-/* -*- 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,
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-
- * 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.
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
#include <float.h>
-#include "typedefs.h"
-#include "string2.h"
-#include "mdebin.h"
-#include "smalloc.h"
-#include "physics.h"
+#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/math/units.h"
#include "gromacs/fileio/enxio.h"
-#include "vec.h"
-#include "disre.h"
-#include "main.h"
-#include "network.h"
-#include "names.h"
-#include "orires.h"
-#include "constr.h"
-#include "mtop_util.h"
-#include "xvgr.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/fileio/gmxfio.h"
-#include "macros.h"
-#include "mdrun.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
#include "mdebin_bar.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/smalloc.h"
static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
{
md->bEner[i] = EEL_FULL(ir->coulombtype);
}
+ else if (i == F_LJ_RECIP)
+ {
+ md->bEner[i] = EVDW_PME(ir->vdwtype);
+ }
else if (i == F_LJ14)
{
md->bEner[i] = b14;
{
ni = groups->grps[egcTC].nm_ind[i];
sprintf(buf, "T-%s", *(groups->grpname[ni]));
- grpnms[i] = strdup(buf);
+ grpnms[i] = gmx_strdup(buf);
}
md->itemp = get_ebin_space(md->ebin, md->nTC, (const char **)grpnms,
unit_temp_K);
for (j = 0; (j < md->nNHC); j++)
{
sprintf(buf, "Xi-%d-%s", j, bufi);
- grpnms[2*(i*md->nNHC+j)] = strdup(buf);
+ grpnms[2*(i*md->nNHC+j)] = gmx_strdup(buf);
sprintf(buf, "vXi-%d-%s", j, bufi);
- grpnms[2*(i*md->nNHC+j)+1] = strdup(buf);
+ grpnms[2*(i*md->nNHC+j)+1] = gmx_strdup(buf);
}
}
md->itc = get_ebin_space(md->ebin, md->mde_n,
for (j = 0; (j < md->nNHC); j++)
{
sprintf(buf, "Xi-%d-%s", j, bufi);
- grpnms[2*(i*md->nNHC+j)] = strdup(buf);
+ grpnms[2*(i*md->nNHC+j)] = gmx_strdup(buf);
sprintf(buf, "vXi-%d-%s", j, bufi);
- grpnms[2*(i*md->nNHC+j)+1] = strdup(buf);
+ grpnms[2*(i*md->nNHC+j)+1] = gmx_strdup(buf);
}
}
md->itcb = get_ebin_space(md->ebin, md->mdeb_n,
ni = groups->grps[egcTC].nm_ind[i];
bufi = *(groups->grpname[ni]);
sprintf(buf, "Xi-%s", bufi);
- grpnms[2*i] = strdup(buf);
+ grpnms[2*i] = gmx_strdup(buf);
sprintf(buf, "vXi-%s", bufi);
- grpnms[2*i+1] = strdup(buf);
+ grpnms[2*i+1] = gmx_strdup(buf);
}
md->itc = get_ebin_space(md->ebin, md->mde_n,
(const char **)grpnms, unit_invtime);
{
ni = groups->grps[egcTC].nm_ind[i];
sprintf(buf, "Lamb-%s", *(groups->grpname[ni]));
- grpnms[i] = strdup(buf);
+ grpnms[i] = gmx_strdup(buf);
}
md->itc = get_ebin_space(md->ebin, md->mde_n, (const char **)grpnms, "");
}
{
ni = groups->grps[egcACC].nm_ind[i];
sprintf(buf, "Ux-%s", *(groups->grpname[ni]));
- grpnms[3*i+XX] = strdup(buf);
+ grpnms[3*i+XX] = gmx_strdup(buf);
sprintf(buf, "Uy-%s", *(groups->grpname[ni]));
- grpnms[3*i+YY] = strdup(buf);
+ grpnms[3*i+YY] = gmx_strdup(buf);
sprintf(buf, "Uz-%s", *(groups->grpname[ni]));
- grpnms[3*i+ZZ] = strdup(buf);
+ grpnms[3*i+ZZ] = gmx_strdup(buf);
}
md->iu = get_ebin_space(md->ebin, 3*md->nU, (const char **)grpnms, unit_vel);
sfree(grpnms);
if (Nsep > 1)
{
/* and add the closing parenthesis */
- str += sprintf(str, ")");
+ sprintf(str, ")");
}
}
bufplace = sprintf(buf, "T = %g (K) ",
ir->opts.ref_t[0]);
}
- if (ir->efep != efepSLOWGROWTH)
+ if ((ir->efep != efepSLOWGROWTH) && (ir->efep != efepEXPANDED))
{
if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
{
nsets += 1; /*add fep state for expanded ensemble */
}
- if (fep->bPrintEnergy)
+ if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
nsets += 1; /* add energy to the dhdl as well */
}
{
/* state for the fep_vals, if we have alchemical sampling */
sprintf(buf, "%s", "Thermodynamic state");
- setname[s] = strdup(buf);
+ setname[s] = gmx_strdup(buf);
s += 1;
}
- if (fep->bPrintEnergy)
+ if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
- sprintf(buf, "%s (%s)", "Energy", unit_energy);
- setname[s] = strdup(buf);
+ switch (fep->edHdLPrintEnergy)
+ {
+ case edHdLPrintEnergyPOTENTIAL:
+ sprintf(buf, "%s (%s)", "Potential Energy", unit_energy);
+ break;
+ case edHdLPrintEnergyTOTAL:
+ case edHdLPrintEnergyYES:
+ default:
+ sprintf(buf, "%s (%s)", "Total Energy", unit_energy);
+ }
+ setname[s] = gmx_strdup(buf);
s += 1;
}
sprintf(buf, "%s %s = %.4f", dhdl, efpt_singular_names[i],
lam);
}
- setname[s] = strdup(buf);
+ setname[s] = gmx_strdup(buf);
s += 1;
}
}
nsetsbegin = 0;
}
- if (fep->bPrintEnergy)
+ if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
nsetsbegin += 1;
}
ir->simtempvals->temperatures[s-(nsetsbegin)],
unit_temp_K);
}
- setname[s] = strdup(buf);
+ setname[s] = gmx_strdup(buf);
s++;
}
if (write_pV)
{
np = sprintf(buf, "pV (%s)", unit_energy);
- setname[nsetsextend-1] = strdup(buf); /* the first entry after
- nsets */
+ setname[nsetsextend-1] = gmx_strdup(buf); /* the first entry after
+ nsets */
}
xvgr_legend(fp, nsetsextend, (const char **)setname, oenv);
fprintf(md->fp_dhdl, " %4d", state->fep_state);
}
/* total energy (for if the temperature changes */
- if (fep->bPrintEnergy)
+
+ if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
- store_energy = enerd->term[F_ETOT];
+ switch (fep->edHdLPrintEnergy)
+ {
+ case edHdLPrintEnergyPOTENTIAL:
+ store_energy = enerd->term[F_EPOT];
+ break;
+ case edHdLPrintEnergyTOTAL:
+ case edHdLPrintEnergyYES:
+ default:
+ store_energy = enerd->term[F_ETOT];
+ }
fprintf(md->fp_dhdl, " %#.8g", store_energy);
}
fprintf(log, "\n");
}
-void print_ebin_header(FILE *log, gmx_large_int_t steps, double time, real lambda)
+void print_ebin_header(FILE *log, gmx_int64_t steps, double time, real lambda)
{
char buf[22];
void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
FILE *log,
- gmx_large_int_t step, double time,
+ gmx_int64_t step, double time,
int mode, gmx_bool bCompact,
t_mdebin *md, t_fcdata *fcd,
gmx_groups_t *groups, t_grpopts *opts)
/* do the actual I/O */
do_enx(fp_ene, &fr);
- gmx_fio_check_file_position(enx_file_pointer(fp_ene));
if (fr.nre)
{
/* We have stored the sums, so reset the sum history */
nj = groups->grps[egcENER].nm_ind[j];
sprintf(buf, "%s-%s", *(groups->grpname[ni]),
*(groups->grpname[nj]));
- md->print_grpnms[n++] = strdup(buf);
+ md->print_grpnms[n++] = gmx_strdup(buf);
}
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff