/*
- *
- * 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.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* 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) 2012,2014, 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.
+ *
+ * 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.
+ *
+ * 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.
+ *
* 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.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <signal.h>
#include <stdlib.h>
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
-double compute_io(t_inputrec *ir,int natoms,gmx_groups_t *groups,
- int nrener,int nrepl)
+static int div_nsteps(int nsteps, int nst)
{
- int nsteps = ir->nsteps;
- int i,nxtcatoms=0;
- int nstx=0,nstv=0,nstf=0,nste=0,nstlog=0,nstxtc=0,nfep=0;
- double cio;
-
- if (ir->nstxout > 0)
- nstx = 1 + nsteps / ir->nstxout;
- if (ir->nstvout > 0)
- nstv = 1 + nsteps / ir->nstvout;
- if (ir->nstfout > 0)
- nstf = (1 + nsteps) / ir->nstfout;
- if (ir->nstxtcout > 0) {
- for(i=0; i<natoms; i++) {
- if (groups->grpnr[egcXTC] == NULL || groups->grpnr[egcXTC][i] == 0)
- nxtcatoms++;
+ if (nst > 0)
+ {
+ return (1 + nsteps + nst - 1)/nst;
+ }
+ else
+ {
+ return 0;
}
- nstxtc = (1 + nsteps) / ir->nstxtcout;
- }
- if (ir->nstlog > 0)
- nstlog = 1 + nsteps / ir->nstlog;
- if (ir->nstenergy > 0)
- nste = 3 + nsteps / ir->nstenergy;
- cio = 80*natoms;
- cio += (nstx+nstf+nstv)*sizeof(real)*(3.0*natoms);
- cio += nstxtc*(14*4 + nxtcatoms*5.0); /* roughly 5 bytes per atom */
- cio += nstlog*(nrener*16*2.0); /* 16 bytes per energy term plus header */
- /* t_energy contains doubles, but real is written to edr */
- cio += (1.0*nste)*nrener*3*sizeof(real);
-
- if (ir->efep != efepNO) {
- int ndh=ir->n_flambda;
- if (ir->dhdl_derivatives == dhdlderivativesYES)
- {
- ndh += 1;
- }
- if (ir->separate_dhdl_file==sepdhdlfileYES)
- {
- int nchars = 8 + ndh*10; /* time data ~8 chars/line,
- dH data ~10 chars/line */
- cio += ((1 + nsteps)/ir->nstdhdl)*nchars;
- }
- else
- {
- /* dH output to ener.edr: */
- if (ir->dh_hist_size <= 0)
- {
- /* as data blocks: 1 real per dH point */
- cio += ((1 + nsteps)/ir->nstdhdl)*ndh*sizeof(real);
- }
- else
- {
- /* as histograms: dh_hist_size ints per histogram */
- cio += ((1 + nsteps)/ir->nstenergy)*
- sizeof(int)*ir->dh_hist_size*ndh;
- }
- }
- }
- if (ir->pull != NULL) {
- if (ir->pull->nstxout > 0) {
- cio += (1 + nsteps)/ir->pull->nstxout*20; /* roughly 20 chars per line */
+}
+
+double compute_io(t_inputrec *ir, int natoms, gmx_groups_t *groups,
+ int nrener, int nrepl)
+{
+
+ int nsteps = ir->nsteps;
+ int i, nxtcatoms = 0;
+ int nstx, nstv, nstf, nste, nstlog, nstxtc, nfep = 0;
+ double cio;
+
+ nstx = div_nsteps(nsteps, ir->nstxout);
+ nstv = div_nsteps(nsteps, ir->nstvout);
+ nstf = div_nsteps(nsteps, ir->nstfout);
+ nstxtc = div_nsteps(nsteps, ir->nstxout_compressed);
+ if (ir->nstxout_compressed > 0)
+ {
+ for (i = 0; i < natoms; i++)
+ {
+ if (groups->grpnr[egcCompressedX] == NULL || groups->grpnr[egcCompressedX][i] == 0)
+ {
+ nxtcatoms++;
+ }
+ }
+ }
+ nstlog = div_nsteps(nsteps, ir->nstlog);
+ /* We add 2 for the header */
+ nste = div_nsteps(2+nsteps, ir->nstenergy);
+
+ cio = 80*natoms;
+ cio += (nstx+nstf+nstv)*sizeof(real)*(3.0*natoms);
+ cio += nstxtc*(14*4 + nxtcatoms*5.0); /* roughly 5 bytes per atom */
+ cio += nstlog*(nrener*16*2.0); /* 16 bytes per energy term plus header */
+ /* t_energy contains doubles, but real is written to edr */
+ cio += (1.0*nste)*nrener*3*sizeof(real);
+
+ if ((ir->efep != efepNO || ir->bSimTemp) && (ir->fepvals->nstdhdl > 0))
+ {
+ int ndh = ir->fepvals->n_lambda;
+ int ndhdl = 0;
+ int nchars = 0;
+
+ for (i = 0; i < efptNR; i++)
+ {
+ if (ir->fepvals->separate_dvdl[i])
+ {
+ ndhdl += 1;
+ }
+ }
+
+ if (ir->fepvals->separate_dhdl_file == esepdhdlfileYES)
+ {
+ nchars = 8 + ndhdl*8 + ndh*10; /* time data ~8 chars/entry, dH data ~10 chars/entry */
+ if (ir->expandedvals->elmcmove > elmcmoveNO)
+ {
+ nchars += 5; /* alchemical state */
+ }
+
+ if (ir->fepvals->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ {
+ nchars += 12; /* energy for dhdl */
+ }
+ cio += div_nsteps(nsteps, ir->fepvals->nstdhdl)*nchars;
+ }
+ else
+ {
+ /* dH output to ener.edr: */
+ if (ir->fepvals->dh_hist_size <= 0)
+ {
+ int ndh_tot = ndh+ndhdl;
+ if (ir->expandedvals->elmcmove > elmcmoveNO)
+ {
+ ndh_tot += 1;
+ }
+ if (ir->fepvals->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ {
+ ndh_tot += 1;
+ }
+ /* as data blocks: 1 real per dH point */
+ cio += div_nsteps(nsteps, ir->fepvals->nstdhdl)*(ndh+ndhdl)*sizeof(real);
+ }
+ else
+ {
+ /* as histograms: dh_hist_size ints per histogram */
+ cio += div_nsteps(nsteps, ir->nstenergy)*
+ sizeof(int)*ir->fepvals->dh_hist_size*ndh;
+ }
+ }
}
- if (ir->pull->nstfout > 0) {
- cio += (1 + nsteps)/ir->pull->nstfout*20; /* roughly 20 chars per line */
+ if (ir->pull != NULL)
+ {
+ cio += div_nsteps(nsteps, ir->pull->nstxout)*20; /* roughly 20 chars per line */
+ cio += div_nsteps(nsteps, ir->pull->nstfout)*20; /* roughly 20 chars per line */
}
- }
- return cio*nrepl/(1024*1024);
+ return cio*nrepl/(1024*1024);
}