-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 2.8)
+ # Keep CMake suitably quiet on Cygwin
+ set(CMAKE_LEGACY_CYGWIN_WIN32 0) # Remove when CMake >= 2.8.4 is required
project(Gromacs)
include(Dart)
# machine with no git.
#
# NOTE: when releasing the "-dev" suffix needs to be stripped off!
-set(PROJECT_VERSION "4.5.5-dev")
+set(PROJECT_VERSION "4.6-dev")
set(CUSTOM_VERSION_STRING ""
CACHE STRING "Custom version string (if empty, use hard-coded default)")
mark_as_advanced(CUSTOM_VERSION_STRING)
set(SOVERSION 6)
# It is a bit irritating, but this has to be set separately for now!
SET(CPACK_PACKAGE_VERSION_MAJOR "4")
-SET(CPACK_PACKAGE_VERSION_MINOR "5")
-SET(CPACK_PACKAGE_VERSION_PATCH "5")
+SET(CPACK_PACKAGE_VERSION_MINOR "6")
+#SET(CPACK_PACKAGE_VERSION_PATCH "0")
# Cmake modules/macros are in a subdirectory to keep this file cleaner
########################################################################
option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
-option(GMX_THREADS "Build a parallel (thread-based) version of GROMACS (cannot be combined with MPI yet)" ON)
+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)
CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec, fortran")
set(GMX_FFT_LIBRARY "fftw3"
- CACHE STRING "FFT library choices: fftw3,fftw2,mkl,fftpack[built-in]")
+ CACHE STRING "FFT library choices: fftw3,mkl,fftpack[built-in]")
option(GMX_DISABLE_FFTW_MEASURE
"Do not optimize FFTW setups (not needed with SSE)" OFF)
mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
option(BUILD_SHARED_LIBS "Enable shared libraries (can be problematic with MPI, Windows)" ${SHARED_LIBS_DEFAULT})
option(GMX_MPI_IN_PLACE "Enable MPI_IN_PLACE for MPIs that have it defined" ON)
mark_as_advanced(GMX_MPI_IN_PLACE)
-option(GMX_DLOPEN "Compile with dlopen, needed to read VMD supported file formats" ON)
-mark_as_advanced(GMX_DLOPEN)
+option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
+mark_as_advanced(GMX_LOAD_PLUGINS)
option(GMX_IA32_ASM "Add SSE assembly files for IA32" OFF)
option(GMX_X86_64_ASM "Add SSE assembly files for X86_64" OFF)
mark_as_advanced(GMX_X86_64_ASM)
+option(GMX_OPENMP "Enable OpenMP-based mutithreading. " ON)
+
option(USE_VERSION_H "Generate development version string/information" ON)
mark_as_advanced(USE_VERSION_H)
set (GMX_LIBS_SUFFIX "_gpu")
endif(GMX_OPENMM)
mark_as_advanced(FORCE GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
- message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
- message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
+ if (NOT SUFFIX_QUIETLY)
+ message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
+ message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
+ endif (NOT SUFFIX_QUIETLY)
else(GMX_DEFAULT_SUFFIX)
mark_as_advanced(CLEAR GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
- message(STATUS "Using manually set binary suffix: \"${GMX_BINARY_SUFFIX}\"")
- message(STATUS "Using manually set library suffix: \"${GMX_LIBS_SUFFIX}\"")
+ if (NOT SUFFIX_QUIETLY)
+ message(STATUS "Using manually set binary suffix: \"${GMX_BINARY_SUFFIX}\"")
+ message(STATUS "Using manually set library suffix: \"${GMX_LIBS_SUFFIX}\"")
+ endif (NOT SUFFIX_QUIETLY)
endif(GMX_DEFAULT_SUFFIX)
+set(SUFFIX_QUIETLY TRUE CACHE INTERNAL "")
set(PKG_CFLAGS "")
if(GMX_DOUBLE)
########################################################################
#Process MPI settings
########################################################################
-include(CheckCSourceCompiles) # for gmxTestMPI_IN_PLACE
-if(GMX_MPI)
- if(GMX_THREADS)
- #message(FATAL_ERROR "Thread-based parallelization conflicts with MPI.")
- set(GMX_THREADS OFF CACHE BOOL
- "Thread-based parallelization conflicts with MPI." FORCE)
- endif(GMX_THREADS)
- find_package(MPI)
- if(MPI_FOUND)
- set(GROMACS_C_FLAGS ${GROMACS_FLAGS} ${MPI_COMPILE_FLAGS})
- set(GROMACS_LINKER_FLAGS ${GROMACS_LINKER_FLAGS} ${MPI_LINK_FLAGS})
-
- include_directories(${MPI_INCLUDE_PATH})
- list(APPEND GMX_EXTRA_LIBRARIES ${MPI_LIBRARIES})
- if(GMX_FAHCORE)
- add_definitions( -DMPI ) #for FAHCORE
- endif(GMX_FAHCORE)
- include(gmxTestMPI_IN_PLACE)
- if (GMX_MPI_IN_PLACE)
- gmx_test_mpi_in_place(MPI_IN_PLACE_EXISTS)
- endif (GMX_MPI_IN_PLACE)
-
- # test for unsuitable versions of OpenMPI
- exec_program(${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 ${MPI_TYPE})
- if(MPI_VERSION VERSION_LESS "1.4.1")
- MESSAGE(WARNING "
- There are known problems with OpenMPI version < 1.4.1.
- Please consider updating your OpenMPI.")
- endif(MPI_VERSION VERSION_LESS "1.4.1")
- unset(MPI_VERSION)
- else(MPI_TYPE MATCHES "Open MPI|OpenRTE")
- # This is not OpenMPI, so give the old generic warning message
- MESSAGE(WARNING "
- There are known problems with some MPI implementations:
- MVAPICH2 version <= 1.4.1
- Please consider updating your MPI if applicable.")
- endif(MPI_TYPE MATCHES "Open MPI|OpenRTE")
- unset(MPI_TYPE)
- endif(MPI_EXEC_RETURN EQUAL 0)
- else(MPI_FOUND)
- message(FATAL_ERROR "MPI support requested, but no MPI compiler found.")
- endif(MPI_FOUND)
- include(gmxTestCatamount)
- gmx_test_catamount(GMX_CRAY_XT3)
- if(GMX_CRAY_XT3)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_CRAY_XT3")
- set(GMX_NO_SYSTEM 1)
- set(GMX_NO_NICE 1)
- endif(GMX_CRAY_XT3)
- set(GMX_LIB_MPI 1)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_LIB_MPI")
-endif(GMX_MPI)
-
+include(gmxManageMPI)
#######################################################################
# Check for options incompatible with OpenMM build #
if(GMX_MPI)
message(FATAL_ERROR "The OpenMM build is not compatible with MPI!")
endif(GMX_MPI)
- if(GMX_THREADS)
- message(STATUS "Threads are not compatible with OpenMM build, disabled!")
- set(GMX_THREADS OFF CACHE BOOL
- "Threads are not compatible with OpenMM build, disabled!" FORCE)
- endif(GMX_THREADS)
+ if(GMX_THREAD_MPI)
+ message(STATUS "Thread-MPI not compatible with OpenMM, disabled!")
+ set(GMX_THREAD_MPI OFF CACHE BOOL
+ "Thread-MPI not compatible with OpenMM build, disabled!" FORCE)
+ endif(GMX_THREAD_MPI)
+ if(GMX_OPENMP)
+ message(STATUS "OpenMP multithreading not compatible with OpenMM, disabled")
+ set(GMX_OPENMP OFF CACHE BOOL
+ "OpenMP multithreading not compatible with OpenMM, disabled!" FORCE)
+ endif()
if(GMX_SOFTWARE_INVSQRT)
set(GMX_SOFTWARE_INVSQRT OFF CACHE STRING
"The OpenMM build does not need GROMACS software 1/sqrt!" FORCE)
endif()
# mark as advanced the unused variables
mark_as_advanced(FORCE GMX_ACCELERATION GMX_MPI GMX_FFT_LIBRARY
- GMX_QMMM_PROGRAM GMX_THREADS GMX_DOUBLE)
+ GMX_QMMM_PROGRAM GMX_THREAD_MPI GMX_DOUBLE)
else(GMX_OPENMM)
mark_as_advanced(CLEAR GMX_ACCELERATION GMX_MPI GMX_FFT_LIBRARY
- GMX_QMMM_PROGRAM GMX_THREADS GMX_DOUBLE)
+ GMX_QMMM_PROGRAM GMX_THREAD_MPI GMX_DOUBLE)
endif(GMX_OPENMM)
endif(X11_FOUND)
endif(GMX_X11)
-if(GMX_THREADS)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREADS")
+if(GMX_THREAD_MPI)
+ set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREAD_MPI")
include(ThreadMPI)
set(THREAD_MPI_LIB thread_mpi)
set(GMX_MPI 1)
string(TOUPPER ${GMX_FFT_LIBRARY} ${GMX_FFT_LIBRARY})
- if(${GMX_FFT_LIBRARY} STREQUAL "FFTW2")
- message(FATAL_ERROR "FFTW2 can't be used with threads. Try fftw3 or mkl.")
- endif()
-endif(GMX_THREADS)
+endif(GMX_THREAD_MPI)
if(GMX_OPENMM)
set(CUDA_BUILD_EMULATION OFF)
find_package(OpenMM)
endif(GMX_OPENMM)
+if(GMX_OPENMP)
+ find_package(OpenMP REQUIRED)
+ set(GROMACS_C_FLAGS "${OpenMP_C_FLAGS} ${GROMACS_C_FLAGS}")
+ set(GROMACS_CXX_FLAGS "${OpenMP_CXX_FLAGS} ${GROMACS_CXX_FLAGS}")
+ add_definitions(-DGMX_OPENMP)
+endif()
+
if(APPLE)
find_library(ACCELERATE_FRAMEWORK Accelerate)
list(APPEND GMX_EXTRA_LIBRARIES ${ACCELERATE_FRAMEWORK})
if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
if(USE_VERSION_H)
# We need at least git v1.5.1 be able to parse git's date output. If not
- # fund or the version is too small, we can't generate version information.
- find_package(Git 1.5.1)
- # this should at some point become VERSION_LESS
- if(NOT Git_FOUND OR Git_VERSION STRLESS "1.5.1")
- message("No compatible git version found, won't be able to generate proper development version information.")
- set(USE_VERSION_H OFF)
+ # found or the version is too small, we can't generate version information.
+ find_package(Git)
+
+ # Find out the git version
+ if(GIT_FOUND AND NOT GIT_VERSION)
+ execute_process(COMMAND ${GIT_EXECUTABLE} "--version"
+ OUTPUT_VARIABLE _exec_out
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+ string(REGEX REPLACE "git version (.*)" "\\1" GIT_VERSION ${_exec_out})
+ set(GIT_VERSION ${GIT_VERSION} CACHE STRING "Git version")
+ mark_as_advanced(GIT_VERSION)
+ endif()
+
+ if(NOT GIT_FOUND OR GIT_VERSION VERSION_LESS "1.5.1")
+ message("No compatible git version found, won't be able to generate proper development version information.")
+ set(USE_VERSION_H OFF)
endif()
endif()
else()
set(USE_VERSION_H OFF)
endif()
-if (GMX_DLOPEN)
- list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS})
- set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
-else(GMX_DLOPEN)
- set(PKG_DL_LIBS)
-endif (GMX_DLOPEN)
-
########################################################################
# Generate development version info for cache
########################################################################
check_function_exists(fseeko HAVE_FSEEKO)
include(gmxTestSignal)
-gmx_test_retsigtype(RETSIGTYPE)
gmx_test_sigusr1(HAVE_SIGUSR1)
include(gmxTestInline)
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_THREADS OFF CACHE BOOL "Threads 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)
elseif(${GMX_ACCELERATION} STREQUAL "POWER6")
set(GMX_POWER6 1)
endif(${GMX_ACCELERATION} STREQUAL "NONE")
if(GMX_FORTRAN OR GMX_POWER6)
- if (GMX_THREADS)
- message(FATAL_ERROR "FORTRAN/POWER6 is incompatible with threads and only provides a speed-up on certain IBM compilers. Disable FORTRAN (or threads if you really want to use FORTRAN kernels).")
- endif(GMX_THREADS)
+ if (GMX_THREAD_MPI)
+ message(FATAL_ERROR "FORTRAN/POWER6 is incompatible with thread-MPI and only provides a speed-up on certain IBM compilers. Disable FORTRAN (or threads if you really want to use FORTRAN kernels).")
+ endif(GMX_THREAD_MPI)
enable_language(Fortran)
include(FortranCInterface)
discover_fortran_mangling(prefix isupper suffix extra_under_score found)
set(PKG_FFT "")
set(PKG_FFT_LIBS "")
if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
-# MESSAGE(STATUS "Using external FFT library - fftw3")
if(GMX_DOUBLE)
- find_package(FFTW3 REQUIRED)
- include_directories(${FFTW3_INCLUDE_DIR})
- set(FFT_LIBRARIES ${FFTW3_LIBRARIES})
- set(PKG_FFT "fftw3")
+ find_package(FFTW 3 COMPONENTS fftw)
else(GMX_DOUBLE)
- find_package(FFTW3F REQUIRED)
- include_directories(${FFTW3F_INCLUDE_DIR})
- set(FFT_LIBRARIES ${FFTW3F_LIBRARIES})
- set(PKG_FFT "fftw3f")
+ find_package(FFTW 3 COMPONENTS fftwf)
endif(GMX_DOUBLE)
-
- if(NOT FFTW3_FOUND AND NOT FFTW3F_FOUND)
- MESSAGE(FATAL_ERROR "Cannot find fftw3 (with correct precision). Fix it, choose another FFT library, or use the Gromacs built-in fftpack (slower)!")
- endif(NOT FFTW3_FOUND AND NOT FFTW3F_FOUND)
+ if(NOT FFTW_FOUND)
+ MESSAGE(FATAL_ERROR "Cannot find FFTW3 (with correct precision - libfftw3f for single precision GROMACS or libfftw3 for double precision GROMACS). Fix it, choose another FFT library, or use the Gromacs built-in fftpack (slower)!")
+ endif(NOT FFTW_FOUND)
+ include_directories(${FFTW_INCLUDE_DIRS})
+ set(FFT_LIBRARIES ${FFTW_LIBRARIES})
+ set(PKG_FFT "${FFTW_PKG}")
set(GMX_FFT_FFTW3 1)
-elseif(${GMX_FFT_LIBRARY} STREQUAL "FFTW2")
-# MESSAGE(STATUS "Using external FFT library - fftw2")
- if(GMX_DOUBLE)
- find_package(FFTW2 REQUIRED)
- else(GMX_DOUBLE)
- find_package(FFTW2F REQUIRED)
- endif(GMX_DOUBLE)
-
- if(NOT FFTW2_FOUND)
- MESSAGE(FATAL_ERROR "Cannot find fftw2 (with correct precision). Fix it, choose another FFT library, or use the Gromacs built-in fftpack (slower)!")
- endif(NOT FFTW2_FOUND)
- include_directories(${FFTW2_INCLUDE_DIR})
- set(FFT_LIBRARIES ${FFTW2_LIBRARIES})
- set(PKG_FFT_LIBS ${FFTW2_LIBRARIES})
-
- if("${FFTW2_LIBRARIES}" MATCHES "dfftw")
- set(FFTW2_NAME_DFFTW 1)
- elseif("${FFTW2_LIBRARIES}" MATCHES "sfftw")
- set(FFTW2_NAME_SFFTW 1)
- else("${FFTW2_LIBRARIES}" MATCHES "dfftw")
- set(FFTW2_NAME_FFTW 1)
- endif("${FFTW2_LIBRARIES}" MATCHES "dfftw")
-
- set(GMX_FFT_FFTW2 1)
elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
# MESSAGE(STATUS "Using external FFT library - Intel MKL")
find_package(MKL REQUIRED)
MESSAGE(STATUS "Using internal FFT library - fftpack")
set(GMX_FFT_FFTPACK 1)
else(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
- MESSAGE(FATAL_ERROR "Invalid FFT library setting: ${GMX_FFT_LIBRARY}. Choose one of: fftw3, fftw2, mkl, acml, fftpack")
+ MESSAGE(FATAL_ERROR "Invalid FFT library setting: ${GMX_FFT_LIBRARY}. Choose one of: fftw3, mkl, fftpack")
endif(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
# MKL has BLAS/LAPACK routines
mark_as_advanced(GMX_EXTERNAL_LAPACK)
mark_as_advanced(GMX_EXTERNAL_BLAS)
+set(GMX_USE_PLUGINS OFF CACHE INTERNAL "Whether GROMACS will really try to compile support for VMD plugins")
+set(GMX_VMD_PLUGIN_PATH)
+mark_as_advanced(GMX_VMD_PLUGIN_PATH)
+
+if(GMX_LOAD_PLUGINS)
+ if(CYGWIN OR NOT WIN32)
+ # Native Windows does not have, nor need dlopen
+ # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
+ include(gmxTestdlopen)
+ gmx_test_dlopen(HAVE_DLOPEN)
+ endif()
+
+ find_package(VMD)
+
+ # Test for unsuitable versions of VMD
+
+ if(VMD_FOUND AND NOT GMX_VMD_PLUGIN_PATH)
+ message(STATUS "Checking for suitable VMD version")
+ exec_program(${VMD_EXECUTABLE}
+ ARGS --help
+ OUTPUT_VARIABLE VMD_HELP
+ RETURN_VALUE VMD_EXEC_RETURN)
+
+ if(VMD_EXEC_RETURN EQUAL 0)
+ # This is the accepted idiom for subexpression matching, unfortunately
+ string(REGEX REPLACE ".*VMD for .*, version ([0-9]+\\.[0-9]*\\.?[0-9]*).*" "\\1" VMD_VERSION ${VMD_HELP})
+ string(REGEX REPLACE ".*VMD for (.*), version .*" "\\1" VMD_ARCH ${VMD_HELP})
+
+ if(VMD_VERSION VERSION_LESS "1.8")
+ MESSAGE(WARNING "Found VMD version ${VMD_VERSION}, but GROMACS needs at least 1.8")
+ unset(VMD_EXECUTABLE)
+ set(VMD_FOUND FALSE)
+ else()
+ message(STATUS "VMD version ${VMD_VERSION} is suitable")
+ if(DEFINED ENV{VMDDIR})
+ # This permits GROMACS to avoid hard-coding a fall-back
+ # path that it can tell right now would be useless.
+ set(GMX_VMD_PLUGIN_PATH "$ENV{VMDDIR}/plugins/${VMD_ARCH}/molfile" CACHE PATH "Path to VMD plugins for molfile I/O")
+ else()
+ set(GMX_VMD_PLUGIN_PATH "/usr/local/lib/vmd/plugins/*/molfile" CACHE PATH "Path to VMD plugins for molfile I/O")
+ endif()
+ endif()
+
+ # clean up
+ unset(VMD_HELP)
+ unset(VMD_VERSION)
+ unset(VMD_ARCH)
+ endif()
+ endif()
+
+ # so, should we use plug-ins?
+ if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
+ if (NOT VMD_QUIETLY)
+ MESSAGE(STATUS "Found the ability to use plug-ins when building shared libaries, so will compile to use plug-ins (e.g. to read VMD-supported file formats).")
+ endif(NOT VMD_QUIETLY)
+ set(GMX_USE_PLUGINS ON)
+ list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
+ set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
+ else()
+ set(PKG_DL_LIBS)
+ endif()
+endif(GMX_LOAD_PLUGINS)
+set(VMD_QUIETLY TRUE CACHE INTERNAL "")
+
# Math and thread libraries must often come after all others when linking...
if(HAVE_LIBM)
list(APPEND GMX_EXTRA_LIBRARIES m)
sfree(model[nwm]);
}
}
- fclose(fp);
+ ffclose(fp);
fprintf(stderr,"%2d: %s\n",nwm+1,"None");
do
else
{
strncpy(ffdir_parent,ffdir,STRLEN-1);
+ ffdir_parent[STRLEN-1]='\0'; /*make sure it is 0-terminated even for long string*/
p=strrchr(ffdir_parent,'/');
*p='\0';
}
static atom_id search_res_atom(const char *type,int resind,
- int natom,t_atom at[],
- char ** const *aname,
+ t_atoms *atoms,
const char *bondtype,gmx_bool bAllowMissing)
{
int i;
- for(i=0; (i<natom); i++)
- if (at[i].resind == resind)
- return search_atom(type,i,natom,at,aname,bondtype,bAllowMissing);
+ for(i=0; (i<atoms->nr); i++)
+ {
+ if (atoms->atom[i].resind == resind)
+ {
+ return search_atom(type,i,atoms,bondtype,bAllowMissing);
+ }
+ }
return NO_ATID;
}
- static void do_ssbonds(t_params *ps,int natoms,t_atom atom[],char **aname[],
+ static void do_ssbonds(t_params *ps,t_atoms *atoms,
int nssbonds,t_ssbond *ssbonds,gmx_bool bAllowMissing)
{
int i,ri,rj;
for(i=0; (i<nssbonds); i++) {
ri = ssbonds[i].res1;
rj = ssbonds[i].res2;
- ai = search_res_atom(ssbonds[i].a1,ri,natoms,atom,aname,
+ ai = search_res_atom(ssbonds[i].a1,ri,atoms,
"special bond",bAllowMissing);
- aj = search_res_atom(ssbonds[i].a2,rj,natoms,atom,aname,
+ aj = search_res_atom(ssbonds[i].a2,rj,atoms,
"special bond",bAllowMissing);
if ((ai == NO_ATID) || (aj == NO_ATID))
gmx_fatal(FARGS,"Trying to make impossible special bond (%s-%s)!",
}
}
-static gmx_bool inter_res_bond(const t_rbonded *b)
-{
- return (b->AI[0] == '-' || b->AI[0] == '+' ||
- b->AJ[0] == '-' || b->AJ[0] == '+');
-}
-
static void at2bonds(t_params *psb, t_hackblock *hb,
- int natoms, t_atom atom[], char **aname[],
- int nres, rvec x[],
+ t_atoms *atoms,
+ rvec x[],
real long_bond_dist, real short_bond_dist,
gmx_bool bAllowMissing)
{
fprintf(stderr,"Making bonds...\n");
i=0;
- for(resind=0; (resind < nres) && (i<natoms); resind++) {
+ for(resind=0; (resind < atoms->nres) && (i<atoms->nr); resind++) {
/* add bonds from list of bonded interactions */
for(j=0; j < hb[resind].rb[ebtsBONDS].nb; j++) {
/* Unfortunately we can not issue errors or warnings
* for missing atoms in bonds, as the hydrogens and terminal atoms
* have not been added yet.
*/
- ai=search_atom(hb[resind].rb[ebtsBONDS].b[j].AI,i,natoms,atom,aname,
+ ai=search_atom(hb[resind].rb[ebtsBONDS].b[j].AI,i,atoms,
ptr,TRUE);
- aj=search_atom(hb[resind].rb[ebtsBONDS].b[j].AJ,i,natoms,atom,aname,
+ aj=search_atom(hb[resind].rb[ebtsBONDS].b[j].AJ,i,atoms,
ptr,TRUE);
if (ai != NO_ATID && aj != NO_ATID) {
dist2 = distance2(x[ai],x[aj]);
}
}
/* add bonds from list of hacks (each added atom gets a bond) */
- while( (i<natoms) && (atom[i].resind == resind) ) {
+ while( (i<atoms->nr) && (atoms->atom[i].resind == resind) ) {
for(j=0; j < hb[resind].nhack; j++)
if ( ( hb[resind].hack[j].tp > 0 ||
hb[resind].hack[j].oname==NULL ) &&
- strcmp(hb[resind].hack[j].AI,*(aname[i])) == 0 ) {
+ strcmp(hb[resind].hack[j].AI,*(atoms->atomname[i])) == 0 ) {
switch(hb[resind].hack[j].tp) {
case 9: /* COOH terminus */
add_param(psb,i,i+1,NULL,NULL); /* C-O */
{
int residx,i,j,k;
const char *ptr;
- int natoms = atoms->nr;
- t_atom *atom = atoms->atom;
- char ***aname = atoms->atomname;
t_resinfo *resinfo = atoms->resinfo;
int nres = atoms->nres;
gmx_bool bAddCMAP;
atom_id cmap_atomid[NUM_CMAP_ATOMS];
- int cmap_chainnum, this_residue_index;
+ int cmap_chainnum=-1, this_residue_index;
if (debug)
ptr = "cmap";
for(k = 0; k < NUM_CMAP_ATOMS && bAddCMAP; k++)
{
cmap_atomid[k] = search_atom(restp[residx].rb[ebtsCMAP].b[j].a[k],
- i,natoms,atom,aname,ptr,TRUE);
+ i,atoms,ptr,TRUE);
bAddCMAP = bAddCMAP && (cmap_atomid[k] != NO_ATID);
if (!bAddCMAP)
{
* into the atom array. */
break;
}
- this_residue_index = atom[cmap_atomid[k]].resind;
+ this_residue_index = atoms->atom[cmap_atomid[k]].resind;
if (0 == k)
{
cmap_chainnum = resinfo[this_residue_index].chainnum;
if(residx<nres-1)
{
- while(atom[i].resind<residx+1)
+ while(atoms->atom[i].resind<residx+1)
{
i++;
}
/* Make bonds */
at2bonds(&(plist[F_BONDS]), hb,
- atoms->nr, atoms->atom, atoms->atomname, atoms->nres, *x,
+ atoms, *x,
long_bond_dist, short_bond_dist, bAllowMissing);
/* specbonds: disulphide bonds & heme-his */
do_ssbonds(&(plist[F_BONDS]),
- atoms->nr, atoms->atom, atoms->atomname, nssbonds, ssbonds,
+ atoms, nssbonds, ssbonds,
bAllowMissing);
nmissat = name2type(atoms, &cgnr, atype, restp, rt);
#endif
#include "string2.h"
#include "pgutil.h"
-#include "string.h"
+#include <string.h>
#include "gmx_fatal.h"
#define BUFSIZE 1024
static void atom_not_found(int fatal_errno,const char *file,int line,
const char *atomname,int resind,
+ const char *resname,
const char *bondtype,gmx_bool bAllowMissing)
{
char message_buffer[BUFSIZE];
if (0 != strcmp(bondtype, "atom"))
{
snprintf(message_buffer, 1024,
- "Atom %s is used in an interaction of type %s in the topology\n"
- "database, but an atom of that name was not found in residue\n"
- "number %d.\n",
- atomname,bondtype,resind+1);
+ "Residue %d named %s of a molecule in the input file was mapped\n"
+ "to an entry in the topology database, but the atom %s used in\n"
+ "an interaction of type %s in that entry is not found in the\n"
+ "input file. Perhaps your atom and/or residue naming needs to be\n"
+ "fixed.\n",
+ resind+1, resname, atomname, bondtype);
}
else
{
snprintf(message_buffer, 1024,
- "Atom %s is used in the topology database, but an atom of that\n"
- "name was not found in residue number %d.\n",
- atomname,resind+1);
+ "Residue %d named %s of a molecule in the input file was mapped\n"
+ "to an entry in the topology database, but the atom %s used in\n"
+ "that entry is not found in the input file. Perhaps your atom\n"
+ "and/or residue naming needs to be fixed.\n",
+ resind+1, resname, atomname);
}
if (bAllowMissing)
{
}
}
- atom_id search_atom(const char *type,int start,int natoms,t_atom at[],
- char ** const * anm,
+ atom_id search_atom(const char *type,int start,
+ t_atoms *atoms,
const char *bondtype,gmx_bool bAllowMissing)
{
int i,resind=-1;
gmx_bool bPrevious,bNext;
+ int natoms = atoms->nr;
+ t_atom *at = atoms->atom;
+ char ** const * anm = atoms->atomname;
bPrevious = (strchr(type,'-') != NULL);
bNext = (strchr(type,'+') != NULL);
return (atom_id) i;
}
if (!(bNext && at[start].resind==at[natoms-1].resind))
- atom_not_found(FARGS,type,at[start].resind,bondtype,bAllowMissing);
+ {
+ atom_not_found(FARGS,type,at[start].resind,*atoms->resinfo[resind].name,bondtype,bAllowMissing);
+ }
}
else {
/* The previous residue */
if (gmx_strcasecmp(type,*(anm[i]))==0)
return (atom_id) i;
if (start > 0)
- atom_not_found(FARGS,type,at[start].resind,bondtype,bAllowMissing);
+ {
+ atom_not_found(FARGS,type,at[start].resind,*atoms->resinfo[resind].name,bondtype,bAllowMissing);
+ }
}
return NO_ATID;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff