set(CPACK_COMPONENT_GROUP_TOOLS_DESCRIPTION "All GROMACS executable tools")
set(CPACK_COMPONENT_GROUP_MDRUN_DESCRIPTION "GROMACS executable for running simulations")
-# override bugs on OS X where Cmake picks gcc (GNU) for C instead of system default cc (Clang).
-if(APPLE)
- set(CMAKE_C_COMPILER_INIT "cc")
-endif(APPLE)
+# CMake modules/macros are in a subdirectory to keep this file cleaner
+# This needs to be set before project() in order to pick up toolchain files
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Platform)
project(Gromacs C)
include(Dart)
# machine with no git.
#
# NOTE: when releasing the "-dev" suffix needs to be stripped off!
-set(PROJECT_VERSION "4.6-beta2-dev")
+set(PROJECT_VERSION "4.6-beta3-dev")
set(CUSTOM_VERSION_STRING ""
CACHE STRING "Custom version string (if empty, use hard-coded default)")
mark_as_advanced(CUSTOM_VERSION_STRING)
# provide backward compatibility of software written against the Gromacs API.
set(API_VERSION ${NUM_VERSION})
-# Cmake modules/macros are in a subdirectory to keep this file cleaner
-set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
-
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
endif()
SET(SHARED_LIBS_DEFAULT OFF)
else()
add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
+ set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
endif()
IF (GMX_PREFER_STATIC_LIBS)
#Workaround for cmake bug 13174. Replace deprecated options.
IF( CMAKE_C_COMPILER_ID MATCHES "Intel" )
+ if(BUILD_SHARED_LIBS)
+ STRING(REPLACE "/INCREMENTAL:YES" "" CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS})
+ SET(CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS} CACHE STRING "" FORCE)
+ endif()
STRING(REPLACE /GZ /RTC1 CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
SET(CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG} CACHE STRING "" FORCE)
ENDIF()
option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
mark_as_advanced(GMX_SOFTWARE_INVSQRT)
-option(GMX_POWERPC_INVSQRT "Use PowerPC hardware 1/sqrt" OFF)
-mark_as_advanced(GMX_POWERPC_INVSQRT)
option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
mark_as_advanced(GMX_FAHCORE)
if(GMX_SOFTWARE_INVSQRT)
set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
endif(GMX_SOFTWARE_INVSQRT)
-if(GMX_POWERPC_INVSQRT)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_POWERPC_INVSQRT")
-endif(GMX_POWERPC_INVSQRT)
########################################################################
#Process MPI settings
set(BUILD_SHARED_LIBS OFF CACHE BOOL "Shared libraries not compatible with BlueGene/L, disabled!" FORCE)
endif (${CMAKE_SYSTEM_NAME} STREQUAL "BlueGeneL")
set(GMX_SOFTWARE_INVSQRT OFF CACHE BOOL "Do not use software reciprocal square root on BlueGene" FORCE)
- set(GMX_POWERPC_INVSQRT ON CACHE BOOL "Use hardware reciprocal square root on BlueGene" FORCE)
set(GMX_X11 OFF CACHE BOOL "X11 not compatible with BlueGene, disabled!" FORCE)
set(GMX_THREAD_MPI OFF CACHE BOOL "Thread-MPI not compatible with BlueGene, disabled!" FORCE)
set(GMX_MPI ON CACHE BOOL "Use MPI on BlueGene" FORCE)
# The automatic testing for endianness does not work for the BlueGene cross-compiler
set(GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER 1 CACHE INTERNAL "BlueGene has big endian FP byte order (by default)" FORCE)
set(GMX_IEEE754_BIG_ENDIAN_WORD_ORDER 1 CACHE INTERNAL "BlueGene has big endian FP word order (by default)" FORCE)
-elseif(${GMX_CPU_ACCELERATION} STREQUAL "POWER6")
- set(GMX_POWER6 1)
- set(GMX_SOFTWARE_INVSQRT OFF CACHE BOOL "Do not use software reciprocal square root on Power6" FORCE)
- set(GMX_POWERPC_INVSQRT ON CACHE BOOL "Use hardware reciprocal square root on Power6" FORCE)
else(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
MESSAGE(FATAL_ERROR "Unrecognized option for accelerated kernels: ${GMX_CPU_ACCELERATION}. Pick one of None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, BlueGene")
endif(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
unset(OpenMP_LINKER_FLAGS CACHE)
unset(OpenMP_SHARED_LINKER_FLAGS)
endif()
+set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
######################################
# Output compiler and CFLAGS used
endif (${FFTW}_FOUND)
set(${FFTW}_HAVE_SIMD FALSE CACHE BOOL "If ${${FFTW}_PKG} was built with SIMD support")
-mark_as_advanced(${FFTW}_INCLUDE_DIR ${FFTW}_LIBRARY ${FFTW}_HAVE_SIMD)
+mark_as_advanced(${FFTW}_INCLUDE_DIR ${FFTW}_LIBRARY ${FFTW}_HAVE_SIMD ${FFTW}_HAVE_AVX)
/* Sets the ED input/output filenames, opens output (.edo) file */
void init_edsam(gmx_mtop_t *mtop,t_inputrec *ir,t_commrec *cr,
- gmx_edsam_t ed, rvec x[], matrix box);
+ gmx_edsam_t ed, rvec x[], matrix box, edsamstate_t *edsamstate);
/* Init routine for ED and flooding. Calls init_edi in a loop for every .edi-cycle
* contained in the input file, creates a NULL terminated list of t_edpar structures */
* and 3 that no shifts could be applied. Negative numbers
* correspond to errors in the arguments provided.
*/
+GMX_LIBGMX_EXPORT
void
F77_FUNC(dsaupd,DSAUPD)(int * ido,
const char * bmat,
* \param lworkl Provide the same argument as you did to dsaupd()
* \param info Provide the same argument as you did to dsaupd()
*/
+GMX_LIBGMX_EXPORT
void
F77_FUNC(dseupd,DSEUPD)(int * rvec,
const char * howmny,
*/
#ifndef GMX_CPUID_H_
#define GMX_CPUID_H_
+
+#include <stdio.h>
+
#include "visibility.h"
+
#ifdef __cplusplus
extern "C" {
#endif
F77_FUNC(dsytrd,DSYTRD)(const char *uplo, int *n, double * a, int *lda, double *d,
double *e, double *tau, double *work, int *lwork, int *info);
+GMX_LIBGMX_EXPORT
void
F77_FUNC(dsyevr,DSYEVR)(const char *jobz, const char *range, const char *uplo, int *n,
double *a, int *lda, double *vl, double *vu, int *
* The string name is used to print to the log file and in a fatal error
* if the val's don't match.
*/
-
+GMX_LIBGMX_EXPORT
void init_multisystem(t_commrec *cr, int nsim, char **multidirs,
int nfile, const t_filenm fnm[], gmx_bool bParFn);
/* Splits the communication into nsim separate simulations
real cuberoot (real a);
GMX_LIBGMX_EXPORT
double gmx_erfd(double x);
+GMX_LIBGMX_EXPORT
double gmx_erfcd(double x);
GMX_LIBGMX_EXPORT
float gmx_erff(float x);
typedef struct gmx_ana_nbsearch_t gmx_ana_nbsearch_t;
/** Create a new neighborhood search data structure. */
+GMX_LIBGMX_EXPORT
int
gmx_ana_nbsearch_create(gmx_ana_nbsearch_t **d, real cutoff, int maxn);
/** Free memory allocated for neighborhood search. */
int
gmx_ana_nbsearch_init(gmx_ana_nbsearch_t *d, t_pbc *pbc, int n, rvec x[]);
/** Initializes neighborhood search for a frame using \c gmx_ana_pos_t. */
+GMX_LIBGMX_EXPORT
int
gmx_ana_nbsearch_pos_init(gmx_ana_nbsearch_t *d, t_pbc *pbc,
struct gmx_ana_pos_t *p);
real
gmx_ana_nbsearch_mindist(gmx_ana_nbsearch_t *d, rvec x);
/** Calculates the minimun distance from the reference points. */
+GMX_LIBGMX_EXPORT
real
gmx_ana_nbsearch_pos_mindist(gmx_ana_nbsearch_t *d,
struct gmx_ana_pos_t *p, int i);
void gmx_sumf_sim(int nr,float r[],const gmx_multisim_t *ms);
/* Calculate the sum over the simulations of an array of floats */
+GMX_LIBGMX_EXPORT
void gmx_sumd_sim(int nr,double r[],const gmx_multisim_t *ms);
/* Calculate the sum over the simulations of an array of doubles */
/* we put all of these on their own cache line by padding the data structure
to the size of a cache line on x86 (64 bytes): */
+#define TMPI_SIZEOF_X86_CACHE_LINE 64
typedef struct tMPI_Atomic
{
int value;
- char padding[64-sizeof(int)];
+ char padding[TMPI_SIZEOF_X86_CACHE_LINE-sizeof(int)];
} tMPI_Atomic_t;
typedef struct tMPI_Atomic_ptr
{
void* value;
- char padding[64-sizeof(void*)];
+ char padding[TMPI_SIZEOF_X86_CACHE_LINE-sizeof(void*)];
} tMPI_Atomic_ptr_t;
typedef struct tMPI_Spinlock
{
unsigned int lock;
- char padding[64-sizeof(unsigned int)];
+ char padding[TMPI_SIZEOF_X86_CACHE_LINE-sizeof(unsigned int)];
} tMPI_Spinlock_t;
as the 486, and gcc on some Linux versions still target 80386 by default).
We also specifically check for icc, because intrinsics are not always
- supported there. */
-#if ( (TMPI_GCC_VERSION >= 40100) && defined(__x86_64__) && \
- !defined(__INTEL_COMPILER) )
+ supported there.
+
+ llvm has issues with inline assembly and also in 32 bits has support for
+ the gcc intrinsics */
+#if ( ( (TMPI_GCC_VERSION >= 40100) && defined(__x86_64__) && \
+ !defined(__INTEL_COMPILER) ) || defined(__llvm__) )
#include "gcc_intrinsics.h"
#else
__asm__ __volatile__("lock ; xaddl %0, %1;"
:"=r"(i) :"m"(a->value), "0"(i) : "memory");
return i + __i;
-}
+}
static inline int tMPI_Atomic_fetch_add(tMPI_Atomic_t *a, int i)
{
static inline int tMPI_Atomic_cas(tMPI_Atomic_t *a, int oldval, int newval)
{
- unsigned int prev;
+ int prev;
__asm__ __volatile__("lock ; cmpxchgl %1,%2"
: "=a"(prev)
int
gmx_ana_add_flags(gmx_ana_traj_t *d, unsigned long flags);
/** Sets the number of reference groups required. */
+GMX_LIBGMX_EXPORT
int
gmx_ana_set_nrefgrps(gmx_ana_traj_t *d, int nrefgrps);
/** Sets the number of analysis groups required. */
int
gmx_ana_get_nanagrps(gmx_ana_traj_t *d, int *nanagrps);
/** Gets the selection object for a reference selection. */
+GMX_LIBGMX_EXPORT
int
gmx_ana_get_refsel(gmx_ana_traj_t *d, int i, gmx_ana_selection_t **sel);
/** Gets the selection object for a reference selection. */
unsigned excl; /* The exclusion (interaction) bits */
} nbnxn_cj_t;
+/* In nbnxn_ci_t the integer shift contains the shift in the lower 7 bits.
+ * The upper bits contain information for non-bonded kernel optimization.
+ * Simply calculating LJ and Coulomb for all pairs in a cluster pair is fine.
+ * But three flags can be used to skip interactions, currently only for subc=0
+ * !(shift & NBNXN_CI_DO_LJ(subc)) => we can skip LJ for all pairs
+ * shift & NBNXN_CI_HALF_LJ(subc) => we can skip LJ for the second half of i
+ * !(shift & NBNXN_CI_DO_COUL(subc)) => we can skip Coulomb for all pairs
+ */
#define NBNXN_CI_SHIFT 127
#define NBNXN_CI_DO_LJ(subc) (1<<(7+3*(subc)))
#define NBNXN_CI_HALF_LJ(subc) (1<<(8+3*(subc)))
/* Simple pair-list i-unit */
typedef struct {
int ci; /* i-cluster */
- int shift; /* Shift vector index plus possible flags */
+ int shift; /* Shift vector index plus possible flags, see above */
int cj_ind_start; /* Start index into cj */
int cj_ind_end; /* End index into cj */
} nbnxn_ci_t;
}
energyhistory_t;
+typedef struct
+{
+ /* If one uses essential dynamics or flooding on a group of atoms from
+ * more than one molecule, we cannot make this group whole with
+ * do_pbc_first_mtop(). We assume that the ED group has the correct PBC
+ * representation at the beginning of the simulation and keep track
+ * of the shifts to always get it into that representation.
+ * For proper restarts from a checkpoint we store the positions of the
+ * reference group at the time of checkpoint writing */
+ gmx_bool bFromCpt; /* Did we start from a checkpoint file? */
+ int nED; /* No. of ED/Flooding data sets, if <1 no ED */
+ int *nref; /* No. of atoms in i'th reference structure */
+ int *nav; /* Same for average structure */
+ rvec **old_sref; /* Positions of the reference atoms
+ at the last time step (with correct PBC
+ representation) */
+ rvec **old_sref_p; /* Pointer to these positions */
+ rvec **old_sav; /* Same for the average positions */
+ rvec **old_sav_p;
+}
+edsamstate_t;
+
typedef struct
{
int natoms;
energyhistory_t enerhist; /* Energy history for statistics */
df_history_t dfhist; /*Free energy history for free energy analysis */
+ edsamstate_t edsamstate; /* Essential dynamics / flooding history */
int ddp_count; /* The DD partitioning count for this state */
int ddp_count_cg_gl; /* The DD part. count for index_gl */
#define INVSQRT_DONE
#endif /* gmx_invsqrt */
-#ifdef GMX_POWERPC_SQRT
-static real gmx_powerpc_invsqrt(real x)
-{
- const real half=0.5;
- const real three=3.0;
- t_convert result,bit_pattern;
- unsigned int exp,fract;
- real lu;
- real y;
-#ifdef GMX_DOUBLE
- real y2;
-#endif
-
- lu = __frsqrte((double)x);
-
- y=(half*lu*(three-((x*lu)*lu)));
-
-#if (GMX_POWERPC_SQRT==2)
- /* Extra iteration required */
- y=(half*y*(three-((x*y)*y)));
-#endif
-
-#ifdef GMX_DOUBLE
- y2=(half*y*(three-((x*y)*y)));
-
- return y2; /* 10 Flops */
-#else
- return y; /* 5 Flops */
-#endif
-}
-#define gmx_invsqrt(x) gmx_powerpc_invsqrt(x)
-#define INVSQRT_DONE
-#endif /* powerpc_invsqrt */
-
#ifndef INVSQRT_DONE
# ifdef GMX_DOUBLE
# ifdef HAVE_RSQRT
# If you only use one shell you can copy that GMXRC.* instead.
-# only csh/tcsh understand 'set'
-set is_csh = 123
-test "$is_csh" = 123 && goto CSH
+# only csh/tcsh set the variable $shell (note: lower case!)
+test $shell && goto CSH
# if we got here, shell is bsh/bash/zsh/ksh
# bsh cannot remove part of a variable with %%
<dl>
<dt>C format
-<dd><tt>"%5d%5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"</tt>
+<dd><tt>"%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"</tt>
<dt>Fortran format
<dd><tt>(i5,2a5,i5,3f8.3,3f8.4)</tt>
<dt>Pascal format
DEPENDS ${GROMACS_HEADERS})
add_custom_target(gromacs_include_links DEPENDS gromacs)
-add_executable(template template.c)
-remove_definitions( -DHAVE_CONFIG_H )
-add_definitions("${PKG_CFLAGS}")
-target_link_libraries(template gmx)
-include_directories("${CMAKE_CURRENT_BINARY_DIR}")
-add_dependencies(template gromacs_include_links)
+option(GMX_BUILD_TEMPLATE "Build gromacs template program" ON)
+mark_as_advanced(GMX_BUILD_TEMPLATE)
+# GMX_PREFER_STATIC_OPENMP=yes is a special case to build binaries
+# to distribute and as the template is not installed it can be
+# ignored.
+# The template is build in a user-like environment, hence we use
+# flags from PKG_CFLAGS. Again GMX_PREFER_STATIC_OPENMP=yes would
+# need special link flags (OpenMP_LINKER_FLAGS), which are not
+# very user-like.
+if (GMX_BUILD_TEMPLATE AND NOT GMX_PREFER_STATIC_OPENMP)
+ add_executable(template template.c)
+ remove_definitions( -DHAVE_CONFIG_H )
+ add_definitions("${PKG_CFLAGS}")
+ target_link_libraries(template gmx)
+ include_directories("${CMAKE_CURRENT_BINARY_DIR}")
+ add_dependencies(template gromacs_include_links)
+endif()
install(FILES README template.c Makefile.pkg
DESTINATION ${DATA_INSTALL_DIR}/template
/* Use the GROMACS software 1/sqrt(x) */
#cmakedefine GMX_SOFTWARE_INVSQRT
-/* Use the PowerPC hardware 1/sqrt(x) */
-#cmakedefine GMX_POWERPC_INVSQRT
-
/* Use sub-counters */
#cmakedefine GMX_CYCLE_SUBCOUNTERS
* But old code can not read a new entry that is present in the file
* (but can read a new format when new entries are not present).
*/
-static const int cpt_version = 14;
+static const int cpt_version = 15;
const char *est_names[estNR]=
}
}
+static void do_cpt_real_err(XDR *xd,const char *desc,real *f)
+{
+ bool_t res=0;
+
+#ifdef GMX_DOUBLE
+ res = xdr_double(xd,f);
+#else
+ res = xdr_float(xd,f);
+#endif
+ if (res == 0)
+ {
+ cp_error();
+ }
+}
+
+static void do_cpt_n_rvecs_err(XDR *xd,const char *desc,int n, rvec f[],FILE *list)
+{
+ int i,j;
+
+ for (i=0; i<n; i++)
+ {
+ for (j=0; j<DIM; j++)
+ {
+ do_cpt_real_err(xd, desc, &f[i][j]);
+ }
+ }
+
+ if (list)
+ {
+ pr_rvecs(list,0,desc,f,n);
+ }
+}
+
/* If nval >= 0, nval is used; on read this should match the passed value.
* If nval n<0, *nptr is used; on read the value is stored in nptr
*/
int *natoms,int *ngtc, int *nnhpres, int *nhchainlength,
int *nlambda, int *flags_state,
int *flags_eks,int *flags_enh, int *flags_dfh,
+ int *nED,
FILE *list)
{
bool_t res=0;
} else {
*flags_dfh = 0;
}
+
+ if (*file_version >= 15)
+ {
+ do_cpt_int_err(xd,"ED data sets",nED,list);
+ }
+ else
+ {
+ *nED = 0;
+ }
}
static int do_cpt_footer(XDR *xd,gmx_bool bRead,int file_version)
return ret;
}
+
+/* This function stores the last whole configuration of the reference and
+ * average structure in the .cpt file
+ */
+static int do_cpt_EDstate(XDR *xd,gmx_bool bRead,
+ edsamstate_t *EDstate, FILE *list)
+{
+ int i,j;
+ int ret=0;
+ char buf[STRLEN];
+
+
+ EDstate->bFromCpt = bRead;
+
+ if (EDstate->nED <= 0)
+ {
+ return ret;
+ }
+
+ /* When reading, init_edsam has not been called yet,
+ * so we have to allocate memory first. */
+ if (bRead)
+ {
+ snew(EDstate->nref , EDstate->nED);
+ snew(EDstate->old_sref, EDstate->nED);
+ snew(EDstate->nav , EDstate->nED);
+ snew(EDstate->old_sav , EDstate->nED);
+ }
+
+ /* Read/write the last whole conformation of SREF and SAV for each ED dataset (usually only one) */
+ for (i=0; i< EDstate->nED; i++)
+ {
+ /* Reference structure SREF */
+ sprintf(buf, "ED%d # of atoms in reference structure", i+1);
+ do_cpt_int_err(xd, buf, &EDstate->nref[i],list);
+ sprintf(buf, "ED%d x_ref", i+1);
+ if (bRead)
+ {
+ snew(EDstate->old_sref[i], EDstate->nref[i]);
+ do_cpt_n_rvecs_err(xd, buf, EDstate->nref[i], EDstate->old_sref[i], list);
+ }
+ else
+ {
+ do_cpt_n_rvecs_err(xd, buf, EDstate->nref[i], EDstate->old_sref_p[i], list);
+ }
+
+ /* Average structure SAV */
+ sprintf(buf, "ED%d # of atoms in average structure", i+1);
+ do_cpt_int_err(xd, buf, &EDstate->nav[i] ,list);
+ sprintf(buf, "ED%d x_av", i+1);
+ if (bRead)
+ {
+ snew(EDstate->old_sav[i], EDstate->nav[i]);
+ do_cpt_n_rvecs_err(xd, buf, EDstate->nav[i], EDstate->old_sav[i], list);
+ }
+ else
+ {
+ do_cpt_n_rvecs_err(xd, buf, EDstate->nav[i], EDstate->old_sav_p[i], list);
+ }
+ }
+
+ return ret;
+}
+
+
static int do_cpt_files(XDR *xd, gmx_bool bRead,
gmx_file_position_t **p_outputfiles, int *nfiles,
FILE *list, int file_version)
DOMAINDECOMP(cr) ? cr->dd->nc : NULL,&npmenodes,
&state->natoms,&state->ngtc,&state->nnhpres,
&state->nhchainlength,&(state->dfhist.nlambda),&state->flags,&flags_eks,&flags_enh,&flags_dfh,
+ &state->edsamstate.nED,
NULL);
sfree(version);
(do_cpt_ekinstate(gmx_fio_getxdr(fp),FALSE,flags_eks,&state->ekinstate,NULL) < 0)||
(do_cpt_enerhist(gmx_fio_getxdr(fp),FALSE,flags_enh,&state->enerhist,NULL) < 0) ||
(do_cpt_df_hist(gmx_fio_getxdr(fp),FALSE,flags_dfh,&state->dfhist,NULL) < 0) ||
+ (do_cpt_EDstate(gmx_fio_getxdr(fp),FALSE,&state->edsamstate,NULL) < 0) ||
(do_cpt_files(gmx_fio_getxdr(fp),FALSE,&outputfiles,&noutputfiles,NULL,
file_version) < 0))
{
&eIntegrator_f,simulation_part,step,t,
&nppnodes_f,dd_nc_f,&npmenodes_f,
&natoms,&ngtc,&nnhpres,&nhchainlength,&nlambda,
- &fflags,&flags_eks,&flags_enh,&flags_dfh,NULL);
+ &fflags,&flags_eks,&flags_enh,&flags_dfh,
+ &state->edsamstate.nED,NULL);
if (bAppendOutputFiles &&
file_version >= 13 && double_prec != GMX_CPT_BUILD_DP)
cp_error();
}
+ ret = do_cpt_EDstate(gmx_fio_getxdr(fp),TRUE,&state->edsamstate,NULL);
+ if (ret)
+ {
+ cp_error();
+ }
+
if (file_version < 6)
{
const char *warn="Reading checkpoint file in old format, assuming that the run that generated this file started at step 0, if this is not the case the averages stored in the energy file will be incorrect.";
&version,&btime,&buser,&bhost,&double_prec,&fprog,&ftime,
&eIntegrator,simulation_part,step,t,&nppnodes,dd_nc,&npme,
&state->natoms,&state->ngtc,&state->nnhpres,&state->nhchainlength,
- &(state->dfhist.nlambda),&state->flags,&flags_eks,&flags_enh,&flags_dfh,NULL);
+ &(state->dfhist.nlambda),&state->flags,&flags_eks,&flags_enh,&flags_dfh,
+ &state->edsamstate.nED,NULL);
ret =
do_cpt_state(gmx_fio_getxdr(fp),TRUE,state->flags,state,bReadRNG,NULL);
if (ret)
cp_error();
}
+ ret = do_cpt_EDstate(gmx_fio_getxdr(fp),TRUE,&state->edsamstate,NULL);
+ if (ret)
+ {
+ cp_error();
+ }
+
ret = do_cpt_files(gmx_fio_getxdr(fp),TRUE,
outputfiles != NULL ? outputfiles : &files_loc,
outputfiles != NULL ? nfiles : &nfiles_loc,
&eIntegrator,&simulation_part,&step,&t,&nppnodes,dd_nc,&npme,
&state.natoms,&state.ngtc,&state.nnhpres,&state.nhchainlength,
&(state.dfhist.nlambda),&state.flags,
- &flags_eks,&flags_enh,&flags_dfh,out);
+ &flags_eks,&flags_enh,&flags_dfh,&state.edsamstate.nED,out);
ret = do_cpt_state(gmx_fio_getxdr(fp),TRUE,state.flags,&state,TRUE,out);
if (ret)
{
ret = do_cpt_df_hist(gmx_fio_getxdr(fp),TRUE,
flags_dfh,&state.dfhist,out);
}
+
+ if (ret == 0)
+ {
+ ret = do_cpt_EDstate(gmx_fio_getxdr(fp),TRUE,&state.edsamstate,out);
+ }
+
if (ret == 0)
{
do_cpt_files(gmx_fio_getxdr(fp),TRUE,&outputfiles,&nfiles,out,file_version);
#include <unistd.h>
#endif
+#include "gmx_cpuid.h"
-#include "gmx_cpuid.h"
-
+/* For convenience, and to enable configure-time invocation, we keep all architectures
+ * in a single file, but to avoid repeated ifdefs we set the overall architecture here.
+ */
+#if defined (__i386__) || defined (__x86_64__) || defined (_M_IX86) || defined (_M_X64)
+# define GMX_CPUID_X86
+#endif
/* Global constant character strings corresponding to our enumerated types */
const char *
#endif
-/* Currently CPUID is only supported (1) if we can use an instruction on MSVC, or (2)
- * if the compiler handles GNU-style inline assembly.
- */
-#if defined (__i386__) || defined (__x86_64__) || defined (_M_IX86) || defined (_M_X64)
+#ifdef GMX_CPUID_X86
/* Execute CPUID on x86 class CPUs. level sets function to exec, and the
* contents of register output is returned. See Intel/AMD docs for details.
{
int rc = 0;
+ /* Currently CPUID is only supported (1) if we can use an instruction on MSVC, or (2)
+ * if the compiler handles GNU-style inline assembly.
+ */
+
#if (defined _MSC_VER)
int CPUInfo[4];
#endif
return rc;
}
-#endif /* architecture is x86 */
/* Identify CPU features common to Intel & AMD - mainly brand string,
}
return 0;
}
+#endif /* GMX_CPUID_X86 */
+
+
/* Try to find the vendor of the current CPU, so we know what specific
* detection routine to call.
/* Set default first */
vendor = GMX_CPUID_VENDOR_UNKNOWN;
+#ifdef GMX_CPUID_X86
execute_x86cpuid(0x0,0,&eax,&ebx,&ecx,&edx);
memcpy(vendorstring,&ebx,4);
vendor = i;
}
}
-
+#else
+ vendor = GMX_CPUID_VENDOR_UNKNOWN;
+#endif
+
return vendor;
}
switch(cpuid->vendor)
{
+#ifdef GMX_CPUID_X86
case GMX_CPUID_VENDOR_INTEL:
cpuid_check_intel_x86(cpuid);
break;
case GMX_CPUID_VENDOR_AMD:
cpuid_check_amd_x86(cpuid);
break;
+#endif
default:
/* Could not find vendor */
strncpy(cpuid->brand,"Unknown CPU brand",GMX_CPUID_BRAND_MAXLEN);
enum gmx_cpuid_x86_smt
gmx_cpuid_x86_smt(gmx_cpuid_t cpuid)
{
-
+#ifdef GMX_CPUID_X86
#if (defined HAVE_SCHED_H && defined HAVE_SCHED_SETAFFINITY && defined HAVE_SYSCONF && defined __linux__)
int i;
int nproc;
return GMX_CPUID_X86_SMT_CANNOTDETECT;
}
#endif
+#else
+ /* not x86 */
+ return GMX_CPUID_X86_SMT_CANNOTDETECT;
+#endif
}
OPTIONS ${_os_def}
RELWITHDEBINFO -g
DEBUG -g -D_DEBUG_=1 )
+#Because this is a static library linked into the (potential) shared library
+#it should have the export of the shared library.
+SET_TARGET_PROPERTIES(gpu_utils PROPERTIES DEFINE_SYMBOL "gmx_EXPORTS" )
CUDA_BUILD_CLEAN_TARGET()
URL: http://www.gromacs.org
Version: @PROJECT_VERSION@
Requires:
-Libs.private: @CMAKE_THREAD_LIBS_INIT@ @PKG_DL_LIBS@
+Libs.private: @CMAKE_THREAD_LIBS_INIT@ @PKG_DL_LIBS@ @OpenMP_LINKER_FLAGS@
Libs: -L${libdir} -lgmx@GMX_LIBS_SUFFIX@ -lm
Cflags: -I${includedir} @PKG_CFLAGS@
/* We tried again, and this time there was a copied buffer.
We use that, and indicate that we're not reading from the
regular buf. This case should be pretty rare. */
- tMPI_Atomic_fetch_add(&(cev->met[rank].buf_readcount),-1);
+ tMPI_Atomic_add_return(&(cev->met[rank].buf_readcount),-1);
tMPI_Atomic_memory_barrier_acq();
srcbuf=try_again_srcbuf;
}
{
/* we decrement the read count; potentially releasing the buffer. */
tMPI_Atomic_memory_barrier_rel();
- tMPI_Atomic_fetch_add( &(cev->met[rank].buf_readcount), -1);
+ tMPI_Atomic_add_return( &(cev->met[rank].buf_readcount), -1);
}
#endif
}
else
{
/* wait until everybody else is done copying the original buffer.
- We use fetch_add because we want to be sure of coherency.
+ We use atomic add-return because we want to be sure of coherency.
This wait is bound to be very short (otherwise it wouldn't
be double-buffering) so we always spin here. */
/*tMPI_Atomic_memory_barrier_rel();*/
-100000))
#endif
#if 0
- while (tMPI_Atomic_fetch_add( &(cev->met[myrank].buf_readcount), 0)
+ while (tMPI_Atomic_add_return( &(cev->met[myrank].buf_readcount), 0)
!= 0)
#endif
#if 1
tMPI_Atomic_memory_barrier_rel();
/* signal that we're done */
- tMPI_Atomic_fetch_add(&(cev->coll.current_sync), 1);
+ tMPI_Atomic_add_return(&(cev->coll.current_sync), 1);
/* we need to keep being in sync */
csync->syncs++;
}
tMPI_Error(TMPI_COMM_WORLD, TMPI_ERR_INIT);
}
}
- /* the main thread now also runs start_fn if we don't want
+ /* the main thread also runs start_fn if we don't want
it to return */
if (!main_returns)
tMPI_Thread_starter((void*)&(threads[0]));
tMPI_Trace_print("tMPI_Init(%p, %p, %p)", argc, argv, start_function);
#endif
-
if (TMPI_COMM_WORLD==0) /* we're the main process */
{
int N=0;
tMPI_Get_N(argc, argv, "-nt", &N);
- tMPI_Start_threads(FALSE, N, TMPI_AFFINITY_ALL_CORES, argc, argv,
+ tMPI_Start_threads(TRUE, N, TMPI_AFFINITY_ALL_CORES, argc, argv,
NULL, NULL, start_function);
}
else
{
nn = rr[i].main;
}
+
if (nn[0] == '-')
{
- gmx_fatal(FARGS,"In the chosen force field there is no residue type for '%s'%s",name,bStart ? " as a starting terminus" : (bEnd ? " as an ending terminus" : ""));
+ gmx_fatal(FARGS,"In the chosen force field there is no residue type for '%s'%s",name,bStart ? ( bEnd ? " as a standalone (starting & ending) residue" : " as a starting terminus") : (bEnd ? " as an ending terminus" : ""));
}
}
}
fprintf(fplog,"\n");
+ /* the "Order After Exchange" is the state label corresponding to the configuration that
+ started in state listed in order, i.e.
+
+ 3 0 1 2
+
+ means that the:
+ configuration starting in simulation 3 is now in simulation 0,
+ configuration starting in simulation 0 is now in simulation 1,
+ configuration starting in simulation 1 is now in simulation 2,
+ configuration starting in simulation 2 is now in simulation 3
+ */
fprintf(fplog,"Order After Exchange: ");
for (i=0;i<n;i++)
{
= [H_b(x_a) + H_a(x_b)] - [H_b(x_b) + H_a(x_a)]
= [H_b(x_a) - H_a(x_a)] + [H_a(x_b) - H_b(x_b)]
= de[b][a] + de[a][b] */
+
/* permuted:
ediff = E_new - E_old
= [H_bp(x_a) + H_ap(x_b)] - [H_bp(x_b) + H_ap(x_a)]
= [H_bp(x_a) - H_a(x_a) + H_a(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_b(x_b) + H_b(x_b) - H_bp(x_b)]
= [H_bp(x_a) - H_a(x_a)] - [H_ap(x_a) - H_a(x_a)] + [H_ap(x_b) - H_b(x_b)] - H_bp(x_b) - H_b(x_b)]
= (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]) */
+ /* but, in the current code implementation, we flip configurations, not indices . . .
+ So let's examine that.
+ = [H_b(x_ap) - H_a(x_a)] - [H_a(x_ap) - H_a(x_a)] + [H_a(x_bp) - H_b(x_b)] - H_b(x_bp) - H_b(x_b)]
+ = [H_b(x_ap) - H_a(x_ap)] + [H_a(x_bp) - H_b(x_pb)]
+ = (de[b][ap] - de[a][ap]) + (de[a][bp] - de[b][bp]
+ So, if we exchange b<=> bp and a<=> ap, we return to the same result.
+ So the simple solution is to flip the
+ position of perturbed and original indices in the tests.
+ */
+
ediff = (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]);
delta = ediff*beta[a]; /* assume all same temperature in this case */
break;
gmx_bool bPrint,bMultiEx;
gmx_bool *bEx = re->bEx;
real *prob = re->prob;
- int *pind = re->destinations;
+ int *pind = re->destinations; /* permuted index */
gmx_bool bEpot=FALSE;
gmx_bool bDLambda=FALSE;
gmx_bool bVol=FALSE;
for (i=0;i<re->nex;i++)
{
/* randomly select a pair */
- /* find out which state it is from, and what label that state currently has */
+ /* in theory, could reduce this by identifying only which switches had a nonneglibible
+ probability of occurring (log p > -100) and only operate on those switches */
+ /* find out which state it is from, and what label that state currently has. Likely
+ more work that useful. */
i0 = (int)(re->nrepl*rando(&(re->seed)));
i1 = (int)(re->nrepl*rando(&(re->seed)));
if (i0==i1)
{
i--;
- continue; /* got the same pair, back up and do it again */
+ continue; /* self-exchange, back up and do it again */
}
- a = re->ind[i0];
+ a = re->ind[i0]; /* what are the indices of these states? */
b = re->ind[i1];
ap = pind[i0];
bp = pind[i1];
bPrint = FALSE; /* too noisy */
- delta = calc_delta(fplog,bPrint,re,a,b,ap,bp); /* calculate the energy difference */
+ /* calculate the energy difference */
+ /* if the code changes to flip the STATES, rather than the configurations,
+ use the commented version of the code */
+ /* delta = calc_delta(fplog,bPrint,re,a,b,ap,bp); */
+ delta = calc_delta(fplog,bPrint,re,ap,bp,a,b);
- /* we actually only use the first space, since there are actually many switches between pairs. */
+ /* we actually only use the first space in the prob and bEx array,
+ since there are actually many switches between pairs. */
if (delta <= 0)
{
re->nmoves[re->ind[i]][pind[i]] +=1;
re->nmoves[pind[i]][re->ind[i]] +=1;
}
+ fflush(fplog); /* make sure we can see what the last exchange was */
}
static void write_debug_x(t_state *state)
/* There will be only one swap cycle with standard replica
* exchange, but there may be multiple swap cycles if we
* allow multiple swaps. */
+
for (j = 0; j < maxswap; j++)
{
exchange_partner = re->order[replica_id][j];
}
else
{
- /* check if some threads failed to set their affinities */
+ /* check & warn if some threads failed to set their affinities */
if (nth_affinity_set != nthread_local)
{
- char sbuf[STRLEN];
- sbuf[0] = '\0';
+ char sbuf1[STRLEN], sbuf2[STRLEN];
+
+ /* sbuf1 contains rank info, while sbuf2 OpenMP thread info */
+ sbuf1[0] = sbuf2[0] = '\0';
#ifdef GMX_MPI
#ifdef GMX_THREAD_MPI
- sprintf(sbuf, "In thread-MPI thread #%d", cr->nodeid);
+ sprintf(sbuf1, "In thread-MPI thread #%d: ", cr->nodeid);
#else /* GMX_LIB_MPI */
+ sprintf(sbuf1, "In MPI process #%d: ", cr->nodeid);
#endif
- sprintf(sbuf, "In MPI process #%d", cr->nodeid);
#endif /* GMX_MPI */
+
+ if (nthread_local > 1)
+ {
+ sprintf(sbuf2, "of %d/%d thread%s ",
+ nthread_local - nth_affinity_set, nthread_local,
+ (nthread_local - nth_affinity_set) > 1 ? "s" : "");
+ }
+
md_print_warn(NULL, fplog,
- "%s%d/%d thread%s failed to set their affinities. "
- "This can cause performance degradation!",
- sbuf, nthread_local - nth_affinity_set, nthread_local,
- (nthread_local - nth_affinity_set) > 1 ? "s" : "");
+ "NOTE: %sAffinity setting %sfailed.\n"
+ " This can cause performance degradation!",
+ sbuf1, sbuf2);
}
}
}
# disabling GMX_BUILD_OWN_FFTW changes dependencies correctly.
add_dependencies(md gmxfftw)
endif()
-set_target_properties(md PROPERTIES OUTPUT_NAME "md${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
+option(GMX_PREFIX_LIBMD "Change install name of libmd to libgmxmd to avoid collision with BSD's/Martin Hinner's libmd, which is used in X11 and zfs" OFF)
+mark_as_advanced(GMX_PREFIX_LIBMD)
+if (GMX_PREFIX_LIBMD)
+ set(MD_PREFIX "gmx")
+else()
+ set(MD_PREFIX)
+endif()
+set_target_properties(md PROPERTIES OUTPUT_NAME "${MD_PREFIX}md${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
COMPILE_FLAGS "${OpenMP_C_FLAGS}")
install(TARGETS md DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libmd.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libmd.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libmd.pc
DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
- RENAME "libmd${GMX_LIBS_SUFFIX}.pc"
+ RENAME "lib${MD_PREFIX}md${GMX_LIBS_SUFFIX}.pc"
COMPONENT development)
/* Initialize the essential dynamics sampling.
* Put the pointer to the ED struct in constr */
constr->ed = ed;
- if (ed != NULL)
+ if (ed != NULL || state->edsamstate.nED > 0)
{
- init_edsam(mtop,ir,cr,ed,state->x,state->box);
+ init_edsam(mtop,ir,cr,ed,state->x,state->box,&state->edsamstate);
}
constr->warn_mtop = mtop;
* 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 */
+ rvec *x_old; /* Last positions which have the correct PBC
+ representation of the ED group. In
+ combination with keeping track of the
+ shift vectors, the ED group can always
+ be made whole */
real *m; /* masses */
real mtot; /* total mass (only used in sref) */
real *sqrtm; /* sqrt of the masses used for mass-
FILE *edo; /* output file pointer */
t_edpar *edpar;
gmx_bool bFirst;
- gmx_bool bStartFromCpt;
} t_gmx_edsam;
for (i=0; i<edi->sav.nr; i++)
+ {
proj += edi->sav.sqrtm[i]*iprod(vec[i], xcoll[i]);
+ }
return proj;
}
/* 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++)
{
/* Add average positions */
for (i = 0; i < edi->sav.nr; i++)
+ {
rvec_inc(x[i], edi->sav.x[i]);
+ }
}
/* 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]);
+ }
}
for (i=0; i<vec->neig; i++)
+ {
rad += pow((vec->refproj[i]-vec->xproj[i]),2);
+ }
return rad=sqrt(rad);
}
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);
}
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");
}
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]);
+ }
}
}
for (i=0; i<dim; i++)
+ {
fprintf(out,"%4d %f %f %f\n",i,x[i][XX],x[i][YY],x[i][ZZ]);
+ }
}
for (i=0;i<dim;i++)
{
for (j=0;j<dim;j++)
+ {
fprintf(out,"%f ",mat[i][j]);
+ }
fprintf(out,"\n");
}
}
gmx_bool bFirst;
if(edi->buf->do_edfit != NULL)
+ {
bFirst = FALSE;
+ }
else
{
bFirst = TRUE;
/* 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[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 */
{
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++)
{
/* 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];
+ 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];
+ vk[1][r]*vh[1][c]-
+ vk[2][r]*vh[2][c];
+ }
+ }
+ }
}
for (i = 0; i < edi->flood.vecs.neig; i++)
{
if (edi->flood.vecs.refprojslope[i] != 0.0)
+ {
bOutputRef=TRUE;
+ }
}
if (bOutputRef)
{
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");
}
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;
}
+ }
}
/* 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++)
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;
}
/* 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, bNS, 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 */
/* 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);
/* 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);
+ }
}
{
/* Call flooding for one matrix */
if (edi->flood.vecs.neig)
+ {
do_single_flood(ed->edo,x,force,edi,step,box,cr,bNS);
+ }
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)
+static void init_flood(t_edpar *edi, gmx_edsam_t ed, real dt, t_commrec *cr, gmx_bool bPrintheader)
{
int i;
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");
+
+ if (bPrintheader)
+ {
+ 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");
+ }
}
}
count++;
}
if (nnames!=count-1)
+ {
gmx_fatal(FARGS,"Number of energies is not consistent with t_edi structure");
+ }
}
/************* END of FLOODING IMPLEMENTATION ****************************/
#endif
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;
}
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);
+ }
}
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 */
+ }
}
}
{
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;
/* 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");
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->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");
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");
- }
+ 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 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)
+static int read_edi_file(gmx_edsam_t ed, t_edpar *edi, int nr_mdatoms, t_commrec *cr)
{
FILE *in;
t_edpar *curr_edi,*last_edi;
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);
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;
/* Close the .edi file again */
gmx_fio_fclose(in);
+
+ return edi_nr;
}
/* 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);
for (i=0; i < s->nr; i++)
+ {
rmsd += distance2(s->x[i], x[i]);
+ }
rmsd /= (real) s->nr;
rmsd = sqrt(rmsd);
/* 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,
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
+ }
+ else
{
xu[XX] = x[XX]-tx*box[XX][XX];
xu[YY] = x[YY]-ty*box[YY][YY];
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 */
/* apply the correction */
proj[i] /= edi->sav.sqrtm[i];
proj[i] *= ratio;
- for (j=0; j<edi->sav.nr; j++) {
+ 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);
}
/* 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]);
+ }
GMX_MPE_LOG(ev_ed_apply_cons_finish);
}
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," 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));
}
{
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));
}
{
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));
}
if (NULL==floodvecs->refproj0)
+ {
snew(floodvecs->refproj0, floodvecs->neig);
+ }
for (i=0; i<floodvecs->neig; i++)
{
}
+/* Call on MASTER only. Check whether the essential dynamics / flooding
+ * datasets of the checkpoint file are consistent with the provided .edi file. */
+static void crosscheck_edi_file_vs_checkpoint(gmx_edsam_t ed, edsamstate_t *EDstate)
+{
+ t_edpar *edi = NULL; /* points to a single edi data set */
+ int i, edinum;
+
+
+ if (NULL == EDstate->nref || NULL == EDstate->nav)
+ {
+ gmx_fatal(FARGS, "Essential dynamics and flooding can only be switched on (or off) at the\n"
+ "start of a new simulation. If a simulation runs with/without ED constraints,\n"
+ "it must also continue with/without ED constraints when checkpointing.\n"
+ "To switch on (or off) ED constraints, please prepare a new .tpr to start\n"
+ "from without a checkpoint.\n");
+ }
+
+ edi=ed->edpar;
+ edinum = 0;
+ while(edi != NULL)
+ {
+ /* Check number of atoms in the reference and average structures */
+ if (EDstate->nref[edinum] != edi->sref.nr)
+ {
+ gmx_fatal(FARGS, "The number of reference structure atoms in ED dataset #%d is\n"
+ "not the same in .cpt (NREF=%d) and .edi (NREF=%d) files!\n",
+ edinum+1, EDstate->nref[edinum], edi->sref.nr);
+ }
+ if (EDstate->nav[edinum] != edi->sav.nr)
+ {
+ gmx_fatal(FARGS, "The number of average structure atoms in ED dataset #%d is\n"
+ "not the same in .cpt (NREF=%d) and .edi (NREF=%d) files!\n",
+ edinum+1, EDstate->nav[edinum], edi->sav.nr);
+ }
+ edi=edi->next_edi;
+ edinum++;
+ }
+
+ if (edinum != EDstate->nED)
+ {
+ gmx_fatal(FARGS, "The number of essential dynamics / flooding datasets is not consistent.\n"
+ "There are %d ED datasets in .cpt file, but %d in .edi file!\n"
+ "Are you shure this is the correct .edi file?\n", EDstate->nED, edinum);
+ }
+}
+
+
+/* The edsamstate struct stores the information we need to make the ED group
+ * whole again after restarts from a checkpoint file. Here we do the following:
+ * a) If we did not start from .cpt, we prepare the struct for proper .cpt writing,
+ * b) if we did start from .cpt, we copy over the last whole structures from .cpt,
+ * c) in any case, for subsequent checkpoint writing, we set the pointers in
+ * edsamstate to the x_old arrays, which contain the correct PBC representation of
+ * all ED structures at the last time step. */
+static void init_edsamstate(gmx_edsam_t ed, edsamstate_t *EDstate)
+{
+ int i, nr_edi;
+ t_edpar *edi;
+
+
+ snew(EDstate->old_sref_p, EDstate->nED);
+ snew(EDstate->old_sav_p , EDstate->nED);
+
+ /* If we did not read in a .cpt file, these arrays are not yet allocated */
+ if (!EDstate->bFromCpt)
+ {
+ snew(EDstate->nref, EDstate->nED);
+ snew(EDstate->nav , EDstate->nED);
+ }
+
+ /* Loop over all ED/flooding data sets (usually only one, though) */
+ edi = ed->edpar;
+ for (nr_edi = 1; nr_edi <= EDstate->nED; nr_edi++)
+ {
+ /* We always need the last reference and average positions such that
+ * in the next time step we can make the ED group whole again
+ * if the atoms do not have the correct PBC representation */
+ if (EDstate->bFromCpt)
+ {
+ /* Copy the last whole positions of reference and average group from .cpt */
+ for (i=0; i<edi->sref.nr; i++)
+ {
+ copy_rvec(EDstate->old_sref[nr_edi-1][i], edi->sref.x_old[i]);
+ }
+ for (i=0; i<edi->sav.nr ; i++)
+ {
+ copy_rvec(EDstate->old_sav [nr_edi-1][i], edi->sav.x_old [i]);
+ }
+ }
+ else
+ {
+ EDstate->nref[nr_edi-1] = edi->sref.nr;
+ EDstate->nav [nr_edi-1] = edi->sav.nr;
+ }
+
+ /* For subsequent checkpoint writing, set the edsamstate pointers to the edi arrays: */
+ EDstate->old_sref_p[nr_edi-1] = edi->sref.x_old;
+ EDstate->old_sav_p [nr_edi-1] = edi->sav.x_old ;
+
+ edi = edi->next_edi;
+ }
+}
+
+
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 */
+ matrix box, /* the box */
+ edsamstate_t *EDstate)
{
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,avindex;
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 *xfit=NULL, *xstart=NULL; /* dummy arrays to determine initial RMSDs */
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.");
+ }
GMX_MPE_LOG(ev_edsam_start);
if (MASTER(cr))
+ {
fprintf(stderr, "ED: Initializing essential dynamics constraints.\n");
+ if (NULL == ed)
+ {
+ gmx_fatal(FARGS, "The checkpoint file you provided is from an essential dynamics or\n"
+ "flooding simulation. Please also provide the correct .edi file with -ei.\n");
+ }
+ }
+
/* Needed for initializing radacc radius in do_edsam */
ed->bFirst = 1;
{
snew(ed->edpar,1);
/* Read the whole edi file at once: */
- read_edi_file(ed,ed->edpar,mtop->natoms,cr);
+ EDstate->nED = read_edi_file(ed,ed->edpar,mtop->natoms,cr);
+
+ /* Make shure the checkpoint was produced in a run using this .edi file */
+ if (EDstate->bFromCpt)
+ {
+ crosscheck_edi_file_vs_checkpoint(ed, EDstate);
+ }
+ init_edsamstate(ed, EDstate);
/* Initialization for every ED/flooding dataset. Flooding uses one edi dataset per
* flooding vector, Essential dynamics can be applied to more than one structure
init_edi(mtop,ir,cr,ed,edi);
/* Init flooding parameters if needed */
- init_flood(edi,ed,ir->delta_t,cr);
+ init_flood(edi,ed,ir->delta_t,cr,!EDstate->bFromCpt);
edi=edi->next_edi;
- numedis++;
}
}
edi=ed->edpar;
/* Loop over all ED/flooding data sets (usually only one, though) */
- for (nr_edi = 1; nr_edi <= numedis; nr_edi++)
+ for (nr_edi = 1; nr_edi <= EDstate->nED; 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++)
+ /* Extract the initial reference and average positions. When starting
+ * from .cpt, these have already been read into sref.x_old
+ * in init_edsamstate() */
+ if (!EDstate->bFromCpt)
{
- copy_rvec(x_pbc[edi->sref.anrs[i]], xfit[i]);
+ /* If this is the first run (i.e. no checkpoint present) we assume
+ * that the starting positions give us the correct PBC representation */
+ for (i=0; i < edi->sref.nr; i++)
+ {
+ copy_rvec(x_pbc[edi->sref.anrs[i]], edi->sref.x_old[i]);
+ }
- /* Save the sref positions such that in the next time step we can make the ED group whole
- * in case any of the atoms do not have the correct PBC representation */
- copy_rvec(xfit[i], edi->sref.x_old[i]);
+ for (i=0; i < edi->sav.nr; i++)
+ {
+ copy_rvec(x_pbc[edi->sav.anrs[i]], edi->sav.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 we can make the ED group whole
- * in case any of the atoms do not have the correct PBC representation */
- copy_rvec(xstart[i], edi->sav.x_old[i]);
- }
+ /* Now we have the PBC-correct start positions of the reference and
+ average structure. We copy that over to dummy arrays on which we
+ can apply fitting to print out the RMSD. We srenew the memory since
+ the size of the buffers is likely different for every ED dataset */
+ srenew(xfit , edi->sref.nr );
+ srenew(xstart, edi->sav.nr );
+ copy_rvecn(edi->sref.x_old, xfit, 0, edi->sref.nr);
+ copy_rvecn(edi->sav.x_old, xstart, 0, edi->sav.nr);
/* Make the fit to the REFERENCE structure, get translation and rotation */
fit_to_reference(xfit, fit_transvec, fit_rotmat, edi);
avindex = edi->star.nr - edi->sav.nr;
}
rad_project(edi, &edi->star.x[avindex], &edi->vecs.radcon, cr);
- } else
+ }
+ 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: 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
{
/* 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 (i=0; i<edi->flood.vecs.neig; i++)
{
- fprintf(stdout, "ED: EV %d flooding potential center: %11.4e", i, edi->flood.vecs.refproj[i]);
+ fprintf(stdout, "ED: EV %d flooding potential center: %11.4e", edi->flood.vecs.ieig[i], edi->flood.vecs.refproj[i]);
if (edi->flood.bHarmonic)
+ {
fprintf(stdout, " (adding %11.4e/timestep)", edi->flood.vecs.refprojslope[i]);
+ }
fprintf(stdout, "\n");
}
}
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))
+ if (ed->edo && !(EDstate->bFromCpt))
+ {
write_edo(nr_edi, edi, ed, -1, 0);
+ }
/* Prepare for the next edi data set: */
edi=edi->next_edi;
if (PAR(cr))
{
/* First let everybody know how many ED data sets to expect */
- gmx_bcast(sizeof(numedis), &numedis, cr);
+ gmx_bcast(sizeof(EDstate->nED), &EDstate->nED, cr);
/* Broadcast the essential dynamics / flooding data to all nodes */
- broadcast_ed_data(cr, ed, numedis);
+ broadcast_ed_data(cr, ed, EDstate->nED);
}
else
{
/* Loop over all ED data sets (usually only one, though) */
edi=ed->edpar;
- for (nr_edi = 1; nr_edi <= numedis; nr_edi++)
+ for (nr_edi = 1; nr_edi <= EDstate->nED; nr_edi++)
{
edi->sref.anrs_loc = edi->sref.anrs;
edi->sav.anrs_loc = edi->sav.anrs;
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;
/* Allocate space for ED buffer variables */
/* Again, loop over ED data sets */
edi=ed->edpar;
- for (nr_edi = 1; nr_edi <= numedis; nr_edi++)
+ for (nr_edi = 1; nr_edi <= EDstate->nED; nr_edi++)
{
/* Allocate space for ED buffer */
snew(edi->buf, 1);
/* Flush the edo file so that the user can check some things
* when the simulation has started */
if (ed->edo)
+ {
fflush(ed->edo);
+ }
GMX_MPE_LOG(ev_edsam_finish);
}
/* 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;
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 */
#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, PAR(cr) ? buf->bUpdateShifts : TRUE, 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 communicate_group_positions.
* We do not need to update the shifts until the next NS step. Note that dd_make_local_ed_indices
/* 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(buf->xcoll, edi);
rad_project(edi, buf->xcoll, &edi->vecs.radacc, cr);
buf->oldrad = 0.0;
- } else
+ }
+ else
+ {
buf->oldrad = edi->vecs.radacc.radius;
+ }
}
/* apply the constraints */
{
project(buf->xcoll, edi);
if (MASTER(cr) && !bSuppress)
+ {
write_edo(edinr, edi, ed, step, rmsdev);
+ }
}
/* Copy back the positions unless monitoring only */
#include "gmxcomplex.h"
#include "gmx_fft.h"
-#ifndef GMX_LIB_MPI
+#ifndef GMX_MPI
double MPI_Wtime();
#endif
#endif
if (getenv("GMX_NBNXN_SIMD_4XN") != NULL)
{
-#ifdef GMX_NBNXN_SIMD_2XNN
+#ifdef GMX_NBNXN_SIMD_4XN
*kernel_type = nbnxnk4xN_SIMD_4xN;
#else
gmx_fatal(FARGS,"SIMD 4xN kernels requested, but Gromacs has been compiled without support for these kernels");
Version: @PROJECT_VERSION@
Requires: libgmx@GMX_LIBS_SUFFIX@ @PKG_FFT@
Libs.private: -lm @CMAKE_THREAD_LIBS_INIT@
-Libs: -L${libdir} -lmd@GMX_LIBS_SUFFIX@ @PKG_FFT_LIBS@
+Libs: -L${libdir} -l@MD_PREFIX@md@GMX_LIBS_SUFFIX@ @PKG_FFT_LIBS@
Cflags: -I${includedir} @PKG_CFLAGS@
OPTIONS
RELWITHDEBINFO -g
DEBUG -g -D_DEBUG_=1)
+ #Because this is a static library linked into the (potential) shared library
+ #it should have the export of the shared library.
+ SET_TARGET_PROPERTIES(nbnxn_cuda PROPERTIES DEFINE_SYMBOL "md_EXPORTS" )
endif()
real *nbfp_i;
int n,ci,ci_sh;
int ish,ishf;
- gmx_bool half_LJ,do_coul;
+ gmx_bool do_LJ,half_LJ,do_coul;
int cjind0,cjind1,cjind;
int ip,jp;
ci = nbln->ci;
ci_sh = (ish == CENTRAL ? ci : -1);
- half_LJ = (nbln->shift & NBNXN_CI_HALF_LJ(0));
+ /* We have 5 LJ/C combinations, but use only three inner loops,
+ * as the other combinations are unlikely and/or not much faster:
+ * inner half-LJ + C for half-LJ + C / no-LJ + C
+ * inner LJ + C for full-LJ + C
+ * inner LJ for full-LJ + no-C / half-LJ + no-C
+ */
+ do_LJ = (nbln->shift & NBNXN_CI_DO_LJ(0));
do_coul = (nbln->shift & NBNXN_CI_DO_COUL(0));
+ half_LJ = ((nbln->shift & NBNXN_CI_HALF_LJ(0)) || !do_LJ) && do_coul;
#ifdef CALC_ENERGIES
#ifndef ENERGY_GROUPS
}
}
- /* With half_LJ we currently always calculate Coulomb interactions */
- if (do_coul || half_LJ)
+ if (do_coul)
{
#ifdef CALC_ENERGIES
real Vc_sub_self;
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/* GMX_MM128_HERE or GMX_MM256_HERE should be set before including this file */
+/* GMX_MM256_HERE should be set before including this file */
#include "gmx_simd_macros.h"
#define SUM_SIMD4(x) (x[0]+x[1]+x[2]+x[3])
#define UNROLLI NBNXN_CPU_CLUSTER_I_SIZE
#define UNROLLJ (GMX_SIMD_WIDTH_HERE/2)
-#if defined GMX_MM128_HERE || defined GMX_DOUBLE
-#define STRIDE 4
-#endif
-#if defined GMX_MM256_HERE && !defined GMX_DOUBLE
+#if defined GMX_MM256_HERE
#define STRIDE 4
#endif
-#ifdef GMX_MM128_HERE
-#ifndef GMX_DOUBLE
-/* SSE single precision 4x4 kernel */
-#define SUM_SIMD(x) SUM_SIMD4(x)
-#define TAB_FDV0
-#else
-/* SSE double precision 4x2 kernel */
-#define SUM_SIMD(x) (x[0]+x[1])
-#endif
-#endif
-
#ifdef GMX_MM256_HERE
#ifndef GMX_DOUBLE
-/* AVX single precision 4x8 kernel */
+/* single precision 2x(4+4) kernel */
#define SUM_SIMD(x) (x[0]+x[1]+x[2]+x[3]+x[4]+x[5]+x[6]+x[7])
#define TAB_FDV0
#else
-/* AVX double precision 4x4 kernel */
-#define SUM_SIMD(x) SUM_SIMD4(x)
+#error "unsupported kernel configuration"
#endif
#endif
int nbfp_stride;
int n,ci,ci_sh;
int ish,ish3;
- gmx_bool half_LJ,do_coul;
+ gmx_bool do_LJ,half_LJ,do_coul;
int sci,scix,sciy,sciz,sci2;
int cjind0,cjind1,cjind;
int ip,jp;
gmx_mm_pr diag_SSE0 = _mm256_castsi256_ps( _mm256_set_epi32( 0xffffffff, 0xffffffff, 0x00000000, 0x00000000, 0xffffffff, 0xffffffff, 0xffffffff, 0x00000000 ));
gmx_mm_pr diag_SSE2 = _mm256_castsi256_ps( _mm256_set_epi32( 0x00000000, 0x00000000, 0x00000000, 0x00000000, 0xffffffff, 0x00000000, 0x00000000, 0x00000000 ));
-#ifndef GMX_MM256_HERE
- __m128i zeroi_SSE = _mm_setzero_si128();
-#endif
#ifdef GMX_X86_SSE4_1
gmx_mm_pr zero_SSE = gmx_set1_pr(0);
#endif
egps_jshift = 2*nbat->neg_2log;
egps_jmask = (1<<egps_jshift) - 1;
egps_jstride = (UNROLLJ>>1)*UNROLLJ;
- /* Major division is over i-particles: divide nVS by 4 for i-stride */
+ /* Major division is over i-particle energy groups, determine the stride */
Vstride_i = nbat->nenergrp*(1<<nbat->neg_2log)*egps_jstride;
#endif
ish = (nbln->shift & NBNXN_CI_SHIFT);
ish3 = ish*3;
- cjind0 = nbln->cj_ind_start;
- cjind1 = nbln->cj_ind_end;
- /* Currently only works super-cells equal to sub-cells */
+ cjind0 = nbln->cj_ind_start;
+ cjind1 = nbln->cj_ind_end;
ci = nbln->ci;
ci_sh = (ish == CENTRAL ? ci : -1);
sci += (ci & 1)*(STRIDE>>1);
#endif
- half_LJ = (nbln->shift & NBNXN_CI_HALF_LJ(0));
+ /* We have 5 LJ/C combinations, but use only three inner loops,
+ * as the other combinations are unlikely and/or not much faster:
+ * inner half-LJ + C for half-LJ + C / no-LJ + C
+ * inner LJ + C for full-LJ + C
+ * inner LJ for full-LJ + no-C / half-LJ + no-C
+ */
+ do_LJ = (nbln->shift & NBNXN_CI_DO_LJ(0));
do_coul = (nbln->shift & NBNXN_CI_DO_COUL(0));
+ half_LJ = ((nbln->shift & NBNXN_CI_HALF_LJ(0)) || !do_LJ) && do_coul;
#ifdef ENERGY_GROUPS
egps_i = nbat->energrp[ci];
iz_SSE0 = gmx_add_pr(gmx_load2_hpr(x+sciz) ,shZ_SSE);
iz_SSE2 = gmx_add_pr(gmx_load2_hpr(x+sciz+2),shZ_SSE);
- /* With half_LJ we currently always calculate Coulomb interactions */
- if (do_coul || half_LJ)
+ if (do_coul)
{
gmx_mm_pr facel_SSE;
#ifdef GMX_MM128_HERE
#ifndef GMX_DOUBLE
-/* SSE single precision 4x4 kernel */
+/* single precision 4x4 kernel */
#define SUM_SIMD(x) SUM_SIMD4(x)
#define TAB_FDV0
#else
-/* SSE double precision 4x2 kernel */
+/* double precision 4x2 kernel */
#define SUM_SIMD(x) (x[0]+x[1])
#endif
#endif
#ifdef GMX_MM256_HERE
#ifndef GMX_DOUBLE
-/* AVX single precision 4x8 kernel */
+/* single precision 4x8 kernel */
#define SUM_SIMD(x) (x[0]+x[1]+x[2]+x[3]+x[4]+x[5]+x[6]+x[7])
#define TAB_FDV0
#else
-/* AVX double precision 4x4 kernel */
+/* double precision 4x4 kernel */
#define SUM_SIMD(x) SUM_SIMD4(x)
#endif
#endif
int nbfp_stride;
int n,ci,ci_sh;
int ish,ish3;
- gmx_bool half_LJ,do_coul;
+ gmx_bool do_LJ,half_LJ,do_coul;
int sci,scix,sciy,sciz,sci2;
int cjind0,cjind1,cjind;
int ip,jp;
__m128d fix2_SSE,fiy2_SSE,fiz2_SSE;
#endif
-#ifndef GMX_MM256_HERE
+#ifdef GMX_MM128_HERE
#ifndef GMX_DOUBLE
__m128i mask0 = _mm_set_epi32( 0x0008, 0x0004, 0x0002, 0x0001 );
__m128i mask1 = _mm_set_epi32( 0x0080, 0x0040, 0x0020, 0x0010 );
__m128i mask2 = _mm_set_epi32( 0x0020, 0x0020, 0x0010, 0x0010 );
__m128i mask3 = _mm_set_epi32( 0x0080, 0x0080, 0x0040, 0x0040 );
#endif
-#else
+#endif
+#ifdef GMX_MM256_HERE
/* AVX: use floating point masks, as there are no integer instructions */
#ifndef GMX_DOUBLE
gmx_mm_pr mask0 = _mm256_castsi256_ps(_mm256_set_epi32( 0x0080, 0x0040, 0x0020, 0x0010, 0x0008, 0x0004, 0x0002, 0x0001 ));
#endif
#endif
-#ifndef GMX_MM256_HERE
+#ifdef GMX_MM128_HERE
#ifndef GMX_DOUBLE
__m128 diag_SSE0 = gmx_mm_castsi128_pr( _mm_set_epi32( 0xffffffff, 0xffffffff, 0xffffffff, 0x00000000 ));
__m128 diag_SSE1 = gmx_mm_castsi128_pr( _mm_set_epi32( 0xffffffff, 0xffffffff, 0x00000000, 0x00000000 ));
__m128d diag1_SSE2 = gmx_mm_castsi128_pd( _mm_set_epi32( 0xffffffff, 0xffffffff, 0x00000000, 0x00000000 ));
__m128d diag1_SSE3 = gmx_mm_castsi128_pd( _mm_set_epi32( 0x00000000, 0x00000000, 0x00000000, 0x00000000 ));
#endif
-#else /* GMX_MM256_HERE */
+#endif
+#ifdef GMX_MM256_HERE
#ifndef GMX_DOUBLE
gmx_mm_pr diag0_SSE0 = _mm256_castsi256_ps( _mm256_set_epi32( 0xffffffff, 0xffffffff, 0xffffffff, 0xffffffff, 0xffffffff, 0xffffffff, 0xffffffff, 0x00000000 ));
gmx_mm_pr diag0_SSE1 = _mm256_castsi256_ps( _mm256_set_epi32( 0xffffffff, 0xffffffff, 0xffffffff, 0xffffffff, 0xffffffff, 0xffffffff, 0x00000000, 0x00000000 ));
#endif
#endif
-#ifndef GMX_MM256_HERE
+#ifdef GMX_MM128_HERE
__m128i zeroi_SSE = _mm_setzero_si128();
#endif
#ifdef GMX_X86_SSE4_1
egps_jshift = 2*nbat->neg_2log;
egps_jmask = (1<<egps_jshift) - 1;
egps_jstride = (UNROLLJ>>1)*UNROLLJ;
- /* Major division is over i-particles: divide nVS by 4 for i-stride */
+ /* Major division is over i-particle energy groups, determine the stride */
Vstride_i = nbat->nenergrp*(1<<nbat->neg_2log)*egps_jstride;
#endif
ish = (nbln->shift & NBNXN_CI_SHIFT);
ish3 = ish*3;
- cjind0 = nbln->cj_ind_start;
- cjind1 = nbln->cj_ind_end;
- /* Currently only works super-cells equal to sub-cells */
+ cjind0 = nbln->cj_ind_start;
+ cjind1 = nbln->cj_ind_end;
ci = nbln->ci;
ci_sh = (ish == CENTRAL ? ci : -1);
sci += (ci & 1)*(STRIDE>>1);
#endif
- half_LJ = (nbln->shift & NBNXN_CI_HALF_LJ(0));
+ /* We have 5 LJ/C combinations, but use only three inner loops,
+ * as the other combinations are unlikely and/or not much faster:
+ * inner half-LJ + C for half-LJ + C / no-LJ + C
+ * inner LJ + C for full-LJ + C
+ * inner LJ for full-LJ + no-C / half-LJ + no-C
+ */
+ do_LJ = (nbln->shift & NBNXN_CI_DO_LJ(0));
do_coul = (nbln->shift & NBNXN_CI_DO_COUL(0));
+ half_LJ = ((nbln->shift & NBNXN_CI_HALF_LJ(0)) || !do_LJ) && do_coul;
#ifdef ENERGY_GROUPS
egps_i = nbat->energrp[ci];
iz_SSE2 = gmx_add_pr(gmx_load1_pr(x+sciz+2),shZ_SSE);
iz_SSE3 = gmx_add_pr(gmx_load1_pr(x+sciz+3),shZ_SSE);
- /* With half_LJ we currently always calculate Coulomb interactions */
- if (do_coul || half_LJ)
+ if (do_coul)
{
iq_SSE0 = gmx_set1_pr(facel*q[sci]);
iq_SSE1 = gmx_set1_pr(facel*q[sci+1]);
{
sort_cj_excl(nbl->cj+nbl->ci[nbl->nci].cj_ind_start,jlen,nbl->work);
- if (nbl->ci[nbl->nci].shift & NBNXN_CI_HALF_LJ(0))
+ /* The counts below are used for non-bonded pair/flop counts
+ * and should therefore match the available kernel setups.
+ */
+ if (!(nbl->ci[nbl->nci].shift & NBNXN_CI_DO_COUL(0)))
{
- nbl->work->ncj_hlj += jlen;
+ nbl->work->ncj_noq += jlen;
}
- else if (!(nbl->ci[nbl->nci].shift & NBNXN_CI_DO_COUL(0)))
+ else if ((nbl->ci[nbl->nci].shift & NBNXN_CI_HALF_LJ(0)) ||
+ !(nbl->ci[nbl->nci].shift & NBNXN_CI_DO_LJ(0)))
{
- nbl->work->ncj_noq += jlen;
+ nbl->work->ncj_hlj += jlen;
}
nbl->nci++;
{
static const char *desc[] = {
"[TT]g_angle[tt] computes the angle distribution for a number of angles",
- "or dihedrals. This way you can check whether your simulation",
- "is correct. With option [TT]-ov[tt] you can plot the average angle of",
- "a group of angles as a function of time. With the [TT]-all[tt] option",
- "the first graph is the average, the rest are the individual angles.[PAR]",
+ "or dihedrals.[PAR]",
+ "With option [TT]-ov[tt], you can plot the average angle of",
+ "a group of angles as a function of time. With the [TT]-all[tt] option,",
+ "the first graph is the average and the rest are the individual angles.[PAR]",
"With the [TT]-of[tt] option, [TT]g_angle[tt] also calculates the fraction of trans",
"dihedrals (only for dihedrals) as function of time, but this is",
- "probably only fun for a selected few.[PAR]",
- "With option [TT]-oc[tt] a dihedral correlation function is calculated.[PAR]",
- "It should be noted that the index file should contain",
- "atom-triples for angles or atom-quadruplets for dihedrals.",
+ "probably only fun for a select few.[PAR]",
+ "With option [TT]-oc[tt], a dihedral correlation function is calculated.[PAR]",
+ "It should be noted that the index file must contain",
+ "atom triplets for angles or atom quadruplets for dihedrals.",
"If this is not the case, the program will crash.[PAR]",
- "With option [TT]-or[tt] a trajectory file is dumped containing cos and",
- "sin of selected dihedral angles which subsequently can be used as",
- "input for a PCA analysis using [TT]g_covar[tt].[PAR]",
+ "With option [TT]-or[tt], a trajectory file is dumped containing cos and",
+ "sin of selected dihedral angles, which subsequently can be used as",
+ "input for a principal components analysis using [TT]g_covar[tt].[PAR]",
"Option [TT]-ot[tt] plots when transitions occur between",
"dihedral rotamers of multiplicity 3 and [TT]-oh[tt]",
"records a histogram of the times between such transitions,",
"of the",
"helix in nm. This is simply the average rise (see above) times the",
"number of helical residues (see below).[BR]",
- "[BB]5.[bb] Number of helical residues (file [TT]n-ahx.xvg[tt]). The title says",
- "it all.[BR]",
- "[BB]6.[bb] Helix dipole, backbone only (file [TT]dip-ahx.xvg[tt]).[BR]",
- "[BB]7.[bb] RMS deviation from ideal helix, calculated for the C[GRK]alpha[grk]",
+ "[BB]5.[bb] Helix dipole, backbone only (file [TT]dip-ahx.xvg[tt]).[BR]",
+ "[BB]6.[bb] RMS deviation from ideal helix, calculated for the C[GRK]alpha[grk]",
"atoms only (file [TT]rms-ahx.xvg[tt]).[BR]",
- "[BB]8.[bb] Average C[GRK]alpha[grk] - C[GRK]alpha[grk] dihedral angle (file [TT]phi-ahx.xvg[tt]).[BR]",
- "[BB]9.[bb] Average [GRK]phi[grk] and [GRK]psi[grk] angles (file [TT]phipsi.xvg[tt]).[BR]",
- "[BB]10.[bb] Ellipticity at 222 nm according to Hirst and Brooks.",
+ "[BB]7.[bb] Average C[GRK]alpha[grk] - C[GRK]alpha[grk] dihedral angle (file [TT]phi-ahx.xvg[tt]).[BR]",
+ "[BB]8.[bb] Average [GRK]phi[grk] and [GRK]psi[grk] angles (file [TT]phipsi.xvg[tt]).[BR]",
+ "[BB]9.[bb] Ellipticity at 222 nm according to Hirst and Brooks.",
"[PAR]"
};
static const char *ppp[efhNR+2] = {
static const char *desc[] = {
"[TT]make_edi[tt] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
"based on eigenvectors of a covariance matrix ([TT]g_covar[tt]) or from a",
- "normal modes anaysis ([TT]g_nmeig[tt]).",
+ "normal modes analysis ([TT]g_nmeig[tt]).",
"ED sampling can be used to manipulate the position along collective coordinates",
"(eigenvectors) of (biological) macromolecules during a simulation. Particularly,",
"it may be used to enhance the sampling efficiency of MD simulations by stimulating",
"before a new cycle is started.[PAR]",
"Note on the parallel implementation: since ED sampling is a 'global' thing",
"(collective coordinates etc.), at least on the 'protein' side, ED sampling",
- "is not very parallel-friendly from an implentation point of view. Because",
+ "is not very parallel-friendly from an implementation point of view. Because",
"parallel ED requires some extra communication, expect the performance to be",
- "lower as in a free MD simulation, especially on a large number of nodes. [PAR]",
- "All output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a .edo file. In the output",
+ "lower as in a free MD simulation, especially on a large number of nodes and/or",
+ "when the ED group contains a lot of atoms. [PAR]",
+ "Please also note that if your ED group contains more than a single protein,",
+ "then the [TT].tpr[tt] file must contain the correct PBC representation of the ED group.",
+ "Take a look on the initial RMSD from the reference structure, which is printed",
+ "out at the start of the simulation; if this is much higher than expected, one",
+ "of the ED molecules might be shifted by a box vector. [PAR]",
+ "All output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [TT].edo[tt] file. In the output",
"file, per OUTFRQ step the following information is present: [PAR]",
"[TT]*[tt] the step number[BR]",
"[TT]*[tt] the number of the ED dataset. ([BB]Note[bb] that you can impose multiple ED constraints in",
"is kept in that region.",
"[PAR]",
"The origin is normally the average structure stored in the [TT]eigvec.trr[tt] file.",
- "It can be changed with [TT]-ori[tt] to an arbitrary position in configurational space.",
+ "It can be changed with [TT]-ori[tt] to an arbitrary position in configuration space.",
"With [TT]-tau[tt], [TT]-deltaF0[tt], and [TT]-Eflnull[tt] you control the flooding behaviour.",
"Efl is the flooding strength, it is updated according to the rule of adaptive flooding.",
"Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth). ",
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff