-/* -*- 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) 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.
+ *
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+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
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+ * in the README & COPYING files - if they are missing, get the
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+ *
* 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.
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <signal.h>
#include <stdlib.h>
-#include "typedefs.h"
-static int div_nsteps(int nsteps,int nst)
+#include "gromacs/legacyheaders/typedefs.h"
+
+static int div_nsteps(int nsteps, int nst)
{
if (nst > 0)
{
}
}
-double compute_io(t_inputrec *ir,int natoms,gmx_groups_t *groups,
- int nrener,int nrepl)
+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->nstxtcout);
- if (ir->nstxtcout > 0)
+
+ 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++)
+ for (i = 0; i < natoms; i++)
{
- if (groups->grpnr[egcXTC] == NULL || groups->grpnr[egcXTC][i] == 0)
+ if (groups->grpnr[egcCompressedX] == NULL || groups->grpnr[egcCompressedX][i] == 0)
{
nxtcatoms++;
}
}
}
- nstlog = div_nsteps(nsteps,ir->nstlog);
+ nstlog = div_nsteps(nsteps, ir->nstlog);
/* We add 2 for the header */
- nste = div_nsteps(2+nsteps,ir->nstenergy);
+ 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;
- 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 += div_nsteps(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 += div_nsteps(nsteps,ir->nstenergy)*ndh*sizeof(real);
- }
- else
- {
- /* as histograms: dh_hist_size ints per histogram */
- cio += div_nsteps(nsteps,ir->nstenergy)*
- sizeof(int)*ir->dh_hist_size*ndh;
- }
- }
- }
+ 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 != 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 */
+ 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);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff