
+ if (dd_simnode2pmenode(cr,rank) == pmenode)
+ {
+ /* This is not the last PP node for pmenode */
+ bReceive = FALSE;
+ }
+ }
+#endif
+ }
+ else
+ {
+ pmenode = dd_simnode2pmenode(cr,cr->sim_nodeid);
+ if (cr->sim_nodeid+1 < cr->nnodes &&
+ dd_simnode2pmenode(cr,cr->sim_nodeid+1) == pmenode)
+ {
+ /* This is not the last PP node for pmenode */
+ bReceive = FALSE;
+ }
+ }
+ }
+
+ return bReceive;
+}
+
+static void set_zones_ncg_home(gmx_domdec_t *dd)
+{
+ gmx_domdec_zones_t *zones;
+ int i;
+
+ zones = &dd->comm->zones;
+
+ zones->cg_range[0] = 0;
+ for(i=1; i<zones->n+1; i++)
+ {
+ zones->cg_range[i] = dd->ncg_home;
+ }
+}
+
+static void rebuild_cgindex(gmx_domdec_t *dd,int *gcgs_index,t_state *state)
+{
+ int nat,i,*ind,*dd_cg_gl,*cgindex,cg_gl;
+
+ ind = state->cg_gl;
+ dd_cg_gl = dd->index_gl;
+ cgindex = dd->cgindex;
+ nat = 0;
+ cgindex[0] = nat;
+ for(i=0; i<state->ncg_gl; i++)
+ {
+ cgindex[i] = nat;
+ cg_gl = ind[i];
+ dd_cg_gl[i] = cg_gl;
+ nat += gcgs_index[cg_gl+1] - gcgs_index[cg_gl];
+ }
+ cgindex[i] = nat;
+
+ dd->ncg_home = state->ncg_gl;
+ dd->nat_home = nat;
+
+ set_zones_ncg_home(dd);
+}
+
+static int ddcginfo(const cginfo_mb_t *cginfo_mb,int cg)
+{
+ while (cg >= cginfo_mb->cg_end)
+ {
+ cginfo_mb++;
+ }
+
+ return cginfo_mb->cginfo[(cg - cginfo_mb->cg_start) % cginfo_mb->cg_mod];
+}
+
+static void dd_set_cginfo(int *index_gl,int cg0,int cg1,
+ t_forcerec *fr,char *bLocalCG)
+{
+ cginfo_mb_t *cginfo_mb;
+ int *cginfo;
+ int cg;
+
+ if (fr != NULL)
+ {
+ cginfo_mb = fr->cginfo_mb;
+ cginfo = fr->cginfo;
+
+ for(cg=cg0; cg<cg1; cg++)
+ {
+ cginfo[cg] = ddcginfo(cginfo_mb,index_gl[cg]);
+ }
+ }
+
+ if (bLocalCG != NULL)
+ {
+ for(cg=cg0; cg<cg1; cg++)
+ {
+ bLocalCG[index_gl[cg]] = TRUE;
+ }
+ }
+}
+
+static void make_dd_indices(gmx_domdec_t *dd,int *gcgs_index,int cg_start)
+{
+ int nzone,zone,zone1,cg0,cg,cg_gl,a,a_gl;
+ int *zone2cg,*zone_ncg1,*index_gl,*gatindex;
+ gmx_ga2la_t *ga2la;
+ char *bLocalCG;
+
+ bLocalCG = dd->comm->bLocalCG;
+
+ if (dd->nat_tot > dd->gatindex_nalloc)
+ {
+ dd->gatindex_nalloc = over_alloc_dd(dd->nat_tot);
+ srenew(dd->gatindex,dd->gatindex_nalloc);
+ }
+
+ nzone = dd->comm->zones.n;
+ zone2cg = dd->comm->zones.cg_range;
+ zone_ncg1 = dd->comm->zone_ncg1;
+ index_gl = dd->index_gl;
+ gatindex = dd->gatindex;
+
+ if (zone2cg[1] != dd->ncg_home)
+ {
+ gmx_incons("dd->ncg_zone is not up to date");
+ }
+
+ /* Make the local to global and global to local atom index */
+ a = dd->cgindex[cg_start];
+ for(zone=0; zone<nzone; zone++)
+ {
+ if (zone == 0)
+ {
+ cg0 = cg_start;
+ }
+ else
+ {
+ cg0 = zone2cg[zone];
+ }
+ for(cg=cg0; cg<zone2cg[zone+1]; cg++)
+ {
+ zone1 = zone;
+ if (cg - cg0 >= zone_ncg1[zone])
+ {
+ /* Signal that this cg is from more than one zone away */
+ zone1 += nzone;
+ }
+ cg_gl = index_gl[cg];
+ for(a_gl=gcgs_index[cg_gl]; a_gl<gcgs_index[cg_gl+1]; a_gl++)
+ {
+ gatindex[a] = a_gl;
+ ga2la_set(dd->ga2la,a_gl,a,zone1);
+ a++;
+ }
+ }
+ }
+}
+
+static int check_bLocalCG(gmx_domdec_t *dd,int ncg_sys,const char *bLocalCG,
+ const char *where)
+{
+ int ncg,i,ngl,nerr;
+
+ nerr = 0;
+ if (bLocalCG == NULL)
+ {
+ return nerr;
+ }
+ for(i=0; i<dd->ncg_tot; i++)
+ {
+ if (!bLocalCG[dd->index_gl[i]])
+ {
+ fprintf(stderr,
+ "DD node %d, %s: cg %d, global cg %d is not marked in bLocalCG (ncg_home %d)\n",dd->rank,where,i+1,dd->index_gl[i]+1,dd->ncg_home);
+ nerr++;
+ }
+ }
+ ngl = 0;
+ for(i=0; i<ncg_sys; i++)
+ {
+ if (bLocalCG[i])
+ {
+ ngl++;
+ }
+ }
+ if (ngl != dd->ncg_tot)
+ {
+ fprintf(stderr,"DD node %d, %s: In bLocalCG %d cgs are marked as local, whereas there are %d\n",dd->rank,where,ngl,dd->ncg_tot);
+ nerr++;
+ }
+
+ return nerr;
+}
+
+static void check_index_consistency(gmx_domdec_t *dd,
+ int natoms_sys,int ncg_sys,
+ const char *where)
+{
+ int nerr,ngl,i,a,cell;
+ int *have;
+
+ nerr = 0;
+
+ if (dd->comm->DD_debug > 1)
+ {
+ snew(have,natoms_sys);
+ for(a=0; a<dd->nat_tot; a++)
+ {
+ if (have[dd->gatindex[a]] > 0)
+ {
+ fprintf(stderr,"DD node %d: global atom %d occurs twice: index %d and %d\n",dd->rank,dd->gatindex[a]+1,have[dd->gatindex[a]],a+1);
+ }
+ else
+ {
+ have[dd->gatindex[a]] = a + 1;
+ }
+ }
+ sfree(have);
+ }
+
+ snew(have,dd->nat_tot);
+
+ ngl = 0;
+ for(i=0; i<natoms_sys; i++)
+ {
+ if (ga2la_get(dd->ga2la,i,&a,&cell))
+ {
+ if (a >= dd->nat_tot)
+ {
+ fprintf(stderr,"DD node %d: global atom %d marked as local atom %d, which is larger than nat_tot (%d)\n",dd->rank,i+1,a+1,dd->nat_tot);
+ nerr++;
+ }
+ else
+ {
+ have[a] = 1;
+ if (dd->gatindex[a] != i)
+ {
+ fprintf(stderr,"DD node %d: global atom %d marked as local atom %d, which has global atom index %d\n",dd->rank,i+1,a+1,dd->gatindex[a]+1);
+ nerr++;
+ }
+ }
+ ngl++;
+ }
+ }
+ if (ngl != dd->nat_tot)
+ {
+ fprintf(stderr,
+ "DD node %d, %s: %d global atom indices, %d local atoms\n",
+ dd->rank,where,ngl,dd->nat_tot);
+ }
+ for(a=0; a<dd->nat_tot; a++)
+ {
+ if (have[a] == 0)
+ {
+ fprintf(stderr,
+ "DD node %d, %s: local atom %d, global %d has no global index\n",
+ dd->rank,where,a+1,dd->gatindex[a]+1);
+ }
+ }
+ sfree(have);
+
+ nerr += check_bLocalCG(dd,ncg_sys,dd->comm->bLocalCG,where);
+
+ if (nerr > 0) {
+ gmx_fatal(FARGS,"DD node %d, %s: %d atom/cg index inconsistencies",
+ dd->rank,where,nerr);
+ }
+}
+
+static void clear_dd_indices(gmx_domdec_t *dd,int cg_start,int a_start)
+{
+ int i;
+ char *bLocalCG;
+
+ if (a_start == 0)
+ {
+ /* Clear the whole list without searching */
+ ga2la_clear(dd->ga2la);
+ }
+ else
+ {
+ for(i=a_start; i<dd->nat_tot; i++)
+ {
+ ga2la_del(dd->ga2la,dd->gatindex[i]);
+ }
+ }
+
+ bLocalCG = dd->comm->bLocalCG;
+ if (bLocalCG)
+ {
+ for(i=cg_start; i<dd->ncg_tot; i++)
+ {
+ bLocalCG[dd->index_gl[i]] = FALSE;
+ }
+ }
+
+ dd_clear_local_vsite_indices(dd);
+
+ if (dd->constraints)
+ {
+ dd_clear_local_constraint_indices(dd);
+ }
+}
+
+static real grid_jump_limit(gmx_domdec_comm_t *comm,int dim_ind)
+{
+ real grid_jump_limit;
+
+ /* The distance between the boundaries of cells at distance
+ * x+-1,y+-1 or y+-1,z+-1 is limited by the cut-off restrictions
+ * and by the fact that cells should not be shifted by more than
+ * half their size, such that cg's only shift by one cell
+ * at redecomposition.
+ */
+ grid_jump_limit = comm->cellsize_limit;
+ if (!comm->bVacDLBNoLimit)
+ {
+ grid_jump_limit = max(grid_jump_limit,
+ comm->cutoff/comm->cd[dim_ind].np);
+ }
+
+ return grid_jump_limit;
+}
+
+static void check_grid_jump(gmx_large_int_t step,gmx_domdec_t *dd,gmx_ddbox_t *ddbox)
+{
+ gmx_domdec_comm_t *comm;
+ int d,dim;
+ real limit,bfac;
+
+ comm = dd->comm;
+
+ for(d=1; d<dd->ndim; d++)
+ {
+ dim = dd->dim[d];
+ limit = grid_jump_limit(comm,d);
+ bfac = ddbox->box_size[dim];
+ if (ddbox->tric_dir[dim])
+ {
+ bfac *= ddbox->skew_fac[dim];
+ }
+ if ((comm->cell_f1[d] - comm->cell_f_max0[d])*bfac < limit ||
+ (comm->cell_f0[d] - comm->cell_f_min1[d])*bfac > -limit)
+ {
+ char buf[22];
+ gmx_fatal(FARGS,"Step %s: The domain decomposition grid has shifted too much in the %c-direction around cell %d %d %d\n",
+ gmx_step_str(step,buf),
+ dim2char(dim),dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
+ }
+ }
+}
+
+static int dd_load_count(gmx_domdec_comm_t *comm)
+{
+ return (comm->eFlop ? comm->flop_n : comm->cycl_n[ddCyclF]);
+}
+
+static float dd_force_load(gmx_domdec_comm_t *comm)
+{
+ float load;
+
+ if (comm->eFlop)
+ {
+ load = comm->flop;
+ if (comm->eFlop > 1)
+ {
+ load *= 1.0 + (comm->eFlop - 1)*(0.1*rand()/RAND_MAX - 0.05);
+ }
+ }
+ else
+ {
+ load = comm->cycl[ddCyclF];
+ if (comm->cycl_n[ddCyclF] > 1)
+ {
+ /* Subtract the maximum of the last n cycle counts
+ * to get rid of possible high counts due to other soures,
+ * for instance system activity, that would otherwise
+ * affect the dynamic load balancing.
+ */
+ load -= comm->cycl_max[ddCyclF];
+ }
+ }
+
+ return load;
+}
+
+static void set_slb_pme_dim_f(gmx_domdec_t *dd,int dim,real **dim_f)
+{
+ gmx_domdec_comm_t *comm;
+ int i;
+
+ comm = dd->comm;
+
+ snew(*dim_f,dd->nc[dim]+1);
+ (*dim_f)[0] = 0;
+ for(i=1; i<dd->nc[dim]; i++)
+ {
+ if (comm->slb_frac[dim])
+ {
+ (*dim_f)[i] = (*dim_f)[i-1] + comm->slb_frac[dim][i-1];
+ }
+ else
+ {
+ (*dim_f)[i] = (real)i/(real)dd->nc[dim];
+ }
+ }
+ (*dim_f)[dd->nc[dim]] = 1;
+}
+
+static void init_ddpme(gmx_domdec_t *dd,gmx_ddpme_t *ddpme,int dimind)
+{
+ int pmeindex,slab,nso,i;
+ ivec xyz;
+
+ if (dimind == 0 && dd->dim[0] == YY && dd->comm->npmenodes_x == 1)
+ {
+ ddpme->dim = YY;
+ }
+ else
+ {
+ ddpme->dim = dimind;
+ }
+ ddpme->dim_match = (ddpme->dim == dd->dim[dimind]);
+
+ ddpme->nslab = (ddpme->dim == 0 ?
+ dd->comm->npmenodes_x :
+ dd->comm->npmenodes_y);
+
+ if (ddpme->nslab <= 1)
+ {
+ return;
+ }
+
+ nso = dd->comm->npmenodes/ddpme->nslab;
+ /* Determine for each PME slab the PP location range for dimension dim */
+ snew(ddpme->pp_min,ddpme->nslab);
+ snew(ddpme->pp_max,ddpme->nslab);
+ for(slab=0; slab<ddpme->nslab; slab++) {
+ ddpme->pp_min[slab] = dd->nc[dd->dim[dimind]] - 1;
+ ddpme->pp_max[slab] = 0;
+ }
+ for(i=0; i<dd->nnodes; i++) {
+ ddindex2xyz(dd->nc,i,xyz);
+ /* For y only use our y/z slab.
+ * This assumes that the PME x grid size matches the DD grid size.
+ */
+ if (dimind == 0 || xyz[XX] == dd->ci[XX]) {
+ pmeindex = ddindex2pmeindex(dd,i);
+ if (dimind == 0) {
+ slab = pmeindex/nso;
+ } else {
+ slab = pmeindex % ddpme->nslab;
+ }
+ ddpme->pp_min[slab] = min(ddpme->pp_min[slab],xyz[dimind]);
+ ddpme->pp_max[slab] = max(ddpme->pp_max[slab],xyz[dimind]);
+ }
+ }
+
+ set_slb_pme_dim_f(dd,ddpme->dim,&ddpme->slb_dim_f);
+}
+
+int dd_pme_maxshift_x(gmx_domdec_t *dd)
+{
+ if (dd->comm->ddpme[0].dim == XX)
+ {
+ return dd->comm->ddpme[0].maxshift;
+ }
+ else
+ {
+ return 0;
+ }
+}
+
+int dd_pme_maxshift_y(gmx_domdec_t *dd)
+{
+ if (dd->comm->ddpme[0].dim == YY)
+ {
+ return dd->comm->ddpme[0].maxshift;
+ }
+ else if (dd->comm->npmedecompdim >= 2 && dd->comm->ddpme[1].dim == YY)
+ {
+ return dd->comm->ddpme[1].maxshift;
+ }
+ else
+ {
+ return 0;
+ }
+}
+
+static void set_pme_maxshift(gmx_domdec_t *dd,gmx_ddpme_t *ddpme,
+ gmx_bool bUniform,gmx_ddbox_t *ddbox,real *cell_f)
+{
+ gmx_domdec_comm_t *comm;
+ int nc,ns,s;
+ int *xmin,*xmax;
+ real range,pme_boundary;
+ int sh;
+
+ comm = dd->comm;
+ nc = dd->nc[ddpme->dim];
+ ns = ddpme->nslab;
+
+ if (!ddpme->dim_match)
+ {
+ /* PP decomposition is not along dim: the worst situation */
+ sh = ns/2;
+ }
+ else if (ns <= 3 || (bUniform && ns == nc))
+ {
+ /* The optimal situation */
+ sh = 1;
+ }
+ else
+ {
+ /* We need to check for all pme nodes which nodes they
+ * could possibly need to communicate with.
+ */
+ xmin = ddpme->pp_min;
+ xmax = ddpme->pp_max;
+ /* Allow for atoms to be maximally 2/3 times the cut-off
+ * out of their DD cell. This is a reasonable balance between
+ * between performance and support for most charge-group/cut-off
+ * combinations.
+ */
+ range = 2.0/3.0*comm->cutoff/ddbox->box_size[ddpme->dim];
+ /* Avoid extra communication when we are exactly at a boundary */
+ range *= 0.999;
+
+ sh = 1;
+ for(s=0; s<ns; s++)
+ {
+ /* PME slab s spreads atoms between box frac. s/ns and (s+1)/ns */
+ pme_boundary = (real)s/ns;
+ while (sh+1 < ns &&
+ ((s-(sh+1) >= 0 &&
+ cell_f[xmax[s-(sh+1) ]+1] + range > pme_boundary) ||
+ (s-(sh+1) < 0 &&
+ cell_f[xmax[s-(sh+1)+ns]+1] - 1 + range > pme_boundary)))
+ {
+ sh++;
+ }
+ pme_boundary = (real)(s+1)/ns;
+ while (sh+1 < ns &&
+ ((s+(sh+1) < ns &&
+ cell_f[xmin[s+(sh+1) ] ] - range < pme_boundary) ||
+ (s+(sh+1) >= ns &&
+ cell_f[xmin[s+(sh+1)-ns] ] + 1 - range < pme_boundary)))
+ {
+ sh++;
+ }
+ }
+ }
+
+ ddpme->maxshift = sh;
+
+ if (debug)
+ {
+ fprintf(debug,"PME slab communication range for dim %d is %d\n",
+ ddpme->dim,ddpme->maxshift);
+ }
+}
+
+static void check_box_size(gmx_domdec_t *dd,gmx_ddbox_t *ddbox)
+{
+ int d,dim;
+
+ for(d=0; d<dd->ndim; d++)
+ {
+ dim = dd->dim[d];
+ if (dim < ddbox->nboundeddim &&
+ ddbox->box_size[dim]*ddbox->skew_fac[dim] <
+ dd->nc[dim]*dd->comm->cellsize_limit*DD_CELL_MARGIN)
+ {
+ gmx_fatal(FARGS,"The %c-size of the box (%f) times the triclinic skew factor (%f) is smaller than the number of DD cells (%d) times the smallest allowed cell size (%f)\n",
+ dim2char(dim),ddbox->box_size[dim],ddbox->skew_fac[dim],
+ dd->nc[dim],dd->comm->cellsize_limit);
+ }
+ }
+}
+
+static void set_dd_cell_sizes_slb(gmx_domdec_t *dd,gmx_ddbox_t *ddbox,
+ gmx_bool bMaster,ivec npulse)
+{
+ gmx_domdec_comm_t *comm;
+ int d,j;
+ rvec cellsize_min;
+ real *cell_x,cell_dx,cellsize;
+
+ comm = dd->comm;
+
+ for(d=0; d<DIM; d++)
+ {
+ cellsize_min[d] = ddbox->box_size[d]*ddbox->skew_fac[d];
+ npulse[d] = 1;
+ if (dd->nc[d] == 1 || comm->slb_frac[d] == NULL)
+ {
+ /* Uniform grid */
+ cell_dx = ddbox->box_size[d]/dd->nc[d];
+ if (bMaster)
+ {
+ for(j=0; j<dd->nc[d]+1; j++)
+ {
+ dd->ma->cell_x[d][j] = ddbox->box0[d] + j*cell_dx;
+ }
+ }
+ else
+ {
+ comm->cell_x0[d] = ddbox->box0[d] + (dd->ci[d] )*cell_dx;
+ comm->cell_x1[d] = ddbox->box0[d] + (dd->ci[d]+1)*cell_dx;
+ }
+ cellsize = cell_dx*ddbox->skew_fac[d];
+ while (cellsize*npulse[d] < comm->cutoff && npulse[d] < dd->nc[d]-1)
+ {
+ npulse[d]++;
+ }
+ cellsize_min[d] = cellsize;
+ }
+ else
+ {
+ /* Statically load balanced grid */
+ /* Also when we are not doing a master distribution we determine
+ * all cell borders in a loop to obtain identical values
+ * to the master distribution case and to determine npulse.
+ */
+ if (bMaster)
+ {
+ cell_x = dd->ma->cell_x[d];
+ }
+ else
+ {
+ snew(cell_x,dd->nc[d]+1);
+ }
+ cell_x[0] = ddbox->box0[d];
+ for(j=0; j<dd->nc[d]; j++)
+ {
+ cell_dx = ddbox->box_size[d]*comm->slb_frac[d][j];
+ cell_x[j+1] = cell_x[j] + cell_dx;
+ cellsize = cell_dx*ddbox->skew_fac[d];
+ while (cellsize*npulse[d] < comm->cutoff &&
+ npulse[d] < dd->nc[d]-1)
+ {
+ npulse[d]++;
+ }
+ cellsize_min[d] = min(cellsize_min[d],cellsize);
+ }
+ if (!bMaster)
+ {
+ comm->cell_x0[d] = cell_x[dd->ci[d]];
+ comm->cell_x1[d] = cell_x[dd->ci[d]+1];
+ sfree(cell_x);
+ }
+ }
+ /* The following limitation is to avoid that a cell would receive
+ * some of its own home charge groups back over the periodic boundary.
+ * Double charge groups cause trouble with the global indices.
+ */
+ if (d < ddbox->npbcdim &&
+ dd->nc[d] > 1 && npulse[d] >= dd->nc[d])
+ {
+ gmx_fatal_collective(FARGS,NULL,dd,
+ "The box size in direction %c (%f) times the triclinic skew factor (%f) is too small for a cut-off of %f with %d domain decomposition cells, use 1 or more than %d %s or increase the box size in this direction",
+ dim2char(d),ddbox->box_size[d],ddbox->skew_fac[d],
+ comm->cutoff,
+ dd->nc[d],dd->nc[d],
+ dd->nnodes > dd->nc[d] ? "cells" : "processors");
+ }
+ }
+
+ if (!comm->bDynLoadBal)
+ {
+ copy_rvec(cellsize_min,comm->cellsize_min);
+ }
+
+ for(d=0; d<comm->npmedecompdim; d++)
+ {
+ set_pme_maxshift(dd,&comm->ddpme[d],
+ comm->slb_frac[dd->dim[d]]==NULL,ddbox,
+ comm->ddpme[d].slb_dim_f);
+ }
+}
+
+
+static void dd_cell_sizes_dlb_root_enforce_limits(gmx_domdec_t *dd,
+ int d,int dim,gmx_domdec_root_t *root,
+ gmx_ddbox_t *ddbox,
+ gmx_bool bUniform,gmx_large_int_t step, real cellsize_limit_f, int range[])
+{
+ gmx_domdec_comm_t *comm;
+ int ncd,i,j,nmin,nmin_old;
+ gmx_bool bLimLo,bLimHi;
+ real *cell_size;
+ real fac,halfway,cellsize_limit_f_i,region_size;
+ gmx_bool bPBC,bLastHi=FALSE;
+ int nrange[]={range[0],range[1]};
+
+ region_size= root->cell_f[range[1]]-root->cell_f[range[0]];
+
+ comm = dd->comm;
+
+ ncd = dd->nc[dim];
+
+ bPBC = (dim < ddbox->npbcdim);
+
+ cell_size = root->buf_ncd;
+
+ if (debug)
+ {
+ fprintf(debug,"enforce_limits: %d %d\n",range[0],range[1]);
+ }
+
+ /* First we need to check if the scaling does not make cells
+ * smaller than the smallest allowed size.
+ * We need to do this iteratively, since if a cell is too small,
+ * it needs to be enlarged, which makes all the other cells smaller,
+ * which could in turn make another cell smaller than allowed.
+ */
+ for(i=range[0]; i<range[1]; i++)
+ {
+ root->bCellMin[i] = FALSE;
+ }
+ nmin = 0;
+ do
+ {
+ nmin_old = nmin;
+ /* We need the total for normalization */
+ fac = 0;
+ for(i=range[0]; i<range[1]; i++)
+ {
+ if (root->bCellMin[i] == FALSE)
+ {
+ fac += cell_size[i];
+ }
+ }
+ fac = ( region_size - nmin*cellsize_limit_f)/fac; /* substracting cells already set to cellsize_limit_f */
+ /* Determine the cell boundaries */
+ for(i=range[0]; i<range[1]; i++)
+ {
+ if (root->bCellMin[i] == FALSE)
+ {
+ cell_size[i] *= fac;
+ if (!bPBC && (i == 0 || i == dd->nc[dim] -1))
+ {
+ cellsize_limit_f_i = 0;
+ }
+ else
+ {
+ cellsize_limit_f_i = cellsize_limit_f;
+ }
+ if (cell_size[i] < cellsize_limit_f_i)
+ {
+ root->bCellMin[i] = TRUE;
+ cell_size[i] = cellsize_limit_f_i;
+ nmin++;
+ }
+ }
+ root->cell_f[i+1] = root->cell_f[i] + cell_size[i];
+ }
+ }
+ while (nmin > nmin_old);
+
+ i=range[1]-1;
+ cell_size[i] = root->cell_f[i+1] - root->cell_f[i];
+ /* For this check we should not use DD_CELL_MARGIN,
+ * but a slightly smaller factor,
+ * since rounding could get use below the limit.
+ */
+ if (bPBC && cell_size[i] < cellsize_limit_f*DD_CELL_MARGIN2/DD_CELL_MARGIN)
+ {
+ char buf[22];
+ gmx_fatal(FARGS,"Step %s: the dynamic load balancing could not balance dimension %c: box size %f, triclinic skew factor %f, #cells %d, minimum cell size %f\n",
+ gmx_step_str(step,buf),
+ dim2char(dim),ddbox->box_size[dim],ddbox->skew_fac[dim],
+ ncd,comm->cellsize_min[dim]);
+ }
+
+ root->bLimited = (nmin > 0) || (range[0]>0) || (range[1]<ncd);
+
+ if (!bUniform)
+ {
+ /* Check if the boundary did not displace more than halfway
+ * each of the cells it bounds, as this could cause problems,
+ * especially when the differences between cell sizes are large.
+ * If changes are applied, they will not make cells smaller
+ * than the cut-off, as we check all the boundaries which
+ * might be affected by a change and if the old state was ok,
+ * the cells will at most be shrunk back to their old size.
+ */
+ for(i=range[0]+1; i<range[1]; i++)
+ {
+ halfway = 0.5*(root->old_cell_f[i] + root->old_cell_f[i-1]);
+ if (root->cell_f[i] < halfway)
+ {
+ root->cell_f[i] = halfway;
+ /* Check if the change also causes shifts of the next boundaries */
+ for(j=i+1; j<range[1]; j++)
+ {
+ if (root->cell_f[j] < root->cell_f[j-1] + cellsize_limit_f)
+ root->cell_f[j] = root->cell_f[j-1] + cellsize_limit_f;
+ }
+ }
+ halfway = 0.5*(root->old_cell_f[i] + root->old_cell_f[i+1]);
+ if (root->cell_f[i] > halfway)
+ {
+ root->cell_f[i] = halfway;
+ /* Check if the change also causes shifts of the next boundaries */
+ for(j=i-1; j>=range[0]+1; j--)
+ {
+ if (root->cell_f[j] > root->cell_f[j+1] - cellsize_limit_f)
+ root->cell_f[j] = root->cell_f[j+1] - cellsize_limit_f;
+ }
+ }
+ }
+ }
+
+ /* nrange is defined as [lower, upper) range for new call to enforce_limits */
+ /* find highest violation of LimLo (a) and the following violation of LimHi (thus the lowest following) (b)
+ * then call enforce_limits for (oldb,a), (a,b). In the next step: (b,nexta). oldb and nexta can be the boundaries.
+ * for a and b nrange is used */
+ if (d > 0)
+ {
+ /* Take care of the staggering of the cell boundaries */
+ if (bUniform)
+ {
+ for(i=range[0]; i<range[1]; i++)
+ {
+ root->cell_f_max0[i] = root->cell_f[i];
+ root->cell_f_min1[i] = root->cell_f[i+1];
+ }
+ }
+ else
+ {
+ for(i=range[0]+1; i<range[1]; i++)
+ {
+ bLimLo = (root->cell_f[i] < root->bound_min[i]);
+ bLimHi = (root->cell_f[i] > root->bound_max[i]);
+ if (bLimLo && bLimHi)
+ {
+ /* Both limits violated, try the best we can */
+ /* For this case we split the original range (range) in two parts and care about the other limitiations in the next iteration. */
+ root->cell_f[i] = 0.5*(root->bound_min[i] + root->bound_max[i]);
+ nrange[0]=range[0];
+ nrange[1]=i;
+ dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);
+
+ nrange[0]=i;
+ nrange[1]=range[1];
+ dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);
+
+ return;
+ }
+ else if (bLimLo)
+ {
+ /* root->cell_f[i] = root->bound_min[i]; */
+ nrange[1]=i; /* only store violation location. There could be a LimLo violation following with an higher index */
+ bLastHi=FALSE;
+ }
+ else if (bLimHi && !bLastHi)
+ {
+ bLastHi=TRUE;
+ if (nrange[1] < range[1]) /* found a LimLo before */
+ {
+ root->cell_f[nrange[1]] = root->bound_min[nrange[1]];
+ dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);
+ nrange[0]=nrange[1];
+ }
+ root->cell_f[i] = root->bound_max[i];
+ nrange[1]=i;
+ dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);
+ nrange[0]=i;
+ nrange[1]=range[1];
+ }
+ }
+ if (nrange[1] < range[1]) /* found last a LimLo */
+ {
+ root->cell_f[nrange[1]] = root->bound_min[nrange[1]];
+ dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);
+ nrange[0]=nrange[1];
+ nrange[1]=range[1];
+ dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);
+ }
+ else if (nrange[0] > range[0]) /* found at least one LimHi */
+ {
+ dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, nrange);
+ }
+ }
+ }
+}
+
+
+static void set_dd_cell_sizes_dlb_root(gmx_domdec_t *dd,
+ int d,int dim,gmx_domdec_root_t *root,
+ gmx_ddbox_t *ddbox,gmx_bool bDynamicBox,
+ gmx_bool bUniform,gmx_large_int_t step)
+{
+ gmx_domdec_comm_t *comm;
+ int ncd,d1,i,j,pos;
+ real *cell_size;
+ real load_aver,load_i,imbalance,change,change_max,sc;
+ real cellsize_limit_f,dist_min_f,dist_min_f_hard,space;
+ real change_limit;
+ real relax = 0.5;
+ gmx_bool bPBC;
+ int range[] = { 0, 0 };
+
+ comm = dd->comm;
+
+ /* Convert the maximum change from the input percentage to a fraction */
+ change_limit = comm->dlb_scale_lim*0.01;
+
+ ncd = dd->nc[dim];
+
+ bPBC = (dim < ddbox->npbcdim);
+
+ cell_size = root->buf_ncd;
+
+ /* Store the original boundaries */
+ for(i=0; i<ncd+1; i++)
+ {
+ root->old_cell_f[i] = root->cell_f[i];
+ }
+ if (bUniform) {
+ for(i=0; i<ncd; i++)
+ {
+ cell_size[i] = 1.0/ncd;
+ }
+ }
+ else if (dd_load_count(comm))
+ {
+ load_aver = comm->load[d].sum_m/ncd;
+ change_max = 0;
+ for(i=0; i<ncd; i++)
+ {
+ /* Determine the relative imbalance of cell i */
+ load_i = comm->load[d].load[i*comm->load[d].nload+2];
+ imbalance = (load_i - load_aver)/(load_aver>0 ? load_aver : 1);
+ /* Determine the change of the cell size using underrelaxation */
+ change = -relax*imbalance;
+ change_max = max(change_max,max(change,-change));
+ }
+ /* Limit the amount of scaling.
+ * We need to use the same rescaling for all cells in one row,
+ * otherwise the load balancing might not converge.
+ */
+ sc = relax;
+ if (change_max > change_limit)
+ {
+ sc *= change_limit/change_max;
+ }
+ for(i=0; i<ncd; i++)
+ {
+ /* Determine the relative imbalance of cell i */
+ load_i = comm->load[d].load[i*comm->load[d].nload+2];
+ imbalance = (load_i - load_aver)/(load_aver>0 ? load_aver : 1);
+ /* Determine the change of the cell size using underrelaxation */
+ change = -sc*imbalance;
+ cell_size[i] = (root->cell_f[i+1]-root->cell_f[i])*(1 + change);
+ }
+ }
+
+ cellsize_limit_f = comm->cellsize_min[dim]/ddbox->box_size[dim];
+ cellsize_limit_f *= DD_CELL_MARGIN;
+ dist_min_f_hard = grid_jump_limit(comm,d)/ddbox->box_size[dim];
+ dist_min_f = dist_min_f_hard * DD_CELL_MARGIN;
+ if (ddbox->tric_dir[dim])
+ {
+ cellsize_limit_f /= ddbox->skew_fac[dim];
+ dist_min_f /= ddbox->skew_fac[dim];
+ }
+ if (bDynamicBox && d > 0)
+ {
+ dist_min_f *= DD_PRES_SCALE_MARGIN;
+ }
+ if (d > 0 && !bUniform)
+ {
+ /* Make sure that the grid is not shifted too much */
+ for(i=1; i<ncd; i++) {
+ if (root->cell_f_min1[i] - root->cell_f_max0[i-1] < 2 * dist_min_f_hard)
+ {
+ gmx_incons("Inconsistent DD boundary staggering limits!");
+ }
+ root->bound_min[i] = root->cell_f_max0[i-1] + dist_min_f;
+ space = root->cell_f[i] - (root->cell_f_max0[i-1] + dist_min_f);
+ if (space > 0) {
+ root->bound_min[i] += 0.5*space;
+ }
+ root->bound_max[i] = root->cell_f_min1[i] - dist_min_f;
+ space = root->cell_f[i] - (root->cell_f_min1[i] - dist_min_f);
+ if (space < 0) {
+ root->bound_max[i] += 0.5*space;
+ }
+ if (debug)
+ {
+ fprintf(debug,
+ "dim %d boundary %d %.3f < %.3f < %.3f < %.3f < %.3f\n",
+ d,i,
+ root->cell_f_max0[i-1] + dist_min_f,
+ root->bound_min[i],root->cell_f[i],root->bound_max[i],
+ root->cell_f_min1[i] - dist_min_f);
+ }
+ }
+ }
+ range[1]=ncd;
+ root->cell_f[0] = 0;
+ root->cell_f[ncd] = 1;
+ dd_cell_sizes_dlb_root_enforce_limits(dd, d, dim, root, ddbox, bUniform, step, cellsize_limit_f, range);
+
+
+ /* After the checks above, the cells should obey the cut-off
+ * restrictions, but it does not hurt to check.
+ */
+ for(i=0; i<ncd; i++)
+ {
+ if (debug)
+ {
+ fprintf(debug,"Relative bounds dim %d cell %d: %f %f\n",
+ dim,i,root->cell_f[i],root->cell_f[i+1]);
+ }
+
+ if ((bPBC || (i != 0 && i != dd->nc[dim]-1)) &&
+ root->cell_f[i+1] - root->cell_f[i] <
+ cellsize_limit_f/DD_CELL_MARGIN)
+ {
+ char buf[22];
+ fprintf(stderr,
+ "\nWARNING step %s: direction %c, cell %d too small: %f\n",
+ gmx_step_str(step,buf),dim2char(dim),i,
+ (root->cell_f[i+1] - root->cell_f[i])
+ *ddbox->box_size[dim]*ddbox->skew_fac[dim]);
+ }
+ }
+
+ pos = ncd + 1;
+ /* Store the cell boundaries of the lower dimensions at the end */
+ for(d1=0; d1<d; d1++)
+ {
+ root->cell_f[pos++] = comm->cell_f0[d1];
+ root->cell_f[pos++] = comm->cell_f1[d1];
+ }
+
+ if (d < comm->npmedecompdim)
+ {
+ /* The master determines the maximum shift for
+ * the coordinate communication between separate PME nodes.
+ */
+ set_pme_maxshift(dd,&comm->ddpme[d],bUniform,ddbox,root->cell_f);
+ }
+ root->cell_f[pos++] = comm->ddpme[0].maxshift;
+ if (d >= 1)
+ {
+ root->cell_f[pos++] = comm->ddpme[1].maxshift;
+ }
+}
+
+static void relative_to_absolute_cell_bounds(gmx_domdec_t *dd,
+ gmx_ddbox_t *ddbox,int dimind)
+{
+ gmx_domdec_comm_t *comm;
+ int dim;
+
+ comm = dd->comm;
+
+ /* Set the cell dimensions */
+ dim = dd->dim[dimind];
+ comm->cell_x0[dim] = comm->cell_f0[dimind]*ddbox->box_size[dim];
+ comm->cell_x1[dim] = comm->cell_f1[dimind]*ddbox->box_size[dim];
+ if (dim >= ddbox->nboundeddim)
+ {
+ comm->cell_x0[dim] += ddbox->box0[dim];
+ comm->cell_x1[dim] += ddbox->box0[dim];
+ }
+}
+
+static void distribute_dd_cell_sizes_dlb(gmx_domdec_t *dd,
+ int d,int dim,real *cell_f_row,
+ gmx_ddbox_t *ddbox)
+{
+ gmx_domdec_comm_t *comm;
+ int d1,dim1,pos;
+
+ comm = dd->comm;
+
+#ifdef GMX_MPI
+ /* Each node would only need to know two fractions,
+ * but it is probably cheaper to broadcast the whole array.
+ */
+ MPI_Bcast(cell_f_row,DD_CELL_F_SIZE(dd,d)*sizeof(real),MPI_BYTE,
+ 0,comm->mpi_comm_load[d]);
+#endif
+ /* Copy the fractions for this dimension from the buffer */
+ comm->cell_f0[d] = cell_f_row[dd->ci[dim] ];
+ comm->cell_f1[d] = cell_f_row[dd->ci[dim]+1];
+ /* The whole array was communicated, so set the buffer position */
+ pos = dd->nc[dim] + 1;
+ for(d1=0; d1<=d; d1++)
+ {
+ if (d1 < d)
+ {
+ /* Copy the cell fractions of the lower dimensions */
+ comm->cell_f0[d1] = cell_f_row[pos++];
+ comm->cell_f1[d1] = cell_f_row[pos++];
+ }
+ relative_to_absolute_cell_bounds(dd,ddbox,d1);
+ }
+ /* Convert the communicated shift from float to int */
+ comm->ddpme[0].maxshift = (int)(cell_f_row[pos++] + 0.5);
+ if (d >= 1)
+ {
+ comm->ddpme[1].maxshift = (int)(cell_f_row[pos++] + 0.5);
+ }
+}
+
+static void set_dd_cell_sizes_dlb_change(gmx_domdec_t *dd,
+ gmx_ddbox_t *ddbox,gmx_bool bDynamicBox,
+ gmx_bool bUniform,gmx_large_int_t step)
+{
+ gmx_domdec_comm_t *comm;
+ int d,dim,d1;
+ gmx_bool bRowMember,bRowRoot;
+ real *cell_f_row;
+
+ comm = dd->comm;
+
+ for(d=0; d<dd->ndim; d++)
+ {
+ dim = dd->dim[d];
+ bRowMember = TRUE;
+ bRowRoot = TRUE;
+ for(d1=d; d1<dd->ndim; d1++)
+ {
+ if (dd->ci[dd->dim[d1]] > 0)
+ {
+ if (d1 > d)
+ {
+ bRowMember = FALSE;
+ }
+ bRowRoot = FALSE;
+ }
+ }
+ if (bRowMember)
+ {
+ if (bRowRoot)
+ {
+ set_dd_cell_sizes_dlb_root(dd,d,dim,comm->root[d],
+ ddbox,bDynamicBox,bUniform,step);
+ cell_f_row = comm->root[d]->cell_f;
+ }
+ else
+ {
+ cell_f_row = comm->cell_f_row;
+ }
+ distribute_dd_cell_sizes_dlb(dd,d,dim,cell_f_row,ddbox);
+ }
+ }
+}
+
+static void set_dd_cell_sizes_dlb_nochange(gmx_domdec_t *dd,gmx_ddbox_t *ddbox)
+{
+ int d;
+
+ /* This function assumes the box is static and should therefore
+ * not be called when the box has changed since the last
+ * call to dd_partition_system.
+ */
+ for(d=0; d<dd->ndim; d++)
+ {
+ relative_to_absolute_cell_bounds(dd,ddbox,d);
+ }
+}
+
+
+
+static void set_dd_cell_sizes_dlb(gmx_domdec_t *dd,
+ gmx_ddbox_t *ddbox,gmx_bool bDynamicBox,
+ gmx_bool bUniform,gmx_bool bDoDLB,gmx_large_int_t step,
+ gmx_wallcycle_t wcycle)
+{
+ gmx_domdec_comm_t *comm;
+ int dim;
+
+ comm = dd->comm;
+
+ if (bDoDLB)
+ {
+ wallcycle_start(wcycle,ewcDDCOMMBOUND);
+ set_dd_cell_sizes_dlb_change(dd,ddbox,bDynamicBox,bUniform,step);
+ wallcycle_stop(wcycle,ewcDDCOMMBOUND);
+ }
+ else if (bDynamicBox)
+ {
+ set_dd_cell_sizes_dlb_nochange(dd,ddbox);
+ }
+
+ /* Set the dimensions for which no DD is used */
+ for(dim=0; dim<DIM; dim++) {
+ if (dd->nc[dim] == 1) {
+ comm->cell_x0[dim] = 0;
+ comm->cell_x1[dim] = ddbox->box_size[dim];
+ if (dim >= ddbox->nboundeddim)
+ {
+ comm->cell_x0[dim] += ddbox->box0[dim];
+ comm->cell_x1[dim] += ddbox->box0[dim];
+ }
+ }
+ }
+}
+
+static void realloc_comm_ind(gmx_domdec_t *dd,ivec npulse)
+{
+ int d,np,i;
+ gmx_domdec_comm_dim_t *cd;
+
+ for(d=0; d<dd->ndim; d++)
+ {
+ cd = &dd->comm->cd[d];
+ np = npulse[dd->dim[d]];
+ if (np > cd->np_nalloc)
+ {
+ if (debug)
+ {
+ fprintf(debug,"(Re)allocing cd for %c to %d pulses\n",
+ dim2char(dd->dim[d]),np);
+ }
+ if (DDMASTER(dd) && cd->np_nalloc > 0)
+ {
+ fprintf(stderr,"\nIncreasing the number of cell to communicate in dimension %c to %d for the first time\n",dim2char(dd->dim[d]),np);
+ }
+ srenew(cd->ind,np);
+ for(i=cd->np_nalloc; i<np; i++)
+ {
+ cd->ind[i].index = NULL;
+ cd->ind[i].nalloc = 0;
+ }
+ cd->np_nalloc = np;
+ }
+ cd->np = np;
+ }
+}
+
+
+static void set_dd_cell_sizes(gmx_domdec_t *dd,
+ gmx_ddbox_t *ddbox,gmx_bool bDynamicBox,
+ gmx_bool bUniform,gmx_bool bDoDLB,gmx_large_int_t step,
+ gmx_wallcycle_t wcycle)
+{
+ gmx_domdec_comm_t *comm;
+ int d;
+ ivec npulse;
+
+ comm = dd->comm;
+
+ /* Copy the old cell boundaries for the cg displacement check */
+ copy_rvec(comm->cell_x0,comm->old_cell_x0);
+ copy_rvec(comm->cell_x1,comm->old_cell_x1);
+
+ if (comm->bDynLoadBal)
+ {
+ if (DDMASTER(dd))
+ {
+ check_box_size(dd,ddbox);
+ }
+ set_dd_cell_sizes_dlb(dd,ddbox,bDynamicBox,bUniform,bDoDLB,step,wcycle);
+ }
+ else
+ {
+ set_dd_cell_sizes_slb(dd,ddbox,FALSE,npulse);
+ realloc_comm_ind(dd,npulse);
+ }
+
+ if (debug)
+ {
+ for(d=0; d<DIM; d++)
+ {
+ fprintf(debug,"cell_x[%d] %f - %f skew_fac %f\n",
+ d,comm->cell_x0[d],comm->cell_x1[d],ddbox->skew_fac[d]);
+ }
+ }
+}
+
+static void comm_dd_ns_cell_sizes(gmx_domdec_t *dd,
+ gmx_ddbox_t *ddbox,
+ rvec cell_ns_x0,rvec cell_ns_x1,
+ gmx_large_int_t step)
+{
+ gmx_domdec_comm_t *comm;
+ int dim_ind,dim;
+
+ comm = dd->comm;
+
+ for(dim_ind=0; dim_ind<dd->ndim; dim_ind++)
+ {
+ dim = dd->dim[dim_ind];
+
+ /* Without PBC we don't have restrictions on the outer cells */
+ if (!(dim >= ddbox->npbcdim &&
+ (dd->ci[dim] == 0 || dd->ci[dim] == dd->nc[dim] - 1)) &&
+ comm->bDynLoadBal &&
+ (comm->cell_x1[dim] - comm->cell_x0[dim])*ddbox->skew_fac[dim] <
+ comm->cellsize_min[dim])
+ {
+ char buf[22];
+ gmx_fatal(FARGS,"Step %s: The %c-size (%f) times the triclinic skew factor (%f) is smaller than the smallest allowed cell size (%f) for domain decomposition grid cell %d %d %d",
+ gmx_step_str(step,buf),dim2char(dim),
+ comm->cell_x1[dim] - comm->cell_x0[dim],
+ ddbox->skew_fac[dim],
+ dd->comm->cellsize_min[dim],
+ dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
+ }
+ }
+
+ if ((dd->bGridJump && dd->ndim > 1) || ddbox->nboundeddim < DIM)
+ {
+ /* Communicate the boundaries and update cell_ns_x0/1 */
+ dd_move_cellx(dd,ddbox,cell_ns_x0,cell_ns_x1);
+ if (dd->bGridJump && dd->ndim > 1)
+ {
+ check_grid_jump(step,dd,ddbox);
+ }
+ }
+}
+
+static void make_tric_corr_matrix(int npbcdim,matrix box,matrix tcm)
+{
+ if (YY < npbcdim)
+ {
+ tcm[YY][XX] = -box[YY][XX]/box[YY][YY];
+ }
+ else
+ {
+ tcm[YY][XX] = 0;
+ }
+ if (ZZ < npbcdim)
+ {
+ tcm[ZZ][XX] = -(box[ZZ][YY]*tcm[YY][XX] + box[ZZ][XX])/box[ZZ][ZZ];
+ tcm[ZZ][YY] = -box[ZZ][YY]/box[ZZ][ZZ];
+ }
+ else
+ {
+ tcm[ZZ][XX] = 0;
+ tcm[ZZ][YY] = 0;
+ }
+}
+
+static void check_screw_box(matrix box)
+{
+ /* Mathematical limitation */
+ if (box[YY][XX] != 0 || box[ZZ][XX] != 0)
+ {
+ gmx_fatal(FARGS,"With screw pbc the unit cell can not have non-zero off-diagonal x-components");
+ }
+
+ /* Limitation due to the asymmetry of the eighth shell method */
+ if (box[ZZ][YY] != 0)
+ {
+ gmx_fatal(FARGS,"pbc=screw with non-zero box_zy is not supported");
+ }
+}
+
+static void distribute_cg(FILE *fplog,gmx_large_int_t step,
+ matrix box,ivec tric_dir,t_block *cgs,rvec pos[],
+ gmx_domdec_t *dd)
+{
+ gmx_domdec_master_t *ma;
+ int **tmp_ind=NULL,*tmp_nalloc=NULL;
+ int i,icg,j,k,k0,k1,d,npbcdim;
+ matrix tcm;
+ rvec box_size,cg_cm;
+ ivec ind;
+ real nrcg,inv_ncg,pos_d;
+ atom_id *cgindex;
+ gmx_bool bUnbounded,bScrew;
+
+ ma = dd->ma;
+
+ if (tmp_ind == NULL)
+ {
+ snew(tmp_nalloc,dd->nnodes);
+ snew(tmp_ind,dd->nnodes);
+ for(i=0; i<dd->nnodes; i++)
+ {
+ tmp_nalloc[i] = over_alloc_large(cgs->nr/dd->nnodes+1);
+ snew(tmp_ind[i],tmp_nalloc[i]);
+ }
+ }
+
+ /* Clear the count */
+ for(i=0; i<dd->nnodes; i++)
+ {
+ ma->ncg[i] = 0;
+ ma->nat[i] = 0;
+ }
+
+ make_tric_corr_matrix(dd->npbcdim,box,tcm);
+
+ cgindex = cgs->index;
+
+ /* Compute the center of geometry for all charge groups */
+ for(icg=0; icg<cgs->nr; icg++)
+ {
+ k0 = cgindex[icg];
+ k1 = cgindex[icg+1];
+ nrcg = k1 - k0;
+ if (nrcg == 1)
+ {
+ copy_rvec(pos[k0],cg_cm);
+ }
+ else
+ {
+ inv_ncg = 1.0/nrcg;
+
+ clear_rvec(cg_cm);
+ for(k=k0; (k<k1); k++)
+ {
+ rvec_inc(cg_cm,pos[k]);
+ }
+ for(d=0; (d<DIM); d++)
+ {
+ cg_cm[d] *= inv_ncg;
+ }
+ }
+ /* Put the charge group in the box and determine the cell index */
+ for(d=DIM-1; d>=0; d--) {
+ pos_d = cg_cm[d];
+ if (d < dd->npbcdim)
+ {
+ bScrew = (dd->bScrewPBC && d == XX);
+ if (tric_dir[d] && dd->nc[d] > 1)
+ {
+ /* Use triclinic coordintates for this dimension */
+ for(j=d+1; j<DIM; j++)
+ {
+ pos_d += cg_cm[j]*tcm[j][d];
+ }
+ }
+ while(pos_d >= box[d][d])
+ {
+ pos_d -= box[d][d];
+ rvec_dec(cg_cm,box[d]);
+ if (bScrew)
+ {
+ cg_cm[YY] = box[YY][YY] - cg_cm[YY];
+ cg_cm[ZZ] = box[ZZ][ZZ] - cg_cm[ZZ];
+ }
+ for(k=k0; (k<k1); k++)
+ {
+ rvec_dec(pos[k],box[d]);
+ if (bScrew)
+ {
+ pos[k][YY] = box[YY][YY] - pos[k][YY];
+ pos[k][ZZ] = box[ZZ][ZZ] - pos[k][ZZ];
+ }
+ }
+ }
+ while(pos_d < 0)
+ {
+ pos_d += box[d][d];
+ rvec_inc(cg_cm,box[d]);
+ if (bScrew)
+ {
+ cg_cm[YY] = box[YY][YY] - cg_cm[YY];
+ cg_cm[ZZ] = box[ZZ][ZZ] - cg_cm[ZZ];
+ }
+ for(k=k0; (k<k1); k++)
+ {
+ rvec_inc(pos[k],box[d]);
+ if (bScrew) {
+ pos[k][YY] = box[YY][YY] - pos[k][YY];
+ pos[k][ZZ] = box[ZZ][ZZ] - pos[k][ZZ];
+ }
+ }
+ }
+ }
+ /* This could be done more efficiently */
+ ind[d] = 0;
+ while(ind[d]+1 < dd->nc[d] && pos_d >= ma->cell_x[d][ind[d]+1])
+ {
+ ind[d]++;
+ }
+ }
+ i = dd_index(dd->nc,ind);
+ if (ma->ncg[i] == tmp_nalloc[i])
+ {
+ tmp_nalloc[i] = over_alloc_large(ma->ncg[i]+1);
+ srenew(tmp_ind[i],tmp_nalloc[i]);
+ }
+ tmp_ind[i][ma->ncg[i]] = icg;
+ ma->ncg[i]++;
+ ma->nat[i] += cgindex[icg+1] - cgindex[icg];
+ }
+
+ k1 = 0;
+ for(i=0; i<dd->nnodes; i++)
+ {
+ ma->index[i] = k1;
+ for(k=0; k<ma->ncg[i]; k++)
+ {
+ ma->cg[k1++] = tmp_ind[i][k];
+ }
+ }
+ ma->index[dd->nnodes] = k1;
+
+ for(i=0; i<dd->nnodes; i++)
+ {
+ sfree(tmp_ind[i]);
+ }
+ sfree(tmp_ind);
+ sfree(tmp_nalloc);
+
+ if (fplog)
+ {
+ char buf[22];
+ fprintf(fplog,"Charge group distribution at step %s:",
+ gmx_step_str(step,buf));
+ for(i=0; i<dd->nnodes; i++)
+ {
+ fprintf(fplog," %d",ma->ncg[i]);
+ }
+ fprintf(fplog,"\n");
+ }
+}
+
+static void get_cg_distribution(FILE *fplog,gmx_large_int_t step,gmx_domdec_t *dd,
+ t_block *cgs,matrix box,gmx_ddbox_t *ddbox,
+ rvec pos[])
+{
+ gmx_domdec_master_t *ma=NULL;
+ ivec npulse;
+ int i,cg_gl;
+ int *ibuf,buf2[2] = { 0, 0 };
+
+ if (DDMASTER(dd))
+ {
+ ma = dd->ma;
+
+ if (dd->bScrewPBC)
+ {
+ check_screw_box(box);
+ }
+
+ set_dd_cell_sizes_slb(dd,ddbox,TRUE,npulse);
+
+ distribute_cg(fplog,step,box,ddbox->tric_dir,cgs,pos,dd);
+ for(i=0; i<dd->nnodes; i++)
+ {
+ ma->ibuf[2*i] = ma->ncg[i];
+ ma->ibuf[2*i+1] = ma->nat[i];
+ }
+ ibuf = ma->ibuf;
+ }
+ else
+ {
+ ibuf = NULL;
+ }
+ dd_scatter(dd,2*sizeof(int),ibuf,buf2);
+
+ dd->ncg_home = buf2[0];
+ dd->nat_home = buf2[1];
+ dd->ncg_tot = dd->ncg_home;
+ dd->nat_tot = dd->nat_home;
+ if (dd->ncg_home > dd->cg_nalloc || dd->cg_nalloc == 0)
+ {
+ dd->cg_nalloc = over_alloc_dd(dd->ncg_home);
+ srenew(dd->index_gl,dd->cg_nalloc);
+ srenew(dd->cgindex,dd->cg_nalloc+1);
+ }
+ if (DDMASTER(dd))
+ {
+ for(i=0; i<dd->nnodes; i++)
+ {
+ ma->ibuf[i] = ma->ncg[i]*sizeof(int);
+ ma->ibuf[dd->nnodes+i] = ma->index[i]*sizeof(int);
+ }
+ }
+
+ dd_scatterv(dd,
+ DDMASTER(dd) ? ma->ibuf : NULL,
+ DDMASTER(dd) ? ma->ibuf+dd->nnodes : NULL,
+ DDMASTER(dd) ? ma->cg : NULL,
+ dd->ncg_home*sizeof(int),dd->index_gl);
+
+ /* Determine the home charge group sizes */
+ dd->cgindex[0] = 0;
+ for(i=0; i<dd->ncg_home; i++)
+ {
+ cg_gl = dd->index_gl[i];
+ dd->cgindex[i+1] =
+ dd->cgindex[i] + cgs->index[cg_gl+1] - cgs->index[cg_gl];
+ }
+
+ if (debug)
+ {
+ fprintf(debug,"Home charge groups:\n");
+ for(i=0; i<dd->ncg_home; i++)
+ {
+ fprintf(debug," %d",dd->index_gl[i]);
+ if (i % 10 == 9)
+ fprintf(debug,"\n");
+ }
+ fprintf(debug,"\n");
+ }
+}
+
+static int compact_and_copy_vec_at(int ncg,int *move,
+ int *cgindex,
+ int nvec,int vec,
+ rvec *src,gmx_domdec_comm_t *comm,
+ gmx_bool bCompact)
+{
+ int m,icg,i,i0,i1,nrcg;
+ int home_pos;
+ int pos_vec[DIM*2];
+
+ home_pos = 0;
+
+ for(m=0; m<DIM*2; m++)
+ {
+ pos_vec[m] = 0;
+ }
+
+ i0 = 0;
+ for(icg=0; icg<ncg; icg++)
+ {
+ i1 = cgindex[icg+1];
+ m = move[icg];
+ if (m == -1)
+ {
+ if (bCompact)
+ {
+ /* Compact the home array in place */
+ for(i=i0; i<i1; i++)
+ {
+ copy_rvec(src[i],src[home_pos++]);
+ }
+ }
+ }
+ else
+ {
+ /* Copy to the communication buffer */
+ nrcg = i1 - i0;
+ pos_vec[m] += 1 + vec*nrcg;
+ for(i=i0; i<i1; i++)
+ {
+ copy_rvec(src[i],comm->cgcm_state[m][pos_vec[m]++]);
+ }
+ pos_vec[m] += (nvec - vec - 1)*nrcg;
+ }
+ if (!bCompact)
+ {
+ home_pos += i1 - i0;
+ }
+ i0 = i1;
+ }
+
+ return home_pos;
+}
+
+static int compact_and_copy_vec_cg(int ncg,int *move,
+ int *cgindex,
+ int nvec,rvec *src,gmx_domdec_comm_t *comm,
+ gmx_bool bCompact)
+{
+ int m,icg,i0,i1,nrcg;
+ int home_pos;
+ int pos_vec[DIM*2];
+
+ home_pos = 0;
+
+ for(m=0; m<DIM*2; m++)
+ {
+ pos_vec[m] = 0;
+ }
+
+ i0 = 0;
+ for(icg=0; icg<ncg; icg++)
+ {
+ i1 = cgindex[icg+1];
+ m = move[icg];
+ if (m == -1)
+ {
+ if (bCompact)
+ {
+ /* Compact the home array in place */
+ copy_rvec(src[icg],src[home_pos++]);
+ }
+ }
+ else
+ {
+ nrcg = i1 - i0;
+ /* Copy to the communication buffer */
+ copy_rvec(src[icg],comm->cgcm_state[m][pos_vec[m]]);
+ pos_vec[m] += 1 + nrcg*nvec;
+ }
+ i0 = i1;
+ }
+ if (!bCompact)
+ {
+ home_pos = ncg;
+ }
+
+ return home_pos;
+}
+
+static int compact_ind(int ncg,int *move,
+ int *index_gl,int *cgindex,
+ int *gatindex,
+ gmx_ga2la_t ga2la,char *bLocalCG,
+ int *cginfo)
+{
+ int cg,nat,a0,a1,a,a_gl;
+ int home_pos;
+
+ home_pos = 0;
+ nat = 0;
+ for(cg=0; cg<ncg; cg++)
+ {
+ a0 = cgindex[cg];
+ a1 = cgindex[cg+1];
+ if (move[cg] == -1)
+ {
+ /* Compact the home arrays in place.
+ * Anything that can be done here avoids access to global arrays.
+ */
+ cgindex[home_pos] = nat;
+ for(a=a0; a<a1; a++)
+ {
+ a_gl = gatindex[a];
+ gatindex[nat] = a_gl;
+ /* The cell number stays 0, so we don't need to set it */
+ ga2la_change_la(ga2la,a_gl,nat);
+ nat++;
+ }
+ index_gl[home_pos] = index_gl[cg];
+ cginfo[home_pos] = cginfo[cg];
+ /* The charge group remains local, so bLocalCG does not change */
+ home_pos++;
+ }
+ else
+ {
+ /* Clear the global indices */
+ for(a=a0; a<a1; a++)
+ {
+ ga2la_del(ga2la,gatindex[a]);
+ }
+ if (bLocalCG)
+ {
+ bLocalCG[index_gl[cg]] = FALSE;
+ }
+ }
+ }
+ cgindex[home_pos] = nat;
+
+ return home_pos;
+}
+
+static void clear_and_mark_ind(int ncg,int *move,
+ int *index_gl,int *cgindex,int *gatindex,
+ gmx_ga2la_t ga2la,char *bLocalCG,
+ int *cell_index)
+{
+ int cg,a0,a1,a;
+
+ for(cg=0; cg<ncg; cg++)
+ {
+ if (move[cg] >= 0)
+ {
+ a0 = cgindex[cg];
+ a1 = cgindex[cg+1];
+ /* Clear the global indices */
+ for(a=a0; a<a1; a++)
+ {
+ ga2la_del(ga2la,gatindex[a]);
+ }
+ if (bLocalCG)
+ {
+ bLocalCG[index_gl[cg]] = FALSE;
+ }
+ /* Signal that this cg has moved using the ns cell index.
+ * Here we set it to -1.
+ * fill_grid will change it from -1 to 4*grid->ncells.
+ */
+ cell_index[cg] = -1;
+ }
+ }
+}
+
+static void print_cg_move(FILE *fplog,
+ gmx_domdec_t *dd,
+ gmx_large_int_t step,int cg,int dim,int dir,
+ gmx_bool bHaveLimitdAndCMOld,real limitd,
+ rvec cm_old,rvec cm_new,real pos_d)
+{
+ gmx_domdec_comm_t *comm;
+ char buf[22];
+
+ comm = dd->comm;
+
+ fprintf(fplog,"\nStep %s:\n",gmx_step_str(step,buf));
+ if (bHaveLimitdAndCMOld)
+ {
+ fprintf(fplog,"The charge group starting at atom %d moved than the distance allowed by the domain decomposition (%f) in direction %c\n",
+ ddglatnr(dd,dd->cgindex[cg]),limitd,dim2char(dim));
+ }
+ else
+ {
+ fprintf(fplog,"The charge group starting at atom %d moved than the distance allowed by the domain decomposition in direction %c\n",
+ ddglatnr(dd,dd->cgindex[cg]),dim2char(dim));
+ }
+ fprintf(fplog,"distance out of cell %f\n",
+ dir==1 ? pos_d - comm->cell_x1[dim] : pos_d - comm->cell_x0[dim]);
+ if (bHaveLimitdAndCMOld)
+ {
+ fprintf(fplog,"Old coordinates: %8.3f %8.3f %8.3f\n",
+ cm_old[XX],cm_old[YY],cm_old[ZZ]);
+ }
+ fprintf(fplog,"New coordinates: %8.3f %8.3f %8.3f\n",
+ cm_new[XX],cm_new[YY],cm_new[ZZ]);
+ fprintf(fplog,"Old cell boundaries in direction %c: %8.3f %8.3f\n",
+ dim2char(dim),
+ comm->old_cell_x0[dim],comm->old_cell_x1[dim]);
+ fprintf(fplog,"New cell boundaries in direction %c: %8.3f %8.3f\n",
+ dim2char(dim),
+ comm->cell_x0[dim],comm->cell_x1[dim]);
+}
+
+static void cg_move_error(FILE *fplog,
+ gmx_domdec_t *dd,
+ gmx_large_int_t step,int cg,int dim,int dir,
+ gmx_bool bHaveLimitdAndCMOld,real limitd,
+ rvec cm_old,rvec cm_new,real pos_d)
+{
+ if (fplog)
+ {
+ print_cg_move(fplog, dd,step,cg,dim,dir,
+ bHaveLimitdAndCMOld,limitd,cm_old,cm_new,pos_d);
+ }
+ print_cg_move(stderr,dd,step,cg,dim,dir,
+ bHaveLimitdAndCMOld,limitd,cm_old,cm_new,pos_d);
+ gmx_fatal(FARGS,
+ "A charge group moved too far between two domain decomposition steps\n"
+ "This usually means that your system is not well equilibrated");
+}
+
+static void rotate_state_atom(t_state *state,int a)
+{
+ int est;
+
+ for(est=0; est<estNR; est++)
+ {
- MPI_Group g_row;
++ if (EST_DISTR(est) && (state->flags & (1<<est))) {
+ switch (est) {
+ case estX:
+ /* Rotate the complete state; for a rectangular box only */
+ state->x[a][YY] = state->box[YY][YY] - state->x[a][YY];
+ state->x[a][ZZ] = state->box[ZZ][ZZ] - state->x[a][ZZ];
+ break;
+ case estV:
+ state->v[a][YY] = -state->v[a][YY];
+ state->v[a][ZZ] = -state->v[a][ZZ];
+ break;
+ case estSDX:
+ state->sd_X[a][YY] = -state->sd_X[a][YY];
+ state->sd_X[a][ZZ] = -state->sd_X[a][ZZ];
+ break;
+ case estCGP:
+ state->cg_p[a][YY] = -state->cg_p[a][YY];
+ state->cg_p[a][ZZ] = -state->cg_p[a][ZZ];
+ break;
+ case estDISRE_INITF:
+ case estDISRE_RM3TAV:
+ case estORIRE_INITF:
+ case estORIRE_DTAV:
+ /* These are distances, so not affected by rotation */
+ break;
+ default:
+ gmx_incons("Unknown state entry encountered in rotate_state_atom");
+ }
+ }
+ }
+}
+
+static int dd_redistribute_cg(FILE *fplog,gmx_large_int_t step,
+ gmx_domdec_t *dd,ivec tric_dir,
+ t_state *state,rvec **f,
+ t_forcerec *fr,t_mdatoms *md,
+ gmx_bool bCompact,
+ t_nrnb *nrnb)
+{
+ int *move;
+ int npbcdim;
+ int ncg[DIM*2],nat[DIM*2];
+ int c,i,cg,k,k0,k1,d,dim,dim2,dir,d2,d3,d4,cell_d;
+ int mc,cdd,nrcg,ncg_recv,nat_recv,nvs,nvr,nvec,vec;
+ int sbuf[2],rbuf[2];
+ int home_pos_cg,home_pos_at,ncg_stay_home,buf_pos;
+ int flag;
+ gmx_bool bV=FALSE,bSDX=FALSE,bCGP=FALSE;
+ gmx_bool bScrew;
+ ivec dev;
+ real inv_ncg,pos_d;
+ matrix tcm;
+ rvec *cg_cm,cell_x0,cell_x1,limitd,limit0,limit1,cm_new;
+ atom_id *cgindex;
+ cginfo_mb_t *cginfo_mb;
+ gmx_domdec_comm_t *comm;
+
+ if (dd->bScrewPBC)
+ {
+ check_screw_box(state->box);
+ }
+
+ comm = dd->comm;
+ cg_cm = fr->cg_cm;
+
+ for(i=0; i<estNR; i++)
+ {
+ if (EST_DISTR(i))
+ {
+ switch (i)
+ {
+ case estX: /* Always present */ break;
+ case estV: bV = (state->flags & (1<<i)); break;
+ case estSDX: bSDX = (state->flags & (1<<i)); break;
+ case estCGP: bCGP = (state->flags & (1<<i)); break;
+ case estLD_RNG:
+ case estLD_RNGI:
+ case estDISRE_INITF:
+ case estDISRE_RM3TAV:
+ case estORIRE_INITF:
+ case estORIRE_DTAV:
+ /* No processing required */
+ break;
+ default:
+ gmx_incons("Unknown state entry encountered in dd_redistribute_cg");
+ }
+ }
+ }
+
+ if (dd->ncg_tot > comm->nalloc_int)
+ {
+ comm->nalloc_int = over_alloc_dd(dd->ncg_tot);
+ srenew(comm->buf_int,comm->nalloc_int);
+ }
+ move = comm->buf_int;
+
+ /* Clear the count */
+ for(c=0; c<dd->ndim*2; c++)
+ {
+ ncg[c] = 0;
+ nat[c] = 0;
+ }
+
+ npbcdim = dd->npbcdim;
+
+ for(d=0; (d<DIM); d++)
+ {
+ limitd[d] = dd->comm->cellsize_min[d];
+ if (d >= npbcdim && dd->ci[d] == 0)
+ {
+ cell_x0[d] = -GMX_FLOAT_MAX;
+ }
+ else
+ {
+ cell_x0[d] = comm->cell_x0[d];
+ }
+ if (d >= npbcdim && dd->ci[d] == dd->nc[d] - 1)
+ {
+ cell_x1[d] = GMX_FLOAT_MAX;
+ }
+ else
+ {
+ cell_x1[d] = comm->cell_x1[d];
+ }
+ if (d < npbcdim)
+ {
+ limit0[d] = comm->old_cell_x0[d] - limitd[d];
+ limit1[d] = comm->old_cell_x1[d] + limitd[d];
+ }
+ else
+ {
+ /* We check after communication if a charge group moved
+ * more than one cell. Set the pre-comm check limit to float_max.
+ */
+ limit0[d] = -GMX_FLOAT_MAX;
+ limit1[d] = GMX_FLOAT_MAX;
+ }
+ }
+
+ make_tric_corr_matrix(npbcdim,state->box,tcm);
+
+ cgindex = dd->cgindex;
+
+ /* Compute the center of geometry for all home charge groups
+ * and put them in the box and determine where they should go.
+ */
+ for(cg=0; cg<dd->ncg_home; cg++)
+ {
+ k0 = cgindex[cg];
+ k1 = cgindex[cg+1];
+ nrcg = k1 - k0;
+ if (nrcg == 1)
+ {
+ copy_rvec(state->x[k0],cm_new);
+ }
+ else
+ {
+ inv_ncg = 1.0/nrcg;
+
+ clear_rvec(cm_new);
+ for(k=k0; (k<k1); k++)
+ {
+ rvec_inc(cm_new,state->x[k]);
+ }
+ for(d=0; (d<DIM); d++)
+ {
+ cm_new[d] = inv_ncg*cm_new[d];
+ }
+ }
+
+ clear_ivec(dev);
+ /* Do pbc and check DD cell boundary crossings */
+ for(d=DIM-1; d>=0; d--)
+ {
+ if (dd->nc[d] > 1)
+ {
+ bScrew = (dd->bScrewPBC && d == XX);
+ /* Determine the location of this cg in lattice coordinates */
+ pos_d = cm_new[d];
+ if (tric_dir[d])
+ {
+ for(d2=d+1; d2<DIM; d2++)
+ {
+ pos_d += cm_new[d2]*tcm[d2][d];
+ }
+ }
+ /* Put the charge group in the triclinic unit-cell */
+ if (pos_d >= cell_x1[d])
+ {
+ if (pos_d >= limit1[d])
+ {
+ cg_move_error(fplog,dd,step,cg,d,1,TRUE,limitd[d],
+ cg_cm[cg],cm_new,pos_d);
+ }
+ dev[d] = 1;
+ if (dd->ci[d] == dd->nc[d] - 1)
+ {
+ rvec_dec(cm_new,state->box[d]);
+ if (bScrew)
+ {
+ cm_new[YY] = state->box[YY][YY] - cm_new[YY];
+ cm_new[ZZ] = state->box[ZZ][ZZ] - cm_new[ZZ];
+ }
+ for(k=k0; (k<k1); k++)
+ {
+ rvec_dec(state->x[k],state->box[d]);
+ if (bScrew)
+ {
+ rotate_state_atom(state,k);
+ }
+ }
+ }
+ }
+ else if (pos_d < cell_x0[d])
+ {
+ if (pos_d < limit0[d])
+ {
+ cg_move_error(fplog,dd,step,cg,d,-1,TRUE,limitd[d],
+ cg_cm[cg],cm_new,pos_d);
+ }
+ dev[d] = -1;
+ if (dd->ci[d] == 0)
+ {
+ rvec_inc(cm_new,state->box[d]);
+ if (bScrew)
+ {
+ cm_new[YY] = state->box[YY][YY] - cm_new[YY];
+ cm_new[ZZ] = state->box[ZZ][ZZ] - cm_new[ZZ];
+ }
+ for(k=k0; (k<k1); k++)
+ {
+ rvec_inc(state->x[k],state->box[d]);
+ if (bScrew)
+ {
+ rotate_state_atom(state,k);
+ }
+ }
+ }
+ }
+ }
+ else if (d < npbcdim)
+ {
+ /* Put the charge group in the rectangular unit-cell */
+ while (cm_new[d] >= state->box[d][d])
+ {
+ rvec_dec(cm_new,state->box[d]);
+ for(k=k0; (k<k1); k++)
+ {
+ rvec_dec(state->x[k],state->box[d]);
+ }
+ }
+ while (cm_new[d] < 0)
+ {
+ rvec_inc(cm_new,state->box[d]);
+ for(k=k0; (k<k1); k++)
+ {
+ rvec_inc(state->x[k],state->box[d]);
+ }
+ }
+ }
+ }
+
+ copy_rvec(cm_new,cg_cm[cg]);
+
+ /* Determine where this cg should go */
+ flag = 0;
+ mc = -1;
+ for(d=0; d<dd->ndim; d++)
+ {
+ dim = dd->dim[d];
+ if (dev[dim] == 1)
+ {
+ flag |= DD_FLAG_FW(d);
+ if (mc == -1)
+ {
+ mc = d*2;
+ }
+ }
+ else if (dev[dim] == -1)
+ {
+ flag |= DD_FLAG_BW(d);
+ if (mc == -1) {
+ if (dd->nc[dim] > 2)
+ {
+ mc = d*2 + 1;
+ }
+ else
+ {
+ mc = d*2;
+ }
+ }
+ }
+ }
+ move[cg] = mc;
+ if (mc >= 0)
+ {
+ if (ncg[mc]+1 > comm->cggl_flag_nalloc[mc])
+ {
+ comm->cggl_flag_nalloc[mc] = over_alloc_dd(ncg[mc]+1);
+ srenew(comm->cggl_flag[mc],comm->cggl_flag_nalloc[mc]*DD_CGIBS);
+ }
+ comm->cggl_flag[mc][ncg[mc]*DD_CGIBS ] = dd->index_gl[cg];
+ /* We store the cg size in the lower 16 bits
+ * and the place where the charge group should go
+ * in the next 6 bits. This saves some communication volume.
+ */
+ comm->cggl_flag[mc][ncg[mc]*DD_CGIBS+1] = nrcg | flag;
+ ncg[mc] += 1;
+ nat[mc] += nrcg;
+ }
+ }
+
+ inc_nrnb(nrnb,eNR_CGCM,dd->nat_home);
+ inc_nrnb(nrnb,eNR_RESETX,dd->ncg_home);
+
+ nvec = 1;
+ if (bV)
+ {
+ nvec++;
+ }
+ if (bSDX)
+ {
+ nvec++;
+ }
+ if (bCGP)
+ {
+ nvec++;
+ }
+
+ /* Make sure the communication buffers are large enough */
+ for(mc=0; mc<dd->ndim*2; mc++)
+ {
+ nvr = ncg[mc] + nat[mc]*nvec;
+ if (nvr > comm->cgcm_state_nalloc[mc])
+ {
+ comm->cgcm_state_nalloc[mc] = over_alloc_dd(nvr);
+ srenew(comm->cgcm_state[mc],comm->cgcm_state_nalloc[mc]);
+ }
+ }
+
+ /* Recalculating cg_cm might be cheaper than communicating,
+ * but that could give rise to rounding issues.
+ */
+ home_pos_cg =
+ compact_and_copy_vec_cg(dd->ncg_home,move,cgindex,
+ nvec,cg_cm,comm,bCompact);
+
+ vec = 0;
+ home_pos_at =
+ compact_and_copy_vec_at(dd->ncg_home,move,cgindex,
+ nvec,vec++,state->x,comm,bCompact);
+ if (bV)
+ {
+ compact_and_copy_vec_at(dd->ncg_home,move,cgindex,
+ nvec,vec++,state->v,comm,bCompact);
+ }
+ if (bSDX)
+ {
+ compact_and_copy_vec_at(dd->ncg_home,move,cgindex,
+ nvec,vec++,state->sd_X,comm,bCompact);
+ }
+ if (bCGP)
+ {
+ compact_and_copy_vec_at(dd->ncg_home,move,cgindex,
+ nvec,vec++,state->cg_p,comm,bCompact);
+ }
+
+ if (bCompact)
+ {
+ compact_ind(dd->ncg_home,move,
+ dd->index_gl,dd->cgindex,dd->gatindex,
+ dd->ga2la,comm->bLocalCG,
+ fr->cginfo);
+ }
+ else
+ {
+ clear_and_mark_ind(dd->ncg_home,move,
+ dd->index_gl,dd->cgindex,dd->gatindex,
+ dd->ga2la,comm->bLocalCG,
+ fr->ns.grid->cell_index);
+ }
+
+ cginfo_mb = fr->cginfo_mb;
+
+ ncg_stay_home = home_pos_cg;
+ for(d=0; d<dd->ndim; d++)
+ {
+ dim = dd->dim[d];
+ ncg_recv = 0;
+ nat_recv = 0;
+ nvr = 0;
+ for(dir=0; dir<(dd->nc[dim]==2 ? 1 : 2); dir++)
+ {
+ cdd = d*2 + dir;
+ /* Communicate the cg and atom counts */
+ sbuf[0] = ncg[cdd];
+ sbuf[1] = nat[cdd];
+ if (debug)
+ {
+ fprintf(debug,"Sending ddim %d dir %d: ncg %d nat %d\n",
+ d,dir,sbuf[0],sbuf[1]);
+ }
+ dd_sendrecv_int(dd, d, dir, sbuf, 2, rbuf, 2);
+
+ if ((ncg_recv+rbuf[0])*DD_CGIBS > comm->nalloc_int)
+ {
+ comm->nalloc_int = over_alloc_dd((ncg_recv+rbuf[0])*DD_CGIBS);
+ srenew(comm->buf_int,comm->nalloc_int);
+ }
+
+ /* Communicate the charge group indices, sizes and flags */
+ dd_sendrecv_int(dd, d, dir,
+ comm->cggl_flag[cdd], sbuf[0]*DD_CGIBS,
+ comm->buf_int+ncg_recv*DD_CGIBS, rbuf[0]*DD_CGIBS);
+
+ nvs = ncg[cdd] + nat[cdd]*nvec;
+ i = rbuf[0] + rbuf[1] *nvec;
+ vec_rvec_check_alloc(&comm->vbuf,nvr+i);
+
+ /* Communicate cgcm and state */
+ dd_sendrecv_rvec(dd, d, dir,
+ comm->cgcm_state[cdd], nvs,
+ comm->vbuf.v+nvr, i);
+ ncg_recv += rbuf[0];
+ nat_recv += rbuf[1];
+ nvr += i;
+ }
+
+ /* Process the received charge groups */
+ buf_pos = 0;
+ for(cg=0; cg<ncg_recv; cg++)
+ {
+ flag = comm->buf_int[cg*DD_CGIBS+1];
+
+ if (dim >= npbcdim && dd->nc[dim] > 2)
+ {
+ /* No pbc in this dim and more than one domain boundary.
+ * We to a separate check if a charge did not move too far.
+ */
+ if (((flag & DD_FLAG_FW(d)) &&
+ comm->vbuf.v[buf_pos][d] > cell_x1[dim]) ||
+ ((flag & DD_FLAG_BW(d)) &&
+ comm->vbuf.v[buf_pos][d] < cell_x0[dim]))
+ {
+ cg_move_error(fplog,dd,step,cg,d,
+ (flag & DD_FLAG_FW(d)) ? 1 : 0,
+ FALSE,0,
+ comm->vbuf.v[buf_pos],
+ comm->vbuf.v[buf_pos],
+ comm->vbuf.v[buf_pos][d]);
+ }
+ }
+
+ mc = -1;
+ if (d < dd->ndim-1)
+ {
+ /* Check which direction this cg should go */
+ for(d2=d+1; (d2<dd->ndim && mc==-1); d2++)
+ {
+ if (dd->bGridJump)
+ {
+ /* The cell boundaries for dimension d2 are not equal
+ * for each cell row of the lower dimension(s),
+ * therefore we might need to redetermine where
+ * this cg should go.
+ */
+ dim2 = dd->dim[d2];
+ /* If this cg crosses the box boundary in dimension d2
+ * we can use the communicated flag, so we do not
+ * have to worry about pbc.
+ */
+ if (!((dd->ci[dim2] == dd->nc[dim2]-1 &&
+ (flag & DD_FLAG_FW(d2))) ||
+ (dd->ci[dim2] == 0 &&
+ (flag & DD_FLAG_BW(d2)))))
+ {
+ /* Clear the two flags for this dimension */
+ flag &= ~(DD_FLAG_FW(d2) | DD_FLAG_BW(d2));
+ /* Determine the location of this cg
+ * in lattice coordinates
+ */
+ pos_d = comm->vbuf.v[buf_pos][dim2];
+ if (tric_dir[dim2])
+ {
+ for(d3=dim2+1; d3<DIM; d3++)
+ {
+ pos_d +=
+ comm->vbuf.v[buf_pos][d3]*tcm[d3][dim2];
+ }
+ }
+ /* Check of we are not at the box edge.
+ * pbc is only handled in the first step above,
+ * but this check could move over pbc while
+ * the first step did not due to different rounding.
+ */
+ if (pos_d >= cell_x1[dim2] &&
+ dd->ci[dim2] != dd->nc[dim2]-1)
+ {
+ flag |= DD_FLAG_FW(d2);
+ }
+ else if (pos_d < cell_x0[dim2] &&
+ dd->ci[dim2] != 0)
+ {
+ flag |= DD_FLAG_BW(d2);
+ }
+ comm->buf_int[cg*DD_CGIBS+1] = flag;
+ }
+ }
+ /* Set to which neighboring cell this cg should go */
+ if (flag & DD_FLAG_FW(d2))
+ {
+ mc = d2*2;
+ }
+ else if (flag & DD_FLAG_BW(d2))
+ {
+ if (dd->nc[dd->dim[d2]] > 2)
+ {
+ mc = d2*2+1;
+ }
+ else
+ {
+ mc = d2*2;
+ }
+ }
+ }
+ }
+
+ nrcg = flag & DD_FLAG_NRCG;
+ if (mc == -1)
+ {
+ if (home_pos_cg+1 > dd->cg_nalloc)
+ {
+ dd->cg_nalloc = over_alloc_dd(home_pos_cg+1);
+ srenew(dd->index_gl,dd->cg_nalloc);
+ srenew(dd->cgindex,dd->cg_nalloc+1);
+ }
+ /* Set the global charge group index and size */
+ dd->index_gl[home_pos_cg] = comm->buf_int[cg*DD_CGIBS];
+ dd->cgindex[home_pos_cg+1] = dd->cgindex[home_pos_cg] + nrcg;
+ /* Copy the state from the buffer */
+ if (home_pos_cg >= fr->cg_nalloc)
+ {
+ dd_realloc_fr_cg(fr,home_pos_cg+1);
+ cg_cm = fr->cg_cm;
+ }
+ copy_rvec(comm->vbuf.v[buf_pos++],cg_cm[home_pos_cg]);
+ /* Set the cginfo */
+ fr->cginfo[home_pos_cg] = ddcginfo(cginfo_mb,
+ dd->index_gl[home_pos_cg]);
+ if (comm->bLocalCG)
+ {
+ comm->bLocalCG[dd->index_gl[home_pos_cg]] = TRUE;
+ }
+
+ if (home_pos_at+nrcg > state->nalloc)
+ {
+ dd_realloc_state(state,f,home_pos_at+nrcg);
+ }
+ for(i=0; i<nrcg; i++)
+ {
+ copy_rvec(comm->vbuf.v[buf_pos++],
+ state->x[home_pos_at+i]);
+ }
+ if (bV)
+ {
+ for(i=0; i<nrcg; i++)
+ {
+ copy_rvec(comm->vbuf.v[buf_pos++],
+ state->v[home_pos_at+i]);
+ }
+ }
+ if (bSDX)
+ {
+ for(i=0; i<nrcg; i++)
+ {
+ copy_rvec(comm->vbuf.v[buf_pos++],
+ state->sd_X[home_pos_at+i]);
+ }
+ }
+ if (bCGP)
+ {
+ for(i=0; i<nrcg; i++)
+ {
+ copy_rvec(comm->vbuf.v[buf_pos++],
+ state->cg_p[home_pos_at+i]);
+ }
+ }
+ home_pos_cg += 1;
+ home_pos_at += nrcg;
+ }
+ else
+ {
+ /* Reallocate the buffers if necessary */
+ if (ncg[mc]+1 > comm->cggl_flag_nalloc[mc])
+ {
+ comm->cggl_flag_nalloc[mc] = over_alloc_dd(ncg[mc]+1);
+ srenew(comm->cggl_flag[mc],comm->cggl_flag_nalloc[mc]*DD_CGIBS);
+ }
+ nvr = ncg[mc] + nat[mc]*nvec;
+ if (nvr + 1 + nrcg*nvec > comm->cgcm_state_nalloc[mc])
+ {
+ comm->cgcm_state_nalloc[mc] = over_alloc_dd(nvr + 1 + nrcg*nvec);
+ srenew(comm->cgcm_state[mc],comm->cgcm_state_nalloc[mc]);
+ }
+ /* Copy from the receive to the send buffers */
+ memcpy(comm->cggl_flag[mc] + ncg[mc]*DD_CGIBS,
+ comm->buf_int + cg*DD_CGIBS,
+ DD_CGIBS*sizeof(int));
+ memcpy(comm->cgcm_state[mc][nvr],
+ comm->vbuf.v[buf_pos],
+ (1+nrcg*nvec)*sizeof(rvec));
+ buf_pos += 1 + nrcg*nvec;
+ ncg[mc] += 1;
+ nat[mc] += nrcg;
+ }
+ }
+ }
+
+ /* With sorting (!bCompact) the indices are now only partially up to date
+ * and ncg_home and nat_home are not the real count, since there are
+ * "holes" in the arrays for the charge groups that moved to neighbors.
+ */
+ dd->ncg_home = home_pos_cg;
+ dd->nat_home = home_pos_at;
+
+ if (debug)
+ {
+ fprintf(debug,"Finished repartitioning\n");
+ }
+
+ return ncg_stay_home;
+}
+
+void dd_cycles_add(gmx_domdec_t *dd,float cycles,int ddCycl)
+{
+ dd->comm->cycl[ddCycl] += cycles;
+ dd->comm->cycl_n[ddCycl]++;
+ if (cycles > dd->comm->cycl_max[ddCycl])
+ {
+ dd->comm->cycl_max[ddCycl] = cycles;
+ }
+}
+
+static double force_flop_count(t_nrnb *nrnb)
+{
+ int i;
+ double sum;
+ const char *name;
+
+ sum = 0;
+ for(i=eNR_NBKERNEL010; i<eNR_NBKERNEL_FREE_ENERGY; i++)
+ {
+ /* To get closer to the real timings, we half the count
+ * for the normal loops and again half it for water loops.
+ */
+ name = nrnb_str(i);
+ if (strstr(name,"W3") != NULL || strstr(name,"W4") != NULL)
+ {
+ sum += nrnb->n[i]*0.25*cost_nrnb(i);
+ }
+ else
+ {
+ sum += nrnb->n[i]*0.50*cost_nrnb(i);
+ }
+ }
+ for(i=eNR_NBKERNEL_FREE_ENERGY; i<=eNR_NB14; i++)
+ {
+ name = nrnb_str(i);
+ if (strstr(name,"W3") != NULL || strstr(name,"W4") != NULL)
+ sum += nrnb->n[i]*cost_nrnb(i);
+ }
+ for(i=eNR_BONDS; i<=eNR_WALLS; i++)
+ {
+ sum += nrnb->n[i]*cost_nrnb(i);
+ }
+
+ return sum;
+}
+
+void dd_force_flop_start(gmx_domdec_t *dd,t_nrnb *nrnb)
+{
+ if (dd->comm->eFlop)
+ {
+ dd->comm->flop -= force_flop_count(nrnb);
+ }
+}
+void dd_force_flop_stop(gmx_domdec_t *dd,t_nrnb *nrnb)
+{
+ if (dd->comm->eFlop)
+ {
+ dd->comm->flop += force_flop_count(nrnb);
+ dd->comm->flop_n++;
+ }
+}
+
+static void clear_dd_cycle_counts(gmx_domdec_t *dd)
+{
+ int i;
+
+ for(i=0; i<ddCyclNr; i++)
+ {
+ dd->comm->cycl[i] = 0;
+ dd->comm->cycl_n[i] = 0;
+ dd->comm->cycl_max[i] = 0;
+ }
+ dd->comm->flop = 0;
+ dd->comm->flop_n = 0;
+}
+
+static void get_load_distribution(gmx_domdec_t *dd,gmx_wallcycle_t wcycle)
+{
+ gmx_domdec_comm_t *comm;
+ gmx_domdec_load_t *load;
+ gmx_domdec_root_t *root=NULL;
+ int d,dim,cid,i,pos;
+ float cell_frac=0,sbuf[DD_NLOAD_MAX];
+ gmx_bool bSepPME;
+
+ if (debug)
+ {
+ fprintf(debug,"get_load_distribution start\n");
+ }
+
+ wallcycle_start(wcycle,ewcDDCOMMLOAD);
+
+ comm = dd->comm;
+
+ bSepPME = (dd->pme_nodeid >= 0);
+
+ for(d=dd->ndim-1; d>=0; d--)
+ {
+ dim = dd->dim[d];
+ /* Check if we participate in the communication in this dimension */
+ if (d == dd->ndim-1 ||
+ (dd->ci[dd->dim[d+1]]==0 && dd->ci[dd->dim[dd->ndim-1]]==0))
+ {
+ load = &comm->load[d];
+ if (dd->bGridJump)
+ {
+ cell_frac = comm->cell_f1[d] - comm->cell_f0[d];
+ }
+ pos = 0;
+ if (d == dd->ndim-1)
+ {
+ sbuf[pos++] = dd_force_load(comm);
+ sbuf[pos++] = sbuf[0];
+ if (dd->bGridJump)
+ {
+ sbuf[pos++] = sbuf[0];
+ sbuf[pos++] = cell_frac;
+ if (d > 0)
+ {
+ sbuf[pos++] = comm->cell_f_max0[d];
+ sbuf[pos++] = comm->cell_f_min1[d];
+ }
+ }
+ if (bSepPME)
+ {
+ sbuf[pos++] = comm->cycl[ddCyclPPduringPME];
+ sbuf[pos++] = comm->cycl[ddCyclPME];
+ }
+ }
+ else
+ {
+ sbuf[pos++] = comm->load[d+1].sum;
+ sbuf[pos++] = comm->load[d+1].max;
+ if (dd->bGridJump)
+ {
+ sbuf[pos++] = comm->load[d+1].sum_m;
+ sbuf[pos++] = comm->load[d+1].cvol_min*cell_frac;
+ sbuf[pos++] = comm->load[d+1].flags;
+ if (d > 0)
+ {
+ sbuf[pos++] = comm->cell_f_max0[d];
+ sbuf[pos++] = comm->cell_f_min1[d];
+ }
+ }
+ if (bSepPME)
+ {
+ sbuf[pos++] = comm->load[d+1].mdf;
+ sbuf[pos++] = comm->load[d+1].pme;
+ }
+ }
+ load->nload = pos;
+ /* Communicate a row in DD direction d.
+ * The communicators are setup such that the root always has rank 0.
+ */
+#ifdef GMX_MPI
+ MPI_Gather(sbuf ,load->nload*sizeof(float),MPI_BYTE,
+ load->load,load->nload*sizeof(float),MPI_BYTE,
+ 0,comm->mpi_comm_load[d]);
+#endif
+ if (dd->ci[dim] == dd->master_ci[dim])
+ {
+ /* We are the root, process this row */
+ if (comm->bDynLoadBal)
+ {
+ root = comm->root[d];
+ }
+ load->sum = 0;
+ load->max = 0;
+ load->sum_m = 0;
+ load->cvol_min = 1;
+ load->flags = 0;
+ load->mdf = 0;
+ load->pme = 0;
+ pos = 0;
+ for(i=0; i<dd->nc[dim]; i++)
+ {
+ load->sum += load->load[pos++];
+ load->max = max(load->max,load->load[pos]);
+ pos++;
+ if (dd->bGridJump)
+ {
+ if (root->bLimited)
+ {
+ /* This direction could not be load balanced properly,
+ * therefore we need to use the maximum iso the average load.
+ */
+ load->sum_m = max(load->sum_m,load->load[pos]);
+ }
+ else
+ {
+ load->sum_m += load->load[pos];
+ }
+ pos++;
+ load->cvol_min = min(load->cvol_min,load->load[pos]);
+ pos++;
+ if (d < dd->ndim-1)
+ {
+ load->flags = (int)(load->load[pos++] + 0.5);
+ }
+ if (d > 0)
+ {
+ root->cell_f_max0[i] = load->load[pos++];
+ root->cell_f_min1[i] = load->load[pos++];
+ }
+ }
+ if (bSepPME)
+ {
+ load->mdf = max(load->mdf,load->load[pos]);
+ pos++;
+ load->pme = max(load->pme,load->load[pos]);
+ pos++;
+ }
+ }
+ if (comm->bDynLoadBal && root->bLimited)
+ {
+ load->sum_m *= dd->nc[dim];
+ load->flags |= (1<<d);
+ }
+ }
+ }
+ }
+
+ if (DDMASTER(dd))
+ {
+ comm->nload += dd_load_count(comm);
+ comm->load_step += comm->cycl[ddCyclStep];
+ comm->load_sum += comm->load[0].sum;
+ comm->load_max += comm->load[0].max;
+ if (comm->bDynLoadBal)
+ {
+ for(d=0; d<dd->ndim; d++)
+ {
+ if (comm->load[0].flags & (1<<d))
+ {
+ comm->load_lim[d]++;
+ }
+ }
+ }
+ if (bSepPME)
+ {
+ comm->load_mdf += comm->load[0].mdf;
+ comm->load_pme += comm->load[0].pme;
+ }
+ }
+
+ wallcycle_stop(wcycle,ewcDDCOMMLOAD);
+
+ if (debug)
+ {
+ fprintf(debug,"get_load_distribution finished\n");
+ }
+}
+
+static float dd_force_imb_perf_loss(gmx_domdec_t *dd)
+{
+ /* Return the relative performance loss on the total run time
+ * due to the force calculation load imbalance.
+ */
+ if (dd->comm->nload > 0)
+ {
+ return
+ (dd->comm->load_max*dd->nnodes - dd->comm->load_sum)/
+ (dd->comm->load_step*dd->nnodes);
+ }
+ else
+ {
+ return 0;
+ }
+}
+
+static void print_dd_load_av(FILE *fplog,gmx_domdec_t *dd)
+{
+ char buf[STRLEN];
+ int npp,npme,nnodes,d,limp;
+ float imbal,pme_f_ratio,lossf,lossp=0;
+ gmx_bool bLim;
+ gmx_domdec_comm_t *comm;
+
+ comm = dd->comm;
+ if (DDMASTER(dd) && comm->nload > 0)
+ {
+ npp = dd->nnodes;
+ npme = (dd->pme_nodeid >= 0) ? comm->npmenodes : 0;
+ nnodes = npp + npme;
+ imbal = comm->load_max*npp/comm->load_sum - 1;
+ lossf = dd_force_imb_perf_loss(dd);
+ sprintf(buf," Average load imbalance: %.1f %%\n",imbal*100);
+ fprintf(fplog,"%s",buf);
+ fprintf(stderr,"\n");
+ fprintf(stderr,"%s",buf);
+ sprintf(buf," Part of the total run time spent waiting due to load imbalance: %.1f %%\n",lossf*100);
+ fprintf(fplog,"%s",buf);
+ fprintf(stderr,"%s",buf);
+ bLim = FALSE;
+ if (comm->bDynLoadBal)
+ {
+ sprintf(buf," Steps where the load balancing was limited by -rdd, -rcon and/or -dds:");
+ for(d=0; d<dd->ndim; d++)
+ {
+ limp = (200*comm->load_lim[d]+1)/(2*comm->nload);
+ sprintf(buf+strlen(buf)," %c %d %%",dim2char(dd->dim[d]),limp);
+ if (limp >= 50)
+ {
+ bLim = TRUE;
+ }
+ }
+ sprintf(buf+strlen(buf),"\n");
+ fprintf(fplog,"%s",buf);
+ fprintf(stderr,"%s",buf);
+ }
+ if (npme > 0)
+ {
+ pme_f_ratio = comm->load_pme/comm->load_mdf;
+ lossp = (comm->load_pme -comm->load_mdf)/comm->load_step;
+ if (lossp <= 0)
+ {
+ lossp *= (float)npme/(float)nnodes;
+ }
+ else
+ {
+ lossp *= (float)npp/(float)nnodes;
+ }
+ sprintf(buf," Average PME mesh/force load: %5.3f\n",pme_f_ratio);
+ fprintf(fplog,"%s",buf);
+ fprintf(stderr,"%s",buf);
+ sprintf(buf," Part of the total run time spent waiting due to PP/PME imbalance: %.1f %%\n",fabs(lossp)*100);
+ fprintf(fplog,"%s",buf);
+ fprintf(stderr,"%s",buf);
+ }
+ fprintf(fplog,"\n");
+ fprintf(stderr,"\n");
+
+ if (lossf >= DD_PERF_LOSS)
+ {
+ sprintf(buf,
+ "NOTE: %.1f %% performance was lost due to load imbalance\n"
+ " in the domain decomposition.\n",lossf*100);
+ if (!comm->bDynLoadBal)
+ {
+ sprintf(buf+strlen(buf)," You might want to use dynamic load balancing (option -dlb.)\n");
+ }
+ else if (bLim)
+ {
+ sprintf(buf+strlen(buf)," You might want to decrease the cell size limit (options -rdd, -rcon and/or -dds).\n");
+ }
+ fprintf(fplog,"%s\n",buf);
+ fprintf(stderr,"%s\n",buf);
+ }
+ if (npme > 0 && fabs(lossp) >= DD_PERF_LOSS)
+ {
+ sprintf(buf,
+ "NOTE: %.1f %% performance was lost because the PME nodes\n"
+ " had %s work to do than the PP nodes.\n"
+ " You might want to %s the number of PME nodes\n"
+ " or %s the cut-off and the grid spacing.\n",
+ fabs(lossp*100),
+ (lossp < 0) ? "less" : "more",
+ (lossp < 0) ? "decrease" : "increase",
+ (lossp < 0) ? "decrease" : "increase");
+ fprintf(fplog,"%s\n",buf);
+ fprintf(stderr,"%s\n",buf);
+ }
+ }
+}
+
+static float dd_vol_min(gmx_domdec_t *dd)
+{
+ return dd->comm->load[0].cvol_min*dd->nnodes;
+}
+
+static gmx_bool dd_load_flags(gmx_domdec_t *dd)
+{
+ return dd->comm->load[0].flags;
+}
+
+static float dd_f_imbal(gmx_domdec_t *dd)
+{
+ return dd->comm->load[0].max*dd->nnodes/dd->comm->load[0].sum - 1;
+}
+
+static float dd_pme_f_ratio(gmx_domdec_t *dd)
+{
+ return dd->comm->load[0].pme/dd->comm->load[0].mdf;
+}
+
+static void dd_print_load(FILE *fplog,gmx_domdec_t *dd,gmx_large_int_t step)
+{
+ int flags,d;
+ char buf[22];
+
+ flags = dd_load_flags(dd);
+ if (flags)
+ {
+ fprintf(fplog,
+ "DD load balancing is limited by minimum cell size in dimension");
+ for(d=0; d<dd->ndim; d++)
+ {
+ if (flags & (1<<d))
+ {
+ fprintf(fplog," %c",dim2char(dd->dim[d]));
+ }
+ }
+ fprintf(fplog,"\n");
+ }
+ fprintf(fplog,"DD step %s",gmx_step_str(step,buf));
+ if (dd->comm->bDynLoadBal)
+ {
+ fprintf(fplog," vol min/aver %5.3f%c",
+ dd_vol_min(dd),flags ? '!' : ' ');
+ }
+ fprintf(fplog," load imb.: force %4.1f%%",dd_f_imbal(dd)*100);
+ if (dd->comm->cycl_n[ddCyclPME])
+ {
+ fprintf(fplog," pme mesh/force %5.3f",dd_pme_f_ratio(dd));
+ }
+ fprintf(fplog,"\n\n");
+}
+
+static void dd_print_load_verbose(gmx_domdec_t *dd)
+{
+ if (dd->comm->bDynLoadBal)
+ {
+ fprintf(stderr,"vol %4.2f%c ",
+ dd_vol_min(dd),dd_load_flags(dd) ? '!' : ' ');
+ }
+ fprintf(stderr,"imb F %2d%% ",(int)(dd_f_imbal(dd)*100+0.5));
+ if (dd->comm->cycl_n[ddCyclPME])
+ {
+ fprintf(stderr,"pme/F %4.2f ",dd_pme_f_ratio(dd));
+ }
+}
+
+#ifdef GMX_MPI
+static void make_load_communicator(gmx_domdec_t *dd,MPI_Group g_all,
+ int dim_ind,ivec loc)
+{
- /* Here we create a new group, that does not necessarily
- * include our process. But MPI_Comm_create needs to be
- * called by all the processes in the original communicator.
- * Calling MPI_Group_free afterwards gives errors, so I assume
- * also the group is needed by all processes. (B. Hess)
- */
- MPI_Group_incl(g_all,dd->nc[dim],rank,&g_row);
++ MPI_Group g_row = MPI_GROUP_EMPTY;
+ MPI_Comm c_row;
+ int dim,i,*rank;
+ ivec loc_c;
+ gmx_domdec_root_t *root;
++ gmx_bool bPartOfGroup = FALSE;
+
+ dim = dd->dim[dim_ind];
+ copy_ivec(loc,loc_c);
+ snew(rank,dd->nc[dim]);
+ for(i=0; i<dd->nc[dim]; i++)
+ {
+ loc_c[dim] = i;
+ rank[i] = dd_index(dd->nc,loc_c);
++ if (rank[i] == dd->rank)
++ {
++ /* This process is part of the group */
++ bPartOfGroup = TRUE;
++ }
++ }
++ if (bPartOfGroup)
++ {
++ MPI_Group_incl(g_all,dd->nc[dim],rank,&g_row);
+ }
- if (c_row != MPI_COMM_NULL)
+ MPI_Comm_create(dd->mpi_comm_all,g_row,&c_row);
- /* This process is part of the group */
++ if (bPartOfGroup)
+ {
- "The number of separate PME node (%d) is larger than the number of PP nodes (%d), this is not supported.",cr->npmenodes,dd->nnodes);
+ dd->comm->mpi_comm_load[dim_ind] = c_row;
+ if (dd->comm->eDLB != edlbNO)
+ {
+ if (dd->ci[dim] == dd->master_ci[dim])
+ {
+ /* This is the root process of this row */
+ snew(dd->comm->root[dim_ind],1);
+ root = dd->comm->root[dim_ind];
+ snew(root->cell_f,DD_CELL_F_SIZE(dd,dim_ind));
+ snew(root->old_cell_f,dd->nc[dim]+1);
+ snew(root->bCellMin,dd->nc[dim]);
+ if (dim_ind > 0)
+ {
+ snew(root->cell_f_max0,dd->nc[dim]);
+ snew(root->cell_f_min1,dd->nc[dim]);
+ snew(root->bound_min,dd->nc[dim]);
+ snew(root->bound_max,dd->nc[dim]);
+ }
+ snew(root->buf_ncd,dd->nc[dim]);
+ }
+ else
+ {
+ /* This is not a root process, we only need to receive cell_f */
+ snew(dd->comm->cell_f_row,DD_CELL_F_SIZE(dd,dim_ind));
+ }
+ }
+ if (dd->ci[dim] == dd->master_ci[dim])
+ {
+ snew(dd->comm->load[dim_ind].load,dd->nc[dim]*DD_NLOAD_MAX);
+ }
+ }
+ sfree(rank);
+}
+#endif
+
+static void make_load_communicators(gmx_domdec_t *dd)
+{
+#ifdef GMX_MPI
+ MPI_Group g_all;
+ int dim0,dim1,i,j;
+ ivec loc;
+
+ if (debug)
+ fprintf(debug,"Making load communicators\n");
+
+ MPI_Comm_group(dd->mpi_comm_all,&g_all);
+
+ snew(dd->comm->load,dd->ndim);
+ snew(dd->comm->mpi_comm_load,dd->ndim);
+
+ clear_ivec(loc);
+ make_load_communicator(dd,g_all,0,loc);
+ if (dd->ndim > 1) {
+ dim0 = dd->dim[0];
+ for(i=0; i<dd->nc[dim0]; i++) {
+ loc[dim0] = i;
+ make_load_communicator(dd,g_all,1,loc);
+ }
+ }
+ if (dd->ndim > 2) {
+ dim0 = dd->dim[0];
+ for(i=0; i<dd->nc[dim0]; i++) {
+ loc[dim0] = i;
+ dim1 = dd->dim[1];
+ for(j=0; j<dd->nc[dim1]; j++) {
+ loc[dim1] = j;
+ make_load_communicator(dd,g_all,2,loc);
+ }
+ }
+ }
+
+ MPI_Group_free(&g_all);
+
+ if (debug)
+ fprintf(debug,"Finished making load communicators\n");
+#endif
+}
+
+void setup_dd_grid(FILE *fplog,gmx_domdec_t *dd)
+{
+ gmx_bool bZYX;
+ int d,dim,i,j,m;
+ ivec tmp,s;
+ int nzone,nzonep;
+ ivec dd_zp[DD_MAXIZONE];
+ gmx_domdec_zones_t *zones;
+ gmx_domdec_ns_ranges_t *izone;
+
+ for(d=0; d<dd->ndim; d++)
+ {
+ dim = dd->dim[d];
+ copy_ivec(dd->ci,tmp);
+ tmp[dim] = (tmp[dim] + 1) % dd->nc[dim];
+ dd->neighbor[d][0] = ddcoord2ddnodeid(dd,tmp);
+ copy_ivec(dd->ci,tmp);
+ tmp[dim] = (tmp[dim] - 1 + dd->nc[dim]) % dd->nc[dim];
+ dd->neighbor[d][1] = ddcoord2ddnodeid(dd,tmp);
+ if (debug)
+ {
+ fprintf(debug,"DD rank %d neighbor ranks in dir %d are + %d - %d\n",
+ dd->rank,dim,
+ dd->neighbor[d][0],
+ dd->neighbor[d][1]);
+ }
+ }
+
+ if (DDMASTER(dd))
+ {
+ fprintf(stderr,"Making %dD domain decomposition %d x %d x %d\n",
+ dd->ndim,dd->nc[XX],dd->nc[YY],dd->nc[ZZ]);
+ }
+ if (fplog)
+ {
+ fprintf(fplog,"\nMaking %dD domain decomposition grid %d x %d x %d, home cell index %d %d %d\n\n",
+ dd->ndim,
+ dd->nc[XX],dd->nc[YY],dd->nc[ZZ],
+ dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
+ }
+ switch (dd->ndim)
+ {
+ case 3:
+ nzone = dd_z3n;
+ nzonep = dd_zp3n;
+ for(i=0; i<nzonep; i++)
+ {
+ copy_ivec(dd_zp3[i],dd_zp[i]);
+ }
+ break;
+ case 2:
+ nzone = dd_z2n;
+ nzonep = dd_zp2n;
+ for(i=0; i<nzonep; i++)
+ {
+ copy_ivec(dd_zp2[i],dd_zp[i]);
+ }
+ break;
+ case 1:
+ nzone = dd_z1n;
+ nzonep = dd_zp1n;
+ for(i=0; i<nzonep; i++)
+ {
+ copy_ivec(dd_zp1[i],dd_zp[i]);
+ }
+ break;
+ default:
+ gmx_fatal(FARGS,"Can only do 1, 2 or 3D domain decomposition");
+ nzone = 0;
+ nzonep = 0;
+ }
+
+ zones = &dd->comm->zones;
+
+ for(i=0; i<nzone; i++)
+ {
+ m = 0;
+ clear_ivec(zones->shift[i]);
+ for(d=0; d<dd->ndim; d++)
+ {
+ zones->shift[i][dd->dim[d]] = dd_zo[i][m++];
+ }
+ }
+
+ zones->n = nzone;
+ for(i=0; i<nzone; i++)
+ {
+ for(d=0; d<DIM; d++)
+ {
+ s[d] = dd->ci[d] - zones->shift[i][d];
+ if (s[d] < 0)
+ {
+ s[d] += dd->nc[d];
+ }
+ else if (s[d] >= dd->nc[d])
+ {
+ s[d] -= dd->nc[d];
+ }
+ }
+ }
+ zones->nizone = nzonep;
+ for(i=0; i<zones->nizone; i++)
+ {
+ if (dd_zp[i][0] != i)
+ {
+ gmx_fatal(FARGS,"Internal inconsistency in the dd grid setup");
+ }
+ izone = &zones->izone[i];
+ izone->j0 = dd_zp[i][1];
+ izone->j1 = dd_zp[i][2];
+ for(dim=0; dim<DIM; dim++)
+ {
+ if (dd->nc[dim] == 1)
+ {
+ /* All shifts should be allowed */
+ izone->shift0[dim] = -1;
+ izone->shift1[dim] = 1;
+ }
+ else
+ {
+ /*
+ izone->shift0[d] = 0;
+ izone->shift1[d] = 0;
+ for(j=izone->j0; j<izone->j1; j++) {
+ if (dd->shift[j][d] > dd->shift[i][d])
+ izone->shift0[d] = -1;
+ if (dd->shift[j][d] < dd->shift[i][d])
+ izone->shift1[d] = 1;
+ }
+ */
+
+ int shift_diff;
+
+ /* Assume the shift are not more than 1 cell */
+ izone->shift0[dim] = 1;
+ izone->shift1[dim] = -1;
+ for(j=izone->j0; j<izone->j1; j++)
+ {
+ shift_diff = zones->shift[j][dim] - zones->shift[i][dim];
+ if (shift_diff < izone->shift0[dim])
+ {
+ izone->shift0[dim] = shift_diff;
+ }
+ if (shift_diff > izone->shift1[dim])
+ {
+ izone->shift1[dim] = shift_diff;
+ }
+ }
+ }
+ }
+ }
+
+ if (dd->comm->eDLB != edlbNO)
+ {
+ snew(dd->comm->root,dd->ndim);
+ }
+
+ if (dd->comm->bRecordLoad)
+ {
+ make_load_communicators(dd);
+ }
+}
+
+static void make_pp_communicator(FILE *fplog,t_commrec *cr,int reorder)
+{
+ gmx_domdec_t *dd;
+ gmx_domdec_comm_t *comm;
+ int i,rank,*buf;
+ ivec periods;
+#ifdef GMX_MPI
+ MPI_Comm comm_cart;
+#endif
+
+ dd = cr->dd;
+ comm = dd->comm;
+
+#ifdef GMX_MPI
+ if (comm->bCartesianPP)
+ {
+ /* Set up cartesian communication for the particle-particle part */
+ if (fplog)
+ {
+ fprintf(fplog,"Will use a Cartesian communicator: %d x %d x %d\n",
+ dd->nc[XX],dd->nc[YY],dd->nc[ZZ]);
+ }
+
+ for(i=0; i<DIM; i++)
+ {
+ periods[i] = TRUE;
+ }
+ MPI_Cart_create(cr->mpi_comm_mygroup,DIM,dd->nc,periods,reorder,
+ &comm_cart);
+ /* We overwrite the old communicator with the new cartesian one */
+ cr->mpi_comm_mygroup = comm_cart;
+ }
+
+ dd->mpi_comm_all = cr->mpi_comm_mygroup;
+ MPI_Comm_rank(dd->mpi_comm_all,&dd->rank);
+
+ if (comm->bCartesianPP_PME)
+ {
+ /* Since we want to use the original cartesian setup for sim,
+ * and not the one after split, we need to make an index.
+ */
+ snew(comm->ddindex2ddnodeid,dd->nnodes);
+ comm->ddindex2ddnodeid[dd_index(dd->nc,dd->ci)] = dd->rank;
+ gmx_sumi(dd->nnodes,comm->ddindex2ddnodeid,cr);
+ /* Get the rank of the DD master,
+ * above we made sure that the master node is a PP node.
+ */
+ if (MASTER(cr))
+ {
+ rank = dd->rank;
+ }
+ else
+ {
+ rank = 0;
+ }
+ MPI_Allreduce(&rank,&dd->masterrank,1,MPI_INT,MPI_SUM,dd->mpi_comm_all);
+ }
+ else if (comm->bCartesianPP)
+ {
+ if (cr->npmenodes == 0)
+ {
+ /* The PP communicator is also
+ * the communicator for this simulation
+ */
+ cr->mpi_comm_mysim = cr->mpi_comm_mygroup;
+ }
+ cr->nodeid = dd->rank;
+
+ MPI_Cart_coords(dd->mpi_comm_all,dd->rank,DIM,dd->ci);
+
+ /* We need to make an index to go from the coordinates
+ * to the nodeid of this simulation.
+ */
+ snew(comm->ddindex2simnodeid,dd->nnodes);
+ snew(buf,dd->nnodes);
+ if (cr->duty & DUTY_PP)
+ {
+ buf[dd_index(dd->nc,dd->ci)] = cr->sim_nodeid;
+ }
+ /* Communicate the ddindex to simulation nodeid index */
+ MPI_Allreduce(buf,comm->ddindex2simnodeid,dd->nnodes,MPI_INT,MPI_SUM,
+ cr->mpi_comm_mysim);
+ sfree(buf);
+
+ /* Determine the master coordinates and rank.
+ * The DD master should be the same node as the master of this sim.
+ */
+ for(i=0; i<dd->nnodes; i++)
+ {
+ if (comm->ddindex2simnodeid[i] == 0)
+ {
+ ddindex2xyz(dd->nc,i,dd->master_ci);
+ MPI_Cart_rank(dd->mpi_comm_all,dd->master_ci,&dd->masterrank);
+ }
+ }
+ if (debug)
+ {
+ fprintf(debug,"The master rank is %d\n",dd->masterrank);
+ }
+ }
+ else
+ {
+ /* No Cartesian communicators */
+ /* We use the rank in dd->comm->all as DD index */
+ ddindex2xyz(dd->nc,dd->rank,dd->ci);
+ /* The simulation master nodeid is 0, so the DD master rank is also 0 */
+ dd->masterrank = 0;
+ clear_ivec(dd->master_ci);
+ }
+#endif
+
+ if (fplog)
+ {
+ fprintf(fplog,
+ "Domain decomposition nodeid %d, coordinates %d %d %d\n\n",
+ dd->rank,dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
+ }
+ if (debug)
+ {
+ fprintf(debug,
+ "Domain decomposition nodeid %d, coordinates %d %d %d\n\n",
+ dd->rank,dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
+ }
+}
+
+static void receive_ddindex2simnodeid(t_commrec *cr)
+{
+ gmx_domdec_t *dd;
+
+ gmx_domdec_comm_t *comm;
+ int *buf;
+
+ dd = cr->dd;
+ comm = dd->comm;
+
+#ifdef GMX_MPI
+ if (!comm->bCartesianPP_PME && comm->bCartesianPP)
+ {
+ snew(comm->ddindex2simnodeid,dd->nnodes);
+ snew(buf,dd->nnodes);
+ if (cr->duty & DUTY_PP)
+ {
+ buf[dd_index(dd->nc,dd->ci)] = cr->sim_nodeid;
+ }
+#ifdef GMX_MPI
+ /* Communicate the ddindex to simulation nodeid index */
+ MPI_Allreduce(buf,comm->ddindex2simnodeid,dd->nnodes,MPI_INT,MPI_SUM,
+ cr->mpi_comm_mysim);
+#endif
+ sfree(buf);
+ }
+#endif
+}
+
+static gmx_domdec_master_t *init_gmx_domdec_master_t(gmx_domdec_t *dd,
+ int ncg,int natoms)
+{
+ gmx_domdec_master_t *ma;
+ int i;
+
+ snew(ma,1);
+
+ snew(ma->ncg,dd->nnodes);
+ snew(ma->index,dd->nnodes+1);
+ snew(ma->cg,ncg);
+ snew(ma->nat,dd->nnodes);
+ snew(ma->ibuf,dd->nnodes*2);
+ snew(ma->cell_x,DIM);
+ for(i=0; i<DIM; i++)
+ {
+ snew(ma->cell_x[i],dd->nc[i]+1);
+ }
+
+ if (dd->nnodes <= GMX_DD_NNODES_SENDRECV)
+ {
+ ma->vbuf = NULL;
+ }
+ else
+ {
+ snew(ma->vbuf,natoms);
+ }
+
+ return ma;
+}
+
+static void split_communicator(FILE *fplog,t_commrec *cr,int dd_node_order,
+ int reorder)
+{
+ gmx_domdec_t *dd;
+ gmx_domdec_comm_t *comm;
+ int i,rank;
+ gmx_bool bDiv[DIM];
+ ivec periods;
+#ifdef GMX_MPI
+ MPI_Comm comm_cart;
+#endif
+
+ dd = cr->dd;
+ comm = dd->comm;
+
+ if (comm->bCartesianPP)
+ {
+ for(i=1; i<DIM; i++)
+ {
+ bDiv[i] = ((cr->npmenodes*dd->nc[i]) % (dd->nnodes) == 0);
+ }
+ if (bDiv[YY] || bDiv[ZZ])
+ {
+ comm->bCartesianPP_PME = TRUE;
+ /* If we have 2D PME decomposition, which is always in x+y,
+ * we stack the PME only nodes in z.
+ * Otherwise we choose the direction that provides the thinnest slab
+ * of PME only nodes as this will have the least effect
+ * on the PP communication.
+ * But for the PME communication the opposite might be better.
+ */
+ if (bDiv[ZZ] && (comm->npmenodes_y > 1 ||
+ !bDiv[YY] ||
+ dd->nc[YY] > dd->nc[ZZ]))
+ {
+ comm->cartpmedim = ZZ;
+ }
+ else
+ {
+ comm->cartpmedim = YY;
+ }
+ comm->ntot[comm->cartpmedim]
+ += (cr->npmenodes*dd->nc[comm->cartpmedim])/dd->nnodes;
+ }
+ else if (fplog)
+ {
+ fprintf(fplog,"#pmenodes (%d) is not a multiple of nx*ny (%d*%d) or nx*nz (%d*%d)\n",cr->npmenodes,dd->nc[XX],dd->nc[YY],dd->nc[XX],dd->nc[ZZ]);
+ fprintf(fplog,
+ "Will not use a Cartesian communicator for PP <-> PME\n\n");
+ }
+ }
+
+#ifdef GMX_MPI
+ if (comm->bCartesianPP_PME)
+ {
+ if (fplog)
+ {
+ fprintf(fplog,"Will use a Cartesian communicator for PP <-> PME: %d x %d x %d\n",comm->ntot[XX],comm->ntot[YY],comm->ntot[ZZ]);
+ }
+
+ for(i=0; i<DIM; i++)
+ {
+ periods[i] = TRUE;
+ }
+ MPI_Cart_create(cr->mpi_comm_mysim,DIM,comm->ntot,periods,reorder,
+ &comm_cart);
+
+ MPI_Comm_rank(comm_cart,&rank);
+ if (MASTERNODE(cr) && rank != 0)
+ {
+ gmx_fatal(FARGS,"MPI rank 0 was renumbered by MPI_Cart_create, we do not allow this");
+ }
+
+ /* With this assigment we loose the link to the original communicator
+ * which will usually be MPI_COMM_WORLD, unless have multisim.
+ */
+ cr->mpi_comm_mysim = comm_cart;
+ cr->sim_nodeid = rank;
+
+ MPI_Cart_coords(cr->mpi_comm_mysim,cr->sim_nodeid,DIM,dd->ci);
+
+ if (fplog)
+ {
+ fprintf(fplog,"Cartesian nodeid %d, coordinates %d %d %d\n\n",
+ cr->sim_nodeid,dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
+ }
+
+ if (dd->ci[comm->cartpmedim] < dd->nc[comm->cartpmedim])
+ {
+ cr->duty = DUTY_PP;
+ }
+ if (cr->npmenodes == 0 ||
+ dd->ci[comm->cartpmedim] >= dd->nc[comm->cartpmedim])
+ {
+ cr->duty = DUTY_PME;
+ }
+
+ /* Split the sim communicator into PP and PME only nodes */
+ MPI_Comm_split(cr->mpi_comm_mysim,
+ cr->duty,
+ dd_index(comm->ntot,dd->ci),
+ &cr->mpi_comm_mygroup);
+ }
+ else
+ {
+ switch (dd_node_order)
+ {
+ case ddnoPP_PME:
+ if (fplog)
+ {
+ fprintf(fplog,"Order of the nodes: PP first, PME last\n");
+ }
+ break;
+ case ddnoINTERLEAVE:
+ /* Interleave the PP-only and PME-only nodes,
+ * as on clusters with dual-core machines this will double
+ * the communication bandwidth of the PME processes
+ * and thus speed up the PP <-> PME and inter PME communication.
+ */
+ if (fplog)
+ {
+ fprintf(fplog,"Interleaving PP and PME nodes\n");
+ }
+ comm->pmenodes = dd_pmenodes(cr);
+ break;
+ case ddnoCARTESIAN:
+ break;
+ default:
+ gmx_fatal(FARGS,"Unknown dd_node_order=%d",dd_node_order);
+ }
+
+ if (dd_simnode2pmenode(cr,cr->sim_nodeid) == -1)
+ {
+ cr->duty = DUTY_PME;
+ }
+ else
+ {
+ cr->duty = DUTY_PP;
+ }
+
+ /* Split the sim communicator into PP and PME only nodes */
+ MPI_Comm_split(cr->mpi_comm_mysim,
+ cr->duty,
+ cr->nodeid,
+ &cr->mpi_comm_mygroup);
+ MPI_Comm_rank(cr->mpi_comm_mygroup,&cr->nodeid);
+ }
+#endif
+
+ if (fplog)
+ {
+ fprintf(fplog,"This is a %s only node\n\n",
+ (cr->duty & DUTY_PP) ? "particle-particle" : "PME-mesh");
+ }
+}
+
+void make_dd_communicators(FILE *fplog,t_commrec *cr,int dd_node_order)
+{
+ gmx_domdec_t *dd;
+ gmx_domdec_comm_t *comm;
+ int CartReorder;
+
+ dd = cr->dd;
+ comm = dd->comm;
+
+ copy_ivec(dd->nc,comm->ntot);
+
+ comm->bCartesianPP = (dd_node_order == ddnoCARTESIAN);
+ comm->bCartesianPP_PME = FALSE;
+
+ /* Reorder the nodes by default. This might change the MPI ranks.
+ * Real reordering is only supported on very few architectures,
+ * Blue Gene is one of them.
+ */
+ CartReorder = (getenv("GMX_NO_CART_REORDER") == NULL);
+
+ if (cr->npmenodes > 0)
+ {
+ /* Split the communicator into a PP and PME part */
+ split_communicator(fplog,cr,dd_node_order,CartReorder);
+ if (comm->bCartesianPP_PME)
+ {
+ /* We (possibly) reordered the nodes in split_communicator,
+ * so it is no longer required in make_pp_communicator.
+ */
+ CartReorder = FALSE;
+ }
+ }
+ else
+ {
+ /* All nodes do PP and PME */
+#ifdef GMX_MPI
+ /* We do not require separate communicators */
+ cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
+#endif
+ }
+
+ if (cr->duty & DUTY_PP)
+ {
+ /* Copy or make a new PP communicator */
+ make_pp_communicator(fplog,cr,CartReorder);
+ }
+ else
+ {
+ receive_ddindex2simnodeid(cr);
+ }
+
+ if (!(cr->duty & DUTY_PME))
+ {
+ /* Set up the commnuication to our PME node */
+ dd->pme_nodeid = dd_simnode2pmenode(cr,cr->sim_nodeid);
+ dd->pme_receive_vir_ener = receive_vir_ener(cr);
+ if (debug)
+ {
+ fprintf(debug,"My pme_nodeid %d receive ener %d\n",
+ dd->pme_nodeid,dd->pme_receive_vir_ener);
+ }
+ }
+ else
+ {
+ dd->pme_nodeid = -1;
+ }
+
+ if (DDMASTER(dd))
+ {
+ dd->ma = init_gmx_domdec_master_t(dd,
+ comm->cgs_gl.nr,
+ comm->cgs_gl.index[comm->cgs_gl.nr]);
+ }
+}
+
+static real *get_slb_frac(FILE *fplog,const char *dir,int nc,const char *size_string)
+{
+ real *slb_frac,tot;
+ int i,n;
+ double dbl;
+
+ slb_frac = NULL;
+ if (nc > 1 && size_string != NULL)
+ {
+ if (fplog)
+ {
+ fprintf(fplog,"Using static load balancing for the %s direction\n",
+ dir);
+ }
+ snew(slb_frac,nc);
+ tot = 0;
+ for (i=0; i<nc; i++)
+ {
+ dbl = 0;
+ sscanf(size_string,"%lf%n",&dbl,&n);
+ if (dbl == 0)
+ {
+ gmx_fatal(FARGS,"Incorrect or not enough DD cell size entries for direction %s: '%s'",dir,size_string);
+ }
+ slb_frac[i] = dbl;
+ size_string += n;
+ tot += slb_frac[i];
+ }
+ /* Normalize */
+ if (fplog)
+ {
+ fprintf(fplog,"Relative cell sizes:");
+ }
+ for (i=0; i<nc; i++)
+ {
+ slb_frac[i] /= tot;
+ if (fplog)
+ {
+ fprintf(fplog," %5.3f",slb_frac[i]);
+ }
+ }
+ if (fplog)
+ {
+ fprintf(fplog,"\n");
+ }
+ }
+
+ return slb_frac;
+}
+
+static int multi_body_bondeds_count(gmx_mtop_t *mtop)
+{
+ int n,nmol,ftype;
+ gmx_mtop_ilistloop_t iloop;
+ t_ilist *il;
+
+ n = 0;
+ iloop = gmx_mtop_ilistloop_init(mtop);
+ while (gmx_mtop_ilistloop_next(iloop,&il,&nmol))
+ {
+ for(ftype=0; ftype<F_NRE; ftype++)
+ {
+ if ((interaction_function[ftype].flags & IF_BOND) &&
+ NRAL(ftype) > 2)
+ {
+ n += nmol*il[ftype].nr/(1 + NRAL(ftype));
+ }
+ }
+ }
+
+ return n;
+}
+
+static int dd_nst_env(FILE *fplog,const char *env_var,int def)
+{
+ char *val;
+ int nst;
+
+ nst = def;
+ val = getenv(env_var);
+ if (val)
+ {
+ if (sscanf(val,"%d",&nst) <= 0)
+ {
+ nst = 1;
+ }
+ if (fplog)
+ {
+ fprintf(fplog,"Found env.var. %s = %s, using value %d\n",
+ env_var,val,nst);
+ }
+ }
+
+ return nst;
+}
+
+static void dd_warning(t_commrec *cr,FILE *fplog,const char *warn_string)
+{
+ if (MASTER(cr))
+ {
+ fprintf(stderr,"\n%s\n",warn_string);
+ }
+ if (fplog)
+ {
+ fprintf(fplog,"\n%s\n",warn_string);
+ }
+}
+
+static void check_dd_restrictions(t_commrec *cr,gmx_domdec_t *dd,
+ t_inputrec *ir,FILE *fplog)
+{
+ if (ir->ePBC == epbcSCREW &&
+ (dd->nc[XX] == 1 || dd->nc[YY] > 1 || dd->nc[ZZ] > 1))
+ {
+ gmx_fatal(FARGS,"With pbc=%s can only do domain decomposition in the x-direction",epbc_names[ir->ePBC]);
+ }
+
+ if (ir->ns_type == ensSIMPLE)
+ {
+ gmx_fatal(FARGS,"Domain decomposition does not support simple neighbor searching, use grid searching or use particle decomposition");
+ }
+
+ if (ir->nstlist == 0)
+ {
+ gmx_fatal(FARGS,"Domain decomposition does not work with nstlist=0");
+ }
+
+ if (ir->comm_mode == ecmANGULAR && ir->ePBC != epbcNONE)
+ {
+ dd_warning(cr,fplog,"comm-mode angular will give incorrect results when the comm group partially crosses a periodic boundary");
+ }
+}
+
+static real average_cellsize_min(gmx_domdec_t *dd,gmx_ddbox_t *ddbox)
+{
+ int di,d;
+ real r;
+
+ r = ddbox->box_size[XX];
+ for(di=0; di<dd->ndim; di++)
+ {
+ d = dd->dim[di];
+ /* Check using the initial average cell size */
+ r = min(r,ddbox->box_size[d]*ddbox->skew_fac[d]/dd->nc[d]);
+ }
+
+ return r;
+}
+
+static int check_dlb_support(FILE *fplog,t_commrec *cr,
+ const char *dlb_opt,gmx_bool bRecordLoad,
+ unsigned long Flags,t_inputrec *ir)
+{
+ gmx_domdec_t *dd;
+ int eDLB=-1;
+ char buf[STRLEN];
+
+ switch (dlb_opt[0])
+ {
+ case 'a': eDLB = edlbAUTO; break;
+ case 'n': eDLB = edlbNO; break;
+ case 'y': eDLB = edlbYES; break;
+ default: gmx_incons("Unknown dlb_opt");
+ }
+
+ if (Flags & MD_RERUN)
+ {
+ return edlbNO;
+ }
+
+ if (!EI_DYNAMICS(ir->eI))
+ {
+ if (eDLB == edlbYES)
+ {
+ sprintf(buf,"NOTE: dynamic load balancing is only supported with dynamics, not with integrator '%s'\n",EI(ir->eI));
+ dd_warning(cr,fplog,buf);
+ }
+
+ return edlbNO;
+ }
+
+ if (!bRecordLoad)
+ {
+ dd_warning(cr,fplog,"NOTE: Cycle counting is not supported on this architecture, will not use dynamic load balancing\n");
+
+ return edlbNO;
+ }
+
+ if (Flags & MD_REPRODUCIBLE)
+ {
+ switch (eDLB)
+ {
+ case edlbNO:
+ break;
+ case edlbAUTO:
+ dd_warning(cr,fplog,"NOTE: reproducibility requested, will not use dynamic load balancing\n");
+ eDLB = edlbNO;
+ break;
+ case edlbYES:
+ dd_warning(cr,fplog,"WARNING: reproducibility requested with dynamic load balancing, the simulation will NOT be binary reproducible\n");
+ break;
+ default:
+ gmx_fatal(FARGS,"Death horror: undefined case (%d) for load balancing choice",eDLB);
+ break;
+ }
+ }
+
+ return eDLB;
+}
+
+static void set_dd_dim(FILE *fplog,gmx_domdec_t *dd)
+{
+ int dim;
+
+ dd->ndim = 0;
+ if (getenv("GMX_DD_ORDER_ZYX") != NULL)
+ {
+ /* Decomposition order z,y,x */
+ if (fplog)
+ {
+ fprintf(fplog,"Using domain decomposition order z, y, x\n");
+ }
+ for(dim=DIM-1; dim>=0; dim--)
+ {
+ if (dd->nc[dim] > 1)
+ {
+ dd->dim[dd->ndim++] = dim;
+ }
+ }
+ }
+ else
+ {
+ /* Decomposition order x,y,z */
+ for(dim=0; dim<DIM; dim++)
+ {
+ if (dd->nc[dim] > 1)
+ {
+ dd->dim[dd->ndim++] = dim;
+ }
+ }
+ }
+}
+
+static gmx_domdec_comm_t *init_dd_comm()
+{
+ gmx_domdec_comm_t *comm;
+ int i;
+
+ snew(comm,1);
+ snew(comm->cggl_flag,DIM*2);
+ snew(comm->cgcm_state,DIM*2);
+ for(i=0; i<DIM*2; i++)
+ {
+ comm->cggl_flag_nalloc[i] = 0;
+ comm->cgcm_state_nalloc[i] = 0;
+ }
+
+ comm->nalloc_int = 0;
+ comm->buf_int = NULL;
+
+ vec_rvec_init(&comm->vbuf);
+
+ comm->n_load_have = 0;
+ comm->n_load_collect = 0;
+
+ for(i=0; i<ddnatNR-ddnatZONE; i++)
+ {
+ comm->sum_nat[i] = 0;
+ }
+ comm->ndecomp = 0;
+ comm->nload = 0;
+ comm->load_step = 0;
+ comm->load_sum = 0;
+ comm->load_max = 0;
+ clear_ivec(comm->load_lim);
+ comm->load_mdf = 0;
+ comm->load_pme = 0;
+
+ return comm;
+}
+
+gmx_domdec_t *init_domain_decomposition(FILE *fplog,t_commrec *cr,
+ unsigned long Flags,
+ ivec nc,
+ real comm_distance_min,real rconstr,
+ const char *dlb_opt,real dlb_scale,
+ const char *sizex,const char *sizey,const char *sizez,
+ gmx_mtop_t *mtop,t_inputrec *ir,
+ matrix box,rvec *x,
+ gmx_ddbox_t *ddbox,
+ int *npme_x,int *npme_y)
+{
+ gmx_domdec_t *dd;
+ gmx_domdec_comm_t *comm;
+ int recload;
+ int d,i,j;
+ real r_2b,r_mb,r_bonded=-1,r_bonded_limit=-1,limit,acs;
+ gmx_bool bC;
+ char buf[STRLEN];
+
+ if (fplog)
+ {
+ fprintf(fplog,
+ "\nInitializing Domain Decomposition on %d nodes\n",cr->nnodes);
+ }
+
+ snew(dd,1);
+
+ dd->comm = init_dd_comm();
+ comm = dd->comm;
+ snew(comm->cggl_flag,DIM*2);
+ snew(comm->cgcm_state,DIM*2);
+
+ dd->npbcdim = ePBC2npbcdim(ir->ePBC);
+ dd->bScrewPBC = (ir->ePBC == epbcSCREW);
+
+ dd->bSendRecv2 = dd_nst_env(fplog,"GMX_DD_SENDRECV2",0);
+ comm->dlb_scale_lim = dd_nst_env(fplog,"GMX_DLB_MAX",10);
+ comm->eFlop = dd_nst_env(fplog,"GMX_DLB_FLOP",0);
+ recload = dd_nst_env(fplog,"GMX_DD_LOAD",1);
+ comm->nstSortCG = dd_nst_env(fplog,"GMX_DD_SORT",1);
+ comm->nstDDDump = dd_nst_env(fplog,"GMX_DD_DUMP",0);
+ comm->nstDDDumpGrid = dd_nst_env(fplog,"GMX_DD_DUMP_GRID",0);
+ comm->DD_debug = dd_nst_env(fplog,"GMX_DD_DEBUG",0);
+
+ dd->pme_recv_f_alloc = 0;
+ dd->pme_recv_f_buf = NULL;
+
+ if (dd->bSendRecv2 && fplog)
+ {
+ fprintf(fplog,"Will use two sequential MPI_Sendrecv calls instead of two simultaneous non-blocking MPI_Irecv and MPI_Isend pairs for constraint and vsite communication\n");
+ }
+ if (comm->eFlop)
+ {
+ if (fplog)
+ {
+ fprintf(fplog,"Will load balance based on FLOP count\n");
+ }
+ if (comm->eFlop > 1)
+ {
+ srand(1+cr->nodeid);
+ }
+ comm->bRecordLoad = TRUE;
+ }
+ else
+ {
+ comm->bRecordLoad = (wallcycle_have_counter() && recload > 0);
+
+ }
+
+ comm->eDLB = check_dlb_support(fplog,cr,dlb_opt,comm->bRecordLoad,Flags,ir);
+
+ comm->bDynLoadBal = (comm->eDLB == edlbYES);
+ if (fplog)
+ {
+ fprintf(fplog,"Dynamic load balancing: %s\n",edlb_names[comm->eDLB]);
+ }
+ dd->bGridJump = comm->bDynLoadBal;
+
+ if (comm->nstSortCG)
+ {
+ if (fplog)
+ {
+ if (comm->nstSortCG == 1)
+ {
+ fprintf(fplog,"Will sort the charge groups at every domain (re)decomposition\n");
+ }
+ else
+ {
+ fprintf(fplog,"Will sort the charge groups every %d steps\n",
+ comm->nstSortCG);
+ }
+ }
+ snew(comm->sort,1);
+ }
+ else
+ {
+ if (fplog)
+ {
+ fprintf(fplog,"Will not sort the charge groups\n");
+ }
+ }
+
+ comm->bInterCGBondeds = (ncg_mtop(mtop) > mtop->mols.nr);
+ if (comm->bInterCGBondeds)
+ {
+ comm->bInterCGMultiBody = (multi_body_bondeds_count(mtop) > 0);
+ }
+ else
+ {
+ comm->bInterCGMultiBody = FALSE;
+ }
+
+ dd->bInterCGcons = inter_charge_group_constraints(mtop);
+
+ if (ir->rlistlong == 0)
+ {
+ /* Set the cut-off to some very large value,
+ * so we don't need if statements everywhere in the code.
+ * We use sqrt, since the cut-off is squared in some places.
+ */
+ comm->cutoff = GMX_CUTOFF_INF;
+ }
+ else
+ {
+ comm->cutoff = ir->rlistlong;
+ }
+ comm->cutoff_mbody = 0;
+
+ comm->cellsize_limit = 0;
+ comm->bBondComm = FALSE;
+
+ if (comm->bInterCGBondeds)
+ {
+ if (comm_distance_min > 0)
+ {
+ comm->cutoff_mbody = comm_distance_min;
+ if (Flags & MD_DDBONDCOMM)
+ {
+ comm->bBondComm = (comm->cutoff_mbody > comm->cutoff);
+ }
+ else
+ {
+ comm->cutoff = max(comm->cutoff,comm->cutoff_mbody);
+ }
+ r_bonded_limit = comm->cutoff_mbody;
+ }
+ else if (ir->bPeriodicMols)
+ {
+ /* Can not easily determine the required cut-off */
+ dd_warning(cr,fplog,"NOTE: Periodic molecules: can not easily determine the required minimum bonded cut-off, using half the non-bonded cut-off\n");
+ comm->cutoff_mbody = comm->cutoff/2;
+ r_bonded_limit = comm->cutoff_mbody;
+ }
+ else
+ {
+ if (MASTER(cr))
+ {
+ dd_bonded_cg_distance(fplog,dd,mtop,ir,x,box,
+ Flags & MD_DDBONDCHECK,&r_2b,&r_mb);
+ }
+ gmx_bcast(sizeof(r_2b),&r_2b,cr);
+ gmx_bcast(sizeof(r_mb),&r_mb,cr);
+
+ /* We use an initial margin of 10% for the minimum cell size,
+ * except when we are just below the non-bonded cut-off.
+ */
+ if (Flags & MD_DDBONDCOMM)
+ {
+ if (max(r_2b,r_mb) > comm->cutoff)
+ {
+ r_bonded = max(r_2b,r_mb);
+ r_bonded_limit = 1.1*r_bonded;
+ comm->bBondComm = TRUE;
+ }
+ else
+ {
+ r_bonded = r_mb;
+ r_bonded_limit = min(1.1*r_bonded,comm->cutoff);
+ }
+ /* We determine cutoff_mbody later */
+ }
+ else
+ {
+ /* No special bonded communication,
+ * simply increase the DD cut-off.
+ */
+ r_bonded_limit = 1.1*max(r_2b,r_mb);
+ comm->cutoff_mbody = r_bonded_limit;
+ comm->cutoff = max(comm->cutoff,comm->cutoff_mbody);
+ }
+ }
+ comm->cellsize_limit = max(comm->cellsize_limit,r_bonded_limit);
+ if (fplog)
+ {
+ fprintf(fplog,
+ "Minimum cell size due to bonded interactions: %.3f nm\n",
+ comm->cellsize_limit);
+ }
+ }
+
+ if (dd->bInterCGcons && rconstr <= 0)
+ {
+ /* There is a cell size limit due to the constraints (P-LINCS) */
+ rconstr = constr_r_max(fplog,mtop,ir);
+ if (fplog)
+ {
+ fprintf(fplog,
+ "Estimated maximum distance required for P-LINCS: %.3f nm\n",
+ rconstr);
+ if (rconstr > comm->cellsize_limit)
+ {
+ fprintf(fplog,"This distance will limit the DD cell size, you can override this with -rcon\n");
+ }
+ }
+ }
+ else if (rconstr > 0 && fplog)
+ {
+ /* Here we do not check for dd->bInterCGcons,
+ * because one can also set a cell size limit for virtual sites only
+ * and at this point we don't know yet if there are intercg v-sites.
+ */
+ fprintf(fplog,
+ "User supplied maximum distance required for P-LINCS: %.3f nm\n",
+ rconstr);
+ }
+ comm->cellsize_limit = max(comm->cellsize_limit,rconstr);
+
+ comm->cgs_gl = gmx_mtop_global_cgs(mtop);
+
+ if (nc[XX] > 0)
+ {
+ copy_ivec(nc,dd->nc);
+ set_dd_dim(fplog,dd);
+ set_ddbox_cr(cr,&dd->nc,ir,box,&comm->cgs_gl,x,ddbox);
+
+ if (cr->npmenodes == -1)
+ {
+ cr->npmenodes = 0;
+ }
+ acs = average_cellsize_min(dd,ddbox);
+ if (acs < comm->cellsize_limit)
+ {
+ if (fplog)
+ {
+ fprintf(fplog,"ERROR: The initial cell size (%f) is smaller than the cell size limit (%f)\n",acs,comm->cellsize_limit);
+ }
+ gmx_fatal_collective(FARGS,cr,NULL,
+ "The initial cell size (%f) is smaller than the cell size limit (%f), change options -dd, -rdd or -rcon, see the log file for details",
+ acs,comm->cellsize_limit);
+ }
+ }
+ else
+ {
+ set_ddbox_cr(cr,NULL,ir,box,&comm->cgs_gl,x,ddbox);
+
+ /* We need to choose the optimal DD grid and possibly PME nodes */
+ limit = dd_choose_grid(fplog,cr,dd,ir,mtop,box,ddbox,
+ comm->eDLB!=edlbNO,dlb_scale,
+ comm->cellsize_limit,comm->cutoff,
+ comm->bInterCGBondeds,comm->bInterCGMultiBody);
+
+ if (dd->nc[XX] == 0)
+ {
+ bC = (dd->bInterCGcons && rconstr > r_bonded_limit);
+ sprintf(buf,"Change the number of nodes or mdrun option %s%s%s",
+ !bC ? "-rdd" : "-rcon",
+ comm->eDLB!=edlbNO ? " or -dds" : "",
+ bC ? " or your LINCS settings" : "");
+
+ gmx_fatal_collective(FARGS,cr,NULL,
+ "There is no domain decomposition for %d nodes that is compatible with the given box and a minimum cell size of %g nm\n"
+ "%s\n"
+ "Look in the log file for details on the domain decomposition",
+ cr->nnodes-cr->npmenodes,limit,buf);
+ }
+ set_dd_dim(fplog,dd);
+ }
+
+ if (fplog)
+ {
+ fprintf(fplog,
+ "Domain decomposition grid %d x %d x %d, separate PME nodes %d\n",
+ dd->nc[XX],dd->nc[YY],dd->nc[ZZ],cr->npmenodes);
+ }
+
+ dd->nnodes = dd->nc[XX]*dd->nc[YY]*dd->nc[ZZ];
+ if (cr->nnodes - dd->nnodes != cr->npmenodes)
+ {
+ gmx_fatal_collective(FARGS,cr,NULL,
+ "The size of the domain decomposition grid (%d) does not match the number of nodes (%d). The total number of nodes is %d",
+ dd->nnodes,cr->nnodes - cr->npmenodes,cr->nnodes);
+ }
+ if (cr->npmenodes > dd->nnodes)
+ {
+ gmx_fatal_collective(FARGS,cr,NULL,
- if (EST_DISTR(i) && state->flags & (1<<i))
++ "The number of separate PME nodes (%d) is larger than the number of PP nodes (%d), this is not supported.",cr->npmenodes,dd->nnodes);
+ }
+ if (cr->npmenodes > 0)
+ {
+ comm->npmenodes = cr->npmenodes;
+ }
+ else
+ {
+ comm->npmenodes = dd->nnodes;
+ }
+
+ if (EEL_PME(ir->coulombtype))
+ {
+ /* The following choices should match those
+ * in comm_cost_est in domdec_setup.c.
+ * Note that here the checks have to take into account
+ * that the decomposition might occur in a different order than xyz
+ * (for instance through the env.var. GMX_DD_ORDER_ZYX),
+ * in which case they will not match those in comm_cost_est,
+ * but since that is mainly for testing purposes that's fine.
+ */
+ if (dd->ndim >= 2 && dd->dim[0] == XX && dd->dim[1] == YY &&
+ comm->npmenodes > dd->nc[XX] && comm->npmenodes % dd->nc[XX] == 0 &&
+ getenv("GMX_PMEONEDD") == NULL)
+ {
+ comm->npmedecompdim = 2;
+ comm->npmenodes_x = dd->nc[XX];
+ comm->npmenodes_y = comm->npmenodes/comm->npmenodes_x;
+ }
+ else
+ {
+ /* In case nc is 1 in both x and y we could still choose to
+ * decompose pme in y instead of x, but we use x for simplicity.
+ */
+ comm->npmedecompdim = 1;
+ if (dd->dim[0] == YY)
+ {
+ comm->npmenodes_x = 1;
+ comm->npmenodes_y = comm->npmenodes;
+ }
+ else
+ {
+ comm->npmenodes_x = comm->npmenodes;
+ comm->npmenodes_y = 1;
+ }
+ }
+ if (fplog)
+ {
+ fprintf(fplog,"PME domain decomposition: %d x %d x %d\n",
+ comm->npmenodes_x,comm->npmenodes_y,1);
+ }
+ }
+ else
+ {
+ comm->npmedecompdim = 0;
+ comm->npmenodes_x = 0;
+ comm->npmenodes_y = 0;
+ }
+
+ /* Technically we don't need both of these,
+ * but it simplifies code not having to recalculate it.
+ */
+ *npme_x = comm->npmenodes_x;
+ *npme_y = comm->npmenodes_y;
+
+ snew(comm->slb_frac,DIM);
+ if (comm->eDLB == edlbNO)
+ {
+ comm->slb_frac[XX] = get_slb_frac(fplog,"x",dd->nc[XX],sizex);
+ comm->slb_frac[YY] = get_slb_frac(fplog,"y",dd->nc[YY],sizey);
+ comm->slb_frac[ZZ] = get_slb_frac(fplog,"z",dd->nc[ZZ],sizez);
+ }
+
+ if (comm->bInterCGBondeds && comm->cutoff_mbody == 0)
+ {
+ if (comm->bBondComm || comm->eDLB != edlbNO)
+ {
+ /* Set the bonded communication distance to halfway
+ * the minimum and the maximum,
+ * since the extra communication cost is nearly zero.
+ */
+ acs = average_cellsize_min(dd,ddbox);
+ comm->cutoff_mbody = 0.5*(r_bonded + acs);
+ if (comm->eDLB != edlbNO)
+ {
+ /* Check if this does not limit the scaling */
+ comm->cutoff_mbody = min(comm->cutoff_mbody,dlb_scale*acs);
+ }
+ if (!comm->bBondComm)
+ {
+ /* Without bBondComm do not go beyond the n.b. cut-off */
+ comm->cutoff_mbody = min(comm->cutoff_mbody,comm->cutoff);
+ if (comm->cellsize_limit >= comm->cutoff)
+ {
+ /* We don't loose a lot of efficieny
+ * when increasing it to the n.b. cut-off.
+ * It can even be slightly faster, because we need
+ * less checks for the communication setup.
+ */
+ comm->cutoff_mbody = comm->cutoff;
+ }
+ }
+ /* Check if we did not end up below our original limit */
+ comm->cutoff_mbody = max(comm->cutoff_mbody,r_bonded_limit);
+
+ if (comm->cutoff_mbody > comm->cellsize_limit)
+ {
+ comm->cellsize_limit = comm->cutoff_mbody;
+ }
+ }
+ /* Without DLB and cutoff_mbody<cutoff, cutoff_mbody is dynamic */
+ }
+
+ if (debug)
+ {
+ fprintf(debug,"Bonded atom communication beyond the cut-off: %d\n"
+ "cellsize limit %f\n",
+ comm->bBondComm,comm->cellsize_limit);
+ }
+
+ if (MASTER(cr))
+ {
+ check_dd_restrictions(cr,dd,ir,fplog);
+ }
+
+ comm->globalcomm_step = INT_MIN;
+ dd->ddp_count = 0;
+
+ clear_dd_cycle_counts(dd);
+
+ return dd;
+}
+
+static void set_dlb_limits(gmx_domdec_t *dd)
+
+{
+ int d;
+
+ for(d=0; d<dd->ndim; d++)
+ {
+ dd->comm->cd[d].np = dd->comm->cd[d].np_dlb;
+ dd->comm->cellsize_min[dd->dim[d]] =
+ dd->comm->cellsize_min_dlb[dd->dim[d]];
+ }
+}
+
+
+static void turn_on_dlb(FILE *fplog,t_commrec *cr,gmx_large_int_t step)
+{
+ gmx_domdec_t *dd;
+ gmx_domdec_comm_t *comm;
+ real cellsize_min;
+ int d,nc,i;
+ char buf[STRLEN];
+
+ dd = cr->dd;
+ comm = dd->comm;
+
+ if (fplog)
+ {
+ fprintf(fplog,"At step %s the performance loss due to force load imbalance is %.1f %%\n",gmx_step_str(step,buf),dd_force_imb_perf_loss(dd)*100);
+ }
+
+ cellsize_min = comm->cellsize_min[dd->dim[0]];
+ for(d=1; d<dd->ndim; d++)
+ {
+ cellsize_min = min(cellsize_min,comm->cellsize_min[dd->dim[d]]);
+ }
+
+ if (cellsize_min < comm->cellsize_limit*1.05)
+ {
+ dd_warning(cr,fplog,"NOTE: the minimum cell size is smaller than 1.05 times the cell size limit, will not turn on dynamic load balancing\n");
+
+ /* Change DLB from "auto" to "no". */
+ comm->eDLB = edlbNO;
+
+ return;
+ }
+
+ dd_warning(cr,fplog,"NOTE: Turning on dynamic load balancing\n");
+ comm->bDynLoadBal = TRUE;
+ dd->bGridJump = TRUE;
+
+ set_dlb_limits(dd);
+
+ /* We can set the required cell size info here,
+ * so we do not need to communicate this.
+ * The grid is completely uniform.
+ */
+ for(d=0; d<dd->ndim; d++)
+ {
+ if (comm->root[d])
+ {
+ comm->load[d].sum_m = comm->load[d].sum;
+
+ nc = dd->nc[dd->dim[d]];
+ for(i=0; i<nc; i++)
+ {
+ comm->root[d]->cell_f[i] = i/(real)nc;
+ if (d > 0)
+ {
+ comm->root[d]->cell_f_max0[i] = i /(real)nc;
+ comm->root[d]->cell_f_min1[i] = (i+1)/(real)nc;
+ }
+ }
+ comm->root[d]->cell_f[nc] = 1.0;
+ }
+ }
+}
+
+static char *init_bLocalCG(gmx_mtop_t *mtop)
+{
+ int ncg,cg;
+ char *bLocalCG;
+
+ ncg = ncg_mtop(mtop);
+ snew(bLocalCG,ncg);
+ for(cg=0; cg<ncg; cg++)
+ {
+ bLocalCG[cg] = FALSE;
+ }
+
+ return bLocalCG;
+}
+
+void dd_init_bondeds(FILE *fplog,
+ gmx_domdec_t *dd,gmx_mtop_t *mtop,
+ gmx_vsite_t *vsite,gmx_constr_t constr,
+ t_inputrec *ir,gmx_bool bBCheck,cginfo_mb_t *cginfo_mb)
+{
+ gmx_domdec_comm_t *comm;
+ gmx_bool bBondComm;
+ int d;
+
+ dd_make_reverse_top(fplog,dd,mtop,vsite,constr,ir,bBCheck);
+
+ comm = dd->comm;
+
+ if (comm->bBondComm)
+ {
+ /* Communicate atoms beyond the cut-off for bonded interactions */
+ comm = dd->comm;
+
+ comm->cglink = make_charge_group_links(mtop,dd,cginfo_mb);
+
+ comm->bLocalCG = init_bLocalCG(mtop);
+ }
+ else
+ {
+ /* Only communicate atoms based on cut-off */
+ comm->cglink = NULL;
+ comm->bLocalCG = NULL;
+ }
+}
+
+static void print_dd_settings(FILE *fplog,gmx_domdec_t *dd,
+ t_inputrec *ir,
+ gmx_bool bDynLoadBal,real dlb_scale,
+ gmx_ddbox_t *ddbox)
+{
+ gmx_domdec_comm_t *comm;
+ int d;
+ ivec np;
+ real limit,shrink;
+ char buf[64];
+
+ if (fplog == NULL)
+ {
+ return;
+ }
+
+ comm = dd->comm;
+
+ if (bDynLoadBal)
+ {
+ fprintf(fplog,"The maximum number of communication pulses is:");
+ for(d=0; d<dd->ndim; d++)
+ {
+ fprintf(fplog," %c %d",dim2char(dd->dim[d]),comm->cd[d].np_dlb);
+ }
+ fprintf(fplog,"\n");
+ fprintf(fplog,"The minimum size for domain decomposition cells is %.3f nm\n",comm->cellsize_limit);
+ fprintf(fplog,"The requested allowed shrink of DD cells (option -dds) is: %.2f\n",dlb_scale);
+ fprintf(fplog,"The allowed shrink of domain decomposition cells is:");
+ for(d=0; d<DIM; d++)
+ {
+ if (dd->nc[d] > 1)
+ {
+ if (d >= ddbox->npbcdim && dd->nc[d] == 2)
+ {
+ shrink = 0;
+ }
+ else
+ {
+ shrink =
+ comm->cellsize_min_dlb[d]/
+ (ddbox->box_size[d]*ddbox->skew_fac[d]/dd->nc[d]);
+ }
+ fprintf(fplog," %c %.2f",dim2char(d),shrink);
+ }
+ }
+ fprintf(fplog,"\n");
+ }
+ else
+ {
+ set_dd_cell_sizes_slb(dd,ddbox,FALSE,np);
+ fprintf(fplog,"The initial number of communication pulses is:");
+ for(d=0; d<dd->ndim; d++)
+ {
+ fprintf(fplog," %c %d",dim2char(dd->dim[d]),np[dd->dim[d]]);
+ }
+ fprintf(fplog,"\n");
+ fprintf(fplog,"The initial domain decomposition cell size is:");
+ for(d=0; d<DIM; d++) {
+ if (dd->nc[d] > 1)
+ {
+ fprintf(fplog," %c %.2f nm",
+ dim2char(d),dd->comm->cellsize_min[d]);
+ }
+ }
+ fprintf(fplog,"\n\n");
+ }
+
+ if (comm->bInterCGBondeds || dd->vsite_comm || dd->constraint_comm)
+ {
+ fprintf(fplog,"The maximum allowed distance for charge groups involved in interactions is:\n");
+ fprintf(fplog,"%40s %-7s %6.3f nm\n",
+ "non-bonded interactions","",comm->cutoff);
+
+ if (bDynLoadBal)
+ {
+ limit = dd->comm->cellsize_limit;
+ }
+ else
+ {
+ if (dynamic_dd_box(ddbox,ir))
+ {
+ fprintf(fplog,"(the following are initial values, they could change due to box deformation)\n");
+ }
+ limit = dd->comm->cellsize_min[XX];
+ for(d=1; d<DIM; d++)
+ {
+ limit = min(limit,dd->comm->cellsize_min[d]);
+ }
+ }
+
+ if (comm->bInterCGBondeds)
+ {
+ fprintf(fplog,"%40s %-7s %6.3f nm\n",
+ "two-body bonded interactions","(-rdd)",
+ max(comm->cutoff,comm->cutoff_mbody));
+ fprintf(fplog,"%40s %-7s %6.3f nm\n",
+ "multi-body bonded interactions","(-rdd)",
+ (comm->bBondComm || dd->bGridJump) ? comm->cutoff_mbody : min(comm->cutoff,limit));
+ }
+ if (dd->vsite_comm)
+ {
+ fprintf(fplog,"%40s %-7s %6.3f nm\n",
+ "virtual site constructions","(-rcon)",limit);
+ }
+ if (dd->constraint_comm)
+ {
+ sprintf(buf,"atoms separated by up to %d constraints",
+ 1+ir->nProjOrder);
+ fprintf(fplog,"%40s %-7s %6.3f nm\n",
+ buf,"(-rcon)",limit);
+ }
+ fprintf(fplog,"\n");
+ }
+
+ fflush(fplog);
+}
+
+void set_dd_parameters(FILE *fplog,gmx_domdec_t *dd,real dlb_scale,
+ t_inputrec *ir,t_forcerec *fr,
+ gmx_ddbox_t *ddbox)
+{
+ gmx_domdec_comm_t *comm;
+ int d,dim,npulse,npulse_d_max,npulse_d;
+ gmx_bool bNoCutOff;
+ int natoms_tot;
+ real vol_frac;
+
+ comm = dd->comm;
+
+ bNoCutOff = (ir->rvdw == 0 || ir->rcoulomb == 0);
+
+ if (EEL_PME(ir->coulombtype))
+ {
+ init_ddpme(dd,&comm->ddpme[0],0);
+ if (comm->npmedecompdim >= 2)
+ {
+ init_ddpme(dd,&comm->ddpme[1],1);
+ }
+ }
+ else
+ {
+ comm->npmenodes = 0;
+ if (dd->pme_nodeid >= 0)
+ {
+ gmx_fatal_collective(FARGS,NULL,dd,
+ "Can not have separate PME nodes without PME electrostatics");
+ }
+ }
+
+ /* If each molecule is a single charge group
+ * or we use domain decomposition for each periodic dimension,
+ * we do not need to take pbc into account for the bonded interactions.
+ */
+ if (fr->ePBC == epbcNONE || !comm->bInterCGBondeds ||
+ (dd->nc[XX]>1 && dd->nc[YY]>1 && (dd->nc[ZZ]>1 || fr->ePBC==epbcXY)))
+ {
+ fr->bMolPBC = FALSE;
+ }
+ else
+ {
+ fr->bMolPBC = TRUE;
+ }
+
+ if (debug)
+ {
+ fprintf(debug,"The DD cut-off is %f\n",comm->cutoff);
+ }
+ if (comm->eDLB != edlbNO)
+ {
+ /* Determine the maximum number of comm. pulses in one dimension */
+
+ comm->cellsize_limit = max(comm->cellsize_limit,comm->cutoff_mbody);
+
+ /* Determine the maximum required number of grid pulses */
+ if (comm->cellsize_limit >= comm->cutoff)
+ {
+ /* Only a single pulse is required */
+ npulse = 1;
+ }
+ else if (!bNoCutOff && comm->cellsize_limit > 0)
+ {
+ /* We round down slightly here to avoid overhead due to the latency
+ * of extra communication calls when the cut-off
+ * would be only slightly longer than the cell size.
+ * Later cellsize_limit is redetermined,
+ * so we can not miss interactions due to this rounding.
+ */
+ npulse = (int)(0.96 + comm->cutoff/comm->cellsize_limit);
+ }
+ else
+ {
+ /* There is no cell size limit */
+ npulse = max(dd->nc[XX]-1,max(dd->nc[YY]-1,dd->nc[ZZ]-1));
+ }
+
+ if (!bNoCutOff && npulse > 1)
+ {
+ /* See if we can do with less pulses, based on dlb_scale */
+ npulse_d_max = 0;
+ for(d=0; d<dd->ndim; d++)
+ {
+ dim = dd->dim[d];
+ npulse_d = (int)(1 + dd->nc[dim]*comm->cutoff
+ /(ddbox->box_size[dim]*ddbox->skew_fac[dim]*dlb_scale));
+ npulse_d_max = max(npulse_d_max,npulse_d);
+ }
+ npulse = min(npulse,npulse_d_max);
+ }
+
+ /* This env var can override npulse */
+ d = dd_nst_env(fplog,"GMX_DD_NPULSE",0);
+ if (d > 0)
+ {
+ npulse = d;
+ }
+
+ comm->maxpulse = 1;
+ comm->bVacDLBNoLimit = (ir->ePBC == epbcNONE);
+ for(d=0; d<dd->ndim; d++)
+ {
+ comm->cd[d].np_dlb = min(npulse,dd->nc[dd->dim[d]]-1);
+ comm->cd[d].np_nalloc = comm->cd[d].np_dlb;
+ snew(comm->cd[d].ind,comm->cd[d].np_nalloc);
+ comm->maxpulse = max(comm->maxpulse,comm->cd[d].np_dlb);
+ if (comm->cd[d].np_dlb < dd->nc[dd->dim[d]]-1)
+ {
+ comm->bVacDLBNoLimit = FALSE;
+ }
+ }
+
+ /* cellsize_limit is set for LINCS in init_domain_decomposition */
+ if (!comm->bVacDLBNoLimit)
+ {
+ comm->cellsize_limit = max(comm->cellsize_limit,
+ comm->cutoff/comm->maxpulse);
+ }
+ comm->cellsize_limit = max(comm->cellsize_limit,comm->cutoff_mbody);
+ /* Set the minimum cell size for each DD dimension */
+ for(d=0; d<dd->ndim; d++)
+ {
+ if (comm->bVacDLBNoLimit ||
+ comm->cd[d].np_dlb*comm->cellsize_limit >= comm->cutoff)
+ {
+ comm->cellsize_min_dlb[dd->dim[d]] = comm->cellsize_limit;
+ }
+ else
+ {
+ comm->cellsize_min_dlb[dd->dim[d]] =
+ comm->cutoff/comm->cd[d].np_dlb;
+ }
+ }
+ if (comm->cutoff_mbody <= 0)
+ {
+ comm->cutoff_mbody = min(comm->cutoff,comm->cellsize_limit);
+ }
+ if (comm->bDynLoadBal)
+ {
+ set_dlb_limits(dd);
+ }
+ }
+
+ print_dd_settings(fplog,dd,ir,comm->bDynLoadBal,dlb_scale,ddbox);
+ if (comm->eDLB == edlbAUTO)
+ {
+ if (fplog)
+ {
+ fprintf(fplog,"When dynamic load balancing gets turned on, these settings will change to:\n");
+ }
+ print_dd_settings(fplog,dd,ir,TRUE,dlb_scale,ddbox);
+ }
+
+ if (ir->ePBC == epbcNONE)
+ {
+ vol_frac = 1 - 1/(double)dd->nnodes;
+ }
+ else
+ {
+ vol_frac =
+ (1 + comm_box_frac(dd->nc,comm->cutoff,ddbox))/(double)dd->nnodes;
+ }
+ if (debug)
+ {
+ fprintf(debug,"Volume fraction for all DD zones: %f\n",vol_frac);
+ }
+ natoms_tot = comm->cgs_gl.index[comm->cgs_gl.nr];
+
+ dd->ga2la = ga2la_init(natoms_tot,vol_frac*natoms_tot);
+}
+
+static void merge_cg_buffers(int ncell,
+ gmx_domdec_comm_dim_t *cd, int pulse,
+ int *ncg_cell,
+ int *index_gl, int *recv_i,
+ rvec *cg_cm, rvec *recv_vr,
+ int *cgindex,
+ cginfo_mb_t *cginfo_mb,int *cginfo)
+{
+ gmx_domdec_ind_t *ind,*ind_p;
+ int p,cell,c,cg,cg0,cg1,cg_gl,nat;
+ int shift,shift_at;
+
+ ind = &cd->ind[pulse];
+
+ /* First correct the already stored data */
+ shift = ind->nrecv[ncell];
+ for(cell=ncell-1; cell>=0; cell--)
+ {
+ shift -= ind->nrecv[cell];
+ if (shift > 0)
+ {
+ /* Move the cg's present from previous grid pulses */
+ cg0 = ncg_cell[ncell+cell];
+ cg1 = ncg_cell[ncell+cell+1];
+ cgindex[cg1+shift] = cgindex[cg1];
+ for(cg=cg1-1; cg>=cg0; cg--)
+ {
+ index_gl[cg+shift] = index_gl[cg];
+ copy_rvec(cg_cm[cg],cg_cm[cg+shift]);
+ cgindex[cg+shift] = cgindex[cg];
+ cginfo[cg+shift] = cginfo[cg];
+ }
+ /* Correct the already stored send indices for the shift */
+ for(p=1; p<=pulse; p++)
+ {
+ ind_p = &cd->ind[p];
+ cg0 = 0;
+ for(c=0; c<cell; c++)
+ {
+ cg0 += ind_p->nsend[c];
+ }
+ cg1 = cg0 + ind_p->nsend[cell];
+ for(cg=cg0; cg<cg1; cg++)
+ {
+ ind_p->index[cg] += shift;
+ }
+ }
+ }
+ }
+
+ /* Merge in the communicated buffers */
+ shift = 0;
+ shift_at = 0;
+ cg0 = 0;
+ for(cell=0; cell<ncell; cell++)
+ {
+ cg1 = ncg_cell[ncell+cell+1] + shift;
+ if (shift_at > 0)
+ {
+ /* Correct the old cg indices */
+ for(cg=ncg_cell[ncell+cell]; cg<cg1; cg++)
+ {
+ cgindex[cg+1] += shift_at;
+ }
+ }
+ for(cg=0; cg<ind->nrecv[cell]; cg++)
+ {
+ /* Copy this charge group from the buffer */
+ index_gl[cg1] = recv_i[cg0];
+ copy_rvec(recv_vr[cg0],cg_cm[cg1]);
+ /* Add it to the cgindex */
+ cg_gl = index_gl[cg1];
+ cginfo[cg1] = ddcginfo(cginfo_mb,cg_gl);
+ nat = GET_CGINFO_NATOMS(cginfo[cg1]);
+ cgindex[cg1+1] = cgindex[cg1] + nat;
+ cg0++;
+ cg1++;
+ shift_at += nat;
+ }
+ shift += ind->nrecv[cell];
+ ncg_cell[ncell+cell+1] = cg1;
+ }
+}
+
+static void make_cell2at_index(gmx_domdec_comm_dim_t *cd,
+ int nzone,int cg0,const int *cgindex)
+{
+ int cg,zone,p;
+
+ /* Store the atom block boundaries for easy copying of communication buffers
+ */
+ cg = cg0;
+ for(zone=0; zone<nzone; zone++)
+ {
+ for(p=0; p<cd->np; p++) {
+ cd->ind[p].cell2at0[zone] = cgindex[cg];
+ cg += cd->ind[p].nrecv[zone];
+ cd->ind[p].cell2at1[zone] = cgindex[cg];
+ }
+ }
+}
+
+static gmx_bool missing_link(t_blocka *link,int cg_gl,char *bLocalCG)
+{
+ int i;
+ gmx_bool bMiss;
+
+ bMiss = FALSE;
+ for(i=link->index[cg_gl]; i<link->index[cg_gl+1]; i++)
+ {
+ if (!bLocalCG[link->a[i]])
+ {
+ bMiss = TRUE;
+ }
+ }
+
+ return bMiss;
+}
+
+static void setup_dd_communication(gmx_domdec_t *dd,
+ matrix box,gmx_ddbox_t *ddbox,t_forcerec *fr)
+{
+ int dim_ind,dim,dim0,dim1=-1,dim2=-1,dimd,p,nat_tot;
+ int nzone,nzone_send,zone,zonei,cg0,cg1;
+ int c,i,j,cg,cg_gl,nrcg;
+ int *zone_cg_range,pos_cg,*index_gl,*cgindex,*recv_i;
+ gmx_domdec_comm_t *comm;
+ gmx_domdec_zones_t *zones;
+ gmx_domdec_comm_dim_t *cd;
+ gmx_domdec_ind_t *ind;
+ cginfo_mb_t *cginfo_mb;
+ gmx_bool bBondComm,bDist2B,bDistMB,bDistMB_pulse,bDistBonded,bScrew;
+ real r_mb,r_comm2,r_scomm2,r_bcomm2,r,r_0,r_1,r2,rb2,r2inc,inv_ncg,tric_sh;
+ rvec rb,rn;
+ real corner[DIM][4],corner_round_0=0,corner_round_1[4];
+ real bcorner[DIM],bcorner_round_1=0;
+ ivec tric_dist;
+ rvec *cg_cm,*normal,*v_d,*v_0=NULL,*v_1=NULL,*recv_vr;
+ real skew_fac2_d,skew_fac_01;
+ rvec sf2_round;
+ int nsend,nat;
+
+ if (debug)
+ {
+ fprintf(debug,"Setting up DD communication\n");
+ }
+
+ comm = dd->comm;
+ cg_cm = fr->cg_cm;
+
+ for(dim_ind=0; dim_ind<dd->ndim; dim_ind++)
+ {
+ dim = dd->dim[dim_ind];
+
+ /* Check if we need to use triclinic distances */
+ tric_dist[dim_ind] = 0;
+ for(i=0; i<=dim_ind; i++)
+ {
+ if (ddbox->tric_dir[dd->dim[i]])
+ {
+ tric_dist[dim_ind] = 1;
+ }
+ }
+ }
+
+ bBondComm = comm->bBondComm;
+
+ /* Do we need to determine extra distances for multi-body bondeds? */
+ bDistMB = (comm->bInterCGMultiBody && dd->bGridJump && dd->ndim > 1);
+
+ /* Do we need to determine extra distances for only two-body bondeds? */
+ bDist2B = (bBondComm && !bDistMB);
+
+ r_comm2 = sqr(comm->cutoff);
+ r_bcomm2 = sqr(comm->cutoff_mbody);
+
+ if (debug)
+ {
+ fprintf(debug,"bBondComm %d, r_bc %f\n",bBondComm,sqrt(r_bcomm2));
+ }
+
+ zones = &comm->zones;
+
+ dim0 = dd->dim[0];
+ /* The first dimension is equal for all cells */
+ corner[0][0] = comm->cell_x0[dim0];
+ if (bDistMB)
+ {
+ bcorner[0] = corner[0][0];
+ }
+ if (dd->ndim >= 2)
+ {
+ dim1 = dd->dim[1];
+ /* This cell row is only seen from the first row */
+ corner[1][0] = comm->cell_x0[dim1];
+ /* All rows can see this row */
+ corner[1][1] = comm->cell_x0[dim1];
+ if (dd->bGridJump)
+ {
+ corner[1][1] = max(comm->cell_x0[dim1],comm->zone_d1[1].mch0);
+ if (bDistMB)
+ {
+ /* For the multi-body distance we need the maximum */
+ bcorner[1] = max(comm->cell_x0[dim1],comm->zone_d1[1].p1_0);
+ }
+ }
+ /* Set the upper-right corner for rounding */
+ corner_round_0 = comm->cell_x1[dim0];
+
+ if (dd->ndim >= 3)
+ {
+ dim2 = dd->dim[2];
+ for(j=0; j<4; j++)
+ {
+ corner[2][j] = comm->cell_x0[dim2];
+ }
+ if (dd->bGridJump)
+ {
+ /* Use the maximum of the i-cells that see a j-cell */
+ for(i=0; i<zones->nizone; i++)
+ {
+ for(j=zones->izone[i].j0; j<zones->izone[i].j1; j++)
+ {
+ if (j >= 4)
+ {
+ corner[2][j-4] =
+ max(corner[2][j-4],
+ comm->zone_d2[zones->shift[i][dim0]][zones->shift[i][dim1]].mch0);
+ }
+ }
+ }
+ if (bDistMB)
+ {
+ /* For the multi-body distance we need the maximum */
+ bcorner[2] = comm->cell_x0[dim2];
+ for(i=0; i<2; i++)
+ {
+ for(j=0; j<2; j++)
+ {
+ bcorner[2] = max(bcorner[2],
+ comm->zone_d2[i][j].p1_0);
+ }
+ }
+ }
+ }
+
+ /* Set the upper-right corner for rounding */
+ /* Cell (0,0,0) and cell (1,0,0) can see cell 4 (0,1,1)
+ * Only cell (0,0,0) can see cell 7 (1,1,1)
+ */
+ corner_round_1[0] = comm->cell_x1[dim1];
+ corner_round_1[3] = comm->cell_x1[dim1];
+ if (dd->bGridJump)
+ {
+ corner_round_1[0] = max(comm->cell_x1[dim1],
+ comm->zone_d1[1].mch1);
+ if (bDistMB)
+ {
+ /* For the multi-body distance we need the maximum */
+ bcorner_round_1 = max(comm->cell_x1[dim1],
+ comm->zone_d1[1].p1_1);
+ }
+ }
+ }
+ }
+
+ /* Triclinic stuff */
+ normal = ddbox->normal;
+ skew_fac_01 = 0;
+ if (dd->ndim >= 2)
+ {
+ v_0 = ddbox->v[dim0];
+ if (ddbox->tric_dir[dim0] && ddbox->tric_dir[dim1])
+ {
+ /* Determine the coupling coefficient for the distances
+ * to the cell planes along dim0 and dim1 through dim2.
+ * This is required for correct rounding.
+ */
+ skew_fac_01 =
+ ddbox->v[dim0][dim1+1][dim0]*ddbox->v[dim1][dim1+1][dim1];
+ if (debug)
+ {
+ fprintf(debug,"\nskew_fac_01 %f\n",skew_fac_01);
+ }
+ }
+ }
+ if (dd->ndim >= 3)
+ {
+ v_1 = ddbox->v[dim1];
+ }
+
+ zone_cg_range = zones->cg_range;
+ index_gl = dd->index_gl;
+ cgindex = dd->cgindex;
+ cginfo_mb = fr->cginfo_mb;
+
+ zone_cg_range[0] = 0;
+ zone_cg_range[1] = dd->ncg_home;
+ comm->zone_ncg1[0] = dd->ncg_home;
+ pos_cg = dd->ncg_home;
+
+ nat_tot = dd->nat_home;
+ nzone = 1;
+ for(dim_ind=0; dim_ind<dd->ndim; dim_ind++)
+ {
+ dim = dd->dim[dim_ind];
+ cd = &comm->cd[dim_ind];
+
+ if (dim >= ddbox->npbcdim && dd->ci[dim] == 0)
+ {
+ /* No pbc in this dimension, the first node should not comm. */
+ nzone_send = 0;
+ }
+ else
+ {
+ nzone_send = nzone;
+ }
+
+ bScrew = (dd->bScrewPBC && dim == XX);
+
+ v_d = ddbox->v[dim];
+ skew_fac2_d = sqr(ddbox->skew_fac[dim]);
+
+ cd->bInPlace = TRUE;
+ for(p=0; p<cd->np; p++)
+ {
+ /* Only atoms communicated in the first pulse are used
+ * for multi-body bonded interactions or for bBondComm.
+ */
+ bDistBonded = ((bDistMB || bDist2B) && p == 0);
+ bDistMB_pulse = (bDistMB && bDistBonded);
+
+ ind = &cd->ind[p];
+ nsend = 0;
+ nat = 0;
+ for(zone=0; zone<nzone_send; zone++)
+ {
+ if (tric_dist[dim_ind] && dim_ind > 0)
+ {
+ /* Determine slightly more optimized skew_fac's
+ * for rounding.
+ * This reduces the number of communicated atoms
+ * by about 10% for 3D DD of rhombic dodecahedra.
+ */
+ for(dimd=0; dimd<dim; dimd++)
+ {
+ sf2_round[dimd] = 1;
+ if (ddbox->tric_dir[dimd])
+ {
+ for(i=dd->dim[dimd]+1; i<DIM; i++)
+ {
+ /* If we are shifted in dimension i
+ * and the cell plane is tilted forward
+ * in dimension i, skip this coupling.
+ */
+ if (!(zones->shift[nzone+zone][i] &&
+ ddbox->v[dimd][i][dimd] >= 0))
+ {
+ sf2_round[dimd] +=
+ sqr(ddbox->v[dimd][i][dimd]);
+ }
+ }
+ sf2_round[dimd] = 1/sf2_round[dimd];
+ }
+ }
+ }
+
+ zonei = zone_perm[dim_ind][zone];
+ if (p == 0)
+ {
+ /* Here we permutate the zones to obtain a convenient order
+ * for neighbor searching
+ */
+ cg0 = zone_cg_range[zonei];
+ cg1 = zone_cg_range[zonei+1];
+ }
+ else
+ {
+ /* Look only at the cg's received in the previous grid pulse
+ */
+ cg1 = zone_cg_range[nzone+zone+1];
+ cg0 = cg1 - cd->ind[p-1].nrecv[zone];
+ }
+ ind->nsend[zone] = 0;
+ for(cg=cg0; cg<cg1; cg++)
+ {
+ r2 = 0;
+ rb2 = 0;
+ if (tric_dist[dim_ind] == 0)
+ {
+ /* Rectangular direction, easy */
+ r = cg_cm[cg][dim] - corner[dim_ind][zone];
+ if (r > 0)
+ {
+ r2 += r*r;
+ }
+ if (bDistMB_pulse)
+ {
+ r = cg_cm[cg][dim] - bcorner[dim_ind];
+ if (r > 0)
+ {
+ rb2 += r*r;
+ }
+ }
+ /* Rounding gives at most a 16% reduction
+ * in communicated atoms
+ */
+ if (dim_ind >= 1 && (zonei == 1 || zonei == 2))
+ {
+ r = cg_cm[cg][dim0] - corner_round_0;
+ /* This is the first dimension, so always r >= 0 */
+ r2 += r*r;
+ if (bDistMB_pulse)
+ {
+ rb2 += r*r;
+ }
+ }
+ if (dim_ind == 2 && (zonei == 2 || zonei == 3))
+ {
+ r = cg_cm[cg][dim1] - corner_round_1[zone];
+ if (r > 0)
+ {
+ r2 += r*r;
+ }
+ if (bDistMB_pulse)
+ {
+ r = cg_cm[cg][dim1] - bcorner_round_1;
+ if (r > 0)
+ {
+ rb2 += r*r;
+ }
+ }
+ }
+ }
+ else
+ {
+ /* Triclinic direction, more complicated */
+ clear_rvec(rn);
+ clear_rvec(rb);
+ /* Rounding, conservative as the skew_fac multiplication
+ * will slightly underestimate the distance.
+ */
+ if (dim_ind >= 1 && (zonei == 1 || zonei == 2))
+ {
+ rn[dim0] = cg_cm[cg][dim0] - corner_round_0;
+ for(i=dim0+1; i<DIM; i++)
+ {
+ rn[dim0] -= cg_cm[cg][i]*v_0[i][dim0];
+ }
+ r2 = rn[dim0]*rn[dim0]*sf2_round[dim0];
+ if (bDistMB_pulse)
+ {
+ rb[dim0] = rn[dim0];
+ rb2 = r2;
+ }
+ /* Take care that the cell planes along dim0 might not
+ * be orthogonal to those along dim1 and dim2.
+ */
+ for(i=1; i<=dim_ind; i++)
+ {
+ dimd = dd->dim[i];
+ if (normal[dim0][dimd] > 0)
+ {
+ rn[dimd] -= rn[dim0]*normal[dim0][dimd];
+ if (bDistMB_pulse)
+ {
+ rb[dimd] -= rb[dim0]*normal[dim0][dimd];
+ }
+ }
+ }
+ }
+ if (dim_ind == 2 && (zonei == 2 || zonei == 3))
+ {
+ rn[dim1] += cg_cm[cg][dim1] - corner_round_1[zone];
+ tric_sh = 0;
+ for(i=dim1+1; i<DIM; i++)
+ {
+ tric_sh -= cg_cm[cg][i]*v_1[i][dim1];
+ }
+ rn[dim1] += tric_sh;
+ if (rn[dim1] > 0)
+ {
+ r2 += rn[dim1]*rn[dim1]*sf2_round[dim1];
+ /* Take care of coupling of the distances
+ * to the planes along dim0 and dim1 through dim2.
+ */
+ r2 -= rn[dim0]*rn[dim1]*skew_fac_01;
+ /* Take care that the cell planes along dim1
+ * might not be orthogonal to that along dim2.
+ */
+ if (normal[dim1][dim2] > 0)
+ {
+ rn[dim2] -= rn[dim1]*normal[dim1][dim2];
+ }
+ }
+ if (bDistMB_pulse)
+ {
+ rb[dim1] +=
+ cg_cm[cg][dim1] - bcorner_round_1 + tric_sh;
+ if (rb[dim1] > 0)
+ {
+ rb2 += rb[dim1]*rb[dim1]*sf2_round[dim1];
+ /* Take care of coupling of the distances
+ * to the planes along dim0 and dim1 through dim2.
+ */
+ rb2 -= rb[dim0]*rb[dim1]*skew_fac_01;
+ /* Take care that the cell planes along dim1
+ * might not be orthogonal to that along dim2.
+ */
+ if (normal[dim1][dim2] > 0)
+ {
+ rb[dim2] -= rb[dim1]*normal[dim1][dim2];
+ }
+ }
+ }
+ }
+ /* The distance along the communication direction */
+ rn[dim] += cg_cm[cg][dim] - corner[dim_ind][zone];
+ tric_sh = 0;
+ for(i=dim+1; i<DIM; i++)
+ {
+ tric_sh -= cg_cm[cg][i]*v_d[i][dim];
+ }
+ rn[dim] += tric_sh;
+ if (rn[dim] > 0)
+ {
+ r2 += rn[dim]*rn[dim]*skew_fac2_d;
+ /* Take care of coupling of the distances
+ * to the planes along dim0 and dim1 through dim2.
+ */
+ if (dim_ind == 1 && zonei == 1)
+ {
+ r2 -= rn[dim0]*rn[dim]*skew_fac_01;
+ }
+ }
+ if (bDistMB_pulse)
+ {
+ clear_rvec(rb);
+ rb[dim] += cg_cm[cg][dim] - bcorner[dim_ind] + tric_sh;
+ if (rb[dim] > 0)
+ {
+ rb2 += rb[dim]*rb[dim]*skew_fac2_d;
+ /* Take care of coupling of the distances
+ * to the planes along dim0 and dim1 through dim2.
+ */
+ if (dim_ind == 1 && zonei == 1)
+ {
+ rb2 -= rb[dim0]*rb[dim]*skew_fac_01;
+ }
+ }
+ }
+ }
+
+ if (r2 < r_comm2 ||
+ (bDistBonded &&
+ ((bDistMB && rb2 < r_bcomm2) ||
+ (bDist2B && r2 < r_bcomm2)) &&
+ (!bBondComm ||
+ (GET_CGINFO_BOND_INTER(fr->cginfo[cg]) &&
+ missing_link(comm->cglink,index_gl[cg],
+ comm->bLocalCG)))))
+ {
+ /* Make an index to the local charge groups */
+ if (nsend+1 > ind->nalloc)
+ {
+ ind->nalloc = over_alloc_large(nsend+1);
+ srenew(ind->index,ind->nalloc);
+ }
+ if (nsend+1 > comm->nalloc_int)
+ {
+ comm->nalloc_int = over_alloc_large(nsend+1);
+ srenew(comm->buf_int,comm->nalloc_int);
+ }
+ ind->index[nsend] = cg;
+ comm->buf_int[nsend] = index_gl[cg];
+ ind->nsend[zone]++;
+ vec_rvec_check_alloc(&comm->vbuf,nsend+1);
+
+ if (dd->ci[dim] == 0)
+ {
+ /* Correct cg_cm for pbc */
+ rvec_add(cg_cm[cg],box[dim],comm->vbuf.v[nsend]);
+ if (bScrew)
+ {
+ comm->vbuf.v[nsend][YY] =
+ box[YY][YY]-comm->vbuf.v[nsend][YY];
+ comm->vbuf.v[nsend][ZZ] =
+ box[ZZ][ZZ]-comm->vbuf.v[nsend][ZZ];
+ }
+ }
+ else
+ {
+ copy_rvec(cg_cm[cg],comm->vbuf.v[nsend]);
+ }
+ nsend++;
+ nat += cgindex[cg+1] - cgindex[cg];
+ }
+ }
+ }
+ /* Clear the counts in case we do not have pbc */
+ for(zone=nzone_send; zone<nzone; zone++)
+ {
+ ind->nsend[zone] = 0;
+ }
+ ind->nsend[nzone] = nsend;
+ ind->nsend[nzone+1] = nat;
+ /* Communicate the number of cg's and atoms to receive */
+ dd_sendrecv_int(dd, dim_ind, dddirBackward,
+ ind->nsend, nzone+2,
+ ind->nrecv, nzone+2);
+
+ /* The rvec buffer is also required for atom buffers of size nsend
+ * in dd_move_x and dd_move_f.
+ */
+ vec_rvec_check_alloc(&comm->vbuf,ind->nsend[nzone+1]);
+
+ if (p > 0)
+ {
+ /* We can receive in place if only the last zone is not empty */
+ for(zone=0; zone<nzone-1; zone++)
+ {
+ if (ind->nrecv[zone] > 0)
+ {
+ cd->bInPlace = FALSE;
+ }
+ }
+ if (!cd->bInPlace)
+ {
+ /* The int buffer is only required here for the cg indices */
+ if (ind->nrecv[nzone] > comm->nalloc_int2)
+ {
+ comm->nalloc_int2 = over_alloc_dd(ind->nrecv[nzone]);
+ srenew(comm->buf_int2,comm->nalloc_int2);
+ }
+ /* The rvec buffer is also required for atom buffers
+ * of size nrecv in dd_move_x and dd_move_f.
+ */
+ i = max(cd->ind[0].nrecv[nzone+1],ind->nrecv[nzone+1]);
+ vec_rvec_check_alloc(&comm->vbuf2,i);
+ }
+ }
+
+ /* Make space for the global cg indices */
+ if (pos_cg + ind->nrecv[nzone] > dd->cg_nalloc
+ || dd->cg_nalloc == 0)
+ {
+ dd->cg_nalloc = over_alloc_dd(pos_cg + ind->nrecv[nzone]);
+ srenew(index_gl,dd->cg_nalloc);
+ srenew(cgindex,dd->cg_nalloc+1);
+ }
+ /* Communicate the global cg indices */
+ if (cd->bInPlace)
+ {
+ recv_i = index_gl + pos_cg;
+ }
+ else
+ {
+ recv_i = comm->buf_int2;
+ }
+ dd_sendrecv_int(dd, dim_ind, dddirBackward,
+ comm->buf_int, nsend,
+ recv_i, ind->nrecv[nzone]);
+
+ /* Make space for cg_cm */
+ if (pos_cg + ind->nrecv[nzone] > fr->cg_nalloc)
+ {
+ dd_realloc_fr_cg(fr,pos_cg + ind->nrecv[nzone]);
+ cg_cm = fr->cg_cm;
+ }
+ /* Communicate cg_cm */
+ if (cd->bInPlace)
+ {
+ recv_vr = cg_cm + pos_cg;
+ }
+ else
+ {
+ recv_vr = comm->vbuf2.v;
+ }
+ dd_sendrecv_rvec(dd, dim_ind, dddirBackward,
+ comm->vbuf.v, nsend,
+ recv_vr, ind->nrecv[nzone]);
+
+ /* Make the charge group index */
+ if (cd->bInPlace)
+ {
+ zone = (p == 0 ? 0 : nzone - 1);
+ while (zone < nzone)
+ {
+ for(cg=0; cg<ind->nrecv[zone]; cg++)
+ {
+ cg_gl = index_gl[pos_cg];
+ fr->cginfo[pos_cg] = ddcginfo(cginfo_mb,cg_gl);
+ nrcg = GET_CGINFO_NATOMS(fr->cginfo[pos_cg]);
+ cgindex[pos_cg+1] = cgindex[pos_cg] + nrcg;
+ if (bBondComm)
+ {
+ /* Update the charge group presence,
+ * so we can use it in the next pass of the loop.
+ */
+ comm->bLocalCG[cg_gl] = TRUE;
+ }
+ pos_cg++;
+ }
+ if (p == 0)
+ {
+ comm->zone_ncg1[nzone+zone] = ind->nrecv[zone];
+ }
+ zone++;
+ zone_cg_range[nzone+zone] = pos_cg;
+ }
+ }
+ else
+ {
+ /* This part of the code is never executed with bBondComm. */
+ merge_cg_buffers(nzone,cd,p,zone_cg_range,
+ index_gl,recv_i,cg_cm,recv_vr,
+ cgindex,fr->cginfo_mb,fr->cginfo);
+ pos_cg += ind->nrecv[nzone];
+ }
+ nat_tot += ind->nrecv[nzone+1];
+ }
+ if (!cd->bInPlace)
+ {
+ /* Store the atom block for easy copying of communication buffers */
+ make_cell2at_index(cd,nzone,zone_cg_range[nzone],cgindex);
+ }
+ nzone += nzone;
+ }
+ dd->index_gl = index_gl;
+ dd->cgindex = cgindex;
+
+ dd->ncg_tot = zone_cg_range[zones->n];
+ dd->nat_tot = nat_tot;
+ comm->nat[ddnatHOME] = dd->nat_home;
+ for(i=ddnatZONE; i<ddnatNR; i++)
+ {
+ comm->nat[i] = dd->nat_tot;
+ }
+
+ if (!bBondComm)
+ {
+ /* We don't need to update cginfo, since that was alrady done above.
+ * So we pass NULL for the forcerec.
+ */
+ dd_set_cginfo(dd->index_gl,dd->ncg_home,dd->ncg_tot,
+ NULL,comm->bLocalCG);
+ }
+
+ if (debug)
+ {
+ fprintf(debug,"Finished setting up DD communication, zones:");
+ for(c=0; c<zones->n; c++)
+ {
+ fprintf(debug," %d",zones->cg_range[c+1]-zones->cg_range[c]);
+ }
+ fprintf(debug,"\n");
+ }
+}
+
+static void set_cg_boundaries(gmx_domdec_zones_t *zones)
+{
+ int c;
+
+ for(c=0; c<zones->nizone; c++)
+ {
+ zones->izone[c].cg1 = zones->cg_range[c+1];
+ zones->izone[c].jcg0 = zones->cg_range[zones->izone[c].j0];
+ zones->izone[c].jcg1 = zones->cg_range[zones->izone[c].j1];
+ }
+}
+
+static int comp_cgsort(const void *a,const void *b)
+{
+ int comp;
+
+ gmx_cgsort_t *cga,*cgb;
+ cga = (gmx_cgsort_t *)a;
+ cgb = (gmx_cgsort_t *)b;
+
+ comp = cga->nsc - cgb->nsc;
+ if (comp == 0)
+ {
+ comp = cga->ind_gl - cgb->ind_gl;
+ }
+
+ return comp;
+}
+
+static void order_int_cg(int n,gmx_cgsort_t *sort,
+ int *a,int *buf)
+{
+ int i;
+
+ /* Order the data */
+ for(i=0; i<n; i++)
+ {
+ buf[i] = a[sort[i].ind];
+ }
+
+ /* Copy back to the original array */
+ for(i=0; i<n; i++)
+ {
+ a[i] = buf[i];
+ }
+}
+
+static void order_vec_cg(int n,gmx_cgsort_t *sort,
+ rvec *v,rvec *buf)
+{
+ int i;
+
+ /* Order the data */
+ for(i=0; i<n; i++)
+ {
+ copy_rvec(v[sort[i].ind],buf[i]);
+ }
+
+ /* Copy back to the original array */
+ for(i=0; i<n; i++)
+ {
+ copy_rvec(buf[i],v[i]);
+ }
+}
+
+static void order_vec_atom(int ncg,int *cgindex,gmx_cgsort_t *sort,
+ rvec *v,rvec *buf)
+{
+ int a,atot,cg,cg0,cg1,i;
+
+ /* Order the data */
+ a = 0;
+ for(cg=0; cg<ncg; cg++)
+ {
+ cg0 = cgindex[sort[cg].ind];
+ cg1 = cgindex[sort[cg].ind+1];
+ for(i=cg0; i<cg1; i++)
+ {
+ copy_rvec(v[i],buf[a]);
+ a++;
+ }
+ }
+ atot = a;
+
+ /* Copy back to the original array */
+ for(a=0; a<atot; a++)
+ {
+ copy_rvec(buf[a],v[a]);
+ }
+}
+
+static void ordered_sort(int nsort2,gmx_cgsort_t *sort2,
+ int nsort_new,gmx_cgsort_t *sort_new,
+ gmx_cgsort_t *sort1)
+{
+ int i1,i2,i_new;
+
+ /* The new indices are not very ordered, so we qsort them */
+ qsort_threadsafe(sort_new,nsort_new,sizeof(sort_new[0]),comp_cgsort);
+
+ /* sort2 is already ordered, so now we can merge the two arrays */
+ i1 = 0;
+ i2 = 0;
+ i_new = 0;
+ while(i2 < nsort2 || i_new < nsort_new)
+ {
+ if (i2 == nsort2)
+ {
+ sort1[i1++] = sort_new[i_new++];
+ }
+ else if (i_new == nsort_new)
+ {
+ sort1[i1++] = sort2[i2++];
+ }
+ else if (sort2[i2].nsc < sort_new[i_new].nsc ||
+ (sort2[i2].nsc == sort_new[i_new].nsc &&
+ sort2[i2].ind_gl < sort_new[i_new].ind_gl))
+ {
+ sort1[i1++] = sort2[i2++];
+ }
+ else
+ {
+ sort1[i1++] = sort_new[i_new++];
+ }
+ }
+}
+
+static void dd_sort_state(gmx_domdec_t *dd,int ePBC,
+ rvec *cgcm,t_forcerec *fr,t_state *state,
+ int ncg_home_old)
+{
+ gmx_domdec_sort_t *sort;
+ gmx_cgsort_t *cgsort,*sort_i;
+ int ncg_new,nsort2,nsort_new,i,cell_index,*ibuf,cgsize;
+ rvec *vbuf;
+
+ sort = dd->comm->sort;
+
+ if (dd->ncg_home > sort->sort_nalloc)
+ {
+ sort->sort_nalloc = over_alloc_dd(dd->ncg_home);
+ srenew(sort->sort1,sort->sort_nalloc);
+ srenew(sort->sort2,sort->sort_nalloc);
+ }
+
+ if (ncg_home_old >= 0)
+ {
+ /* The charge groups that remained in the same ns grid cell
+ * are completely ordered. So we can sort efficiently by sorting
+ * the charge groups that did move into the stationary list.
+ */
+ ncg_new = 0;
+ nsort2 = 0;
+ nsort_new = 0;
+ for(i=0; i<dd->ncg_home; i++)
+ {
+ /* Check if this cg did not move to another node */
+ cell_index = fr->ns.grid->cell_index[i];
+ if (cell_index != 4*fr->ns.grid->ncells)
+ {
+ if (i >= ncg_home_old || cell_index != sort->sort1[i].nsc)
+ {
+ /* This cg is new on this node or moved ns grid cell */
+ if (nsort_new >= sort->sort_new_nalloc)
+ {
+ sort->sort_new_nalloc = over_alloc_dd(nsort_new+1);
+ srenew(sort->sort_new,sort->sort_new_nalloc);
+ }
+ sort_i = &(sort->sort_new[nsort_new++]);
+ }
+ else
+ {
+ /* This cg did not move */
+ sort_i = &(sort->sort2[nsort2++]);
+ }
+ /* Sort on the ns grid cell indices
+ * and the global topology index
+ */
+ sort_i->nsc = cell_index;
+ sort_i->ind_gl = dd->index_gl[i];
+ sort_i->ind = i;
+ ncg_new++;
+ }
+ }
+ if (debug)
+ {
+ fprintf(debug,"ordered sort cgs: stationary %d moved %d\n",
+ nsort2,nsort_new);
+ }
+ /* Sort efficiently */
+ ordered_sort(nsort2,sort->sort2,nsort_new,sort->sort_new,sort->sort1);
+ }
+ else
+ {
+ cgsort = sort->sort1;
+ ncg_new = 0;
+ for(i=0; i<dd->ncg_home; i++)
+ {
+ /* Sort on the ns grid cell indices
+ * and the global topology index
+ */
+ cgsort[i].nsc = fr->ns.grid->cell_index[i];
+ cgsort[i].ind_gl = dd->index_gl[i];
+ cgsort[i].ind = i;
+ if (cgsort[i].nsc != 4*fr->ns.grid->ncells)
+ {
+ ncg_new++;
+ }
+ }
+ if (debug)
+ {
+ fprintf(debug,"qsort cgs: %d new home %d\n",dd->ncg_home,ncg_new);
+ }
+ /* Determine the order of the charge groups using qsort */
+ qsort_threadsafe(cgsort,dd->ncg_home,sizeof(cgsort[0]),comp_cgsort);
+ }
+ cgsort = sort->sort1;
+
+ /* We alloc with the old size, since cgindex is still old */
+ vec_rvec_check_alloc(&dd->comm->vbuf,dd->cgindex[dd->ncg_home]);
+ vbuf = dd->comm->vbuf.v;
+
+ /* Remove the charge groups which are no longer at home here */
+ dd->ncg_home = ncg_new;
+
+ /* Reorder the state */
+ for(i=0; i<estNR; i++)
+ {
- (step + ir->nstlist > ir->init_step + ir->nsteps));
++ if (EST_DISTR(i) && (state->flags & (1<<i)))
+ {
+ switch (i)
+ {
+ case estX:
+ order_vec_atom(dd->ncg_home,dd->cgindex,cgsort,state->x,vbuf);
+ break;
+ case estV:
+ order_vec_atom(dd->ncg_home,dd->cgindex,cgsort,state->v,vbuf);
+ break;
+ case estSDX:
+ order_vec_atom(dd->ncg_home,dd->cgindex,cgsort,state->sd_X,vbuf);
+ break;
+ case estCGP:
+ order_vec_atom(dd->ncg_home,dd->cgindex,cgsort,state->cg_p,vbuf);
+ break;
+ case estLD_RNG:
+ case estLD_RNGI:
+ case estDISRE_INITF:
+ case estDISRE_RM3TAV:
+ case estORIRE_INITF:
+ case estORIRE_DTAV:
+ /* No ordering required */
+ break;
+ default:
+ gmx_incons("Unknown state entry encountered in dd_sort_state");
+ break;
+ }
+ }
+ }
+ /* Reorder cgcm */
+ order_vec_cg(dd->ncg_home,cgsort,cgcm,vbuf);
+
+ if (dd->ncg_home+1 > sort->ibuf_nalloc)
+ {
+ sort->ibuf_nalloc = over_alloc_dd(dd->ncg_home+1);
+ srenew(sort->ibuf,sort->ibuf_nalloc);
+ }
+ ibuf = sort->ibuf;
+ /* Reorder the global cg index */
+ order_int_cg(dd->ncg_home,cgsort,dd->index_gl,ibuf);
+ /* Reorder the cginfo */
+ order_int_cg(dd->ncg_home,cgsort,fr->cginfo,ibuf);
+ /* Rebuild the local cg index */
+ ibuf[0] = 0;
+ for(i=0; i<dd->ncg_home; i++)
+ {
+ cgsize = dd->cgindex[cgsort[i].ind+1] - dd->cgindex[cgsort[i].ind];
+ ibuf[i+1] = ibuf[i] + cgsize;
+ }
+ for(i=0; i<dd->ncg_home+1; i++)
+ {
+ dd->cgindex[i] = ibuf[i];
+ }
+ /* Set the home atom number */
+ dd->nat_home = dd->cgindex[dd->ncg_home];
+
+ /* Copy the sorted ns cell indices back to the ns grid struct */
+ for(i=0; i<dd->ncg_home; i++)
+ {
+ fr->ns.grid->cell_index[i] = cgsort[i].nsc;
+ }
+ fr->ns.grid->nr = dd->ncg_home;
+}
+
+static void add_dd_statistics(gmx_domdec_t *dd)
+{
+ gmx_domdec_comm_t *comm;
+ int ddnat;
+
+ comm = dd->comm;
+
+ for(ddnat=ddnatZONE; ddnat<ddnatNR; ddnat++)
+ {
+ comm->sum_nat[ddnat-ddnatZONE] +=
+ comm->nat[ddnat] - comm->nat[ddnat-1];
+ }
+ comm->ndecomp++;
+}
+
+void reset_dd_statistics_counters(gmx_domdec_t *dd)
+{
+ gmx_domdec_comm_t *comm;
+ int ddnat;
+
+ comm = dd->comm;
+
+ /* Reset all the statistics and counters for total run counting */
+ for(ddnat=ddnatZONE; ddnat<ddnatNR; ddnat++)
+ {
+ comm->sum_nat[ddnat-ddnatZONE] = 0;
+ }
+ comm->ndecomp = 0;
+ comm->nload = 0;
+ comm->load_step = 0;
+ comm->load_sum = 0;
+ comm->load_max = 0;
+ clear_ivec(comm->load_lim);
+ comm->load_mdf = 0;
+ comm->load_pme = 0;
+}
+
+void print_dd_statistics(t_commrec *cr,t_inputrec *ir,FILE *fplog)
+{
+ gmx_domdec_comm_t *comm;
+ int ddnat;
+ double av;
+
+ comm = cr->dd->comm;
+
+ gmx_sumd(ddnatNR-ddnatZONE,comm->sum_nat,cr);
+
+ if (fplog == NULL)
+ {
+ return;
+ }
+
+ fprintf(fplog,"\n D O M A I N D E C O M P O S I T I O N S T A T I S T I C S\n\n");
+
+ for(ddnat=ddnatZONE; ddnat<ddnatNR; ddnat++)
+ {
+ av = comm->sum_nat[ddnat-ddnatZONE]/comm->ndecomp;
+ switch(ddnat)
+ {
+ case ddnatZONE:
+ fprintf(fplog,
+ " av. #atoms communicated per step for force: %d x %.1f\n",
+ 2,av);
+ break;
+ case ddnatVSITE:
+ if (cr->dd->vsite_comm)
+ {
+ fprintf(fplog,
+ " av. #atoms communicated per step for vsites: %d x %.1f\n",
+ (EEL_PME(ir->coulombtype) || ir->coulombtype==eelEWALD) ? 3 : 2,
+ av);
+ }
+ break;
+ case ddnatCON:
+ if (cr->dd->constraint_comm)
+ {
+ fprintf(fplog,
+ " av. #atoms communicated per step for LINCS: %d x %.1f\n",
+ 1 + ir->nLincsIter,av);
+ }
+ break;
+ default:
+ gmx_incons(" Unknown type for DD statistics");
+ }
+ }
+ fprintf(fplog,"\n");
+
+ if (comm->bRecordLoad && EI_DYNAMICS(ir->eI))
+ {
+ print_dd_load_av(fplog,cr->dd);
+ }
+}
+
+void dd_partition_system(FILE *fplog,
+ gmx_large_int_t step,
+ t_commrec *cr,
+ gmx_bool bMasterState,
+ int nstglobalcomm,
+ t_state *state_global,
+ gmx_mtop_t *top_global,
+ t_inputrec *ir,
+ t_state *state_local,
+ rvec **f,
+ t_mdatoms *mdatoms,
+ gmx_localtop_t *top_local,
+ t_forcerec *fr,
+ gmx_vsite_t *vsite,
+ gmx_shellfc_t shellfc,
+ gmx_constr_t constr,
+ t_nrnb *nrnb,
+ gmx_wallcycle_t wcycle,
+ gmx_bool bVerbose)
+{
+ gmx_domdec_t *dd;
+ gmx_domdec_comm_t *comm;
+ gmx_ddbox_t ddbox={0};
+ t_block *cgs_gl;
+ gmx_large_int_t step_pcoupl;
+ rvec cell_ns_x0,cell_ns_x1;
+ int i,j,n,cg0=0,ncg_home_old=-1,nat_f_novirsum;
+ gmx_bool bBoxChanged,bNStGlobalComm,bDoDLB,bCheckDLB,bTurnOnDLB,bLogLoad;
+ gmx_bool bRedist,bSortCG,bResortAll;
+ ivec ncells_old,np;
+ real grid_density;
+ char sbuf[22];
+
+ dd = cr->dd;
+ comm = dd->comm;
+
+ bBoxChanged = (bMasterState || DEFORM(*ir));
+ if (ir->epc != epcNO)
+ {
+ /* With nstpcouple > 1 pressure coupling happens.
+ * one step after calculating the pressure.
+ * Box scaling happens at the end of the MD step,
+ * after the DD partitioning.
+ * We therefore have to do DLB in the first partitioning
+ * after an MD step where P-coupling occured.
+ * We need to determine the last step in which p-coupling occurred.
+ * MRS -- need to validate this for vv?
+ */
+ n = ir->nstpcouple;
+ if (n == 1)
+ {
+ step_pcoupl = step - 1;
+ }
+ else
+ {
+ step_pcoupl = ((step - 1)/n)*n + 1;
+ }
+ if (step_pcoupl >= comm->globalcomm_step)
+ {
+ bBoxChanged = TRUE;
+ }
+ }
+
+ bNStGlobalComm = (step >= comm->globalcomm_step + nstglobalcomm);
+
+ if (!comm->bDynLoadBal)
+ {
+ bDoDLB = FALSE;
+ }
+ else
+ {
+ /* Should we do dynamic load balacing this step?
+ * Since it requires (possibly expensive) global communication,
+ * we might want to do DLB less frequently.
+ */
+ if (bBoxChanged || ir->epc != epcNO)
+ {
+ bDoDLB = bBoxChanged;
+ }
+ else
+ {
+ bDoDLB = bNStGlobalComm;
+ }
+ }
+
+ /* Check if we have recorded loads on the nodes */
+ if (comm->bRecordLoad && dd_load_count(comm))
+ {
+ if (comm->eDLB == edlbAUTO && !comm->bDynLoadBal)
+ {
+ /* Check if we should use DLB at the second partitioning
+ * and every 100 partitionings,
+ * so the extra communication cost is negligible.
+ */
+ n = max(100,nstglobalcomm);
+ bCheckDLB = (comm->n_load_collect == 0 ||
+ comm->n_load_have % n == n-1);
+ }
+ else
+ {
+ bCheckDLB = FALSE;
+ }
+
+ /* Print load every nstlog, first and last step to the log file */
+ bLogLoad = ((ir->nstlog > 0 && step % ir->nstlog == 0) ||
+ comm->n_load_collect == 0 ||
++ (ir->nsteps >= 0 &&
++ (step + ir->nstlist > ir->init_step + ir->nsteps)));
+
+ /* Avoid extra communication due to verbose screen output
+ * when nstglobalcomm is set.
+ */
+ if (bDoDLB || bLogLoad || bCheckDLB ||
+ (bVerbose && (ir->nstlist == 0 || nstglobalcomm <= ir->nstlist)))
+ {
+ get_load_distribution(dd,wcycle);
+ if (DDMASTER(dd))
+ {
+ if (bLogLoad)
+ {
+ dd_print_load(fplog,dd,step-1);
+ }
+ if (bVerbose)
+ {
+ dd_print_load_verbose(dd);
+ }
+ }
+ comm->n_load_collect++;
+
+ if (bCheckDLB) {
+ /* Since the timings are node dependent, the master decides */
+ if (DDMASTER(dd))
+ {
+ bTurnOnDLB =
+ (dd_force_imb_perf_loss(dd) >= DD_PERF_LOSS);
+ if (debug)
+ {
+ fprintf(debug,"step %s, imb loss %f\n",
+ gmx_step_str(step,sbuf),
+ dd_force_imb_perf_loss(dd));
+ }
+ }
+ dd_bcast(dd,sizeof(bTurnOnDLB),&bTurnOnDLB);
+ if (bTurnOnDLB)
+ {
+ turn_on_dlb(fplog,cr,step);
+ bDoDLB = TRUE;
+ }
+ }
+ }
+ comm->n_load_have++;
+ }
+
+ cgs_gl = &comm->cgs_gl;
+
+ bRedist = FALSE;
+ if (bMasterState)
+ {
+ /* Clear the old state */
+ clear_dd_indices(dd,0,0);
+
+ set_ddbox(dd,bMasterState,cr,ir,state_global->box,
+ TRUE,cgs_gl,state_global->x,&ddbox);
+
+ get_cg_distribution(fplog,step,dd,cgs_gl,
+ state_global->box,&ddbox,state_global->x);
+
+ dd_distribute_state(dd,cgs_gl,
+ state_global,state_local,f);
+
+ dd_make_local_cgs(dd,&top_local->cgs);
+
+ if (dd->ncg_home > fr->cg_nalloc)
+ {
+ dd_realloc_fr_cg(fr,dd->ncg_home);
+ }
+ calc_cgcm(fplog,0,dd->ncg_home,
+ &top_local->cgs,state_local->x,fr->cg_cm);
+
+ inc_nrnb(nrnb,eNR_CGCM,dd->nat_home);
+
+ dd_set_cginfo(dd->index_gl,0,dd->ncg_home,fr,comm->bLocalCG);
+
+ cg0 = 0;
+ }
+ else if (state_local->ddp_count != dd->ddp_count)
+ {
+ if (state_local->ddp_count > dd->ddp_count)
+ {
+ gmx_fatal(FARGS,"Internal inconsistency state_local->ddp_count (%d) > dd->ddp_count (%d)",state_local->ddp_count,dd->ddp_count);
+ }
+
+ if (state_local->ddp_count_cg_gl != state_local->ddp_count)
+ {
+ gmx_fatal(FARGS,"Internal inconsistency state_local->ddp_count_cg_gl (%d) != state_local->ddp_count (%d)",state_local->ddp_count_cg_gl,state_local->ddp_count);
+ }
+
+ /* Clear the old state */
+ clear_dd_indices(dd,0,0);
+
+ /* Build the new indices */
+ rebuild_cgindex(dd,cgs_gl->index,state_local);
+ make_dd_indices(dd,cgs_gl->index,0);
+
+ /* Redetermine the cg COMs */
+ calc_cgcm(fplog,0,dd->ncg_home,
+ &top_local->cgs,state_local->x,fr->cg_cm);
+
+ inc_nrnb(nrnb,eNR_CGCM,dd->nat_home);
+
+ dd_set_cginfo(dd->index_gl,0,dd->ncg_home,fr,comm->bLocalCG);
+
+ set_ddbox(dd,bMasterState,cr,ir,state_local->box,
+ TRUE,&top_local->cgs,state_local->x,&ddbox);
+
+ bRedist = comm->bDynLoadBal;
+ }
+ else
+ {
+ /* We have the full state, only redistribute the cgs */
+
+ /* Clear the non-home indices */
+ clear_dd_indices(dd,dd->ncg_home,dd->nat_home);
+
+ /* Avoid global communication for dim's without pbc and -gcom */
+ if (!bNStGlobalComm)
+ {
+ copy_rvec(comm->box0 ,ddbox.box0 );
+ copy_rvec(comm->box_size,ddbox.box_size);
+ }
+ set_ddbox(dd,bMasterState,cr,ir,state_local->box,
+ bNStGlobalComm,&top_local->cgs,state_local->x,&ddbox);
+
+ bBoxChanged = TRUE;
+ bRedist = TRUE;
+ }
+ /* For dim's without pbc and -gcom */
+ copy_rvec(ddbox.box0 ,comm->box0 );
+ copy_rvec(ddbox.box_size,comm->box_size);
+
+ set_dd_cell_sizes(dd,&ddbox,dynamic_dd_box(&ddbox,ir),bMasterState,bDoDLB,
+ step,wcycle);
+
+ if (comm->nstDDDumpGrid > 0 && step % comm->nstDDDumpGrid == 0)
+ {
+ write_dd_grid_pdb("dd_grid",step,dd,state_local->box,&ddbox);
+ }
+
+ /* Check if we should sort the charge groups */
+ if (comm->nstSortCG > 0)
+ {
+ bSortCG = (bMasterState ||
+ (bRedist && (step % comm->nstSortCG == 0)));
+ }
+ else
+ {
+ bSortCG = FALSE;
+ }
+
+ ncg_home_old = dd->ncg_home;
+
+ if (bRedist)
+ {
+ cg0 = dd_redistribute_cg(fplog,step,dd,ddbox.tric_dir,
+ state_local,f,fr,mdatoms,
+ !bSortCG,nrnb);
+ }
+
+ get_nsgrid_boundaries(fr->ns.grid,dd,
+ state_local->box,&ddbox,&comm->cell_x0,&comm->cell_x1,
+ dd->ncg_home,fr->cg_cm,
+ cell_ns_x0,cell_ns_x1,&grid_density);
+
+ if (bBoxChanged)
+ {
+ comm_dd_ns_cell_sizes(dd,&ddbox,cell_ns_x0,cell_ns_x1,step);
+ }
+
+ copy_ivec(fr->ns.grid->n,ncells_old);
+ grid_first(fplog,fr->ns.grid,dd,&ddbox,fr->ePBC,
+ state_local->box,cell_ns_x0,cell_ns_x1,
+ fr->rlistlong,grid_density);
+ /* We need to store tric_dir for dd_get_ns_ranges called from ns.c */
+ copy_ivec(ddbox.tric_dir,comm->tric_dir);
+
+ if (bSortCG)
+ {
+ /* Sort the state on charge group position.
+ * This enables exact restarts from this step.
+ * It also improves performance by about 15% with larger numbers
+ * of atoms per node.
+ */
+
+ /* Fill the ns grid with the home cell,
+ * so we can sort with the indices.
+ */
+ set_zones_ncg_home(dd);
+ fill_grid(fplog,&comm->zones,fr->ns.grid,dd->ncg_home,
+ 0,dd->ncg_home,fr->cg_cm);
+
+ /* Check if we can user the old order and ns grid cell indices
+ * of the charge groups to sort the charge groups efficiently.
+ */
+ bResortAll = (bMasterState ||
+ fr->ns.grid->n[XX] != ncells_old[XX] ||
+ fr->ns.grid->n[YY] != ncells_old[YY] ||
+ fr->ns.grid->n[ZZ] != ncells_old[ZZ]);
+
+ if (debug)
+ {
+ fprintf(debug,"Step %s, sorting the %d home charge groups\n",
+ gmx_step_str(step,sbuf),dd->ncg_home);
+ }
+ dd_sort_state(dd,ir->ePBC,fr->cg_cm,fr,state_local,
+ bResortAll ? -1 : ncg_home_old);
+ /* Rebuild all the indices */
+ cg0 = 0;
+ ga2la_clear(dd->ga2la);
+ }
+
+ /* Setup up the communication and communicate the coordinates */
+ setup_dd_communication(dd,state_local->box,&ddbox,fr);
+
+ /* Set the indices */
+ make_dd_indices(dd,cgs_gl->index,cg0);
+
+ /* Set the charge group boundaries for neighbor searching */
+ set_cg_boundaries(&comm->zones);
+
+ /*
+ write_dd_pdb("dd_home",step,"dump",top_global,cr,
+ -1,state_local->x,state_local->box);
+ */
+
+ /* Extract a local topology from the global topology */
+ for(i=0; i<dd->ndim; i++)
+ {
+ np[dd->dim[i]] = comm->cd[i].np;
+ }
+ dd_make_local_top(fplog,dd,&comm->zones,dd->npbcdim,state_local->box,
+ comm->cellsize_min,np,
+ fr,vsite,top_global,top_local);
+
+ /* Set up the special atom communication */
+ n = comm->nat[ddnatZONE];
+ for(i=ddnatZONE+1; i<ddnatNR; i++)
+ {
+ switch(i)
+ {
+ case ddnatVSITE:
+ if (vsite && vsite->n_intercg_vsite)
+ {
+ n = dd_make_local_vsites(dd,n,top_local->idef.il);
+ }
+ break;
+ case ddnatCON:
+ if (dd->bInterCGcons)
+ {
+ /* Only for inter-cg constraints we need special code */
+ n = dd_make_local_constraints(dd,n,top_global,
+ constr,ir->nProjOrder,
+ &top_local->idef.il[F_CONSTR]);
+ }
+ break;
+ default:
+ gmx_incons("Unknown special atom type setup");
+ }
+ comm->nat[i] = n;
+ }
+
+ /* Make space for the extra coordinates for virtual site
+ * or constraint communication.
+ */
+ state_local->natoms = comm->nat[ddnatNR-1];
+ if (state_local->natoms > state_local->nalloc)
+ {
+ dd_realloc_state(state_local,f,state_local->natoms);
+ }
+
+ if (fr->bF_NoVirSum)
+ {
+ if (vsite && vsite->n_intercg_vsite)
+ {
+ nat_f_novirsum = comm->nat[ddnatVSITE];
+ }
+ else
+ {
+ if (EEL_FULL(ir->coulombtype) && dd->n_intercg_excl > 0)
+ {
+ nat_f_novirsum = dd->nat_tot;
+ }
+ else
+ {
+ nat_f_novirsum = dd->nat_home;
+ }
+ }
+ }
+ else
+ {
+ nat_f_novirsum = 0;
+ }
+
+ /* Set the number of atoms required for the force calculation.
+ * Forces need to be constrained when using a twin-range setup
+ * or with energy minimization. For simple simulations we could
+ * avoid some allocation, zeroing and copying, but this is
+ * probably not worth the complications ande checking.
+ */
+ forcerec_set_ranges(fr,dd->ncg_home,dd->ncg_tot,
+ dd->nat_tot,comm->nat[ddnatCON],nat_f_novirsum);
+
+ /* We make the all mdatoms up to nat_tot_con.
+ * We could save some work by only setting invmass
+ * between nat_tot and nat_tot_con.
+ */
+ /* This call also sets the new number of home particles to dd->nat_home */
+ atoms2md(top_global,ir,
+ comm->nat[ddnatCON],dd->gatindex,0,dd->nat_home,mdatoms);
+
+ /* Now we have the charges we can sort the FE interactions */
+ dd_sort_local_top(dd,mdatoms,top_local);
+
+ if (shellfc)
+ {
+ /* Make the local shell stuff, currently no communication is done */
+ make_local_shells(cr,mdatoms,shellfc);
+ }
+
+ if (ir->implicit_solvent)
+ {
+ make_local_gb(cr,fr->born,ir->gb_algorithm);
+ }
+
+ if (!(cr->duty & DUTY_PME))
+ {
+ /* Send the charges to our PME only node */
+ gmx_pme_send_q(cr,mdatoms->nChargePerturbed,
+ mdatoms->chargeA,mdatoms->chargeB,
+ dd_pme_maxshift_x(dd),dd_pme_maxshift_y(dd));
+ }
+
+ if (constr)
+ {
+ set_constraints(constr,top_local,ir,mdatoms,cr);
+ }
+
+ if (ir->ePull != epullNO)
+ {
+ /* Update the local pull groups */
+ dd_make_local_pull_groups(dd,ir->pull,mdatoms);
+ }
+
+ if (ir->bRot)
+ {
+ /* Update the local rotation groups */
+ dd_make_local_rotation_groups(dd,ir->rot);
+ }
+
+
+ add_dd_statistics(dd);
+
+ /* Make sure we only count the cycles for this DD partitioning */
+ clear_dd_cycle_counts(dd);
+
+ /* Because the order of the atoms might have changed since
+ * the last vsite construction, we need to communicate the constructing
+ * atom coordinates again (for spreading the forces this MD step).
+ */
+ dd_move_x_vsites(dd,state_local->box,state_local->x);
+
+ if (comm->nstDDDump > 0 && step % comm->nstDDDump == 0)
+ {
+ dd_move_x(dd,state_local->box,state_local->x);
+ write_dd_pdb("dd_dump",step,"dump",top_global,cr,
+ -1,state_local->x,state_local->box);
+ }
+
+ if (bNStGlobalComm)
+ {
+ /* Store the global communication step */
+ comm->globalcomm_step = step;
+ }
+
+ /* Increase the DD partitioning counter */
+ dd->ddp_count++;
+ /* The state currently matches this DD partitioning count, store it */
+ state_local->ddp_count = dd->ddp_count;
+ if (bMasterState)
+ {
+ /* The DD master node knows the complete cg distribution,
+ * store the count so we can possibly skip the cg info communication.
+ */
+ comm->master_cg_ddp_count = (bSortCG ? 0 : dd->ddp_count);
+ }
+
+ if (comm->DD_debug > 0)
+ {
+ /* Set the env var GMX_DD_DEBUG if you suspect corrupted indices */
+ check_index_consistency(dd,top_global->natoms,ncg_mtop(top_global),
+ "after partitioning");
+ }
+}
--- /dev/null
- else if (readmagic == 669)
- ;
- else
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * GROwing Monsters And Cloning Shrimps
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+#include <time.h>
+#include "typedefs.h"
+#include "string2.h"
+#include "smalloc.h"
+#include "names.h"
+#include "confio.h"
+#include "mvdata.h"
+#include "txtdump.h"
+#include "vec.h"
+#include "time.h"
+#include "nrnb.h"
+#include "mshift.h"
+#include "mdrun.h"
+#include "update.h"
+#include "physics.h"
+#include "nrjac.h"
+#include "mtop_util.h"
+#include "edsam.h"
+#include "gmxfio.h"
+#include "groupcoord.h"
+
+
+/* We use the same defines as in mvdata.c here */
+#define block_bc(cr, d) gmx_bcast( sizeof(d), &(d),(cr))
+#define nblock_bc(cr,nr,d) gmx_bcast((nr)*sizeof((d)[0]), (d),(cr))
+#define snew_bc(cr,d,nr) { if (!MASTER(cr)) snew((d),(nr)); }
+
+
+/* enum to identify the type of ED: none, normal ED, flooding */
+enum {eEDnone, eEDedsam, eEDflood, eEDnr};
+
+/* enum to identify operations on reference, average, origin, target structures */
+enum {eedREF, eedAV, eedORI, eedTAR, eedNR};
+
+
+typedef struct
+{
+ int neig; /* nr of eigenvectors */
+ int *ieig; /* index nrs of eigenvectors */
+ real *stpsz; /* stepsizes (per eigenvector) */
+ rvec **vec; /* eigenvector components */
+ real *xproj; /* instantaneous x projections */
+ real *fproj; /* instantaneous f projections */
+ real radius; /* instantaneous radius */
+ real *refproj; /* starting or target projecions */
+ /* When using flooding as harmonic restraint: The current reference projection
+ * is at each step calculated from the initial refproj0 and the slope. */
+ real *refproj0,*refprojslope;
+} t_eigvec;
+
+
+typedef struct
+{
+ t_eigvec mon; /* only monitored, no constraints */
+ t_eigvec linfix; /* fixed linear constraints */
+ t_eigvec linacc; /* acceptance linear constraints */
+ t_eigvec radfix; /* fixed radial constraints (exp) */
+ t_eigvec radacc; /* acceptance radial constraints (exp) */
+ t_eigvec radcon; /* acceptance rad. contraction constr. */
+} t_edvecs;
+
+
+typedef struct
+{
+ real deltaF0;
+ gmx_bool bHarmonic; /* Use flooding for harmonic restraint on
+ the eigenvector */
+ gmx_bool bConstForce; /* Do not calculate a flooding potential,
+ instead flood with a constant force */
+ real tau;
+ real deltaF;
+ real Efl;
+ real kT;
+ real Vfl;
+ real dt;
+ real constEfl;
+ real alpha2;
+ int flood_id;
+ rvec *forces_cartesian;
+ t_eigvec vecs; /* use flooding for these */
+} t_edflood;
+
+
+/* This type is for the average, reference, target, and origin structure */
+typedef struct gmx_edx
+{
+ int nr; /* number of atoms this structure contains */
+ int nr_loc; /* number of atoms on local node */
+ int *anrs; /* atom index numbers */
+ int *anrs_loc; /* local atom index numbers */
+ int nalloc_loc; /* allocation size of anrs_loc */
+ int *c_ind; /* at which position of the whole anrs
+ * array is a local atom?, i.e.
+ * c_ind[0...nr_loc-1] gives the atom index
+ * with respect to the collective
+ * anrs[0...nr-1] array */
+ rvec *x; /* positions for this structure */
+ rvec *x_old; /* used to keep track of the shift vectors
+ such that the ED molecule can always be
+ made whole in the parallel case */
+ real *m; /* masses */
+ real mtot; /* total mass (only used in sref) */
+ real *sqrtm; /* sqrt of the masses used for mass-
+ * weighting of analysis (only used in sav) */
+} t_gmx_edx;
+
+
+typedef struct edpar
+{
+ int nini; /* total Nr of atoms */
+ gmx_bool fitmas; /* true if trans fit with cm */
+ gmx_bool pcamas; /* true if mass-weighted PCA */
+ int presteps; /* number of steps to run without any
+ * perturbations ... just monitoring */
+ int outfrq; /* freq (in steps) of writing to edo */
+ int maxedsteps; /* max nr of steps per cycle */
+
+ /* all gmx_edx datasets are copied to all nodes in the parallel case */
+ struct gmx_edx sref; /* reference positions, to these fitting
+ * will be done */
+ gmx_bool bRefEqAv; /* If true, reference & average indices
+ * are the same. Used for optimization */
+ struct gmx_edx sav; /* average positions */
+ struct gmx_edx star; /* target positions */
+ struct gmx_edx sori; /* origin positions */
+
+ t_edvecs vecs; /* eigenvectors */
+ real slope; /* minimal slope in acceptance radexp */
+
+ gmx_bool bNeedDoEdsam; /* if any of the options mon, linfix, ...
+ * is used (i.e. apart from flooding) */
+ t_edflood flood; /* parameters especially for flooding */
+ struct t_ed_buffer *buf; /* handle to local buffers */
+ struct edpar *next_edi; /* Pointer to another ed dataset */
+} t_edpar;
+
+
+typedef struct gmx_edsam
+{
+ int eEDtype; /* Type of ED: see enums above */
+ const char *edinam; /* name of ED sampling input file */
+ const char *edonam; /* output */
+ FILE *edo; /* output file pointer */
+ t_edpar *edpar;
+ gmx_bool bFirst;
+ gmx_bool bStartFromCpt;
+} t_gmx_edsam;
+
+
+struct t_do_edsam
+{
+ matrix old_rotmat;
+ real oldrad;
+ rvec old_transvec,older_transvec,transvec_compact;
+ rvec *xcoll; /* Positions from all nodes, this is the
+ collective set we work on.
+ These are the positions of atoms with
+ average structure indices */
+ rvec *xc_ref; /* same but with reference structure indices */
+ ivec *shifts_xcoll; /* Shifts for xcoll */
+ ivec *extra_shifts_xcoll; /* xcoll shift changes since last NS step */
+ ivec *shifts_xc_ref; /* Shifts for xc_ref */
+ ivec *extra_shifts_xc_ref; /* xc_ref shift changes since last NS step */
+ gmx_bool bUpdateShifts; /* TRUE in NS steps to indicate that the
+ ED shifts for this ED dataset need to
+ be updated */
+};
+
+
+/* definition of ED buffer structure */
+struct t_ed_buffer
+{
+ struct t_fit_to_ref * fit_to_ref;
+ struct t_do_edfit * do_edfit;
+ struct t_do_edsam * do_edsam;
+ struct t_do_radcon * do_radcon;
+};
+
+
+/* Function declarations */
+static void fit_to_reference(rvec *xcoll,rvec transvec,matrix rotmat,t_edpar *edi);
+
+static void translate_and_rotate(rvec *x,int nat,rvec transvec,matrix rotmat);
+/* End function declarations */
+
+
+/* Does not subtract average positions, projection on single eigenvector is returned
+ * used by: do_linfix, do_linacc, do_radfix, do_radacc, do_radcon
+ * Average position is subtracted in ed_apply_constraints prior to calling projectx
+ */
+static real projectx(t_edpar *edi, rvec *xcoll, rvec *vec)
+{
+ int i;
+ real proj=0.0;
+
+
+ for (i=0; i<edi->sav.nr; i++)
+ proj += edi->sav.sqrtm[i]*iprod(vec[i], xcoll[i]);
+
+ return proj;
+}
+
+
+/* Specialized: projection is stored in vec->refproj
+ * -> used for radacc, radfix, radcon and center of flooding potential
+ * subtracts average positions, projects vector x */
+static void rad_project(t_edpar *edi, rvec *x, t_eigvec *vec, t_commrec *cr)
+{
+ int i;
+ real rad=0.0;
+
+ /* Subtract average positions */
+ for (i = 0; i < edi->sav.nr; i++)
+ rvec_dec(x[i], edi->sav.x[i]);
+
+ for (i = 0; i < vec->neig; i++)
+ {
+ vec->refproj[i] = projectx(edi,x,vec->vec[i]);
+ rad += pow((vec->refproj[i]-vec->xproj[i]),2);
+ }
+ vec->radius=sqrt(rad);
+
+ /* Add average positions */
+ for (i = 0; i < edi->sav.nr; i++)
+ rvec_inc(x[i], edi->sav.x[i]);
+}
+
+
+/* Project vector x, subtract average positions prior to projection and add
+ * them afterwards to retain the unchanged vector. Store in xproj. Mass-weighting
+ * is applied. */
+static void project_to_eigvectors(rvec *x, /* The positions to project to an eigenvector */
+ t_eigvec *vec, /* The eigenvectors */
+ t_edpar *edi)
+{
+ int i;
+
+
+ if (!vec->neig) return;
+
+ /* Subtract average positions */
+ for (i=0; i<edi->sav.nr; i++)
+ rvec_dec(x[i], edi->sav.x[i]);
+
+ for (i=0; i<vec->neig; i++)
+ vec->xproj[i] = projectx(edi, x, vec->vec[i]);
+
+ /* Add average positions */
+ for (i=0; i<edi->sav.nr; i++)
+ rvec_inc(x[i], edi->sav.x[i]);
+}
+
+
+/* Project vector x onto all edi->vecs (mon, linfix,...) */
+static void project(rvec *x, /* positions to project */
+ t_edpar *edi) /* edi data set */
+{
+ /* It is not more work to subtract the average position in every
+ * subroutine again, because these routines are rarely used simultanely */
+ project_to_eigvectors(x, &edi->vecs.mon , edi);
+ project_to_eigvectors(x, &edi->vecs.linfix, edi);
+ project_to_eigvectors(x, &edi->vecs.linacc, edi);
+ project_to_eigvectors(x, &edi->vecs.radfix, edi);
+ project_to_eigvectors(x, &edi->vecs.radacc, edi);
+ project_to_eigvectors(x, &edi->vecs.radcon, edi);
+}
+
+
+static real calc_radius(t_eigvec *vec)
+{
+ int i;
+ real rad=0.0;
+
+
+ for (i=0; i<vec->neig; i++)
+ rad += pow((vec->refproj[i]-vec->xproj[i]),2);
+
+ return rad=sqrt(rad);
+}
+
+
+/* Debug helper */
+#ifdef DEBUGHELPERS
+static void dump_xcoll(t_edpar *edi, struct t_do_edsam *buf, t_commrec *cr,
+ int step)
+{
+ int i;
+ FILE *fp;
+ char fn[STRLEN];
+ rvec *xcoll;
+ ivec *shifts, *eshifts;
+
+
+ if (!MASTER(cr))
+ return;
+
+ xcoll = buf->xcoll;
+ shifts = buf->shifts_xcoll;
+ eshifts = buf->extra_shifts_xcoll;
+
+ sprintf(fn, "xcolldump_step%d.txt", step);
+ fp = fopen(fn, "w");
+
+ for (i=0; i<edi->sav.nr; i++)
+ fprintf(fp, "%d %9.5f %9.5f %9.5f %d %d %d %d %d %d\n",
+ edi->sav.anrs[i]+1,
+ xcoll[i][XX] , xcoll[i][YY] , xcoll[i][ZZ],
+ shifts[i][XX] , shifts[i][YY] , shifts[i][ZZ],
+ eshifts[i][XX], eshifts[i][YY], eshifts[i][ZZ]);
+
+ fclose(fp);
+}
+
+
+/* Debug helper */
+static void dump_edi_positions(FILE *out, struct gmx_edx *s, const char name[])
+{
+ int i;
+
+
+ fprintf(out, "#%s positions:\n%d\n", name, s->nr);
+ if (s->nr == 0)
+ return;
+
+ fprintf(out, "#index, x, y, z");
+ if (s->sqrtm)
+ fprintf(out, ", sqrt(m)");
+ for (i=0; i<s->nr; i++)
+ {
+ fprintf(out, "\n%6d %11.6f %11.6f %11.6f",s->anrs[i], s->x[i][XX], s->x[i][YY], s->x[i][ZZ]);
+ if (s->sqrtm)
+ fprintf(out,"%9.3f",s->sqrtm[i]);
+ }
+ fprintf(out, "\n");
+}
+
+
+/* Debug helper */
+static void dump_edi_eigenvecs(FILE *out, t_eigvec *ev,
+ const char name[], int length)
+{
+ int i,j;
+
+
+ fprintf(out, "#%s eigenvectors:\n%d\n", name, ev->neig);
+ /* Dump the data for every eigenvector: */
+ for (i=0; i<ev->neig; i++)
+ {
+ fprintf(out, "EV %4d\ncomponents %d\nstepsize %f\nxproj %f\nfproj %f\nrefproj %f\nradius %f\nComponents:\n",
+ ev->ieig[i], length, ev->stpsz[i], ev->xproj[i], ev->fproj[i], ev->refproj[i], ev->radius);
+ for (j=0; j<length; j++)
+ fprintf(out, "%11.6f %11.6f %11.6f\n", ev->vec[i][j][XX], ev->vec[i][j][YY], ev->vec[i][j][ZZ]);
+ }
+}
+
+
+/* Debug helper */
+static void dump_edi(t_edpar *edpars, t_commrec *cr, int nr_edi)
+{
+ FILE *out;
+ char fn[STRLEN];
+
+
+ sprintf(fn, "EDdump_node%d_edi%d", cr->nodeid, nr_edi);
+ out = ffopen(fn, "w");
+
+ fprintf(out,"#NINI\n %d\n#FITMAS\n %d\n#ANALYSIS_MAS\n %d\n",
+ edpars->nini,edpars->fitmas,edpars->pcamas);
+ fprintf(out,"#OUTFRQ\n %d\n#MAXLEN\n %d\n#SLOPECRIT\n %f\n",
+ edpars->outfrq,edpars->maxedsteps,edpars->slope);
+ fprintf(out,"#PRESTEPS\n %d\n#DELTA_F0\n %f\n#TAU\n %f\n#EFL_NULL\n %f\n#ALPHA2\n %f\n",
+ edpars->presteps,edpars->flood.deltaF0,edpars->flood.tau,
+ edpars->flood.constEfl,edpars->flood.alpha2);
+
+ /* Dump reference, average, target, origin positions */
+ dump_edi_positions(out, &edpars->sref, "REFERENCE");
+ dump_edi_positions(out, &edpars->sav , "AVERAGE" );
+ dump_edi_positions(out, &edpars->star, "TARGET" );
+ dump_edi_positions(out, &edpars->sori, "ORIGIN" );
+
+ /* Dump eigenvectors */
+ dump_edi_eigenvecs(out, &edpars->vecs.mon , "MONITORED", edpars->sav.nr);
+ dump_edi_eigenvecs(out, &edpars->vecs.linfix, "LINFIX" , edpars->sav.nr);
+ dump_edi_eigenvecs(out, &edpars->vecs.linacc, "LINACC" , edpars->sav.nr);
+ dump_edi_eigenvecs(out, &edpars->vecs.radfix, "RADFIX" , edpars->sav.nr);
+ dump_edi_eigenvecs(out, &edpars->vecs.radacc, "RADACC" , edpars->sav.nr);
+ dump_edi_eigenvecs(out, &edpars->vecs.radcon, "RADCON" , edpars->sav.nr);
+
+ /* Dump flooding eigenvectors */
+ dump_edi_eigenvecs(out, &edpars->flood.vecs, "FLOODING" , edpars->sav.nr);
+
+ /* Dump ed local buffer */
+ fprintf(out, "buf->do_edfit =%p\n", (void*)edpars->buf->do_edfit );
+ fprintf(out, "buf->do_edsam =%p\n", (void*)edpars->buf->do_edsam );
+ fprintf(out, "buf->do_radcon =%p\n", (void*)edpars->buf->do_radcon );
+
+ ffclose(out);
+}
+
+
+/* Debug helper */
+static void dump_rotmat(FILE* out,matrix rotmat)
+{
+ fprintf(out,"ROTMAT: %12.8f %12.8f %12.8f\n",rotmat[XX][XX],rotmat[XX][YY],rotmat[XX][ZZ]);
+ fprintf(out,"ROTMAT: %12.8f %12.8f %12.8f\n",rotmat[YY][XX],rotmat[YY][YY],rotmat[YY][ZZ]);
+ fprintf(out,"ROTMAT: %12.8f %12.8f %12.8f\n",rotmat[ZZ][XX],rotmat[ZZ][YY],rotmat[ZZ][ZZ]);
+}
+
+
+/* Debug helper */
+static void dump_rvec(FILE *out, int dim, rvec *x)
+{
+ int i;
+
+
+ for (i=0; i<dim; i++)
+ fprintf(out,"%4d %f %f %f\n",i,x[i][XX],x[i][YY],x[i][ZZ]);
+}
+
+
+/* Debug helper */
+static void dump_mat(FILE* out, int dim, double** mat)
+{
+ int i,j;
+
+
+ fprintf(out,"MATRIX:\n");
+ for (i=0;i<dim;i++)
+ {
+ for (j=0;j<dim;j++)
+ fprintf(out,"%f ",mat[i][j]);
+ fprintf(out,"\n");
+ }
+}
+#endif
+
+
+struct t_do_edfit {
+ double **omega;
+ double **om;
+};
+
+static void do_edfit(int natoms,rvec *xp,rvec *x,matrix R,t_edpar *edi)
+{
+ /* this is a copy of do_fit with some modifications */
+ int c,r,n,j,i,irot;
+ double d[6],xnr,xpc;
+ matrix vh,vk,u;
+ int index;
+ real max_d;
+
+ struct t_do_edfit *loc;
+ gmx_bool bFirst;
+
+ if(edi->buf->do_edfit != NULL)
+ bFirst = FALSE;
+ else
+ {
+ bFirst = TRUE;
+ snew(edi->buf->do_edfit,1);
+ }
+ loc = edi->buf->do_edfit;
+
+ if (bFirst)
+ {
+ snew(loc->omega,2*DIM);
+ snew(loc->om,2*DIM);
+ for(i=0; i<2*DIM; i++)
+ {
+ snew(loc->omega[i],2*DIM);
+ snew(loc->om[i],2*DIM);
+ }
+ }
+
+ for(i=0;(i<6);i++)
+ {
+ d[i]=0;
+ for(j=0;(j<6);j++)
+ {
+ loc->omega[i][j]=0;
+ loc->om[i][j]=0;
+ }
+ }
+
+ /* calculate the matrix U */
+ clear_mat(u);
+ for(n=0;(n<natoms);n++)
+ {
+ for(c=0; (c<DIM); c++)
+ {
+ xpc=xp[n][c];
+ for(r=0; (r<DIM); r++)
+ {
+ xnr=x[n][r];
+ u[c][r]+=xnr*xpc;
+ }
+ }
+ }
+
+ /* construct loc->omega */
+ /* loc->omega is symmetric -> loc->omega==loc->omega' */
+ for(r=0;(r<6);r++)
+ for(c=0;(c<=r);c++)
+ if ((r>=3) && (c<3))
+ {
+ loc->omega[r][c]=u[r-3][c];
+ loc->omega[c][r]=u[r-3][c];
+ }
+ else
+ {
+ loc->omega[r][c]=0;
+ loc->omega[c][r]=0;
+ }
+
+ /* determine h and k */
+#ifdef DEBUG
+ {
+ int i;
+ dump_mat(stderr,2*DIM,loc->omega);
+ for (i=0; i<6; i++)
+ fprintf(stderr,"d[%d] = %f\n",i,d[i]);
+ }
+#endif
+ jacobi(loc->omega,6,d,loc->om,&irot);
+
+ if (irot==0)
+ fprintf(stderr,"IROT=0\n");
+
+ index=0; /* For the compiler only */
+
+ for(j=0;(j<3);j++)
+ {
+ max_d=-1000;
+ for(i=0;(i<6);i++)
+ if (d[i]>max_d)
+ {
+ max_d=d[i];
+ index=i;
+ }
+ d[index]=-10000;
+ for(i=0;(i<3);i++)
+ {
+ vh[j][i]=M_SQRT2*loc->om[i][index];
+ vk[j][i]=M_SQRT2*loc->om[i+DIM][index];
+ }
+ }
+
+ /* determine R */
+ for(c=0;(c<3);c++)
+ for(r=0;(r<3);r++)
+ R[c][r]=vk[0][r]*vh[0][c]+
+ vk[1][r]*vh[1][c]+
+ vk[2][r]*vh[2][c];
+ if (det(R) < 0)
+ for(c=0;(c<3);c++)
+ for(r=0;(r<3);r++)
+ R[c][r]=vk[0][r]*vh[0][c]+
+ vk[1][r]*vh[1][c]-
+ vk[2][r]*vh[2][c];
+}
+
+
+static void rmfit(int nat, rvec *xcoll, rvec transvec, matrix rotmat)
+{
+ rvec vec;
+ matrix tmat;
+
+
+ /* Remove rotation.
+ * The inverse rotation is described by the transposed rotation matrix */
+ transpose(rotmat,tmat);
+ rotate_x(xcoll, nat, tmat);
+
+ /* Remove translation */
+ vec[XX]=-transvec[XX];
+ vec[YY]=-transvec[YY];
+ vec[ZZ]=-transvec[ZZ];
+ translate_x(xcoll, nat, vec);
+}
+
+
+/**********************************************************************************
+ ******************** FLOODING ****************************************************
+ **********************************************************************************
+
+The flooding ability was added later to edsam. Many of the edsam functionality could be reused for that purpose.
+The flooding covariance matrix, i.e. the selected eigenvectors and their corresponding eigenvalues are
+read as 7th Component Group. The eigenvalues are coded into the stepsize parameter (as used by -linfix or -linacc).
+
+do_md clls right in the beginning the function init_edsam, which reads the edi file, saves all the necessary information in
+the edi structure and calls init_flood, to initialise some extra fields in the edi->flood structure.
+
+since the flooding acts on forces do_flood is called from the function force() (force.c), while the other
+edsam functionality is hooked into md via the update() (update.c) function acting as constraint on positions.
+
+do_flood makes a copy of the positions,
+fits them, projects them computes flooding_energy, and flooding forces. The forces are computed in the
+space of the eigenvectors and are then blown up to the full cartesian space and rotated back to remove the
+fit. Then do_flood adds these forces to the forcefield-forces
+(given as parameter) and updates the adaptive flooding parameters Efl and deltaF.
+
+To center the flooding potential at a different location one can use the -ori option in make_edi. The ori
+structure is projected to the system of eigenvectors and then this position in the subspace is used as
+center of the flooding potential. If the option is not used, the center will be zero in the subspace,
+i.e. the average structure as given in the make_edi file.
+
+To use the flooding potential as restraint, make_edi has the option -restrain, which leads to inverted
+signs of alpha2 and Efl, such that the sign in the exponential of Vfl is not inverted but the sign of
+Vfl is inverted. Vfl = Efl * exp (- .../Efl/alpha2*x^2...) With tau>0 the negative Efl will grow slowly
+so that the restraint is switched off slowly. When Efl==0 and inverted flooding is ON is reached no
+ further adaption is applied, Efl will stay constant at zero.
+
+To use restraints with harmonic potentials switch -restrain and -harmonic. Then the eigenvalues are
+used as spring constants for the harmonic potential.
+Note that eq3 in the flooding paper (J. Comp. Chem. 2006, 27, 1693-1702) defines the parameter lambda \
+as the inverse of the spring constant, whereas the implementation uses lambda as the spring constant.
+
+To use more than one flooding matrix just concatenate several .edi files (cat flood1.edi flood2.edi > flood_all.edi)
+the routine read_edi_file reads all of theses flooding files.
+The structure t_edi is now organized as a list of t_edis and the function do_flood cycles through the list
+calling the do_single_flood() routine for every single entry. Since every state variables have been kept in one
+edi there is no interdependence whatsoever. The forces are added together.
+
+ To write energies into the .edr file, call the function
+ get_flood_enx_names(char**, int *nnames) to get the Header (Vfl1 Vfl2... Vfln)
+and call
+ get_flood_energies(real Vfl[],int nnames);
+
+ TODO:
+- one could program the whole thing such that Efl, Vfl and deltaF is written to the .edr file. -- i dont know how to do that, yet.
+
+ Maybe one should give a range of atoms for which to remove motion, so that motion is removed with
+ two edsam files from two peptide chains
+*/
+
+static void write_edo_flood(t_edpar *edi, FILE *fp, gmx_large_int_t step)
+{
+ int i;
+ char buf[22];
+ gmx_bool bOutputRef=FALSE;
+
+
+ fprintf(fp,"%d.th FL: %s %12.5e %12.5e %12.5e\n",
+ edi->flood.flood_id, gmx_step_str(step,buf),
+ edi->flood.Efl, edi->flood.Vfl, edi->flood.deltaF);
+
+
+ /* Check whether any of the references changes with time (this can happen
+ * in case flooding is used as harmonic restraint). If so, output all the
+ * current reference projections. */
+ if (edi->flood.bHarmonic)
+ {
+ for (i = 0; i < edi->flood.vecs.neig; i++)
+ {
+ if (edi->flood.vecs.refprojslope[i] != 0.0)
+ bOutputRef=TRUE;
+ }
+ if (bOutputRef)
+ {
+ fprintf(fp, "Ref. projs.: ");
+ for (i = 0; i < edi->flood.vecs.neig; i++)
+ {
+ fprintf(fp, "%12.5e ", edi->flood.vecs.refproj[i]);
+ }
+ fprintf(fp, "\n");
+ }
+ }
+ fprintf(fp,"FL_FORCES: ");
+
+ for (i=0; i<edi->flood.vecs.neig; i++)
+ fprintf(fp," %12.5e",edi->flood.vecs.fproj[i]);
+
+ fprintf(fp,"\n");
+}
+
+
+/* From flood.xproj compute the Vfl(x) at this point */
+static real flood_energy(t_edpar *edi, gmx_large_int_t step)
+{
+ /* compute flooding energy Vfl
+ Vfl = Efl * exp( - \frac {kT} {2Efl alpha^2} * sum_i { \lambda_i c_i^2 } )
+ \lambda_i is the reciprocal eigenvalue 1/\sigma_i
+ it is already computed by make_edi and stored in stpsz[i]
+ bHarmonic:
+ Vfl = - Efl * 1/2(sum _i {\frac 1{\lambda_i} c_i^2})
+ */
+ real sum;
+ real Vfl;
+ int i;
+
+
+ /* Each time this routine is called (i.e. each time step), we add a small
+ * value to the reference projection. This way a harmonic restraint towards
+ * a moving reference is realized. If no value for the additive constant
+ * is provided in the edi file, the reference will not change. */
+ if (edi->flood.bHarmonic)
+ {
+ for (i=0; i<edi->flood.vecs.neig; i++)
+ {
+ edi->flood.vecs.refproj[i] = edi->flood.vecs.refproj0[i] + step * edi->flood.vecs.refprojslope[i];
+ }
+ }
+
+ sum=0.0;
+ /* Compute sum which will be the exponent of the exponential */
+ for (i=0; i<edi->flood.vecs.neig; i++)
+ {
+ /* stpsz stores the reciprocal eigenvalue 1/sigma_i */
+ sum += edi->flood.vecs.stpsz[i]*(edi->flood.vecs.xproj[i]-edi->flood.vecs.refproj[i])*(edi->flood.vecs.xproj[i]-edi->flood.vecs.refproj[i]);
+ }
+
+ /* Compute the Gauss function*/
+ if (edi->flood.bHarmonic)
+ {
+ Vfl = -0.5*edi->flood.Efl*sum; /* minus sign because Efl is negative, if restrain is on. */
+ }
+ else
+ {
+ Vfl = edi->flood.Efl!=0 ? edi->flood.Efl*exp(-edi->flood.kT/2/edi->flood.Efl/edi->flood.alpha2*sum) :0;
+ }
+
+ return Vfl;
+}
+
+
+/* From the position and from Vfl compute forces in subspace -> store in edi->vec.flood.fproj */
+static void flood_forces(t_edpar *edi)
+{
+ /* compute the forces in the subspace of the flooding eigenvectors
+ * by the formula F_i= V_{fl}(c) * ( \frac {kT} {E_{fl}} \lambda_i c_i */
+
+ int i;
+ real energy=edi->flood.Vfl;
+
+
+ if (edi->flood.bHarmonic)
+ for (i=0; i<edi->flood.vecs.neig; i++)
+ {
+ edi->flood.vecs.fproj[i] = edi->flood.Efl* edi->flood.vecs.stpsz[i]*(edi->flood.vecs.xproj[i]-edi->flood.vecs.refproj[i]);
+ }
+ else
+ for (i=0; i<edi->flood.vecs.neig; i++)
+ {
+ /* if Efl is zero the forces are zero if not use the formula */
+ edi->flood.vecs.fproj[i] = edi->flood.Efl!=0 ? edi->flood.kT/edi->flood.Efl/edi->flood.alpha2*energy*edi->flood.vecs.stpsz[i]*(edi->flood.vecs.xproj[i]-edi->flood.vecs.refproj[i]) : 0;
+ }
+}
+
+
+/* Raise forces from subspace into cartesian space */
+static void flood_blowup(t_edpar *edi, rvec *forces_cart)
+{
+ /* this function lifts the forces from the subspace to the cartesian space
+ all the values not contained in the subspace are assumed to be zero and then
+ a coordinate transformation from eigenvector to cartesian vectors is performed
+ The nonexistent values don't have to be set to zero explicitly, they would occur
+ as zero valued summands, hence we just stop to compute this part of the sum.
+
+ for every atom we add all the contributions to this atom from all the different eigenvectors.
+
+ NOTE: one could add directly to the forcefield forces, would mean we wouldn't have to clear the
+ field forces_cart prior the computation, but we compute the forces separately
+ to have them accessible for diagnostics
+ */
+ int j,eig;
+ rvec dum;
+ real *forces_sub;
+
+
+ forces_sub = edi->flood.vecs.fproj;
+
+
+ /* Calculate the cartesian forces for the local atoms */
+
+ /* Clear forces first */
+ for (j=0; j<edi->sav.nr_loc; j++)
+ clear_rvec(forces_cart[j]);
+
+ /* Now compute atomwise */
+ for (j=0; j<edi->sav.nr_loc; j++)
+ {
+ /* Compute forces_cart[edi->sav.anrs[j]] */
+ for (eig=0; eig<edi->flood.vecs.neig; eig++)
+ {
+ /* Force vector is force * eigenvector (compute only atom j) */
+ svmul(forces_sub[eig],edi->flood.vecs.vec[eig][edi->sav.c_ind[j]],dum);
+ /* Add this vector to the cartesian forces */
+ rvec_inc(forces_cart[j],dum);
+ }
+ }
+}
+
+
+/* Update the values of Efl, deltaF depending on tau and Vfl */
+static void update_adaption(t_edpar *edi)
+{
+ /* this function updates the parameter Efl and deltaF according to the rules given in
+ * 'predicting unimolecular chemical reactions: chemical flooding' M Mueller et al,
+ * J. chem Phys. */
+
+ if ((edi->flood.tau < 0 ? -edi->flood.tau : edi->flood.tau ) > 0.00000001)
+ {
+ edi->flood.Efl = edi->flood.Efl+edi->flood.dt/edi->flood.tau*(edi->flood.deltaF0-edi->flood.deltaF);
+ /* check if restrain (inverted flooding) -> don't let EFL become positive */
+ if (edi->flood.alpha2<0 && edi->flood.Efl>-0.00000001)
+ edi->flood.Efl = 0;
+
+ edi->flood.deltaF = (1-edi->flood.dt/edi->flood.tau)*edi->flood.deltaF+edi->flood.dt/edi->flood.tau*edi->flood.Vfl;
+ }
+}
+
+
+static void do_single_flood(
+ FILE *edo,
+ rvec x[],
+ rvec force[],
+ t_edpar *edi,
+ gmx_large_int_t step,
+ matrix box,
+ t_commrec *cr)
+{
+ int i;
+ matrix rotmat; /* rotation matrix */
+ matrix tmat; /* inverse rotation */
+ rvec transvec; /* translation vector */
+ struct t_do_edsam *buf;
+
+
+ buf=edi->buf->do_edsam;
+
+ /* Broadcast the positions of the AVERAGE structure such that they are known on
+ * every processor. Each node contributes its local positions x and stores them in
+ * the collective ED array buf->xcoll */
+ communicate_group_positions(cr, buf->xcoll, buf->shifts_xcoll, buf->extra_shifts_xcoll, buf->bUpdateShifts, x,
+ edi->sav.nr, edi->sav.nr_loc, edi->sav.anrs_loc, edi->sav.c_ind, edi->sav.x_old, box);
+
+ /* Only assembly REFERENCE positions if their indices differ from the average ones */
+ if (!edi->bRefEqAv)
+ communicate_group_positions(cr, buf->xc_ref, buf->shifts_xc_ref, buf->extra_shifts_xc_ref, buf->bUpdateShifts, x,
+ edi->sref.nr, edi->sref.nr_loc, edi->sref.anrs_loc, edi->sref.c_ind, edi->sref.x_old, box);
+
+ /* If bUpdateShifts was TRUE, the shifts have just been updated in get_positions.
+ * We do not need to update the shifts until the next NS step */
+ buf->bUpdateShifts = FALSE;
+
+ /* Now all nodes have all of the ED/flooding positions in edi->sav->xcoll,
+ * as well as the indices in edi->sav.anrs */
+
+ /* Fit the reference indices to the reference structure */
+ if (edi->bRefEqAv)
+ fit_to_reference(buf->xcoll , transvec, rotmat, edi);
+ else
+ fit_to_reference(buf->xc_ref, transvec, rotmat, edi);
+
+ /* Now apply the translation and rotation to the ED structure */
+ translate_and_rotate(buf->xcoll, edi->sav.nr, transvec, rotmat);
+
+ /* Project fitted structure onto supbspace -> store in edi->flood.vecs.xproj */
+ project_to_eigvectors(buf->xcoll,&edi->flood.vecs,edi);
+
+ if (FALSE == edi->flood.bConstForce)
+ {
+ /* Compute Vfl(x) from flood.xproj */
+ edi->flood.Vfl = flood_energy(edi, step);
+
+ update_adaption(edi);
+
+ /* Compute the flooding forces */
+ flood_forces(edi);
+ }
+
+ /* Translate them into cartesian positions */
+ flood_blowup(edi, edi->flood.forces_cartesian);
+
+ /* Rotate forces back so that they correspond to the given structure and not to the fitted one */
+ /* Each node rotates back its local forces */
+ transpose(rotmat,tmat);
+ rotate_x(edi->flood.forces_cartesian, edi->sav.nr_loc, tmat);
+
+ /* Finally add forces to the main force variable */
+ for (i=0; i<edi->sav.nr_loc; i++)
+ rvec_inc(force[edi->sav.anrs_loc[i]],edi->flood.forces_cartesian[i]);
+
+ /* Output is written by the master process */
+ if (do_per_step(step,edi->outfrq) && MASTER(cr))
+ write_edo_flood(edi,edo,step);
+}
+
+
+/* Main flooding routine, called from do_force */
+extern void do_flood(
+ FILE *log, /* md.log file */
+ t_commrec *cr, /* Communication record */
+ rvec x[], /* Positions on the local processor */
+ rvec force[], /* forcefield forces, to these the flooding forces are added */
+ gmx_edsam_t ed, /* ed data structure contains all ED and flooding datasets */
+ matrix box, /* the box */
+ gmx_large_int_t step) /* The relative time step since ir->init_step is already subtracted */
+{
+ t_edpar *edi;
+
+
+ if (ed->eEDtype != eEDflood)
+ return;
+
+ edi = ed->edpar;
+ while (edi)
+ {
+ /* Call flooding for one matrix */
+ if (edi->flood.vecs.neig)
+ do_single_flood(ed->edo,x,force,edi,step,box,cr);
+ edi = edi->next_edi;
+ }
+}
+
+
+/* Called by init_edi, configure some flooding related variables and structures,
+ * print headers to output files */
+static void init_flood(t_edpar *edi, gmx_edsam_t ed, real dt, t_commrec *cr)
+{
+ int i;
+
+
+ edi->flood.Efl = edi->flood.constEfl;
+ edi->flood.Vfl = 0;
+ edi->flood.dt = dt;
+
+ if (edi->flood.vecs.neig)
+ {
+ /* If in any of the datasets we find a flooding vector, flooding is turned on */
+ ed->eEDtype = eEDflood;
+
+ fprintf(stderr,"ED: Flooding of matrix %d is switched on.\n", edi->flood.flood_id);
+
+ if (edi->flood.bConstForce)
+ {
+ /* We have used stpsz as a vehicle to carry the fproj values for constant
+ * force flooding. Now we copy that to flood.vecs.fproj. Note that
+ * in const force flooding, fproj is never changed. */
+ for (i=0; i<edi->flood.vecs.neig; i++)
+ {
+ edi->flood.vecs.fproj[i] = edi->flood.vecs.stpsz[i];
+
+ fprintf(stderr, "ED: applying on eigenvector %d a constant force of %g\n",
+ edi->flood.vecs.ieig[i], edi->flood.vecs.fproj[i]);
+ }
+ }
+ fprintf(ed->edo,"FL_HEADER: Flooding of matrix %d is switched on! The flooding output will have the following format:\n",
+ edi->flood.flood_id);
+ fprintf(ed->edo,"FL_HEADER: Step Efl Vfl deltaF\n");
+ }
+}
+
+
+#ifdef DEBUGHELPERS
+/*********** Energy book keeping ******/
+static void get_flood_enx_names(t_edpar *edi, char** names, int *nnames) /* get header of energies */
+{
+ t_edpar *actual;
+ int count;
+ char buf[STRLEN];
+ actual=edi;
+ count = 1;
+ while (actual)
+ {
+ srenew(names,count);
+ sprintf(buf,"Vfl_%d",count);
+ names[count-1]=strdup(buf);
+ actual=actual->next_edi;
+ count++;
+ }
+ *nnames=count-1;
+}
+
+
+static void get_flood_energies(t_edpar *edi, real Vfl[],int nnames)
+{
+ /*fl has to be big enough to capture nnames-many entries*/
+ t_edpar *actual;
+ int count;
+
+
+ actual=edi;
+ count = 1;
+ while (actual)
+ {
+ Vfl[count-1]=actual->flood.Vfl;
+ actual=actual->next_edi;
+ count++;
+ }
+ if (nnames!=count-1)
+ gmx_fatal(FARGS,"Number of energies is not consistent with t_edi structure");
+}
+/************* END of FLOODING IMPLEMENTATION ****************************/
+#endif
+
+
+gmx_edsam_t ed_open(int nfile,const t_filenm fnm[],unsigned long Flags,t_commrec *cr)
+{
+ gmx_edsam_t ed;
+
+
+ /* Allocate space for the ED data structure */
+ snew(ed, 1);
+
+ /* We want to perform ED (this switch might later be upgraded to eEDflood) */
+ ed->eEDtype = eEDedsam;
+
+ if (MASTER(cr))
+ {
+ /* Open .edi input file: */
+ ed->edinam=ftp2fn(efEDI,nfile,fnm);
+ /* The master opens the .edo output file */
+ fprintf(stderr,"ED sampling will be performed!\n");
+ ed->edonam = ftp2fn(efEDO,nfile,fnm);
+ ed->edo = gmx_fio_fopen(ed->edonam,(Flags & MD_APPENDFILES)? "a+" : "w+");
+ ed->bStartFromCpt = Flags & MD_STARTFROMCPT;
+ }
+ return ed;
+}
+
+
+/* Broadcasts the structure data */
+static void bc_ed_positions(t_commrec *cr, struct gmx_edx *s, int stype)
+{
+ snew_bc(cr, s->anrs, s->nr ); /* Index numbers */
+ snew_bc(cr, s->x , s->nr ); /* Positions */
+ nblock_bc(cr, s->nr, s->anrs );
+ nblock_bc(cr, s->nr, s->x );
+
+ /* For the average & reference structures we need an array for the collective indices,
+ * and we need to broadcast the masses as well */
+ if (stype == eedAV || stype == eedREF)
+ {
+ /* We need these additional variables in the parallel case: */
+ snew(s->c_ind , s->nr ); /* Collective indices */
+ /* Local atom indices get assigned in dd_make_local_group_indices.
+ * There, also memory is allocated */
+ s->nalloc_loc = 0; /* allocation size of s->anrs_loc */
+ snew_bc(cr, s->x_old, s->nr); /* To be able to always make the ED molecule whole, ... */
+ nblock_bc(cr, s->nr, s->x_old); /* ... keep track of shift changes with the help of old coords */
+ }
+
+ /* broadcast masses for the reference structure (for mass-weighted fitting) */
+ if (stype == eedREF)
+ {
+ snew_bc(cr, s->m, s->nr);
+ nblock_bc(cr, s->nr, s->m);
+ }
+
+ /* For the average structure we might need the masses for mass-weighting */
+ if (stype == eedAV)
+ {
+ snew_bc(cr, s->sqrtm, s->nr);
+ nblock_bc(cr, s->nr, s->sqrtm);
+ snew_bc(cr, s->m, s->nr);
+ nblock_bc(cr, s->nr, s->m);
+ }
+}
+
+
+/* Broadcasts the eigenvector data */
+static void bc_ed_vecs(t_commrec *cr, t_eigvec *ev, int length, gmx_bool bHarmonic)
+{
+ int i;
+
+ snew_bc(cr, ev->ieig , ev->neig); /* index numbers of eigenvector */
+ snew_bc(cr, ev->stpsz , ev->neig); /* stepsizes per eigenvector */
+ snew_bc(cr, ev->xproj , ev->neig); /* instantaneous x projection */
+ snew_bc(cr, ev->fproj , ev->neig); /* instantaneous f projection */
+ snew_bc(cr, ev->refproj, ev->neig); /* starting or target projection */
+
+ nblock_bc(cr, ev->neig, ev->ieig );
+ nblock_bc(cr, ev->neig, ev->stpsz );
+ nblock_bc(cr, ev->neig, ev->xproj );
+ nblock_bc(cr, ev->neig, ev->fproj );
+ nblock_bc(cr, ev->neig, ev->refproj);
+
+ snew_bc(cr, ev->vec, ev->neig); /* Eigenvector components */
+ for (i=0; i<ev->neig; i++)
+ {
+ snew_bc(cr, ev->vec[i], length);
+ nblock_bc(cr, length, ev->vec[i]);
+ }
+
+ /* For harmonic restraints the reference projections can change with time */
+ if (bHarmonic)
+ {
+ snew_bc(cr, ev->refproj0 , ev->neig);
+ snew_bc(cr, ev->refprojslope, ev->neig);
+ nblock_bc(cr, ev->neig, ev->refproj0 );
+ nblock_bc(cr, ev->neig, ev->refprojslope);
+ }
+}
+
+
+/* Broadcasts the ED / flooding data to other nodes
+ * and allocates memory where needed */
+static void broadcast_ed_data(t_commrec *cr, gmx_edsam_t ed, int numedis)
+{
+ int nr;
+ t_edpar *edi;
+
+
+ /* Master lets the other nodes know if its ED only or also flooding */
+ gmx_bcast(sizeof(ed->eEDtype), &(ed->eEDtype), cr);
+
+ snew_bc(cr, ed->edpar,1);
+ /* Now transfer the ED data set(s) */
+ edi = ed->edpar;
+ for (nr=0; nr<numedis; nr++)
+ {
+ /* Broadcast a single ED data set */
+ block_bc(cr, *edi);
+
+ /* Broadcast positions */
+ bc_ed_positions(cr, &(edi->sref), eedREF); /* reference positions (don't broadcast masses) */
+ bc_ed_positions(cr, &(edi->sav ), eedAV ); /* average positions (do broadcast masses as well) */
+ bc_ed_positions(cr, &(edi->star), eedTAR); /* target positions */
+ bc_ed_positions(cr, &(edi->sori), eedORI); /* origin positions */
+
+ /* Broadcast eigenvectors */
+ bc_ed_vecs(cr, &edi->vecs.mon , edi->sav.nr, FALSE);
+ bc_ed_vecs(cr, &edi->vecs.linfix, edi->sav.nr, FALSE);
+ bc_ed_vecs(cr, &edi->vecs.linacc, edi->sav.nr, FALSE);
+ bc_ed_vecs(cr, &edi->vecs.radfix, edi->sav.nr, FALSE);
+ bc_ed_vecs(cr, &edi->vecs.radacc, edi->sav.nr, FALSE);
+ bc_ed_vecs(cr, &edi->vecs.radcon, edi->sav.nr, FALSE);
+ /* Broadcast flooding eigenvectors and, if needed, values for the moving reference */
+ bc_ed_vecs(cr, &edi->flood.vecs, edi->sav.nr, edi->flood.bHarmonic);
+
+ /* Set the pointer to the next ED dataset */
+ if (edi->next_edi)
+ {
+ snew_bc(cr, edi->next_edi, 1);
+ edi = edi->next_edi;
+ }
+ }
+}
+
+
+/* init-routine called for every *.edi-cycle, initialises t_edpar structure */
+static void init_edi(gmx_mtop_t *mtop,t_inputrec *ir,
+ t_commrec *cr,gmx_edsam_t ed,t_edpar *edi)
+{
+ int i;
+ real totalmass = 0.0;
+ rvec com;
+ t_atom *atom;
+
+ /* NOTE Init_edi is executed on the master process only
+ * The initialized data sets are then transmitted to the
+ * other nodes in broadcast_ed_data */
+
+ edi->bNeedDoEdsam = edi->vecs.mon.neig
+ || edi->vecs.linfix.neig
+ || edi->vecs.linacc.neig
+ || edi->vecs.radfix.neig
+ || edi->vecs.radacc.neig
+ || edi->vecs.radcon.neig;
+
+ /* evaluate masses (reference structure) */
+ snew(edi->sref.m, edi->sref.nr);
+ for (i = 0; i < edi->sref.nr; i++)
+ {
+ if (edi->fitmas)
+ {
+ gmx_mtop_atomnr_to_atom(mtop,edi->sref.anrs[i],&atom);
+ edi->sref.m[i] = atom->m;
+ }
+ else
+ {
+ edi->sref.m[i] = 1.0;
+ }
+
+ /* Check that every m > 0. Bad things will happen otherwise. */
+ if (edi->sref.m[i] <= 0.0)
+ {
+ gmx_fatal(FARGS, "Reference structure atom %d (sam.edi index %d) has a mass of %g.\n"
+ "For a mass-weighted fit, all reference structure atoms need to have a mass >0.\n"
+ "Either make the covariance analysis non-mass-weighted, or exclude massless\n"
+ "atoms from the reference structure by creating a proper index group.\n",
+ i, edi->sref.anrs[i]+1, edi->sref.m[i]);
+ }
+
+ totalmass += edi->sref.m[i];
+ }
+ edi->sref.mtot = totalmass;
+
+ /* Masses m and sqrt(m) for the average structure. Note that m
+ * is needed if forces have to be evaluated in do_edsam */
+ snew(edi->sav.sqrtm, edi->sav.nr );
+ snew(edi->sav.m , edi->sav.nr );
+ for (i = 0; i < edi->sav.nr; i++)
+ {
+ gmx_mtop_atomnr_to_atom(mtop,edi->sav.anrs[i],&atom);
+ edi->sav.m[i] = atom->m;
+ if (edi->pcamas)
+ {
+ edi->sav.sqrtm[i] = sqrt(atom->m);
+ }
+ else
+ {
+ edi->sav.sqrtm[i] = 1.0;
+ }
+
+ /* Check that every m > 0. Bad things will happen otherwise. */
+ if (edi->sav.sqrtm[i] <= 0.0)
+ {
+ gmx_fatal(FARGS, "Average structure atom %d (sam.edi index %d) has a mass of %g.\n"
+ "For ED with mass-weighting, all average structure atoms need to have a mass >0.\n"
+ "Either make the covariance analysis non-mass-weighted, or exclude massless\n"
+ "atoms from the average structure by creating a proper index group.\n",
+ i, edi->sav.anrs[i]+1, atom->m);
+ }
+ }
+
+ /* put reference structure in origin */
+ get_center(edi->sref.x, edi->sref.m, edi->sref.nr, com);
+ com[XX] = -com[XX];
+ com[YY] = -com[YY];
+ com[ZZ] = -com[ZZ];
+ translate_x(edi->sref.x, edi->sref.nr, com);
+
+ /* Init ED buffer */
+ snew(edi->buf, 1);
+}
+
+
+static void check(const char *line, const char *label)
+{
+ if (!strstr(line,label))
+ gmx_fatal(FARGS,"Could not find input parameter %s at expected position in edsam input-file (.edi)\nline read instead is %s",label,line);
+}
+
+
+static int read_checked_edint(FILE *file,const char *label)
+{
+ char line[STRLEN+1];
+ int idum;
+
+
+ fgets2 (line,STRLEN,file);
+ check(line,label);
+ fgets2 (line,STRLEN,file);
+ sscanf (line,"%d",&idum);
+ return idum;
+}
+
+
+static int read_edint(FILE *file,gmx_bool *bEOF)
+{
+ char line[STRLEN+1];
+ int idum;
+ char *eof;
+
+
+ eof=fgets2 (line,STRLEN,file);
+ if (eof==NULL)
+ {
+ *bEOF = TRUE;
+ return -1;
+ }
+ eof=fgets2 (line,STRLEN,file);
+ if (eof==NULL)
+ {
+ *bEOF = TRUE;
+ return -1;
+ }
+ sscanf (line,"%d",&idum);
+ *bEOF = FALSE;
+ return idum;
+}
+
+
+static real read_checked_edreal(FILE *file,const char *label)
+{
+ char line[STRLEN+1];
+ double rdum;
+
+
+ fgets2 (line,STRLEN,file);
+ check(line,label);
+ fgets2 (line,STRLEN,file);
+ sscanf (line,"%lf",&rdum);
+ return (real) rdum; /* always read as double and convert to single */
+}
+
+
+static void read_edx(FILE *file,int number,int *anrs,rvec *x)
+{
+ int i,j;
+ char line[STRLEN+1];
+ double d[3];
+
+
+ for(i=0; i<number; i++)
+ {
+ fgets2 (line,STRLEN,file);
+ sscanf (line,"%d%lf%lf%lf",&anrs[i],&d[0],&d[1],&d[2]);
+ anrs[i]--; /* we are reading FORTRAN indices */
+ for(j=0; j<3; j++)
+ x[i][j]=d[j]; /* always read as double and convert to single */
+ }
+}
+
+
+static void scan_edvec(FILE *in,int nr,rvec *vec)
+{
+ char line[STRLEN+1];
+ int i;
+ double x,y,z;
+
+
+ for(i=0; (i < nr); i++)
+ {
+ fgets2 (line,STRLEN,in);
+ sscanf (line,"%le%le%le",&x,&y,&z);
+ vec[i][XX]=x;
+ vec[i][YY]=y;
+ vec[i][ZZ]=z;
+ }
+}
+
+
+static void read_edvec(FILE *in,int nr,t_eigvec *tvec,gmx_bool bReadRefproj, gmx_bool *bHaveReference)
+{
+ int i,idum,nscan;
+ double rdum,refproj_dum=0.0,refprojslope_dum=0.0;
+ char line[STRLEN+1];
+
+
+ tvec->neig=read_checked_edint(in,"NUMBER OF EIGENVECTORS");
+ if (tvec->neig >0)
+ {
+ snew(tvec->ieig ,tvec->neig);
+ snew(tvec->stpsz ,tvec->neig);
+ snew(tvec->vec ,tvec->neig);
+ snew(tvec->xproj ,tvec->neig);
+ snew(tvec->fproj ,tvec->neig);
+ snew(tvec->refproj,tvec->neig);
+ if (bReadRefproj)
+ {
+ snew(tvec->refproj0 ,tvec->neig);
+ snew(tvec->refprojslope,tvec->neig);
+ }
+
+ for(i=0; (i < tvec->neig); i++)
+ {
+ fgets2 (line,STRLEN,in);
+ if (bReadRefproj) /* ONLY when using flooding as harmonic restraint */
+ {
+ nscan = sscanf(line,"%d%lf%lf%lf",&idum,&rdum,&refproj_dum,&refprojslope_dum);
+ /* Zero out values which were not scanned */
+ switch(nscan)
+ {
+ case 4:
+ /* Every 4 values read, including reference position */
+ *bHaveReference = TRUE;
+ break;
+ case 3:
+ /* A reference position is provided */
+ *bHaveReference = TRUE;
+ /* No value for slope, set to 0 */
+ refprojslope_dum = 0.0;
+ break;
+ case 2:
+ /* No values for reference projection and slope, set to 0 */
+ refproj_dum = 0.0;
+ refprojslope_dum = 0.0;
+ break;
+ default:
+ gmx_fatal(FARGS,"Expected 2 - 4 (not %d) values for flooding vec: <nr> <spring const> <refproj> <refproj-slope>\n", nscan);
+ break;
+ }
+ tvec->refproj[i]=refproj_dum;
+ tvec->refproj0[i]=refproj_dum;
+ tvec->refprojslope[i]=refprojslope_dum;
+ }
+ else /* Normal flooding */
+ {
+ nscan = sscanf(line,"%d%lf",&idum,&rdum);
+ if (nscan != 2)
+ gmx_fatal(FARGS,"Expected 2 values for flooding vec: <nr> <stpsz>\n");
+ }
+ tvec->ieig[i]=idum;
+ tvec->stpsz[i]=rdum;
+ } /* end of loop over eigenvectors */
+
+ for(i=0; (i < tvec->neig); i++)
+ {
+ snew(tvec->vec[i],nr);
+ scan_edvec(in,nr,tvec->vec[i]);
+ }
+ }
+}
+
+
+/* calls read_edvec for the vector groups, only for flooding there is an extra call */
+static void read_edvecs(FILE *in,int nr,t_edvecs *vecs)
+{
+ gmx_bool bHaveReference = FALSE;
+
+
+ read_edvec(in, nr, &vecs->mon , FALSE, &bHaveReference);
+ read_edvec(in, nr, &vecs->linfix, FALSE, &bHaveReference);
+ read_edvec(in, nr, &vecs->linacc, FALSE, &bHaveReference);
+ read_edvec(in, nr, &vecs->radfix, FALSE, &bHaveReference);
+ read_edvec(in, nr, &vecs->radacc, FALSE, &bHaveReference);
+ read_edvec(in, nr, &vecs->radcon, FALSE, &bHaveReference);
+}
+
+
+/* Check if the same atom indices are used for reference and average positions */
+static gmx_bool check_if_same(struct gmx_edx sref, struct gmx_edx sav)
+{
+ int i;
+
+
+ /* If the number of atoms differs between the two structures,
+ * they cannot be identical */
+ if (sref.nr != sav.nr)
+ return FALSE;
+
+ /* Now that we know that both stuctures have the same number of atoms,
+ * check if also the indices are identical */
+ for (i=0; i < sav.nr; i++)
+ {
+ if (sref.anrs[i] != sav.anrs[i])
+ return FALSE;
+ }
+ fprintf(stderr, "ED: Note: Reference and average structure are composed of the same atom indices.\n");
+
+ return TRUE;
+}
+
+
+static int read_edi(FILE* in, gmx_edsam_t ed,t_edpar *edi,int nr_mdatoms, int edi_nr, t_commrec *cr)
+{
+ int readmagic;
+ const int magic=670;
+ gmx_bool bEOF;
+
+ /* Was a specific reference point for the flooding/umbrella potential provided in the edi file? */
+ gmx_bool bHaveReference = FALSE;
+
+
+ /* the edi file is not free format, so expect problems if the input is corrupt. */
+
+ /* check the magic number */
+ readmagic=read_edint(in,&bEOF);
+ /* Check whether we have reached the end of the input file */
+ if (bEOF)
+ return 0;
+
+ if (readmagic != magic)
+ {
+ if (readmagic==666 || readmagic==667 || readmagic==668)
+ gmx_fatal(FARGS,"Wrong magic number: Use newest version of make_edi to produce edi file");
++ else if (readmagic != 669)
+ gmx_fatal(FARGS,"Wrong magic number %d in %s",readmagic,ed->edinam);
+ }
+
+ /* check the number of atoms */
+ edi->nini=read_edint(in,&bEOF);
+ if (edi->nini != nr_mdatoms)
+ gmx_fatal(FARGS,"Nr of atoms in %s (%d) does not match nr of md atoms (%d)",
+ ed->edinam,edi->nini,nr_mdatoms);
+
+ /* Done checking. For the rest we blindly trust the input */
+ edi->fitmas = read_checked_edint(in,"FITMAS");
+ edi->pcamas = read_checked_edint(in,"ANALYSIS_MAS");
+ edi->outfrq = read_checked_edint(in,"OUTFRQ");
+ edi->maxedsteps = read_checked_edint(in,"MAXLEN");
+ edi->slope = read_checked_edreal(in,"SLOPECRIT");
+
+ edi->presteps = read_checked_edint(in,"PRESTEPS");
+ edi->flood.deltaF0 = read_checked_edreal(in,"DELTA_F0");
+ edi->flood.deltaF = read_checked_edreal(in,"INIT_DELTA_F");
+ edi->flood.tau = read_checked_edreal(in,"TAU");
+ edi->flood.constEfl = read_checked_edreal(in,"EFL_NULL");
+ edi->flood.alpha2 = read_checked_edreal(in,"ALPHA2");
+ edi->flood.kT = read_checked_edreal(in,"KT");
+ edi->flood.bHarmonic = read_checked_edint(in,"HARMONIC");
+ if (readmagic > 669)
+ edi->flood.bConstForce = read_checked_edint(in,"CONST_FORCE_FLOODING");
+ else
+ edi->flood.bConstForce = FALSE;
+ edi->flood.flood_id = edi_nr;
+ edi->sref.nr = read_checked_edint(in,"NREF");
+
+ /* allocate space for reference positions and read them */
+ snew(edi->sref.anrs,edi->sref.nr);
+ snew(edi->sref.x ,edi->sref.nr);
+ if (PAR(cr))
+ snew(edi->sref.x_old,edi->sref.nr);
+ edi->sref.sqrtm =NULL;
+ read_edx(in,edi->sref.nr,edi->sref.anrs,edi->sref.x);
+
+ /* average positions. they define which atoms will be used for ED sampling */
+ edi->sav.nr=read_checked_edint(in,"NAV");
+ snew(edi->sav.anrs,edi->sav.nr);
+ snew(edi->sav.x ,edi->sav.nr);
+ if (PAR(cr))
+ snew(edi->sav.x_old,edi->sav.nr);
+ read_edx(in,edi->sav.nr,edi->sav.anrs,edi->sav.x);
+
+ /* Check if the same atom indices are used for reference and average positions */
+ edi->bRefEqAv = check_if_same(edi->sref, edi->sav);
+
+ /* eigenvectors */
+ read_edvecs(in,edi->sav.nr,&edi->vecs);
+ read_edvec(in,edi->sav.nr,&edi->flood.vecs,edi->flood.bHarmonic, &bHaveReference);
+
+ /* target positions */
+ edi->star.nr=read_edint(in,&bEOF);
+ if (edi->star.nr > 0)
+ {
+ snew(edi->star.anrs,edi->star.nr);
+ snew(edi->star.x ,edi->star.nr);
+ edi->star.sqrtm =NULL;
+ read_edx(in,edi->star.nr,edi->star.anrs,edi->star.x);
+ }
+
+ /* positions defining origin of expansion circle */
+ edi->sori.nr=read_edint(in,&bEOF);
+ if (edi->sori.nr > 0)
+ {
+ if (bHaveReference)
+ {
+ /* Both an -ori structure and a at least one manual reference point have been
+ * specified. That's ambiguous and probably not intentional. */
+ gmx_fatal(FARGS, "ED: An origin structure has been provided and a at least one (moving) reference\n"
+ " point was manually specified in the edi file. That is ambiguous. Aborting.\n");
+ }
+ snew(edi->sori.anrs,edi->sori.nr);
+ snew(edi->sori.x ,edi->sori.nr);
+ edi->sori.sqrtm =NULL;
+ read_edx(in,edi->sori.nr,edi->sori.anrs,edi->sori.x);
+ }
+
+ /* all done */
+ return 1;
+}
+
+
+
+/* Read in the edi input file. Note that it may contain several ED data sets which were
+ * achieved by concatenating multiple edi files. The standard case would be a single ED
+ * data set, though. */
+static void read_edi_file(gmx_edsam_t ed, t_edpar *edi, int nr_mdatoms, t_commrec *cr)
+{
+ FILE *in;
+ t_edpar *curr_edi,*last_edi;
+ t_edpar *edi_read;
+ int edi_nr = 0;
+
+
+ /* This routine is executed on the master only */
+
+ /* Open the .edi parameter input file */
+ in = gmx_fio_fopen(ed->edinam,"r");
+ fprintf(stderr, "ED: Reading edi file %s\n", ed->edinam);
+
+ /* Now read a sequence of ED input parameter sets from the edi file */
+ curr_edi=edi;
+ last_edi=edi;
+ while( read_edi(in, ed, curr_edi, nr_mdatoms, edi_nr, cr) )
+ {
+ edi_nr++;
+ /* Make shure that the number of atoms in each dataset is the same as in the tpr file */
+ if (edi->nini != nr_mdatoms)
+ gmx_fatal(FARGS,"edi file %s (dataset #%d) was made for %d atoms, but the simulation contains %d atoms.",
+ ed->edinam, edi_nr, edi->nini, nr_mdatoms);
+ /* Since we arrived within this while loop we know that there is still another data set to be read in */
+ /* We need to allocate space for the data: */
+ snew(edi_read,1);
+ /* Point the 'next_edi' entry to the next edi: */
+ curr_edi->next_edi=edi_read;
+ /* Keep the curr_edi pointer for the case that the next dataset is empty: */
+ last_edi = curr_edi;
+ /* Let's prepare to read in the next edi data set: */
+ curr_edi = edi_read;
+ }
+ if (edi_nr == 0)
+ gmx_fatal(FARGS, "No complete ED data set found in edi file %s.", ed->edinam);
+
+ /* Terminate the edi dataset list with a NULL pointer: */
+ last_edi->next_edi = NULL;
+
+ fprintf(stderr, "ED: Found %d ED dataset%s.\n", edi_nr, edi_nr>1? "s" : "");
+
+ /* Close the .edi file again */
+ gmx_fio_fclose(in);
+}
+
+
+struct t_fit_to_ref {
+ rvec *xcopy; /* Working copy of the positions in fit_to_reference */
+};
+
+/* Fit the current positions to the reference positions
+ * Do not actually do the fit, just return rotation and translation.
+ * Note that the COM of the reference structure was already put into
+ * the origin by init_edi. */
+static void fit_to_reference(rvec *xcoll, /* The positions to be fitted */
+ rvec transvec, /* The translation vector */
+ matrix rotmat, /* The rotation matrix */
+ t_edpar *edi) /* Just needed for do_edfit */
+{
+ rvec com; /* center of mass */
+ int i;
+ struct t_fit_to_ref *loc;
+
+
+ /* Allocate memory the first time this routine is called for each edi dataset */
+ if (NULL == edi->buf->fit_to_ref)
+ {
+ snew(edi->buf->fit_to_ref, 1);
+ snew(edi->buf->fit_to_ref->xcopy, edi->sref.nr);
+ }
+ loc = edi->buf->fit_to_ref;
+
+ /* We do not touch the original positions but work on a copy. */
+ for (i=0; i<edi->sref.nr; i++)
+ copy_rvec(xcoll[i], loc->xcopy[i]);
+
+ /* Calculate the center of mass */
+ get_center(loc->xcopy, edi->sref.m, edi->sref.nr, com);
+
+ transvec[XX] = -com[XX];
+ transvec[YY] = -com[YY];
+ transvec[ZZ] = -com[ZZ];
+
+ /* Subtract the center of mass from the copy */
+ translate_x(loc->xcopy, edi->sref.nr, transvec);
+
+ /* Determine the rotation matrix */
+ do_edfit(edi->sref.nr, edi->sref.x, loc->xcopy, rotmat, edi);
+}
+
+
+static void translate_and_rotate(rvec *x, /* The positions to be translated and rotated */
+ int nat, /* How many positions are there? */
+ rvec transvec, /* The translation vector */
+ matrix rotmat) /* The rotation matrix */
+{
+ /* Translation */
+ translate_x(x, nat, transvec);
+
+ /* Rotation */
+ rotate_x(x, nat, rotmat);
+}
+
+
+/* Gets the rms deviation of the positions to the structure s */
+/* fit_to_structure has to be called before calling this routine! */
+static real rmsd_from_structure(rvec *x, /* The positions under consideration */
+ struct gmx_edx *s) /* The structure from which the rmsd shall be computed */
+{
+ real rmsd=0.0;
+ int i;
+
+
+ for (i=0; i < s->nr; i++)
+ rmsd += distance2(s->x[i], x[i]);
+
+ rmsd /= (real) s->nr;
+ rmsd = sqrt(rmsd);
+
+ return rmsd;
+}
+
+
+void dd_make_local_ed_indices(gmx_domdec_t *dd, struct gmx_edsam *ed)
+{
+ t_edpar *edi;
+
+
+ if (ed->eEDtype != eEDnone)
+ {
+ /* Loop over ED datasets (usually there is just one dataset, though) */
+ edi=ed->edpar;
+ while (edi)
+ {
+ /* Local atoms of the reference structure (for fitting), need only be assembled
+ * if their indices differ from the average ones */
+ if (!edi->bRefEqAv)
+ dd_make_local_group_indices(dd->ga2la, edi->sref.nr, edi->sref.anrs,
+ &edi->sref.nr_loc, &edi->sref.anrs_loc, &edi->sref.nalloc_loc, edi->sref.c_ind);
+
+ /* Local atoms of the average structure (on these ED will be performed) */
+ dd_make_local_group_indices(dd->ga2la, edi->sav.nr, edi->sav.anrs,
+ &edi->sav.nr_loc, &edi->sav.anrs_loc, &edi->sav.nalloc_loc, edi->sav.c_ind);
+
+ /* Indicate that the ED shift vectors for this structure need to be updated
+ * at the next call to communicate_group_positions, since obviously we are in a NS step */
+ edi->buf->do_edsam->bUpdateShifts = TRUE;
+
+ /* Set the pointer to the next ED dataset (if any) */
+ edi=edi->next_edi;
+ }
+ }
+}
+
+
+static inline void ed_unshift_single_coord(matrix box, const rvec x, const ivec is, rvec xu)
+{
+ int tx,ty,tz;
+
+
+ tx=is[XX];
+ ty=is[YY];
+ tz=is[ZZ];
+
+ if(TRICLINIC(box))
+ {
+ xu[XX] = x[XX]-tx*box[XX][XX]-ty*box[YY][XX]-tz*box[ZZ][XX];
+ xu[YY] = x[YY]-ty*box[YY][YY]-tz*box[ZZ][YY];
+ xu[ZZ] = x[ZZ]-tz*box[ZZ][ZZ];
+ } else
+ {
+ xu[XX] = x[XX]-tx*box[XX][XX];
+ xu[YY] = x[YY]-ty*box[YY][YY];
+ xu[ZZ] = x[ZZ]-tz*box[ZZ][ZZ];
+ }
+}
+
+
+static void do_linfix(rvec *xcoll, t_edpar *edi, int step, t_commrec *cr)
+{
+ int i, j;
+ real proj, add;
+ rvec vec_dum;
+
+
+ /* loop over linfix vectors */
+ for (i=0; i<edi->vecs.linfix.neig; i++)
+ {
+ /* calculate the projection */
+ proj = projectx(edi, xcoll, edi->vecs.linfix.vec[i]);
+
+ /* calculate the correction */
+ add = edi->vecs.linfix.refproj[i] + step*edi->vecs.linfix.stpsz[i] - proj;
+
+ /* apply the correction */
+ add /= edi->sav.sqrtm[i];
+ for (j=0; j<edi->sav.nr; j++)
+ {
+ svmul(add, edi->vecs.linfix.vec[i][j], vec_dum);
+ rvec_inc(xcoll[j], vec_dum);
+ }
+ }
+}
+
+
+static void do_linacc(rvec *xcoll, t_edpar *edi, t_commrec *cr)
+{
+ int i, j;
+ real proj, add;
+ rvec vec_dum;
+
+
+ /* loop over linacc vectors */
+ for (i=0; i<edi->vecs.linacc.neig; i++)
+ {
+ /* calculate the projection */
+ proj=projectx(edi, xcoll, edi->vecs.linacc.vec[i]);
+
+ /* calculate the correction */
+ add = 0.0;
+ if (edi->vecs.linacc.stpsz[i] > 0.0)
+ {
+ if ((proj-edi->vecs.linacc.refproj[i]) < 0.0)
+ add = edi->vecs.linacc.refproj[i] - proj;
+ }
+ if (edi->vecs.linacc.stpsz[i] < 0.0)
+ {
+ if ((proj-edi->vecs.linacc.refproj[i]) > 0.0)
+ add = edi->vecs.linacc.refproj[i] - proj;
+ }
+
+ /* apply the correction */
+ add /= edi->sav.sqrtm[i];
+ for (j=0; j<edi->sav.nr; j++)
+ {
+ svmul(add, edi->vecs.linacc.vec[i][j], vec_dum);
+ rvec_inc(xcoll[j], vec_dum);
+ }
+
+ /* new positions will act as reference */
+ edi->vecs.linacc.refproj[i] = proj + add;
+ }
+}
+
+
+static void do_radfix(rvec *xcoll, t_edpar *edi, int step, t_commrec *cr)
+{
+ int i,j;
+ real *proj, rad=0.0, ratio;
+ rvec vec_dum;
+
+
+ if (edi->vecs.radfix.neig == 0)
+ return;
+
+ snew(proj, edi->vecs.radfix.neig);
+
+ /* loop over radfix vectors */
+ for (i=0; i<edi->vecs.radfix.neig; i++)
+ {
+ /* calculate the projections, radius */
+ proj[i] = projectx(edi, xcoll, edi->vecs.radfix.vec[i]);
+ rad += pow(proj[i] - edi->vecs.radfix.refproj[i], 2);
+ }
+
+ rad = sqrt(rad);
+ ratio = (edi->vecs.radfix.stpsz[0]+edi->vecs.radfix.radius)/rad - 1.0;
+ edi->vecs.radfix.radius += edi->vecs.radfix.stpsz[0];
+
+ /* loop over radfix vectors */
+ for (i=0; i<edi->vecs.radfix.neig; i++)
+ {
+ proj[i] -= edi->vecs.radfix.refproj[i];
+
+ /* apply the correction */
+ proj[i] /= edi->sav.sqrtm[i];
+ proj[i] *= ratio;
+ for (j=0; j<edi->sav.nr; j++) {
+ svmul(proj[i], edi->vecs.radfix.vec[i][j], vec_dum);
+ rvec_inc(xcoll[j], vec_dum);
+ }
+ }
+
+ sfree(proj);
+}
+
+
+static void do_radacc(rvec *xcoll, t_edpar *edi, t_commrec *cr)
+{
+ int i,j;
+ real *proj, rad=0.0, ratio=0.0;
+ rvec vec_dum;
+
+
+ if (edi->vecs.radacc.neig == 0)
+ return;
+
+ snew(proj,edi->vecs.radacc.neig);
+
+ /* loop over radacc vectors */
+ for (i=0; i<edi->vecs.radacc.neig; i++)
+ {
+ /* calculate the projections, radius */
+ proj[i] = projectx(edi, xcoll, edi->vecs.radacc.vec[i]);
+ rad += pow(proj[i] - edi->vecs.radacc.refproj[i], 2);
+ }
+ rad = sqrt(rad);
+
+ /* only correct when radius decreased */
+ if (rad < edi->vecs.radacc.radius)
+ {
+ ratio = edi->vecs.radacc.radius/rad - 1.0;
+ rad = edi->vecs.radacc.radius;
+ }
+ else
+ edi->vecs.radacc.radius = rad;
+
+ /* loop over radacc vectors */
+ for (i=0; i<edi->vecs.radacc.neig; i++)
+ {
+ proj[i] -= edi->vecs.radacc.refproj[i];
+
+ /* apply the correction */
+ proj[i] /= edi->sav.sqrtm[i];
+ proj[i] *= ratio;
+ for (j=0; j<edi->sav.nr; j++)
+ {
+ svmul(proj[i], edi->vecs.radacc.vec[i][j], vec_dum);
+ rvec_inc(xcoll[j], vec_dum);
+ }
+ }
+ sfree(proj);
+}
+
+
+struct t_do_radcon {
+ real *proj;
+};
+
+static void do_radcon(rvec *xcoll, t_edpar *edi, t_commrec *cr)
+{
+ int i,j;
+ real rad=0.0, ratio=0.0;
+ struct t_do_radcon *loc;
+ gmx_bool bFirst;
+ rvec vec_dum;
+
+
+ if(edi->buf->do_radcon != NULL)
+ {
+ bFirst = FALSE;
+ loc = edi->buf->do_radcon;
+ }
+ else
+ {
+ bFirst = TRUE;
+ snew(edi->buf->do_radcon, 1);
+ }
+ loc = edi->buf->do_radcon;
+
+ if (edi->vecs.radcon.neig == 0)
+ return;
+
+ if (bFirst)
+ snew(loc->proj, edi->vecs.radcon.neig);
+
+ /* loop over radcon vectors */
+ for (i=0; i<edi->vecs.radcon.neig; i++)
+ {
+ /* calculate the projections, radius */
+ loc->proj[i] = projectx(edi, xcoll, edi->vecs.radcon.vec[i]);
+ rad += pow(loc->proj[i] - edi->vecs.radcon.refproj[i], 2);
+ }
+ rad = sqrt(rad);
+ /* only correct when radius increased */
+ if (rad > edi->vecs.radcon.radius)
+ {
+ ratio = edi->vecs.radcon.radius/rad - 1.0;
+
+ /* loop over radcon vectors */
+ for (i=0; i<edi->vecs.radcon.neig; i++)
+ {
+ /* apply the correction */
+ loc->proj[i] -= edi->vecs.radcon.refproj[i];
+ loc->proj[i] /= edi->sav.sqrtm[i];
+ loc->proj[i] *= ratio;
+
+ for (j=0; j<edi->sav.nr; j++)
+ {
+ svmul(loc->proj[i], edi->vecs.radcon.vec[i][j], vec_dum);
+ rvec_inc(xcoll[j], vec_dum);
+ }
+ }
+ }
+ else
+ edi->vecs.radcon.radius = rad;
+
+ if (rad != edi->vecs.radcon.radius)
+ {
+ rad = 0.0;
+ for (i=0; i<edi->vecs.radcon.neig; i++)
+ {
+ /* calculate the projections, radius */
+ loc->proj[i] = projectx(edi, xcoll, edi->vecs.radcon.vec[i]);
+ rad += pow(loc->proj[i] - edi->vecs.radcon.refproj[i], 2);
+ }
+ rad = sqrt(rad);
+ }
+}
+
+
+static void ed_apply_constraints(rvec *xcoll, t_edpar *edi, gmx_large_int_t step, t_commrec *cr)
+{
+ int i;
+
+
+ /* subtract the average positions */
+ for (i=0; i<edi->sav.nr; i++)
+ rvec_dec(xcoll[i], edi->sav.x[i]);
+
+ /* apply the constraints */
+ if (step >= 0)
+ do_linfix(xcoll, edi, step, cr);
+ do_linacc(xcoll, edi, cr);
+ if (step >= 0)
+ do_radfix(xcoll, edi, step, cr);
+ do_radacc(xcoll, edi, cr);
+ do_radcon(xcoll, edi, cr);
+
+ /* add back the average positions */
+ for (i=0; i<edi->sav.nr; i++)
+ rvec_inc(xcoll[i], edi->sav.x[i]);
+}
+
+
+/* Write out the projections onto the eigenvectors */
+static void write_edo(int nr_edi, t_edpar *edi, gmx_edsam_t ed, gmx_large_int_t step,real rmsd)
+{
+ int i;
+ char buf[22];
+
+
+ if (edi->bNeedDoEdsam)
+ {
+ if (step == -1)
+ fprintf(ed->edo, "Initial projections:\n");
+ else
+ {
+ fprintf(ed->edo,"Step %s, ED #%d ", gmx_step_str(step, buf), nr_edi);
+ fprintf(ed->edo," RMSD %f nm\n",rmsd);
+ }
+
+ if (edi->vecs.mon.neig)
+ {
+ fprintf(ed->edo," Monitor eigenvectors");
+ for (i=0; i<edi->vecs.mon.neig; i++)
+ fprintf(ed->edo," %d: %12.5e ",edi->vecs.mon.ieig[i],edi->vecs.mon.xproj[i]);
+ fprintf(ed->edo,"\n");
+ }
+ if (edi->vecs.linfix.neig)
+ {
+ fprintf(ed->edo," Linfix eigenvectors");
+ for (i=0; i<edi->vecs.linfix.neig; i++)
+ fprintf(ed->edo," %d: %12.5e ",edi->vecs.linfix.ieig[i],edi->vecs.linfix.xproj[i]);
+ fprintf(ed->edo,"\n");
+ }
+ if (edi->vecs.linacc.neig)
+ {
+ fprintf(ed->edo," Linacc eigenvectors");
+ for (i=0; i<edi->vecs.linacc.neig; i++)
+ fprintf(ed->edo," %d: %12.5e ",edi->vecs.linacc.ieig[i],edi->vecs.linacc.xproj[i]);
+ fprintf(ed->edo,"\n");
+ }
+ if (edi->vecs.radfix.neig)
+ {
+ fprintf(ed->edo," Radfix eigenvectors");
+ for (i=0; i<edi->vecs.radfix.neig; i++)
+ fprintf(ed->edo," %d: %12.5e ",edi->vecs.radfix.ieig[i],edi->vecs.radfix.xproj[i]);
+ fprintf(ed->edo,"\n");
+ fprintf(ed->edo," fixed increment radius = %f\n", calc_radius(&edi->vecs.radfix));
+ }
+ if (edi->vecs.radacc.neig)
+ {
+ fprintf(ed->edo," Radacc eigenvectors");
+ for (i=0; i<edi->vecs.radacc.neig; i++)
+ fprintf(ed->edo," %d: %12.5e ",edi->vecs.radacc.ieig[i],edi->vecs.radacc.xproj[i]);
+ fprintf(ed->edo,"\n");
+ fprintf(ed->edo," acceptance radius = %f\n", calc_radius(&edi->vecs.radacc));
+ }
+ if (edi->vecs.radcon.neig)
+ {
+ fprintf(ed->edo," Radcon eigenvectors");
+ for (i=0; i<edi->vecs.radcon.neig; i++)
+ fprintf(ed->edo," %d: %12.5e ",edi->vecs.radcon.ieig[i],edi->vecs.radcon.xproj[i]);
+ fprintf(ed->edo,"\n");
+ fprintf(ed->edo," contracting radius = %f\n", calc_radius(&edi->vecs.radcon));
+ }
+ }
+}
+
+/* Returns if any constraints are switched on */
+static int ed_constraints(gmx_bool edtype, t_edpar *edi)
+{
+ if (edtype == eEDedsam || edtype == eEDflood)
+ {
+ return (edi->vecs.linfix.neig || edi->vecs.linacc.neig ||
+ edi->vecs.radfix.neig || edi->vecs.radacc.neig ||
+ edi->vecs.radcon.neig);
+ }
+ return 0;
+}
+
+
+/* Copies reference projection 'refproj' to fixed 'refproj0' variable for flooding/
+ * umbrella sampling simulations. */
+static void copyEvecReference(t_eigvec* floodvecs)
+{
+ int i;
+
+
+ for (i=0; i<floodvecs->neig; i++)
+ {
+ floodvecs->refproj0[i] = floodvecs->refproj[i];
+ }
+}
+
+
+void init_edsam(gmx_mtop_t *mtop, /* global topology */
+ t_inputrec *ir, /* input record */
+ t_commrec *cr, /* communication record */
+ gmx_edsam_t ed, /* contains all ED data */
+ rvec x[], /* positions of the whole MD system */
+ matrix box) /* the box */
+{
+ t_edpar *edi = NULL; /* points to a single edi data set */
+ int numedis=0; /* keep track of the number of ED data sets in edi file */
+ int i,nr_edi;
+ rvec *x_pbc = NULL; /* positions of the whole MD system with pbc removed */
+ rvec *xfit = NULL; /* the positions which will be fitted to the reference structure */
+ rvec *xstart = NULL; /* the positions which are subject to ED sampling */
+ rvec fit_transvec; /* translation ... */
+ matrix fit_rotmat; /* ... and rotation from fit to reference structure */
+
+
+ if (!DOMAINDECOMP(cr) && PAR(cr) && MASTER(cr))
+ gmx_fatal(FARGS, "Please switch on domain decomposition to use essential dynamics in parallel.");
+
+ if (MASTER(cr))
+ fprintf(stderr, "ED: Initializing essential dynamics constraints.\n");
+
+ /* Needed for initializing radacc radius in do_edsam */
+ ed->bFirst = 1;
+
+ /* The input file is read by the master and the edi structures are
+ * initialized here. Input is stored in ed->edpar. Then the edi
+ * structures are transferred to the other nodes */
+ if (MASTER(cr))
+ {
+ snew(ed->edpar,1);
+ /* Read the whole edi file at once: */
+ read_edi_file(ed,ed->edpar,mtop->natoms,cr);
+
+ /* Initialization for every ED/flooding dataset. Flooding uses one edi dataset per
+ * flooding vector, Essential dynamics can be applied to more than one structure
+ * as well, but will be done in the order given in the edi file, so
+ * expect different results for different order of edi file concatenation! */
+ edi=ed->edpar;
+ while(edi != NULL)
+ {
+ init_edi(mtop,ir,cr,ed,edi);
+
+ /* Init flooding parameters if needed */
+ init_flood(edi,ed,ir->delta_t,cr);
+
+ edi=edi->next_edi;
+ numedis++;
+ }
+ }
+
+ /* The master does the work here. The other nodes get the positions
+ * not before dd_partition_system which is called after init_edsam */
+ if (MASTER(cr))
+ {
+ /* Remove pbc, make molecule whole.
+ * When ir->bContinuation=TRUE this has already been done, but ok.
+ */
+ snew(x_pbc,mtop->natoms);
+ m_rveccopy(mtop->natoms,x,x_pbc);
+ do_pbc_first_mtop(NULL,ir->ePBC,box,mtop,x_pbc);
+
+ /* Reset pointer to first ED data set which contains the actual ED data */
+ edi=ed->edpar;
+
+ /* Loop over all ED/flooding data sets (usually only one, though) */
+ for (nr_edi = 1; nr_edi <= numedis; nr_edi++)
+ {
+ /* We use srenew to allocate memory since the size of the buffers
+ * is likely to change with every ED dataset */
+ srenew(xfit , edi->sref.nr );
+ srenew(xstart, edi->sav.nr );
+
+ /* Extract the positions of the atoms to which will be fitted */
+ for (i=0; i < edi->sref.nr; i++)
+ {
+ copy_rvec(x_pbc[edi->sref.anrs[i]], xfit[i]);
+
+ /* Save the sref positions such that in the next time step the molecule can
+ * be made whole again (in the parallel case) */
+ if (PAR(cr))
+ copy_rvec(xfit[i], edi->sref.x_old[i]);
+ }
+
+ /* Extract the positions of the atoms subject to ED sampling */
+ for (i=0; i < edi->sav.nr; i++)
+ {
+ copy_rvec(x_pbc[edi->sav.anrs[i]], xstart[i]);
+
+ /* Save the sav positions such that in the next time step the molecule can
+ * be made whole again (in the parallel case) */
+ if (PAR(cr))
+ copy_rvec(xstart[i], edi->sav.x_old[i]);
+ }
+
+ /* Make the fit to the REFERENCE structure, get translation and rotation */
+ fit_to_reference(xfit, fit_transvec, fit_rotmat, edi);
+
+ /* Output how well we fit to the reference at the start */
+ translate_and_rotate(xfit, edi->sref.nr, fit_transvec, fit_rotmat);
+ fprintf(stderr, "ED: Initial RMSD from reference after fit = %f nm (dataset #%d)\n",
+ rmsd_from_structure(xfit, &edi->sref), nr_edi);
+
+ /* Now apply the translation and rotation to the atoms on which ED sampling will be performed */
+ translate_and_rotate(xstart, edi->sav.nr, fit_transvec, fit_rotmat);
+
+ /* calculate initial projections */
+ project(xstart, edi);
+
+ /* process target structure, if required */
+ if (edi->star.nr > 0)
+ {
+ fprintf(stderr, "ED: Fitting target structure to reference structure\n");
+ /* get translation & rotation for fit of target structure to reference structure */
+ fit_to_reference(edi->star.x, fit_transvec, fit_rotmat, edi);
+ /* do the fit */
+ translate_and_rotate(edi->star.x, edi->sav.nr, fit_transvec, fit_rotmat);
+ rad_project(edi, edi->star.x, &edi->vecs.radcon, cr);
+ } else
+ rad_project(edi, xstart, &edi->vecs.radcon, cr);
+
+ /* process structure that will serve as origin of expansion circle */
+ if ( (eEDflood == ed->eEDtype) && (FALSE == edi->flood.bConstForce) )
+ fprintf(stderr, "ED: Setting center of flooding potential (0 = average structure)\n");
+ if (edi->sori.nr > 0)
+ {
+ fprintf(stderr, "ED: Fitting origin structure to reference structure\n");
+ /* fit this structure to reference structure */
+ fit_to_reference(edi->sori.x, fit_transvec, fit_rotmat, edi);
+ /* do the fit */
+ translate_and_rotate(edi->sori.x, edi->sav.nr, fit_transvec, fit_rotmat);
+ rad_project(edi, edi->sori.x, &edi->vecs.radacc, cr);
+ rad_project(edi, edi->sori.x, &edi->vecs.radfix, cr);
+ if ( (eEDflood == ed->eEDtype) && (FALSE == edi->flood.bConstForce) )
+ {
+ fprintf(stderr, "ED: The ORIGIN structure will define the flooding potential center.\n");
+ /* Set center of flooding potential to the ORIGIN structure */
+ rad_project(edi, edi->sori.x, &edi->flood.vecs, cr);
+ /* We already know that no (moving) reference position was provided,
+ * therefore we can overwrite refproj[0]*/
+ copyEvecReference(&edi->flood.vecs);
+ }
+ }
+ else /* No origin structure given */
+ {
+ rad_project(edi, xstart, &edi->vecs.radacc, cr);
+ rad_project(edi, xstart, &edi->vecs.radfix, cr);
+ if ( (eEDflood == ed->eEDtype) && (FALSE == edi->flood.bConstForce) )
+ {
+ if (edi->flood.bHarmonic)
+ {
+ fprintf(stderr, "ED: A (possibly changing) ref. projection will define the flooding potential center.\n");
+ for (i=0; i<edi->flood.vecs.neig; i++)
+ edi->flood.vecs.refproj[i] = edi->flood.vecs.refproj0[i];
+ }
+ else
+ {
+ fprintf(stderr, "ED: The AVERAGE structure will define the flooding potential center.\n");
+ /* Set center of flooding potential to the center of the covariance matrix,
+ * i.e. the average structure, i.e. zero in the projected system */
+ for (i=0; i<edi->flood.vecs.neig; i++)
+ edi->flood.vecs.refproj[i] = 0.0;
+ }
+ }
+ }
+ /* For convenience, output the center of the flooding potential for the eigenvectors */
+ if ( (eEDflood == ed->eEDtype) && (FALSE == edi->flood.bConstForce) )
+ {
+ for (i=0; i<edi->flood.vecs.neig; i++)
+ {
+ fprintf(stdout, "ED: EV %d flooding potential center: %11.4e", i, edi->flood.vecs.refproj[i]);
+ if (edi->flood.bHarmonic)
+ fprintf(stdout, " (adding %11.4e/timestep)", edi->flood.vecs.refprojslope[i]);
+ fprintf(stdout, "\n");
+ }
+ }
+
+ /* set starting projections for linsam */
+ rad_project(edi, xstart, &edi->vecs.linacc, cr);
+ rad_project(edi, xstart, &edi->vecs.linfix, cr);
+
+ /* Output to file, set the step to -1 so that write_edo knows it was called from init_edsam */
+ if (ed->edo && !(ed->bStartFromCpt))
+ write_edo(nr_edi, edi, ed, -1, 0);
+
+ /* Prepare for the next edi data set: */
+ edi=edi->next_edi;
+ }
+ /* Cleaning up on the master node: */
+ sfree(x_pbc);
+ sfree(xfit);
+ sfree(xstart);
+
+ } /* end of MASTER only section */
+
+ if (PAR(cr))
+ {
+ /* First let everybody know how many ED data sets to expect */
+ gmx_bcast(sizeof(numedis), &numedis, cr);
+ /* Broadcast the essential dynamics / flooding data to all nodes */
+ broadcast_ed_data(cr, ed, numedis);
+ }
+ else
+ {
+ /* In the single-CPU case, point the local atom numbers pointers to the global
+ * one, so that we can use the same notation in serial and parallel case: */
+
+ /* Loop over all ED data sets (usually only one, though) */
+ edi=ed->edpar;
+ for (nr_edi = 1; nr_edi <= numedis; nr_edi++)
+ {
+ edi->sref.anrs_loc = edi->sref.anrs;
+ edi->sav.anrs_loc = edi->sav.anrs;
+ edi->star.anrs_loc = edi->star.anrs;
+ edi->sori.anrs_loc = edi->sori.anrs;
+ /* For the same reason as above, make a dummy c_ind array: */
+ snew(edi->sav.c_ind, edi->sav.nr);
+ /* Initialize the array */
+ for (i=0; i<edi->sav.nr; i++)
+ edi->sav.c_ind[i] = i;
+ /* In the general case we will need a different-sized array for the reference indices: */
+ if (!edi->bRefEqAv)
+ {
+ snew(edi->sref.c_ind, edi->sref.nr);
+ for (i=0; i<edi->sref.nr; i++)
+ edi->sref.c_ind[i] = i;
+ }
+ /* Point to the very same array in case of other structures: */
+ edi->star.c_ind = edi->sav.c_ind;
+ edi->sori.c_ind = edi->sav.c_ind;
+ /* In the serial case, the local number of atoms is the global one: */
+ edi->sref.nr_loc = edi->sref.nr;
+ edi->sav.nr_loc = edi->sav.nr;
+ edi->star.nr_loc = edi->star.nr;
+ edi->sori.nr_loc = edi->sori.nr;
+
+ /* An on we go to the next edi dataset */
+ edi=edi->next_edi;
+ }
+ }
+
+ /* Allocate space for ED buffer variables */
+ /* Again, loop over ED data sets */
+ edi=ed->edpar;
+ for (nr_edi = 1; nr_edi <= numedis; nr_edi++)
+ {
+ /* Allocate space for ED buffer */
+ snew(edi->buf, 1);
+ snew(edi->buf->do_edsam, 1);
+
+ /* Space for collective ED buffer variables */
+
+ /* Collective positions of atoms with the average indices */
+ snew(edi->buf->do_edsam->xcoll , edi->sav.nr);
+ snew(edi->buf->do_edsam->shifts_xcoll , edi->sav.nr); /* buffer for xcoll shifts */
+ snew(edi->buf->do_edsam->extra_shifts_xcoll , edi->sav.nr);
+ /* Collective positions of atoms with the reference indices */
+ if (!edi->bRefEqAv)
+ {
+ snew(edi->buf->do_edsam->xc_ref , edi->sref.nr);
+ snew(edi->buf->do_edsam->shifts_xc_ref , edi->sref.nr); /* To store the shifts in */
+ snew(edi->buf->do_edsam->extra_shifts_xc_ref, edi->sref.nr);
+ }
+
+ /* Get memory for flooding forces */
+ snew(edi->flood.forces_cartesian , edi->sav.nr);
+
+#ifdef DUMPEDI
+ /* Dump it all into one file per process */
+ dump_edi(edi, cr, nr_edi);
+#endif
+
+ /* An on we go to the next edi dataset */
+ edi=edi->next_edi;
+ }
+
+ /* Flush the edo file so that the user can check some things
+ * when the simulation has started */
+ if (ed->edo)
+ fflush(ed->edo);
+}
+
+
+void do_edsam(t_inputrec *ir,
+ gmx_large_int_t step,
+ t_mdatoms *md,
+ t_commrec *cr,
+ rvec xs[], /* The local current positions on this processor */
+ rvec v[], /* The velocities */
+ matrix box,
+ gmx_edsam_t ed)
+{
+ int i,edinr,iupdate=500;
+ matrix rotmat; /* rotation matrix */
+ rvec transvec; /* translation vector */
+ rvec dv,dx,x_unsh; /* tmp vectors for velocity, distance, unshifted x coordinate */
+ real dt_1; /* 1/dt */
+ struct t_do_edsam *buf;
+ t_edpar *edi;
+ real rmsdev=-1; /* RMSD from reference structure prior to applying the constraints */
+ gmx_bool bSuppress=FALSE; /* Write .edo file on master? */
+
+
+ /* Check if ED sampling has to be performed */
+ if ( ed->eEDtype==eEDnone )
+ return;
+
+ /* Suppress output on first call of do_edsam if
+ * two-step sd2 integrator is used */
+ if ( (ir->eI==eiSD2) && (v != NULL) )
+ bSuppress = TRUE;
+
+ dt_1 = 1.0/ir->delta_t;
+
+ /* Loop over all ED datasets (usually one) */
+ edi = ed->edpar;
+ edinr = 0;
+ while (edi != NULL)
+ {
+ edinr++;
+ if (edi->bNeedDoEdsam)
+ {
+
+ buf=edi->buf->do_edsam;
+
+ if (ed->bFirst)
+ /* initialise radacc radius for slope criterion */
+ buf->oldrad=calc_radius(&edi->vecs.radacc);
+
+ /* Copy the positions into buf->xc* arrays and after ED
+ * feed back corrections to the official positions */
+
+ /* Broadcast the ED positions such that every node has all of them
+ * Every node contributes its local positions xs and stores it in
+ * the collective buf->xcoll array. Note that for edinr > 1
+ * xs could already have been modified by an earlier ED */
+
+ communicate_group_positions(cr, buf->xcoll, buf->shifts_xcoll, buf->extra_shifts_xcoll, buf->bUpdateShifts, xs,
+ edi->sav.nr, edi->sav.nr_loc, edi->sav.anrs_loc, edi->sav.c_ind, edi->sav.x_old, box);
+
+#ifdef DEBUG_ED
+ dump_xcoll(edi, buf, cr, step);
+#endif
+ /* Only assembly reference positions if their indices differ from the average ones */
+ if (!edi->bRefEqAv)
+ communicate_group_positions(cr, buf->xc_ref, buf->shifts_xc_ref, buf->extra_shifts_xc_ref, buf->bUpdateShifts, xs,
+ edi->sref.nr, edi->sref.nr_loc, edi->sref.anrs_loc, edi->sref.c_ind, edi->sref.x_old, box);
+
+ /* If bUpdateShifts was TRUE then the shifts have just been updated in get_positions.
+ * We do not need to uptdate the shifts until the next NS step */
+ buf->bUpdateShifts = FALSE;
+
+ /* Now all nodes have all of the ED positions in edi->sav->xcoll,
+ * as well as the indices in edi->sav.anrs */
+
+ /* Fit the reference indices to the reference structure */
+ if (edi->bRefEqAv)
+ fit_to_reference(buf->xcoll , transvec, rotmat, edi);
+ else
+ fit_to_reference(buf->xc_ref, transvec, rotmat, edi);
+
+ /* Now apply the translation and rotation to the ED structure */
+ translate_and_rotate(buf->xcoll, edi->sav.nr, transvec, rotmat);
+
+ /* Find out how well we fit to the reference (just for output steps) */
+ if (do_per_step(step,edi->outfrq) && MASTER(cr))
+ {
+ if (edi->bRefEqAv)
+ {
+ /* Indices of reference and average structures are identical,
+ * thus we can calculate the rmsd to SREF using xcoll */
+ rmsdev = rmsd_from_structure(buf->xcoll,&edi->sref);
+ }
+ else
+ {
+ /* We have to translate & rotate the reference atoms first */
+ translate_and_rotate(buf->xc_ref, edi->sref.nr, transvec, rotmat);
+ rmsdev = rmsd_from_structure(buf->xc_ref,&edi->sref);
+ }
+ }
+
+ /* update radsam references, when required */
+ if (do_per_step(step,edi->maxedsteps) && step >= edi->presteps)
+ {
+ project(buf->xcoll, edi);
+ rad_project(edi, buf->xcoll, &edi->vecs.radacc, cr);
+ rad_project(edi, buf->xcoll, &edi->vecs.radfix, cr);
+ buf->oldrad=-1.e5;
+ }
+
+ /* update radacc references, when required */
+ if (do_per_step(step,iupdate) && step >= edi->presteps)
+ {
+ edi->vecs.radacc.radius = calc_radius(&edi->vecs.radacc);
+ if (edi->vecs.radacc.radius - buf->oldrad < edi->slope)
+ {
+ project(buf->xcoll, edi);
+ rad_project(edi, buf->xcoll, &edi->vecs.radacc, cr);
+ buf->oldrad = 0.0;
+ } else
+ buf->oldrad = edi->vecs.radacc.radius;
+ }
+
+ /* apply the constraints */
+ if (step >= edi->presteps && ed_constraints(ed->eEDtype, edi))
+ {
+ /* ED constraints should be applied already in the first MD step
+ * (which is step 0), therefore we pass step+1 to the routine */
+ ed_apply_constraints(buf->xcoll, edi, step+1 - ir->init_step, cr);
+ }
+
+ /* write to edo, when required */
+ if (do_per_step(step,edi->outfrq))
+ {
+ project(buf->xcoll, edi);
+ if (MASTER(cr) && !bSuppress)
+ write_edo(edinr, edi, ed, step, rmsdev);
+ }
+
+ /* Copy back the positions unless monitoring only */
+ if (ed_constraints(ed->eEDtype, edi))
+ {
+ /* remove fitting */
+ rmfit(edi->sav.nr, buf->xcoll, transvec, rotmat);
+
+ /* Copy the ED corrected positions into the coordinate array */
+ /* Each node copies its local part. In the serial case, nat_loc is the
+ * total number of ED atoms */
+ for (i=0; i<edi->sav.nr_loc; i++)
+ {
+ /* Unshift local ED coordinate and store in x_unsh */
+ ed_unshift_single_coord(box, buf->xcoll[edi->sav.c_ind[i]],
+ buf->shifts_xcoll[edi->sav.c_ind[i]], x_unsh);
+
+ /* dx is the ED correction to the positions: */
+ rvec_sub(x_unsh, xs[edi->sav.anrs_loc[i]], dx);
+
+ if (v != NULL)
+ {
+ /* dv is the ED correction to the velocity: */
+ svmul(dt_1, dx, dv);
+ /* apply the velocity correction: */
+ rvec_inc(v[edi->sav.anrs_loc[i]], dv);
+ }
+ /* Finally apply the position correction due to ED: */
+ copy_rvec(x_unsh, xs[edi->sav.anrs_loc[i]]);
+ }
+ }
+ } /* END of if (edi->bNeedDoEdsam) */
+
+ /* Prepare for the next ED dataset */
+ edi = edi->next_edi;
+
+ } /* END of loop over ED datasets */
+
+ ed->bFirst = FALSE;
+}
--- /dev/null
- static gmx_bool bTricl,bDynBox;
- static int f_nre=0,epc,etc,nCrmsd;
-
-
-
-
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * GROwing Monsters And Cloning Shrimps
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <string.h>
+#include <float.h>
+#include "typedefs.h"
+#include "string2.h"
+#include "mdebin.h"
+#include "smalloc.h"
+#include "physics.h"
+#include "enxio.h"
+#include "vec.h"
+#include "disre.h"
+#include "main.h"
+#include "network.h"
+#include "names.h"
+#include "orires.h"
+#include "constr.h"
+#include "mtop_util.h"
+#include "xvgr.h"
+#include "gmxfio.h"
+
+#include "mdebin_bar.h"
+
+
+static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
+
+static const char *boxs_nm[] = { "Box-X", "Box-Y", "Box-Z" };
+
+static const char *tricl_boxs_nm[] = {
+ "Box-XX", "Box-YY", "Box-ZZ",
+ "Box-YX", "Box-ZX", "Box-ZY"
+};
+
+static const char *vol_nm[] = { "Volume" };
+
+static const char *dens_nm[] = {"Density" };
+
+static const char *pv_nm[] = {"pV" };
+
+static const char *enthalpy_nm[] = {"Enthalpy" };
+
+static const char *boxvel_nm[] = {
+ "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
+ "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
+};
+
+#define NBOXS asize(boxs_nm)
+#define NTRICLBOXS asize(tricl_boxs_nm)
+
- for (i=0;i<DIM;i++)
- {
- for (j=0;j<DIM;j++)
- {
- md->ref_p[i][j] = ir->ref_p[i][j];
- }
- }
+
+t_mdebin *init_mdebin(ener_file_t fp_ene,
+ const gmx_mtop_t *mtop,
+ const t_inputrec *ir,
+ FILE *fp_dhdl)
+{
+ const char *ener_nm[F_NRE];
+ static const char *vir_nm[] = {
+ "Vir-XX", "Vir-XY", "Vir-XZ",
+ "Vir-YX", "Vir-YY", "Vir-YZ",
+ "Vir-ZX", "Vir-ZY", "Vir-ZZ"
+ };
+ static const char *sv_nm[] = {
+ "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
+ "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
+ "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
+ };
+ static const char *fv_nm[] = {
+ "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
+ "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
+ "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
+ };
+ static const char *pres_nm[] = {
+ "Pres-XX","Pres-XY","Pres-XZ",
+ "Pres-YX","Pres-YY","Pres-YZ",
+ "Pres-ZX","Pres-ZY","Pres-ZZ"
+ };
+ static const char *surft_nm[] = {
+ "#Surf*SurfTen"
+ };
+ static const char *mu_nm[] = {
+ "Mu-X", "Mu-Y", "Mu-Z"
+ };
+ static const char *vcos_nm[] = {
+ "2CosZ*Vel-X"
+ };
+ static const char *visc_nm[] = {
+ "1/Viscosity"
+ };
+ static const char *baro_nm[] = {
+ "Barostat"
+ };
+
+ char **grpnms;
+ const gmx_groups_t *groups;
+ char **gnm;
+ char buf[256];
+ const char *bufi;
+ t_mdebin *md;
+ int i,j,ni,nj,n,nh,k,kk,ncon,nset;
+ gmx_bool bBHAM,bNoseHoover,b14;
+
+ snew(md,1);
+
+ if (EI_DYNAMICS(ir->eI))
+ {
+ md->delta_t = ir->delta_t;
+ }
+ else
+ {
+ md->delta_t = 0;
+ }
+
+ groups = &mtop->groups;
+
+ bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
+ b14 = (gmx_mtop_ftype_count(mtop,F_LJ14) > 0 ||
+ gmx_mtop_ftype_count(mtop,F_LJC14_Q) > 0);
+
+ ncon = gmx_mtop_ftype_count(mtop,F_CONSTR);
+ nset = gmx_mtop_ftype_count(mtop,F_SETTLE);
+ md->bConstr = (ncon > 0 || nset > 0);
+ md->bConstrVir = FALSE;
+ if (md->bConstr) {
+ if (ncon > 0 && ir->eConstrAlg == econtLINCS) {
+ if (ir->eI == eiSD2)
+ md->nCrmsd = 2;
+ else
+ md->nCrmsd = 1;
+ }
+ md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
+ } else {
+ md->nCrmsd = 0;
+ }
+
+ /* Energy monitoring */
+ for(i=0;i<egNR;i++)
+ {
+ md->bEInd[i]=FALSE;
+ }
+
+#ifndef GMX_OPENMM
+ for(i=0; i<F_NRE; i++)
+ {
+ md->bEner[i] = FALSE;
+ if (i == F_LJ)
+ md->bEner[i] = !bBHAM;
+ else if (i == F_BHAM)
+ md->bEner[i] = bBHAM;
+ else if (i == F_EQM)
+ md->bEner[i] = ir->bQMMM;
+ else if (i == F_COUL_LR)
+ md->bEner[i] = (ir->rcoulomb > ir->rlist);
+ else if (i == F_LJ_LR)
+ md->bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
+ else if (i == F_BHAM_LR)
+ md->bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
+ else if (i == F_RF_EXCL)
+ md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC);
+ else if (i == F_COUL_RECIP)
+ md->bEner[i] = EEL_FULL(ir->coulombtype);
+ else if (i == F_LJ14)
+ md->bEner[i] = b14;
+ else if (i == F_COUL14)
+ md->bEner[i] = b14;
+ else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
+ md->bEner[i] = FALSE;
+ else if ((i == F_DVDL) || (i == F_DKDL))
+ md->bEner[i] = (ir->efep != efepNO);
+ else if (i == F_DHDL_CON)
+ md->bEner[i] = (ir->efep != efepNO && md->bConstr);
+ else if ((interaction_function[i].flags & IF_VSITE) ||
+ (i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
+ md->bEner[i] = FALSE;
+ else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i==F_EQM))
+ md->bEner[i] = TRUE;
+ else if ((i == F_GBPOL) && ir->implicit_solvent==eisGBSA)
+ md->bEner[i] = TRUE;
+ else if ((i == F_NPSOLVATION) && ir->implicit_solvent==eisGBSA && (ir->sa_algorithm != esaNO))
+ md->bEner[i] = TRUE;
+ else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14))
+ md->bEner[i] = FALSE;
+ else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
+ md->bEner[i] = EI_DYNAMICS(ir->eI);
+ else if (i==F_VTEMP)
+ md->bEner[i] = (EI_DYNAMICS(ir->eI) && getenv("GMX_VIRIAL_TEMPERATURE"));
+ else if (i == F_DISPCORR || i == F_PDISPCORR)
+ md->bEner[i] = (ir->eDispCorr != edispcNO);
+ else if (i == F_DISRESVIOL)
+ md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0);
+ else if (i == F_ORIRESDEV)
+ md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0);
+ else if (i == F_CONNBONDS)
+ md->bEner[i] = FALSE;
+ else if (i == F_COM_PULL)
+ md->bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F || ir->bRot);
+ else if (i == F_ECONSERVED)
+ md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
+ (ir->epc == epcNO || ir->epc==epcMTTK));
+ else
+ md->bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
+ }
+#else
+ /* OpenMM always produces only the following 4 energy terms */
+ md->bEner[F_EPOT] = TRUE;
+ md->bEner[F_EKIN] = TRUE;
+ md->bEner[F_ETOT] = TRUE;
+ md->bEner[F_TEMP] = TRUE;
+#endif
+
+ md->f_nre=0;
+ for(i=0; i<F_NRE; i++)
+ {
+ if (md->bEner[i])
+ {
+ /* FIXME: The constness should not be cast away */
+ /*ener_nm[f_nre]=(char *)interaction_function[i].longname;*/
+ ener_nm[md->f_nre]=interaction_function[i].longname;
+ md->f_nre++;
+ }
+ }
+
+ md->epc = ir->epc;
- md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
- md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy);
++ md->bDiagPres = !TRICLINIC(ir->ref_p);
++ md->ref_p = (ir->ref_p[XX][XX]+ir->ref_p[YY][YY]+ir->ref_p[ZZ][ZZ])/DIM;
+ md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
+ md->bDynBox = DYNAMIC_BOX(*ir);
+ md->etc = ir->etc;
+ md->bNHC_trotter = IR_NVT_TROTTER(ir);
+ md->bMTTK = IR_NPT_TROTTER(ir);
+
+ md->ebin = mk_ebin();
+ /* Pass NULL for unit to let get_ebin_space determine the units
+ * for interaction_function[i].longname
+ */
+ md->ie = get_ebin_space(md->ebin,md->f_nre,ener_nm,NULL);
+ if (md->nCrmsd)
+ {
+ /* This should be called directly after the call for md->ie,
+ * such that md->iconrmsd follows directly in the list.
+ */
+ md->iconrmsd = get_ebin_space(md->ebin,md->nCrmsd,conrmsd_nm,"");
+ }
+ if (md->bDynBox)
+ {
+ md->ib = get_ebin_space(md->ebin,
+ md->bTricl ? NTRICLBOXS : NBOXS,
+ md->bTricl ? tricl_boxs_nm : boxs_nm,
+ unit_length);
+ md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume);
+ md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI);
- /* This is pV (in kJ/mol). The pressure is the reference pressure,
- not the instantaneous pressure */
- pv = 0;
- for (i=0;i<DIM;i++)
- {
- for (j=0;j<DIM;j++)
- {
- if (i>j)
- {
- pv += box[i][j]*md->ref_p[i][j]/PRESFAC;
- }
- else
- {
- pv += box[j][i]*md->ref_p[j][i]/PRESFAC;
- }
- }
- }
-
++ if (md->bDiagPres)
++ {
++ md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
++ md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy);
++ }
+ }
+ if (md->bConstrVir)
+ {
+ md->isvir = get_ebin_space(md->ebin,asize(sv_nm),sv_nm,unit_energy);
+ md->ifvir = get_ebin_space(md->ebin,asize(fv_nm),fv_nm,unit_energy);
+ }
+ md->ivir = get_ebin_space(md->ebin,asize(vir_nm),vir_nm,unit_energy);
+ md->ipres = get_ebin_space(md->ebin,asize(pres_nm),pres_nm,unit_pres_bar);
+ md->isurft = get_ebin_space(md->ebin,asize(surft_nm),surft_nm,
+ unit_surft_bar);
+ if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
+ {
+ md->ipc = get_ebin_space(md->ebin,md->bTricl ? 6 : 3,
+ boxvel_nm,unit_vel);
+ }
+ md->imu = get_ebin_space(md->ebin,asize(mu_nm),mu_nm,unit_dipole_D);
+ if (ir->cos_accel != 0)
+ {
+ md->ivcos = get_ebin_space(md->ebin,asize(vcos_nm),vcos_nm,unit_vel);
+ md->ivisc = get_ebin_space(md->ebin,asize(visc_nm),visc_nm,
+ unit_invvisc_SI);
+ }
+
+ /* Energy monitoring */
+ for(i=0;i<egNR;i++)
+ {
+ md->bEInd[i] = FALSE;
+ }
+ md->bEInd[egCOULSR] = TRUE;
+ md->bEInd[egLJSR ] = TRUE;
+
+ if (ir->rcoulomb > ir->rlist)
+ {
+ md->bEInd[egCOULLR] = TRUE;
+ }
+ if (!bBHAM)
+ {
+ if (ir->rvdw > ir->rlist)
+ {
+ md->bEInd[egLJLR] = TRUE;
+ }
+ }
+ else
+ {
+ md->bEInd[egLJSR] = FALSE;
+ md->bEInd[egBHAMSR] = TRUE;
+ if (ir->rvdw > ir->rlist)
+ {
+ md->bEInd[egBHAMLR] = TRUE;
+ }
+ }
+ if (b14)
+ {
+ md->bEInd[egLJ14] = TRUE;
+ md->bEInd[egCOUL14] = TRUE;
+ }
+ md->nEc=0;
+ for(i=0; (i<egNR); i++)
+ {
+ if (md->bEInd[i])
+ {
+ md->nEc++;
+ }
+ }
+
+ n=groups->grps[egcENER].nr;
+ md->nEg=n;
+ md->nE=(n*(n+1))/2;
+ snew(md->igrp,md->nE);
+ if (md->nE > 1)
+ {
+ n=0;
+ snew(gnm,md->nEc);
+ for(k=0; (k<md->nEc); k++)
+ {
+ snew(gnm[k],STRLEN);
+ }
+ for(i=0; (i<groups->grps[egcENER].nr); i++)
+ {
+ ni=groups->grps[egcENER].nm_ind[i];
+ for(j=i; (j<groups->grps[egcENER].nr); j++)
+ {
+ nj=groups->grps[egcENER].nm_ind[j];
+ for(k=kk=0; (k<egNR); k++)
+ {
+ if (md->bEInd[k])
+ {
+ sprintf(gnm[kk],"%s:%s-%s",egrp_nm[k],
+ *(groups->grpname[ni]),*(groups->grpname[nj]));
+ kk++;
+ }
+ }
+ md->igrp[n]=get_ebin_space(md->ebin,md->nEc,
+ (const char **)gnm,unit_energy);
+ n++;
+ }
+ }
+ for(k=0; (k<md->nEc); k++)
+ {
+ sfree(gnm[k]);
+ }
+ sfree(gnm);
+
+ if (n != md->nE)
+ {
+ gmx_incons("Number of energy terms wrong");
+ }
+ }
+
+ md->nTC=groups->grps[egcTC].nr;
+ md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */
+ if (md->bMTTK)
+ {
+ md->nTCP = 1; /* assume only one possible coupling system for barostat
+ for now */
+ }
+ else
+ {
+ md->nTCP = 0;
+ }
+
+ if (md->etc == etcNOSEHOOVER) {
+ if (md->bNHC_trotter) {
+ md->mde_n = 2*md->nNHC*md->nTC;
+ }
+ else
+ {
+ md->mde_n = 2*md->nTC;
+ }
+ if (md->epc == epcMTTK)
+ {
+ md->mdeb_n = 2*md->nNHC*md->nTCP;
+ }
+ } else {
+ md->mde_n = md->nTC;
+ md->mdeb_n = 0;
+ }
+
+ snew(md->tmp_r,md->mde_n);
+ snew(md->tmp_v,md->mde_n);
+ snew(md->grpnms,md->mde_n);
+ grpnms = md->grpnms;
+
+ for(i=0; (i<md->nTC); i++)
+ {
+ ni=groups->grps[egcTC].nm_ind[i];
+ sprintf(buf,"T-%s",*(groups->grpname[ni]));
+ grpnms[i]=strdup(buf);
+ }
+ md->itemp=get_ebin_space(md->ebin,md->nTC,(const char **)grpnms,
+ unit_temp_K);
+
+ bNoseHoover = (getenv("GMX_NOSEHOOVER_CHAINS") != NULL); /* whether to print Nose-Hoover chains */
+
+ if (md->etc == etcNOSEHOOVER)
+ {
+ if (bNoseHoover)
+ {
+ if (md->bNHC_trotter)
+ {
+ for(i=0; (i<md->nTC); i++)
+ {
+ ni=groups->grps[egcTC].nm_ind[i];
+ bufi = *(groups->grpname[ni]);
+ for(j=0; (j<md->nNHC); j++)
+ {
+ sprintf(buf,"Xi-%d-%s",j,bufi);
+ grpnms[2*(i*md->nNHC+j)]=strdup(buf);
+ sprintf(buf,"vXi-%d-%s",j,bufi);
+ grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
+ }
+ }
+ md->itc=get_ebin_space(md->ebin,md->mde_n,
+ (const char **)grpnms,unit_invtime);
+ if (md->bMTTK)
+ {
+ for(i=0; (i<md->nTCP); i++)
+ {
+ bufi = baro_nm[0]; /* All barostat DOF's together for now. */
+ for(j=0; (j<md->nNHC); j++)
+ {
+ sprintf(buf,"Xi-%d-%s",j,bufi);
+ grpnms[2*(i*md->nNHC+j)]=strdup(buf);
+ sprintf(buf,"vXi-%d-%s",j,bufi);
+ grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
+ }
+ }
+ md->itcb=get_ebin_space(md->ebin,md->mdeb_n,
+ (const char **)grpnms,unit_invtime);
+ }
+ }
+ else
+ {
+ for(i=0; (i<md->nTC); i++)
+ {
+ ni=groups->grps[egcTC].nm_ind[i];
+ bufi = *(groups->grpname[ni]);
+ sprintf(buf,"Xi-%s",bufi);
+ grpnms[2*i]=strdup(buf);
+ sprintf(buf,"vXi-%s",bufi);
+ grpnms[2*i+1]=strdup(buf);
+ }
+ md->itc=get_ebin_space(md->ebin,md->mde_n,
+ (const char **)grpnms,unit_invtime);
+ }
+ }
+ }
+ else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
+ md->etc == etcVRESCALE)
+ {
+ for(i=0; (i<md->nTC); i++)
+ {
+ ni=groups->grps[egcTC].nm_ind[i];
+ sprintf(buf,"Lamb-%s",*(groups->grpname[ni]));
+ grpnms[i]=strdup(buf);
+ }
+ md->itc=get_ebin_space(md->ebin,md->mde_n,(const char **)grpnms,"");
+ }
+
+ sfree(grpnms);
+
+
+ md->nU=groups->grps[egcACC].nr;
+ if (md->nU > 1)
+ {
+ snew(grpnms,3*md->nU);
+ for(i=0; (i<md->nU); i++)
+ {
+ ni=groups->grps[egcACC].nm_ind[i];
+ sprintf(buf,"Ux-%s",*(groups->grpname[ni]));
+ grpnms[3*i+XX]=strdup(buf);
+ sprintf(buf,"Uy-%s",*(groups->grpname[ni]));
+ grpnms[3*i+YY]=strdup(buf);
+ sprintf(buf,"Uz-%s",*(groups->grpname[ni]));
+ grpnms[3*i+ZZ]=strdup(buf);
+ }
+ md->iu=get_ebin_space(md->ebin,3*md->nU,(const char **)grpnms,unit_vel);
+ sfree(grpnms);
+ }
+
+ if ( fp_ene )
+ {
+ do_enxnms(fp_ene,&md->ebin->nener,&md->ebin->enm);
+ }
+
+ md->print_grpnms=NULL;
+
+ /* check whether we're going to write dh histograms */
+ md->dhc=NULL;
+ if (ir->separate_dhdl_file == sepdhdlfileNO )
+ {
+ int i;
+ snew(md->dhc, 1);
+
+ mde_delta_h_coll_init(md->dhc, ir);
+ md->fp_dhdl = NULL;
+ }
+ else
+ {
+ md->fp_dhdl = fp_dhdl;
+ }
+ md->dhdl_derivatives = (ir->dhdl_derivatives==dhdlderivativesYES);
+ return md;
+}
+
+FILE *open_dhdl(const char *filename,const t_inputrec *ir,
+ const output_env_t oenv)
+{
+ FILE *fp;
+ const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda";
+ char title[STRLEN],label_x[STRLEN],label_y[STRLEN];
+ char **setname;
+ char buf[STRLEN];
+
+ sprintf(label_x,"%s (%s)","Time",unit_time);
+ if (ir->n_flambda == 0)
+ {
+ sprintf(title,"%s",dhdl);
+ sprintf(label_y,"%s (%s %s)",
+ dhdl,unit_energy,"[\\lambda]\\S-1\\N");
+ }
+ else
+ {
+ sprintf(title,"%s, %s",dhdl,deltag);
+ sprintf(label_y,"(%s)",unit_energy);
+ }
+ fp = gmx_fio_fopen(filename,"w+");
+ xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv);
+
+ if (ir->delta_lambda == 0)
+ {
+ sprintf(buf,"T = %g (K), %s = %g",
+ ir->opts.ref_t[0],lambda,ir->init_lambda);
+ }
+ else
+ {
+ sprintf(buf,"T = %g (K)",
+ ir->opts.ref_t[0]);
+ }
+ xvgr_subtitle(fp,buf,oenv);
+
+ if (ir->n_flambda > 0)
+ {
+ int nsets,s,nsi=0;
+ /* g_bar has to determine the lambda values used in this simulation
+ * from this xvg legend. */
+ nsets = ( (ir->dhdl_derivatives==dhdlderivativesYES) ? 1 : 0) +
+ ir->n_flambda;
+ snew(setname,nsets);
+ if (ir->dhdl_derivatives == dhdlderivativesYES)
+ {
+ sprintf(buf,"%s %s %g",dhdl,lambda,ir->init_lambda);
+ setname[nsi++] = gmx_strdup(buf);
+ }
+ for(s=0; s<ir->n_flambda; s++)
+ {
+ sprintf(buf,"%s %s %g",deltag,lambda,ir->flambda[s]);
+ setname[nsi++] = gmx_strdup(buf);
+ }
+ xvgr_legend(fp,nsets,(const char**)setname,oenv);
+
+ for(s=0; s<nsets; s++)
+ {
+ sfree(setname[s]);
+ }
+ sfree(setname);
+ }
+
+ return fp;
+}
+
+static void copy_energy(t_mdebin *md, real e[],real ecpy[])
+{
+ int i,j;
+
+ for(i=j=0; (i<F_NRE); i++)
+ if (md->bEner[i])
+ ecpy[j++] = e[i];
+ if (j != md->f_nre)
+ gmx_incons("Number of energy terms wrong");
+}
+
+void upd_mdebin(t_mdebin *md, gmx_bool write_dhdl,
+ gmx_bool bSum,
+ double time,
+ real tmass,
+ gmx_enerdata_t *enerd,
+ t_state *state,
+ matrix box,
+ tensor svir,
+ tensor fvir,
+ tensor vir,
+ tensor pres,
+ gmx_ekindata_t *ekind,
+ rvec mu_tot,
+ gmx_constr_t constr)
+{
+ int i,j,k,kk,m,n,gid;
+ real crmsd[2],tmp6[6];
+ real bs[NTRICLBOXS],vol,dens,pv,enthalpy;
+ real eee[egNR];
+ real ecopy[F_NRE];
+ real tmp;
+ gmx_bool bNoseHoover;
+
+ /* Do NOT use the box in the state variable, but the separate box provided
+ * as an argument. This is because we sometimes need to write the box from
+ * the last timestep to match the trajectory frames.
+ */
+ copy_energy(md, enerd->term,ecopy);
+ add_ebin(md->ebin,md->ie,md->f_nre,ecopy,bSum);
+ if (md->nCrmsd)
+ {
+ crmsd[0] = constr_rmsd(constr,FALSE);
+ if (md->nCrmsd > 1)
+ {
+ crmsd[1] = constr_rmsd(constr,TRUE);
+ }
+ add_ebin(md->ebin,md->iconrmsd,md->nCrmsd,crmsd,FALSE);
+ }
+ if (md->bDynBox)
+ {
+ int nboxs;
+ if(md->bTricl)
+ {
+ bs[0] = box[XX][XX];
+ bs[1] = box[YY][YY];
+ bs[2] = box[ZZ][ZZ];
+ bs[3] = box[YY][XX];
+ bs[4] = box[ZZ][XX];
+ bs[5] = box[ZZ][YY];
+ nboxs=NTRICLBOXS;
+ }
+ else
+ {
+ bs[0] = box[XX][XX];
+ bs[1] = box[YY][YY];
+ bs[2] = box[ZZ][ZZ];
+ nboxs=NBOXS;
+ }
+ vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
+ dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
+
- add_ebin(md->ebin,md->ipv ,1 ,&pv ,bSum);
- enthalpy = pv + enerd->term[F_ETOT];
- add_ebin(md->ebin,md->ienthalpy ,1 ,&enthalpy ,bSum);
+ add_ebin(md->ebin,md->ib ,nboxs,bs ,bSum);
+ add_ebin(md->ebin,md->ivol ,1 ,&vol ,bSum);
+ add_ebin(md->ebin,md->idens,1 ,&dens,bSum);
++
++ if (md->bDiagPres)
++ {
++ /* This is pV (in kJ/mol). The pressure is the reference pressure,
++ not the instantaneous pressure */
++ pv = vol*md->ref_p/PRESFAC;
++
++ add_ebin(md->ebin,md->ipv ,1 ,&pv ,bSum);
++ enthalpy = pv + enerd->term[F_ETOT];
++ add_ebin(md->ebin,md->ienthalpy ,1 ,&enthalpy ,bSum);
++ }
+ }
+ if (md->bConstrVir)
+ {
+ add_ebin(md->ebin,md->isvir,9,svir[0],bSum);
+ add_ebin(md->ebin,md->ifvir,9,fvir[0],bSum);
+ }
+ add_ebin(md->ebin,md->ivir,9,vir[0],bSum);
+ add_ebin(md->ebin,md->ipres,9,pres[0],bSum);
+ tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
+ add_ebin(md->ebin,md->isurft,1,&tmp,bSum);
+ if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
+ {
+ tmp6[0] = state->boxv[XX][XX];
+ tmp6[1] = state->boxv[YY][YY];
+ tmp6[2] = state->boxv[ZZ][ZZ];
+ tmp6[3] = state->boxv[YY][XX];
+ tmp6[4] = state->boxv[ZZ][XX];
+ tmp6[5] = state->boxv[ZZ][YY];
+ add_ebin(md->ebin,md->ipc,md->bTricl ? 6 : 3,tmp6,bSum);
+ }
+ add_ebin(md->ebin,md->imu,3,mu_tot,bSum);
+ if (ekind && ekind->cosacc.cos_accel != 0)
+ {
+ vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
+ dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
+ add_ebin(md->ebin,md->ivcos,1,&(ekind->cosacc.vcos),bSum);
+ /* 1/viscosity, unit 1/(kg m^-1 s^-1) */
+ tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
+ *dens*vol*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
+ add_ebin(md->ebin,md->ivisc,1,&tmp,bSum);
+ }
+ if (md->nE > 1)
+ {
+ n=0;
+ for(i=0; (i<md->nEg); i++)
+ {
+ for(j=i; (j<md->nEg); j++)
+ {
+ gid=GID(i,j,md->nEg);
+ for(k=kk=0; (k<egNR); k++)
+ {
+ if (md->bEInd[k])
+ {
+ eee[kk++] = enerd->grpp.ener[k][gid];
+ }
+ }
+ add_ebin(md->ebin,md->igrp[n],md->nEc,eee,bSum);
+ n++;
+ }
+ }
+ }
+
+ if (ekind)
+ {
+ for(i=0; (i<md->nTC); i++)
+ {
+ md->tmp_r[i] = ekind->tcstat[i].T;
+ }
+ add_ebin(md->ebin,md->itemp,md->nTC,md->tmp_r,bSum);
+
+ /* whether to print Nose-Hoover chains: */
+ bNoseHoover = (getenv("GMX_NOSEHOOVER_CHAINS") != NULL);
+
+ if (md->etc == etcNOSEHOOVER)
+ {
+ if (bNoseHoover)
+ {
+ if (md->bNHC_trotter)
+ {
+ for(i=0; (i<md->nTC); i++)
+ {
+ for (j=0;j<md->nNHC;j++)
+ {
+ k = i*md->nNHC+j;
+ md->tmp_r[2*k] = state->nosehoover_xi[k];
+ md->tmp_r[2*k+1] = state->nosehoover_vxi[k];
+ }
+ }
+ add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
+
+ if (md->bMTTK) {
+ for(i=0; (i<md->nTCP); i++)
+ {
+ for (j=0;j<md->nNHC;j++)
+ {
+ k = i*md->nNHC+j;
+ md->tmp_r[2*k] = state->nhpres_xi[k];
+ md->tmp_r[2*k+1] = state->nhpres_vxi[k];
+ }
+ }
+ add_ebin(md->ebin,md->itcb,md->mdeb_n,md->tmp_r,bSum);
+ }
+
+ }
+ else
+ {
+ for(i=0; (i<md->nTC); i++)
+ {
+ md->tmp_r[2*i] = state->nosehoover_xi[i];
+ md->tmp_r[2*i+1] = state->nosehoover_vxi[i];
+ }
+ add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
+ }
+ }
+ }
+ else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
+ md->etc == etcVRESCALE)
+ {
+ for(i=0; (i<md->nTC); i++)
+ {
+ md->tmp_r[i] = ekind->tcstat[i].lambda;
+ }
+ add_ebin(md->ebin,md->itc,md->nTC,md->tmp_r,bSum);
+ }
+ }
+
+ if (ekind && md->nU > 1)
+ {
+ for(i=0; (i<md->nU); i++)
+ {
+ copy_rvec(ekind->grpstat[i].u,md->tmp_v[i]);
+ }
+ add_ebin(md->ebin,md->iu,3*md->nU,md->tmp_v[0],bSum);
+ }
+
+ ebin_increase_count(md->ebin,bSum);
+
+ /* BAR + thermodynamic integration values */
+ if (write_dhdl)
+ {
+ if (md->fp_dhdl)
+ {
+ fprintf(md->fp_dhdl,"%.4f", time);
+
+ if (md->dhdl_derivatives)
+ {
+ fprintf(md->fp_dhdl," %g", enerd->term[F_DVDL]+
+ enerd->term[F_DKDL]+
+ enerd->term[F_DHDL_CON]);
+ }
+ for(i=1; i<enerd->n_lambda; i++)
+ {
+ fprintf(md->fp_dhdl," %g",
+ enerd->enerpart_lambda[i]-enerd->enerpart_lambda[0]);
+ }
+ fprintf(md->fp_dhdl,"\n");
+ }
+ /* and the binary BAR output */
+ if (md->dhc)
+ {
+ mde_delta_h_coll_add_dh(md->dhc,
+ enerd->term[F_DVDL]+ enerd->term[F_DKDL]+
+ enerd->term[F_DHDL_CON],
+ enerd->enerpart_lambda, time,
+ state->lambda);
+ }
+ }
+}
+
+void upd_mdebin_step(t_mdebin *md)
+{
+ ebin_increase_count(md->ebin,FALSE);
+}
+
+static void npr(FILE *log,int n,char c)
+{
+ for(; (n>0); n--) fprintf(log,"%c",c);
+}
+
+static void pprint(FILE *log,const char *s,t_mdebin *md)
+{
+ char CHAR='#';
+ int slen;
+ char buf1[22],buf2[22];
+
+ slen = strlen(s);
+ fprintf(log,"\t<====== ");
+ npr(log,slen,CHAR);
+ fprintf(log," ==>\n");
+ fprintf(log,"\t<==== %s ====>\n",s);
+ fprintf(log,"\t<== ");
+ npr(log,slen,CHAR);
+ fprintf(log," ======>\n\n");
+
+ fprintf(log,"\tStatistics over %s steps using %s frames\n",
+ gmx_step_str(md->ebin->nsteps_sim,buf1),
+ gmx_step_str(md->ebin->nsum_sim,buf2));
+ fprintf(log,"\n");
+}
+
+void print_ebin_header(FILE *log,gmx_large_int_t steps,double time,real lamb)
+{
+ char buf[22];
+
+ fprintf(log," %12s %12s %12s\n"
+ " %12s %12.5f %12.5f\n\n",
+ "Step","Time","Lambda",gmx_step_str(steps,buf),time,lamb);
+}
+
+void print_ebin(ener_file_t fp_ene,gmx_bool bEne,gmx_bool bDR,gmx_bool bOR,
+ FILE *log,
+ gmx_large_int_t step,double time,
+ int mode,gmx_bool bCompact,
+ t_mdebin *md,t_fcdata *fcd,
+ gmx_groups_t *groups,t_grpopts *opts)
+{
+ /*static char **grpnms=NULL;*/
+ char buf[246];
+ int i,j,n,ni,nj,ndr,nor,b;
+ int ndisre=0;
+ real *disre_rm3tav, *disre_rt;
+
+ /* these are for the old-style blocks (1 subblock, only reals), because
+ there can be only one per ID for these */
+ int nr[enxNR];
+ int id[enxNR];
+ real *block[enxNR];
+
+ /* temporary arrays for the lambda values to write out */
+ double enxlambda_data[2];
+
+ t_enxframe fr;
+
+ switch (mode)
+ {
+ case eprNORMAL:
+ init_enxframe(&fr);
+ fr.t = time;
+ fr.step = step;
+ fr.nsteps = md->ebin->nsteps;
+ fr.dt = md->delta_t;
+ fr.nsum = md->ebin->nsum;
+ fr.nre = (bEne) ? md->ebin->nener : 0;
+ fr.ener = md->ebin->e;
+ ndisre = bDR ? fcd->disres.npair : 0;
+ disre_rm3tav = fcd->disres.rm3tav;
+ disre_rt = fcd->disres.rt;
+ /* Optional additional old-style (real-only) blocks. */
+ for(i=0; i<enxNR; i++)
+ {
+ nr[i] = 0;
+ }
+ if (fcd->orires.nr > 0 && bOR)
+ {
+ diagonalize_orires_tensors(&(fcd->orires));
+ nr[enxOR] = fcd->orires.nr;
+ block[enxOR] = fcd->orires.otav;
+ id[enxOR] = enxOR;
+ nr[enxORI] = (fcd->orires.oinsl != fcd->orires.otav) ?
+ fcd->orires.nr : 0;
+ block[enxORI] = fcd->orires.oinsl;
+ id[enxORI] = enxORI;
+ nr[enxORT] = fcd->orires.nex*12;
+ block[enxORT] = fcd->orires.eig;
+ id[enxORT] = enxORT;
+ }
+
+ /* whether we are going to wrte anything out: */
+ if (fr.nre || ndisre || nr[enxOR] || nr[enxORI])
+ {
+
+ /* the old-style blocks go first */
+ fr.nblock = 0;
+ for(i=0; i<enxNR; i++)
+ {
+ if (nr[i] > 0)
+ {
+ fr.nblock = i + 1;
+ }
+ }
+ add_blocks_enxframe(&fr, fr.nblock);
+ for(b=0;b<fr.nblock;b++)
+ {
+ add_subblocks_enxblock(&(fr.block[b]), 1);
+ fr.block[b].id=id[b];
+ fr.block[b].sub[0].nr = nr[b];
+#ifndef GMX_DOUBLE
+ fr.block[b].sub[0].type = xdr_datatype_float;
+ fr.block[b].sub[0].fval = block[b];
+#else
+ fr.block[b].sub[0].type = xdr_datatype_double;
+ fr.block[b].sub[0].dval = block[b];
+#endif
+ }
+
+ /* check for disre block & fill it. */
+ if (ndisre>0)
+ {
+ int db = fr.nblock;
+ fr.nblock+=1;
+ add_blocks_enxframe(&fr, fr.nblock);
+
+ add_subblocks_enxblock(&(fr.block[db]), 2);
+ fr.block[db].id=enxDISRE;
+ fr.block[db].sub[0].nr=ndisre;
+ fr.block[db].sub[1].nr=ndisre;
+#ifndef GMX_DOUBLE
+ fr.block[db].sub[0].type=xdr_datatype_float;
+ fr.block[db].sub[1].type=xdr_datatype_float;
+ fr.block[db].sub[0].fval=disre_rt;
+ fr.block[db].sub[1].fval=disre_rm3tav;
+#else
+ fr.block[db].sub[0].type=xdr_datatype_double;
+ fr.block[db].sub[1].type=xdr_datatype_double;
+ fr.block[db].sub[0].dval=disre_rt;
+ fr.block[db].sub[1].dval=disre_rm3tav;
+#endif
+ }
+ /* here we can put new-style blocks */
+
+ /* Free energy perturbation blocks */
+ if (md->dhc)
+ {
+ mde_delta_h_coll_handle_block(md->dhc, &fr, fr.nblock);
+ }
+
+ /* do the actual I/O */
+ do_enx(fp_ene,&fr);
+ gmx_fio_check_file_position(enx_file_pointer(fp_ene));
+ if (fr.nre)
+ {
+ /* We have stored the sums, so reset the sum history */
+ reset_ebin_sums(md->ebin);
+ }
+
+ /* we can now free & reset the data in the blocks */
+ if (md->dhc)
+ mde_delta_h_coll_reset(md->dhc);
+ }
+ free_enxframe(&fr);
+ break;
+ case eprAVER:
+ if (log)
+ {
+ pprint(log,"A V E R A G E S",md);
+ }
+ break;
+ case eprRMS:
+ if (log)
+ {
+ pprint(log,"R M S - F L U C T U A T I O N S",md);
+ }
+ break;
+ default:
+ gmx_fatal(FARGS,"Invalid print mode (%d)",mode);
+ }
+
+ if (log)
+ {
+ for(i=0;i<opts->ngtc;i++)
+ {
+ if(opts->annealing[i]!=eannNO)
+ {
+ fprintf(log,"Current ref_t for group %s: %8.1f\n",
+ *(groups->grpname[groups->grps[egcTC].nm_ind[i]]),
+ opts->ref_t[i]);
+ }
+ }
+ if (mode==eprNORMAL && fcd->orires.nr>0)
+ {
+ print_orires_log(log,&(fcd->orires));
+ }
+ fprintf(log," Energies (%s)\n",unit_energy);
+ pr_ebin(log,md->ebin,md->ie,md->f_nre+md->nCrmsd,5,mode,TRUE);
+ fprintf(log,"\n");
+
+ if (!bCompact)
+ {
+ if (md->bDynBox)
+ {
+ pr_ebin(log,md->ebin,md->ib, md->bTricl ? NTRICLBOXS : NBOXS,5,
+ mode,TRUE);
+ fprintf(log,"\n");
+ }
+ if (md->bConstrVir)
+ {
+ fprintf(log," Constraint Virial (%s)\n",unit_energy);
+ pr_ebin(log,md->ebin,md->isvir,9,3,mode,FALSE);
+ fprintf(log,"\n");
+ fprintf(log," Force Virial (%s)\n",unit_energy);
+ pr_ebin(log,md->ebin,md->ifvir,9,3,mode,FALSE);
+ fprintf(log,"\n");
+ }
+ fprintf(log," Total Virial (%s)\n",unit_energy);
+ pr_ebin(log,md->ebin,md->ivir,9,3,mode,FALSE);
+ fprintf(log,"\n");
+ fprintf(log," Pressure (%s)\n",unit_pres_bar);
+ pr_ebin(log,md->ebin,md->ipres,9,3,mode,FALSE);
+ fprintf(log,"\n");
+ fprintf(log," Total Dipole (%s)\n",unit_dipole_D);
+ pr_ebin(log,md->ebin,md->imu,3,3,mode,FALSE);
+ fprintf(log,"\n");
+
+ if (md->nE > 1)
+ {
+ if (md->print_grpnms==NULL)
+ {
+ snew(md->print_grpnms,md->nE);
+ n=0;
+ for(i=0; (i<md->nEg); i++)
+ {
+ ni=groups->grps[egcENER].nm_ind[i];
+ for(j=i; (j<md->nEg); j++)
+ {
+ nj=groups->grps[egcENER].nm_ind[j];
+ sprintf(buf,"%s-%s",*(groups->grpname[ni]),
+ *(groups->grpname[nj]));
+ md->print_grpnms[n++]=strdup(buf);
+ }
+ }
+ }
+ sprintf(buf,"Epot (%s)",unit_energy);
+ fprintf(log,"%15s ",buf);
+ for(i=0; (i<egNR); i++)
+ {
+ if (md->bEInd[i])
+ {
+ fprintf(log,"%12s ",egrp_nm[i]);
+ }
+ }
+ fprintf(log,"\n");
+ for(i=0; (i<md->nE); i++)
+ {
+ fprintf(log,"%15s",md->print_grpnms[i]);
+ pr_ebin(log,md->ebin,md->igrp[i],md->nEc,md->nEc,mode,
+ FALSE);
+ }
+ fprintf(log,"\n");
+ }
+ if (md->nTC > 1)
+ {
+ pr_ebin(log,md->ebin,md->itemp,md->nTC,4,mode,TRUE);
+ fprintf(log,"\n");
+ }
+ if (md->nU > 1)
+ {
+ fprintf(log,"%15s %12s %12s %12s\n",
+ "Group","Ux","Uy","Uz");
+ for(i=0; (i<md->nU); i++)
+ {
+ ni=groups->grps[egcACC].nm_ind[i];
+ fprintf(log,"%15s",*groups->grpname[ni]);
+ pr_ebin(log,md->ebin,md->iu+3*i,3,3,mode,FALSE);
+ }
+ fprintf(log,"\n");
+ }
+ }
+ }
+
+}
+
+void update_energyhistory(energyhistory_t * enerhist,t_mdebin * mdebin)
+{
+ int i;
+
+ enerhist->nsteps = mdebin->ebin->nsteps;
+ enerhist->nsum = mdebin->ebin->nsum;
+ enerhist->nsteps_sim = mdebin->ebin->nsteps_sim;
+ enerhist->nsum_sim = mdebin->ebin->nsum_sim;
+ enerhist->nener = mdebin->ebin->nener;
+
+ if (mdebin->ebin->nsum > 0)
+ {
+ /* Check if we need to allocate first */
+ if(enerhist->ener_ave == NULL)
+ {
+ snew(enerhist->ener_ave,enerhist->nener);
+ snew(enerhist->ener_sum,enerhist->nener);
+ }
+
+ for(i=0;i<enerhist->nener;i++)
+ {
+ enerhist->ener_ave[i] = mdebin->ebin->e[i].eav;
+ enerhist->ener_sum[i] = mdebin->ebin->e[i].esum;
+ }
+ }
+
+ if (mdebin->ebin->nsum_sim > 0)
+ {
+ /* Check if we need to allocate first */
+ if(enerhist->ener_sum_sim == NULL)
+ {
+ snew(enerhist->ener_sum_sim,enerhist->nener);
+ }
+
+ for(i=0;i<enerhist->nener;i++)
+ {
+ enerhist->ener_sum_sim[i] = mdebin->ebin->e_sim[i].esum;
+ }
+ }
+ if (mdebin->dhc)
+ {
+ mde_delta_h_coll_update_energyhistory(mdebin->dhc, enerhist);
+ }
+}
+
+void restore_energyhistory_from_state(t_mdebin * mdebin,
+ energyhistory_t * enerhist)
+{
+ int i;
+
+ if ((enerhist->nsum > 0 || enerhist->nsum_sim > 0) &&
+ mdebin->ebin->nener != enerhist->nener)
+ {
+ gmx_fatal(FARGS,"Mismatch between number of energies in run input (%d) and checkpoint file (%d).",
+ mdebin->ebin->nener,enerhist->nener);
+ }
+
+ mdebin->ebin->nsteps = enerhist->nsteps;
+ mdebin->ebin->nsum = enerhist->nsum;
+ mdebin->ebin->nsteps_sim = enerhist->nsteps_sim;
+ mdebin->ebin->nsum_sim = enerhist->nsum_sim;
+
+ for(i=0; i<mdebin->ebin->nener; i++)
+ {
+ mdebin->ebin->e[i].eav =
+ (enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
+ mdebin->ebin->e[i].esum =
+ (enerhist->nsum > 0 ? enerhist->ener_sum[i] : 0);
+ mdebin->ebin->e_sim[i].esum =
+ (enerhist->nsum_sim > 0 ? enerhist->ener_sum_sim[i] : 0);
+ }
+ if (mdebin->dhc)
+ {
+ mde_delta_h_coll_restore_energyhistory(mdebin->dhc, enerhist);
+ }
+}
--- /dev/null
- if (!fr->bExcl_IntraCGAll_InterCGNone)
- {
- gmx_fatal(FARGS,"The charge-group - charge-group force loops only support systems with all intra-cg interactions excluded and no inter-cg exclusions, this is not the case for this system.");
- }
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * GROwing Monsters And Cloning Shrimps
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifdef GMX_THREAD_SHM_FDECOMP
+#include <pthread.h>
+#endif
+
+#include <math.h>
+#include <string.h>
+#include "sysstuff.h"
+#include "smalloc.h"
+#include "macros.h"
+#include "maths.h"
+#include "vec.h"
+#include "network.h"
+#include "nsgrid.h"
+#include "force.h"
+#include "nonbonded.h"
+#include "ns.h"
+#include "pbc.h"
+#include "names.h"
+#include "gmx_fatal.h"
+#include "nrnb.h"
+#include "txtdump.h"
+#include "mtop_util.h"
+
+#include "domdec.h"
+
+
+/*
+ * E X C L U S I O N H A N D L I N G
+ */
+
+#ifdef DEBUG
+static void SETEXCL_(t_excl e[],atom_id i,atom_id j)
+{ e[j] = e[j] | (1<<i); }
+static void RMEXCL_(t_excl e[],atom_id i,atom_id j)
+{ e[j]=e[j] & ~(1<<i); }
+static gmx_bool ISEXCL_(t_excl e[],atom_id i,atom_id j)
+{ return (gmx_bool)(e[j] & (1<<i)); }
+static gmx_bool NOTEXCL_(t_excl e[],atom_id i,atom_id j)
+{ return !(ISEXCL(e,i,j)); }
+#else
+#define SETEXCL(e,i,j) (e)[((atom_id) (j))] |= (1<<((atom_id) (i)))
+#define RMEXCL(e,i,j) (e)[((atom_id) (j))] &= (~(1<<((atom_id) (i))))
+#define ISEXCL(e,i,j) (gmx_bool) ((e)[((atom_id) (j))] & (1<<((atom_id) (i))))
+#define NOTEXCL(e,i,j) !(ISEXCL(e,i,j))
+#endif
+
+/************************************************
+ *
+ * U T I L I T I E S F O R N S
+ *
+ ************************************************/
+
+static void reallocate_nblist(t_nblist *nl)
+{
+ if (gmx_debug_at)
+ {
+ fprintf(debug,"reallocating neigborlist il_code=%d, maxnri=%d\n",
+ nl->il_code,nl->maxnri);
+ }
+ srenew(nl->iinr, nl->maxnri);
+ if (nl->enlist == enlistCG_CG)
+ {
+ srenew(nl->iinr_end,nl->maxnri);
+ }
+ srenew(nl->gid, nl->maxnri);
+ srenew(nl->shift, nl->maxnri);
+ srenew(nl->jindex, nl->maxnri+1);
+}
+
+/* ivdw/icoul are used to determine the type of interaction, so we
+ * can set an innerloop index here. The obvious choice for this would have
+ * been the vdwtype/coultype values in the forcerecord, but unfortunately
+ * those types are braindead - for instance both Buckingham and normal
+ * Lennard-Jones use the same value (evdwCUT), and a separate gmx_boolean variable
+ * to determine which interaction is used. There is further no special value
+ * for 'no interaction'. For backward compatibility with old TPR files we won't
+ * change this in the 3.x series, so when calling this routine you should use:
+ *
+ * icoul=0 no coulomb interaction
+ * icoul=1 cutoff standard coulomb
+ * icoul=2 reaction-field coulomb
+ * icoul=3 tabulated coulomb
+ *
+ * ivdw=0 no vdw interaction
+ * ivdw=1 standard L-J interaction
+ * ivdw=2 Buckingham
+ * ivdw=3 tabulated vdw.
+ *
+ * Kind of ugly, but it works.
+ */
+static void init_nblist(t_nblist *nl_sr,t_nblist *nl_lr,
+ int maxsr,int maxlr,
+ int ivdw, int icoul,
+ gmx_bool bfree, int enlist)
+{
+ t_nblist *nl;
+ int homenr;
+ int i,nn;
+
+ int inloop[20] =
+ {
+ eNR_NBKERNEL_NONE,
+ eNR_NBKERNEL010,
+ eNR_NBKERNEL020,
+ eNR_NBKERNEL030,
+ eNR_NBKERNEL100,
+ eNR_NBKERNEL110,
+ eNR_NBKERNEL120,
+ eNR_NBKERNEL130,
+ eNR_NBKERNEL200,
+ eNR_NBKERNEL210,
+ eNR_NBKERNEL220,
+ eNR_NBKERNEL230,
+ eNR_NBKERNEL300,
+ eNR_NBKERNEL310,
+ eNR_NBKERNEL320,
+ eNR_NBKERNEL330,
+ eNR_NBKERNEL400,
+ eNR_NBKERNEL410,
+ eNR_NBKERNEL_NONE,
+ eNR_NBKERNEL430
+ };
+
+ for(i=0; (i<2); i++)
+ {
+ nl = (i == 0) ? nl_sr : nl_lr;
+ homenr = (i == 0) ? maxsr : maxlr;
+
+ if (nl == NULL)
+ {
+ continue;
+ }
+
+ /* Set coul/vdw in neighborlist, and for the normal loops we determine
+ * an index of which one to call.
+ */
+ nl->ivdw = ivdw;
+ nl->icoul = icoul;
+ nl->free_energy = bfree;
+
+ if (bfree)
+ {
+ nl->enlist = enlistATOM_ATOM;
+ nl->il_code = eNR_NBKERNEL_FREE_ENERGY;
+ }
+ else
+ {
+ nl->enlist = enlist;
+
+ nn = inloop[4*icoul + ivdw];
+
+ /* solvent loops follow directly after the corresponding
+ * ordinary loops, in the order:
+ *
+ * SPC, SPC-SPC, TIP4p, TIP4p-TIP4p
+ *
+ */
+ switch (enlist) {
+ case enlistATOM_ATOM:
+ case enlistCG_CG:
+ break;
+ case enlistSPC_ATOM: nn += 1; break;
+ case enlistSPC_SPC: nn += 2; break;
+ case enlistTIP4P_ATOM: nn += 3; break;
+ case enlistTIP4P_TIP4P: nn += 4; break;
+ }
+
+ nl->il_code = nn;
+ }
+
+ if (debug)
+ fprintf(debug,"Initiating neighbourlist type %d for %s interactions,\nwith %d SR, %d LR atoms.\n",
+ nl->il_code,ENLISTTYPE(enlist),maxsr,maxlr);
+
+ /* maxnri is influenced by the number of shifts (maximum is 8)
+ * and the number of energy groups.
+ * If it is not enough, nl memory will be reallocated during the run.
+ * 4 seems to be a reasonable factor, which only causes reallocation
+ * during runs with tiny and many energygroups.
+ */
+ nl->maxnri = homenr*4;
+ nl->maxnrj = 0;
+ nl->maxlen = 0;
+ nl->nri = -1;
+ nl->nrj = 0;
+ nl->iinr = NULL;
+ nl->gid = NULL;
+ nl->shift = NULL;
+ nl->jindex = NULL;
+ reallocate_nblist(nl);
+ nl->jindex[0] = 0;
+#ifdef GMX_THREAD_SHM_FDECOMP
+ nl->counter = 0;
+ snew(nl->mtx,1);
+ pthread_mutex_init(nl->mtx,NULL);
+#endif
+ }
+}
+
+void init_neighbor_list(FILE *log,t_forcerec *fr,int homenr)
+{
+ /* Make maxlr tunable! (does not seem to be a big difference though)
+ * This parameter determines the number of i particles in a long range
+ * neighbourlist. Too few means many function calls, too many means
+ * cache trashing.
+ */
+ int maxsr,maxsr_wat,maxlr,maxlr_wat;
+ int icoul,icoulf,ivdw;
+ int solvent;
+ int enlist_def,enlist_w,enlist_ww;
+ int i;
+ t_nblists *nbl;
+
+ /* maxsr = homenr-fr->nWatMol*3; */
+ maxsr = homenr;
+
+ if (maxsr < 0)
+ {
+ gmx_fatal(FARGS,"%s, %d: Negative number of short range atoms.\n"
+ "Call your Gromacs dealer for assistance.",__FILE__,__LINE__);
+ }
+ /* This is just for initial allocation, so we do not reallocate
+ * all the nlist arrays many times in a row.
+ * The numbers seem very accurate, but they are uncritical.
+ */
+ maxsr_wat = min(fr->nWatMol,(homenr+2)/3);
+ if (fr->bTwinRange)
+ {
+ maxlr = 50;
+ maxlr_wat = min(maxsr_wat,maxlr);
+ }
+ else
+ {
+ maxlr = maxlr_wat = 0;
+ }
+
+ /* Determine the values for icoul/ivdw. */
+ /* Start with GB */
+ if(fr->bGB)
+ {
+ icoul=4;
+ }
+ else if (fr->bcoultab)
+ {
+ icoul = 3;
+ }
+ else if (EEL_RF(fr->eeltype))
+ {
+ icoul = 2;
+ }
+ else
+ {
+ icoul = 1;
+ }
+
+ if (fr->bvdwtab)
+ {
+ ivdw = 3;
+ }
+ else if (fr->bBHAM)
+ {
+ ivdw = 2;
+ }
+ else
+ {
+ ivdw = 1;
+ }
+
+ fr->ns.bCGlist = (getenv("GMX_NBLISTCG") != 0);
+ if (!fr->ns.bCGlist)
+ {
+ enlist_def = enlistATOM_ATOM;
+ }
+ else
+ {
+ enlist_def = enlistCG_CG;
+ if (log != NULL)
+ {
+ fprintf(log,"\nUsing charge-group - charge-group neighbor lists and kernels\n\n");
+ }
- t_excl *bexcl,gmx_bool bLR)
+ }
+
+ if (fr->solvent_opt == esolTIP4P) {
+ enlist_w = enlistTIP4P_ATOM;
+ enlist_ww = enlistTIP4P_TIP4P;
+ } else {
+ enlist_w = enlistSPC_ATOM;
+ enlist_ww = enlistSPC_SPC;
+ }
+
+ for(i=0; i<fr->nnblists; i++)
+ {
+ nbl = &(fr->nblists[i]);
+ init_nblist(&nbl->nlist_sr[eNL_VDWQQ],&nbl->nlist_lr[eNL_VDWQQ],
+ maxsr,maxlr,ivdw,icoul,FALSE,enlist_def);
+ init_nblist(&nbl->nlist_sr[eNL_VDW],&nbl->nlist_lr[eNL_VDW],
+ maxsr,maxlr,ivdw,0,FALSE,enlist_def);
+ init_nblist(&nbl->nlist_sr[eNL_QQ],&nbl->nlist_lr[eNL_QQ],
+ maxsr,maxlr,0,icoul,FALSE,enlist_def);
+ init_nblist(&nbl->nlist_sr[eNL_VDWQQ_WATER],&nbl->nlist_lr[eNL_VDWQQ_WATER],
+ maxsr_wat,maxlr_wat,ivdw,icoul, FALSE,enlist_w);
+ init_nblist(&nbl->nlist_sr[eNL_QQ_WATER],&nbl->nlist_lr[eNL_QQ_WATER],
+ maxsr_wat,maxlr_wat,0,icoul, FALSE,enlist_w);
+ init_nblist(&nbl->nlist_sr[eNL_VDWQQ_WATERWATER],&nbl->nlist_lr[eNL_VDWQQ_WATERWATER],
+ maxsr_wat,maxlr_wat,ivdw,icoul, FALSE,enlist_ww);
+ init_nblist(&nbl->nlist_sr[eNL_QQ_WATERWATER],&nbl->nlist_lr[eNL_QQ_WATERWATER],
+ maxsr_wat,maxlr_wat,0,icoul, FALSE,enlist_ww);
+
+ if (fr->efep != efepNO)
+ {
+ if (fr->bEwald)
+ {
+ icoulf = 5;
+ }
+ else
+ {
+ icoulf = icoul;
+ }
+
+ init_nblist(&nbl->nlist_sr[eNL_VDWQQ_FREE],&nbl->nlist_lr[eNL_VDWQQ_FREE],
+ maxsr,maxlr,ivdw,icoulf,TRUE,enlistATOM_ATOM);
+ init_nblist(&nbl->nlist_sr[eNL_VDW_FREE],&nbl->nlist_lr[eNL_VDW_FREE],
+ maxsr,maxlr,ivdw,0,TRUE,enlistATOM_ATOM);
+ init_nblist(&nbl->nlist_sr[eNL_QQ_FREE],&nbl->nlist_lr[eNL_QQ_FREE],
+ maxsr,maxlr,0,icoulf,TRUE,enlistATOM_ATOM);
+ }
+ }
+ /* QMMM MM list */
+ if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
+ {
+ init_nblist(&fr->QMMMlist,NULL,
+ maxsr,maxlr,0,icoul,FALSE,enlistATOM_ATOM);
+ }
+
+ fr->ns.nblist_initialized=TRUE;
+}
+
+static void reset_nblist(t_nblist *nl)
+{
+ nl->nri = -1;
+ nl->nrj = 0;
+ nl->maxlen = 0;
+ if (nl->jindex)
+ {
+ nl->jindex[0] = 0;
+ }
+}
+
+static void reset_neighbor_list(t_forcerec *fr,gmx_bool bLR,int nls,int eNL)
+{
+ int n,i;
+
+ if (bLR)
+ {
+ reset_nblist(&(fr->nblists[nls].nlist_lr[eNL]));
+ }
+ else
+ {
+ for(n=0; n<fr->nnblists; n++)
+ {
+ for(i=0; i<eNL_NR; i++)
+ {
+ reset_nblist(&(fr->nblists[n].nlist_sr[i]));
+ }
+ }
+ if (fr->bQMMM)
+ {
+ /* only reset the short-range nblist */
+ reset_nblist(&(fr->QMMMlist));
+ }
+ }
+}
+
+
+
+
+static inline void new_i_nblist(t_nblist *nlist,
+ gmx_bool bLR,atom_id i_atom,int shift,int gid)
+{
+ int i,k,nri,nshift;
+
+ nri = nlist->nri;
+
+ /* Check whether we have to increase the i counter */
+ if ((nri == -1) ||
+ (nlist->iinr[nri] != i_atom) ||
+ (nlist->shift[nri] != shift) ||
+ (nlist->gid[nri] != gid))
+ {
+ /* This is something else. Now see if any entries have
+ * been added in the list of the previous atom.
+ */
+ if ((nri == -1) ||
+ ((nlist->jindex[nri+1] > nlist->jindex[nri]) &&
+ (nlist->gid[nri] != -1)))
+ {
+ /* If so increase the counter */
+ nlist->nri++;
+ nri++;
+ if (nlist->nri >= nlist->maxnri)
+ {
+ nlist->maxnri += over_alloc_large(nlist->nri);
+ reallocate_nblist(nlist);
+ }
+ }
+ /* Set the number of neighbours and the atom number */
+ nlist->jindex[nri+1] = nlist->jindex[nri];
+ nlist->iinr[nri] = i_atom;
+ nlist->gid[nri] = gid;
+ nlist->shift[nri] = shift;
+ }
+}
+
+static inline void close_i_nblist(t_nblist *nlist)
+{
+ int nri = nlist->nri;
+ int len;
+
+ if (nri >= 0)
+ {
+ nlist->jindex[nri+1] = nlist->nrj;
+
+ len=nlist->nrj - nlist->jindex[nri];
+
+ /* nlist length for water i molecules is treated statically
+ * in the innerloops
+ */
+ if (len > nlist->maxlen)
+ {
+ nlist->maxlen = len;
+ }
+ }
+}
+
+static inline void close_nblist(t_nblist *nlist)
+{
+ /* Only close this nblist when it has been initialized.
+ * Avoid the creation of i-lists with no j-particles.
+ */
+ if (nlist->nrj == 0)
+ {
+ /* Some assembly kernels do not support empty lists,
+ * make sure here that we don't generate any empty lists.
+ * With the current ns code this branch is taken in two cases:
+ * No i-particles at all: nri=-1 here
+ * There are i-particles, but no j-particles; nri=0 here
+ */
+ nlist->nri = 0;
+ }
+ else
+ {
+ /* Close list number nri by incrementing the count */
+ nlist->nri++;
+ }
+}
+
+static inline void close_neighbor_list(t_forcerec *fr,gmx_bool bLR,int nls,int eNL,
+ gmx_bool bMakeQMMMnblist)
+{
+ int n,i;
+
+ if (bMakeQMMMnblist) {
+ if (!bLR)
+ {
+ close_nblist(&(fr->QMMMlist));
+ }
+ }
+ else
+ {
+ if (bLR)
+ {
+ close_nblist(&(fr->nblists[nls].nlist_lr[eNL]));
+ }
+ else
+ {
+ for(n=0; n<fr->nnblists; n++)
+ {
+ for(i=0; (i<eNL_NR); i++)
+ {
+ close_nblist(&(fr->nblists[n].nlist_sr[i]));
+ }
+ }
+ }
+ }
+}
+
+static inline void add_j_to_nblist(t_nblist *nlist,atom_id j_atom,gmx_bool bLR)
+{
+ int nrj=nlist->nrj;
+
+ if (nlist->nrj >= nlist->maxnrj)
+ {
+ nlist->maxnrj = over_alloc_small(nlist->nrj + 1);
+ if (gmx_debug_at)
+ fprintf(debug,"Increasing %s nblist %s j size to %d\n",
+ bLR ? "LR" : "SR",nrnb_str(nlist->il_code),nlist->maxnrj);
+
+ srenew(nlist->jjnr,nlist->maxnrj);
+ }
+
+ nlist->jjnr[nrj] = j_atom;
+ nlist->nrj ++;
+}
+
+static inline void add_j_to_nblist_cg(t_nblist *nlist,
+ atom_id j_start,int j_end,
- add_j_to_nblist_cg(vdwc,index[jcg],index[jcg+1],bExcl,bLR);
++ t_excl *bexcl,gmx_bool i_is_j,
++ gmx_bool bLR)
+{
+ int nrj=nlist->nrj;
+ int j;
+
+ if (nlist->nrj >= nlist->maxnrj)
+ {
+ nlist->maxnrj = over_alloc_small(nlist->nrj + 1);
+ if (gmx_debug_at)
+ fprintf(debug,"Increasing %s nblist %s j size to %d\n",
+ bLR ? "LR" : "SR",nrnb_str(nlist->il_code),nlist->maxnrj);
+
+ srenew(nlist->jjnr ,nlist->maxnrj);
+ srenew(nlist->jjnr_end,nlist->maxnrj);
+ srenew(nlist->excl ,nlist->maxnrj*MAX_CGCGSIZE);
+ }
+
+ nlist->jjnr[nrj] = j_start;
+ nlist->jjnr_end[nrj] = j_end;
+
+ if (j_end - j_start > MAX_CGCGSIZE)
+ {
+ gmx_fatal(FARGS,"The charge-group - charge-group neighborlist do not support charge groups larger than %d, found a charge group of size %d",MAX_CGCGSIZE,j_end-j_start);
+ }
+
+ /* Set the exclusions */
+ for(j=j_start; j<j_end; j++)
+ {
+ nlist->excl[nrj*MAX_CGCGSIZE + j - j_start] = bexcl[j];
+ }
++ if (i_is_j)
++ {
++ /* Avoid double counting of intra-cg interactions */
++ for(j=1; j<j_end-j_start; j++)
++ {
++ nlist->excl[nrj*MAX_CGCGSIZE + j] |= (1<<j) - 1;
++ }
++ }
+
+ nlist->nrj ++;
+}
+
+typedef void
+put_in_list_t(gmx_bool bHaveVdW[],
+ int ngid,
+ t_mdatoms * md,
+ int icg,
+ int jgid,
+ int nj,
+ atom_id jjcg[],
+ atom_id index[],
+ t_excl bExcl[],
+ int shift,
+ t_forcerec * fr,
+ gmx_bool bLR,
+ gmx_bool bDoVdW,
+ gmx_bool bDoCoul);
+
+static void
+put_in_list_at(gmx_bool bHaveVdW[],
+ int ngid,
+ t_mdatoms * md,
+ int icg,
+ int jgid,
+ int nj,
+ atom_id jjcg[],
+ atom_id index[],
+ t_excl bExcl[],
+ int shift,
+ t_forcerec * fr,
+ gmx_bool bLR,
+ gmx_bool bDoVdW,
+ gmx_bool bDoCoul)
+{
+ /* The a[] index has been removed,
+ * to put it back in i_atom should be a[i0] and jj should be a[jj].
+ */
+ t_nblist * vdwc;
+ t_nblist * vdw;
+ t_nblist * coul;
+ t_nblist * vdwc_free = NULL;
+ t_nblist * vdw_free = NULL;
+ t_nblist * coul_free = NULL;
+ t_nblist * vdwc_ww = NULL;
+ t_nblist * coul_ww = NULL;
+
+ int i,j,jcg,igid,gid,nbl_ind,ind_ij;
+ atom_id jj,jj0,jj1,i_atom;
+ int i0,nicg,len;
+
+ int *cginfo;
+ int *type,*typeB;
+ real *charge,*chargeB;
+ real qi,qiB,qq,rlj;
+ gmx_bool bFreeEnergy,bFree,bFreeJ,bNotEx,*bPert;
+ gmx_bool bDoVdW_i,bDoCoul_i,bDoCoul_i_sol;
+ int iwater,jwater;
+ t_nblist *nlist;
+
+ /* Copy some pointers */
+ cginfo = fr->cginfo;
+ charge = md->chargeA;
+ chargeB = md->chargeB;
+ type = md->typeA;
+ typeB = md->typeB;
+ bPert = md->bPerturbed;
+
+ /* Get atom range */
+ i0 = index[icg];
+ nicg = index[icg+1]-i0;
+
+ /* Get the i charge group info */
+ igid = GET_CGINFO_GID(cginfo[icg]);
+ iwater = GET_CGINFO_SOLOPT(cginfo[icg]);
+
+ bFreeEnergy = FALSE;
+ if (md->nPerturbed)
+ {
+ /* Check if any of the particles involved are perturbed.
+ * If not we can do the cheaper normal put_in_list
+ * and use more solvent optimization.
+ */
+ for(i=0; i<nicg; i++)
+ {
+ bFreeEnergy |= bPert[i0+i];
+ }
+ /* Loop over the j charge groups */
+ for(j=0; (j<nj && !bFreeEnergy); j++)
+ {
+ jcg = jjcg[j];
+ jj0 = index[jcg];
+ jj1 = index[jcg+1];
+ /* Finally loop over the atoms in the j-charge group */
+ for(jj=jj0; jj<jj1; jj++)
+ {
+ bFreeEnergy |= bPert[jj];
+ }
+ }
+ }
+
+ /* Unpack pointers to neighbourlist structs */
+ if (fr->nnblists == 1)
+ {
+ nbl_ind = 0;
+ }
+ else
+ {
+ nbl_ind = fr->gid2nblists[GID(igid,jgid,ngid)];
+ }
+ if (bLR)
+ {
+ nlist = fr->nblists[nbl_ind].nlist_lr;
+ }
+ else
+ {
+ nlist = fr->nblists[nbl_ind].nlist_sr;
+ }
+
+ if (iwater != esolNO)
+ {
+ vdwc = &nlist[eNL_VDWQQ_WATER];
+ vdw = &nlist[eNL_VDW];
+ coul = &nlist[eNL_QQ_WATER];
+#ifndef DISABLE_WATERWATER_NLIST
+ vdwc_ww = &nlist[eNL_VDWQQ_WATERWATER];
+ coul_ww = &nlist[eNL_QQ_WATERWATER];
+#endif
+ }
+ else
+ {
+ vdwc = &nlist[eNL_VDWQQ];
+ vdw = &nlist[eNL_VDW];
+ coul = &nlist[eNL_QQ];
+ }
+
+ if (!bFreeEnergy)
+ {
+ if (iwater != esolNO)
+ {
+ /* Loop over the atoms in the i charge group */
+ i_atom = i0;
+ gid = GID(igid,jgid,ngid);
+ /* Create new i_atom for each energy group */
+ if (bDoCoul && bDoVdW)
+ {
+ new_i_nblist(vdwc,bLR,i_atom,shift,gid);
+#ifndef DISABLE_WATERWATER_NLIST
+ new_i_nblist(vdwc_ww,bLR,i_atom,shift,gid);
+#endif
+ }
+ if (bDoVdW)
+ {
+ new_i_nblist(vdw,bLR,i_atom,shift,gid);
+ }
+ if (bDoCoul)
+ {
+ new_i_nblist(coul,bLR,i_atom,shift,gid);
+#ifndef DISABLE_WATERWATER_NLIST
+ new_i_nblist(coul_ww,bLR,i_atom,shift,gid);
+#endif
+ }
+ /* Loop over the j charge groups */
+ for(j=0; (j<nj); j++)
+ {
+ jcg=jjcg[j];
+
+ if (jcg == icg)
+ {
+ continue;
+ }
+
+ jj0 = index[jcg];
+ jwater = GET_CGINFO_SOLOPT(cginfo[jcg]);
+
+ if (iwater == esolSPC && jwater == esolSPC)
+ {
+ /* Interaction between two SPC molecules */
+ if (!bDoCoul)
+ {
+ /* VdW only - only first atoms in each water interact */
+ add_j_to_nblist(vdw,jj0,bLR);
+ }
+ else
+ {
+#ifdef DISABLE_WATERWATER_NLIST
+ /* Add entries for the three atoms - only do VdW if we need to */
+ if (!bDoVdW)
+ {
+ add_j_to_nblist(coul,jj0,bLR);
+ }
+ else
+ {
+ add_j_to_nblist(vdwc,jj0,bLR);
+ }
+ add_j_to_nblist(coul,jj0+1,bLR);
+ add_j_to_nblist(coul,jj0+2,bLR);
+#else
+ /* One entry for the entire water-water interaction */
+ if (!bDoVdW)
+ {
+ add_j_to_nblist(coul_ww,jj0,bLR);
+ }
+ else
+ {
+ add_j_to_nblist(vdwc_ww,jj0,bLR);
+ }
+#endif
+ }
+ }
+ else if (iwater == esolTIP4P && jwater == esolTIP4P)
+ {
+ /* Interaction between two TIP4p molecules */
+ if (!bDoCoul)
+ {
+ /* VdW only - only first atoms in each water interact */
+ add_j_to_nblist(vdw,jj0,bLR);
+ }
+ else
+ {
+#ifdef DISABLE_WATERWATER_NLIST
+ /* Add entries for the four atoms - only do VdW if we need to */
+ if (bDoVdW)
+ {
+ add_j_to_nblist(vdw,jj0,bLR);
+ }
+ add_j_to_nblist(coul,jj0+1,bLR);
+ add_j_to_nblist(coul,jj0+2,bLR);
+ add_j_to_nblist(coul,jj0+3,bLR);
+#else
+ /* One entry for the entire water-water interaction */
+ if (!bDoVdW)
+ {
+ add_j_to_nblist(coul_ww,jj0,bLR);
+ }
+ else
+ {
+ add_j_to_nblist(vdwc_ww,jj0,bLR);
+ }
+#endif
+ }
+ }
+ else
+ {
+ /* j charge group is not water, but i is.
+ * Add entries to the water-other_atom lists; the geometry of the water
+ * molecule doesn't matter - that is taken care of in the nonbonded kernel,
+ * so we don't care if it is SPC or TIP4P...
+ */
+
+ jj1 = index[jcg+1];
+
+ if (!bDoVdW)
+ {
+ for(jj=jj0; (jj<jj1); jj++)
+ {
+ if (charge[jj] != 0)
+ {
+ add_j_to_nblist(coul,jj,bLR);
+ }
+ }
+ }
+ else if (!bDoCoul)
+ {
+ for(jj=jj0; (jj<jj1); jj++)
+ {
+ if (bHaveVdW[type[jj]])
+ {
+ add_j_to_nblist(vdw,jj,bLR);
+ }
+ }
+ }
+ else
+ {
+ /* _charge_ _groups_ interact with both coulomb and LJ */
+ /* Check which atoms we should add to the lists! */
+ for(jj=jj0; (jj<jj1); jj++)
+ {
+ if (bHaveVdW[type[jj]])
+ {
+ if (charge[jj] != 0)
+ {
+ add_j_to_nblist(vdwc,jj,bLR);
+ }
+ else
+ {
+ add_j_to_nblist(vdw,jj,bLR);
+ }
+ }
+ else if (charge[jj] != 0)
+ {
+ add_j_to_nblist(coul,jj,bLR);
+ }
+ }
+ }
+ }
+ }
+ close_i_nblist(vdw);
+ close_i_nblist(coul);
+ close_i_nblist(vdwc);
+#ifndef DISABLE_WATERWATER_NLIST
+ close_i_nblist(coul_ww);
+ close_i_nblist(vdwc_ww);
+#endif
+ }
+ else
+ {
+ /* no solvent as i charge group */
+ /* Loop over the atoms in the i charge group */
+ for(i=0; i<nicg; i++)
+ {
+ i_atom = i0+i;
+ gid = GID(igid,jgid,ngid);
+ qi = charge[i_atom];
+
+ /* Create new i_atom for each energy group */
+ if (bDoVdW && bDoCoul)
+ {
+ new_i_nblist(vdwc,bLR,i_atom,shift,gid);
+ }
+ if (bDoVdW)
+ {
+ new_i_nblist(vdw,bLR,i_atom,shift,gid);
+ }
+ if (bDoCoul)
+ {
+ new_i_nblist(coul,bLR,i_atom,shift,gid);
+ }
+ bDoVdW_i = (bDoVdW && bHaveVdW[type[i_atom]]);
+ bDoCoul_i = (bDoCoul && qi!=0);
+
+ if (bDoVdW_i || bDoCoul_i)
+ {
+ /* Loop over the j charge groups */
+ for(j=0; (j<nj); j++)
+ {
+ jcg=jjcg[j];
+
+ /* Check for large charge groups */
+ if (jcg == icg)
+ {
+ jj0 = i0 + i + 1;
+ }
+ else
+ {
+ jj0 = index[jcg];
+ }
+
+ jj1=index[jcg+1];
+ /* Finally loop over the atoms in the j-charge group */
+ for(jj=jj0; jj<jj1; jj++)
+ {
+ bNotEx = NOTEXCL(bExcl,i,jj);
+
+ if (bNotEx)
+ {
+ if (!bDoVdW_i)
+ {
+ if (charge[jj] != 0)
+ {
+ add_j_to_nblist(coul,jj,bLR);
+ }
+ }
+ else if (!bDoCoul_i)
+ {
+ if (bHaveVdW[type[jj]])
+ {
+ add_j_to_nblist(vdw,jj,bLR);
+ }
+ }
+ else
+ {
+ if (bHaveVdW[type[jj]])
+ {
+ if (charge[jj] != 0)
+ {
+ add_j_to_nblist(vdwc,jj,bLR);
+ }
+ else
+ {
+ add_j_to_nblist(vdw,jj,bLR);
+ }
+ }
+ else if (charge[jj] != 0)
+ {
+ add_j_to_nblist(coul,jj,bLR);
+ }
+ }
+ }
+ }
+ }
+ }
+ close_i_nblist(vdw);
+ close_i_nblist(coul);
+ close_i_nblist(vdwc);
+ }
+ }
+ }
+ else
+ {
+ /* we are doing free energy */
+ vdwc_free = &nlist[eNL_VDWQQ_FREE];
+ vdw_free = &nlist[eNL_VDW_FREE];
+ coul_free = &nlist[eNL_QQ_FREE];
+ /* Loop over the atoms in the i charge group */
+ for(i=0; i<nicg; i++)
+ {
+ i_atom = i0+i;
+ gid = GID(igid,jgid,ngid);
+ qi = charge[i_atom];
+ qiB = chargeB[i_atom];
+
+ /* Create new i_atom for each energy group */
+ if (bDoVdW && bDoCoul)
+ new_i_nblist(vdwc,bLR,i_atom,shift,gid);
+ if (bDoVdW)
+ new_i_nblist(vdw,bLR,i_atom,shift,gid);
+ if (bDoCoul)
+ new_i_nblist(coul,bLR,i_atom,shift,gid);
+
+ new_i_nblist(vdw_free,bLR,i_atom,shift,gid);
+ new_i_nblist(coul_free,bLR,i_atom,shift,gid);
+ new_i_nblist(vdwc_free,bLR,i_atom,shift,gid);
+
+ bDoVdW_i = (bDoVdW &&
+ (bHaveVdW[type[i_atom]] || bHaveVdW[typeB[i_atom]]));
+ bDoCoul_i = (bDoCoul && (qi!=0 || qiB!=0));
+ /* For TIP4P the first atom does not have a charge,
+ * but the last three do. So we should still put an atom
+ * without LJ but with charge in the water-atom neighborlist
+ * for a TIP4p i charge group.
+ * For SPC type water the first atom has LJ and charge,
+ * so there is no such problem.
+ */
+ if (iwater == esolNO)
+ {
+ bDoCoul_i_sol = bDoCoul_i;
+ }
+ else
+ {
+ bDoCoul_i_sol = bDoCoul;
+ }
+
+ if (bDoVdW_i || bDoCoul_i_sol)
+ {
+ /* Loop over the j charge groups */
+ for(j=0; (j<nj); j++)
+ {
+ jcg=jjcg[j];
+
+ /* Check for large charge groups */
+ if (jcg == icg)
+ {
+ jj0 = i0 + i + 1;
+ }
+ else
+ {
+ jj0 = index[jcg];
+ }
+
+ jj1=index[jcg+1];
+ /* Finally loop over the atoms in the j-charge group */
+ bFree = bPert[i_atom];
+ for(jj=jj0; (jj<jj1); jj++)
+ {
+ bFreeJ = bFree || bPert[jj];
+ /* Complicated if, because the water H's should also
+ * see perturbed j-particles
+ */
+ if (iwater==esolNO || i==0 || bFreeJ)
+ {
+ bNotEx = NOTEXCL(bExcl,i,jj);
+
+ if (bNotEx)
+ {
+ if (bFreeJ)
+ {
+ if (!bDoVdW_i)
+ {
+ if (charge[jj]!=0 || chargeB[jj]!=0)
+ {
+ add_j_to_nblist(coul_free,jj,bLR);
+ }
+ }
+ else if (!bDoCoul_i)
+ {
+ if (bHaveVdW[type[jj]] || bHaveVdW[typeB[jj]])
+ {
+ add_j_to_nblist(vdw_free,jj,bLR);
+ }
+ }
+ else
+ {
+ if (bHaveVdW[type[jj]] || bHaveVdW[typeB[jj]])
+ {
+ if (charge[jj]!=0 || chargeB[jj]!=0)
+ {
+ add_j_to_nblist(vdwc_free,jj,bLR);
+ }
+ else
+ {
+ add_j_to_nblist(vdw_free,jj,bLR);
+ }
+ }
+ else if (charge[jj]!=0 || chargeB[jj]!=0)
+ add_j_to_nblist(coul_free,jj,bLR);
+ }
+ }
+ else if (!bDoVdW_i)
+ {
+ /* This is done whether or not bWater is set */
+ if (charge[jj] != 0)
+ {
+ add_j_to_nblist(coul,jj,bLR);
+ }
+ }
+ else if (!bDoCoul_i_sol)
+ {
+ if (bHaveVdW[type[jj]])
+ {
+ add_j_to_nblist(vdw,jj,bLR);
+ }
+ }
+ else
+ {
+ if (bHaveVdW[type[jj]])
+ {
+ if (charge[jj] != 0)
+ {
+ add_j_to_nblist(vdwc,jj,bLR);
+ }
+ else
+ {
+ add_j_to_nblist(vdw,jj,bLR);
+ }
+ }
+ else if (charge[jj] != 0)
+ {
+ add_j_to_nblist(coul,jj,bLR);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ close_i_nblist(vdw);
+ close_i_nblist(coul);
+ close_i_nblist(vdwc);
+ close_i_nblist(vdw_free);
+ close_i_nblist(coul_free);
+ close_i_nblist(vdwc_free);
+ }
+ }
+}
+
+static void
+put_in_list_qmmm(gmx_bool bHaveVdW[],
+ int ngid,
+ t_mdatoms * md,
+ int icg,
+ int jgid,
+ int nj,
+ atom_id jjcg[],
+ atom_id index[],
+ t_excl bExcl[],
+ int shift,
+ t_forcerec * fr,
+ gmx_bool bLR,
+ gmx_bool bDoVdW,
+ gmx_bool bDoCoul)
+{
+ t_nblist * coul;
+ int i,j,jcg,igid,gid;
+ atom_id jj,jj0,jj1,i_atom;
+ int i0,nicg;
+ gmx_bool bNotEx;
+
+ /* Get atom range */
+ i0 = index[icg];
+ nicg = index[icg+1]-i0;
+
+ /* Get the i charge group info */
+ igid = GET_CGINFO_GID(fr->cginfo[icg]);
+
+ coul = &fr->QMMMlist;
+
+ /* Loop over atoms in the ith charge group */
+ for (i=0;i<nicg;i++)
+ {
+ i_atom = i0+i;
+ gid = GID(igid,jgid,ngid);
+ /* Create new i_atom for each energy group */
+ new_i_nblist(coul,bLR,i_atom,shift,gid);
+
+ /* Loop over the j charge groups */
+ for (j=0;j<nj;j++)
+ {
+ jcg=jjcg[j];
+
+ /* Charge groups cannot have QM and MM atoms simultaneously */
+ if (jcg!=icg)
+ {
+ jj0 = index[jcg];
+ jj1 = index[jcg+1];
+ /* Finally loop over the atoms in the j-charge group */
+ for(jj=jj0; jj<jj1; jj++)
+ {
+ bNotEx = NOTEXCL(bExcl,i,jj);
+ if(bNotEx)
+ add_j_to_nblist(coul,jj,bLR);
+ }
+ }
+ }
+ close_i_nblist(coul);
+ }
+}
+
+static void
+put_in_list_cg(gmx_bool bHaveVdW[],
+ int ngid,
+ t_mdatoms * md,
+ int icg,
+ int jgid,
+ int nj,
+ atom_id jjcg[],
+ atom_id index[],
+ t_excl bExcl[],
+ int shift,
+ t_forcerec * fr,
+ gmx_bool bLR,
+ gmx_bool bDoVdW,
+ gmx_bool bDoCoul)
+{
+ int cginfo;
+ int igid,gid,nbl_ind;
+ t_nblist * vdwc;
+ int j,jcg;
+
+ cginfo = fr->cginfo[icg];
+
+ igid = GET_CGINFO_GID(cginfo);
+ gid = GID(igid,jgid,ngid);
+
+ /* Unpack pointers to neighbourlist structs */
+ if (fr->nnblists == 1)
+ {
+ nbl_ind = 0;
+ }
+ else
+ {
+ nbl_ind = fr->gid2nblists[gid];
+ }
+ if (bLR)
+ {
+ vdwc = &fr->nblists[nbl_ind].nlist_lr[eNL_VDWQQ];
+ }
+ else
+ {
+ vdwc = &fr->nblists[nbl_ind].nlist_sr[eNL_VDWQQ];
+ }
+
+ /* Make a new neighbor list for charge group icg.
+ * Currently simply one neighbor list is made with LJ and Coulomb.
+ * If required, zero interactions could be removed here
+ * or in the force loop.
+ */
+ new_i_nblist(vdwc,bLR,index[icg],shift,gid);
+ vdwc->iinr_end[vdwc->nri] = index[icg+1];
+
+ for(j=0; (j<nj); j++)
+ {
+ jcg = jjcg[j];
+ /* Skip the icg-icg pairs if all self interactions are excluded */
+ if (!(jcg == icg && GET_CGINFO_EXCL_INTRA(cginfo)))
+ {
+ /* Here we add the j charge group jcg to the list,
+ * exclusions are also added to the list.
+ */
++ add_j_to_nblist_cg(vdwc,index[jcg],index[jcg+1],bExcl,icg==jcg,bLR);
+ }
+ }
+
+ close_i_nblist(vdwc);
+}
+
+static void setexcl(atom_id start,atom_id end,t_blocka *excl,gmx_bool b,
+ t_excl bexcl[])
+{
+ atom_id i,k;
+
+ if (b)
+ {
+ for(i=start; i<end; i++)
+ {
+ for(k=excl->index[i]; k<excl->index[i+1]; k++)
+ {
+ SETEXCL(bexcl,i-start,excl->a[k]);
+ }
+ }
+ }
+ else
+ {
+ for(i=start; i<end; i++)
+ {
+ for(k=excl->index[i]; k<excl->index[i+1]; k++)
+ {
+ RMEXCL(bexcl,i-start,excl->a[k]);
+ }
+ }
+ }
+}
+
+int calc_naaj(int icg,int cgtot)
+{
+ int naaj;
+
+ if ((cgtot % 2) == 1)
+ {
+ /* Odd number of charge groups, easy */
+ naaj = 1 + (cgtot/2);
+ }
+ else if ((cgtot % 4) == 0)
+ {
+ /* Multiple of four is hard */
+ if (icg < cgtot/2)
+ {
+ if ((icg % 2) == 0)
+ {
+ naaj=1+(cgtot/2);
+ }
+ else
+ {
+ naaj=cgtot/2;
+ }
+ }
+ else
+ {
+ if ((icg % 2) == 1)
+ {
+ naaj=1+(cgtot/2);
+ }
+ else
+ {
+ naaj=cgtot/2;
+ }
+ }
+ }
+ else
+ {
+ /* cgtot/2 = odd */
+ if ((icg % 2) == 0)
+ {
+ naaj=1+(cgtot/2);
+ }
+ else
+ {
+ naaj=cgtot/2;
+ }
+ }
+#ifdef DEBUG
+ fprintf(log,"naaj=%d\n",naaj);
+#endif
+
+ return naaj;
+}
+
+/************************************************
+ *
+ * S I M P L E C O R E S T U F F
+ *
+ ************************************************/
+
+static real calc_image_tric(rvec xi,rvec xj,matrix box,
+ rvec b_inv,int *shift)
+{
+ /* This code assumes that the cut-off is smaller than
+ * a half times the smallest diagonal element of the box.
+ */
+ const real h25=2.5;
+ real dx,dy,dz;
+ real r2;
+ int tx,ty,tz;
+
+ /* Compute diff vector */
+ dz = xj[ZZ] - xi[ZZ];
+ dy = xj[YY] - xi[YY];
+ dx = xj[XX] - xi[XX];
+
+ /* Perform NINT operation, using trunc operation, therefore
+ * we first add 2.5 then subtract 2 again
+ */
+ tz = dz*b_inv[ZZ] + h25;
+ tz -= 2;
+ dz -= tz*box[ZZ][ZZ];
+ dy -= tz*box[ZZ][YY];
+ dx -= tz*box[ZZ][XX];
+
+ ty = dy*b_inv[YY] + h25;
+ ty -= 2;
+ dy -= ty*box[YY][YY];
+ dx -= ty*box[YY][XX];
+
+ tx = dx*b_inv[XX]+h25;
+ tx -= 2;
+ dx -= tx*box[XX][XX];
+
+ /* Distance squared */
+ r2 = (dx*dx) + (dy*dy) + (dz*dz);
+
+ *shift = XYZ2IS(tx,ty,tz);
+
+ return r2;
+}
+
+static real calc_image_rect(rvec xi,rvec xj,rvec box_size,
+ rvec b_inv,int *shift)
+{
+ const real h15=1.5;
+ real ddx,ddy,ddz;
+ real dx,dy,dz;
+ real r2;
+ int tx,ty,tz;
+
+ /* Compute diff vector */
+ dx = xj[XX] - xi[XX];
+ dy = xj[YY] - xi[YY];
+ dz = xj[ZZ] - xi[ZZ];
+
+ /* Perform NINT operation, using trunc operation, therefore
+ * we first add 1.5 then subtract 1 again
+ */
+ tx = dx*b_inv[XX] + h15;
+ ty = dy*b_inv[YY] + h15;
+ tz = dz*b_inv[ZZ] + h15;
+ tx--;
+ ty--;
+ tz--;
+
+ /* Correct diff vector for translation */
+ ddx = tx*box_size[XX] - dx;
+ ddy = ty*box_size[YY] - dy;
+ ddz = tz*box_size[ZZ] - dz;
+
+ /* Distance squared */
+ r2 = (ddx*ddx) + (ddy*ddy) + (ddz*ddz);
+
+ *shift = XYZ2IS(tx,ty,tz);
+
+ return r2;
+}
+
+static void add_simple(t_ns_buf *nsbuf,int nrj,atom_id cg_j,
+ gmx_bool bHaveVdW[],int ngid,t_mdatoms *md,
+ int icg,int jgid,t_block *cgs,t_excl bexcl[],
+ int shift,t_forcerec *fr,put_in_list_t *put_in_list)
+{
+ if (nsbuf->nj + nrj > MAX_CG)
+ {
+ put_in_list(bHaveVdW,ngid,md,icg,jgid,nsbuf->ncg,nsbuf->jcg,
+ cgs->index,bexcl,shift,fr,FALSE,TRUE,TRUE);
+ /* Reset buffer contents */
+ nsbuf->ncg = nsbuf->nj = 0;
+ }
+ nsbuf->jcg[nsbuf->ncg++] = cg_j;
+ nsbuf->nj += nrj;
+}
+
+static void ns_inner_tric(rvec x[],int icg,int *i_egp_flags,
+ int njcg,atom_id jcg[],
+ matrix box,rvec b_inv,real rcut2,
+ t_block *cgs,t_ns_buf **ns_buf,
+ gmx_bool bHaveVdW[],int ngid,t_mdatoms *md,
+ t_excl bexcl[],t_forcerec *fr,
+ put_in_list_t *put_in_list)
+{
+ int shift;
+ int j,nrj,jgid;
+ int *cginfo=fr->cginfo;
+ atom_id cg_j,*cgindex;
+ t_ns_buf *nsbuf;
+
+ cgindex = cgs->index;
+ shift = CENTRAL;
+ for(j=0; (j<njcg); j++)
+ {
+ cg_j = jcg[j];
+ nrj = cgindex[cg_j+1]-cgindex[cg_j];
+ if (calc_image_tric(x[icg],x[cg_j],box,b_inv,&shift) < rcut2)
+ {
+ jgid = GET_CGINFO_GID(cginfo[cg_j]);
+ if (!(i_egp_flags[jgid] & EGP_EXCL))
+ {
+ add_simple(&ns_buf[jgid][shift],nrj,cg_j,
+ bHaveVdW,ngid,md,icg,jgid,cgs,bexcl,shift,fr,
+ put_in_list);
+ }
+ }
+ }
+}
+
+static void ns_inner_rect(rvec x[],int icg,int *i_egp_flags,
+ int njcg,atom_id jcg[],
+ gmx_bool bBox,rvec box_size,rvec b_inv,real rcut2,
+ t_block *cgs,t_ns_buf **ns_buf,
+ gmx_bool bHaveVdW[],int ngid,t_mdatoms *md,
+ t_excl bexcl[],t_forcerec *fr,
+ put_in_list_t *put_in_list)
+{
+ int shift;
+ int j,nrj,jgid;
+ int *cginfo=fr->cginfo;
+ atom_id cg_j,*cgindex;
+ t_ns_buf *nsbuf;
+
+ cgindex = cgs->index;
+ if (bBox)
+ {
+ shift = CENTRAL;
+ for(j=0; (j<njcg); j++)
+ {
+ cg_j = jcg[j];
+ nrj = cgindex[cg_j+1]-cgindex[cg_j];
+ if (calc_image_rect(x[icg],x[cg_j],box_size,b_inv,&shift) < rcut2)
+ {
+ jgid = GET_CGINFO_GID(cginfo[cg_j]);
+ if (!(i_egp_flags[jgid] & EGP_EXCL))
+ {
+ add_simple(&ns_buf[jgid][shift],nrj,cg_j,
+ bHaveVdW,ngid,md,icg,jgid,cgs,bexcl,shift,fr,
+ put_in_list);
+ }
+ }
+ }
+ }
+ else
+ {
+ for(j=0; (j<njcg); j++)
+ {
+ cg_j = jcg[j];
+ nrj = cgindex[cg_j+1]-cgindex[cg_j];
+ if ((rcut2 == 0) || (distance2(x[icg],x[cg_j]) < rcut2)) {
+ jgid = GET_CGINFO_GID(cginfo[cg_j]);
+ if (!(i_egp_flags[jgid] & EGP_EXCL))
+ {
+ add_simple(&ns_buf[jgid][CENTRAL],nrj,cg_j,
+ bHaveVdW,ngid,md,icg,jgid,cgs,bexcl,CENTRAL,fr,
+ put_in_list);
+ }
+ }
+ }
+ }
+}
+
+/* ns_simple_core needs to be adapted for QMMM still 2005 */
+
+static int ns_simple_core(t_forcerec *fr,
+ gmx_localtop_t *top,
+ t_mdatoms *md,
+ matrix box,rvec box_size,
+ t_excl bexcl[],atom_id *aaj,
+ int ngid,t_ns_buf **ns_buf,
+ put_in_list_t *put_in_list,gmx_bool bHaveVdW[])
+{
+ int naaj,k;
+ real rlist2;
+ int nsearch,icg,jcg,igid,i0,nri,nn;
+ int *cginfo;
+ t_ns_buf *nsbuf;
+ /* atom_id *i_atoms; */
+ t_block *cgs=&(top->cgs);
+ t_blocka *excl=&(top->excls);
+ rvec b_inv;
+ int m;
+ gmx_bool bBox,bTriclinic;
+ int *i_egp_flags;
+
+ rlist2 = sqr(fr->rlist);
+
+ bBox = (fr->ePBC != epbcNONE);
+ if (bBox)
+ {
+ for(m=0; (m<DIM); m++)
+ {
+ b_inv[m] = divide_err(1.0,box_size[m]);
+ }
+ bTriclinic = TRICLINIC(box);
+ }
+ else
+ {
+ bTriclinic = FALSE;
+ }
+
+ cginfo = fr->cginfo;
+
+ nsearch=0;
+ for (icg=fr->cg0; (icg<fr->hcg); icg++)
+ {
+ /*
+ i0 = cgs->index[icg];
+ nri = cgs->index[icg+1]-i0;
+ i_atoms = &(cgs->a[i0]);
+ i_eg_excl = fr->eg_excl + ngid*md->cENER[*i_atoms];
+ setexcl(nri,i_atoms,excl,TRUE,bexcl);
+ */
+ igid = GET_CGINFO_GID(cginfo[icg]);
+ i_egp_flags = fr->egp_flags + ngid*igid;
+ setexcl(cgs->index[icg],cgs->index[icg+1],excl,TRUE,bexcl);
+
+ naaj=calc_naaj(icg,cgs->nr);
+ if (bTriclinic)
+ {
+ ns_inner_tric(fr->cg_cm,icg,i_egp_flags,naaj,&(aaj[icg]),
+ box,b_inv,rlist2,cgs,ns_buf,
+ bHaveVdW,ngid,md,bexcl,fr,put_in_list);
+ }
+ else
+ {
+ ns_inner_rect(fr->cg_cm,icg,i_egp_flags,naaj,&(aaj[icg]),
+ bBox,box_size,b_inv,rlist2,cgs,ns_buf,
+ bHaveVdW,ngid,md,bexcl,fr,put_in_list);
+ }
+ nsearch += naaj;
+
+ for(nn=0; (nn<ngid); nn++)
+ {
+ for(k=0; (k<SHIFTS); k++)
+ {
+ nsbuf = &(ns_buf[nn][k]);
+ if (nsbuf->ncg > 0)
+ {
+ put_in_list(bHaveVdW,ngid,md,icg,nn,nsbuf->ncg,nsbuf->jcg,
+ cgs->index,bexcl,k,fr,FALSE,TRUE,TRUE);
+ nsbuf->ncg=nsbuf->nj=0;
+ }
+ }
+ }
+ /* setexcl(nri,i_atoms,excl,FALSE,bexcl); */
+ setexcl(cgs->index[icg],cgs->index[icg+1],excl,FALSE,bexcl);
+ }
+ close_neighbor_list(fr,FALSE,-1,-1,FALSE);
+
+ return nsearch;
+}
+
+/************************************************
+ *
+ * N S 5 G R I D S T U F F
+ *
+ ************************************************/
+
+static inline void get_dx(int Nx,real gridx,real rc2,int xgi,real x,
+ int *dx0,int *dx1,real *dcx2)
+{
+ real dcx,tmp;
+ int xgi0,xgi1,i;
+
+ if (xgi < 0)
+ {
+ *dx0 = 0;
+ xgi0 = -1;
+ *dx1 = -1;
+ xgi1 = 0;
+ }
+ else if (xgi >= Nx)
+ {
+ *dx0 = Nx;
+ xgi0 = Nx-1;
+ *dx1 = Nx-1;
+ xgi1 = Nx;
+ }
+ else
+ {
+ dcx2[xgi] = 0;
+ *dx0 = xgi;
+ xgi0 = xgi-1;
+ *dx1 = xgi;
+ xgi1 = xgi+1;
+ }
+
+ for(i=xgi0; i>=0; i--)
+ {
+ dcx = (i+1)*gridx-x;
+ tmp = dcx*dcx;
+ if (tmp >= rc2)
+ break;
+ *dx0 = i;
+ dcx2[i] = tmp;
+ }
+ for(i=xgi1; i<Nx; i++)
+ {
+ dcx = i*gridx-x;
+ tmp = dcx*dcx;
+ if (tmp >= rc2)
+ {
+ break;
+ }
+ *dx1 = i;
+ dcx2[i] = tmp;
+ }
+}
+
+static inline void get_dx_dd(int Nx,real gridx,real rc2,int xgi,real x,
+ int ncpddc,int shift_min,int shift_max,
+ int *g0,int *g1,real *dcx2)
+{
+ real dcx,tmp;
+ int g_min,g_max,shift_home;
+
+ if (xgi < 0)
+ {
+ g_min = 0;
+ g_max = Nx - 1;
+ *g0 = 0;
+ *g1 = -1;
+ }
+ else if (xgi >= Nx)
+ {
+ g_min = 0;
+ g_max = Nx - 1;
+ *g0 = Nx;
+ *g1 = Nx - 1;
+ }
+ else
+ {
+ if (ncpddc == 0)
+ {
+ g_min = 0;
+ g_max = Nx - 1;
+ }
+ else
+ {
+ if (xgi < ncpddc)
+ {
+ shift_home = 0;
+ }
+ else
+ {
+ shift_home = -1;
+ }
+ g_min = (shift_min == shift_home ? 0 : ncpddc);
+ g_max = (shift_max == shift_home ? ncpddc - 1 : Nx - 1);
+ }
+ if (shift_min > 0)
+ {
+ *g0 = g_min;
+ *g1 = g_min - 1;
+ }
+ else if (shift_max < 0)
+ {
+ *g0 = g_max + 1;
+ *g1 = g_max;
+ }
+ else
+ {
+ *g0 = xgi;
+ *g1 = xgi;
+ dcx2[xgi] = 0;
+ }
+ }
+
+ while (*g0 > g_min)
+ {
+ /* Check one grid cell down */
+ dcx = ((*g0 - 1) + 1)*gridx - x;
+ tmp = dcx*dcx;
+ if (tmp >= rc2)
+ {
+ break;
+ }
+ (*g0)--;
+ dcx2[*g0] = tmp;
+ }
+
+ while (*g1 < g_max)
+ {
+ /* Check one grid cell up */
+ dcx = (*g1 + 1)*gridx - x;
+ tmp = dcx*dcx;
+ if (tmp >= rc2)
+ {
+ break;
+ }
+ (*g1)++;
+ dcx2[*g1] = tmp;
+ }
+}
+
+
+#define sqr(x) ((x)*(x))
+#define calc_dx2(XI,YI,ZI,y) (sqr(XI-y[XX]) + sqr(YI-y[YY]) + sqr(ZI-y[ZZ]))
+#define calc_cyl_dx2(XI,YI,y) (sqr(XI-y[XX]) + sqr(YI-y[YY]))
+/****************************************************
+ *
+ * F A S T N E I G H B O R S E A R C H I N G
+ *
+ * Optimized neighboursearching routine using grid
+ * at least 1x1x1, see GROMACS manual
+ *
+ ****************************************************/
+
+static void do_longrange(t_commrec *cr,gmx_localtop_t *top,t_forcerec *fr,
+ int ngid,t_mdatoms *md,int icg,
+ int jgid,int nlr,
+ atom_id lr[],t_excl bexcl[],int shift,
+ rvec x[],rvec box_size,t_nrnb *nrnb,
+ real lambda,real *dvdlambda,
+ gmx_grppairener_t *grppener,
+ gmx_bool bDoVdW,gmx_bool bDoCoul,
+ gmx_bool bEvaluateNow,put_in_list_t *put_in_list,
+ gmx_bool bHaveVdW[],
+ gmx_bool bDoForces,rvec *f)
+{
+ int n,i;
+ t_nblist *nl;
+
+ for(n=0; n<fr->nnblists; n++)
+ {
+ for(i=0; (i<eNL_NR); i++)
+ {
+ nl = &fr->nblists[n].nlist_lr[i];
+ if ((nl->nri > nl->maxnri-32) || bEvaluateNow)
+ {
+ close_neighbor_list(fr,TRUE,n,i,FALSE);
+ /* Evaluate the energies and forces */
+ do_nonbonded(cr,fr,x,f,md,NULL,
+ grppener->ener[fr->bBHAM ? egBHAMLR : egLJLR],
+ grppener->ener[egCOULLR],
+ grppener->ener[egGB],box_size,
+ nrnb,lambda,dvdlambda,n,i,
+ GMX_DONB_LR | GMX_DONB_FORCES);
+
+ reset_neighbor_list(fr,TRUE,n,i);
+ }
+ }
+ }
+
+ if (!bEvaluateNow)
+ {
+ /* Put the long range particles in a list */
+ /* do_longrange is never called for QMMM */
+ put_in_list(bHaveVdW,ngid,md,icg,jgid,nlr,lr,top->cgs.index,
+ bexcl,shift,fr,TRUE,bDoVdW,bDoCoul);
+ }
+}
+
+static void get_cutoff2(t_forcerec *fr,gmx_bool bDoLongRange,
+ real *rvdw2,real *rcoul2,
+ real *rs2,real *rm2,real *rl2)
+{
+ *rs2 = sqr(fr->rlist);
+ if (bDoLongRange && fr->bTwinRange)
+ {
+ /* The VdW and elec. LR cut-off's could be different,
+ * so we can not simply set them to rlistlong.
+ */
+ if (EVDW_MIGHT_BE_ZERO_AT_CUTOFF(fr->vdwtype) &&
+ fr->rvdw > fr->rlist)
+ {
+ *rvdw2 = sqr(fr->rlistlong);
+ }
+ else
+ {
+ *rvdw2 = sqr(fr->rvdw);
+ }
+ if (EEL_MIGHT_BE_ZERO_AT_CUTOFF(fr->eeltype) &&
+ fr->rcoulomb > fr->rlist)
+ {
+ *rcoul2 = sqr(fr->rlistlong);
+ }
+ else
+ {
+ *rcoul2 = sqr(fr->rcoulomb);
+ }
+ }
+ else
+ {
+ /* Workaround for a gcc -O3 or -ffast-math problem */
+ *rvdw2 = *rs2;
+ *rcoul2 = *rs2;
+ }
+ *rm2 = min(*rvdw2,*rcoul2);
+ *rl2 = max(*rvdw2,*rcoul2);
+}
+
+static void init_nsgrid_lists(t_forcerec *fr,int ngid,gmx_ns_t *ns)
+{
+ real rvdw2,rcoul2,rs2,rm2,rl2;
+ int j;
+
+ get_cutoff2(fr,TRUE,&rvdw2,&rcoul2,&rs2,&rm2,&rl2);
+
+ /* Short range buffers */
+ snew(ns->nl_sr,ngid);
+ /* Counters */
+ snew(ns->nsr,ngid);
+ snew(ns->nlr_ljc,ngid);
+ snew(ns->nlr_one,ngid);
+
+ if (rm2 > rs2)
+ {
+ /* Long range VdW and Coul buffers */
+ snew(ns->nl_lr_ljc,ngid);
+ }
+ if (rl2 > rm2)
+ {
+ /* Long range VdW or Coul only buffers */
+ snew(ns->nl_lr_one,ngid);
+ }
+ for(j=0; (j<ngid); j++) {
+ snew(ns->nl_sr[j],MAX_CG);
+ if (rm2 > rs2)
+ {
+ snew(ns->nl_lr_ljc[j],MAX_CG);
+ }
+ if (rl2 > rm2)
+ {
+ snew(ns->nl_lr_one[j],MAX_CG);
+ }
+ }
+ if (debug)
+ {
+ fprintf(debug,
+ "ns5_core: rs2 = %g, rm2 = %g, rl2 = %g (nm^2)\n",
+ rs2,rm2,rl2);
+ }
+}
+
+static int nsgrid_core(FILE *log,t_commrec *cr,t_forcerec *fr,
+ matrix box,rvec box_size,int ngid,
+ gmx_localtop_t *top,
+ t_grid *grid,rvec x[],
+ t_excl bexcl[],gmx_bool *bExcludeAlleg,
+ t_nrnb *nrnb,t_mdatoms *md,
+ real lambda,real *dvdlambda,
+ gmx_grppairener_t *grppener,
+ put_in_list_t *put_in_list,
+ gmx_bool bHaveVdW[],
+ gmx_bool bDoLongRange,gmx_bool bDoForces,rvec *f,
+ gmx_bool bMakeQMMMnblist)
+{
+ gmx_ns_t *ns;
+ atom_id **nl_lr_ljc,**nl_lr_one,**nl_sr;
+ int *nlr_ljc,*nlr_one,*nsr;
+ gmx_domdec_t *dd=NULL;
+ t_block *cgs=&(top->cgs);
+ int *cginfo=fr->cginfo;
+ /* atom_id *i_atoms,*cgsindex=cgs->index; */
+ ivec sh0,sh1,shp;
+ int cell_x,cell_y,cell_z;
+ int d,tx,ty,tz,dx,dy,dz,cj;
+#ifdef ALLOW_OFFDIAG_LT_HALFDIAG
+ int zsh_ty,zsh_tx,ysh_tx;
+#endif
+ int dx0,dx1,dy0,dy1,dz0,dz1;
+ int Nx,Ny,Nz,shift=-1,j,nrj,nns,nn=-1;
+ real gridx,gridy,gridz,grid_x,grid_y,grid_z;
+ real *dcx2,*dcy2,*dcz2;
+ int zgi,ygi,xgi;
+ int cg0,cg1,icg=-1,cgsnr,i0,igid,nri,naaj,max_jcg;
+ int jcg0,jcg1,jjcg,cgj0,jgid;
+ int *grida,*gridnra,*gridind;
+ gmx_bool rvdw_lt_rcoul,rcoul_lt_rvdw;
+ rvec xi,*cgcm,grid_offset;
+ real r2,rs2,rvdw2,rcoul2,rm2,rl2,XI,YI,ZI,dcx,dcy,dcz,tmp1,tmp2;
+ int *i_egp_flags;
+ gmx_bool bDomDec,bTriclinicX,bTriclinicY;
+ ivec ncpddc;
+
+ ns = &fr->ns;
+
+ bDomDec = DOMAINDECOMP(cr);
+ if (bDomDec)
+ {
+ dd = cr->dd;
+ }
+
+ bTriclinicX = ((YY < grid->npbcdim &&
+ (!bDomDec || dd->nc[YY]==1) && box[YY][XX] != 0) ||
+ (ZZ < grid->npbcdim &&
+ (!bDomDec || dd->nc[ZZ]==1) && box[ZZ][XX] != 0));
+ bTriclinicY = (ZZ < grid->npbcdim &&
+ (!bDomDec || dd->nc[ZZ]==1) && box[ZZ][YY] != 0);
+
+ cgsnr = cgs->nr;
+
+ get_cutoff2(fr,bDoLongRange,&rvdw2,&rcoul2,&rs2,&rm2,&rl2);
+
+ rvdw_lt_rcoul = (rvdw2 >= rcoul2);
+ rcoul_lt_rvdw = (rcoul2 >= rvdw2);
+
+ if (bMakeQMMMnblist)
+ {
+ rm2 = rl2;
+ rs2 = rl2;
+ }
+
+ nl_sr = ns->nl_sr;
+ nsr = ns->nsr;
+ nl_lr_ljc = ns->nl_lr_ljc;
+ nl_lr_one = ns->nl_lr_one;
+ nlr_ljc = ns->nlr_ljc;
+ nlr_one = ns->nlr_one;
+
+ /* Unpack arrays */
+ cgcm = fr->cg_cm;
+ Nx = grid->n[XX];
+ Ny = grid->n[YY];
+ Nz = grid->n[ZZ];
+ grida = grid->a;
+ gridind = grid->index;
+ gridnra = grid->nra;
+ nns = 0;
+
+ gridx = grid->cell_size[XX];
+ gridy = grid->cell_size[YY];
+ gridz = grid->cell_size[ZZ];
+ grid_x = 1/gridx;
+ grid_y = 1/gridy;
+ grid_z = 1/gridz;
+ copy_rvec(grid->cell_offset,grid_offset);
+ copy_ivec(grid->ncpddc,ncpddc);
+ dcx2 = grid->dcx2;
+ dcy2 = grid->dcy2;
+ dcz2 = grid->dcz2;
+
+#ifdef ALLOW_OFFDIAG_LT_HALFDIAG
+ zsh_ty = floor(-box[ZZ][YY]/box[YY][YY]+0.5);
+ zsh_tx = floor(-box[ZZ][XX]/box[XX][XX]+0.5);
+ ysh_tx = floor(-box[YY][XX]/box[XX][XX]+0.5);
+ if (zsh_tx!=0 && ysh_tx!=0)
+ {
+ /* This could happen due to rounding, when both ratios are 0.5 */
+ ysh_tx = 0;
+ }
+#endif
+
+ debug_gmx();
+
+ if (fr->n_tpi)
+ {
+ /* We only want a list for the test particle */
+ cg0 = cgsnr - 1;
+ }
+ else
+ {
+ cg0 = grid->icg0;
+ }
+ cg1 = grid->icg1;
+
+ /* Set the shift range */
+ for(d=0; d<DIM; d++)
+ {
+ sh0[d] = -1;
+ sh1[d] = 1;
+ /* Check if we need periodicity shifts.
+ * Without PBC or with domain decomposition we don't need them.
+ */
+ if (d >= ePBC2npbcdim(fr->ePBC) || (bDomDec && dd->nc[d] > 1))
+ {
+ shp[d] = 0;
+ }
+ else
+ {
+ if (d == XX &&
+ box[XX][XX] - fabs(box[YY][XX]) - fabs(box[ZZ][XX]) < sqrt(rl2))
+ {
+ shp[d] = 2;
+ }
+ else
+ {
+ shp[d] = 1;
+ }
+ }
+ }
+
+ /* Loop over charge groups */
+ for(icg=cg0; (icg < cg1); icg++)
+ {
+ igid = GET_CGINFO_GID(cginfo[icg]);
+ /* Skip this charge group if all energy groups are excluded! */
+ if (bExcludeAlleg[igid])
+ {
+ continue;
+ }
+
+ i0 = cgs->index[icg];
+
+ if (bMakeQMMMnblist)
+ {
+ /* Skip this charge group if it is not a QM atom while making a
+ * QM/MM neighbourlist
+ */
+ if (md->bQM[i0]==FALSE)
+ {
+ continue; /* MM particle, go to next particle */
+ }
+
+ /* Compute the number of charge groups that fall within the control
+ * of this one (icg)
+ */
+ naaj = calc_naaj(icg,cgsnr);
+ jcg0 = icg;
+ jcg1 = icg + naaj;
+ max_jcg = cgsnr;
+ }
+ else
+ {
+ /* make a normal neighbourlist */
+
+ if (bDomDec)
+ {
+ /* Get the j charge-group and dd cell shift ranges */
+ dd_get_ns_ranges(cr->dd,icg,&jcg0,&jcg1,sh0,sh1);
+ max_jcg = 0;
+ }
+ else
+ {
+ /* Compute the number of charge groups that fall within the control
+ * of this one (icg)
+ */
+ naaj = calc_naaj(icg,cgsnr);
+ jcg0 = icg;
+ jcg1 = icg + naaj;
+
+ if (fr->n_tpi)
+ {
+ /* The i-particle is awlways the test particle,
+ * so we want all j-particles
+ */
+ max_jcg = cgsnr - 1;
+ }
+ else
+ {
+ max_jcg = jcg1 - cgsnr;
+ }
+ }
+ }
+
+ i_egp_flags = fr->egp_flags + igid*ngid;
+
+ /* Set the exclusions for the atoms in charge group icg using a bitmask */
+ setexcl(i0,cgs->index[icg+1],&top->excls,TRUE,bexcl);
+
+ ci2xyz(grid,icg,&cell_x,&cell_y,&cell_z);
+
+ /* Changed iicg to icg, DvdS 990115
+ * (but see consistency check above, DvdS 990330)
+ */
+#ifdef NS5DB
+ fprintf(log,"icg=%5d, naaj=%5d, cell %d %d %d\n",
+ icg,naaj,cell_x,cell_y,cell_z);
+#endif
+ /* Loop over shift vectors in three dimensions */
+ for (tz=-shp[ZZ]; tz<=shp[ZZ]; tz++)
+ {
+ ZI = cgcm[icg][ZZ]+tz*box[ZZ][ZZ];
+ /* Calculate range of cells in Z direction that have the shift tz */
+ zgi = cell_z + tz*Nz;
+#define FAST_DD_NS
+#ifndef FAST_DD_NS
+ get_dx(Nz,gridz,rl2,zgi,ZI,&dz0,&dz1,dcz2);
+#else
+ get_dx_dd(Nz,gridz,rl2,zgi,ZI-grid_offset[ZZ],
+ ncpddc[ZZ],sh0[ZZ],sh1[ZZ],&dz0,&dz1,dcz2);
+#endif
+ if (dz0 > dz1)
+ {
+ continue;
+ }
+ for (ty=-shp[YY]; ty<=shp[YY]; ty++)
+ {
+ YI = cgcm[icg][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
+ /* Calculate range of cells in Y direction that have the shift ty */
+ if (bTriclinicY)
+ {
+ ygi = (int)(Ny + (YI - grid_offset[YY])*grid_y) - Ny;
+ }
+ else
+ {
+ ygi = cell_y + ty*Ny;
+ }
+#ifndef FAST_DD_NS
+ get_dx(Ny,gridy,rl2,ygi,YI,&dy0,&dy1,dcy2);
+#else
+ get_dx_dd(Ny,gridy,rl2,ygi,YI-grid_offset[YY],
+ ncpddc[YY],sh0[YY],sh1[YY],&dy0,&dy1,dcy2);
+#endif
+ if (dy0 > dy1)
+ {
+ continue;
+ }
+ for (tx=-shp[XX]; tx<=shp[XX]; tx++)
+ {
+ XI = cgcm[icg][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
+ /* Calculate range of cells in X direction that have the shift tx */
+ if (bTriclinicX)
+ {
+ xgi = (int)(Nx + (XI - grid_offset[XX])*grid_x) - Nx;
+ }
+ else
+ {
+ xgi = cell_x + tx*Nx;
+ }
+#ifndef FAST_DD_NS
+ get_dx(Nx,gridx,rl2,xgi*Nx,XI,&dx0,&dx1,dcx2);
+#else
+ get_dx_dd(Nx,gridx,rl2,xgi,XI-grid_offset[XX],
+ ncpddc[XX],sh0[XX],sh1[XX],&dx0,&dx1,dcx2);
+#endif
+ if (dx0 > dx1)
+ {
+ continue;
+ }
+ /* Get shift vector */
+ shift=XYZ2IS(tx,ty,tz);
+#ifdef NS5DB
+ range_check(shift,0,SHIFTS);
+#endif
+ for(nn=0; (nn<ngid); nn++)
+ {
+ nsr[nn] = 0;
+ nlr_ljc[nn] = 0;
+ nlr_one[nn] = 0;
+ }
+#ifdef NS5DB
+ fprintf(log,"shift: %2d, dx0,1: %2d,%2d, dy0,1: %2d,%2d, dz0,1: %2d,%2d\n",
+ shift,dx0,dx1,dy0,dy1,dz0,dz1);
+ fprintf(log,"cgcm: %8.3f %8.3f %8.3f\n",cgcm[icg][XX],
+ cgcm[icg][YY],cgcm[icg][ZZ]);
+ fprintf(log,"xi: %8.3f %8.3f %8.3f\n",XI,YI,ZI);
+#endif
+ for (dx=dx0; (dx<=dx1); dx++)
+ {
+ tmp1 = rl2 - dcx2[dx];
+ for (dy=dy0; (dy<=dy1); dy++)
+ {
+ tmp2 = tmp1 - dcy2[dy];
+ if (tmp2 > 0)
+ {
+ for (dz=dz0; (dz<=dz1); dz++) {
+ if (tmp2 > dcz2[dz]) {
+ /* Find grid-cell cj in which possible neighbours are */
+ cj = xyz2ci(Ny,Nz,dx,dy,dz);
+
+ /* Check out how many cgs (nrj) there in this cell */
+ nrj = gridnra[cj];
+
+ /* Find the offset in the cg list */
+ cgj0 = gridind[cj];
+
+ /* Check if all j's are out of range so we
+ * can skip the whole cell.
+ * Should save some time, especially with DD.
+ */
+ if (nrj == 0 ||
+ (grida[cgj0] >= max_jcg &&
+ (grida[cgj0] >= jcg1 || grida[cgj0+nrj-1] < jcg0)))
+ {
+ continue;
+ }
+
+ /* Loop over cgs */
+ for (j=0; (j<nrj); j++)
+ {
+ jjcg = grida[cgj0+j];
+
+ /* check whether this guy is in range! */
+ if ((jjcg >= jcg0 && jjcg < jcg1) ||
+ (jjcg < max_jcg))
+ {
+ r2=calc_dx2(XI,YI,ZI,cgcm[jjcg]);
+ if (r2 < rl2) {
+ /* jgid = gid[cgsatoms[cgsindex[jjcg]]]; */
+ jgid = GET_CGINFO_GID(cginfo[jjcg]);
+ /* check energy group exclusions */
+ if (!(i_egp_flags[jgid] & EGP_EXCL))
+ {
+ if (r2 < rs2)
+ {
+ if (nsr[jgid] >= MAX_CG)
+ {
+ put_in_list(bHaveVdW,ngid,md,icg,jgid,
+ nsr[jgid],nl_sr[jgid],
+ cgs->index,/* cgsatoms, */ bexcl,
+ shift,fr,FALSE,TRUE,TRUE);
+ nsr[jgid]=0;
+ }
+ nl_sr[jgid][nsr[jgid]++]=jjcg;
+ }
+ else if (r2 < rm2)
+ {
+ if (nlr_ljc[jgid] >= MAX_CG)
+ {
+ do_longrange(cr,top,fr,ngid,md,icg,jgid,
+ nlr_ljc[jgid],
+ nl_lr_ljc[jgid],bexcl,shift,x,
+ box_size,nrnb,
+ lambda,dvdlambda,
+ grppener,
+ TRUE,TRUE,FALSE,
+ put_in_list,
+ bHaveVdW,
+ bDoForces,f);
+ nlr_ljc[jgid]=0;
+ }
+ nl_lr_ljc[jgid][nlr_ljc[jgid]++]=jjcg;
+ }
+ else
+ {
+ if (nlr_one[jgid] >= MAX_CG) {
+ do_longrange(cr,top,fr,ngid,md,icg,jgid,
+ nlr_one[jgid],
+ nl_lr_one[jgid],bexcl,shift,x,
+ box_size,nrnb,
+ lambda,dvdlambda,
+ grppener,
+ rvdw_lt_rcoul,rcoul_lt_rvdw,FALSE,
+ put_in_list,
+ bHaveVdW,
+ bDoForces,f);
+ nlr_one[jgid]=0;
+ }
+ nl_lr_one[jgid][nlr_one[jgid]++]=jjcg;
+ }
+ }
+ }
+ nns++;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ /* CHECK whether there is anything left in the buffers */
+ for(nn=0; (nn<ngid); nn++)
+ {
+ if (nsr[nn] > 0)
+ {
+ put_in_list(bHaveVdW,ngid,md,icg,nn,nsr[nn],nl_sr[nn],
+ cgs->index, /* cgsatoms, */ bexcl,
+ shift,fr,FALSE,TRUE,TRUE);
+ }
+
+ if (nlr_ljc[nn] > 0)
+ {
+ do_longrange(cr,top,fr,ngid,md,icg,nn,nlr_ljc[nn],
+ nl_lr_ljc[nn],bexcl,shift,x,box_size,nrnb,
+ lambda,dvdlambda,grppener,TRUE,TRUE,FALSE,
+ put_in_list,bHaveVdW,bDoForces,f);
+ }
+
+ if (nlr_one[nn] > 0)
+ {
+ do_longrange(cr,top,fr,ngid,md,icg,nn,nlr_one[nn],
+ nl_lr_one[nn],bexcl,shift,x,box_size,nrnb,
+ lambda,dvdlambda,grppener,
+ rvdw_lt_rcoul,rcoul_lt_rvdw,FALSE,
+ put_in_list,bHaveVdW,bDoForces,f);
+ }
+ }
+ }
+ }
+ }
+ /* setexcl(nri,i_atoms,&top->atoms.excl,FALSE,bexcl); */
+ setexcl(cgs->index[icg],cgs->index[icg+1],&top->excls,FALSE,bexcl);
+ }
+ /* Perform any left over force calculations */
+ for (nn=0; (nn<ngid); nn++)
+ {
+ if (rm2 > rs2)
+ {
+ do_longrange(cr,top,fr,0,md,icg,nn,nlr_ljc[nn],
+ nl_lr_ljc[nn],bexcl,shift,x,box_size,nrnb,
+ lambda,dvdlambda,grppener,
+ TRUE,TRUE,TRUE,put_in_list,bHaveVdW,bDoForces,f);
+ }
+ if (rl2 > rm2) {
+ do_longrange(cr,top,fr,0,md,icg,nn,nlr_one[nn],
+ nl_lr_one[nn],bexcl,shift,x,box_size,nrnb,
+ lambda,dvdlambda,grppener,
+ rvdw_lt_rcoul,rcoul_lt_rvdw,
+ TRUE,put_in_list,bHaveVdW,bDoForces,f);
+ }
+ }
+ debug_gmx();
+
+ /* Close off short range neighbourlists */
+ close_neighbor_list(fr,FALSE,-1,-1,bMakeQMMMnblist);
+
+ return nns;
+}
+
+void ns_realloc_natoms(gmx_ns_t *ns,int natoms)
+{
+ int i;
+
+ if (natoms > ns->nra_alloc)
+ {
+ ns->nra_alloc = over_alloc_dd(natoms);
+ srenew(ns->bexcl,ns->nra_alloc);
+ for(i=0; i<ns->nra_alloc; i++)
+ {
+ ns->bexcl[i] = 0;
+ }
+ }
+}
+
+void init_ns(FILE *fplog,const t_commrec *cr,
+ gmx_ns_t *ns,t_forcerec *fr,
+ const gmx_mtop_t *mtop,
+ matrix box)
+{
+ int mt,icg,nr_in_cg,maxcg,i,j,jcg,ngid,ncg;
+ t_block *cgs;
+ char *ptr;
+
+ /* Compute largest charge groups size (# atoms) */
+ nr_in_cg=1;
+ for(mt=0; mt<mtop->nmoltype; mt++) {
+ cgs = &mtop->moltype[mt].cgs;
+ for (icg=0; (icg < cgs->nr); icg++)
+ {
+ nr_in_cg=max(nr_in_cg,(int)(cgs->index[icg+1]-cgs->index[icg]));
+ }
+ }
+
+ /* Verify whether largest charge group is <= max cg.
+ * This is determined by the type of the local exclusion type
+ * Exclusions are stored in bits. (If the type is not large
+ * enough, enlarge it, unsigned char -> unsigned short -> unsigned long)
+ */
+ maxcg = sizeof(t_excl)*8;
+ if (nr_in_cg > maxcg)
+ {
+ gmx_fatal(FARGS,"Max #atoms in a charge group: %d > %d\n",
+ nr_in_cg,maxcg);
+ }
+
+ ngid = mtop->groups.grps[egcENER].nr;
+ snew(ns->bExcludeAlleg,ngid);
+ for(i=0; i<ngid; i++) {
+ ns->bExcludeAlleg[i] = TRUE;
+ for(j=0; j<ngid; j++)
+ {
+ if (!(fr->egp_flags[i*ngid+j] & EGP_EXCL))
+ {
+ ns->bExcludeAlleg[i] = FALSE;
+ }
+ }
+ }
+
+ if (fr->bGrid) {
+ /* Grid search */
+ ns->grid = init_grid(fplog,fr);
+ init_nsgrid_lists(fr,ngid,ns);
+ }
+ else
+ {
+ /* Simple search */
+ snew(ns->ns_buf,ngid);
+ for(i=0; (i<ngid); i++)
+ {
+ snew(ns->ns_buf[i],SHIFTS);
+ }
+ ncg = ncg_mtop(mtop);
+ snew(ns->simple_aaj,2*ncg);
+ for(jcg=0; (jcg<ncg); jcg++)
+ {
+ ns->simple_aaj[jcg] = jcg;
+ ns->simple_aaj[jcg+ncg] = jcg;
+ }
+ }
+
+ /* Create array that determines whether or not atoms have VdW */
+ snew(ns->bHaveVdW,fr->ntype);
+ for(i=0; (i<fr->ntype); i++)
+ {
+ for(j=0; (j<fr->ntype); j++)
+ {
+ ns->bHaveVdW[i] = (ns->bHaveVdW[i] ||
+ (fr->bBHAM ?
+ ((BHAMA(fr->nbfp,fr->ntype,i,j) != 0) ||
+ (BHAMB(fr->nbfp,fr->ntype,i,j) != 0) ||
+ (BHAMC(fr->nbfp,fr->ntype,i,j) != 0)) :
+ ((C6(fr->nbfp,fr->ntype,i,j) != 0) ||
+ (C12(fr->nbfp,fr->ntype,i,j) != 0))));
+ }
+ }
+ if (debug)
+ pr_bvec(debug,0,"bHaveVdW",ns->bHaveVdW,fr->ntype,TRUE);
+
+ ns->nra_alloc = 0;
+ ns->bexcl = NULL;
+ if (!DOMAINDECOMP(cr))
+ {
+ /* This could be reduced with particle decomposition */
+ ns_realloc_natoms(ns,mtop->natoms);
+ }
+
+ ns->nblist_initialized=FALSE;
+
+ /* nbr list debug dump */
+ {
+ char *ptr=getenv("GMX_DUMP_NL");
+ if (ptr)
+ {
+ ns->dump_nl=strtol(ptr,NULL,10);
+ if (fplog)
+ {
+ fprintf(fplog, "GMX_DUMP_NL = %d", ns->dump_nl);
+ }
+ }
+ else
+ {
+ ns->dump_nl=0;
+ }
+ }
+}
+
+
+int search_neighbours(FILE *log,t_forcerec *fr,
+ rvec x[],matrix box,
+ gmx_localtop_t *top,
+ gmx_groups_t *groups,
+ t_commrec *cr,
+ t_nrnb *nrnb,t_mdatoms *md,
+ real lambda,real *dvdlambda,
+ gmx_grppairener_t *grppener,
+ gmx_bool bFillGrid,
+ gmx_bool bDoLongRange,
+ gmx_bool bDoForces,rvec *f)
+{
+ t_block *cgs=&(top->cgs);
+ rvec box_size,grid_x0,grid_x1;
+ int i,j,m,ngid;
+ real min_size,grid_dens;
+ int nsearch;
+ gmx_bool bGrid;
+ char *ptr;
+ gmx_bool *i_egp_flags;
+ int cg_start,cg_end,start,end;
+ gmx_ns_t *ns;
+ t_grid *grid;
+ gmx_domdec_zones_t *dd_zones;
+ put_in_list_t *put_in_list;
+
+ ns = &fr->ns;
+
+ /* Set some local variables */
+ bGrid = fr->bGrid;
+ ngid = groups->grps[egcENER].nr;
+
+ for(m=0; (m<DIM); m++)
+ {
+ box_size[m] = box[m][m];
+ }
+
+ if (fr->ePBC != epbcNONE)
+ {
+ if (sqr(fr->rlistlong) >= max_cutoff2(fr->ePBC,box))
+ {
+ gmx_fatal(FARGS,"One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.");
+ }
+ if (!bGrid)
+ {
+ min_size = min(box_size[XX],min(box_size[YY],box_size[ZZ]));
+ if (2*fr->rlistlong >= min_size)
+ gmx_fatal(FARGS,"One of the box diagonal elements has become smaller than twice the cut-off length.");
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ ns_realloc_natoms(ns,cgs->index[cgs->nr]);
+ }
+ debug_gmx();
+
+ /* Reset the neighbourlists */
+ reset_neighbor_list(fr,FALSE,-1,-1);
+
+ if (bGrid && bFillGrid)
+ {
+
+ grid = ns->grid;
+ if (DOMAINDECOMP(cr))
+ {
+ dd_zones = domdec_zones(cr->dd);
+ }
+ else
+ {
+ dd_zones = NULL;
+
+ get_nsgrid_boundaries(grid,NULL,box,NULL,NULL,NULL,
+ cgs->nr,fr->cg_cm,grid_x0,grid_x1,&grid_dens);
+
+ grid_first(log,grid,NULL,NULL,fr->ePBC,box,grid_x0,grid_x1,
+ fr->rlistlong,grid_dens);
+ }
+ debug_gmx();
+
+ /* Don't know why this all is... (DvdS 3/99) */
+#ifndef SEGV
+ start = 0;
+ end = cgs->nr;
+#else
+ start = fr->cg0;
+ end = (cgs->nr+1)/2;
+#endif
+
+ if (DOMAINDECOMP(cr))
+ {
+ end = cgs->nr;
+ fill_grid(log,dd_zones,grid,end,-1,end,fr->cg_cm);
+ grid->icg0 = 0;
+ grid->icg1 = dd_zones->izone[dd_zones->nizone-1].cg1;
+ }
+ else
+ {
+ fill_grid(log,NULL,grid,cgs->nr,fr->cg0,fr->hcg,fr->cg_cm);
+ grid->icg0 = fr->cg0;
+ grid->icg1 = fr->hcg;
+ debug_gmx();
+
+ if (PARTDECOMP(cr))
+ mv_grid(cr,grid);
+ debug_gmx();
+ }
+
+ calc_elemnr(log,grid,start,end,cgs->nr);
+ calc_ptrs(grid);
+ grid_last(log,grid,start,end,cgs->nr);
+
+ if (gmx_debug_at)
+ {
+ check_grid(debug,grid);
+ print_grid(debug,grid);
+ }
+ }
+ else if (fr->n_tpi)
+ {
+ /* Set the grid cell index for the test particle only.
+ * The cell to cg index is not corrected, but that does not matter.
+ */
+ fill_grid(log,NULL,ns->grid,fr->hcg,fr->hcg-1,fr->hcg,fr->cg_cm);
+ }
+ debug_gmx();
+
+ if (!fr->ns.bCGlist)
+ {
+ put_in_list = put_in_list_at;
+ }
+ else
+ {
+ put_in_list = put_in_list_cg;
+ }
+
+ /* Do the core! */
+ if (bGrid)
+ {
+ grid = ns->grid;
+ nsearch = nsgrid_core(log,cr,fr,box,box_size,ngid,top,
+ grid,x,ns->bexcl,ns->bExcludeAlleg,
+ nrnb,md,lambda,dvdlambda,grppener,
+ put_in_list,ns->bHaveVdW,
+ bDoLongRange,bDoForces,f,
+ FALSE);
+
+ /* neighbour searching withouth QMMM! QM atoms have zero charge in
+ * the classical calculation. The charge-charge interaction
+ * between QM and MM atoms is handled in the QMMM core calculation
+ * (see QMMM.c). The VDW however, we'd like to compute classically
+ * and the QM MM atom pairs have just been put in the
+ * corresponding neighbourlists. in case of QMMM we still need to
+ * fill a special QMMM neighbourlist that contains all neighbours
+ * of the QM atoms. If bQMMM is true, this list will now be made:
+ */
+ if (fr->bQMMM && fr->qr->QMMMscheme!=eQMMMschemeoniom)
+ {
+ nsearch += nsgrid_core(log,cr,fr,box,box_size,ngid,top,
+ grid,x,ns->bexcl,ns->bExcludeAlleg,
+ nrnb,md,lambda,dvdlambda,grppener,
+ put_in_list_qmmm,ns->bHaveVdW,
+ bDoLongRange,bDoForces,f,
+ TRUE);
+ }
+ }
+ else
+ {
+ nsearch = ns_simple_core(fr,top,md,box,box_size,
+ ns->bexcl,ns->simple_aaj,
+ ngid,ns->ns_buf,put_in_list,ns->bHaveVdW);
+ }
+ debug_gmx();
+
+#ifdef DEBUG
+ pr_nsblock(log);
+#endif
+
+ inc_nrnb(nrnb,eNR_NS,nsearch);
+ /* inc_nrnb(nrnb,eNR_LR,fr->nlr); */
+
+ return nsearch;
+}
+
+int natoms_beyond_ns_buffer(t_inputrec *ir,t_forcerec *fr,t_block *cgs,
+ matrix scale_tot,rvec *x)
+{
+ int cg0,cg1,cg,a0,a1,a,i,j;
+ real rint,hbuf2,scale;
+ rvec *cg_cm,cgsc;
+ gmx_bool bIsotropic;
+ int nBeyond;
+
+ nBeyond = 0;
+
+ rint = max(ir->rcoulomb,ir->rvdw);
+ if (ir->rlist < rint)
+ {
+ gmx_fatal(FARGS,"The neighbor search buffer has negative size: %f nm",
+ ir->rlist - rint);
+ }
+ cg_cm = fr->cg_cm;
+
+ cg0 = fr->cg0;
+ cg1 = fr->hcg;
+
+ if (!EI_DYNAMICS(ir->eI) || !DYNAMIC_BOX(*ir))
+ {
+ hbuf2 = sqr(0.5*(ir->rlist - rint));
+ for(cg=cg0; cg<cg1; cg++)
+ {
+ a0 = cgs->index[cg];
+ a1 = cgs->index[cg+1];
+ for(a=a0; a<a1; a++)
+ {
+ if (distance2(cg_cm[cg],x[a]) > hbuf2)
+ {
+ nBeyond++;
+ }
+ }
+ }
+ }
+ else
+ {
+ bIsotropic = TRUE;
+ scale = scale_tot[0][0];
+ for(i=1; i<DIM; i++)
+ {
+ /* With anisotropic scaling, the original spherical ns volumes become
+ * ellipsoids. To avoid costly transformations we use the minimum
+ * eigenvalue of the scaling matrix for determining the buffer size.
+ * Since the lower half is 0, the eigenvalues are the diagonal elements.
+ */
+ scale = min(scale,scale_tot[i][i]);
+ if (scale_tot[i][i] != scale_tot[i-1][i-1])
+ {
+ bIsotropic = FALSE;
+ }
+ for(j=0; j<i; j++)
+ {
+ if (scale_tot[i][j] != 0)
+ {
+ bIsotropic = FALSE;
+ }
+ }
+ }
+ hbuf2 = sqr(0.5*(scale*ir->rlist - rint));
+ if (bIsotropic)
+ {
+ for(cg=cg0; cg<cg1; cg++)
+ {
+ svmul(scale,cg_cm[cg],cgsc);
+ a0 = cgs->index[cg];
+ a1 = cgs->index[cg+1];
+ for(a=a0; a<a1; a++)
+ {
+ if (distance2(cgsc,x[a]) > hbuf2)
+ {
+ nBeyond++;
+ }
+ }
+ }
+ }
+ else
+ {
+ /* Anistropic scaling */
+ for(cg=cg0; cg<cg1; cg++)
+ {
+ /* Since scale_tot contains the transpose of the scaling matrix,
+ * we need to multiply with the transpose.
+ */
+ tmvmul_ur0(scale_tot,cg_cm[cg],cgsc);
+ a0 = cgs->index[cg];
+ a1 = cgs->index[cg+1];
+ for(a=a0; a<a1; a++)
+ {
+ if (distance2(cgsc,x[a]) > hbuf2)
+ {
+ nBeyond++;
+ }
+ }
+ }
+ }
+ }
+
+ return nBeyond;
+}
--- /dev/null
- cutoff = HUGE_VAL;
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2009, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ */
+/*! \page nbsearch Neighborhood search routines
+ *
+ * Functions to find particles within a neighborhood of a set of particles
+ * are defined in nbsearch.h.
+ * The usage is simple: a data structure is allocated with
+ * gmx_ana_nbsearch_create(), and the box shape and reference positions for a
+ * frame are set using gmx_ana_nbsearch_init() or gmx_ana_nbsearch_pos_init().
+ * Searches can then be performed with gmx_ana_nbsearch_is_within() and
+ * gmx_ana_nbsearch_mindist(), or with versions that take the \c gmx_ana_pos_t
+ * data structure.
+ * When the data structure is no longer required, it can be freed with
+ * gmx_ana_nbsearch_free().
+ *
+ * \internal
+ *
+ * \todo
+ * The grid implementation could still be optimized in several different ways:
+ * - Triclinic grid cells are not the most efficient shape, but make PBC
+ * handling easier.
+ * - Precalculating the required PBC shift for a pair of cells outside the
+ * inner loop. After this is done, it should be quite straightforward to
+ * move to rectangular cells.
+ * - Pruning grid cells from the search list if they are completely outside
+ * the sphere that is being considered.
+ * - A better heuristic could be added for falling back to simple loops for a
+ * small number of reference particles.
+ * - A better heuristic for selecting the grid size.
+ * - A multi-level grid implementation could be used to be able to use small
+ * grids for short cutoffs with very inhomogeneous particle distributions
+ * without a memory cost.
+ */
+/*! \internal \file
+ * \brief
+ * Implements functions in nbsearch.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \ingroup module_selection
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include <smalloc.h>
+#include <typedefs.h>
+#include <pbc.h>
+#include <vec.h>
+
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/selection/position.h"
+
+/*! \internal \brief
+ * Data structure for neighborhood searches.
+ */
+struct gmx_ana_nbsearch_t
+{
+ /** The cutoff. */
+ real cutoff;
+ /** The cutoff squared. */
+ real cutoff2;
+ /** Maximum number of reference points. */
+ int maxnref;
+
+ /** Number of reference points for the current frame. */
+ int nref;
+ /** Reference point positions. */
+ rvec *xref;
+ /** Reference position ids (NULL if not available). */
+ int *refid;
+ /** PBC data. */
+ t_pbc *pbc;
+
+ /** Number of excluded reference positions for current test particle. */
+ int nexcl;
+ /** Exclusions for current test particle. */
+ int *excl;
+
+ /** Whether to try grid searching. */
+ gmx_bool bTryGrid;
+ /** Whether grid searching is actually used for the current positions. */
+ gmx_bool bGrid;
+ /** Array allocated for storing in-unit-cell reference positions. */
+ rvec *xref_alloc;
+ /** FALSE if the box is rectangular. */
+ gmx_bool bTric;
+ /** Box vectors of a single grid cell. */
+ matrix cellbox;
+ /** The reciprocal cell vectors as columns; the inverse of \p cellbox. */
+ matrix recipcell;
+ /** Number of cells along each dimension. */
+ ivec ncelldim;
+ /** Total number of cells. */
+ int ncells;
+ /** Number of reference positions in each cell. */
+ int *ncatoms;
+ /** List of reference positions in each cell. */
+ atom_id **catom;
+ /** Allocation counts for each \p catom[i]. */
+ int *catom_nalloc;
+ /** Allocation count for the per-cell arrays. */
+ int cells_nalloc;
+ /** Number of neighboring cells to consider. */
+ int ngridnb;
+ /** Offsets of the neighboring cells to consider. */
+ ivec *gnboffs;
+ /** Allocation count for \p gnboffs. */
+ int gnboffs_nalloc;
+
+ /** Stores test position during a pair loop. */
+ rvec xtest;
+ /** Stores the previous returned position during a pair loop. */
+ int previ;
+ /** Stores the current exclusion index during loops. */
+ int exclind;
+ /** Stores the test particle cell index during loops. */
+ ivec testcell;
+ /** Stores the current cell neighbor index during pair loops. */
+ int prevnbi;
+ /** Stores the index within the current cell during pair loops. */
+ int prevcai;
+};
+
+/*!
+ * \param[in] cutoff Cutoff distance for the search
+ * (<=0 stands for no cutoff).
+ * \param[in] maxn Maximum number of reference particles.
+ * \returns Created neighborhood search data structure.
+ */
+gmx_ana_nbsearch_t *
+gmx_ana_nbsearch_create(real cutoff, int maxn)
+{
+ gmx_ana_nbsearch_t *d;
+
+ snew(d, 1);
+ d->bTryGrid = TRUE;
+ if (cutoff <= 0)
+ {
++ cutoff = GMX_REAL_MAX;
+ d->bTryGrid = FALSE;
+ }
+ d->cutoff = cutoff;
+ d->cutoff2 = sqr(cutoff);
+ d->maxnref = maxn;
+
+ d->xref = NULL;
+ d->nexcl = 0;
+ d->exclind = 0;
+
+ d->xref_alloc = NULL;
+ d->ncells = 0;
+ d->ncatoms = NULL;
+ d->catom = NULL;
+ d->catom_nalloc = 0;
+ d->cells_nalloc = 0;
+
+ d->ngridnb = 0;
+ d->gnboffs = NULL;
+ d->gnboffs_nalloc = 0;
+
+ return d;
+}
+
+/*!
+ * \param d Data structure to free.
+ *
+ * After the call, the pointer \p d is no longer valid.
+ */
+void
+gmx_ana_nbsearch_free(gmx_ana_nbsearch_t *d)
+{
+ sfree(d->xref_alloc);
+ sfree(d->ncatoms);
+ if (d->catom)
+ {
+ int ci;
+
+ for (ci = 0; ci < d->ncells; ++ci)
+ {
+ sfree(d->catom[ci]);
+ }
+ sfree(d->catom);
+ }
+ sfree(d->catom_nalloc);
+ sfree(d->gnboffs);
+ sfree(d);
+}
+
+/*! \brief
+ * Calculates offsets to neighboring grid cells that should be considered.
+ *
+ * \param[in,out] d Grid information.
+ * \param[in] pbc Information about the box.
+ */
+static void
+grid_init_cell_nblist(gmx_ana_nbsearch_t *d, t_pbc *pbc)
+{
+ int maxx, maxy, maxz;
+ int x, y, z, i;
+ real rvnorm;
+
+ /* Find the extent of the sphere in triclinic coordinates */
+ maxz = (int)(d->cutoff * d->recipcell[ZZ][ZZ]) + 1;
+ rvnorm = sqrt(sqr(d->recipcell[YY][YY]) + sqr(d->recipcell[ZZ][YY]));
+ maxy = (int)(d->cutoff * rvnorm) + 1;
+ rvnorm = sqrt(sqr(d->recipcell[XX][XX]) + sqr(d->recipcell[YY][XX])
+ + sqr(d->recipcell[ZZ][XX]));
+ maxx = (int)(d->cutoff * rvnorm) + 1;
+
+ /* Calculate the number of cells and reallocate if necessary */
+ d->ngridnb = (2 * maxx + 1) * (2 * maxy + 1) * (2 * maxz + 1);
+ if (d->gnboffs_nalloc < d->ngridnb)
+ {
+ d->gnboffs_nalloc = d->ngridnb;
+ srenew(d->gnboffs, d->gnboffs_nalloc);
+ }
+
+ /* Store the whole cube */
+ /* TODO: Prune off corners that are not needed */
+ i = 0;
+ for (x = -maxx; x <= maxx; ++x)
+ {
+ for (y = -maxy; y <= maxy; ++y)
+ {
+ for (z = -maxz; z <= maxz; ++z)
+ {
+ d->gnboffs[i][XX] = x;
+ d->gnboffs[i][YY] = y;
+ d->gnboffs[i][ZZ] = z;
+ ++i;
+ }
+ }
+ }
+}
+
+/*! \brief
+ * Determines a suitable grid size.
+ *
+ * \param[in,out] d Grid information.
+ * \param[in] pbc Information about the box.
+ * \returns FALSE if grid search is not suitable.
+ */
+static gmx_bool
+grid_setup_cells(gmx_ana_nbsearch_t *d, t_pbc *pbc)
+{
+ real targetsize;
+ int dd;
+
+#ifdef HAVE_CBRT
+ targetsize = cbrt(pbc->box[XX][XX] * pbc->box[YY][YY] * pbc->box[ZZ][ZZ]
+ * 10 / d->nref);
+#else
+ targetsize = pow(pbc->box[XX][XX] * pbc->box[YY][YY] * pbc->box[ZZ][ZZ]
+ * 10 / d->nref, 1./3.);
+#endif
+
+ d->ncells = 1;
+ for (dd = 0; dd < DIM; ++dd)
+ {
+ d->ncelldim[dd] = (int)(pbc->box[dd][dd] / targetsize);
+ d->ncells *= d->ncelldim[dd];
+ if (d->ncelldim[dd] < 3)
+ {
+ return FALSE;
+ }
+ }
+ /* Reallocate if necessary */
+ if (d->cells_nalloc < d->ncells)
+ {
+ int i;
+
+ srenew(d->ncatoms, d->ncells);
+ srenew(d->catom, d->ncells);
+ srenew(d->catom_nalloc, d->ncells);
+ for (i = d->cells_nalloc; i < d->ncells; ++i)
+ {
+ d->catom[i] = NULL;
+ d->catom_nalloc[i] = 0;
+ }
+ d->cells_nalloc = d->ncells;
+ }
+ return TRUE;
+}
+
+/*! \brief
+ * Sets ua a search grid for a given box.
+ *
+ * \param[in,out] d Grid information.
+ * \param[in] pbc Information about the box.
+ * \returns FALSE if grid search is not suitable.
+ */
+static gmx_bool
+grid_set_box(gmx_ana_nbsearch_t *d, t_pbc *pbc)
+{
+ int dd;
+
+ /* TODO: This check could be improved. */
+ if (0.5*pbc->max_cutoff2 < d->cutoff2)
+ {
+ return FALSE;
+ }
+
+ if (!grid_setup_cells(d, pbc))
+ {
+ return FALSE;
+ }
+
+ d->bTric = TRICLINIC(pbc->box);
+ if (d->bTric)
+ {
+ for (dd = 0; dd < DIM; ++dd)
+ {
+ svmul(1.0 / d->ncelldim[dd], pbc->box[dd], d->cellbox[dd]);
+ }
+ m_inv_ur0(d->cellbox, d->recipcell);
+ }
+ else
+ {
+ for (dd = 0; dd < DIM; ++dd)
+ {
+ d->cellbox[dd][dd] = pbc->box[dd][dd] / d->ncelldim[dd];
+ d->recipcell[dd][dd] = 1 / d->cellbox[dd][dd];
+ }
+ }
+ grid_init_cell_nblist(d, pbc);
+ return TRUE;
+}
+
+/*! \brief
+ * Maps a point into a grid cell.
+ *
+ * \param[in] d Grid information.
+ * \param[in] x Point to map.
+ * \param[out] cell Indices of the grid cell in which \p x lies.
+ *
+ * \p x should be in the triclinic unit cell.
+ */
+static void
+grid_map_onto(gmx_ana_nbsearch_t *d, const rvec x, ivec cell)
+{
+ int dd;
+
+ if (d->bTric)
+ {
+ rvec tx;
+
+ tmvmul_ur0(d->recipcell, x, tx);
+ for (dd = 0; dd < DIM; ++dd)
+ {
+ cell[dd] = (int)tx[dd];
+ }
+ }
+ else
+ {
+ for (dd = 0; dd < DIM; ++dd)
+ {
+ cell[dd] = (int)(x[dd] * d->recipcell[dd][dd]);
+ }
+ }
+}
+
+/*! \brief
+ * Calculates linear index of a grid cell.
+ *
+ * \param[in] d Grid information.
+ * \param[in] cell Cell indices.
+ * \returns Linear index of \p cell.
+ */
+static int
+grid_index(gmx_ana_nbsearch_t *d, const ivec cell)
+{
+ return cell[XX] + cell[YY] * d->ncelldim[XX]
+ + cell[ZZ] * d->ncelldim[XX] * d->ncelldim[YY];
+}
+
+/*! \brief
+ * Clears all grid cells.
+ *
+ * \param[in,out] d Grid information.
+ */
+static void
+grid_clear_cells(gmx_ana_nbsearch_t *d)
+{
+ int ci;
+
+ for (ci = 0; ci < d->ncells; ++ci)
+ {
+ d->ncatoms[ci] = 0;
+ }
+}
+
+/*! \brief
+ * Adds an index into a grid cell.
+ *
+ * \param[in,out] d Grid information.
+ * \param[in] cell Cell into which \p i should be added.
+ * \param[in] i Index to add.
+ */
+static void
+grid_add_to_cell(gmx_ana_nbsearch_t *d, const ivec cell, int i)
+{
+ int ci = grid_index(d, cell);
+
+ if (d->ncatoms[ci] == d->catom_nalloc[ci])
+ {
+ d->catom_nalloc[ci] += 10;
+ srenew(d->catom[ci], d->catom_nalloc[ci]);
+ }
+ d->catom[ci][d->ncatoms[ci]++] = i;
+}
+
+/*!
+ * \param[in,out] d Neighborhood search data structure.
+ * \param[in] pbc PBC information for the frame.
+ * \param[in] n Number of reference positions for the frame.
+ * \param[in] x \p n reference positions for the frame.
+ *
+ * Initializes the data structure \p d such that it can be used to search
+ * for the neighbors of \p x.
+ */
+void
+gmx_ana_nbsearch_init(gmx_ana_nbsearch_t *d, t_pbc *pbc, int n, const rvec x[])
+{
+ d->pbc = pbc;
+ d->nref = n;
+ if (!pbc)
+ {
+ d->bGrid = FALSE;
+ }
+ else if (d->bTryGrid)
+ {
+ d->bGrid = grid_set_box(d, pbc);
+ }
+ if (d->bGrid)
+ {
+ int i;
+
+ if (!d->xref_alloc)
+ {
+ snew(d->xref_alloc, d->maxnref);
+ }
+ d->xref = d->xref_alloc;
+ grid_clear_cells(d);
+
+ for (i = 0; i < n; ++i)
+ {
+ copy_rvec(x[i], d->xref[i]);
+ }
+ put_atoms_in_triclinic_unitcell(ecenterTRIC, pbc->box, n, d->xref);
+ for (i = 0; i < n; ++i)
+ {
+ ivec refcell;
+
+ grid_map_onto(d, d->xref[i], refcell);
+ grid_add_to_cell(d, refcell, i);
+ }
+ }
+ else
+ {
+ // Won't be modified in this case, but when a grid is used,
+ // xref _is_ modified, so it can't be const.
+ d->xref = const_cast<rvec *>(x);
+ }
+ d->refid = NULL;
+}
+
+/*!
+ * \param[in,out] d Neighborhood search data structure.
+ * \param[in] pbc PBC information for the frame.
+ * \param[in] p Reference positions for the frame.
+ *
+ * A convenience wrapper for gmx_ana_nbsearch_init().
+ */
+void
+gmx_ana_nbsearch_pos_init(gmx_ana_nbsearch_t *d, t_pbc *pbc, const gmx_ana_pos_t *p)
+{
+ gmx_ana_nbsearch_init(d, pbc, p->nr, p->x);
+ d->refid = (p->nr < d->maxnref ? p->m.refid : NULL);
+}
+
+/*!
+ * \param[in,out] d Neighborhood search data structure.
+ * \param[in] nexcl Number of reference positions to exclude from next
+ * search.
+ * \param[in] excl Indices of reference positions to exclude.
+ *
+ * The set exclusions remain in effect until the next call of this function.
+ */
+void
+gmx_ana_nbsearch_set_excl(gmx_ana_nbsearch_t *d, int nexcl, int excl[])
+{
+
+ d->nexcl = nexcl;
+ d->excl = excl;
+}
+
+/*! \brief
+ * Helper function to check whether a reference point should be excluded.
+ */
+static gmx_bool
+is_excluded(gmx_ana_nbsearch_t *d, int j)
+{
+ if (d->exclind < d->nexcl)
+ {
+ if (d->refid)
+ {
+ while (d->exclind < d->nexcl && d->refid[j] > d->excl[d->exclind])
+ {
+ ++d->exclind;
+ }
+ if (d->exclind < d->nexcl && d->refid[j] == d->excl[d->exclind])
+ {
+ ++d->exclind;
+ return TRUE;
+ }
+ }
+ else
+ {
+ while (d->bGrid && d->exclind < d->nexcl && d->excl[d->exclind] < j)
+ {
+ ++d->exclind;
+ }
+ if (d->excl[d->exclind] == j)
+ {
+ ++d->exclind;
+ return TRUE;
+ }
+ }
+ }
+ return FALSE;
+}
+
+/*! \brief
+ * Initializes a grid search to find reference positions neighboring \p x.
+ */
+static void
+grid_search_start(gmx_ana_nbsearch_t *d, const rvec x)
+{
+ copy_rvec(x, d->xtest);
+ if (d->bGrid)
+ {
+ put_atoms_in_triclinic_unitcell(ecenterTRIC, d->pbc->box, 1, &d->xtest);
+ grid_map_onto(d, d->xtest, d->testcell);
+ d->prevnbi = 0;
+ d->prevcai = -1;
+ }
+ else
+ {
+ d->previ = -1;
+ }
+ d->exclind = 0;
+}
+
+/*! \brief
+ * Does a grid search.
+ */
+static gmx_bool
+grid_search(gmx_ana_nbsearch_t *d,
+ gmx_bool (*action)(gmx_ana_nbsearch_t *d, int i, real r2))
+{
+ int i;
+ rvec dx;
+ real r2;
+
+ if (d->bGrid)
+ {
+ int nbi, ci, cai;
+
+ nbi = d->prevnbi;
+ cai = d->prevcai + 1;
+
+ for ( ; nbi < d->ngridnb; ++nbi)
+ {
+ ivec cell;
+
+ ivec_add(d->testcell, d->gnboffs[nbi], cell);
+ /* TODO: Support for 2D and screw PBC */
+ cell[XX] = (cell[XX] + d->ncelldim[XX]) % d->ncelldim[XX];
+ cell[YY] = (cell[YY] + d->ncelldim[YY]) % d->ncelldim[YY];
+ cell[ZZ] = (cell[ZZ] + d->ncelldim[ZZ]) % d->ncelldim[ZZ];
+ ci = grid_index(d, cell);
+ /* TODO: Calculate the required PBC shift outside the inner loop */
+ for ( ; cai < d->ncatoms[ci]; ++cai)
+ {
+ i = d->catom[ci][cai];
+ if (is_excluded(d, i))
+ {
+ continue;
+ }
+ pbc_dx_aiuc(d->pbc, d->xtest, d->xref[i], dx);
+ r2 = norm2(dx);
+ if (r2 <= d->cutoff2)
+ {
+ if (action(d, i, r2))
+ {
+ d->prevnbi = nbi;
+ d->prevcai = cai;
+ d->previ = i;
+ return TRUE;
+ }
+ }
+ }
+ d->exclind = 0;
+ cai = 0;
+ }
+ }
+ else
+ {
+ i = d->previ + 1;
+ for ( ; i < d->nref; ++i)
+ {
+ if (is_excluded(d, i))
+ {
+ continue;
+ }
+ if (d->pbc)
+ {
+ pbc_dx(d->pbc, d->xtest, d->xref[i], dx);
+ }
+ else
+ {
+ rvec_sub(d->xtest, d->xref[i], dx);
+ }
+ r2 = norm2(dx);
+ if (r2 <= d->cutoff2)
+ {
+ if (action(d, i, r2))
+ {
+ d->previ = i;
+ return TRUE;
+ }
+ }
+ }
+ }
+ return FALSE;
+}
+
+/*! \brief
+ * Helper function to use with grid_search() to find the next neighbor.
+ *
+ * Simply breaks the loop on the first found neighbor.
+ */
+static gmx_bool
+within_action(gmx_ana_nbsearch_t *d, int i, real r2)
+{
+ return TRUE;
+}
+
+/*! \brief
+ * Helper function to use with grid_search() to find the minimum distance.
+ */
+static gmx_bool
+mindist_action(gmx_ana_nbsearch_t *d, int i, real r2)
+{
+ d->cutoff2 = r2;
+ return FALSE;
+}
+
+/*!
+ * \param[in] d Neighborhood search data structure.
+ * \param[in] x Test position.
+ * \returns TRUE if \p x is within the cutoff of any reference position,
+ * FALSE otherwise.
+ */
+gmx_bool
+gmx_ana_nbsearch_is_within(gmx_ana_nbsearch_t *d, const rvec x)
+{
+ grid_search_start(d, x);
+ return grid_search(d, &within_action);
+}
+
+/*!
+ * \param[in] d Neighborhood search data structure.
+ * \param[in] p Test positions.
+ * \param[in] i Use the i'th position in \p p for testing.
+ * \returns TRUE if the test position is within the cutoff of any reference
+ * position, FALSE otherwise.
+ */
+gmx_bool
+gmx_ana_nbsearch_pos_is_within(gmx_ana_nbsearch_t *d, const gmx_ana_pos_t *p, int i)
+{
+ return gmx_ana_nbsearch_is_within(d, p->x[i]);
+}
+
+/*!
+ * \param[in] d Neighborhood search data structure.
+ * \param[in] x Test position.
+ * \returns The distance to the nearest reference position, or the cutoff
+ * value if there are no reference positions within the cutoff.
+ */
+real
+gmx_ana_nbsearch_mindist(gmx_ana_nbsearch_t *d, const rvec x)
+{
+ real mind;
+
+ grid_search_start(d, x);
+ grid_search(d, &mindist_action);
+ mind = sqrt(d->cutoff2);
+ d->cutoff2 = sqr(d->cutoff);
+ return mind;
+}
+
+/*!
+ * \param[in] d Neighborhood search data structure.
+ * \param[in] p Test positions.
+ * \param[in] i Use the i'th position in \p p for testing.
+ * \returns The distance to the nearest reference position, or the cutoff
+ * value if there are no reference positions within the cutoff.
+ */
+real
+gmx_ana_nbsearch_pos_mindist(gmx_ana_nbsearch_t *d, const gmx_ana_pos_t *p, int i)
+{
+ return gmx_ana_nbsearch_mindist(d, p->x[i]);
+}
+
+/*!
+ * \param[in] d Neighborhood search data structure.
+ * \param[in] x Test positions.
+ * \param[out] jp Index of the reference position in the first pair.
+ * \returns TRUE if there are positions within the cutoff.
+ */
+gmx_bool
+gmx_ana_nbsearch_first_within(gmx_ana_nbsearch_t *d, const rvec x, int *jp)
+{
+ grid_search_start(d, x);
+ return gmx_ana_nbsearch_next_within(d, jp);
+}
+
+/*!
+ * \param[in] d Neighborhood search data structure.
+ * \param[in] p Test positions.
+ * \param[in] i Use the i'th position in \p p.
+ * \param[out] jp Index of the reference position in the first pair.
+ * \returns TRUE if there are positions within the cutoff.
+ */
+gmx_bool
+gmx_ana_nbsearch_pos_first_within(gmx_ana_nbsearch_t *d, const gmx_ana_pos_t *p,
+ int i, int *jp)
+{
+ return gmx_ana_nbsearch_first_within(d, p->x[i], jp);
+}
+
+/*!
+ * \param[in] d Neighborhood search data structure.
+ * \param[out] jp Index of the test position in the next pair.
+ * \returns TRUE if there are positions within the cutoff.
+ */
+gmx_bool
+gmx_ana_nbsearch_next_within(gmx_ana_nbsearch_t *d, int *jp)
+{
+ if (grid_search(d, &within_action))
+ {
+ *jp = d->previ;
+ return TRUE;
+ }
+ *jp = -1;
+ return FALSE;
+}
--- /dev/null
- value->u.r.r1 = (real)value->u.i.i1;
- value->u.r.r2 = (real)value->u.i.i2;
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2009, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ */
+/*! \internal \file
+ * \brief
+ * Implements functions in selparam.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \ingroup module_selection
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <smalloc.h>
+#include <string2.h>
+#include <vec.h>
+
+#include "gromacs/fatalerror/errorcodes.h"
+#include "gromacs/fatalerror/messagestringcollector.h"
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selmethod.h"
+#include "gromacs/selection/selparam.h"
+#include "gromacs/utility/format.h"
+
+#include "parsetree.h"
+#include "position.h"
+#include "scanner.h"
+#include "selelem.h"
+
+template <typename T>
+static T min(T a, T b)
+{
+ return (a < b) ? a : b;
+}
+
+template <typename T>
+static T max(T a, T b)
+{
+ return (a > b) ? a : b;
+}
+
+/*!
+ * \param[in] name Name of the parameter to search.
+ * \param[in] nparam Number of parameters in the \p param array.
+ * \param[in] param Parameter array to search.
+ * \returns Pointer to the parameter in the \p param
+ * or NULL if no parameter with name \p name was found.
+ *
+ * The comparison is case-sensitive.
+ */
+gmx_ana_selparam_t *
+gmx_ana_selparam_find(const char *name, int nparam, gmx_ana_selparam_t *param)
+{
+ int i;
+
+ if (nparam == 0)
+ {
+ return NULL;
+ }
+ /* Find the first non-null parameter */
+ i = 0;
+ while (i < nparam && param[i].name == NULL)
+ {
+ ++i;
+ }
+ /* Process the special case of a NULL parameter */
+ if (name == NULL)
+ {
+ return (i == 0) ? NULL : ¶m[i-1];
+ }
+ for ( ; i < nparam; ++i)
+ {
+ if (!strcmp(param[i].name, name))
+ {
+ return ¶m[i];
+ }
+ /* Check for 'no' prefix on gmx_boolean parameters */
+ if (param[i].val.type == NO_VALUE
+ && strlen(name) > 2 && name[0] == 'n' && name[1] == 'o'
+ && !strcmp(param[i].name, name+2))
+ {
+ return ¶m[i];
+ }
+ }
+ return NULL;
+}
+
+/*! \brief
+ * Does a type conversion on a \c t_selexpr_value.
+ *
+ * \param[in,out] value Value to convert.
+ * \param[in] type Type to convert to.
+ * \param[in] scanner Scanner data structure.
+ * \returns 0 on success, a non-zero value on error.
+ */
+static int
+convert_value(t_selexpr_value *value, e_selvalue_t type, void *scanner)
+{
+ if (value->type == type || type == NO_VALUE)
+ {
+ return 0;
+ }
+ if (value->bExpr)
+ {
+ /* Conversion from atom selection to position using default
+ * reference positions. */
+ if (value->type == GROUP_VALUE && type == POS_VALUE)
+ {
+ value->u.expr =
+ _gmx_sel_init_position(value->u.expr, NULL, scanner);
+ if (value->u.expr == NULL)
+ {
+ return -1;
+ }
+ value->type = type;
+ return 0;
+ }
+ return -1;
+ }
+ else
+ {
+ /* Integers to floating point are easy */
+ if (value->type == INT_VALUE && type == REAL_VALUE)
+ {
- value->u.i.i1 = (int)value->u.r.r1;
- value->u.i.i2 = (int)value->u.r.r2;
++ real r1 = (real)value->u.i.i1;
++ real r2 = (real)value->u.i.i2;
++ value->u.r.r1 = r1;
++ value->u.r.r2 = r2;
+ value->type = type;
+ return 0;
+ }
+ /* Reals that are integer-valued can also be converted */
+ if (value->type == REAL_VALUE && type == INT_VALUE
+ && gmx_within_tol(value->u.r.r1, (int)value->u.r.r1, GMX_REAL_EPS)
+ && gmx_within_tol(value->u.r.r2, (int)value->u.r.r2, GMX_REAL_EPS))
+ {
++ int i1 = (int)value->u.r.r1;
++ int i2 = (int)value->u.r.r2;
++ value->u.i.i1 = i1;
++ value->u.i.i2 = i2;
+ value->type = type;
+ return 0;
+ }
+ }
+ return -1;
+}
+
+/*! \brief
+ * Does a type conversion on a list of values.
+ *
+ * \param[in,out] values Values to convert.
+ * \param[in] type Type to convert to.
+ * \param[in] scanner Scanner data structure.
+ * \returns 0 on success, a non-zero value on error.
+ */
+static int
+convert_values(t_selexpr_value *values, e_selvalue_t type, void *scanner)
+{
+ t_selexpr_value *value;
+ int rc, rc1;
+
+ rc = 0;
+ value = values;
+ while (value)
+ {
+ rc1 = convert_value(value, type, scanner);
+ if (rc1 != 0 && rc == 0)
+ {
+ rc = rc1;
+ }
+ value = value->next;
+ }
+ /* FIXME: More informative error messages */
+ return rc;
+}
+
+/*! \brief
+ * Adds a child element for a parameter, keeping the parameter order.
+ *
+ * \param[in,out] root Root element to which the child is added.
+ * \param[in] child Child to add.
+ * \param[in] param Parameter for which this child is a value.
+ *
+ * Puts \p child in the child list of \p root such that the list remains
+ * in the same order as the corresponding parameters.
+ */
+static void
+place_child(t_selelem *root, t_selelem *child, gmx_ana_selparam_t *param)
+{
+ gmx_ana_selparam_t *ps;
+ int n;
+
+ ps = root->u.expr.method->param;
+ n = param - ps;
+ /* Put the child element in the correct place */
+ if (!root->child || n < root->child->u.param - ps)
+ {
+ child->next = root->child;
+ root->child = child;
+ }
+ else
+ {
+ t_selelem *prev;
+
+ prev = root->child;
+ while (prev->next && prev->next->u.param - ps >= n)
+ {
+ prev = prev->next;
+ }
+ child->next = prev->next;
+ prev->next = child;
+ }
+}
+
+/*! \brief
+ * Comparison function for sorting integer ranges.
+ *
+ * \param[in] a Pointer to the first range.
+ * \param[in] b Pointer to the second range.
+ * \returns -1, 0, or 1 depending on the relative order of \p a and \p b.
+ *
+ * The ranges are primarily sorted based on their starting point, and
+ * secondarily based on length (longer ranges come first).
+ */
+static int
+cmp_int_range(const void *a, const void *b)
+{
+ if (((int *)a)[0] < ((int *)b)[0])
+ {
+ return -1;
+ }
+ if (((int *)a)[0] > ((int *)b)[0])
+ {
+ return 1;
+ }
+ if (((int *)a)[1] > ((int *)b)[1])
+ {
+ return -1;
+ }
+ return 0;
+}
+
+/*! \brief
+ * Comparison function for sorting real ranges.
+ *
+ * \param[in] a Pointer to the first range.
+ * \param[in] b Pointer to the second range.
+ * \returns -1, 0, or 1 depending on the relative order of \p a and \p b.
+ *
+ * The ranges are primarily sorted based on their starting point, and
+ * secondarily based on length (longer ranges come first).
+ */
+static int
+cmp_real_range(const void *a, const void *b)
+{
+ if (((real *)a)[0] < ((real *)b)[0])
+ {
+ return -1;
+ }
+ if (((real *)a)[0] > ((real *)b)[0])
+ {
+ return 1;
+ }
+ if (((real *)a)[1] > ((real *)b)[1])
+ {
+ return -1;
+ }
+ return 0;
+}
+
+/*! \brief
+ * Parses the values for a parameter that takes integer or real ranges.
+ *
+ * \param[in] nval Number of values in \p values.
+ * \param[in] values Pointer to the list of values.
+ * \param param Parameter to parse.
+ * \param[in] scanner Scanner data structure.
+ * \returns TRUE if the values were parsed successfully, FALSE otherwise.
+ */
+static gmx_bool
+parse_values_range(int nval, t_selexpr_value *values, gmx_ana_selparam_t *param,
+ void *scanner)
+{
+ t_selexpr_value *value;
+ int *idata;
+ real *rdata;
+ int i, j, n;
+
+ param->flags &= ~SPAR_DYNAMIC;
+ if (param->val.type != INT_VALUE && param->val.type != REAL_VALUE)
+ {
+ GMX_ERROR_NORET(gmx::eeInternalError, "Invalid range parameter type");
+ return FALSE;
+ }
+ idata = NULL;
+ rdata = NULL;
+ if (param->val.type == INT_VALUE)
+ {
+ snew(idata, nval*2);
+ }
+ else
+ {
+ snew(rdata, nval*2);
+ }
+ value = values;
+ i = 0;
+ while (value)
+ {
+ if (value->bExpr)
+ {
+ _gmx_selparser_error(scanner, "expressions not supported within range parameters");
+ return FALSE;
+ }
+ if (value->type != param->val.type)
+ {
+ GMX_ERROR_NORET(gmx::eeInternalError, "Invalid range value type");
+ return FALSE;
+ }
+ if (param->val.type == INT_VALUE)
+ {
+ /* Make sure the input range is in increasing order */
+ if (value->u.i.i1 > value->u.i.i2)
+ {
+ int tmp = value->u.i.i1;
+ value->u.i.i1 = value->u.i.i2;
+ value->u.i.i2 = tmp;
+ }
+ /* Check if the new range overlaps or extends the previous one */
+ if (i > 0 && value->u.i.i1 <= idata[i-1]+1 && value->u.i.i2 >= idata[i-2]-1)
+ {
+ idata[i-2] = min(idata[i-2], value->u.i.i1);
+ idata[i-1] = max(idata[i-1], value->u.i.i2);
+ }
+ else
+ {
+ idata[i++] = value->u.i.i1;
+ idata[i++] = value->u.i.i2;
+ }
+ }
+ else
+ {
+ /* Make sure the input range is in increasing order */
+ if (value->u.r.r1 > value->u.r.r2)
+ {
+ real tmp = value->u.r.r1;
+ value->u.r.r1 = value->u.r.r2;
+ value->u.r.r2 = tmp;
+ }
+ /* Check if the new range overlaps or extends the previous one */
+ if (i > 0 && value->u.r.r1 <= rdata[i-1] && value->u.r.r2 >= rdata[i-2])
+ {
+ rdata[i-2] = min(rdata[i-2], value->u.r.r1);
+ rdata[i-1] = max(rdata[i-1], value->u.r.r2);
+ }
+ else
+ {
+ rdata[i++] = value->u.r.r1;
+ rdata[i++] = value->u.r.r2;
+ }
+ }
+ value = value->next;
+ }
+ n = i/2;
+ /* Sort the ranges and merge consequent ones */
+ if (param->val.type == INT_VALUE)
+ {
+ qsort(idata, n, 2*sizeof(int), &cmp_int_range);
+ for (i = j = 2; i < 2*n; i += 2)
+ {
+ if (idata[j-1]+1 >= idata[i])
+ {
+ if (idata[i+1] > idata[j-1])
+ {
+ idata[j-1] = idata[i+1];
+ }
+ }
+ else
+ {
+ idata[j] = idata[i];
+ idata[j+1] = idata[i+1];
+ j += 2;
+ }
+ }
+ }
+ else
+ {
+ qsort(rdata, n, 2*sizeof(real), &cmp_real_range);
+ for (i = j = 2; i < 2*n; i += 2)
+ {
+ if (rdata[j-1]+1 >= rdata[i])
+ {
+ if (rdata[i+1] > rdata[j-1])
+ {
+ rdata[j-1] = rdata[i+1];
+ }
+ }
+ else
+ {
+ rdata[j] = rdata[i];
+ rdata[j+1] = rdata[i+1];
+ j += 2;
+ }
+ }
+ }
+ n = j/2;
+ /* Store the values */
+ if (param->flags & SPAR_VARNUM)
+ {
+ param->val.nr = n;
+ if (param->val.type == INT_VALUE)
+ {
+ srenew(idata, j);
+ _gmx_selvalue_setstore_alloc(¶m->val, idata, j);
+ }
+ else
+ {
+ srenew(rdata, j);
+ _gmx_selvalue_setstore_alloc(¶m->val, rdata, j);
+ }
+ }
+ else
+ {
+ if (n != param->val.nr)
+ {
+ _gmx_selparser_error(scanner, "the value should consist of exactly one range");
+ sfree(idata);
+ sfree(rdata);
+ return FALSE;
+ }
+ if (param->val.type == INT_VALUE)
+ {
+ memcpy(param->val.u.i, idata, 2*n*sizeof(int));
+ sfree(idata);
+ }
+ else
+ {
+ memcpy(param->val.u.r, rdata, 2*n*sizeof(real));
+ sfree(rdata);
+ }
+ }
+ if (param->nvalptr)
+ {
+ *param->nvalptr = param->val.nr;
+ }
+ param->nvalptr = NULL;
+
+ return TRUE;
+}
+
+/*! \brief
+ * Parses the values for a parameter that takes a variable number of values.
+ *
+ * \param[in] nval Number of values in \p values.
+ * \param[in] values Pointer to the list of values.
+ * \param param Parameter to parse.
+ * \param root Selection element to which child expressions are added.
+ * \param[in] scanner Scanner data structure.
+ * \returns TRUE if the values were parsed successfully, FALSE otherwise.
+ *
+ * For integer ranges, the sequence of numbers from the first to second value
+ * is stored, each as a separate value.
+ */
+static gmx_bool
+parse_values_varnum(int nval, t_selexpr_value *values,
+ gmx_ana_selparam_t *param, t_selelem *root, void *scanner)
+{
+ t_selexpr_value *value;
+ int i, j;
+
+ param->flags &= ~SPAR_DYNAMIC;
+ /* Update nval if there are integer ranges. */
+ if (param->val.type == INT_VALUE)
+ {
+ value = values;
+ while (value)
+ {
+ if (value->type == INT_VALUE && !value->bExpr)
+ {
+ nval += abs(value->u.i.i2 - value->u.i.i1);
+ }
+ value = value->next;
+ }
+ }
+
+ /* Check that the value type is actually implemented */
+ if (param->val.type != INT_VALUE && param->val.type != REAL_VALUE
+ && param->val.type != STR_VALUE && param->val.type != POS_VALUE)
+ {
+ GMX_ERROR_NORET(gmx::eeInternalError,
+ "Variable-count value type not implemented");
+ return FALSE;
+ }
+
+ /* Reserve appropriate amount of memory */
+ if (param->val.type == POS_VALUE)
+ {
+ gmx_ana_pos_reserve(param->val.u.p, nval, 0);
+ gmx_ana_pos_set_nr(param->val.u.p, nval);
+ gmx_ana_indexmap_init(¶m->val.u.p->m, NULL, NULL, INDEX_UNKNOWN);
+ }
+ else
+ {
+ _gmx_selvalue_reserve(¶m->val, nval);
+ }
+
+ value = values;
+ i = 0;
+ while (value)
+ {
+ if (value->bExpr)
+ {
+ _gmx_selparser_error(scanner, "expressions not supported within value lists");
+ return FALSE;
+ }
+ if (value->type != param->val.type)
+ {
+ GMX_ERROR_NORET(gmx::eeInternalError, "Invalid value type");
+ return FALSE;
+ }
+ switch (param->val.type)
+ {
+ case INT_VALUE:
+ if (value->u.i.i1 <= value->u.i.i2)
+ {
+ for (j = value->u.i.i1; j <= value->u.i.i2; ++j)
+ {
+ param->val.u.i[i++] = j;
+ }
+ }
+ else
+ {
+ for (j = value->u.i.i1; j >= value->u.i.i2; --j)
+ {
+ param->val.u.i[i++] = j;
+ }
+ }
+ break;
+ case REAL_VALUE:
+ if (value->u.r.r1 != value->u.r.r2)
+ {
+ _gmx_selparser_error(scanner, "real ranges not supported");
+ return FALSE;
+ }
+ param->val.u.r[i++] = value->u.r.r1;
+ break;
+ case STR_VALUE: param->val.u.s[i++] = strdup(value->u.s); break;
+ case POS_VALUE: copy_rvec(value->u.x, param->val.u.p->x[i++]); break;
+ default: /* Should not be reached */
+ GMX_ERROR_NORET(gmx::eeInternalError, "Invalid value type");
+ return FALSE;
+ }
+ value = value->next;
+ }
+ param->val.nr = i;
+ if (param->nvalptr)
+ {
+ *param->nvalptr = param->val.nr;
+ }
+ param->nvalptr = NULL;
+ /* Create a dummy child element to store the string values.
+ * This element is responsible for freeing the values, but carries no
+ * other function. */
+ if (param->val.type == STR_VALUE)
+ {
+ t_selelem *child;
+
+ child = _gmx_selelem_create(SEL_CONST);
+ _gmx_selelem_set_vtype(child, STR_VALUE);
+ child->name = param->name;
+ child->flags &= ~SEL_ALLOCVAL;
+ child->flags |= SEL_FLAGSSET | SEL_VARNUMVAL | SEL_ALLOCDATA;
+ child->v.nr = param->val.nr;
+ _gmx_selvalue_setstore(&child->v, param->val.u.s);
+ /* Because the child is not group-valued, the u union is not used
+ * for anything, so we can abuse it by storing the parameter value
+ * as place_child() expects, but this is really ugly... */
+ child->u.param = param;
+ place_child(root, child, param);
+ }
+
+ return TRUE;
+}
+
+/*! \brief
+ * Adds a new subexpression reference to a selection element.
+ *
+ * \param[in,out] root Root element to which the subexpression is added.
+ * \param[in] param Parameter for which this expression is a value.
+ * \param[in] expr Expression to add.
+ * \param[in] scanner Scanner data structure.
+ * \returns The created child element.
+ *
+ * Creates a new \ref SEL_SUBEXPRREF element and adds it into the child
+ * list of \p root.
+ * If \p expr is already a \ref SEL_SUBEXPRREF, it is used as it is.
+ * \ref SEL_ALLOCVAL is cleared for the returned element.
+ */
+static t_selelem *
+add_child(t_selelem *root, gmx_ana_selparam_t *param, t_selelem *expr,
+ void *scanner)
+{
+ t_selelem *child;
+ int rc;
+
+ if (root->type != SEL_EXPRESSION && root->type != SEL_MODIFIER)
+ {
+ GMX_ERROR_NORET(gmx::eeInternalError,
+ "Unsupported root element for selection parameter parser");
+ return NULL;
+ }
+ /* Create a subexpression reference element if necessary */
+ if (expr->type == SEL_SUBEXPRREF)
+ {
+ child = expr;
+ }
+ else
+ {
+ child = _gmx_selelem_create(SEL_SUBEXPRREF);
+ if (!child)
+ {
+ return NULL;
+ }
+ _gmx_selelem_set_vtype(child, expr->v.type);
+ child->child = expr;
+ }
+ /* Setup the child element */
+ child->flags &= ~SEL_ALLOCVAL;
+ child->u.param = param;
+ if (child->v.type != param->val.type)
+ {
+ _gmx_selparser_error(scanner, "invalid expression value");
+ goto on_error;
+ }
+ rc = _gmx_selelem_update_flags(child, scanner);
+ if (rc != 0)
+ {
+ goto on_error;
+ }
+ if ((child->flags & SEL_DYNAMIC) && !(param->flags & SPAR_DYNAMIC))
+ {
+ _gmx_selparser_error(scanner, "dynamic values not supported");
+ goto on_error;
+ }
+ if (!(child->flags & SEL_DYNAMIC))
+ {
+ param->flags &= ~SPAR_DYNAMIC;
+ }
+ /* Put the child element in the correct place */
+ place_child(root, child, param);
+ return child;
+
+on_error:
+ if (child != expr)
+ {
+ _gmx_selelem_free(child);
+ }
+ return NULL;
+}
+
+/*! \brief
+ * Parses an expression value for a parameter that takes a variable number of values.
+ *
+ * \param[in] nval Number of values in \p values.
+ * \param[in] values Pointer to the list of values.
+ * \param param Parameter to parse.
+ * \param root Selection element to which child expressions are added.
+ * \param[in] scanner Scanner data structure.
+ * \returns TRUE if the values were parsed successfully, FALSE otherwise.
+ */
+static gmx_bool
+parse_values_varnum_expr(int nval, t_selexpr_value *values,
+ gmx_ana_selparam_t *param, t_selelem *root,
+ void *scanner)
+{
+ t_selexpr_value *value;
+ t_selelem *child;
+ t_selelem *expr;
+
+ if (nval != 1 || !values->bExpr)
+ {
+ GMX_ERROR_NORET(gmx::eeInternalError, "Invalid expression value");
+ return FALSE;
+ }
+
+ value = values;
+ child = add_child(root, param, value->u.expr, scanner);
+ value->u.expr = NULL;
+ if (!child)
+ {
+ return FALSE;
+ }
+
+ /* Process single-valued expressions */
+ /* TODO: We should also handle SEL_SINGLEVAL expressions here */
+ if (child->v.type == POS_VALUE || child->v.type == GROUP_VALUE)
+ {
+ /* Set the value storage */
+ _gmx_selvalue_setstore(&child->v, param->val.u.ptr);
+ param->val.nr = 1;
+ if (param->nvalptr)
+ {
+ *param->nvalptr = param->val.nr;
+ }
+ param->nvalptr = NULL;
+ return TRUE;
+ }
+
+ if (!(child->flags & SEL_VARNUMVAL))
+ {
+ _gmx_selparser_error(scanner, "invalid expression value");
+ return FALSE;
+ }
+
+ child->flags |= SEL_ALLOCVAL;
+ param->val.nr = -1;
+ *param->nvalptr = param->val.nr;
+ /* Rest of the initialization is done during compilation in
+ * init_method(). */
+
+ return TRUE;
+}
+
+/*! \brief
+ * Initializes the storage of an expression value.
+ *
+ * \param[in,out] sel Selection element that evaluates the value.
+ * \param[in] param Parameter to receive the value.
+ * \param[in] i The value of \p sel evaluates the value \p i for
+ * \p param.
+ * \param[in] scanner Scanner data structure.
+ *
+ * Initializes the data pointer of \p sel such that the result is stored
+ * as the value \p i of \p param.
+ * This function is used internally by parse_values_std().
+ */
+static gmx_bool
+set_expr_value_store(t_selelem *sel, gmx_ana_selparam_t *param, int i,
+ void *scanner)
+{
+ if (sel->v.type != GROUP_VALUE && !(sel->flags & SEL_SINGLEVAL))
+ {
+ _gmx_selparser_error(scanner, "invalid expression value");
+ return FALSE;
+ }
+ switch (sel->v.type)
+ {
+ case INT_VALUE: sel->v.u.i = ¶m->val.u.i[i]; break;
+ case REAL_VALUE: sel->v.u.r = ¶m->val.u.r[i]; break;
+ case STR_VALUE: sel->v.u.s = ¶m->val.u.s[i]; break;
+ case POS_VALUE: sel->v.u.p = ¶m->val.u.p[i]; break;
+ case GROUP_VALUE: sel->v.u.g = ¶m->val.u.g[i]; break;
+ default: /* Error */
+ GMX_ERROR_NORET(gmx::eeInternalError, "Invalid value type");
+ return FALSE;
+ }
+ sel->v.nr = 1;
+ sel->v.nalloc = -1;
+ return TRUE;
+}
+
+/*! \brief
+ * Parses the values for a parameter that takes a constant number of values.
+ *
+ * \param[in] nval Number of values in \p values.
+ * \param[in] values Pointer to the list of values.
+ * \param param Parameter to parse.
+ * \param root Selection element to which child expressions are added.
+ * \param[in] scanner Scanner data structure.
+ * \returns TRUE if the values were parsed successfully, FALSE otherwise.
+ *
+ * For integer ranges, the sequence of numbers from the first to second value
+ * is stored, each as a separate value.
+ */
+static gmx_bool
+parse_values_std(int nval, t_selexpr_value *values, gmx_ana_selparam_t *param,
+ t_selelem *root, void *scanner)
+{
+ t_selexpr_value *value;
+ t_selelem *child;
+ int i, j;
+ gmx_bool bDynamic;
+
+ /* Handle atom-valued parameters */
+ if (param->flags & SPAR_ATOMVAL)
+ {
+ if (nval > 1)
+ {
+ _gmx_selparser_error(scanner, "more than one value not supported");
+ return FALSE;
+ }
+ value = values;
+ if (value->bExpr)
+ {
+ child = add_child(root, param, value->u.expr, scanner);
+ value->u.expr = NULL;
+ if (!child)
+ {
+ return FALSE;
+ }
+ child->flags |= SEL_ALLOCVAL;
+ if (child->v.type != GROUP_VALUE && (child->flags & SEL_ATOMVAL))
+ {
+ /* Rest of the initialization is done during compilation in
+ * init_method(). */
+ /* TODO: Positions are not correctly handled */
+ param->val.nr = -1;
+ if (param->nvalptr)
+ {
+ *param->nvalptr = -1;
+ }
+ return TRUE;
+ }
+ param->flags &= ~SPAR_ATOMVAL;
+ param->val.nr = 1;
+ if (param->nvalptr)
+ {
+ *param->nvalptr = 1;
+ }
+ param->nvalptr = NULL;
+ if (param->val.type == INT_VALUE || param->val.type == REAL_VALUE
+ || param->val.type == STR_VALUE)
+ {
+ _gmx_selvalue_reserve(¶m->val, 1);
+ }
+ return set_expr_value_store(child, param, 0, scanner);
+ }
+ /* If we reach here, proceed with normal parameter handling */
+ param->val.nr = 1;
+ if (param->val.type == INT_VALUE || param->val.type == REAL_VALUE
+ || param->val.type == STR_VALUE)
+ {
+ _gmx_selvalue_reserve(¶m->val, 1);
+ }
+ param->flags &= ~SPAR_ATOMVAL;
+ param->flags &= ~SPAR_DYNAMIC;
+ }
+
+ value = values;
+ i = 0;
+ bDynamic = FALSE;
+ while (value && i < param->val.nr)
+ {
+ if (value->type != param->val.type)
+ {
+ _gmx_selparser_error(scanner, "incorrect value skipped");
+ value = value->next;
+ continue;
+ }
+ if (value->bExpr)
+ {
+ child = add_child(root, param, value->u.expr, scanner);
+ /* Clear the expression from the value once it is stored */
+ value->u.expr = NULL;
+ /* Check that the expression is valid */
+ if (!child)
+ {
+ return FALSE;
+ }
+ if (!set_expr_value_store(child, param, i, scanner))
+ {
+ return FALSE;
+ }
+ if (child->flags & SEL_DYNAMIC)
+ {
+ bDynamic = TRUE;
+ }
+ }
+ else
+ {
+ /* Value is not an expression */
+ switch (value->type)
+ {
+ case INT_VALUE:
+ if (value->u.i.i1 <= value->u.i.i2)
+ {
+ for (j = value->u.i.i1; j <= value->u.i.i2 && i < param->val.nr; ++j)
+ {
+ param->val.u.i[i++] = j;
+ }
+ if (j != value->u.i.i2 + 1)
+ {
+ _gmx_selparser_error(scanner, "extra values skipped");
+ }
+ }
+ else
+ {
+ for (j = value->u.i.i1; j >= value->u.i.i2 && i < param->val.nr; --j)
+ {
+ param->val.u.i[i++] = j;
+ }
+ if (j != value->u.i.i2 - 1)
+ {
+ _gmx_selparser_error(scanner, "extra values skipped");
+ }
+ }
+ --i;
+ break;
+ case REAL_VALUE:
+ if (value->u.r.r1 != value->u.r.r2)
+ {
+ _gmx_selparser_error(scanner, "real ranges not supported");
+ return FALSE;
+ }
+ param->val.u.r[i] = value->u.r.r1;
+ break;
+ case STR_VALUE:
+ param->val.u.s[i] = strdup(value->u.s);
+ break;
+ case POS_VALUE:
+ gmx_ana_pos_init_const(¶m->val.u.p[i], value->u.x);
+ break;
+ case NO_VALUE:
+ case GROUP_VALUE:
+ GMX_ERROR_NORET(gmx::eeInternalError,
+ "Invalid non-expression value");
+ return FALSE;
+ }
+ }
+ ++i;
+ value = value->next;
+ }
+ if (value != NULL)
+ {
+ _gmx_selparser_error(scanner, "extra values'");
+ return FALSE;
+ }
+ if (i < param->val.nr)
+ {
+ _gmx_selparser_error(scanner, "not enough values");
+ return FALSE;
+ }
+ if (!bDynamic)
+ {
+ param->flags &= ~SPAR_DYNAMIC;
+ }
+ if (param->nvalptr)
+ {
+ *param->nvalptr = param->val.nr;
+ }
+ param->nvalptr = NULL;
+
+ return TRUE;
+}
+
+/*! \brief
+ * Parses the values for a boolean parameter.
+ *
+ * \param[in] name Name by which the parameter was given.
+ * \param[in] nval Number of values in \p values.
+ * \param[in] values Pointer to the list of values.
+ * \param param Parameter to parse.
+ * \param[in] scanner Scanner data structure.
+ * \returns TRUE if the values were parsed successfully, FALSE otherwise.
+ */
+static gmx_bool
+parse_values_bool(const char *name, int nval, t_selexpr_value *values,
+ gmx_ana_selparam_t *param, void *scanner)
+{
+ gmx_bool bSetNo;
+ int len;
+
+ if (param->val.type != NO_VALUE)
+ {
+ GMX_ERROR_NORET(gmx::eeInternalError, "Invalid boolean parameter");
+ return FALSE;
+ }
+ if (nval > 1 || (values && values->type != INT_VALUE))
+ {
+ _gmx_selparser_error(scanner, "parameter takes only a yes/no/on/off/0/1 value");
+ return FALSE;
+ }
+
+ bSetNo = FALSE;
+ /* Check if the parameter name is given with a 'no' prefix */
+ len = strlen(name);
+ if (len > 2 && name[0] == 'n' && name[1] == 'o'
+ && strncmp(name+2, param->name, len-2) == 0)
+ {
+ bSetNo = TRUE;
+ }
+ if (bSetNo && nval > 0)
+ {
+ _gmx_selparser_error(scanner, "parameter 'no%s' should not have a value",
+ param->name);
+ return FALSE;
+ }
+ if (values && values->u.i.i1 == 0)
+ {
+ bSetNo = TRUE;
+ }
+
+ *param->val.u.b = bSetNo ? FALSE : TRUE;
+ return TRUE;
+}
+
+/*! \brief
+ * Parses the values for an enumeration parameter.
+ *
+ * \param[in] nval Number of values in \p values.
+ * \param[in] values Pointer to the list of values.
+ * \param param Parameter to parse.
+ * \param[in] scanner Scanner data structure.
+ * \returns TRUE if the values were parsed successfully, FALSE otherwise.
+ */
+static gmx_bool
+parse_values_enum(int nval, t_selexpr_value *values, gmx_ana_selparam_t *param,
+ void *scanner)
+{
+ int i, len, match;
+
+ if (nval != 1)
+ {
+ _gmx_selparser_error(scanner, "a single value is required");
+ return FALSE;
+ }
+ if (values->type != STR_VALUE || param->val.type != STR_VALUE)
+ {
+ GMX_ERROR_NORET(gmx::eeInternalError, "Invalid enum parameter");
+ return FALSE;
+ }
+ if (values->bExpr)
+ {
+ _gmx_selparser_error(scanner, "expression value for enumerated parameter not supported");
+ return FALSE;
+ }
+
+ len = strlen(values->u.s);
+ i = 1;
+ match = 0;
+ while (param->val.u.s[i] != NULL)
+ {
+ if (strncmp(values->u.s, param->val.u.s[i], len) == 0)
+ {
+ /* Check if there is a duplicate match */
+ if (match > 0)
+ {
+ _gmx_selparser_error(scanner, "ambiguous value");
+ return FALSE;
+ }
+ match = i;
+ }
+ ++i;
+ }
+ if (match == 0)
+ {
+ _gmx_selparser_error(scanner, "invalid value");
+ return FALSE;
+ }
+ param->val.u.s[0] = param->val.u.s[match];
+ return TRUE;
+}
+
+/*! \brief
+ * Replaces constant expressions with their values.
+ *
+ * \param[in,out] values First element in the value list to process.
+ */
+static void
+convert_const_values(t_selexpr_value *values)
+{
+ t_selexpr_value *val;
+
+ val = values;
+ while (val)
+ {
+ if (val->bExpr && val->u.expr->v.type != GROUP_VALUE &&
+ val->u.expr->type == SEL_CONST)
+ {
+ t_selelem *expr = val->u.expr;
+ val->bExpr = FALSE;
+ switch (expr->v.type)
+ {
+ case INT_VALUE:
+ val->u.i.i1 = val->u.i.i2 = expr->v.u.i[0];
+ break;
+ case REAL_VALUE:
+ val->u.r.r1 = val->u.r.r2 = expr->v.u.r[0];
+ break;
+ case STR_VALUE:
+ val->u.s = expr->v.u.s[0];
+ break;
+ case POS_VALUE:
+ copy_rvec(expr->v.u.p->x[0], val->u.x);
+ break;
+ default:
+ GMX_ERROR_NORET(gmx::eeInternalError,
+ "Unsupported value type");
+ break;
+ }
+ _gmx_selelem_free(expr);
+ }
+ val = val->next;
+ }
+}
+
+/*!
+ * \param pparams List of parameters from the selection parser.
+ * \param[in] nparam Number of parameters in \p params.
+ * \param params Array of parameters to parse.
+ * \param root Selection element to which child expressions are added.
+ * \param[in] scanner Scanner data structure.
+ * \returns TRUE if the parameters were parsed successfully, FALSE otherwise.
+ *
+ * Initializes the \p params array based on the parameters in \p pparams.
+ * See the documentation of \c gmx_ana_selparam_t for different options
+ * available for parsing.
+ *
+ * The list \p pparams and any associated values are freed after the parameters
+ * have been processed, no matter is there was an error or not.
+ */
+gmx_bool
+_gmx_sel_parse_params(t_selexpr_param *pparams, int nparam, gmx_ana_selparam_t *params,
+ t_selelem *root, void *scanner)
+{
+ gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
+ t_selexpr_param *pparam;
+ gmx_ana_selparam_t *oparam;
+ gmx_bool bOk, rc;
+ int i;
+
+ /* Check that the value pointers of SPAR_VARNUM parameters are NULL and
+ * that they are not NULL for other parameters */
+ bOk = TRUE;
+ for (i = 0; i < nparam; ++i)
+ {
+ std::string contextStr = gmx::formatString("In parameter '%s'", params[i].name);
+ gmx::MessageStringContext context(errors, contextStr);
+ if (params[i].val.type != POS_VALUE && (params[i].flags & (SPAR_VARNUM | SPAR_ATOMVAL)))
+ {
+ if (params[i].val.u.ptr != NULL)
+ {
+ _gmx_selparser_error(scanner, "value pointer is not NULL "
+ "although it should be for SPAR_VARNUM "
+ "and SPAR_ATOMVAL parameters");
+ }
+ if ((params[i].flags & SPAR_VARNUM)
+ && (params[i].flags & SPAR_DYNAMIC) && !params[i].nvalptr)
+ {
+ _gmx_selparser_error(scanner, "nvalptr is NULL but both "
+ "SPAR_VARNUM and SPAR_DYNAMIC are specified");
+ bOk = FALSE;
+ }
+ }
+ else
+ {
+ if (params[i].val.u.ptr == NULL)
+ {
+ _gmx_selparser_error(scanner, "value pointer is NULL");
+ bOk = FALSE;
+ }
+ }
+ }
+ if (!bOk)
+ {
+ _gmx_selexpr_free_params(pparams);
+ return FALSE;
+ }
+ /* Parse the parameters */
+ pparam = pparams;
+ i = 0;
+ while (pparam)
+ {
+ std::string contextStr;
+ /* Find the parameter and make some checks */
+ if (pparam->name != NULL)
+ {
+ contextStr = gmx::formatString("In parameter '%s'", pparam->name);
+ i = -1;
+ oparam = gmx_ana_selparam_find(pparam->name, nparam, params);
+ }
+ else if (i >= 0)
+ {
+ contextStr = gmx::formatString("In value %d", i + 1);
+ oparam = ¶ms[i];
+ if (oparam->name != NULL)
+ {
+ oparam = NULL;
+ _gmx_selparser_error(scanner, "too many NULL parameters provided");
+ bOk = FALSE;
+ pparam = pparam->next;
+ continue;
+ }
+ ++i;
+ }
+ else
+ {
+ _gmx_selparser_error(scanner, "all NULL parameters should appear in the beginning of the list");
+ bOk = FALSE;
+ pparam = pparam->next;
+ continue;
+ }
+ gmx::MessageStringContext context(errors, contextStr);
+ if (!oparam)
+ {
+ _gmx_selparser_error(scanner, "unknown parameter skipped");
+ bOk = FALSE;
+ goto next_param;
+ }
+ if (oparam->flags & SPAR_SET)
+ {
+ _gmx_selparser_error(scanner, "parameter set multiple times, extra values skipped");
+ bOk = FALSE;
+ goto next_param;
+ }
+ oparam->flags |= SPAR_SET;
+ /* Process the values for the parameter */
+ convert_const_values(pparam->value);
+ if (convert_values(pparam->value, oparam->val.type, scanner) != 0)
+ {
+ _gmx_selparser_error(scanner, "invalid value");
+ bOk = FALSE;
+ goto next_param;
+ }
+ if (oparam->val.type == NO_VALUE)
+ {
+ rc = parse_values_bool(pparam->name, pparam->nval, pparam->value, oparam, scanner);
+ }
+ else if (oparam->flags & SPAR_RANGES)
+ {
+ rc = parse_values_range(pparam->nval, pparam->value, oparam, scanner);
+ }
+ else if (oparam->flags & SPAR_VARNUM)
+ {
+ if (pparam->nval == 1 && pparam->value->bExpr)
+ {
+ rc = parse_values_varnum_expr(pparam->nval, pparam->value, oparam, root, scanner);
+ }
+ else
+ {
+ rc = parse_values_varnum(pparam->nval, pparam->value, oparam, root, scanner);
+ }
+ }
+ else if (oparam->flags & SPAR_ENUMVAL)
+ {
+ rc = parse_values_enum(pparam->nval, pparam->value, oparam, scanner);
+ }
+ else
+ {
+ rc = parse_values_std(pparam->nval, pparam->value, oparam, root, scanner);
+ }
+ if (!rc)
+ {
+ bOk = FALSE;
+ }
+ /* Advance to the next parameter */
+next_param:
+ pparam = pparam->next;
+ }
+ /* Check that all required parameters are present */
+ for (i = 0; i < nparam; ++i)
+ {
+ if (!(params[i].flags & SPAR_OPTIONAL) && !(params[i].flags & SPAR_SET))
+ {
+ _gmx_selparser_error(scanner, "required parameter '%s' not specified", params[i].name);
+ bOk = FALSE;
+ }
+ }
+
+ _gmx_selexpr_free_params(pparams);
+ return bOk;
+}
--- /dev/null
- /** Sets the COM/COG data for the \p insolidangle selection method. */
- static void
- set_comg_insolidangle(gmx_ana_pos_t *pos, void *data);
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2009, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ */
+/*! \page page_module_selection_insolidangle Selection method: insolidangle
+ *
+ * This method selects a subset of particles that are located in a solid
+ * angle defined by a center and a set of points.
+ * The solid angle is constructed as a union of small cones whose axis
+ * goes through the center and a point.
+ * So there's such a cone for each position, and a
+ * point is in the solid angle if it lies within any of these cones.
+ * The width of the cones can be adjusted.
+ *
+ * \internal
+ *
+ * The method is implemented by partitioning the surface of the unit sphere
+ * into bins using the polar coordinates \f$(\theta, \phi)\f$.
+ * The partitioning is always uniform in the zenith angle \f$\theta\f$,
+ * while the partitioning in the azimuthal angle \f$\phi\f$ varies.
+ * For each reference point, the unit vector from the center to the point
+ * is constructed, and it is stored in all the bins that overlap with the
+ * cone defined by the point.
+ * Bins that are completely covered by a single cone are marked as such.
+ * Checking whether a point is in the solid angle is then straightforward
+ * with this data structure: one finds the bin that corresponds to the point,
+ * and checks whether the bin is completely covered. If it is not, one
+ * additionally needs to check whether it is within the specified cutoff of
+ * any of the stored points.
+ *
+ * The above construction gives quite a lot of flexibility for constructing
+ * the bins without modifying the rest of the code.
+ * The current (quite inefficient) implementation is discussed below, but
+ * it should be optimized to get the most out of the code.
+ *
+ * The current way of constructing the bins constructs the boundaries
+ * statically: the bin size in the zenith direction is set to approximately
+ * half the angle cutoff, and the bins in the azimuthal direction have
+ * sizes such that the shortest edge of the bin is approximately equal to
+ * half the angle cutoff (for the regions close to the poles, a single bin
+ * is used).
+ * Each reference point is then added to the bins as follows:
+ * -# Find the zenith angle range that is spanned by the cone centered at the
+ * point (this is simple addition/subtraction).
+ * -# Calculate the maximal span of the cone in the azimuthal direction using
+ * the formula
+ * \f[\sin \Delta \phi_{max} = \frac{\sin \alpha}{\sin \theta}\f]
+ * (a sine formula in spherical coordinates),
+ * where \f$\alpha\f$ is the width of the cone and \f$\theta\f$ is the
+ * zenith angle of the cone center.
+ * Similarly, the zenith angle at which this extent is achieved is
+ * calculated using
+ * \f[\cos \theta_{max} = \frac{\cos \theta}{\cos \alpha}\f]
+ * (Pythagoras's theorem in spherical coordinates).
+ * -# For each zenith angle bin that is at least partially covered by the
+ * cone, calculate the span of the cone at the edges using
+ * \f[\sin^2 \frac{\Delta \phi}{2} = \frac{\sin^2 \frac{\alpha}{2} - \sin^2 \frac{\theta - \theta'}{2}}{\sin \theta \sin \theta'}\f]
+ * (distance in spherical geometry),
+ * where \f$\theta'\f$ is the zenith angle of the bin edge.
+ * -# Using the values calculated above, loop through the azimuthal bins that
+ * are partially or completely covered by the cone and update them.
+ *
+ * The total solid angle (for covered fraction calculations) is estimated by
+ * taking the total area of completely covered bins plus
+ * half the area of partially covered bins.
+ * The second one is an approximation, but should give reasonable estimates
+ * for the averages as well as in cases where the bin size is small.
+ */
+/*! \internal \file
+ * \brief
+ * Implements the \ref sm_insolidangle "insolidangle" selection method.
+ *
+ * \todo
+ * The implementation could be optimized quite a bit.
+ *
+ * \todo
+ * Move the covered fraction stuff somewhere else and make it more generic
+ * (along the lines it is handled in selection.h and trajana.h in the old C
+ * API).
+ *
+ * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \ingroup module_selection
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include <macros.h>
+#include <maths.h>
+#include <pbc.h>
+#include <physics.h>
+#include <smalloc.h>
+#include <vec.h>
+
+// FIXME: Should really be in the beginning, but causes compilation errors
+#include <algorithm>
+
+#include "gromacs/fatalerror/exceptions.h"
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selmethod.h"
+
+#include "selelem.h"
+
+using std::min;
+using std::max;
+
+/*! \internal \brief
+ * Internal data structure for the \p insolidangle selection method.
+ *
+ * \see \c t_partition
+ */
+typedef struct
+{
+ /** Left edge of the partition. */
+ real left;
+ /** Bin index corresponding to this partition. */
+ int bin;
+} t_partition_item;
+
+/*! \internal \brief
+ * Internal data structure for the \p insolidangle selection method.
+ *
+ * Describes the surface partitioning within one slice along the zenith angle.
+ * The slice from azimuthal angle \p p[i].left to \p p[i+1].left belongs to
+ * bin \p p[i].bin.
+ */
+typedef struct
+{
+ /** Number of partition items (\p p contains \p n+1 items). */
+ int n;
+ /** Array of partition edges and corresponding bins. */
+ t_partition_item *p;
+} t_partition;
+
+/*! \internal \brief
+ * Internal data structure for the \p insolidangle selection method.
+ *
+ * Contains the reference points that partially cover a certain region on the
+ * surface of the unit sphere.
+ * If \p n is -1, the whole region described by the bin is covered.
+ */
+typedef struct
+{
+ /** Number of points in the array \p x, -1 if whole bin covered. */
+ int n;
+ /** Number of elements allocated for \p x. */
+ int n_alloc;
+ /** Array of points that partially cover the bin. */
+ rvec *x;
+} t_spheresurfacebin;
+
+/*! \internal \brief
+ * Data structure for the \p insolidangle selection method.
+ *
+ * All angle values are in the units of radians.
+ */
+typedef struct
+{
+ /** Center of the solid angle. */
+ gmx_ana_pos_t center;
+ /** Positions that span the solid angle. */
+ gmx_ana_pos_t span;
+ /** Cutoff angle. */
+ real angcut;
+ /** Estimate of the covered fraction. */
+ real cfrac;
+
+ /** Cutoff for the cosine (equals cos(angcut)). */
+ real distccut;
+ /** Bin size to be used as the target bin size when constructing the bins. */
+ real targetbinsize;
+
+ /** Number of bins in the \p tbin array. */
+ int ntbins;
+ /** Size of one bin in the zenith angle direction. */
+ real tbinsize;
+ /** Array of zenith angle slices. */
+ t_partition *tbin;
+ /** Number of elements allocated for the \p bin array. */
+ int maxbins;
+ /** Number of elements used in the \p bin array. */
+ int nbins;
+ /** Array of individual bins. */
+ t_spheresurfacebin *bin;
+} t_methoddata_insolidangle;
+
+/** Allocates data for the \p insolidangle selection method. */
+static void *
+init_data_insolidangle(int npar, gmx_ana_selparam_t *param);
+/** Initializes the \p insolidangle selection method. */
+static void
+init_insolidangle(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+/** Frees the data allocated for the \p insolidangle selection method. */
+static void
+free_data_insolidangle(void *data);
+/** Initializes the evaluation of the \p insolidangle selection method for a frame. */
+static void
+init_frame_insolidangle(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
+/** Internal helper function for evaluate_insolidangle(). */
+static gmx_bool
+accept_insolidangle(rvec x, t_pbc *pbc, void *data);
+/** Evaluates the \p insolidangle selection method. */
+static void
+evaluate_insolidangle(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+ gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
+
+/** Calculates the distance between unit vectors. */
+static real
+sph_distc(rvec x1, rvec x2);
+/** Does a binary search on a \p t_partition to find a bin for a value. */
+static int
+find_partition_bin(t_partition *p, real value);
+/** Finds a bin that corresponds to a location on the unit sphere surface. */
+static int
+find_surface_bin(t_methoddata_insolidangle *surf, rvec x);
+/** Clears/initializes the bins on the unit sphere surface. */
+static void
+clear_surface_points(t_methoddata_insolidangle *surf);
+/** Frees memory allocated for storing the reference points in the surface bins. */
+static void
+free_surface_points(t_methoddata_insolidangle *surf);
+/** Adds a reference point to a given bin. */
+static void
+add_surface_point(t_methoddata_insolidangle *surf, int tbin, int pbin, rvec x);
+/** Marks a bin as completely covered. */
+static void
+mark_surface_covered(t_methoddata_insolidangle *surf, int tbin, int pbin);
+/** Helper function for store_surface_point() to update a single zenith angle bin. */
+static void
+update_surface_bin(t_methoddata_insolidangle *surf, int tbin,
+ real phi, real pdelta1, real pdelta2, real pdeltamax,
+ rvec x);
+/** Adds a single reference point and updates the surface bins. */
+static void
+store_surface_point(t_methoddata_insolidangle *surf, rvec x);
+/** Optimizes the surface bins for faster searching. */
+static void
+optimize_surface_points(t_methoddata_insolidangle *surf);
+/** Estimates the area covered by the reference cones. */
+static real
+estimate_covered_fraction(t_methoddata_insolidangle *surf);
+/** Checks whether a point lies within a solid angle. */
+static gmx_bool
+is_surface_covered(t_methoddata_insolidangle *surf, rvec x);
+
+/** Parameters for the \p insolidangle selection method. */
+static gmx_ana_selparam_t smparams_insolidangle[] = {
+ {"center", {POS_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
+ {"span", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
+ {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
+};
+
+/** Help text for the \p insolidangle selection method. */
+static const char *help_insolidangle[] = {
+ "SELECTING ATOMS IN A SOLID ANGLE[PAR]",
+
+ "[TT]insolidangle center POS span POS_EXPR [cutoff REAL][tt][PAR]",
+
+ "This keyword selects atoms that are within [TT]REAL[tt] degrees",
+ "(default=5) of any position in [TT]POS_EXPR[tt] as seen from [TT]POS[tt]",
+ "a position expression that evaluates to a single position), i.e., atoms",
+ "in the solid angle spanned by the positions in [TT]POS_EXPR[tt] and",
+ "centered at [TT]POS[tt].[PAR]"
+
+ "Technically, the solid angle is constructed as a union of small cones",
+ "whose tip is at [TT]POS[tt] and the axis goes through a point in",
+ "[TT]POS_EXPR[tt]. There is such a cone for each position in",
+ "[TT]POS_EXPR[tt], and point is in the solid angle if it lies within any",
+ "of these cones. The cutoff determines the width of the cones.",
+};
+
+/** \internal Selection method data for the \p insolidangle method. */
+gmx_ana_selmethod_t sm_insolidangle = {
+ "insolidangle", GROUP_VALUE, SMETH_DYNAMIC,
+ asize(smparams_insolidangle), smparams_insolidangle,
+ &init_data_insolidangle,
+ NULL,
+ &init_insolidangle,
+ NULL,
+ &free_data_insolidangle,
+ &init_frame_insolidangle,
+ NULL,
+ &evaluate_insolidangle,
+ {"insolidangle center POS span POS_EXPR [cutoff REAL]",
+ asize(help_insolidangle), help_insolidangle},
+};
+
+/*!
+ * \param[in] npar Not used (should be 3).
+ * \param[in,out] param Method parameters (should point to
+ * \ref smparams_insolidangle).
+ * \returns Pointer to the allocated data (\ref t_methoddata_insolidangle).
+ *
+ * Allocates memory for a \ref t_methoddata_insolidangle structure and
+ * initializes the parameter as follows:
+ * - \p center defines the value for t_methoddata_insolidangle::center.
+ * - \p span defines the value for t_methoddata_insolidangle::span.
+ * - \p cutoff defines the value for t_methoddata_insolidangle::angcut.
+ */
+static void *
+init_data_insolidangle(int npar, gmx_ana_selparam_t *param)
+{
+ t_methoddata_insolidangle *data;
+
+ snew(data, 1);
+ data->angcut = 5.0;
+ param[0].val.u.p = &data->center;
+ param[1].val.u.p = &data->span;
+ param[2].val.u.r = &data->angcut;
+ return data;
+}
+
+/*!
+ * \param top Not used.
+ * \param npar Not used.
+ * \param param Not used.
+ * \param data Pointer to \ref t_methoddata_insolidangle to initialize.
+ * \returns 0 on success, -1 on failure.
+ *
+ * Converts t_methoddata_insolidangle::angcut to radians and allocates
+ * and allocates memory for the bins used during the evaluation.
+ */
+static void
+init_insolidangle(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+{
+ t_methoddata_insolidangle *surf = (t_methoddata_insolidangle *)data;
+ int i, c;
+
+ if (surf->angcut <= 0)
+ {
+ GMX_THROW(gmx::InvalidInputError("Angle cutoff should be > 0"));
+ }
+
+ surf->angcut *= DEG2RAD;
+
+ surf->distccut = -cos(surf->angcut);
+ surf->targetbinsize = surf->angcut / 2;
+ surf->ntbins = (int) (M_PI / surf->targetbinsize);
+ surf->tbinsize = (180.0 / surf->ntbins)*DEG2RAD;
+
+ snew(surf->tbin, (int)(M_PI/surf->tbinsize) + 1);
+ surf->maxbins = 0;
+ for (i = 0; i < surf->ntbins; ++i)
+ {
+ c = max(sin(surf->tbinsize*i), sin(surf->tbinsize*(i+1)))
+ * M_2PI / surf->targetbinsize + 1;
+ snew(surf->tbin[i].p, c+1);
+ surf->maxbins += c;
+ }
+ surf->nbins = 0;
+ snew(surf->bin, surf->maxbins);
+}
+
+/*!
+ * \param data Data to free (should point to a \ref t_methoddata_insolidangle).
+ *
+ * Frees the memory allocated for \c t_methoddata_insolidangle::center and
+ * \c t_methoddata_insolidangle::span, as well as the memory for the internal
+ * bin structure.
+ */
+static void
+free_data_insolidangle(void *data)
+{
+ t_methoddata_insolidangle *d = (t_methoddata_insolidangle *)data;
+ int i;
+
+ if (d->tbin)
+ {
+ for (i = 0; i < d->ntbins; ++i)
+ {
+ sfree(d->tbin[i].p);
+ }
+ sfree(d->tbin);
+ }
+ free_surface_points(d);
+ sfree(d->bin);
+}
+
+/*!
+ * \param[in] top Not used.
+ * \param[in] fr Current frame.
+ * \param[in] pbc PBC structure.
+ * \param data Should point to a \ref t_methoddata_insolidangle.
+ *
+ * Creates a lookup structure that enables fast queries of whether a point
+ * is within the solid angle or not.
+ */
+static void
+init_frame_insolidangle(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data)
+{
+ t_methoddata_insolidangle *d = (t_methoddata_insolidangle *)data;
+ rvec dx;
+ int i;
+
+ free_surface_points(d);
+ clear_surface_points(d);
+ for (i = 0; i < d->span.nr; ++i)
+ {
+ if (pbc)
+ {
+ pbc_dx(pbc, d->span.x[i], d->center.x[0], dx);
+ }
+ else
+ {
+ rvec_sub(d->span.x[i], d->center.x[0], dx);
+ }
+ unitv(dx, dx);
+ store_surface_point(d, dx);
+ }
+ optimize_surface_points(d);
+ d->cfrac = -1;
+}
+
+/*!
+ * \param[in] x Test point.
+ * \param[in] pbc PBC data (if NULL, no PBC are used).
+ * \param[in] data Pointer to a \c t_methoddata_insolidangle data structure.
+ * \returns TRUE if \p x is within the solid angle, FALSE otherwise.
+ */
+static gmx_bool
+accept_insolidangle(rvec x, t_pbc *pbc, void *data)
+{
+ t_methoddata_insolidangle *d = (t_methoddata_insolidangle *)data;
+ rvec dx;
+
+ if (pbc)
+ {
+ pbc_dx(pbc, x, d->center.x[0], dx);
+ }
+ else
+ {
+ rvec_sub(x, d->center.x[0], dx);
+ }
+ unitv(dx, dx);
+ return is_surface_covered(d, dx);
+}
+
+/*!
+ * See sel_updatefunc() for description of the parameters.
+ * \p data should point to a \c t_methoddata_insolidangle.
+ *
+ * Calculates which atoms in \p g are within the solid angle spanned by
+ * \c t_methoddata_insolidangle::span and centered at
+ * \c t_methoddata_insolidangle::center, and stores the result in \p out->u.g.
+ */
+static void
+evaluate_insolidangle(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+ gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
+{
+ t_methoddata_insolidangle *d = (t_methoddata_insolidangle *)data;
+ int b;
+
+ out->u.g->isize = 0;
+ for (b = 0; b < pos->nr; ++b)
+ {
+ if (accept_insolidangle(pos->x[b], pbc, data))
+ {
+ gmx_ana_pos_append(NULL, out->u.g, pos, b, 0);
+ }
+ }
+}
+
+/*!
+ * \param[in] sel Selection element to query.
+ * \returns TRUE if the covered fraction can be estimated for \p sel with
+ * _gmx_selelem_estimate_coverfrac(), FALSE otherwise.
+ */
+gmx_bool
+_gmx_selelem_can_estimate_cover(t_selelem *sel)
+{
+ t_selelem *child;
+ gmx_bool bFound;
+ gmx_bool bDynFound;
+
+ if (sel->type == SEL_BOOLEAN && sel->u.boolt == BOOL_OR)
+ {
+ return FALSE;
+ }
+ bFound = FALSE;
+ bDynFound = FALSE;
+ child = sel->child;
+ while (child)
+ {
+ if (child->type == SEL_EXPRESSION)
+ {
+ if (child->u.expr.method->name == sm_insolidangle.name)
+ {
+ if (bFound || bDynFound)
+ {
+ return FALSE;
+ }
+ bFound = TRUE;
+ }
+ else if (child->u.expr.method
+ && (child->u.expr.method->flags & SMETH_DYNAMIC))
+ {
+ if (bFound)
+ {
+ return FALSE;
+ }
+ bDynFound = TRUE;
+ }
+ }
+ else if (!_gmx_selelem_can_estimate_cover(child))
+ {
+ return FALSE;
+ }
+ child = child->next;
+ }
+ return TRUE;
+}
+
+/*!
+ * \param[in] sel Selection for which the fraction should be calculated.
+ * \returns Fraction of angles covered by the selection (between zero and one).
+ *
+ * The return value is undefined if _gmx_selelem_can_estimate_cover() returns
+ * FALSE.
+ * Should be called after gmx_ana_evaluate_selections() has been called for the
+ * frame.
+ */
+real
+_gmx_selelem_estimate_coverfrac(t_selelem *sel)
+{
+ t_selelem *child;
+ real cfrac;
+
+ if (sel->type == SEL_EXPRESSION && sel->u.expr.method->name == sm_insolidangle.name)
+ {
+ t_methoddata_insolidangle *d = (t_methoddata_insolidangle *)sel->u.expr.mdata;
+ if (d->cfrac < 0)
+ {
+ d->cfrac = estimate_covered_fraction(d);
+ }
+ return d->cfrac;
+ }
+ if (sel->type == SEL_BOOLEAN && sel->u.boolt == BOOL_NOT)
+ {
+ cfrac = _gmx_selelem_estimate_coverfrac(sel->child);
+ if (cfrac < 1.0)
+ {
+ return 1 - cfrac;
+ }
+ return 1;
+ }
+
+ /* Here, we assume that the selection is simple enough */
+ child = sel->child;
+ while (child)
+ {
+ cfrac = _gmx_selelem_estimate_coverfrac(child);
+ if (cfrac < 1.0)
+ {
+ return cfrac;
+ }
+ child = child->next;
+ }
+ return 1.0;
+}
+
+/*!
+ * \param[in] x1 Unit vector 1.
+ * \param[in] x2 Unit vector 2.
+ * \returns Minus the dot product of \p x1 and \p x2.
+ *
+ * This function is used internally to calculate the distance between the
+ * unit vectors \p x1 and \p x2 to find out whether \p x2 is within the
+ * cone centered at \p x1. Currently, the cosine of the angle is used
+ * for efficiency, and the minus is there to make it behave like a normal
+ * distance (larger values mean longer distances).
+ */
+static real
+sph_distc(rvec x1, rvec x2)
+{
+ return -iprod(x1, x2);
+}
+
+/*!
+ * \param[in] p Partition to search.
+ * \param[in] value Value to search for.
+ * \returns The partition index in \p p that contains \p value.
+ *
+ * If \p value is outside the range of \p p, the first/last index is returned.
+ * Otherwise, the return value \c i satisfies \c p->p[i].left<=value and
+ * \c p->p[i+1].left>value
+ */
+static int
+find_partition_bin(t_partition *p, real value)
+{
+ int pmin, pmax, pbin;
+
+ /* Binary search the partition */
+ pmin = 0; pmax = p->n;
+ while (pmax > pmin + 1)
+ {
+ pbin = pmin + (pmax - pmin) / 2;
+ if (p->p[pbin].left <= value)
+ {
+ pmin = pbin;
+ }
+ else
+ {
+ pmax = pbin;
+ }
+ }
+ pbin = pmin;
+ return pbin;
+}
+
+/*!
+ * \param[in] surf Surface data structure to search.
+ * \param[in] x Unit vector to find.
+ * \returns The bin index that contains \p x.
+ *
+ * The return value is an index to the \p surf->bin array.
+ */
+static int
+find_surface_bin(t_methoddata_insolidangle *surf, rvec x)
+{
+ real theta, phi;
+ int tbin, pbin;
+
+ theta = acos(x[ZZ]);
+ phi = atan2(x[YY], x[XX]);
+ tbin = floor(theta / surf->tbinsize);
+ if (tbin >= surf->ntbins)
+ {
+ tbin = surf->ntbins - 1;
+ }
+ pbin = find_partition_bin(&surf->tbin[tbin], phi);
+ return surf->tbin[tbin].p[pbin].bin;
+}
+
+/*!
+ * \param[in,out] surf Surface data structure.
+ *
+ * Clears the reference points from the bins and (re)initializes the edges
+ * of the azimuthal bins.
+ */
+static void
+clear_surface_points(t_methoddata_insolidangle *surf)
+{
+ int i, j, c;
+
+ surf->nbins = 0;
+ for (i = 0; i < surf->ntbins; ++i)
+ {
+ c = min(sin(surf->tbinsize*i), sin(surf->tbinsize*(i+1)))
+ * M_2PI / surf->targetbinsize + 1;
+ if (c <= 0)
+ {
+ c = 1;
+ }
+ surf->tbin[i].n = c;
+ for (j = 0; j < c; ++j)
+ {
+ surf->tbin[i].p[j].left = -M_PI + j*M_2PI/c - 0.0001;
+ surf->tbin[i].p[j].bin = surf->nbins;
+ surf->bin[surf->nbins].n = 0;
+ surf->nbins++;
+ }
+ surf->tbin[i].p[c].left = M_PI + 0.0001;
+ surf->tbin[i].p[c].bin = -1;
+ }
+}
+
+/*!
+ * \param[in,out] surf Surface data structure.
+ */
+static void
+free_surface_points(t_methoddata_insolidangle *surf)
+{
+ int i;
+
+ for (i = 0; i < surf->nbins; ++i)
+ {
+ if (surf->bin[i].x)
+ {
+ sfree(surf->bin[i].x);
+ }
+ surf->bin[i].n_alloc = 0;
+ surf->bin[i].x = NULL;
+ }
+}
+
+/*!
+ * \param[in,out] surf Surface data structure.
+ * \param[in] tbin Bin number in the zenith angle direction.
+ * \param[in] pbin Bin number in the azimuthal angle direction.
+ * \param[in] x Point to store.
+ */
+static void
+add_surface_point(t_methoddata_insolidangle *surf, int tbin, int pbin, rvec x)
+{
+ int bin;
+
+ bin = surf->tbin[tbin].p[pbin].bin;
+ /* Return if bin is already completely covered */
+ if (surf->bin[bin].n == -1)
+ return;
+ /* Allocate more space if necessary */
+ if (surf->bin[bin].n == surf->bin[bin].n_alloc) {
+ surf->bin[bin].n_alloc += 10;
+ srenew(surf->bin[bin].x, surf->bin[bin].n_alloc);
+ }
+ /* Add the point to the bin */
+ copy_rvec(x, surf->bin[bin].x[surf->bin[bin].n]);
+ ++surf->bin[bin].n;
+}
+
+/*!
+ * \param[in,out] surf Surface data structure.
+ * \param[in] tbin Bin number in the zenith angle direction.
+ * \param[in] pbin Bin number in the azimuthal angle direction.
+ */
+static void
+mark_surface_covered(t_methoddata_insolidangle *surf, int tbin, int pbin)
+{
+ int bin;
+
+ bin = surf->tbin[tbin].p[pbin].bin;
+ surf->bin[bin].n = -1;
+}
+
+/*!
+ * \param[in,out] surf Surface data structure.
+ * \param[in] tbin Bin number in the zenith angle direction.
+ * \param[in] phi Azimuthal angle of \p x.
+ * \param[in] pdelta1 Width of the cone at the lower edge of \p tbin.
+ * \param[in] pdelta2 Width of the cone at the uppper edge of \p tbin.
+ * \param[in] pdeltamax Max. width of the cone inside \p tbin.
+ * \param[in] x Point to store (should have unit length).
+ */
+static void
+update_surface_bin(t_methoddata_insolidangle *surf, int tbin,
+ real phi, real pdelta1, real pdelta2, real pdeltamax,
+ rvec x)
+{
+ real pdelta, phi1, phi2;
+ int pbin1, pbin2, pbin;
+
+ /* Find the edges of the bins affected */
+ pdelta = max(max(pdelta1, pdelta2), pdeltamax);
+ phi1 = phi - pdelta;
+ if (phi1 < -M_PI)
+ {
+ phi1 += M_2PI;
+ }
+ phi2 = phi + pdelta;
+ if (phi2 > M_PI)
+ {
+ phi2 -= M_2PI;
+ }
+ pbin1 = find_partition_bin(&surf->tbin[tbin], phi1);
+ pbin2 = find_partition_bin(&surf->tbin[tbin], phi2);
+ /* Find the edges of completely covered region */
+ pdelta = min(pdelta1, pdelta2);
+ phi1 = phi - pdelta;
+ if (phi1 < -M_PI)
+ {
+ phi1 += M_2PI;
+ }
+ phi2 = phi + pdelta;
+ /* Loop over all affected bins */
+ pbin = pbin1;
+ do
+ {
+ /* Wrap bin around if end reached */
+ if (pbin == surf->tbin[tbin].n)
+ {
+ pbin = 0;
+ phi1 -= M_2PI;
+ phi2 -= M_2PI;
+ }
+ /* Check if bin is completely covered and update */
+ if (surf->tbin[tbin].p[pbin].left >= phi1
+ && surf->tbin[tbin].p[pbin+1].left <= phi2)
+ {
+ mark_surface_covered(surf, tbin, pbin);
+ }
+ else
+ {
+ add_surface_point(surf, tbin, pbin, x);
+ }
+ }
+ while (pbin++ != pbin2); /* Loop including pbin2 */
+}
+
+/*!
+ * \param[in,out] surf Surface data structure.
+ * \param[in] x Point to store (should have unit length).
+ *
+ * Finds all the bins covered by the cone centered at \p x and calls
+ * update_surface_bin() to update them.
+ */
+static void
+store_surface_point(t_methoddata_insolidangle *surf, rvec x)
+{
+ real theta, phi;
+ real pdeltamax, tmax;
+ real theta1, theta2, pdelta1, pdelta2;
+ int tbin, pbin, bin;
+
+ theta = acos(x[ZZ]);
+ phi = atan2(x[YY], x[XX]);
+ /* Find the maximum extent in the phi direction */
+ if (theta <= surf->angcut)
+ {
+ pdeltamax = M_PI;
+ tmax = 0;
+ }
+ else if (theta >= M_PI - surf->angcut)
+ {
+ pdeltamax = M_PI;
+ tmax = M_PI;
+ }
+ else
+ {
+ pdeltamax = asin(sin(surf->angcut) / sin(theta));
+ tmax = acos(cos(theta) / cos(surf->angcut));
+ }
+ /* Find the first affected bin */
+ tbin = max(floor((theta - surf->angcut) / surf->tbinsize), 0.0);
+ theta1 = tbin * surf->tbinsize;
+ if (theta1 < theta - surf->angcut)
+ {
+ pdelta1 = 0;
+ }
+ else
+ {
+ pdelta1 = M_PI;
+ }
+ /* Loop through all affected bins */
+ while (tbin < ceil((theta + surf->angcut) / surf->tbinsize)
+ && tbin < surf->ntbins)
+ {
+ /* Calculate the next boundaries */
+ theta2 = (tbin+1) * surf->tbinsize;
+ if (theta2 > theta + surf->angcut)
+ {
+ pdelta2 = 0;
+ }
+ else if (tbin == surf->ntbins - 1)
+ {
+ pdelta2 = M_PI;
+ }
+ else
+ {
+ pdelta2 = 2*asin(sqrt(
+ (sqr(sin(surf->angcut/2)) - sqr(sin((theta2-theta)/2))) /
+ (sin(theta) * sin(theta2))));
+ }
+ /* Update the bin */
+ if (tmax >= theta1 && tmax <= theta2)
+ {
+ update_surface_bin(surf, tbin, phi, pdelta1, pdelta2, pdeltamax, x);
+ }
+ else
+ {
+ update_surface_bin(surf, tbin, phi, pdelta1, pdelta2, 0, x);
+ }
+ /* Next bin */
+ theta1 = theta2;
+ pdelta1 = pdelta2;
+ ++tbin;
+ }
+}
+
+/*!
+ * \param[in,out] surf Surface data structure.
+ *
+ * Currently, this function does nothing.
+ */
+static void
+optimize_surface_points(t_methoddata_insolidangle *surf)
+{
+ /* TODO: Implement */
+}
+
+/*!
+ * \param[in] surf Surface data structure.
+ * \returns An estimate for the area covered by the reference points.
+ */
+static real
+estimate_covered_fraction(t_methoddata_insolidangle *surf)
+{
+ int t, p, n;
+ real cfrac, tfrac, pfrac;
+
+ cfrac = 0.0;
+ for (t = 0; t < surf->ntbins; ++t)
+ {
+ tfrac = cos(t * surf->tbinsize) - cos((t+1) * surf->tbinsize);
+ for (p = 0; p < surf->tbin[t].n; ++p)
+ {
+ pfrac = surf->tbin[t].p[p+1].left - surf->tbin[t].p[p].left;
+ n = surf->bin[surf->tbin[t].p[p].bin].n;
+ if (n == -1) /* Bin completely covered */
+ {
+ cfrac += tfrac * pfrac;
+ }
+ else if (n > 0) /* Bin partially covered */
+ {
+ cfrac += tfrac * pfrac / 2; /* A rough estimate */
+ }
+ }
+ }
+ return cfrac / (4*M_PI);
+}
+
+/*!
+ * \param[in] surf Surface data structure to search.
+ * \param[in] x Unit vector to check.
+ * \returns TRUE if \p x is within the solid angle, FALSE otherwise.
+ */
+static gmx_bool
+is_surface_covered(t_methoddata_insolidangle *surf, rvec x)
+{
+ int bin, i;
+
+ bin = find_surface_bin(surf, x);
+ /* Check for completely covered bin */
+ if (surf->bin[bin].n == -1)
+ {
+ return TRUE;
+ }
+ /* Check each point that partially covers the bin */
+ for (i = 0; i < surf->bin[bin].n; ++i)
+ {
+ if (sph_distc(x, surf->bin[bin].x[i]) < surf->distccut)
+ {
+ return TRUE;
+ }
+ }
+ return FALSE;
+}
--- /dev/null
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "typedefs.h"
+#include "macros.h"
+#include "copyrite.h"
+#include "main.h"
+#include "statutil.h"
+#include "smalloc.h"
+#include "futil.h"
+#include "smalloc.h"
+#include "edsam.h"
+#include "mdrun.h"
+#include "xmdrun.h"
+#include "checkpoint.h"
+#ifdef GMX_THREADS
+#include "thread_mpi.h"
+#endif
+
+/* afm stuf */
+#include "pull.h"
+
+int main(int argc,char *argv[])
+{
+ const char *desc[] = {
+ #ifdef GMX_OPENMM
+ "This is an experimental release of GROMACS for accelerated",
+ "Molecular Dynamics simulations on GPU processors. Support is provided",
+ "by the OpenMM library (https://simtk.org/home/openmm).[PAR]",
+ "*Warning*[BR]",
+ "This release is targeted at developers and advanced users and",
+ "care should be taken before production use. The following should be",
+ "noted before using the program:[PAR]",
+ " * The current release runs only on modern nVidia GPU hardware with CUDA support.",
+ "Make sure that the necessary CUDA drivers and libraries for your operating system",
+ "are already installed. The CUDA SDK also should be installed in order to compile",
+ "the program from source (http://www.nvidia.com/object/cuda_home.html).[PAR]",
+ " * Multiple GPU cards are not supported.[PAR]",
+ " * Only a small subset of the GROMACS features and options are supported on the GPUs.",
+ "See below for a detailed list.[PAR]",
+ " * Consumer level GPU cards are known to often have problems with faulty memory.",
+ "It is recommended that a full memory check of the cards is done at least once",
+ "(for example, using the memtest=full option).",
+ "A partial memory check (for example, memtest=15) before and",
+ "after the simulation run would help spot",
+ "problems resulting from processor overheating.[PAR]",
+ " * The maximum size of the simulated systems depends on the available",
+ "GPU memory,for example, a GTX280 with 1GB memory has been tested with systems",
+ "of up to about 100,000 atoms.[PAR]",
+ " * In order to take a full advantage of the GPU platform features, many algorithms",
+ "have been implemented in a very different way than they are on the CPUs.",
+ "Therefore numercal correspondence between properties of the state of",
+ "simulated systems should not be expected. Moreover, the values will likely vary",
+ "when simulations are done on different GPU hardware.[PAR]",
+ " * Frequent retrieval of system state information such as",
+ "trajectory coordinates and energies can greatly influence the performance",
+ "of the program due to slow CPU<->GPU memory transfer speed.[PAR]",
+ " * MD algorithms are complex, and although the Gromacs code is highly tuned for them,",
+ "they often do not translate very well onto the streaming architetures.",
+ "Realistic expectations about the achievable speed-up from test with GTX280:",
+ "For small protein systems in implicit solvent using all-vs-all kernels the acceleration",
+ "can be as high as 20 times, but in most other setups involving cutoffs and PME the",
+ "acceleration is usually only ~4 times relative to a 3GHz CPU.[PAR]",
+ "Supported features:[PAR]",
+ " * Integrators: md/md-vv/md-vv-avek, sd/sd1 and bd.\n",
+ " * Long-range interactions (option coulombtype): Reaction-Field, Ewald, PME, and cut-off (for Implicit Solvent only)\n",
+ " * Temperature control: Supported only with the md/md-vv/md-vv-avek, sd/sd1 and bd integrators.\n",
+ " * Pressure control: Supported.\n",
+ " * Implicit solvent: Supported.\n",
+ "A detailed description can be found on the GROMACS website:\n",
+ "http://www.gromacs.org/gpu[PAR]",
+/* From the original mdrun documentaion */
+ "The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
+ "and distributes the topology over nodes if needed.",
+ "[TT]mdrun[tt] produces at least four output files.",
+ "A single log file ([TT]-g[tt]) is written, unless the option",
+ "[TT]-seppot[tt] is used, in which case each node writes a log file.",
+ "The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
+ "optionally forces.",
+ "The structure file ([TT]-c[tt]) contains the coordinates and",
+ "velocities of the last step.",
+ "The energy file ([TT]-e[tt]) contains energies, the temperature,",
+ "pressure, etc, a lot of these things are also printed in the log file.",
+ "Optionally coordinates can be written to a compressed trajectory file",
+ "([TT]-x[tt]).[PAR]",
+/* openmm specific information */
+ "Usage with OpenMM:[BR]",
+ "[TT]mdrun -device \"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no\"[tt][PAR]",
+ "Options:[PAR]",
+ " [TT]platform[tt] = Cuda\t\t:\tThe only available value. OpenCL support will be available in future.\n",
+ " [TT]memtest[tt] = 15\t\t:\tRun a partial, random GPU memory test for the given amount of seconds. A full test",
+ "(recommended!) can be run with \"memtest=full\". Memory testing can be disabled with \"memtest=off\".\n",
+ " [TT]deviceid[tt] = 0\t\t:\tSpecify the target device when multiple cards are present.",
+ "Only one card can be used at any given time though.\n",
+ " [TT]force-device[tt] = no\t\t:\tIf set to \"yes\" [TT]mdrun[tt] will be forced to execute on",
+ "hardware that is not officially supported. GPU acceleration can also be achieved on older",
+ "but Cuda capable cards, although the simulation might be too slow, and the memory limits too strict.",
+#else
+ "The [TT]mdrun[tt] program is the main computational chemistry engine",
+ "within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
+ "but it can also perform Stochastic Dynamics, Energy Minimization,",
+ "test particle insertion or (re)calculation of energies.",
+ "Normal mode analysis is another option. In this case [TT]mdrun[tt]",
+ "builds a Hessian matrix from single conformation.",
+ "For usual Normal Modes-like calculations, make sure that",
+ "the structure provided is properly energy-minimized.",
+ "The generated matrix can be diagonalized by [TT]g_nmeig[tt].[PAR]",
+ "The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
+ "and distributes the topology over nodes if needed.",
+ "[TT]mdrun[tt] produces at least four output files.",
+ "A single log file ([TT]-g[tt]) is written, unless the option",
+ "[TT]-seppot[tt] is used, in which case each node writes a log file.",
+ "The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
+ "optionally forces.",
+ "The structure file ([TT]-c[tt]) contains the coordinates and",
+ "velocities of the last step.",
+ "The energy file ([TT]-e[tt]) contains energies, the temperature,",
+ "pressure, etc, a lot of these things are also printed in the log file.",
+ "Optionally coordinates can be written to a compressed trajectory file",
+ "([TT]-x[tt]).[PAR]",
+ "The option [TT]-dhdl[tt] is only used when free energy calculation is",
+ "turned on.[PAR]",
+ "When [TT]mdrun[tt] is started using MPI with more than 1 node, parallelization",
+ "is used. By default domain decomposition is used, unless the [TT]-pd[tt]",
+ "option is set, which selects particle decomposition.[PAR]",
+ "With domain decomposition, the spatial decomposition can be set",
+ "with option [TT]-dd[tt]. By default [TT]mdrun[tt] selects a good decomposition.",
+ "The user only needs to change this when the system is very inhomogeneous.",
+ "Dynamic load balancing is set with the option [TT]-dlb[tt],",
+ "which can give a significant performance improvement,",
+ "especially for inhomogeneous systems. The only disadvantage of",
+ "dynamic load balancing is that runs are no longer binary reproducible,",
+ "but in most cases this is not important.",
+ "By default the dynamic load balancing is automatically turned on",
+ "when the measured performance loss due to load imbalance is 5% or more.",
+ "At low parallelization these are the only important options",
+ "for domain decomposition.",
+ "At high parallelization the options in the next two sections",
+ "could be important for increasing the performace.",
+ "[PAR]",
+ "When PME is used with domain decomposition, separate nodes can",
+ "be assigned to do only the PME mesh calculation;",
+ "this is computationally more efficient starting at about 12 nodes.",
+ "The number of PME nodes is set with option [TT]-npme[tt],",
+ "this can not be more than half of the nodes.",
+ "By default [TT]mdrun[tt] makes a guess for the number of PME",
+ "nodes when the number of nodes is larger than 11 or performance wise",
+ "not compatible with the PME grid x dimension.",
+ "But the user should optimize npme. Performance statistics on this issue",
+ "are written at the end of the log file.",
+ "For good load balancing at high parallelization, the PME grid x and y",
+ "dimensions should be divisible by the number of PME nodes",
+ "(the simulation will run correctly also when this is not the case).",
+ "[PAR]",
+ "This section lists all options that affect the domain decomposition.",
+ "[PAR]",
+ "Option [TT]-rdd[tt] can be used to set the required maximum distance",
+ "for inter charge-group bonded interactions.",
+ "Communication for two-body bonded interactions below the non-bonded",
+ "cut-off distance always comes for free with the non-bonded communication.",
+ "Atoms beyond the non-bonded cut-off are only communicated when they have",
+ "missing bonded interactions; this means that the extra cost is minor",
+ "and nearly indepedent of the value of [TT]-rdd[tt].",
+ "With dynamic load balancing option [TT]-rdd[tt] also sets",
+ "the lower limit for the domain decomposition cell sizes.",
+ "By default [TT]-rdd[tt] is determined by [TT]mdrun[tt] based on",
+ "the initial coordinates. The chosen value will be a balance",
+ "between interaction range and communication cost.",
+ "[PAR]",
+ "When inter charge-group bonded interactions are beyond",
+ "the bonded cut-off distance, [TT]mdrun[tt] terminates with an error message.",
+ "For pair interactions and tabulated bonds",
+ "that do not generate exclusions, this check can be turned off",
+ "with the option [TT]-noddcheck[tt].",
+ "[PAR]",
+ "When constraints are present, option [TT]-rcon[tt] influences",
+ "the cell size limit as well.",
+ "Atoms connected by NC constraints, where NC is the LINCS order plus 1,",
+ "should not be beyond the smallest cell size. A error message is",
+ "generated when this happens and the user should change the decomposition",
+ "or decrease the LINCS order and increase the number of LINCS iterations.",
+ "By default [TT]mdrun[tt] estimates the minimum cell size required for P-LINCS",
+ "in a conservative fashion. For high parallelization it can be useful",
+ "to set the distance required for P-LINCS with the option [TT]-rcon[tt].",
+ "[PAR]",
+ "The [TT]-dds[tt] option sets the minimum allowed x, y and/or z scaling",
+ "of the cells with dynamic load balancing. [TT]mdrun[tt] will ensure that",
+ "the cells can scale down by at least this factor. This option is used",
+ "for the automated spatial decomposition (when not using [TT]-dd[tt])",
+ "as well as for determining the number of grid pulses, which in turn",
+ "sets the minimum allowed cell size. Under certain circumstances",
+ "the value of [TT]-dds[tt] might need to be adjusted to account for",
+ "high or low spatial inhomogeneity of the system.",
+ "[PAR]",
+ "The option [TT]-gcom[tt] can be used to only do global communication",
+ "every n steps.",
+ "This can improve performance for highly parallel simulations",
+ "where this global communication step becomes the bottleneck.",
+ "For a global thermostat and/or barostat the temperature",
+ "and/or pressure will also only be updated every [TT]-gcom[tt] steps.",
+ "By default it is set to the minimum of nstcalcenergy and nstlist.[PAR]",
+ "With [TT]-rerun[tt] an input trajectory can be given for which ",
+ "forces and energies will be (re)calculated. Neighbor searching will be",
+ "performed for every frame, unless [TT]nstlist[tt] is zero",
+ "(see the [TT].mdp[tt] file).[PAR]",
+ "ED (essential dynamics) sampling is switched on by using the [TT]-ei[tt]",
+ "flag followed by an [TT].edi[tt] file.",
+ "The [TT].edi[tt] file can be produced using options in the essdyn",
+ "menu of the WHAT IF program. [TT]mdrun[tt] produces a [TT].edo[tt] file that",
+ "contains projections of positions, velocities and forces onto selected",
+ "eigenvectors.[PAR]",
+ "When user-defined potential functions have been selected in the",
+ "[TT].mdp[tt] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
+ "a formatted table with potential functions. The file is read from",
+ "either the current directory or from the [TT]GMXLIB[tt] directory.",
+ "A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
+ "for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
+ "normal Coulomb.",
+ "When pair interactions are present, a separate table for pair interaction",
+ "functions is read using the [TT]-tablep[tt] option.[PAR]",
+ "When tabulated bonded functions are present in the topology,",
+ "interaction functions are read using the [TT]-tableb[tt] option.",
+ "For each different tabulated interaction type the table file name is",
+ "modified in a different way: before the file extension an underscore is",
+ "appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
+ "and finally the table number of the interaction type.[PAR]",
+ "The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
+ "coordinates and forces when pulling is selected",
+ "in the [TT].mdp[tt] file.[PAR]",
+ "With [TT]-multi[tt] or [TT]-multidir[tt], multiple systems can be ",
+ "simulated in parallel.",
+ "As many input files/directories are required as the number of systems. ",
+ "The [TT]-multidir[tt] option takes a list of directories (one for each ",
+ "system) and runs in each of them, using the input/output file names, ",
+ "such as specified by e.g. the [TT]-s[tt] option, relative to these ",
+ "directories.",
+ "With [TT]-multi[tt], the system number is appended to the run input ",
+ "and each output filename, for instance [TT]topol.tpr[tt] becomes",
+ "[TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.",
+ "The number of nodes per system is the total number of nodes",
+ "divided by the number of systems.",
+ "One use of this option is for NMR refinement: when distance",
+ "or orientation restraints are present these can be ensemble averaged",
+ "over all the systems.[PAR]",
+ "With [TT]-replex[tt] replica exchange is attempted every given number",
+ "of steps. The number of replicas is set with the [TT]-multi[tt] or ",
+ "[TT]-multidir[tt] option, described above.",
+ "All run input files should use a different coupling temperature,",
+ "the order of the files is not important. The random seed is set with",
+ "[TT]-reseed[tt]. The velocities are scaled and neighbor searching",
+ "is performed after every exchange.[PAR]",
+ "Finally some experimental algorithms can be tested when the",
+ "appropriate options have been given. Currently under",
+ "investigation are: polarizability and X-ray bombardments.",
+ "[PAR]",
+ "The option [TT]-membed[dd] does what used to be g_membed, i.e. embed",
+ "a protein into a membrane. The data file should contain the options",
+ "that where passed to g_membed before. The [TT]-mn[tt] and [TT]-mp[tt]",
+ "both apply to this as well.",
+ "[PAR]",
+ "The option [TT]-pforce[tt] is useful when you suspect a simulation",
+ "crashes due to too large forces. With this option coordinates and",
+ "forces of atoms with a force larger than a certain value will",
+ "be printed to stderr.",
+ "[PAR]",
+ "Checkpoints containing the complete state of the system are written",
+ "at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
+ "unless option [TT]-cpt[tt] is set to -1.",
+ "The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
+ "make sure that a recent state of the system is always available,",
+ "even when the simulation is terminated while writing a checkpoint.",
+ "With [TT]-cpnum[tt] all checkpoint files are kept and appended",
+ "with the step number.",
+ "A simulation can be continued by reading the full state from file",
+ "with option [TT]-cpi[tt]. This option is intelligent in the way that",
+ "if no checkpoint file is found, Gromacs just assumes a normal run and",
+ "starts from the first step of the [TT].tpr[tt] file. By default the output",
+ "will be appending to the existing output files. The checkpoint file",
+ "contains checksums of all output files, such that you will never",
+ "loose data when some output files are modified, corrupt or removed.",
+ "There are three scenarios with [TT]-cpi[tt]:[PAR]",
+ "[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
+ "[TT]*[tt] all files are present with names and checksums matching those stored",
+ "in the checkpoint file: files are appended[PAR]",
+ "[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
+ "With [TT]-noappend[tt] new output files are opened and the simulation",
+ "part number is added to all output file names.",
+ "Note that in all cases the checkpoint file itself is not renamed",
+ "and will be overwritten, unless its name does not match",
+ "the [TT]-cpo[tt] option.",
+ "[PAR]",
+ "With checkpointing the output is appended to previously written",
+ "output files, unless [TT]-noappend[tt] is used or none of the previous",
+ "output files are present (except for the checkpoint file).",
+ "The integrity of the files to be appended is verified using checksums",
+ "which are stored in the checkpoint file. This ensures that output can",
+ "not be mixed up or corrupted due to file appending. When only some",
+ "of the previous output files are present, a fatal error is generated",
+ "and no old output files are modified and no new output files are opened.",
+ "The result with appending will be the same as from a single run.",
+ "The contents will be binary identical, unless you use a different number",
+ "of nodes or dynamic load balancing or the FFT library uses optimizations",
+ "through timing.",
+ "[PAR]",
+ "With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
+ "file is written at the first neighbor search step where the run time",
+ "exceeds [TT]-maxh[tt]*0.99 hours.",
+ "[PAR]",
+ "When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
+ "step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
+ "pressed), it will stop after the next neighbor search step ",
+ "(with nstlist=0 at the next step).",
+ "In both cases all the usual output will be written to file.",
+ "When running with MPI, a signal to one of the [TT]mdrun[tt] processes",
+ "is sufficient, this signal should not be sent to mpirun or",
+ "the [TT]mdrun[tt] process that is the parent of the others.",
+ "[PAR]",
+ "When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
+#endif
+ };
+ t_commrec *cr;
+ t_filenm fnm[] = {
+ { efTPX, NULL, NULL, ffREAD },
+ { efTRN, "-o", NULL, ffWRITE },
+ { efXTC, "-x", NULL, ffOPTWR },
+ { efCPT, "-cpi", NULL, ffOPTRD },
+ { efCPT, "-cpo", NULL, ffOPTWR },
+ { efSTO, "-c", "confout", ffWRITE },
+ { efEDR, "-e", "ener", ffWRITE },
+ { efLOG, "-g", "md", ffWRITE },
+ { efXVG, "-dhdl", "dhdl", ffOPTWR },
+ { efXVG, "-field", "field", ffOPTWR },
+ { efXVG, "-table", "table", ffOPTRD },
+ { efXVG, "-tablep", "tablep", ffOPTRD },
+ { efXVG, "-tableb", "table", ffOPTRD },
+ { efTRX, "-rerun", "rerun", ffOPTRD },
+ { efXVG, "-tpi", "tpi", ffOPTWR },
+ { efXVG, "-tpid", "tpidist", ffOPTWR },
+ { efEDI, "-ei", "sam", ffOPTRD },
+ { efEDO, "-eo", "sam", ffOPTWR },
+ { efGCT, "-j", "wham", ffOPTRD },
+ { efGCT, "-jo", "bam", ffOPTWR },
+ { efXVG, "-ffout", "gct", ffOPTWR },
+ { efXVG, "-devout", "deviatie", ffOPTWR },
+ { efXVG, "-runav", "runaver", ffOPTWR },
+ { efXVG, "-px", "pullx", ffOPTWR },
+ { efXVG, "-pf", "pullf", ffOPTWR },
+ { efXVG, "-ro", "rotation", ffOPTWR },
+ { efLOG, "-ra", "rotangles",ffOPTWR },
+ { efLOG, "-rs", "rotslabs", ffOPTWR },
+ { efLOG, "-rt", "rottorque",ffOPTWR },
+ { efMTX, "-mtx", "nm", ffOPTWR },
+ { efNDX, "-dn", "dipole", ffOPTWR },
+ { efDAT, "-membed", "membed", ffOPTRD },
+ { efTOP, "-mp", "membed", ffOPTRD },
+ { efNDX, "-mn", "membed", ffOPTRD },
+ { efRND, "-multidir",NULL, ffOPTRDMULT}
+ };
+#define NFILE asize(fnm)
+
+ /* Command line options ! */
+ gmx_bool bCart = FALSE;
+ gmx_bool bPPPME = FALSE;
+ gmx_bool bPartDec = FALSE;
+ gmx_bool bDDBondCheck = TRUE;
+ gmx_bool bDDBondComm = TRUE;
+ gmx_bool bVerbose = FALSE;
+ gmx_bool bCompact = TRUE;
+ gmx_bool bSepPot = FALSE;
+ gmx_bool bRerunVSite = FALSE;
+ gmx_bool bIonize = FALSE;
+ gmx_bool bConfout = TRUE;
+ gmx_bool bReproducible = FALSE;
+
+ int npme=-1;
+ int nmultisim=0;
+ int nstglobalcomm=-1;
+ int repl_ex_nst=0;
+ int repl_ex_seed=-1;
+ int nstepout=100;
+ int nthreads=0; /* set to determine # of threads automatically */
+ int resetstep=-1;
+
+ rvec realddxyz={0,0,0};
+ const char *ddno_opt[ddnoNR+1] =
+ { NULL, "interleave", "pp_pme", "cartesian", NULL };
+ const char *dddlb_opt[] =
+ { NULL, "auto", "no", "yes", NULL };
+ real rdd=0.0,rconstr=0.0,dlb_scale=0.8,pforce=-1;
+ char *ddcsx=NULL,*ddcsy=NULL,*ddcsz=NULL;
+ real cpt_period=15.0,max_hours=-1;
+ gmx_bool bAppendFiles=TRUE;
+ gmx_bool bKeepAndNumCPT=FALSE;
+ gmx_bool bResetCountersHalfWay=FALSE;
+ output_env_t oenv=NULL;
+ const char *deviceOptions = "";
+
+ t_pargs pa[] = {
+
+ { "-pd", FALSE, etBOOL,{&bPartDec},
+ "Use particle decompostion" },
+ { "-dd", FALSE, etRVEC,{&realddxyz},
+ "Domain decomposition grid, 0 is optimize" },
+#ifdef GMX_THREADS
+ { "-nt", FALSE, etINT, {&nthreads},
+ "Number of threads to start (0 is guess)" },
+#endif
+ { "-npme", FALSE, etINT, {&npme},
+ "Number of separate nodes to be used for PME, -1 is guess" },
+ { "-ddorder", FALSE, etENUM, {ddno_opt},
+ "DD node order" },
+ { "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
+ "Check for all bonded interactions with DD" },
+ { "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
+ "HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
+ { "-rdd", FALSE, etREAL, {&rdd},
+ "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
+ { "-rcon", FALSE, etREAL, {&rconstr},
+ "Maximum distance for P-LINCS (nm), 0 is estimate" },
+ { "-dlb", FALSE, etENUM, {dddlb_opt},
+ "Dynamic load balancing (with DD)" },
+ { "-dds", FALSE, etREAL, {&dlb_scale},
+ "Minimum allowed dlb scaling of the DD cell size" },
+ { "-ddcsx", FALSE, etSTR, {&ddcsx},
+ "HIDDENThe DD cell sizes in x" },
+ { "-ddcsy", FALSE, etSTR, {&ddcsy},
+ "HIDDENThe DD cell sizes in y" },
+ { "-ddcsz", FALSE, etSTR, {&ddcsz},
+ "HIDDENThe DD cell sizes in z" },
+ { "-gcom", FALSE, etINT,{&nstglobalcomm},
+ "Global communication frequency" },
+ { "-v", FALSE, etBOOL,{&bVerbose},
+ "Be loud and noisy" },
+ { "-compact", FALSE, etBOOL,{&bCompact},
+ "Write a compact log file" },
+ { "-seppot", FALSE, etBOOL, {&bSepPot},
+ "Write separate V and dVdl terms for each interaction type and node to the log file(s)" },
+ { "-pforce", FALSE, etREAL, {&pforce},
+ "Print all forces larger than this (kJ/mol nm)" },
+ { "-reprod", FALSE, etBOOL,{&bReproducible},
+ "Try to avoid optimizations that affect binary reproducibility" },
+ { "-cpt", FALSE, etREAL, {&cpt_period},
+ "Checkpoint interval (minutes)" },
+ { "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
+ "Keep and number checkpoint files" },
+ { "-append", FALSE, etBOOL, {&bAppendFiles},
+ "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
+ { "-maxh", FALSE, etREAL, {&max_hours},
+ "Terminate after 0.99 times this time (hours)" },
+ { "-multi", FALSE, etINT,{&nmultisim},
+ "Do multiple simulations in parallel" },
+ { "-replex", FALSE, etINT, {&repl_ex_nst},
+ "Attempt replica exchange every # steps" },
+ { "-reseed", FALSE, etINT, {&repl_ex_seed},
+ "Seed for replica exchange, -1 is generate a seed" },
+ { "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
+ "HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
+ { "-ionize", FALSE, etBOOL,{&bIonize},
+ "Do a simulation including the effect of an X-Ray bombardment on your system" },
+ { "-confout", FALSE, etBOOL, {&bConfout},
+ "HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
+ { "-stepout", FALSE, etINT, {&nstepout},
+ "HIDDENFrequency of writing the remaining runtime" },
+ { "-resetstep", FALSE, etINT, {&resetstep},
+ "HIDDENReset cycle counters after these many time steps" },
+ { "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
+ "HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
+#ifdef GMX_OPENMM
+ ,
+ { "-device", FALSE, etSTR, {&deviceOptions},
+ "Device option string" }
+#endif
+ };
+ gmx_edsam_t ed;
+ unsigned long Flags, PCA_Flags;
+ ivec ddxyz;
+ int dd_node_order;
+ gmx_bool bAddPart;
+ FILE *fplog,*fptest;
+ int sim_part,sim_part_fn;
+ const char *part_suffix=".part";
+ char suffix[STRLEN];
+ int rc;
+ char **multidir=NULL;
+
+
+ cr = init_par(&argc,&argv);
+
+ if (MASTER(cr))
+ CopyRight(stderr, argv[0]);
+
+ PCA_Flags = (PCA_KEEP_ARGS | PCA_NOEXIT_ON_ARGS | PCA_CAN_SET_DEFFNM
+ | (MASTER(cr) ? 0 : PCA_QUIET));
+
+
+ /* Comment this in to do fexist calls only on master
+ * works not with rerun or tables at the moment
+ * also comment out the version of init_forcerec in md.c
+ * with NULL instead of opt2fn
+ */
+ /*
+ if (!MASTER(cr))
+ {
+ PCA_Flags |= PCA_NOT_READ_NODE;
+ }
+ */
+
+ parse_common_args(&argc,argv,PCA_Flags, NFILE,fnm,asize(pa),pa,
+ asize(desc),desc,0,NULL, &oenv);
+
+
+
+ /* we set these early because they might be used in init_multisystem()
+ Note that there is the potential for npme>nnodes until the number of
+ threads is set later on, if there's thread parallelization. That shouldn't
+ lead to problems. */
+ dd_node_order = nenum(ddno_opt);
+ cr->npmenodes = npme;
+
+#ifndef GMX_THREADS
+ nthreads=1;
+#endif
+
+ /* now check the -multi and -multidir option */
+ if (opt2bSet("-multidir", NFILE, fnm))
+ {
+ int i;
+ if (nmultisim > 0)
+ {
+ gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
+ }
+ nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
+ }
+
+
+ if (repl_ex_nst != 0 && nmultisim < 2)
+ gmx_fatal(FARGS,"Need at least two replicas for replica exchange (option -multi)");
+
+ if (nmultisim > 1) {
+#ifndef GMX_THREADS
+ gmx_bool bParFn = (multidir == NULL);
+ init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
+#else
+ gmx_fatal(FARGS,"mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support");
+#endif
+ }
+
+ bAddPart = !bAppendFiles;
+
+ /* Check if there is ANY checkpoint file available */
+ sim_part = 1;
+ sim_part_fn = sim_part;
+ if (opt2bSet("-cpi",NFILE,fnm))
+ {
+ if (bSepPot && bAppendFiles)
+ {
+ gmx_fatal(FARGS,"Output file appending is not supported with -seppot");
+ }
+
+ bAppendFiles =
+ read_checkpoint_simulation_part(opt2fn_master("-cpi", NFILE,
+ fnm,cr),
+ &sim_part_fn,NULL,cr,
+ bAppendFiles,NFILE,fnm,
+ part_suffix,&bAddPart);
+ if (sim_part_fn==0 && MASTER(cr))
+ {
+ fprintf(stdout,"No previous checkpoint file present, assuming this is a new run.\n");
+ }
+ else
+ {
+ sim_part = sim_part_fn + 1;
+ }
++
++ if (MULTISIM(cr) && MASTER(cr))
++ {
++ check_multi_int(stdout,cr->ms,sim_part,"simulation part");
++ }
+ }
+ else
+ {
+ bAppendFiles = FALSE;
+ }
+
+ if (!bAppendFiles)
+ {
+ sim_part_fn = sim_part;
+ }
+
+ if (bAddPart)
+ {
+ /* Rename all output files (except checkpoint files) */
+ /* create new part name first (zero-filled) */
+ sprintf(suffix,"%s%04d",part_suffix,sim_part_fn);
+
+ add_suffix_to_output_names(fnm,NFILE,suffix);
+ if (MASTER(cr))
+ {
+ fprintf(stdout,"Checkpoint file is from part %d, new output files will be suffixed '%s'.\n",sim_part-1,suffix);
+ }
+ }
+
+ Flags = opt2bSet("-rerun",NFILE,fnm) ? MD_RERUN : 0;
+ Flags = Flags | (bSepPot ? MD_SEPPOT : 0);
+ Flags = Flags | (bIonize ? MD_IONIZE : 0);
+ Flags = Flags | (bPartDec ? MD_PARTDEC : 0);
+ Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
+ Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
+ Flags = Flags | (bConfout ? MD_CONFOUT : 0);
+ Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
+ Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
+ Flags = Flags | (bAppendFiles ? MD_APPENDFILES : 0);
+ Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
+ Flags = Flags | (sim_part>1 ? MD_STARTFROMCPT : 0);
+ Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
+
+
+ /* We postpone opening the log file if we are appending, so we can
+ first truncate the old log file and append to the correct position
+ there instead. */
+ if ((MASTER(cr) || bSepPot) && !bAppendFiles)
+ {
+ gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,!bSepPot,Flags,&fplog);
+ CopyRight(fplog,argv[0]);
+ please_cite(fplog,"Hess2008b");
+ please_cite(fplog,"Spoel2005a");
+ please_cite(fplog,"Lindahl2001a");
+ please_cite(fplog,"Berendsen95a");
+ }
+ else if (!MASTER(cr) && bSepPot)
+ {
+ gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,!bSepPot,Flags,&fplog);
+ }
+ else
+ {
+ fplog = NULL;
+ }
+
+ ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
+ ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
+ ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
+
+ rc = mdrunner(nthreads, fplog,cr,NFILE,fnm,oenv,bVerbose,bCompact,
+ nstglobalcomm, ddxyz,dd_node_order,rdd,rconstr,
+ dddlb_opt[0],dlb_scale,ddcsx,ddcsy,ddcsz,
+ nstepout,resetstep,nmultisim,repl_ex_nst,repl_ex_seed,
+ pforce, cpt_period,max_hours,deviceOptions,Flags);
+
+ if (gmx_parallel_env_initialized())
+ gmx_finalize();
+
+ if (MULTIMASTER(cr)) {
+ thanx(stderr);
+ }
+
+ /* Log file has to be closed in mdrunner if we are appending to it
+ (fplog not set here) */
+ if (MASTER(cr) && !bAppendFiles)
+ {
+ gmx_log_close(fplog);
+ }
+
+ return rc;
+}
+
gmx_polystat.c gmx_potential.c gmx_rama.c
gmx_rdf.c gmx_rms.c gmx_rmsf.c
gmx_rotacf.c gmx_saltbr.c gmx_sas.c
- gmx_rmsdist.c gmx_rotmat.c
- gmx_select.c gmx_rmsdist.c gmx_rotmat.c
++ gmx_rmsdist.c gmx_rotmat.c
gmx_sgangle.c gmx_sorient.c gmx_spol.c gmx_tcaf.c
gmx_traj.c gmx_velacc.c gmx_helixorient.c
gmx_clustsize.c gmx_mdmat.c gmx_wham.c
gmx_editconf.c gmx_genbox.c gmx_genion.c gmx_genconf.c
gmx_genpr.c gmx_eneconv.c gmx_vanhove.c gmx_wheel.c
addconf.c calcpot.c edittop.c gmx_bar.c
- gmx_pme_error.c gmx_options.c
- gmx_membed.c gmx_pme_error.c gmx_options.c gmx_dos.c
++ gmx_pme_error.c gmx_options.c gmx_dos.c
+ gmx_hydorder.c gmx_densorder.c powerspect.c dens_filter.c
+ binsearch.c
)
g_dyndom g_enemat g_energy g_lie g_filter g_gyrate
g_h2order g_hbond g_helix g_mindist g_msd g_morph g_nmeig
g_nmens g_order g_kinetics g_polystat g_potential g_rama g_rdf g_rms
- g_rmsf g_rotacf g_saltbr g_sas g_select g_sgangle g_sham g_sorient
+ g_rmsf g_rotacf g_saltbr g_sas g_sgangle g_sham g_sorient
g_spol g_spatial g_tcaf g_traj g_tune_pme g_vanhove
g_velacc g_clustsize g_mdmat g_wham g_sigeps g_bar
- g_membed g_pme_error g_rmsdist g_rotmat g_options
+ g_pme_error g_rmsdist g_rotmat g_options
+ g_dos g_hydorder g_densorder
)
set(GMX_TOOLS_PROGRAMS_NOT_FOR_INSTALLATION
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff