########################################################################
include(CheckCSourceCompiles) # for gmxTestMPI_IN_PLACE
if(GMX_MPI)
- MESSAGE(WARNING "
- There are known problems with some MPI implementations:
- OpenMPI version < 1.4.1
- MVAPICH2 version <= 1.4.1 *")
if(GMX_THREADS)
#message(FATAL_ERROR "Thread-based parallelization conflicts with MPI.")
set(GMX_THREADS OFF CACHE BOOL
if (GMX_MPI_IN_PLACE)
gmx_test_mpi_in_place(MPI_IN_PLACE_EXISTS)
endif (GMX_MPI_IN_PLACE)
+
+ # test for unsuitable versions of OpenMPI
+ exec_program(${MPIEXEC}
+ ARGS --version
+ OUTPUT_VARIABLE MPI_TYPE
+ RETURN_VALUE MPI_EXEC_RETURN)
+ if(MPI_EXEC_RETURN EQUAL 0)
+ if(MPI_TYPE MATCHES "Open MPI|OpenRTE")
+ string(REGEX MATCH "[0-9]+\\.[0-9]*\\.?[0-9]*" MPI_VERSION ${MPI_TYPE})
+ if(MPI_VERSION VERSION_LESS "1.4.1")
+ MESSAGE(WARNING "
+ There are known problems with OpenMPI version < 1.4.1.
+ Please consider updating your OpenMPI.")
+ endif(MPI_VERSION VERSION_LESS "1.4.1")
+ unset(MPI_VERSION)
+ else(MPI_TYPE MATCHES "Open MPI|OpenRTE")
+ # This is not OpenMPI, so give the old generic warning message
+ MESSAGE(WARNING "
+ There are known problems with some MPI implementations:
+ MVAPICH2 version <= 1.4.1
+ Please consider updating your MPI if applicable.")
+ endif(MPI_TYPE MATCHES "Open MPI|OpenRTE")
+ unset(MPI_TYPE)
+ endif(MPI_EXEC_RETURN EQUAL 0)
else(MPI_FOUND)
message(FATAL_ERROR "MPI support requested, but no MPI compiler found.")
endif(MPI_FOUND)
check_function_exists(fseeko HAVE_FSEEKO)
include(gmxTestSignal)
-gmx_test_retsigtype(RETSIGTYPE)
gmx_test_sigusr1(HAVE_SIGUSR1)
include(gmxTestInline)
# turn on SSE if supported with reasonable defaults.
if (${GMX_ACCELERATION} STREQUAL "auto" AND NOT GMX_OPENMM)
- if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(i.86|x86|x64|x86_64|AMD64|amd64)")
+ if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(i.86|x86|x64|x86_64|AMD64|amd64)" OR CYGWIN)
set(GMX_ACCELERATION "SSE" CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec, fortran" FORCE)
set(GMX_X11 OFF CACHE BOOL "X11 not compatible with BlueGene, disabled!" FORCE)
set(GMX_THREADS OFF CACHE BOOL "Threads not compatible with BlueGene, disabled!" FORCE)
set(GMX_MPI ON CACHE BOOL "Use MPI on BlueGene" FORCE)
- set(GMX_EXTERNAL_BLAS TRUE CACHE BOOL "Use MASSV for BLAS on BlueGene" FORCE)
- set(GMX_EXTERNAL_LAPACK TRUE CACHE BOOL "Use MASSV for LAPACK on BlueGene" FORCE)
- list(APPEND GMX_EXTRA_LIBRARIES massv)
elseif(${GMX_ACCELERATION} STREQUAL "POWER6")
set(GMX_POWER6 1)
set(GMX_SOFTWARE_INVSQRT OFF CACHE BOOL "Do not use software reciprocal square root on Power6" FORCE)
mark_as_advanced(BUILD_TESTING)
IF(BUILD_TESTING)
enable_testing()
- add_test(TestBuildAll make)
add_subdirectory(tests)
ENDIF()
--- /dev/null
+SET(CTEST_PROJECT_NAME "Gromacs")
+SET(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
+
+IF(NOT DEFINED CTEST_DROP_METHOD)
+ SET(CTEST_DROP_METHOD "http")
+ENDIF(NOT DEFINED CTEST_DROP_METHOD)
+
+IF(CTEST_DROP_METHOD STREQUAL "http")
+ SET(CTEST_DROP_SITE "cdash.gromacs.org")
+ SET(CTEST_DROP_LOCATION "/submit.php?project=Gromacs")
+ SET(CTEST_DROP_SITE_CDASH TRUE)
+ENDIF(CTEST_DROP_METHOD STREQUAL "http")
+
--- /dev/null
+#!/bin/sh -x
+if [ -n "${CMakeVersion}" ] ; then
+ export PATH=$HOME/tools/cmake-${CMakeVersion}/bin:$PATH
+fi
+CC=gcc-${CompilerVersion} CXX=g++-${CompilerVersion} cmake -D GMX_DOUBLE=${GMX_DOUBLE} -D GMX_MPI=${GMX_MPI} -D GMX_OPENMP=${GMX_OPENMP} -DGMX_DEFAULT_SUFFIX=off -DCMAKE_BUILD_TYPE=Debug . &&
+make &&
+ctest -D ExperimentalTest -V
--- /dev/null
+REM Requires Windows SDK and CMake to be in the path
+REM Run Windows SDK SetEnv script
+SetEnv && ^
+cmake -G "Visual Studio 10 Win64" -D GMX_DOUBLE=%GMX_DOUBLE% -D GMX_MPI=%GMX_MPI% -D GMX_OPENMP=%GMX_OPENMP% -DGMX_DEFAULT_SUFFIX=off -DCMAKE_BUILD_TYPE=Debug . && ^
+msbuild All_Build.vcxproj && ^
+REM currently the test one example test doesn't work on Windows
+REM ctest -D ExperimentalTest -V
+
--- /dev/null
+# The module defines the following variables:
+# GIT_EXECUTABLE - path to git command line client
+# GIT_FOUND - true if the command line client was found
+# Example usage:
+# find_package(Git)
+# if(GIT_FOUND)
+# message("git found: ${GIT_EXECUTABLE}")
+# endif()
+
+#=============================================================================
+# Copyright 2010 Kitware, Inc.
+#
+# Distributed under the OSI-approved BSD License (the "License");
+# see accompanying file Copyright.txt for details.
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#=============================================================================
+# (To distributed this file outside of CMake, substitute the full
+# License text for the above reference.)
+
+# Look for 'git' or 'eg' (easy git)
+#
+set(git_names git eg)
+
+# Prefer .cmd variants on Windows unless running in a Makefile
+# in the MSYS shell.
+#
+if(WIN32)
+ if(NOT CMAKE_GENERATOR MATCHES "MSYS")
+ set(git_names git.cmd git eg.cmd eg)
+ endif()
+endif()
+
+find_program(GIT_EXECUTABLE
+ NAMES ${git_names}
+ DOC "git command line client"
+ )
+mark_as_advanced(GIT_EXECUTABLE)
+
+# Handle the QUIETLY and REQUIRED arguments and set GIT_FOUND to TRUE if
+# all listed variables are TRUE
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(Git DEFAULT_MSG GIT_EXECUTABLE)
# GEN_VERSION_INFO_INTERNAL has to be set ON.
#
# The following variables have to be previously defined:
-# Git_EXECUTABLE - path to git binary
-# Git_VERSION - git version (if not defined it's assumed that >=1.5.3)
+# GIT_EXECUTABLE - path to git binary
+# GIT_VERSION - git version (if not defined it's assumed that >=1.5.3)
# PROJECT_VERSION - hard-coded version string, should have the following structure:
# VERSION[-dev-SUFFIX] where the VERSION can have any form and the suffix
# is optional but should start with -dev
# if git executable xists and it's compatible version
# build the development version string
# this should at some point become VERSION_LESS
-if(EXISTS ${Git_EXECUTABLE} AND NOT Git_VERSION STRLESS "1.5.1")
+if(EXISTS ${GIT_EXECUTABLE} AND NOT ${GIT_VERSION} STRLESS "1.5.1")
# refresh git index
- execute_process(COMMAND ${Git_EXECUTABLE} update-index -q --refresh
+ execute_process(COMMAND ${GIT_EXECUTABLE} update-index -q --refresh
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
TIMEOUT 5
OUTPUT_QUIET
)
# get the full hash of the current HEAD
- execute_process(COMMAND ${Git_EXECUTABLE} rev-parse HEAD
+ execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse HEAD
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
OUTPUT_VARIABLE GMX_GIT_HEAD_HASH
ERROR_VARIABLE EXEC_ERR
string(SUBSTRING ${GMX_GIT_HEAD_HASH} 0 5 HEAD_HASH_SHORT)
# if there are local uncommitted changes, the build gets labeled "dirty"
- execute_process(COMMAND ${Git_EXECUTABLE} diff-index --name-only HEAD
+ execute_process(COMMAND ${GIT_EXECUTABLE} diff-index --name-only HEAD
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
OUTPUT_VARIABLE SRC_LOCAL_CHANGES
ERROR_VARIABLE EXEC_ERR
# if git is older then 1.5.3 we need to extract the RFC2822 style date
# and massage it, otherwise the ISO 8601 format is more trusworthy
# this should at some point become VERSION_LESS
- if (NOT Git_VERSION STREQUAL "" AND Git_VERSION STRLESS "1.5.3")
- execute_process(COMMAND ${Git_EXECUTABLE} rev-list -n1 "--pretty=format:%cD" HEAD
+ if (NOT GIT_VERSION STREQUAL "" AND GIT_VERSION STRLESS "1.5.3")
+ execute_process(COMMAND ${GIT_EXECUTABLE} rev-list -n1 "--pretty=format:%cD" HEAD
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
OUTPUT_VARIABLE HEAD_DATE
ERROR_VARIABLE EXEC_ERR
string(REGEX REPLACE "DEC" "12" HEAD_DATE ${HEAD_DATE})
else()
# get the date of the HEAD commit
- execute_process(COMMAND ${Git_EXECUTABLE} rev-list -n1 "--pretty=format:%ci" HEAD
+ execute_process(COMMAND ${GIT_EXECUTABLE} rev-list -n1 "--pretty=format:%ci" HEAD
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
OUTPUT_VARIABLE HEAD_DATE
ERROR_VARIABLE EXEC_ERR
set(VERSION_STR_SUFFIX "${HEAD_DATE}-${HEAD_HASH_SHORT}${DIRTY_STR}")
# find the name of the remote which is located on the official gromacs git server
- execute_process(COMMAND ${Git_EXECUTABLE} config --get-regexp
+ execute_process(COMMAND ${GIT_EXECUTABLE} config --get-regexp
"remote\\..*\\.url" "git\\.gromacs\\.org[:|/]gromacs"
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
OUTPUT_VARIABLE GMX_REMOTE
# find the first ancestor in the list provided by rev-list (not
# necessarily the last though) which is in GMX_REMOTE, extract the
# hash and the number of commits HEAD is ahead with
- execute_process(COMMAND ${Git_EXECUTABLE} rev-list --max-count=100 HEAD
+ execute_process(COMMAND ${GIT_EXECUTABLE} rev-list --max-count=100 HEAD
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
OUTPUT_VARIABLE ANCESTOR_LIST
)
set(AHEAD 0)
set(GMX_GIT_REMOTE_HASH "")
foreach(OBJ ${ANCESTOR_LIST})
- execute_process(COMMAND ${Git_EXECUTABLE} name-rev --refs=refs/remotes/${GMX_REMOTE}/* ${OBJ}
+ execute_process(COMMAND ${GIT_EXECUTABLE} name-rev --refs=refs/remotes/${GMX_REMOTE}/* ${OBJ}
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
OUTPUT_VARIABLE HASH_AND_REVNAME
OUTPUT_STRIP_TRAILING_WHITESPACE
+++ /dev/null
-# - Define macro to check return type of signals (int/void)
-#
-# GMX_TEST_RETSIGTYPE(VARIABLE)
-#
-# VARIABLE will be set to the return type of signals - "int" or "void"
-#
-# Remember to have a cmakedefine for it too...
-
-MACRO(GMX_TEST_RETSIGTYPE VARIABLE)
- IF(NOT DEFINED ${VARIABLE})
-
- MESSAGE(STATUS "Checking for return type of signals")
-
- # First check without any special flags
- TRY_COMPILE(RETSIGTYPE_INT_OK "${CMAKE_BINARY_DIR}"
- "${CMAKE_SOURCE_DIR}/cmake/TestRetSigType.c")
-
- if(RETSIGTYPE_INT_OK)
- MESSAGE(STATUS "Checking for return type of signals - int")
- set(${VARIABLE} "int" CACHE INTERNAL "Result of test for signal return type" FORCE)
- else(RETSIGTYPE_INT_OK)
- MESSAGE(STATUS "Checking for return type of signals - void")
- set(${VARIABLE} "void" CACHE INTERNAL "Result of test for signal return type" FORCE)
- endif(RETSIGTYPE_INT_OK)
-
- ENDIF(NOT DEFINED ${VARIABLE})
-ENDMACRO(GMX_TEST_RETSIGTYPE VARIABLE)
-
-
-
-# - Define macro to check return type of signals (int/void)
-#
-# GMX_TEST_RETSIGTYPE(VARIABLE)
-#
-# VARIABLE will be set to the return type of signals - "int" or "void"
-#
-# Remember to have a cmakedefine for it too...
-
-MACRO(GMX_TEST_RETSIGTYPE VARIABLE)
- IF(NOT DEFINED ${VARIABLE})
-
- MESSAGE(STATUS "Checking for return type of signals")
-
- # First check without any special flags
- TRY_COMPILE(RETSIGTYPE_INT_OK "${CMAKE_BINARY_DIR}"
- "${CMAKE_SOURCE_DIR}/cmake/TestRetSigType.c")
-
- if(RETSIGTYPE_INT_OK)
- MESSAGE(STATUS "Checking for return type of signals - int")
- set(${VARIABLE} "int" CACHE INTERNAL "Result of test for signal return type" FORCE)
- else(RETSIGTYPE_INT_OK)
- MESSAGE(STATUS "Checking for return type of signals - void")
- set(${VARIABLE} "void" CACHE INTERNAL "Result of test for signal return type" FORCE)
- endif(RETSIGTYPE_INT_OK)
-
- ENDIF(NOT DEFINED ${VARIABLE})
-ENDMACRO(GMX_TEST_RETSIGTYPE VARIABLE)
-
-
-
# - Define macro to check if SIGUSR1 is defined
#
# GMX_TEST_SIGUSR1(VARIABLE)
gmx_bool bHisto, const char *fn_histo, int maxchi,
real **dih, int nlist, t_dlist dlist[],
int nframes, int nangles, const char *grpname,
- int xity[], real t0, real dt, gmx_bool bRb,
+ int multiplicity[], real t0, real dt, gmx_bool bRb,
real core_frac, const output_env_t oenv);
- /* as above but passes dlist so can copy occupancies into it, and xity[]
+ /* as above but passes dlist so can copy occupancies into it, and multiplicity[]
* (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
* rotamers. Also production of xvg output files is conditional
* and the fractional width of each rotamer can be set ie for a 3 fold
void mk_chi_lookup (int **lookup, int maxchi, real **dih,
int nlist, t_dlist dlist[]) ;
-void mk_multiplicity_lookup (int *xity, int maxchi, real **dih,
+void mk_multiplicity_lookup (int *multiplicity, int maxchi, real **dih,
int nlist, t_dlist dlist[],int nangle) ;
void get_chi_product_traj (real **dih,int nframes,int nangles,
int nlist,int maxchi, t_dlist dlist[],
- real time[], int **lookup,int *xity,
+ real time[], int **lookup,int *multiplicity,
gmx_bool bRb,gmx_bool bNormalize,
real core_frac,gmx_bool bAll,const char *fnall,
const output_env_t oenv);
* structure is simply nrow*ncol floating-point elements. The sparse
* matrix structure should be freed with gmx_sparsematrix_destroy() when you are done.
*
- * To determine the format you should set full_matrix and sparse_matrix to NULL
+ * To determine the format you should set *full_matrix and *sparse_matrix to NULL
* before calling this routine, and check which one is non-NULL on return.
*/
void
#define NRFP(ftype) (NRFPA(ftype)+NRFPB(ftype))
#define NRAL(ftype) (interaction_function[(ftype)].nratoms)
-#define IS_CHEMBOND(ftype) (interaction_function[(ftype)].nratoms==2 && interaction_function[(ftype)].flags & IF_CHEMBOND)
+#define IS_CHEMBOND(ftype) (interaction_function[(ftype)].nratoms==2 && (interaction_function[(ftype)].flags & IF_CHEMBOND))
/* IS_CHEMBOND tells if function type ftype represents a chemical bond */
/* IS_ANGLE tells if a function type ftype represents an angle
* Per Larsson, 2007-11-06
*/
-#define IS_ANGLE(ftype) (interaction_function[(ftype)].nratoms==3 && interaction_function[(ftype)].flags & IF_ATYPE)
+#define IS_ANGLE(ftype) (interaction_function[(ftype)].nratoms==3 && (interaction_function[(ftype)].flags & IF_ATYPE))
#define IS_VSITE(ftype) (interaction_function[(ftype)].flags & IF_VSITE)
#define IS_TABULATED(ftype) (interaction_function[(ftype)].flags & IF_TABULATED)
The GROMACS xpm file format is compatible with the XPixMap format
and is used for storing matrix data.
Thus GROMACS xpm files can be viewed directly with programs like XV.
+Alternatively, they can be imported into GIMP and scaled to 300 DPI,
+using strong antialiasing for font and graphics.
The first matrix data line in an xpm file corresponds to the last matrix
row.
In addition to the XPixMap format, GROMACS xpm files may contain
[ atoms ]
; id at type res nr residu name at name cg nr charge
-1 ZN 1 ZN ZN 1 -2
+1 ZN 1 ZN ZN 1 2
order! Only relevant when FLOAT_FORMAT_IEEE754 is defined. */
#cmakedefine GMX_IEEE754_BIG_ENDIAN_WORD_ORDER
-/* Define as the return type of signal handlers (int or void). */
-#cmakedefine RETSIGTYPE @RETSIGTYPE@
-
/* Define if SIGUSR1 is present */
#cmakedefine HAVE_SIGUSR1
if(USE_VERSION_H)
add_custom_target(gmx_version ALL
COMMAND ${CMAKE_COMMAND}
- -D Git_EXECUTABLE="${Git_EXECUTABLE}"
- -D Git_VERSION="${Git_VERSION}"
+ -D GIT_EXECUTABLE="${GIT_EXECUTABLE}"
+ -D GIT_VERSION="${GIT_VERSION}"
-D PROJECT_VERSION="${PROJECT_VERSION}"
-D PROJECT_SOURCE_DIR="${PROJECT_SOURCE_DIR}"
-D VERSION_C_CMAKEIN="${CMAKE_SOURCE_DIR}/src/gmxlib/version.c.cmakein"
/* Loop over all bonded force types to calculate the bonded forces */
for(ftype=0; (ftype<F_NRE); ftype++) {
if(ftype<F_GB12 || ftype>F_GB14) {
- if (interaction_function[ftype].flags & IF_BOND &&
+ if ((interaction_function[ftype].flags & IF_BOND) &&
!(ftype == F_CONNBONDS || ftype == F_POSRES)) {
nbonds=idef->il[ftype].nr;
if (nbonds > 0) {
for(ftype=0; (ftype<F_NRE); ftype++) {
if(ftype<F_GB12 || ftype>F_GB14) {
- if (interaction_function[ftype].flags & IF_BOND &&
+ if ((interaction_function[ftype].flags & IF_BOND) &&
!(ftype == F_CONNBONDS || ftype == F_POSRES))
{
nbonds_np = idef->il[ftype].nr_nonperturbed;
cp_error();
}
*bReadEkin = ((flags_eks & (1<<eeksEKINH)) || (flags_eks & (1<<eeksEKINF)) || (flags_eks & (1<<eeksEKINO)) ||
- (flags_eks & (1<<eeksEKINSCALEF)) | (flags_eks & (1<<eeksEKINSCALEH)) | (flags_eks & (1<<eeksVSCALE)));
+ ((flags_eks & (1<<eeksEKINSCALEF)) | (flags_eks & (1<<eeksEKINSCALEH)) | (flags_eks & (1<<eeksVSCALE))));
ret = do_cpt_enerhist(gmx_fio_getxdr(fp),TRUE,
flags_enh,&state->enerhist,NULL);
gmx_fio_do_int(fio, i);
- if(i==GMX_MTXIO_FULL_MATRIX)
+ if(i==GMX_MTXIO_FULL_MATRIX && NULL != full_matrix)
{
printf("Full matrix storage format, nrow=%d, ncols=%d\n",*nrow,*ncol);
snew((*full_matrix),sz);
bDum=gmx_fio_ndo_real(fio, (*full_matrix),sz);
}
- else
+ else if (NULL != sparse_matrix)
{
/* Sparse storage */
printf("Sparse matrix storage format, nrow=%d, ncols=%d\n",*nrow,*ncol);
};
const char *epull_names[epullNR+1] = {
- "no", "umbrella", "constraint", "constant_force", NULL
+ "no", "umbrella", "constraint", "constant-force", NULL
};
const char *epullg_names[epullgNR+1] = {
- "distance", "direction", "cylinder", "position", "direction_periodic", NULL
+ "distance", "direction", "cylinder", "position", "direction-periodic", NULL
};
const char *eQMmethod_names[eQMmethodNR+1] = {
ntype = *p_ntype;
nthreads = *p_nthreads;
_facel = *p_facel;
- _tabscale = *p_tabscale;
- _gbtabscale = *p_gbtabscale;
- _krf = *p_krf;
- _crf = *p_crf;
+#if (COULOMB == COULOMB_TAB || VDW == VDW_TAB)
+ _tabscale = *p_tabscale;
+#else
+ _tabscale = 0.0;
+#endif
+#if COULOMB == REACTION_FIELD
+ _krf = *p_krf;
+ _crf = *p_crf;
+#else
+ _krf = 0.0;
+ _crf = 0.0;
+#endif
+#if COULOMB == GENERALIZED_BORN
+ _gbtabscale = *p_gbtabscale;
+#else
+ _gbtabscale = 0.0;
+#endif
nj1 = 0;
for(n=0; (n<nri); n++)
int k,ggid;
real _iq = _facel * charge[ii];
+#if COULOMB == GENERALIZED_BORN
real _isai = invsqrta[ii];
+#else
+ real _isai = 0.0;
+#endif
// add the shift vector to all water atoms
#if COULOMB == GENERALIZED_BORN
dvda[jnr11] -= __creal(dvdaj);
- dvda[jnr21] -= __creal(dvdaj);
+ dvda[jnr21] -= __cimag(dvdaj);
dvdaj = __cmplx(dvda[jnr12],dvda[jnr22]);
#endif
#if COULOMB == GENERALIZED_BORN
dvda[jnr12] -= __creal(dvdaj);
- dvda[jnr22] -= __creal(dvdaj);
+ dvda[jnr22] -= __cimag(dvdaj);
dvdaj = __cmplx(dvda[jnr13],dvda[jnr23]);
#endif
#if COULOMB == GENERALIZED_BORN
dvda[jnr13] -= __creal(dvdaj);
- dvda[jnr23] -= __creal(dvdaj);
+ dvda[jnr23] -= __cimag(dvdaj);
#endif
#ifndef NO_FORCE
ntype = *p_ntype;
nthreads = *p_nthreads;
_facel = *p_facel;
+#if (COULOMB == COULOMB_TAB || VDW == VDW_TAB)
_tabscale = *p_tabscale;
- _gbtabscale = *p_gbtabscale;
+#else
+ _tabscale = 0.0;
+#endif
+#if COULOMB == REACTION_FIELD
_krf = *p_krf;
_crf = *p_crf;
+#else
+ _krf = 0.0;
+ _crf = 0.0;
+#endif
+#if COULOMB == GENERALIZED_BORN
+ _gbtabscale = *p_gbtabscale;
+#else
+ _gbtabscale = 0.0;
+#endif
ii = iinr[0];
_qO = _facel * charge[ii];
ntype = *p_ntype;
nthreads = *p_nthreads;
_facel = *p_facel;
+#if (COULOMB == COULOMB_TAB || VDW == VDW_TAB)
_tabscale = *p_tabscale;
+#else
+ _tabscale = 0.0;
+#endif
+#if COULOMB == REACTION_FIELD
_krf = *p_krf;
_crf = *p_crf;
- _gbtabscale = *p_gbtabscale;
+#else
+ _krf = 0.0;
+ _crf = 0.0;
+#endif
+#if COULOMB == GENERALIZED_BORN
+ _gbtabscale = *p_gbtabscale;
+#else
+ _gbtabscale = 0.0;
+#endif
ii = iinr[0];
ntype = *p_ntype;
nthreads = *p_nthreads;
_facel = *p_facel;
+#if (COULOMB == COULOMB_TAB || VDW == VDW_TAB)
_tabscale = *p_tabscale;
- _gbtabscale = *p_gbtabscale;
+#else
+ _tabscale = 0.0;
+#endif
+#if COULOMB == REACTION_FIELD
_krf = *p_krf;
_crf = *p_crf;
+#else
+ _krf = 0.0;
+ _crf = 0.0;
+#endif
+#if COULOMB == GENERALIZED_BORN
+ _gbtabscale = *p_gbtabscale;
+#else
+ _gbtabscale = 0.0;
+#endif
ii = iinr[0];
_qH = _facel * charge[ii+1];
ntype = *p_ntype;
nthreads = *p_nthreads;
_facel = *p_facel;
+#if (COULOMB == COULOMB_TAB || VDW == VDW_TAB)
_tabscale = *p_tabscale;
+#else
+ _tabscale = 0.0;
+#endif
+#if COULOMB == REACTION_FIELD
_krf = *p_krf;
_crf = *p_crf;
- _gbtabscale = *p_gbtabscale;
+#else
+ _krf = 0.0;
+ _crf = 0.0;
+#endif
+#if COULOMB == GENERALIZED_BORN
+ _gbtabscale = *p_gbtabscale;
+#else
+ _gbtabscale = 0.0;
+#endif
ii = iinr[0];
/** Initializes the \p insolidangle selection method. */
static int
init_insolidangle(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
-/** Sets the COM/COG data for the \p insolidangle selection method. */
-static void
-set_comg_insolidangle(gmx_ana_pos_t *pos, void *data);
/** Frees the data allocated for the \p insolidangle selection method. */
static void
free_data_insolidangle(void *data);
static volatile sig_atomic_t usr_condition=0;
-static RETSIGTYPE signal_handler(int n)
+static void signal_handler(int n)
{
switch (n) {
/* windows doesn't do SIGINT correctly according to ANSI (yes, signals are in
static tMPI_Thread_mutex_t tc_mutex=TMPI_THREAD_MUTEX_INITIALIZER;
#endif
-typedef struct {
- real tfactor;
- const char *tstr,*xvgstr;
-} t_timeconvert;
-
-static const t_timeconvert timeconvert[] = {
- { 0, NULL, NULL },
- { 1e3, "fs", "fs" },
- { 1, "ps", "ps" },
- { 1e-3, "ns", "ns" },
- { 1e-6, "us", "\\mus" },
- { 1e-9, "ms", "ms" },
- { 1e-12, "s", "s" },
- { (1.0/60.0)*1e-12, "m", "m" },
- { (1.0/3600.0)*1e-12, "h", "h" },
- { 0, NULL, NULL }
-};
-
gmx_bool bTimeSet(int tcontrol)
{
gmx_bool ret;
for(i=0; i<nind; i++)
copy_rvec(fr->f[ind[i]],fout[i]);
}
+ /* no break */
case efXTC:
case efG87:
if (fr->bX) {
case efTRR:
if (vout) sfree(vout);
if (fout) sfree(fout);
+ /* no break */
case efXTC:
case efG87:
sfree(xout);
}
if (bRet) {
- bMissingData = ((fr->flags & TRX_NEED_X && !fr->bX) ||
- (fr->flags & TRX_NEED_V && !fr->bV) ||
- (fr->flags & TRX_NEED_F && !fr->bF));
+ bMissingData = (((fr->flags & TRX_NEED_X) && !fr->bX) ||
+ ((fr->flags & TRX_NEED_V) && !fr->bV) ||
+ ((fr->flags & TRX_NEED_F) && !fr->bF));
bSkip = FALSE;
if (!bMissingData) {
ct=check_times2(fr->time,fr->t0,fr->tpf,fr->tppf,fr->bDouble);
- if (ct == 0 || (fr->flags & TRX_DONT_SKIP && ct<0)) {
+ if (ct == 0 || ((fr->flags & TRX_DONT_SKIP) && ct<0)) {
printcount(status, oenv,fr->time,FALSE);
} else if (ct > 0)
bRet = FALSE;
fprintf(out,"\n");
pr_indent(out,indent);
- fprintf(out,"ref_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,"tau_t%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");
fprintf(out," %10s",EANNEAL(opts->annealing[i]));
fprintf(out,"\n");
- fprintf(out,"ann_npoints%s",bMDPformat ? " = " : ":");
+ 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->ngener); i++) {
pr_indent(out,indent);
- fprintf(out,"energygrp_flags[%3d]:",i);
+ 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");
static void pr_pullgrp(FILE *fp,int indent,int g,t_pullgrp *pg)
{
pr_indent(fp,indent);
- fprintf(fp,"pull_group %d:\n",g);
+ 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);
{
int g;
- 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);
+ 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]);
}
indent=pr_title(fp,indent,title);
PS("integrator",EI(ir->eI));
PSTEP("nsteps",ir->nsteps);
- PSTEP("init_step",ir->init_step);
- PS("ns_type",ENS(ir->ns_type));
+ 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);
- PS("comm_mode",ECOM(ir->comm_mode));
+ PS("comm-mode",ECOM(ir->comm_mode));
PI("nstlog",ir->nstlog);
PI("nstxout",ir->nstxout);
PI("nstvout",ir->nstvout);
PI("nstcalcenergy",ir->nstcalcenergy);
PI("nstenergy",ir->nstenergy);
PI("nstxtcout",ir->nstxtcout);
- PR("init_t",ir->init_t);
- PR("delta_t",ir->delta_t);
+ 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);
- 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));
+ 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("epc",EPCOUPLTYPE(ir->epc));
PS("epctype",EPCOUPLTYPETYPE(ir->epct));
PI("nstpcouple",ir->nstpcouple);
- PR("tau_p",ir->tau_p);
- pr_matrix(fp,indent,"ref_p",ir->ref_p,bMDPformat);
+ PR("tau-p",ir->tau_p);
+ pr_matrix(fp,indent,"ref-p",ir->ref_p,bMDPformat);
pr_matrix(fp,indent,"compress",ir->compress,bMDPformat);
- PS("refcoord_scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
+ PS("refcoord-scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
if (bMDPformat)
- fprintf(fp,"posres_com = %g %g %g\n",ir->posres_com[XX],
+ fprintf(fp,"posres-com = %g %g %g\n",ir->posres_com[XX],
ir->posres_com[YY],ir->posres_com[ZZ]);
else
- pr_rvec(fp,indent,"posres_com",ir->posres_com,DIM,TRUE);
+ pr_rvec(fp,indent,"posres-com",ir->posres_com,DIM,TRUE);
if (bMDPformat)
- fprintf(fp,"posres_comB = %g %g %g\n",ir->posres_comB[XX],
+ fprintf(fp,"posres-comB = %g %g %g\n",ir->posres_comB[XX],
ir->posres_comB[YY],ir->posres_comB[ZZ]);
else
- pr_rvec(fp,indent,"posres_comB",ir->posres_comB,DIM,TRUE);
- PI("andersen_seed",ir->andersen_seed);
+ 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("rcoulomb_switch",ir->rcoulomb_switch);
+ PR("rcoulomb-switch",ir->rcoulomb_switch);
PR("rcoulomb",ir->rcoulomb);
PS("vdwtype",EVDWTYPE(ir->vdwtype));
- PR("rvdw_switch",ir->rvdw_switch);
+ PR("rvdw-switch",ir->rvdw_switch);
PR("rvdw",ir->rvdw);
if (ir->epsilon_r != 0)
- PR("epsilon_r",ir->epsilon_r);
+ PR("epsilon-r",ir->epsilon_r);
else
- PS("epsilon_r",infbuf);
+ PS("epsilon-r",infbuf);
if (ir->epsilon_rf != 0)
- PR("epsilon_rf",ir->epsilon_rf);
+ PR("epsilon-rf",ir->epsilon_rf);
else
- PS("epsilon_rf",infbuf);
+ PS("epsilon-rf",infbuf);
PR("tabext",ir->tabext);
- PS("implicit_solvent",EIMPLICITSOL(ir->implicit_solvent));
- PS("gb_algorithm",EGBALGORITHM(ir->gb_algorithm));
- PR("gb_epsilon_solvent",ir->gb_epsilon_solvent);
+ 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);
- 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);
+ 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));
- PS("free_energy",EFEPTYPE(ir->efep));
- PR("init_lambda",ir->init_lambda);
- PR("delta_lambda",ir->delta_lambda);
+ PS("free-energy",EFEPTYPE(ir->efep));
+ PR("init-lambda",ir->init_lambda);
+ PR("delta-lambda",ir->delta_lambda);
if (!bMDPformat)
{
- PI("n_foreign_lambda",ir->n_flambda);
+ PI("n-foreign-lambda",ir->n_flambda);
}
if (ir->n_flambda > 0)
{
pr_indent(fp,indent);
- fprintf(fp,"foreign_lambda%s",bMDPformat ? " = " : ":");
+ fprintf(fp,"foreign-lambda%s",bMDPformat ? " = " : ":");
for(i=0; i<ir->n_flambda; i++)
{
fprintf(fp," %10g",ir->flambda[i]);
}
fprintf(fp,"\n");
}
- 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);
+ 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("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);
+ 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("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("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("disre",EDISRETYPE(ir->eDisre));
- 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("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("orires_fc",ir->orires_fc);
- PR("orires_tau",ir->orires_tau);
+ PR("orires-fc",ir->orires_fc);
+ PR("orires-tau",ir->orires_tau);
PR("nstorireout",ir->nstorireout);
PR("dihre-fc",ir->dihre_fc);
- PR("em_stepsize",ir->em_stepsize);
- PR("em_tol",ir->em_tol);
+ PR("em-stepsize",ir->em_stepsize);
+ PR("em-tol",ir->em_tol);
PI("niter",ir->niter);
- PR("fc_stepsize",ir->fc_stepsize);
+ PR("fc-stepsize",ir->fc_stepsize);
PI("nstcgsteep",ir->nstcgsteep);
PI("nbfgscorr",ir->nbfgscorr);
PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
- 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("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("QMconstraints",ir->QMconstraints);
PI("QMMMscheme",ir->QMMMscheme);
PR("scalefactor",ir->scalefactor);
- pr_qm_opts(fp,indent,"qm_opts",&(ir->opts));
+ pr_qm_opts(fp,indent,"qm-opts",&(ir->opts));
}
}
#undef PS
for(j=2; (pa[i].u.c[j] != NULL); j++)
fprintf(out,",'%s'",pa[i].u.c[j]);
fprintf(out,"],%d))\n",is_hidden(&(pa[i])));
+ break;
default:
break;
}
sinalpha=sqrt(1-cosalpha*cosalpha);
x[atCG] = - sinalpha*dCGCE1;
y[atCG] = 0;
+ x[atHE1] = x[atHE2] = x[atHD1] = x[atHD2] = 0;
+ y[atHE1] = y[atHE2] = y[atHD1] = y[atHD2] = 0;
/* calculate ND1 and CD2 positions from CE1 and NE2 */
gmx_bool bShowTimestep=TRUE,bOK,newline=FALSE;
t_trxstatus *status;
gmx_mtop_t mtop;
- gmx_localtop_t *top;
+ gmx_localtop_t *top=NULL;
t_state state;
t_inputrec ir;
if (tpr) {
read_tpx_state(tpr,&ir,&state,NULL,&mtop);
+ top = gmx_mtop_generate_local_top(&mtop,&ir);
}
new_natoms = -1;
natoms = -1;
}
natoms=new_natoms;
if (tpr) {
- top = gmx_mtop_generate_local_top(&mtop,&ir);
chk_bonds(&top->idef,ir.ePBC,fr.x,fr.box,tol);
}
if (fr.bX)
sim_part = sim_part_fn + 1;
}
- if (MULTISIM(cr))
+ if (MULTISIM(cr) && MASTER(cr))
{
check_multi_int(stdout,cr->ms,sim_part,"simulation part");
}
{
dt_pcoupl = ir->nstpcouple*ir->delta_t;
- sprintf(err_buf,"tau_p must be > 0 instead of %g\n",ir->tau_p);
+ 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,"For proper integration of the %s barostat, tau_p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
+ 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);
}
}
if (ir->epsilon_r!=1 && ir->implicit_solvent==eisGBSA) {
- sprintf(warn_buf,"epsilon_r = %g with GB implicit solvent, will use this value for inner dielectric",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(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 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,"epsilon_r must be >= 0 instead of %g\n",ir->epsilon_r);
+ sprintf(err_buf,"epsilon-r must be >= 0 instead of %g\n",ir->epsilon_r);
CHECK(ir->epsilon_r < 0);
}
/* reaction field (at the cut-off) */
if (ir->coulombtype == eelRF_ZERO) {
- sprintf(err_buf,"With coulombtype = %s, epsilon_rf must be 0",
+ sprintf(err_buf,"With coulombtype = %s, epsilon-rf must be 0",
eel_names[ir->coulombtype]);
CHECK(ir->epsilon_rf != 0);
}
- sprintf(err_buf,"epsilon_rf must be >= epsilon_r");
+ 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) {
- sprintf(warn_buf,"Using epsilon_rf = epsilon_r with %s does not make sense",
+ sprintf(warn_buf,"Using epsilon-rf = epsilon-r with %s does not make sense",
eel_names[ir->coulombtype]);
warning(wi,warn_buf);
}
if (EEL_PME(ir->coulombtype)) {
if (ir->pme_order < 3) {
- warning_error(wi,"pme_order can not be smaller than 3");
+ 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(warn_buf,"With pbc=%s you should use ewald_geometry=%s",
+ 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,"wall_ewald_zfac should be >= 2");
+ sprintf(err_buf,"wall-ewald-zfac should be >= 2");
CHECK(ir->wall_ewald_zfac < 2);
}
if (EVDW_SWITCHED(ir->vdwtype)) {
- sprintf(err_buf,"With vdwtype = %s rvdw_switch must be < rvdw",
+ 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) {
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"
- "setting implicit_solvent value to \"GBSA\" in input section.\n");
+ "setting implicit-solvent value to \"GBSA\" in input section.\n");
}
if(ir->sa_algorithm==esaSTILL)
nstr = str_nelem(wall_density,MAXPTR,names);
if (nstr != ir->nwall)
{
- gmx_fatal(FARGS,"Expected %d elements for wall_density, found %d",ir->nwall,nstr);
+ 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)
{
- gmx_fatal(FARGS,"wall_density[%d] = %f\n",i,dbl);
+ gmx_fatal(FARGS,"wall-density[%d] = %f\n",i,dbl);
}
ir->wall_density[i] = dbl;
}
RTYPE ("dt", ir->delta_t, 0.001);
STEPTYPE ("nsteps", ir->nsteps, 0);
CTYPE ("For exact run continuation or redoing part of a run");
- STEPTYPE ("init_step",ir->init_step, 0);
+ STEPTYPE ("init-step",ir->init_step, 0);
CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
- ITYPE ("simulation_part", ir->simulation_part, 1);
+ 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");
CTYPE ("Force tolerance and initial step-size");
RTYPE ("emtol", ir->em_tol, 10.0);
RTYPE ("emstep", ir->em_stepsize,0.01);
- CTYPE ("Max number of iterations in relax_shells");
+ 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);
ir->ndelta = 2;
CTYPE ("Periodic boundary conditions: xyz, no, xy");
EETYPE("pbc", ir->ePBC, epbc_names);
- EETYPE("periodic_molecules", ir->bPeriodicMols, yesno_names);
+ 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 ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
CTYPE ("Relative dielectric constant for the medium and the reaction field");
- RTYPE ("epsilon_r", ir->epsilon_r, 1.0);
- RTYPE ("epsilon_rf", ir->epsilon_rf, 1.0);
+ 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");
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");
- STYPE ("energygrp_table", egptable, NULL);
+ 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 ("fourier_nx", ir->nkx, 0);
- ITYPE ("fourier_ny", ir->nky, 0);
- ITYPE ("fourier_nz", ir->nkz, 0);
+ ITYPE ("fourier-nx", ir->nkx, 0);
+ ITYPE ("fourier-ny", ir->nky, 0);
+ ITYPE ("fourier-nz", ir->nkz, 0);
CTYPE ("EWALD/PME/PPPM parameters");
- 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 ("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("implicit_solvent", ir->implicit_solvent, eis_names);
+ EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
CTYPE ("Algorithm for calculating Born radii");
- EETYPE("gb_algorithm", ir->gb_algorithm, egb_names);
+ 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_epsilon_solvent",ir->gb_epsilon_solvent, 80.0);
+ RTYPE ("gb-epsilon-solvent",ir->gb_epsilon_solvent, 80.0);
CTYPE ("Salt concentration in M for Generalized Born models");
- RTYPE ("gb_saltconc", ir->gb_saltconc, 0.0);
+ RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
- 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-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.");
- RTYPE ("sa_surface_tension", ir->sa_surface_tension, -1);
+ RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
/* Coupling stuff */
CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
CTYPE ("Time constant (ps) and reference temperature (K)");
STYPE ("tau-t", tau_t, NULL);
STYPE ("ref-t", ref_t, NULL);
- CTYPE ("Pressure coupling");
- EETYPE("Pcoupl", ir->epc, epcoupl_names);
- EETYPE("Pcoupltype", ir->epct, epcoupltype_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");
- EETYPE ("refcoord_scaling",ir->refcoord_scaling,erefscaling_names);
+ EETYPE ("refcoord-scaling",ir->refcoord_scaling,erefscaling_names);
CTYPE ("Random seed for Andersen thermostat");
- ITYPE ("andersen_seed", ir->andersen_seed, 815131);
+ ITYPE ("andersen-seed", ir->andersen_seed, 815131);
/* QMMM */
CCTYPE ("OPTIONS FOR QMMM calculations");
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_npoints", anneal_npoints, NULL);
+ STYPE ("annealing-npoints", anneal_npoints, NULL);
CTYPE ("List of times at the annealing points for each group");
- STYPE ("annealing_time", anneal_time, NULL);
+ STYPE ("annealing-time", anneal_time, NULL);
CTYPE ("Temp. at each annealing point, for each group.");
- STYPE ("annealing_temp", anneal_temp, NULL);
+ STYPE ("annealing-temp", anneal_temp, NULL);
/* Startup run */
CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
/* Energy group exclusions */
CCTYPE ("ENERGY GROUP EXCLUSIONS");
CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
- STYPE ("energygrp_excl", egpexcl, NULL);
+ 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);
- 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);
+ 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");
- CTYPE("Pull type: no, umbrella, constraint or constant_force");
+ CTYPE("Pull type: no, umbrella, constraint or constant-force");
EETYPE("pull", ir->ePull, epull_names);
if (ir->ePull != epullNO) {
snew(ir->pull,1);
EETYPE("free-energy", ir->efep, efep_names);
RTYPE ("init-lambda", ir->init_lambda,0.0);
RTYPE ("delta-lambda",ir->delta_lambda,0.0);
- STYPE ("foreign_lambda", foreign_lambda, NULL);
+ 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);
EETYPE("separate-dhdl-file", ir->separate_dhdl_file,
separate_dhdl_file_names);
EETYPE("dhdl-derivatives", ir->dhdl_derivatives, dhdl_derivatives_names);
- ITYPE ("dh_hist_size", ir->dh_hist_size, 0);
- RTYPE ("dh_hist_spacing", ir->dh_hist_spacing, 0.1);
+ 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);
warning(wi,"For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
}
} else {
- warning(wi,"Can not couple a molecule with free_energy = no");
+ warning(wi,"Can not couple a molecule with free-energy = no");
}
}
nref_t = str_nelem(ref_t,MAXPTR,ptr2);
ntcg = str_nelem(tcgrps,MAXPTR,ptr3);
if ((ntau_t != ntcg) || (nref_t != ntcg)) {
- gmx_fatal(FARGS,"Invalid T coupling input: %d groups, %d ref_t values and "
- "%d tau_t values",ntcg,nref_t,ntau_t);
+ 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));
snew(ir->opts.tau_t,nr);
snew(ir->opts.ref_t,nr);
if (ir->eI==eiBD && ir->bd_fric==0) {
- fprintf(stderr,"bd_fric=0, so tau_t will be used as the inverse friction constant(s)\n");
+ fprintf(stderr,"bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
}
if (bSetTCpar)
{
if (nr != nref_t)
{
- gmx_fatal(FARGS,"Not enough ref_t and tau_t values!");
+ gmx_fatal(FARGS,"Not enough ref-t and tau-t values!");
}
tau_min = 1e20;
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,"With integrator %s tau_t should be larger than 0",ei_names[ir->eI]);
+ 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) ||
{
if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
{
- 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,"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);
ir->opts.ref_t[i] = strtod(ptr2[i],NULL);
if (ir->opts.ref_t[i] < 0)
{
- gmx_fatal(FARGS,"ref_t for group %d negative",i);
+ gmx_fatal(FARGS,"ref-t for group %d negative",i);
}
}
}
/* Read the other fields too */
nSA_points = str_nelem(anneal_npoints,MAXPTR,ptr1);
if(nSA_points!=nSA)
- gmx_fatal(FARGS,"Found %d annealing_npoints values for %d groups\n",nSA_points,nSA);
+ 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)
nSA_time = str_nelem(anneal_time,MAXPTR,ptr1);
if(nSA_time!=k)
- gmx_fatal(FARGS,"Found %d annealing_time values, wanter %d\n",nSA_time,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)
- gmx_fatal(FARGS,"Found %d annealing_temp values, wanted %d\n",nSA_temp,k);
+ gmx_fatal(FARGS,"Found %d annealing-temp values, wanted %d\n",nSA_temp,k);
for(i=0,k=0;i<nr;i++) {
nr = groups->grps[egcENER].nr;
snew(ir->opts.egp_flags,nr*nr);
- bExcl = do_egp_flag(ir,groups,"energygrp_excl",egpexcl,EGP_EXCL);
+ 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");
- bTable = do_egp_flag(ir,groups,"energygrp_table",egptable,EGP_TABLE);
+ 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))
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) {
- 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",
+ 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);
}
if (bConstr && ir->eConstrAlg == econtSHAKE) {
if (ir->shake_tol <= 0.0) {
- sprintf(warn_buf,"ERROR: shake_tol must be > 0 instead of %g\n",
+ sprintf(warn_buf,"ERROR: shake-tol must be > 0 instead of %g\n",
ir->shake_tol);
warning_error(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]);
+ 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) {
gmx_fatal(FARGS,"Invalid bond type %d",type);
break;
}
+ break;
case d_angles:
case d_angletypes:
switch (type) {
gmx_fatal(FARGS,"Invalid angle type %d",type);
break;
}
- case d_pairs:
+ break;
+ case d_pairs:
case d_pairtypes:
if (type == 1 || (d == d_pairtypes && type == 2))
return F_LJ14;
return F_LJC14_Q;
else
gmx_fatal(FARGS,"Invalid pairs type %d",type);
+ break;
case d_pairs_nb:
return F_LJC_PAIRS_NB;
case d_dihedrals:
default:
gmx_fatal(FARGS,"Invalid vsites3 type %d",type);
}
+ break;
case d_vsites4:
switch (type) {
case 1:
default:
gmx_fatal(FARGS,"Invalid vsites4 type %d",type);
}
+ break;
case d_vsitesn:
return F_VSITEN;
case d_constraints:
default:
gmx_fatal(FARGS,"Invalid constraints type %d",type);
}
+ break;
case d_settles:
return F_SETTLE;
case d_position_restraints:
return F_POSRES;
case 2:
gmx_fatal(FARGS,"Water polarization should now be listed under [ water_polarization ]\n");
+ break;
default:
gmx_fatal(FARGS,"Invalid position restraint type %d",type);
}
+ break;
case d_polarization:
return F_POLARIZATION;
case d_thole_polarization:
}
for(est=0; est<estNR; est++)
{
- if (EST_DISTR(est) && state_local->flags & (1<<est))
+ if (EST_DISTR(est) && (state_local->flags & (1<<est)))
{
switch (est) {
case estX:
for(est=0; est<estNR; est++)
{
- if (EST_DISTR(est) && state->flags & (1<<est))
+ if (EST_DISTR(est) && (state->flags & (1<<est)))
{
switch(est) {
case estX:
}
for(i=0; i<estNR; i++)
{
- if (EST_DISTR(i) && state_local->flags & (1<<i))
+ if (EST_DISTR(i) && (state_local->flags & (1<<i)))
{
switch (i) {
case estX:
for(est=0; est<estNR; est++)
{
- if (EST_DISTR(est) && state->flags & (1<<est)) {
+ if (EST_DISTR(est) && (state->flags & (1<<est))) {
switch (est) {
case estX:
/* Rotate the complete state; for a rectangular box only */
/* Reorder the state */
for(i=0; i<estNR; i++)
{
- if (EST_DISTR(i) && state->flags & (1<<i))
+ if (EST_DISTR(i) && (state->flags & (1<<i)))
{
switch (i)
{
/* 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 ||
- (step + ir->nstlist > ir->init_step + ir->nsteps));
+ (ir->nsteps >= 0 &&
+ (step + ir->nstlist > ir->init_step + ir->nsteps)));
/* Avoid extra communication due to verbose screen output
* when nstglobalcomm is set.
{
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)
- ;
- else
+ else if (readmagic != 669)
gmx_fatal(FARGS,"Wrong magic number %d in %s",readmagic,ed->edinam);
}
int i;
for (i=sqrt(z);;i--)
if (z%i==0) return i;
+ return 1;
}
/* largest factor */
if (z==1) return 1;
for (i=z/2;;i--)
if (z%i==0) return i;
+ return 1;
}
/* largest prime factor: WARNING: slow recursion, only use for small numbers */
rotate(NG);
}
}
- if (plan->flags&FFT5D_REALCOMPLEX && ((!(plan->flags&FFT5D_BACKWARD) && s==0) || (plan->flags&FFT5D_BACKWARD && s==2))) {
+ if ((plan->flags&FFT5D_REALCOMPLEX) && ((!(plan->flags&FFT5D_BACKWARD) && s==0) || ((plan->flags&FFT5D_BACKWARD) && s==2))) {
xl[0] = rC[s];
}
}
int x,y,z,l;
int *coor = plan->coor;
int ll=2; /*compare ll values per element (has to be 2 for complex)*/
- if (plan->flags&FFT5D_REALCOMPLEX && plan->flags&FFT5D_BACKWARD)
+ if ((plan->flags&FFT5D_REALCOMPLEX) && (plan->flags&FFT5D_BACKWARD))
{
ll=1;
}
case egbSTILL:
if(fr->UseOptimizedKernels)
{
- calc_gb_rad_still_sse2_double(cr,fr,md->nr,top, atype, x[0], nl, born);
+ calc_gb_rad_still_sse2_double(cr,fr,born->nr,top, atype, x[0], nl, born);
}
else
{
for(m=0; m<DIM; m++)
{
dr[m] *= pull->dim[m];
- dr2 += dr[m];
+ dr2 += dr[m]*dr[m];
}
if (max_dist2 >= 0 && dr2 > 0.98*0.98*max_dist2)
{
- gmx_fatal(FARGS,"Distance of pull group %d (%f nm) is larger than 0.49 times the box size (%f)",g,sqrt(dr2),max_dist2);
+ gmx_fatal(FARGS,"Distance of pull group %d (%f nm) is larger than 0.49 times the box size (%f)",g,sqrt(dr2),sqrt(max_dist2));
}
if (pull->eGeom == epullgDIRPBC)
}
}
- bConverged_all = TRUE;
+ bConverged_all = FALSE;
while (!bConverged_all && niter < max_iter)
{
bConverged_all = TRUE;
at = type[i];
Cd = nbfp[ntw[w]+2*at];
Cr = nbfp[ntw[w]+2*at+1];
- if (!((Cd==0 && Cr==0) || egp_flags[ggid] & EGP_EXCL))
+ if (!((Cd==0 && Cr==0) || (egp_flags[ggid] & EGP_EXCL)))
{
if (w == 0)
{
case ClientMessage:
ew->etype=event->xclient.data.l[0];
ExposeWin(x11->disp,ew->wd.self);
- /* Fall thru... */
+ /* no break */
case ButtonRelease:
hide_menu(x11,ew->selener);
break;
void init_gmx(t_x11 *x11,char *program,int nfile,t_filenm fnm[],
const output_env_t oenv);
-int EventSignaller(t_manager *man);
-
static void dump_xw(char *dispname,Window w,char *fn)
{
char comm[256];
break;
case 5:
if (i==0)
- data[i] = 1;
+ data[i] = 1;
else
- data[i] = sin(x)/(x);
+ data[i] = sin(x)/(x);
+ break;
default:
/* Data remains 0.0 */
break;
/* just a wrapper; declare extra args, then chuck away at end. */
int maxchi = 0 ;
t_dlist *dlist ;
- int *xity;
+ int *multiplicity;
int nlist = nangles ;
int k ;
snew(dlist,nlist);
- snew(xity,nangles);
+ snew(multiplicity,nangles);
for(k=0; (k<nangles); k++) {
- xity[k]=3 ;
+ multiplicity[k]=3 ;
}
low_ana_dih_trans(TRUE, fn_trans,TRUE, fn_histo, maxchi,
dih, nlist, dlist, nframes,
- nangles, grpname, xity, t0, dt, bRb, 0.5,oenv);
+ nangles, grpname, multiplicity, t0, dt, bRb, 0.5,oenv);
sfree(dlist);
- sfree(xity);
+ sfree(multiplicity);
}
void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
gmx_bool bHisto, const char *fn_histo, int maxchi,
real **dih, int nlist, t_dlist dlist[], int nframes,
- int nangles, const char *grpname, int xity[],
+ int nangles, const char *grpname, int multiplicity[],
real t0, real dt, gmx_bool bRb, real core_frac,
const output_env_t oenv)
{
#ifdef OLDIE
mind = maxd = prev = dih[i][0];
#else
- cur_bin = calc_bin(dih[i][0],xity[i],core_frac);
+ cur_bin = calc_bin(dih[i][0],multiplicity[i],core_frac);
rot_occ[cur_bin][i]++ ;
#endif
for (j=1; (j<nframes); j++)
{
- new_bin = calc_bin(dih[i][j],xity[i],core_frac);
+ new_bin = calc_bin(dih[i][j],multiplicity[i],core_frac);
rot_occ[new_bin][i]++ ;
#ifndef OLDIE
if (cur_bin == 0)
}
-void mk_multiplicity_lookup (int *xity, int maxchi, real **dih,
+void mk_multiplicity_lookup (int *multiplicity, int maxchi, real **dih,
int nlist, t_dlist dlist[],int nangles)
{
/* new by grs - for dihedral j (as in dih[j]) get multiplicity from dlist
- * and store in xity[j]
+ * and store in multiplicity[j]
*/
int j, Dih, i ;
((Dih == edOmega) && (has_dihedral(edOmega,&(dlist[i])))) ||
((Dih > edOmega) && (dlist[i].atm.Cn[Dih-NONCHI+3] != -1))) {
/* default - we will correct the rest below */
- xity[j] = 3 ;
+ multiplicity[j] = 3 ;
/* make omegas 2fold, though doesn't make much more sense than 3 */
if (Dih == edOmega && (has_dihedral(edOmega,&(dlist[i])))) {
- xity[j] = 2 ;
+ multiplicity[j] = 2 ;
}
/* dihedrals to aromatic rings, COO, CONH2 or guanidinium are 2fold*/
((strstr(name,"GLN") != NULL) && (Dih == edChi3)) ||
((strstr(name,"ASN") != NULL) && (Dih == edChi2)) ||
((strstr(name,"ARG") != NULL) && (Dih == edChi4)) ) {
- xity[j] = 2;
+ multiplicity[j] = 2;
}
}
j++ ;
j,nangles);
/* Check for remaining dihedrals */
for(;(j < nangles); j++)
- xity[j] = 3;
+ multiplicity[j] = 3;
}
void get_chi_product_traj (real **dih,int nframes,int nangles, int nlist,
int maxchi, t_dlist dlist[], real time[],
- int **lookup, int *xity,gmx_bool bRb, gmx_bool bNormalize,
+ int **lookup, int *multiplicity,gmx_bool bRb, gmx_bool bNormalize,
real core_frac, gmx_bool bAll, const char *fnall,
const output_env_t oenv)
{
for (Xi = 0 ; Xi < maxchi ; Xi ++ ) {
index = lookup[i][Xi] ; /* chi_(Xi+1) of res i (-1 if off end) */
if ( index >= 0 ) {
- n = xity[index];
+ n = multiplicity[index];
nbin = n*nbin ;
}
}
bRotZero = TRUE ;
bHaveChi = FALSE ;
} else {
- b = calc_bin(dih[index][j],xity[index],core_frac) ;
+ b = calc_bin(dih[index][j],multiplicity[index],core_frac) ;
accum = b - 1 ;
if (b == 0 )
bRotZero = TRUE ;
for (Xi = 1 ; Xi < maxchi ; Xi ++ ) {
index = lookup[i][Xi] ; /* chi_(Xi+1) of res i (-1 if off end) */
if ( index >= 0 ) {
- n = xity[index];
+ n = multiplicity[index];
b = calc_bin(dih[index][j],n,core_frac);
accum = n * accum + b - 1 ;
if (b == 0 )
#include "tpxio.h"
#include "viewit.h"
-/* defined in gmx_wheel.c*/
-extern gmx_bool *bPhobics(int ,char *);
static int strip_dssp(char *dsspfile,int nres,
gmx_bool bPhobres[],real t,
return nr;
}
+static gmx_bool *bPhobics(t_atoms *atoms)
+{
+ int i,nb;
+ char **cb;
+ gmx_bool *bb;
+
+
+ nb = get_strings("phbres.dat",&cb);
+ snew(bb,atoms->nres);
+
+ for (i=0; (i<atoms->nres); i++)
+ {
+ if ( -1 != search_str(nb,cb,*atoms->resinfo[i].name) )
+ {
+ bb[i]=TRUE;
+ }
+ }
+ return bb;
+}
+
static void check_oo(t_atoms *atoms)
{
char *OOO;
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xp,NULL,box,FALSE);
atoms=&(top.atoms);
check_oo(atoms);
- bPhbres=bPhobics((int)atoms->nres,(char *)atoms->resinfo);
+ bPhbres = bPhobics(atoms);
get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpnm);
nres=0;
"y = a2*ee(a1,x) + (1-a2)*ee(a2,x)"
};
-extern gmx_bool mrqmin(real x[],real y[],real sig[],int ndata,real a[],
- int ma,int lista[],int mfit,real **covar,real **alpha,
- real *chisq,
- void (*funcs)(real x,real a[],real *y,real dyda[]),
- real *alamda);
-
extern gmx_bool mrqmin_new(real x[],real y[],real sig[],int ndata,real a[],
int ia[],int ma,real **covar,real **alpha,real *chisq,
void (*funcs)(real, real [], real *, real []),
"and fourth cumulant from those of a Gaussian distribution with the same",
"standard deviation.[PAR]",
- "Option [TT]-ac[tt] produces the autocorrelation function(s).[PAR]",
+ "Option [TT]-ac[tt] produces the autocorrelation function(s).",
+ "Be sure that the time interval between data points is",
+ "much shorter than the time scale of the autocorrelation.[PAR]",
"Option [TT]-cc[tt] plots the resemblance of set i with a cosine of",
"i/2 periods. The formula is:[BR]"
static void dump_dih_trn(int nframes,int nangles,real **dih,const char *fn,
- real dt)
+ real *time)
{
int i,j,k,l,m,na;
t_fileio *trn;
}
}
}
- fwrite_trn(trn,i,(real)i*dt,0,box,na,x,NULL,NULL);
+ fwrite_trn(trn,i,time[i],0,box,na,x,NULL,NULL);
}
close_trn(trn);
sfree(x);
bAver=opt2bSet("-ov",NFILE,fnm);
bTrans=opt2bSet("-ot",NFILE,fnm);
bFrac=opt2bSet("-of",NFILE,fnm);
-
+ if (bTrans && opt[0][0] != 'd') {
+ fprintf(stderr, "Option -ot should only accompany -type dihedral. Disabling -ot.\n");
+ bTrans = FALSE;
+ }
+
if (bChandler && !bCorr)
bCorr=TRUE;
ffclose(out);
}
if (opt2bSet("-or",NFILE,fnm))
- dump_dih_trn(nframes,nangles,dih,opt2fn("-or",NFILE,fnm),dt);
+ dump_dih_trn(nframes,nangles,dih,opt2fn("-or",NFILE,fnm),time);
if (bFrac) {
sprintf(title,"Trans fraction: %s",grpname);
atom_id isize,*index;
int ndih,nactdih,nf;
real **dih,*trans_frac,*aver_angle,*time;
- int i,j,**chi_lookup,*xity;
+ int i,j,**chi_lookup,*multiplicity;
t_filenm fnm[] = {
{ efSTX, "-s", NULL, ffREAD },
*
* added multiplicity */
- snew(xity,ndih) ;
- mk_multiplicity_lookup(xity, maxchi, dih, nlist, dlist,ndih);
+ snew(multiplicity,ndih) ;
+ mk_multiplicity_lookup(multiplicity, maxchi, dih, nlist, dlist,ndih);
strcpy(grpname, "All residues, ");
if(bPhi)
low_ana_dih_trans(bDo_ot, opt2fn("-ot",NFILE,fnm),
bDo_oh, opt2fn("-oh",NFILE,fnm),maxchi,
- dih, nlist, dlist, nf, nactdih, grpname, xity,
+ dih, nlist, dlist, nf, nactdih, grpname, multiplicity,
*time, dt, FALSE, core_frac,oenv) ;
/* Order parameters */
mk_chi_lookup(chi_lookup, maxchi, dih, nlist, dlist);
get_chi_product_traj(dih,nf,nactdih,nlist,
- maxchi,dlist,time,chi_lookup,xity,
+ maxchi,dlist,time,chi_lookup,multiplicity,
FALSE,bNormHisto, core_frac,bAll,
opt2fn("-cp",NFILE,fnm),oenv);
int nsatm;
t_simat sat[3];
} t_simlist;
-static const char *pdbtp[epdbNR] =
- { "ATOM ", "HETATM" };
real calc_mass(t_atoms *atoms, gmx_bool bGetMass, gmx_atomprop_t aps)
{
}
emid = 0.0;/*(emin+emax)*0.5;*/
- for(m=0; (m<egNR); m++)
- egrp_nm[m]=egrp_nm[m];
egrp_nm[egTotal]="total";
for (m=0; (m<egNR+egSP); m++)
if (egrp_use[m]) {
"[TT]rect[tt] is the ordinary brick shape.",
"[TT]tric[tt] is the triclinic unit cell.",
"[TT]compact[tt] puts all atoms at the closest distance from the center",
- "of the box. This can be useful for visualizing e.g. truncated",
- "octahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
+ "of the box. This can be useful for visualizing e.g. truncated octahedra",
+ "or rhombic dodecahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
"is [TT]tric[tt] (see below), unless the option [TT]-boxcenter[tt]",
"is set differently.[PAR]",
if (!gmx_fexist(opt2fn("-s",nfile,fnm)))
gmx_fatal(FARGS, "File %s not found.", opt2fn("-s",nfile,fnm));
- /* Make sure that the checkpoint file is not overwritten by the benchmark runs */
- if ( (0 == strcmp(opt2fn("-cpi",nfile,fnm), opt2fn("-cpo",nfile,fnm)) ) && (sim_part > 1) )
- gmx_fatal(FARGS, "Checkpoint input and output file must not be identical,\nbecause then the input file might change during the benchmarks.");
-
+ /* Make sure that the checkpoint file is not overwritten during benchmarking */
+ if ( (0 == strcmp(opt2fn("-cpi",nfile,fnm), opt2fn("-bcpo",nfile,fnm)) ) && (sim_part > 1) )
+ gmx_fatal(FARGS, "Checkpoint input (-cpi) and benchmark checkpoint output (-bcpo) files must not be identical.\n"
+ "The checkpoint input file must not be overwritten during the benchmarks.\n");
+
/* Make sure that repeats is >= 0 (if == 0, only write tpr files) */
if (repeats < 0)
gmx_fatal(FARGS, "Number of repeats < 0!");
"function is calculated.[PAR]",
"With option [TT]-mol[tt] the velocity autocorrelation function of",
"molecules is calculated. In this case the index group should consist",
- "of molecule numbers instead of atom numbers."
+ "of molecule numbers instead of atom numbers.[PAR]",
+ "Be sure that your trajectory contains frames with velocity information",
+ "(i.e. [TT]nstvout[tt] was set in your original [TT].mdp[tt] file),",
+ "and that the time interval between data collection points is",
+ "much shorter than the time scale of the autocorrelation."
};
static gmx_bool bM=FALSE,bMol=FALSE;
#include "strdb.h"
#include "gmx_ana.h"
-gmx_bool *bPhobics(int nres,char *resnm[])
+static gmx_bool *bPhobics(int nres,char *resnm[])
{
int i,nb;
char **cb;
/* format error occured */
case sError:
- gmx_fatal(FARGS,"Error in the list of eigenvectors for %s at pos %d with char %c",listname,pos-startpos,*(pos-1));
-
+ gmx_fatal(FARGS,"Error in the list of eigenvectors for %s at pos %d with char %c",listname,pos-startpos,*(pos-1));
+ break;
/* logical error occured */
case sZero:
- gmx_fatal(FARGS,"Error in the list of eigenvectors for %s at pos %d: eigenvector 0 is not valid",listname,pos-startpos);
+ gmx_fatal(FARGS,"Error in the list of eigenvectors for %s at pos %d: eigenvector 0 is not valid",listname,pos-startpos);
+ break;
case sSmaller:
- gmx_fatal(FARGS,"Error in the list of eigenvectors for %s at pos %d: second index %d is not bigger than %d",listname,pos-startpos,end_number,number);
-
+ gmx_fatal(FARGS,"Error in the list of eigenvectors for %s at pos %d: second index %d is not bigger than %d",listname,pos-startpos,end_number,number);
+ break;
}
++pos; /* read next character */
} /*scanner has finished */
if (opt[0] == 'a') {
*mult = 3;
for(ftype=0; ftype<F_NRE; ftype++) {
- if (interaction_function[ftype].flags & IF_ATYPE ||
+ if ((interaction_function[ftype].flags & IF_ATYPE) ||
ftype == F_TABANGLES) {
(*nft)++;
srenew(ft,*nft);
extern void get_chi_product_traj (real **dih,int nframes,int nangles,
int nlist,int maxchi, t_dlist dlist[], real time[],
- int **lookup,int *xity,gmx_bool bRb,gmx_bool bNormalize,
+ int **lookup,int *multiplicity,gmx_bool bRb,gmx_bool bNormalize,
real core_frac);
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff