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)
* 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,
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. */
#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 %%
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
#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" : ""));
}
}
# 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)
#include "gmxcomplex.h"
#include "gmx_fft.h"
-#ifndef GMX_LIB_MPI
+#ifndef GMX_MPI
double MPI_Wtime();
#endif
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()
{
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,",
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff