*/
#include "gmxpre.h"
-#include "config.h"
-
-#include <algorithm>
+#include "fft5d.h"
+#include <assert.h>
+#include <float.h>
+#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
+#include <algorithm>
+
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "config.h"
+
#ifdef NOGMX
#define GMX_PARALLEL_ENV_INITIALIZED 1
#else
#endif
#endif
-#include "gromacs/utility/gmxmpi.h"
-
#ifdef GMX_OPENMP
/* TODO: Do we still need this? Are we still planning ot use fftw + OpenMP? */
#define FFT5D_THREADS
/* #define FFT5D_FFTW_THREADS (now set by cmake) */
#endif
-#include "fft5d.h"
-#include <float.h>
-#include <math.h>
-#include <assert.h>
-#include "gromacs/utility/smalloc.h"
-
#ifndef __FLT_EPSILON__
#define __FLT_EPSILON__ FLT_EPSILON
#define __DBL_EPSILON__ DBL_EPSILON
FILE* debug = 0;
#endif
-#include "gromacs/utility/fatalerror.h"
-
-
#ifdef GMX_FFT_FFTW3
#include "thread_mpi/mutex.h"
+
#include "gromacs/utility/exceptions.h"
/* none of the fftw3 calls, except execute(), are thread-safe, so
we need to serialize them with this mutex. */
*/
#include "gmxpre.h"
-#include "config.h"
-
#include <errno.h>
#include <stdlib.h>
#include <fftw3.h>
+#include "thread_mpi/mutex.h"
+
#include "gromacs/fft/fft.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "config.h"
+
#ifdef GMX_DOUBLE
#define FFTWPREFIX(name) fftw_ ## name
#else
#define FFTWPREFIX(name) fftwf_ ## name
#endif
-#include "thread_mpi/mutex.h"
-#include "gromacs/utility/exceptions.h"
-
/* none of the fftw3 calls, except execute(), are thread-safe, so
we need to serialize them with this mutex. */
static tMPI::mutex big_fftw_mutex;
*/
#include "gmxpre.h"
-#include "config.h"
+#include "gmxfio.h"
#include <errno.h>
#include <stdio.h>
#include <string.h>
+
+#include "config.h"
+
#ifdef HAVE_IO_H
#include <io.h>
#endif
#include "thread_mpi/threads.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "filenm.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/* This is the new improved and thread safe version of gmxfio. */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-
#include "gmxpre.h"
-#include "config.h"
-
#include <ctype.h>
#include <errno.h>
#include <stdio.h>
#include <string.h>
+
+#include "config.h"
+
#ifdef HAVE_IO_H
#include <io.h>
#endif
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "filenm.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/* This is the part that reads dummy and ascii files. */
*/
#include "gmxpre.h"
-#include "config.h"
-
#include <errno.h>
#include <stdio.h>
#include <string.h>
+
+#include "config.h"
+
#ifdef HAVE_IO_H
#include <io.h>
#endif
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
+#include "gromacs/utility/smalloc.h"
/* This is the part that reads dummy and ascii files. */
*/
#include "gmxpre.h"
+#include <errno.h>
+#include <stdio.h>
+
#include "config.h"
-#include <stdio.h>
-#include <errno.h>
#ifdef HAVE_IO_H
#include <io.h>
#endif
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
+#include "gromacs/utility/smalloc.h"
/*******************************************************************
*/
#include "gmxpre.h"
-#include "config.h"
-
#include <errno.h>
#include <stdio.h>
#include <string.h>
+
+#include "config.h"
+
#ifdef HAVE_IO_H
#include <io.h>
#endif
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
+#include "gromacs/utility/smalloc.h"
/* This is the part that reads xdr files. */
#include "tngio_for_tools.h"
-#include "config.h"
-
#include <math.h>
-#include "tngio.h"
-#include "trx.h"
+#include "config.h"
#ifdef GMX_USE_TNG
#include "tng/tng_io.h"
#endif
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/trx.h"
#include "gromacs/math/units.h"
#include "gromacs/utility/common.h"
#include "gromacs/utility/fatalerror.h"
#include "trxio.h"
-#include "config.h"
-
#include <assert.h>
#include <math.h>
-#ifdef GMX_USE_PLUGINS
-#include "vmdio.h"
-#endif
-#include "gmxfio.h"
-#include "trxio.h"
-#include "tpxio.h"
-#include "trnio.h"
-#include "tngio.h"
-#include "tngio_for_tools.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "xtcio.h"
-#include "pdbio.h"
-#include "confio.h"
-#include "gromacs/legacyheaders/checkpoint.h"
-#include "xdrf.h"
-
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/timecontrol.h"
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/tngio_for_tools.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/trx.h"
+#include "gromacs/fileio/xdrf.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/vec.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
+#include "config.h"
+
+#ifdef GMX_USE_PLUGINS
+#include "gromacs/fileio/vmdio.h"
+#endif
+
/* defines for frame counter output */
#define SKIP1 10
#define SKIP2 100
*/
#include "gmxpre.h"
-#include "config.h"
#include <math.h>
-/*#define HAVE_NN_LOOPS*/
-
#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/correl.h"
+#include "gromacs/gmxana/geminate.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/smalloc.h"
#include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gstat.h"
-#include "gromacs/utility/cstringutil.h"
#include "gromacs/pbcutil/pbc.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "geminate.h"
-
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "config.h"
+
+/*#define HAVE_NN_LOOPS*/
typedef short int t_E;
typedef int t_EEst;
*/
#include "gmxpre.h"
-#include "config.h"
-
#include <math.h>
#include <stdlib.h>
#include <string.h>
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/typedefs.h"
+#include "config.h"
+
+#ifdef HAVE_UNISTD_H
+#include <unistd.h>
+#endif
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tngio_for_tools.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/tngio_for_tools.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xtcio.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
-
enum {
euSel, euRect, euTric, euCompact, euNR
};
*/
#include "gmxpre.h"
-#include "config.h"
-
#include <stdlib.h>
#include <time.h>
+
+#include "config.h"
+
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/legacyheaders/calcgrid.h"
#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/inputrec.h"
#include "gromacs/legacyheaders/macros.h"
-#include "gmx_ana.h"
#include "gromacs/legacyheaders/names.h"
#include "gromacs/legacyheaders/perf_est.h"
-#include "gromacs/legacyheaders/inputrec.h"
-#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/math/utilities.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/utility/baseversion.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/legacyheaders/checkpoint.h"
-#include "config.h"
-
#include <errno.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <fcntl.h>
+
+#include "config.h"
+
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
-
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
-
#ifdef GMX_NATIVE_WINDOWS
/* _chsize_s */
#include <io.h>
#include <sys/locking.h>
#endif
+#include "buildinfo.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xdr_datatype.h"
+#include "gromacs/fileio/xdrf.h"
#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/txtdump.h"
#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/network.h"
-
-#include "gromacs/fileio/filenm.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/xdrf.h"
-#include "gromacs/fileio/xdr_datatype.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "buildinfo.h"
-
#ifdef GMX_FAHCORE
#include "corewrap.h"
#endif
#include "gromacs/legacyheaders/copyrite.h"
-#include "config.h"
-
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
+#include "config.h"
+
#ifdef HAVE_LIBMKL
#include <mkl.h>
#endif
-
#ifdef HAVE_EXTRAE
- #include "extrae_user_events.h"
+#include <extrae_user_events.h>
#endif
-
#include <boost/version.hpp>
/* This file is completely threadsafe - keep it that way! */
-#include "gromacs/legacyheaders/macros.h"
-
+#include "buildinfo.h"
#include "gromacs/fft/fft.h"
#include "gromacs/fileio/strdb.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
-#include "buildinfo.h"
-
static gmx_bool be_cool(void)
{
/* Yes, it is bad to check the environment variable every call,
*/
#include "gmxpre.h"
-#include "config.h"
-
-#include <string>
-#include <vector>
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
#include <assert.h>
#include <errno.h>
#include <stdlib.h>
#include <string.h>
+#include <string>
+#include <vector>
+
+#include "config.h"
+
#ifdef HAVE_UNISTD_H
/* For sysconf */
#include <unistd.h>
#endif
+#ifdef GMX_NATIVE_WINDOWS
+#include <windows.h>
+#endif
-#include "gromacs/legacyheaders/types/enums.h"
-#include "gromacs/legacyheaders/types/hw_info.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/md_logging.h"
+#include "thread_mpi/threads.h"
+
+#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/legacyheaders/gmx_cpuid.h"
#include "gromacs/legacyheaders/gpu_utils.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_detect_hardware.h"
#include "gromacs/legacyheaders/md_logging.h"
-
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/hw_info.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
-#include "thread_mpi/threads.h"
-
-#ifdef GMX_NATIVE_WINDOWS
-#include <windows.h>
-#endif
-
#ifdef GMX_GPU
const gmx_bool bGPUBinary = TRUE;
#else
#include "gmxpre.h"
#include "config.h"
+
#ifdef HAVE_SCHED_AFFINITY
# ifndef _GNU_SOURCE
# define _GNU_SOURCE 1
# include <sched.h>
# include <sys/syscall.h>
#endif
-#include <string.h>
-#include <errno.h>
+
+#include "gromacs/legacyheaders/gmx_thread_affinity.h"
+
#include <assert.h>
+#include <errno.h>
#include <stdio.h>
+#include <string.h>
#include "thread_mpi/threads.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/types/hw_info.h"
#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/legacyheaders/gmx_cpuid.h"
#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/gmx_thread_affinity.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/hw_info.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
*/
#include "gmxpre.h"
-#include "config.h"
+#include "gromacs/legacyheaders/main.h"
+#include <limits.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include <limits.h>
#include <time.h>
+#include "config.h"
+
+#ifdef GMX_NATIVE_WINDOWS
+#include <process.h>
+#endif
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
-#ifdef GMX_NATIVE_WINDOWS
-#include <process.h>
-#endif
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
#include "gromacs/fileio/filenm.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/legacyheaders/copyrite.h"
-
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
*/
#include "gmxpre.h"
-#include "config.h"
+#include "fflibutil.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <fcntl.h>
-#include <sys/types.h>
#include <sys/stat.h>
+#include <sys/types.h>
+
+#include "config.h"
+
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#include "gromacs/legacyheaders/network.h"
-#include "fflibutil.h"
-
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
-#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
/* This file is completely threadsafe - keep it that way! */
#include "gmxpre.h"
-#include <stdlib.h>
-
-/* #define DEBUG_NNB */
#include "gpp_nextnb.h"
-#include "toputil.h"
+#include <stdlib.h>
+
+#include "gromacs/gmxpreprocess/toputil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+/* #define DEBUG_NNB */
+
typedef struct {
int ai, aj;
} sortable;
*
* \ingroup module_imd
*/
-
#include "gmxpre.h"
-#include "config.h"
+#include "imd.h"
#include <errno.h>
#include <string.h>
+#include "config.h"
+
#ifdef GMX_NATIVE_WINDOWS
#include <windows.h>
#else
#include <unistd.h>
#endif
-#include "imd.h"
-#include "imdsocket.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/sighandler.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/mdlib/groupcoord.h"
#include "gromacs/fileio/confio.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/timing/wallcycle.h"
-
#include "gromacs/fileio/xvgr.h"
+#include "gromacs/imd/imdsocket.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/sighandler.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/groupcoord.h"
#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
*/
#include "gmxpre.h"
-#include "gromacs/math/utilities.h"
-
-#include "config.h"
+#include "utilities.h"
#include <assert.h>
-#include <math.h>
#include <limits.h>
+#include <math.h>
+
+#include "config.h"
+
#ifdef HAVE__FINITE
#include <float.h>
#endif
*/
#include "gmxpre.h"
-#include "config.h"
+#include "nbnxn_cuda.h"
-#include <stdlib.h>
#include <assert.h>
+#include <stdlib.h>
+
+#include "config.h"
#if defined(_MSVC)
#include <limits>
#include <cuda.h>
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/mdlib/nbnxn_pairlist.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/legacyheaders/types/force_flags.h"
-#include "../nbnxn_consts.h"
-
#ifdef TMPI_ATOMICS
#include "thread_mpi/atomic.h"
#endif
-#include "nbnxn_cuda_types.h"
-#include "../../gmxlib/cuda_tools/cudautils.cuh"
-#include "nbnxn_cuda.h"
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
-
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/utility/cstringutil.h"
#define CL_SIZE (NBNXN_GPU_CLUSTER_SIZE)
/***** The kernels come here *****/
-#include "nbnxn_cuda_kernel_utils.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh"
/* Top-level kernel generation: will generate through multiple inclusion the
* following flavors for all kernels:
* - force and energy output with pair list pruning.
*/
/** Force only **/
-#include "nbnxn_cuda_kernels.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
/** Force & energy **/
#define CALC_ENERGIES
-#include "nbnxn_cuda_kernels.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
#undef CALC_ENERGIES
/*** Pair-list pruning kernels ***/
/** Force only **/
#define PRUNE_NBL
-#include "nbnxn_cuda_kernels.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
/** Force & energy **/
#define CALC_ENERGIES
-#include "nbnxn_cuda_kernels.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
#undef CALC_ENERGIES
#undef PRUNE_NBL
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
#ifndef NBNXN_CUDA_H
#define NBNXN_CUDA_H
-#include "config.h"
-
#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
#include "gromacs/legacyheaders/types/simple.h"
+#include "config.h"
+
#ifdef GMX_GPU
#define FUNC_TERM ;
#else
extern "C" {
#endif
+struct nbnxn_atomdata_t;
+
/*! \brief
* Launch asynchronously the nonbonded force calculations.
*
* The local and non-local interaction calculations are launched in two
* separate streams.
*/
-void nbnxn_cuda_launch_kernel(nbnxn_cuda_ptr_t gmx_unused cu_nb,
- const nbnxn_atomdata_t gmx_unused *nbdata,
- int gmx_unused flags,
- int gmx_unused iloc) FUNC_TERM
+void nbnxn_cuda_launch_kernel(nbnxn_cuda_ptr_t gmx_unused cu_nb,
+ const struct nbnxn_atomdata_t gmx_unused *nbdata,
+ int gmx_unused flags,
+ int gmx_unused iloc) FUNC_TERM
/*! \brief
* Launch asynchronously the download of nonbonded forces from the GPU
* (and energies/shift forces if required).
*/
-void nbnxn_cuda_launch_cpyback(nbnxn_cuda_ptr_t gmx_unused cu_nb,
- const nbnxn_atomdata_t gmx_unused *nbatom,
- int gmx_unused flags,
- int gmx_unused aloc) FUNC_TERM
+void nbnxn_cuda_launch_cpyback(nbnxn_cuda_ptr_t gmx_unused cu_nb,
+ const struct nbnxn_atomdata_t gmx_unused *nbatom,
+ int gmx_unused flags,
+ int gmx_unused aloc) FUNC_TERM
/*! \brief
* Wait for the asynchronously launched nonbonded calculations and data
* transfers to finish.
*/
-void nbnxn_cuda_wait_gpu(nbnxn_cuda_ptr_t gmx_unused cu_nb,
- const nbnxn_atomdata_t gmx_unused *nbatom,
- int gmx_unused flags,
- int gmx_unused aloc,
- real gmx_unused *e_lj,
- real gmx_unused *e_el,
- rvec gmx_unused *fshift) FUNC_TERM
+void nbnxn_cuda_wait_gpu(nbnxn_cuda_ptr_t gmx_unused cu_nb,
+ const struct nbnxn_atomdata_t gmx_unused *nbatom,
+ int gmx_unused flags,
+ int gmx_unused aloc,
+ real gmx_unused *e_lj,
+ real gmx_unused *e_el,
+ rvec gmx_unused *fshift) FUNC_TERM
#ifdef __cplusplus
}
#include "gmxpre.h"
-#include "config.h"
+#include "nbnxn_search.h"
+#include <assert.h>
#include <math.h>
#include <string.h>
-#include <assert.h>
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
-#include "nbnxn_consts.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "config.h"
+
/* nbnxn_internal.h included gromacs/simd/macros.h */
-#include "nbnxn_internal.h"
+#include "gromacs/mdlib/nbnxn_internal.h"
#ifdef GMX_SIMD
#include "gromacs/simd/vector_operations.h"
#endif
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
-
-#include "gromacs/pbcutil/ishift.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/smalloc.h"
#ifdef NBNXN_SEARCH_BB_SIMD4
/* Always use 4-wide SIMD for bounding box calculations */
}
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_search_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_search_simd_4xn.h"
#endif
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_search_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_search_simd_2xnn.h"
#endif
/* Plain C or SIMD4 code for making a pair list of super-cell sci vs scj.
*/
#include "gmxpre.h"
-#include "config.h"
+#include "gromacs/legacyheaders/sim_util.h"
#include <assert.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
+
+#include "config.h"
+
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/chargegroup.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/orires.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/imd/imd.h"
#include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/legacyheaders/chargegroup.h"
#include "gromacs/legacyheaders/constr.h"
#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/disre.h"
#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
#include "gromacs/legacyheaders/genborn.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "nbnxn_kernels/nbnxn_kernel_ref.h"
-#include "nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
-#include "nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
-#include "nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
#include "gromacs/legacyheaders/nonbonded.h"
-#include "../gmxlib/nonbonded/nb_kernel.h"
-#include "../gmxlib/nonbonded/nb_free_energy.h"
-
-#include "gromacs/bonded/bonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/adress.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h"
#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/pulling/pull_rotation.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/essentialdynamics/edsam.h"
-#include "gromacs/pulling/pull.h"
-#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/imd/imd.h"
-#include "adress.h"
-#include "gromacs/legacyheaders/qmmm.h"
-
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
-#include "nbnxn_cuda/nbnxn_cuda.h"
-
-#include "nb_verlet.h"
void print_time(FILE *out,
gmx_walltime_accounting_t walltime_accounting,
*/
#include "gmxpre.h"
-#include "config.h"
-
#include "random.h"
+#include <math.h>
#include <stdio.h>
#include <stdlib.h>
+#include <time.h>
+
+#include "config.h"
+
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
-#include <time.h>
-#include <math.h>
#ifdef GMX_NATIVE_WINDOWS
#include <process.h>
#endif
-#include "external/Random123-1.08/include/Random123/threefry.h"
-
#include "gromacs/math/utilities.h"
-#include "random_gausstable.h"
+#include "gromacs/random/random_gausstable.h"
+
+#include "external/Random123-1.08/include/Random123/threefry.h"
#define RNG_N 624
#define RNG_M 397
*/
#include "gmxpre.h"
-#include "gromacs/timing/cyclecounter.h"
+#include "cyclecounter.h"
+
+#include <time.h>
#include "config.h"
-#include <time.h>
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
-
#ifdef _MSC_VER
#include <windows.h>
#endif
*/
#include "gmxpre.h"
-#include "gromacs/timing/walltime_accounting.h"
+#include "walltime_accounting.h"
+
+#include <time.h>
#include "config.h"
-#include <time.h>
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
*/
#include "gmxpre.h"
-#include "config.h"
-
#include <assert.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/checkpoint.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/fileio/xtcio.h"
-#include "gromacs/fileio/enxio.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/tngio.h"
-#include "gromacs/fileio/tngio_for_tools.h"
+#include "config.h"
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/mtxio.h"
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/tngio_for_tools.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xtcio.h"
#include "gromacs/gmxpreprocess/gmxcpp.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn,
*/
#include "gmxpre.h"
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
+#include "nsc.h"
+
#include <math.h>
#include <stdarg.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
-/* Modified DvdS */
-#include "gromacs/pbcutil/pbc.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/smalloc.h"
-#include "nsc.h"
#define TEST_NSC 0
#include "cstringutil.h"
-#include "config.h"
-
#include <assert.h>
#include <ctype.h>
#include <stdio.h>
#include <time.h>
#include <sys/types.h>
+
+#include "config.h"
+
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
#include <string>
#include <vector>
+#include <sys/stat.h>
+
#include "config.h"
-#include <sys/stat.h>
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#include "config.h"
#if defined(HAVE_POSIX_REGEX)
-// old Mac needs sys/types.h before regex.h
#include <sys/types.h>
+// old Mac needs sys/types.h before regex.h
#include <regex.h>
#define USE_POSIX_REGEX
#elif defined(HAVE_CXX11_REGEX)
#define USE_CXX11_REGEX
#endif
-#include "exceptions.h"
-#include "stringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/stringutil.h"
namespace gmx
{
#include <algorithm>
+#include <sys/stat.h>
+
#include "config.h"
-#include <sys/stat.h>
#ifdef GMX_NATIVE_WINDOWS
#include <direct.h>
#else