/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Gromacs Runs On Most of All Computer Systems
+ * 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 _sim_util_h
#define _sim_util_h
-#include "typedefs.h"
-#include "../fileio/enxio.h"
-#include "mdebin.h"
-#include "update.h"
-#include "vcm.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/mdoutf.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
-#include "../fileio/mdoutf.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_graph;
+
typedef struct gmx_global_stat *gmx_global_stat_t;
void do_pbc_first(FILE *log, matrix box, t_forcerec *fr,
- t_graph *graph, rvec x[]);
+ struct t_graph *graph, rvec x[]);
void do_pbc_first_mtop(FILE *fplog, int ePBC, matrix box,
gmx_mtop_t *mtop, rvec x[]);
gmx_bool bSumEkinhOld, int flags);
/* Communicate statistics over cr->mpi_comm_mysim */
-int do_per_step(gmx_large_int_t step, gmx_large_int_t nstep);
+int do_per_step(gmx_int64_t step, gmx_int64_t nstep);
/* Return TRUE if io should be done */
/* ROUTINES from sim_util.c */
void print_time(FILE *out, gmx_walltime_accounting_t walltime_accounting,
- gmx_large_int_t step, t_inputrec *ir, t_commrec *cr);
+ gmx_int64_t step, t_inputrec *ir, t_commrec *cr);
+
+/*! \brief Print date, time, MPI rank and a description of this point
+ * in time.
+ *
+ * \param[in] log logfile, or NULL to suppress output
+ * \param[in] rank MPI rank to include in the output
+ * \param[in] title Description to include in the output
+ * \param[in] the_time Seconds since the epoch, e.g. as reported by gmx_gettime
+ */
+void print_date_and_time(FILE *log, int rank, const char *title,
+ double the_time);
-void print_date_and_time(FILE *log, int pid, const char *title,
- const gmx_walltime_accounting_t walltime_accounting);
+void print_start(FILE *fplog, t_commrec *cr,
+ gmx_walltime_accounting_t walltime_accounting,
+ const char *name);
void finish_run(FILE *log, t_commrec *cr,
t_inputrec *inputrec,
t_nrnb nrnb[], gmx_wallcycle_t wcycle,
gmx_walltime_accounting_t walltime_accounting,
- wallclock_gpu_t *gputimes,
+ struct nonbonded_verlet_t *nbv,
gmx_bool bWriteStat);
void calc_enervirdiff(FILE *fplog, int eDispCorr, t_forcerec *fr);
-void calc_dispcorr(FILE *fplog, t_inputrec *ir, t_forcerec *fr,
- gmx_large_int_t step, int natoms,
+void calc_dispcorr(t_inputrec *ir, t_forcerec *fr,
+ int natoms,
matrix box, real lambda, tensor pres, tensor virial,
real *prescorr, real *enercorr, real *dvdlcorr);
t_nrnb *nrnb, gmx_mtop_t *mtop,
gmx_update_t *upd,
int nfile, const t_filenm fnm[],
- gmx_mdoutf_t **outf, t_mdebin **mdebin,
+ gmx_mdoutf_t *outf, t_mdebin **mdebin,
tensor force_vir, tensor shake_vir,
rvec mu_tot,
- gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags);
+ gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags,
+ gmx_wallcycle_t wcycle);
/* Routine in sim_util.c */
+gmx_bool use_GPU(const struct nonbonded_verlet_t *nbv);
+
#ifdef __cplusplus
}
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff