-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * 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:
- * GROningen Mixture of Alchemy and Childrens' Stories
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <string.h>
#include <stdio.h>
-#include "typedefs.h"
-#include "sysstuff.h"
-#include "gmx_fatal.h"
-#include "network.h"
-#include "txtdump.h"
-#include "names.h"
-#include "physics.h"
-#include "vec.h"
-#include "maths.h"
-#include "mvdata.h"
-#include "main.h"
-#include "force.h"
-#include "vcm.h"
-#include "smalloc.h"
-#include "futil.h"
-#include "network.h"
-#include "rbin.h"
-#include "tgroup.h"
-#include "xtcio.h"
-#include "gmxfio.h"
-#include "trnio.h"
-#include "statutil.h"
-#include "domdec.h"
-#include "partdec.h"
-#include "constr.h"
-#include "checkpoint.h"
-#include "xvgr.h"
-#include "md_support.h"
-#include "mdrun.h"
-#include "sim_util.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/rbin.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/sim_util.h"
typedef struct gmx_global_stat
{
where();
}
-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)
{
if (nstep != 0)
{
return 0;
}
}
-
-static void moveit(t_commrec *cr,
- int left, int right, const char *s, rvec xx[])
-{
- if (!xx)
- {
- return;
- }
-
- move_rvecs(cr, FALSE, FALSE, left, right,
- xx, NULL, (cr->nnodes-cr->npmenodes)-1, NULL);
-}
-
-gmx_mdoutf_t *init_mdoutf(int nfile, const t_filenm fnm[], int mdrun_flags,
- const t_commrec *cr, const t_inputrec *ir,
- const output_env_t oenv)
-{
- gmx_mdoutf_t *of;
- char filemode[3];
- gmx_bool bAppendFiles;
-
- snew(of, 1);
-
- of->fp_trn = NULL;
- of->fp_ene = NULL;
- of->fp_xtc = NULL;
- of->fp_dhdl = NULL;
- of->fp_field = NULL;
-
- of->eIntegrator = ir->eI;
- of->bExpanded = ir->bExpanded;
- of->elamstats = ir->expandedvals->elamstats;
- of->simulation_part = ir->simulation_part;
-
- if (MASTER(cr))
- {
- bAppendFiles = (mdrun_flags & MD_APPENDFILES);
-
- of->bKeepAndNumCPT = (mdrun_flags & MD_KEEPANDNUMCPT);
-
- sprintf(filemode, bAppendFiles ? "a+" : "w+");
-
- if ((EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
-#ifndef GMX_FAHCORE
- &&
- !(EI_DYNAMICS(ir->eI) &&
- ir->nstxout == 0 &&
- ir->nstvout == 0 &&
- ir->nstfout == 0)
-#endif
- )
- {
- of->fp_trn = open_trn(ftp2fn(efTRN, nfile, fnm), filemode);
- }
- if (EI_DYNAMICS(ir->eI) &&
- ir->nstxtcout > 0)
- {
- of->fp_xtc = open_xtc(ftp2fn(efXTC, nfile, fnm), filemode);
- of->xtc_prec = ir->xtcprec;
- }
- if (EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
- {
- of->fp_ene = open_enx(ftp2fn(efEDR, nfile, fnm), filemode);
- }
- of->fn_cpt = opt2fn("-cpo", nfile, fnm);
-
- if ((ir->efep != efepNO || ir->bSimTemp) && ir->fepvals->nstdhdl > 0 &&
- (ir->fepvals->separate_dhdl_file == esepdhdlfileYES ) &&
- EI_DYNAMICS(ir->eI))
- {
- if (bAppendFiles)
- {
- of->fp_dhdl = gmx_fio_fopen(opt2fn("-dhdl", nfile, fnm), filemode);
- }
- else
- {
- of->fp_dhdl = open_dhdl(opt2fn("-dhdl", nfile, fnm), ir, oenv);
- }
- }
-
- if (opt2bSet("-field", nfile, fnm) &&
- (ir->ex[XX].n || ir->ex[YY].n || ir->ex[ZZ].n))
- {
- if (bAppendFiles)
- {
- of->fp_dhdl = gmx_fio_fopen(opt2fn("-field", nfile, fnm),
- filemode);
- }
- else
- {
- of->fp_field = xvgropen(opt2fn("-field", nfile, fnm),
- "Applied electric field", "Time (ps)",
- "E (V/nm)", oenv);
- }
- }
- }
-
- return of;
-}
-
-void done_mdoutf(gmx_mdoutf_t *of)
-{
- if (of->fp_ene != NULL)
- {
- close_enx(of->fp_ene);
- }
- if (of->fp_xtc)
- {
- close_xtc(of->fp_xtc);
- }
- if (of->fp_trn)
- {
- close_trn(of->fp_trn);
- }
- if (of->fp_dhdl != NULL)
- {
- gmx_fio_fclose(of->fp_dhdl);
- }
- if (of->fp_field != NULL)
- {
- gmx_fio_fclose(of->fp_field);
- }
-
- sfree(of);
-}
-
-void write_traj(FILE *fplog, t_commrec *cr,
- gmx_mdoutf_t *of,
- int mdof_flags,
- gmx_mtop_t *top_global,
- gmx_large_int_t step, double t,
- t_state *state_local, t_state *state_global,
- rvec *f_local, rvec *f_global,
- int *n_xtc, rvec **x_xtc)
-{
- int i, j;
- gmx_groups_t *groups;
- rvec *xxtc;
- rvec *local_v;
- rvec *global_v;
-
-#define MX(xvf) moveit(cr, GMX_LEFT, GMX_RIGHT,#xvf, xvf)
-
- /* MRS -- defining these variables is to manage the difference
- * between half step and full step velocities, but there must be a better way . . . */
-
- local_v = state_local->v;
- global_v = state_global->v;
-
- if (DOMAINDECOMP(cr))
- {
- if (mdof_flags & MDOF_CPT)
- {
- dd_collect_state(cr->dd, state_local, state_global);
- }
- else
- {
- if (mdof_flags & (MDOF_X | MDOF_XTC))
- {
- dd_collect_vec(cr->dd, state_local, state_local->x,
- state_global->x);
- }
- if (mdof_flags & MDOF_V)
- {
- dd_collect_vec(cr->dd, state_local, local_v,
- global_v);
- }
- }
- if (mdof_flags & MDOF_F)
- {
- dd_collect_vec(cr->dd, state_local, f_local, f_global);
- }
- }
- else
- {
- if (mdof_flags & MDOF_CPT)
- {
- /* All pointers in state_local are equal to state_global,
- * but we need to copy the non-pointer entries.
- */
- state_global->lambda = state_local->lambda;
- state_global->veta = state_local->veta;
- state_global->vol0 = state_local->vol0;
- copy_mat(state_local->box, state_global->box);
- copy_mat(state_local->boxv, state_global->boxv);
- copy_mat(state_local->svir_prev, state_global->svir_prev);
- copy_mat(state_local->fvir_prev, state_global->fvir_prev);
- copy_mat(state_local->pres_prev, state_global->pres_prev);
- }
- if (cr->nnodes > 1)
- {
- /* Particle decomposition, collect the data on the master node */
- if (mdof_flags & MDOF_CPT)
- {
- if (state_local->flags & (1<<estX))
- {
- MX(state_global->x);
- }
- if (state_local->flags & (1<<estV))
- {
- MX(state_global->v);
- }
- if (state_local->flags & (1<<estSDX))
- {
- MX(state_global->sd_X);
- }
- if (state_global->nrngi > 1)
- {
- if (state_local->flags & (1<<estLD_RNG))
- {
-#ifdef GMX_MPI
- MPI_Gather(state_local->ld_rng,
- state_local->nrng*sizeof(state_local->ld_rng[0]), MPI_BYTE,
- state_global->ld_rng,
- state_local->nrng*sizeof(state_local->ld_rng[0]), MPI_BYTE,
- MASTERRANK(cr), cr->mpi_comm_mygroup);
-#endif
- }
- if (state_local->flags & (1<<estLD_RNGI))
- {
-#ifdef GMX_MPI
- MPI_Gather(state_local->ld_rngi,
- sizeof(state_local->ld_rngi[0]), MPI_BYTE,
- state_global->ld_rngi,
- sizeof(state_local->ld_rngi[0]), MPI_BYTE,
- MASTERRANK(cr), cr->mpi_comm_mygroup);
-#endif
- }
- }
- }
- else
- {
- if (mdof_flags & (MDOF_X | MDOF_XTC))
- {
- MX(state_global->x);
- }
- if (mdof_flags & MDOF_V)
- {
- MX(global_v);
- }
- }
- if (mdof_flags & MDOF_F)
- {
- MX(f_global);
- }
- }
- }
-
- if (MASTER(cr))
- {
- if (mdof_flags & MDOF_CPT)
- {
- write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT,
- fplog, cr, of->eIntegrator, of->simulation_part,
- of->bExpanded, of->elamstats, step, t, state_global);
- }
-
- if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
- {
- fwrite_trn(of->fp_trn, step, t, state_local->lambda[efptFEP],
- state_local->box, top_global->natoms,
- (mdof_flags & MDOF_X) ? state_global->x : NULL,
- (mdof_flags & MDOF_V) ? global_v : NULL,
- (mdof_flags & MDOF_F) ? f_global : NULL);
- if (gmx_fio_flush(of->fp_trn) != 0)
- {
- gmx_file("Cannot write trajectory; maybe you are out of disk space?");
- }
- gmx_fio_check_file_position(of->fp_trn);
- }
- if (mdof_flags & MDOF_XTC)
- {
- groups = &top_global->groups;
- if (*n_xtc == -1)
- {
- *n_xtc = 0;
- for (i = 0; (i < top_global->natoms); i++)
- {
- if (ggrpnr(groups, egcXTC, i) == 0)
- {
- (*n_xtc)++;
- }
- }
- if (*n_xtc != top_global->natoms)
- {
- snew(*x_xtc, *n_xtc);
- }
- }
- if (*n_xtc == top_global->natoms)
- {
- xxtc = state_global->x;
- }
- else
- {
- xxtc = *x_xtc;
- j = 0;
- for (i = 0; (i < top_global->natoms); i++)
- {
- if (ggrpnr(groups, egcXTC, i) == 0)
- {
- copy_rvec(state_global->x[i], xxtc[j++]);
- }
- }
- }
- if (write_xtc(of->fp_xtc, *n_xtc, step, t,
- state_local->box, xxtc, of->xtc_prec) == 0)
- {
- gmx_fatal(FARGS, "XTC error - maybe you are out of disk space?");
- }
- gmx_fio_check_file_position(of->fp_xtc);
- }
- }
-}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff