-/* -*- 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
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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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+ * GROMACS is distributed in the hope that it will be useful,
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+ * Lesser General Public License for more details.
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- * the papers on the package - you can find them in the top README file.
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*
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+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
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+ * 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.
*
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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 "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 "gmxfio.h"
-#include "macros.h"
-#include "mdrun.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 "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 "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" };
#define NBOXS asize(boxs_nm)
#define NTRICLBOXS asize(tricl_boxs_nm)
-t_mdebin *init_mdebin(ener_file_t fp_ene,
+t_mdebin *init_mdebin(ener_file_t fp_ene,
const gmx_mtop_t *mtop,
const t_inputrec *ir,
- FILE *fp_dhdl)
+ FILE *fp_dhdl)
{
- const char *ener_nm[F_NRE];
- static const char *vir_nm[] = {
+ const char *ener_nm[F_NRE];
+ static const char *vir_nm[] = {
"Vir-XX", "Vir-XY", "Vir-XZ",
"Vir-YX", "Vir-YY", "Vir-YZ",
"Vir-ZX", "Vir-ZY", "Vir-ZZ"
};
- static const char *sv_nm[] = {
+ static const char *sv_nm[] = {
"ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
"ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
"ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
};
- static const char *fv_nm[] = {
+ static const char *fv_nm[] = {
"ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
"ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
"ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
};
- static const char *pres_nm[] = {
- "Pres-XX","Pres-XY","Pres-XZ",
- "Pres-YX","Pres-YY","Pres-YZ",
- "Pres-ZX","Pres-ZY","Pres-ZZ"
+ static const char *pres_nm[] = {
+ "Pres-XX", "Pres-XY", "Pres-XZ",
+ "Pres-YX", "Pres-YY", "Pres-YZ",
+ "Pres-ZX", "Pres-ZY", "Pres-ZZ"
};
- static const char *surft_nm[] = {
+ static const char *surft_nm[] = {
"#Surf*SurfTen"
};
- static const char *mu_nm[] = {
+ static const char *mu_nm[] = {
"Mu-X", "Mu-Y", "Mu-Z"
};
- static const char *vcos_nm[] = {
+ static const char *vcos_nm[] = {
"2CosZ*Vel-X"
};
- static const char *visc_nm[] = {
+ static const char *visc_nm[] = {
"1/Viscosity"
};
- static const char *baro_nm[] = {
+ static const char *baro_nm[] = {
"Barostat"
};
- char **grpnms;
+ char **grpnms;
const gmx_groups_t *groups;
- char **gnm;
- char buf[256];
- const char *bufi;
- t_mdebin *md;
- int i,j,ni,nj,n,nh,k,kk,ncon,nset;
- gmx_bool bBHAM,bNoseHoover,b14;
+ char **gnm;
+ char buf[256];
+ const char *bufi;
+ t_mdebin *md;
+ int i, j, ni, nj, n, nh, k, kk, ncon, nset;
+ gmx_bool bBHAM, bNoseHoover, b14;
- snew(md,1);
+ snew(md, 1);
- md->bVir=TRUE;
- md->bPress=TRUE;
- md->bSurft=TRUE;
- md->bMu=TRUE;
+ md->bVir = TRUE;
+ md->bPress = TRUE;
+ md->bSurft = TRUE;
+ md->bMu = TRUE;
if (EI_DYNAMICS(ir->eI))
{
groups = &mtop->groups;
bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
- b14 = (gmx_mtop_ftype_count(mtop,F_LJ14) > 0 ||
- gmx_mtop_ftype_count(mtop,F_LJC14_Q) > 0);
+ b14 = (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
+ gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0);
- ncon = gmx_mtop_ftype_count(mtop,F_CONSTR);
- nset = gmx_mtop_ftype_count(mtop,F_SETTLE);
+ ncon = gmx_mtop_ftype_count(mtop, F_CONSTR);
+ nset = gmx_mtop_ftype_count(mtop, F_SETTLE);
md->bConstr = (ncon > 0 || nset > 0);
md->bConstrVir = FALSE;
- if (md->bConstr) {
- if (ncon > 0 && ir->eConstrAlg == econtLINCS) {
+ if (md->bConstr)
+ {
+ if (ncon > 0 && ir->eConstrAlg == econtLINCS)
+ {
if (ir->eI == eiSD2)
+ {
md->nCrmsd = 2;
+ }
else
+ {
md->nCrmsd = 1;
+ }
}
md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
- } else {
+ }
+ else
+ {
md->nCrmsd = 0;
}
/* Energy monitoring */
- for(i=0;i<egNR;i++)
+ for (i = 0; i < egNR; i++)
{
- md->bEInd[i]=FALSE;
+ md->bEInd[i] = FALSE;
}
-#ifndef GMX_OPENMM
- for(i=0; i<F_NRE; i++)
+ for (i = 0; i < F_NRE; i++)
{
md->bEner[i] = FALSE;
if (i == F_LJ)
+ {
md->bEner[i] = !bBHAM;
+ }
else if (i == F_BHAM)
+ {
md->bEner[i] = bBHAM;
+ }
else if (i == F_EQM)
+ {
md->bEner[i] = ir->bQMMM;
+ }
else if (i == F_COUL_LR)
+ {
md->bEner[i] = (ir->rcoulomb > ir->rlist);
+ }
else if (i == F_LJ_LR)
+ {
md->bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
+ }
else if (i == F_BHAM_LR)
+ {
md->bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
+ }
else if (i == F_RF_EXCL)
- md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC);
+ {
+ md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC && ir->cutoff_scheme == ecutsGROUP);
+ }
else if (i == F_COUL_RECIP)
+ {
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;
+ }
else if (i == F_COUL14)
+ {
md->bEner[i] = b14;
+ }
else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
+ {
md->bEner[i] = FALSE;
+ }
else if ((i == F_DVDL_COUL && ir->fepvals->separate_dvdl[efptCOUL]) ||
(i == F_DVDL_VDW && ir->fepvals->separate_dvdl[efptVDW]) ||
(i == F_DVDL_BONDED && ir->fepvals->separate_dvdl[efptBONDED]) ||
(i == F_DVDL_RESTRAINT && ir->fepvals->separate_dvdl[efptRESTRAINT]) ||
(i == F_DKDL && ir->fepvals->separate_dvdl[efptMASS]) ||
(i == F_DVDL && ir->fepvals->separate_dvdl[efptFEP]))
+ {
md->bEner[i] = (ir->efep != efepNO);
+ }
else if ((interaction_function[i].flags & IF_VSITE) ||
(i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
+ {
md->bEner[i] = FALSE;
- else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i==F_EQM))
+ }
+ else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i == F_EQM))
+ {
md->bEner[i] = TRUE;
- else if ((i == F_GBPOL) && ir->implicit_solvent==eisGBSA)
+ }
+ else if ((i == F_GBPOL) && ir->implicit_solvent == eisGBSA)
+ {
md->bEner[i] = TRUE;
- else if ((i == F_NPSOLVATION) && ir->implicit_solvent==eisGBSA && (ir->sa_algorithm != esaNO))
+ }
+ else if ((i == F_NPSOLVATION) && ir->implicit_solvent == eisGBSA && (ir->sa_algorithm != esaNO))
+ {
md->bEner[i] = TRUE;
+ }
else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14))
+ {
md->bEner[i] = FALSE;
+ }
else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
+ {
md->bEner[i] = EI_DYNAMICS(ir->eI);
- else if (i==F_VTEMP)
- md->bEner[i] = (EI_DYNAMICS(ir->eI) && getenv("GMX_VIRIAL_TEMPERATURE"));
+ }
else if (i == F_DISPCORR || i == F_PDISPCORR)
+ {
md->bEner[i] = (ir->eDispCorr != edispcNO);
+ }
else if (i == F_DISRESVIOL)
- md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0);
+ {
+ md->bEner[i] = (gmx_mtop_ftype_count(mtop, F_DISRES) > 0);
+ }
else if (i == F_ORIRESDEV)
- md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0);
+ {
+ md->bEner[i] = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0);
+ }
else if (i == F_CONNBONDS)
+ {
md->bEner[i] = FALSE;
+ }
else if (i == F_COM_PULL)
+ {
md->bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F || ir->bRot);
+ }
else if (i == F_ECONSERVED)
+ {
md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
- (ir->epc == epcNO || ir->epc==epcMTTK));
+ (ir->epc == epcNO || ir->epc == epcMTTK));
+ }
else
- md->bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
+ {
+ md->bEner[i] = (gmx_mtop_ftype_count(mtop, i) > 0);
+ }
}
-#else
- /* OpenMM always produces only the following 4 energy terms */
- md->bEner[F_EPOT] = TRUE;
- md->bEner[F_EKIN] = TRUE;
- md->bEner[F_ETOT] = TRUE;
- md->bEner[F_TEMP] = TRUE;
-#endif
/* for adress simulations, most energy terms are not meaningfull, and thus disabled*/
- if (ir->bAdress && !debug) {
- for (i = 0; i < F_NRE; i++) {
+ if (ir->bAdress && !debug)
+ {
+ for (i = 0; i < F_NRE; i++)
+ {
md->bEner[i] = FALSE;
- if(i == F_EKIN){ md->bEner[i] = TRUE;}
- if(i == F_TEMP){ md->bEner[i] = TRUE;}
+ if (i == F_EKIN)
+ {
+ md->bEner[i] = TRUE;
+ }
+ if (i == F_TEMP)
+ {
+ md->bEner[i] = TRUE;
+ }
}
- md->bVir=FALSE;
- md->bPress=FALSE;
- md->bSurft=FALSE;
- md->bMu=FALSE;
+ md->bVir = FALSE;
+ md->bPress = FALSE;
+ md->bSurft = FALSE;
+ md->bMu = FALSE;
}
- md->f_nre=0;
- for(i=0; i<F_NRE; i++)
+ md->f_nre = 0;
+ for (i = 0; i < F_NRE; i++)
{
if (md->bEner[i])
{
- /* FIXME: The constness should not be cast away */
- /*ener_nm[f_nre]=(char *)interaction_function[i].longname;*/
- ener_nm[md->f_nre]=interaction_function[i].longname;
+ ener_nm[md->f_nre] = interaction_function[i].longname;
md->f_nre++;
}
}
- md->epc = ir->epc;
- md->bDiagPres = !TRICLINIC(ir->ref_p);
- md->ref_p = (ir->ref_p[XX][XX]+ir->ref_p[YY][YY]+ir->ref_p[ZZ][ZZ])/DIM;
- md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
- md->bDynBox = DYNAMIC_BOX(*ir);
- md->etc = ir->etc;
- md->bNHC_trotter = IR_NVT_TROTTER(ir);
- md->bPrintNHChains = ir-> bPrintNHChains;
- md->bMTTK = (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir));
+ md->epc = ir->epc;
+ md->bDiagPres = !TRICLINIC(ir->ref_p);
+ md->ref_p = (ir->ref_p[XX][XX]+ir->ref_p[YY][YY]+ir->ref_p[ZZ][ZZ])/DIM;
+ md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
+ md->bDynBox = DYNAMIC_BOX(*ir);
+ md->etc = ir->etc;
+ md->bNHC_trotter = IR_NVT_TROTTER(ir);
+ md->bPrintNHChains = ir->bPrintNHChains;
+ md->bMTTK = (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir));
+ md->bMu = NEED_MUTOT(*ir);
md->ebin = mk_ebin();
/* Pass NULL for unit to let get_ebin_space determine the units
* for interaction_function[i].longname
*/
- md->ie = get_ebin_space(md->ebin,md->f_nre,ener_nm,NULL);
+ md->ie = get_ebin_space(md->ebin, md->f_nre, ener_nm, NULL);
if (md->nCrmsd)
{
/* This should be called directly after the call for md->ie,
* such that md->iconrmsd follows directly in the list.
*/
- md->iconrmsd = get_ebin_space(md->ebin,md->nCrmsd,conrmsd_nm,"");
+ md->iconrmsd = get_ebin_space(md->ebin, md->nCrmsd, conrmsd_nm, "");
}
if (md->bDynBox)
{
md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI);
if (md->bDiagPres)
{
- md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
+ md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy);
}
}
if (md->bConstrVir)
{
- md->isvir = get_ebin_space(md->ebin,asize(sv_nm),sv_nm,unit_energy);
- md->ifvir = get_ebin_space(md->ebin,asize(fv_nm),fv_nm,unit_energy);
+ md->isvir = get_ebin_space(md->ebin, asize(sv_nm), sv_nm, unit_energy);
+ md->ifvir = get_ebin_space(md->ebin, asize(fv_nm), fv_nm, unit_energy);
}
if (md->bVir)
- md->ivir = get_ebin_space(md->ebin,asize(vir_nm),vir_nm,unit_energy);
+ {
+ md->ivir = get_ebin_space(md->ebin, asize(vir_nm), vir_nm, unit_energy);
+ }
if (md->bPress)
- md->ipres = get_ebin_space(md->ebin,asize(pres_nm),pres_nm,unit_pres_bar);
+ {
+ md->ipres = get_ebin_space(md->ebin, asize(pres_nm), pres_nm, unit_pres_bar);
+ }
if (md->bSurft)
- md->isurft = get_ebin_space(md->ebin,asize(surft_nm),surft_nm,
- unit_surft_bar);
+ {
+ md->isurft = get_ebin_space(md->ebin, asize(surft_nm), surft_nm,
+ unit_surft_bar);
+ }
if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
{
- md->ipc = get_ebin_space(md->ebin,md->bTricl ? 6 : 3,
- boxvel_nm,unit_vel);
+ md->ipc = get_ebin_space(md->ebin, md->bTricl ? 6 : 3,
+ boxvel_nm, unit_vel);
}
if (md->bMu)
- md->imu = get_ebin_space(md->ebin,asize(mu_nm),mu_nm,unit_dipole_D);
+ {
+ md->imu = get_ebin_space(md->ebin, asize(mu_nm), mu_nm, unit_dipole_D);
+ }
if (ir->cos_accel != 0)
{
- md->ivcos = get_ebin_space(md->ebin,asize(vcos_nm),vcos_nm,unit_vel);
- md->ivisc = get_ebin_space(md->ebin,asize(visc_nm),visc_nm,
+ md->ivcos = get_ebin_space(md->ebin, asize(vcos_nm), vcos_nm, unit_vel);
+ md->ivisc = get_ebin_space(md->ebin, asize(visc_nm), visc_nm,
unit_invvisc_SI);
}
/* Energy monitoring */
- for(i=0;i<egNR;i++)
+ for (i = 0; i < egNR; i++)
{
md->bEInd[i] = FALSE;
}
}
if (b14)
{
- md->bEInd[egLJ14] = TRUE;
+ md->bEInd[egLJ14] = TRUE;
md->bEInd[egCOUL14] = TRUE;
}
- md->nEc=0;
- for(i=0; (i<egNR); i++)
+ md->nEc = 0;
+ for (i = 0; (i < egNR); i++)
{
if (md->bEInd[i])
{
}
}
- n=groups->grps[egcENER].nr;
+ n = groups->grps[egcENER].nr;
/* for adress simulations, most energy terms are not meaningfull, and thus disabled*/
- if (!ir->bAdress){
+ if (!ir->bAdress)
+ {
/*standard simulation*/
- md->nEg=n;
- md->nE=(n*(n+1))/2;
+ md->nEg = n;
+ md->nE = (n*(n+1))/2;
}
- else if (!debug) {
+ else if (!debug)
+ {
/*AdResS simulation*/
- md->nU=0;
- md->nEg=0;
- md->nE=0;
- md->nEc=0;
- md->isvir=FALSE;
+ md->nU = 0;
+ md->nEg = 0;
+ md->nE = 0;
+ md->nEc = 0;
+ md->isvir = FALSE;
}
- snew(md->igrp,md->nE);
+ snew(md->igrp, md->nE);
if (md->nE > 1)
{
- n=0;
- snew(gnm,md->nEc);
- for(k=0; (k<md->nEc); k++)
+ n = 0;
+ snew(gnm, md->nEc);
+ for (k = 0; (k < md->nEc); k++)
{
- snew(gnm[k],STRLEN);
+ snew(gnm[k], STRLEN);
}
- for(i=0; (i<groups->grps[egcENER].nr); i++)
+ for (i = 0; (i < groups->grps[egcENER].nr); i++)
{
- ni=groups->grps[egcENER].nm_ind[i];
- for(j=i; (j<groups->grps[egcENER].nr); j++)
+ ni = groups->grps[egcENER].nm_ind[i];
+ for (j = i; (j < groups->grps[egcENER].nr); j++)
{
- nj=groups->grps[egcENER].nm_ind[j];
- for(k=kk=0; (k<egNR); k++)
+ nj = groups->grps[egcENER].nm_ind[j];
+ for (k = kk = 0; (k < egNR); k++)
{
if (md->bEInd[k])
{
- sprintf(gnm[kk],"%s:%s-%s",egrp_nm[k],
- *(groups->grpname[ni]),*(groups->grpname[nj]));
+ sprintf(gnm[kk], "%s:%s-%s", egrp_nm[k],
+ *(groups->grpname[ni]), *(groups->grpname[nj]));
kk++;
}
}
- md->igrp[n]=get_ebin_space(md->ebin,md->nEc,
- (const char **)gnm,unit_energy);
+ md->igrp[n] = get_ebin_space(md->ebin, md->nEc,
+ (const char **)gnm, unit_energy);
n++;
}
}
- for(k=0; (k<md->nEc); k++)
+ for (k = 0; (k < md->nEc); k++)
{
sfree(gnm[k]);
}
}
}
- md->nTC=groups->grps[egcTC].nr;
+ md->nTC = groups->grps[egcTC].nr;
md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */
if (md->bMTTK)
{
{
md->mdeb_n = 2*md->nNHC*md->nTCP;
}
- } else {
- md->mde_n = md->nTC;
+ }
+ else
+ {
+ md->mde_n = md->nTC;
md->mdeb_n = 0;
}
- snew(md->tmp_r,md->mde_n);
- snew(md->tmp_v,md->mde_n);
- snew(md->grpnms,md->mde_n);
+ snew(md->tmp_r, md->mde_n);
+ snew(md->tmp_v, md->mde_n);
+ snew(md->grpnms, md->mde_n);
grpnms = md->grpnms;
- for(i=0; (i<md->nTC); i++)
+ for (i = 0; (i < md->nTC); i++)
{
- ni=groups->grps[egcTC].nm_ind[i];
- sprintf(buf,"T-%s",*(groups->grpname[ni]));
- grpnms[i]=strdup(buf);
+ ni = groups->grps[egcTC].nm_ind[i];
+ sprintf(buf, "T-%s", *(groups->grpname[ni]));
+ grpnms[i] = gmx_strdup(buf);
}
- md->itemp=get_ebin_space(md->ebin,md->nTC,(const char **)grpnms,
- unit_temp_K);
+ md->itemp = get_ebin_space(md->ebin, md->nTC, (const char **)grpnms,
+ unit_temp_K);
if (md->etc == etcNOSEHOOVER)
{
{
if (md->bNHC_trotter)
{
- for(i=0; (i<md->nTC); i++)
+ for (i = 0; (i < md->nTC); i++)
{
- ni=groups->grps[egcTC].nm_ind[i];
+ ni = groups->grps[egcTC].nm_ind[i];
bufi = *(groups->grpname[ni]);
- for(j=0; (j<md->nNHC); j++)
+ for (j = 0; (j < md->nNHC); j++)
{
- sprintf(buf,"Xi-%d-%s",j,bufi);
- grpnms[2*(i*md->nNHC+j)]=strdup(buf);
- sprintf(buf,"vXi-%d-%s",j,bufi);
- grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
+ sprintf(buf, "Xi-%d-%s", j, bufi);
+ grpnms[2*(i*md->nNHC+j)] = gmx_strdup(buf);
+ sprintf(buf, "vXi-%d-%s", j, bufi);
+ grpnms[2*(i*md->nNHC+j)+1] = gmx_strdup(buf);
}
}
- md->itc=get_ebin_space(md->ebin,md->mde_n,
- (const char **)grpnms,unit_invtime);
+ md->itc = get_ebin_space(md->ebin, md->mde_n,
+ (const char **)grpnms, unit_invtime);
if (md->bMTTK)
{
- for(i=0; (i<md->nTCP); i++)
+ for (i = 0; (i < md->nTCP); i++)
{
bufi = baro_nm[0]; /* All barostat DOF's together for now. */
- for(j=0; (j<md->nNHC); j++)
+ for (j = 0; (j < md->nNHC); j++)
{
- sprintf(buf,"Xi-%d-%s",j,bufi);
- grpnms[2*(i*md->nNHC+j)]=strdup(buf);
- sprintf(buf,"vXi-%d-%s",j,bufi);
- grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
+ sprintf(buf, "Xi-%d-%s", j, bufi);
+ grpnms[2*(i*md->nNHC+j)] = gmx_strdup(buf);
+ sprintf(buf, "vXi-%d-%s", j, bufi);
+ grpnms[2*(i*md->nNHC+j)+1] = gmx_strdup(buf);
}
}
- md->itcb=get_ebin_space(md->ebin,md->mdeb_n,
- (const char **)grpnms,unit_invtime);
+ md->itcb = get_ebin_space(md->ebin, md->mdeb_n,
+ (const char **)grpnms, unit_invtime);
}
}
else
{
- for(i=0; (i<md->nTC); i++)
+ for (i = 0; (i < md->nTC); i++)
{
- ni=groups->grps[egcTC].nm_ind[i];
+ ni = groups->grps[egcTC].nm_ind[i];
bufi = *(groups->grpname[ni]);
- sprintf(buf,"Xi-%s",bufi);
- grpnms[2*i]=strdup(buf);
- sprintf(buf,"vXi-%s",bufi);
- grpnms[2*i+1]=strdup(buf);
+ sprintf(buf, "Xi-%s", bufi);
+ grpnms[2*i] = gmx_strdup(buf);
+ sprintf(buf, "vXi-%s", bufi);
+ grpnms[2*i+1] = gmx_strdup(buf);
}
- md->itc=get_ebin_space(md->ebin,md->mde_n,
- (const char **)grpnms,unit_invtime);
+ md->itc = get_ebin_space(md->ebin, md->mde_n,
+ (const char **)grpnms, unit_invtime);
}
}
}
else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
md->etc == etcVRESCALE)
{
- for(i=0; (i<md->nTC); i++)
+ for (i = 0; (i < md->nTC); i++)
{
- ni=groups->grps[egcTC].nm_ind[i];
- sprintf(buf,"Lamb-%s",*(groups->grpname[ni]));
- grpnms[i]=strdup(buf);
+ ni = groups->grps[egcTC].nm_ind[i];
+ sprintf(buf, "Lamb-%s", *(groups->grpname[ni]));
+ grpnms[i] = gmx_strdup(buf);
}
- md->itc=get_ebin_space(md->ebin,md->mde_n,(const char **)grpnms,"");
+ md->itc = get_ebin_space(md->ebin, md->mde_n, (const char **)grpnms, "");
}
sfree(grpnms);
- md->nU=groups->grps[egcACC].nr;
+ md->nU = groups->grps[egcACC].nr;
if (md->nU > 1)
{
- snew(grpnms,3*md->nU);
- for(i=0; (i<md->nU); i++)
+ snew(grpnms, 3*md->nU);
+ for (i = 0; (i < md->nU); i++)
{
- ni=groups->grps[egcACC].nm_ind[i];
- sprintf(buf,"Ux-%s",*(groups->grpname[ni]));
- grpnms[3*i+XX]=strdup(buf);
- sprintf(buf,"Uy-%s",*(groups->grpname[ni]));
- grpnms[3*i+YY]=strdup(buf);
- sprintf(buf,"Uz-%s",*(groups->grpname[ni]));
- grpnms[3*i+ZZ]=strdup(buf);
+ ni = groups->grps[egcACC].nm_ind[i];
+ sprintf(buf, "Ux-%s", *(groups->grpname[ni]));
+ grpnms[3*i+XX] = gmx_strdup(buf);
+ sprintf(buf, "Uy-%s", *(groups->grpname[ni]));
+ grpnms[3*i+YY] = gmx_strdup(buf);
+ sprintf(buf, "Uz-%s", *(groups->grpname[ni]));
+ grpnms[3*i+ZZ] = gmx_strdup(buf);
}
- md->iu=get_ebin_space(md->ebin,3*md->nU,(const char **)grpnms,unit_vel);
+ md->iu = get_ebin_space(md->ebin, 3*md->nU, (const char **)grpnms, unit_vel);
sfree(grpnms);
}
- if ( fp_ene )
+ if (fp_ene)
{
- do_enxnms(fp_ene,&md->ebin->nener,&md->ebin->enm);
+ do_enxnms(fp_ene, &md->ebin->nener, &md->ebin->enm);
}
- md->print_grpnms=NULL;
+ md->print_grpnms = NULL;
/* check whether we're going to write dh histograms */
- md->dhc=NULL;
- if (ir->fepvals->separate_dhdl_file == esepdhdlfileNO )
+ md->dhc = NULL;
+ if (ir->fepvals->separate_dhdl_file == esepdhdlfileNO)
{
/* Currently dh histograms are only written with dynamics */
if (EI_DYNAMICS(ir->eI))
mde_delta_h_coll_init(md->dhc, ir);
}
md->fp_dhdl = NULL;
+ snew(md->dE, ir->fepvals->n_lambda);
}
else
{
md->fp_dhdl = fp_dhdl;
+ snew(md->dE, ir->fepvals->n_lambda);
}
- if (ir->bSimTemp) {
+ if (ir->bSimTemp)
+ {
int i;
- snew(md->temperatures,ir->fepvals->n_lambda);
- for (i=0;i<ir->fepvals->n_lambda;i++)
+ snew(md->temperatures, ir->fepvals->n_lambda);
+ for (i = 0; i < ir->fepvals->n_lambda; i++)
{
md->temperatures[i] = ir->simtempvals->temperatures[i];
}
return md;
}
-extern FILE *open_dhdl(const char *filename,const t_inputrec *ir,
+/* print a lambda vector to a string
+ fep = the inputrec's FEP input data
+ i = the index of the lambda vector
+ get_native_lambda = whether to print the native lambda
+ get_names = whether to print the names rather than the values
+ str = the pre-allocated string buffer to print to. */
+static void print_lambda_vector(t_lambda *fep, int i,
+ gmx_bool get_native_lambda, gmx_bool get_names,
+ char *str)
+{
+ size_t nps = 0, np;
+ int j, k = 0;
+ int Nsep = 0;
+
+ for (j = 0; j < efptNR; j++)
+ {
+ if (fep->separate_dvdl[j])
+ {
+ Nsep++;
+ }
+ }
+ str[0] = 0; /* reset the string */
+ if (Nsep > 1)
+ {
+ str += sprintf(str, "("); /* set the opening parenthesis*/
+ }
+ for (j = 0; j < efptNR; j++)
+ {
+ if (fep->separate_dvdl[j])
+ {
+ double lam;
+ if (!get_names)
+ {
+ if (get_native_lambda && fep->init_lambda >= 0)
+ {
+ str += sprintf(str, "%.4f", fep->init_lambda);
+ }
+ else
+ {
+ str += sprintf(str, "%.4f", fep->all_lambda[j][i]);
+ }
+ }
+ else
+ {
+ str += sprintf(str, "%s", efpt_singular_names[j]);
+ }
+ /* print comma for the next item */
+ if (k < Nsep-1)
+ {
+ str += sprintf(str, ", ");
+ }
+ k++;
+ }
+ }
+ if (Nsep > 1)
+ {
+ /* and add the closing parenthesis */
+ sprintf(str, ")");
+ }
+}
+
+
+extern FILE *open_dhdl(const char *filename, const t_inputrec *ir,
const output_env_t oenv)
{
- FILE *fp;
- const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda",
- *lambdastate="\\lambda state",*remain="remaining";
- char title[STRLEN],label_x[STRLEN],label_y[STRLEN];
- int i,np,nps,nsets,nsets_de,nsetsbegin;
- t_lambda *fep;
- char **setname;
- char buf[STRLEN];
- int bufplace=0;
-
- int nsets_dhdl = 0;
- int s = 0;
- int nsetsextend;
-
- /* for simplicity */
- fep = ir->fepvals;
+ FILE *fp;
+ const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda",
+ *lambdastate = "\\lambda state", *remain = "remaining";
+ char title[STRLEN], label_x[STRLEN], label_y[STRLEN];
+ int i, np, nps, nsets, nsets_de, nsetsbegin;
+ int n_lambda_terms = 0;
+ t_lambda *fep = ir->fepvals; /* for simplicity */
+ t_expanded *expand = ir->expandedvals;
+ char **setname;
+ char buf[STRLEN], lambda_vec_str[STRLEN], lambda_name_str[STRLEN];
+ int bufplace = 0;
+
+ int nsets_dhdl = 0;
+ int s = 0;
+ int nsetsextend;
+ gmx_bool write_pV = FALSE;
+
+ /* count the number of different lambda terms */
+ for (i = 0; i < efptNR; i++)
+ {
+ if (fep->separate_dvdl[i])
+ {
+ n_lambda_terms++;
+ }
+ }
if (fep->n_lambda == 0)
{
- sprintf(title,"%s",dhdl);
- sprintf(label_x,"Time (ps)");
- sprintf(label_y,"%s (%s %s)",
- dhdl,unit_energy,"[\\lambda]\\S-1\\N");
+ sprintf(title, "%s", dhdl);
+ sprintf(label_x, "Time (ps)");
+ sprintf(label_y, "%s (%s %s)",
+ dhdl, unit_energy, "[\\lambda]\\S-1\\N");
}
else
{
- sprintf(title,"%s and %s",dhdl,deltag);
- sprintf(label_x,"Time (ps)");
- sprintf(label_y,"%s and %s (%s %s)",
- dhdl,deltag,unit_energy,"[\\8l\\4]\\S-1\\N");
+ sprintf(title, "%s and %s", dhdl, deltag);
+ sprintf(label_x, "Time (ps)");
+ sprintf(label_y, "%s and %s (%s %s)",
+ dhdl, deltag, unit_energy, "[\\8l\\4]\\S-1\\N");
}
- fp = gmx_fio_fopen(filename,"w+");
- xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv);
+ fp = gmx_fio_fopen(filename, "w+");
+ xvgr_header(fp, title, label_x, label_y, exvggtXNY, oenv);
if (!(ir->bSimTemp))
{
- bufplace = sprintf(buf,"T = %g (K) ",
- ir->opts.ref_t[0]);
+ bufplace = sprintf(buf, "T = %g (K) ",
+ ir->opts.ref_t[0]);
}
- if (ir->efep != efepSLOWGROWTH)
+ if ((ir->efep != efepSLOWGROWTH) && (ir->efep != efepEXPANDED))
{
- if (fep->n_lambda == 0)
+ if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
{
- sprintf(&(buf[bufplace]),"%s = %g",
- lambda,fep->init_lambda);
+ /* compatibility output */
+ sprintf(&(buf[bufplace]), "%s = %.4f", lambda, fep->init_lambda);
}
else
{
- sprintf(&(buf[bufplace]),"%s = %d",
- lambdastate,fep->init_fep_state);
+ print_lambda_vector(fep, fep->init_fep_state, TRUE, FALSE,
+ lambda_vec_str);
+ print_lambda_vector(fep, fep->init_fep_state, TRUE, TRUE,
+ lambda_name_str);
+ sprintf(&(buf[bufplace]), "%s %d: %s = %s",
+ lambdastate, fep->init_fep_state,
+ lambda_name_str, lambda_vec_str);
}
}
- xvgr_subtitle(fp,buf,oenv);
+ xvgr_subtitle(fp, buf, oenv);
+
- for (i=0;i<efptNR;i++)
+ nsets_dhdl = 0;
+ if (fep->dhdl_derivatives == edhdlderivativesYES)
{
- if (fep->separate_dvdl[i]) {nsets_dhdl++;}
+ nsets_dhdl = n_lambda_terms;
}
-
/* count the number of delta_g states */
- nsets_de = fep->n_lambda;
+ nsets_de = fep->lambda_stop_n - fep->lambda_start_n;
nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
- if (fep->n_lambda>0 && ir->bExpanded)
+ if (fep->n_lambda > 0 && (expand->elmcmove > elmcmoveNO))
{
nsets += 1; /*add fep state for expanded ensemble */
}
- if (fep->bPrintEnergy)
+ if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
nsets += 1; /* add energy to the dhdl as well */
}
nsetsextend = nsets;
- if ((ir->epc!=epcNO) && (fep->n_lambda>0))
+ if ((ir->epc != epcNO) && (fep->n_lambda > 0) && (fep->init_lambda < 0))
{
- nsetsextend += 1; /* for PV term, other terms possible if required for the reduced potential (only needed with foreign lambda) */
+ nsetsextend += 1; /* for PV term, other terms possible if required for
+ the reduced potential (only needed with foreign
+ lambda, and only output when init_lambda is not
+ set in order to maintain compatibility of the
+ dhdl.xvg file) */
+ write_pV = TRUE;
}
- snew(setname,nsetsextend);
+ snew(setname, nsetsextend);
- if (ir->bExpanded)
+ if (expand->elmcmove > elmcmoveNO)
{
/* state for the fep_vals, if we have alchemical sampling */
- sprintf(buf,"%s","Thermodynamic state");
- setname[s] = strdup(buf);
- s+=1;
+ sprintf(buf, "%s", "Thermodynamic state");
+ 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);
- s+=1;
+ 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;
}
- for (i=0;i<efptNR;i++)
+ if (fep->dhdl_derivatives == edhdlderivativesYES)
{
- if (fep->separate_dvdl[i]) {
- sprintf(buf,"%s (%s)",dhdl,efpt_names[i]);
- setname[s] = strdup(buf);
- s+=1;
+ for (i = 0; i < efptNR; i++)
+ {
+ if (fep->separate_dvdl[i])
+ {
+
+ if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
+ {
+ /* compatibility output */
+ sprintf(buf, "%s %s %.4f", dhdl, lambda, fep->init_lambda);
+ }
+ else
+ {
+ double lam = fep->init_lambda;
+ if (fep->init_lambda < 0)
+ {
+ lam = fep->all_lambda[i][fep->init_fep_state];
+ }
+ sprintf(buf, "%s %s = %.4f", dhdl, efpt_singular_names[i],
+ lam);
+ }
+ setname[s] = gmx_strdup(buf);
+ s += 1;
+ }
}
}
* from this xvg legend.
*/
- if (ir->bExpanded) {
+ if (expand->elmcmove > elmcmoveNO)
+ {
nsetsbegin = 1; /* for including the expanded ensemble */
- } else {
+ }
+ else
+ {
nsetsbegin = 0;
}
- if (fep->bPrintEnergy)
+ if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
nsetsbegin += 1;
}
nsetsbegin += nsets_dhdl;
- for(s=nsetsbegin; s<nsets; s++)
+ for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
{
- nps = sprintf(buf,"%s %s (",deltag,lambda);
- for (i=0;i<efptNR;i++)
+ print_lambda_vector(fep, i, FALSE, FALSE, lambda_vec_str);
+ if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
{
- if (fep->separate_dvdl[i])
- {
- np = sprintf(&buf[nps],"%g,",fep->all_lambda[i][s-(nsetsbegin)]);
- nps += np;
- }
+ /* for compatible dhdl.xvg files */
+ nps = sprintf(buf, "%s %s %s", deltag, lambda, lambda_vec_str);
}
- if (ir->bSimTemp)
+ else
{
- /* print the temperature for this state if doing simulated annealing */
- sprintf(&buf[nps],"T = %g (%s))",ir->simtempvals->temperatures[s-(nsetsbegin)],unit_temp_K);
+ nps = sprintf(buf, "%s %s to %s", deltag, lambda, lambda_vec_str);
}
- else
+
+ if (ir->bSimTemp)
{
- sprintf(&buf[nps-1],")"); /* -1 to overwrite the last comma */
+ /* print the temperature for this state if doing simulated annealing */
+ sprintf(&buf[nps], "T = %g (%s)",
+ ir->simtempvals->temperatures[s-(nsetsbegin)],
+ unit_temp_K);
}
- setname[s] = strdup(buf);
+ setname[s] = gmx_strdup(buf);
+ s++;
}
- if (ir->epc!=epcNO) {
- np = sprintf(buf,"pV (%s)",unit_energy);
- setname[nsetsextend-1] = strdup(buf); /* the first entry after nsets */
+ if (write_pV)
+ {
+ np = sprintf(buf, "pV (%s)", unit_energy);
+ setname[nsetsextend-1] = gmx_strdup(buf); /* the first entry after
+ nsets */
}
- xvgr_legend(fp,nsetsextend,(const char **)setname,oenv);
+ xvgr_legend(fp, nsetsextend, (const char **)setname, oenv);
- for(s=0; s<nsetsextend; s++)
+ for (s = 0; s < nsetsextend; s++)
{
sfree(setname[s]);
}
return fp;
}
-static void copy_energy(t_mdebin *md, real e[],real ecpy[])
+static void copy_energy(t_mdebin *md, real e[], real ecpy[])
{
- int i,j;
+ int i, j;
- for(i=j=0; (i<F_NRE); i++)
+ for (i = j = 0; (i < F_NRE); i++)
+ {
if (md->bEner[i])
+ {
ecpy[j++] = e[i];
+ }
+ }
if (j != md->f_nre)
+ {
gmx_incons("Number of energy terms wrong");
+ }
}
-void upd_mdebin(t_mdebin *md,
- gmx_bool bDoDHDL,
- gmx_bool bSum,
- double time,
- real tmass,
+void upd_mdebin(t_mdebin *md,
+ gmx_bool bDoDHDL,
+ gmx_bool bSum,
+ double time,
+ real tmass,
gmx_enerdata_t *enerd,
- t_state *state,
- t_lambda *fep,
- t_expanded *expand,
- matrix box,
- tensor svir,
- tensor fvir,
- tensor vir,
- tensor pres,
+ t_state *state,
+ t_lambda *fep,
+ t_expanded *expand,
+ matrix box,
+ tensor svir,
+ tensor fvir,
+ tensor vir,
+ tensor pres,
gmx_ekindata_t *ekind,
- rvec mu_tot,
- gmx_constr_t constr)
+ rvec mu_tot,
+ gmx_constr_t constr)
{
- int i,j,k,kk,m,n,gid;
- real crmsd[2],tmp6[6];
- real bs[NTRICLBOXS],vol,dens,pv,enthalpy;
+ int i, j, k, kk, m, n, gid;
+ real crmsd[2], tmp6[6];
+ real bs[NTRICLBOXS], vol, dens, pv, enthalpy;
real eee[egNR];
real ecopy[F_NRE];
double store_dhdl[efptNR];
- double *dE=NULL;
- real store_energy=0;
+ real store_energy = 0;
real tmp;
/* Do NOT use the box in the state variable, but the separate box provided
* as an argument. This is because we sometimes need to write the box from
* the last timestep to match the trajectory frames.
*/
- copy_energy(md, enerd->term,ecopy);
- add_ebin(md->ebin,md->ie,md->f_nre,ecopy,bSum);
+ copy_energy(md, enerd->term, ecopy);
+ add_ebin(md->ebin, md->ie, md->f_nre, ecopy, bSum);
if (md->nCrmsd)
{
- crmsd[0] = constr_rmsd(constr,FALSE);
+ crmsd[0] = constr_rmsd(constr, FALSE);
if (md->nCrmsd > 1)
{
- crmsd[1] = constr_rmsd(constr,TRUE);
+ crmsd[1] = constr_rmsd(constr, TRUE);
}
- add_ebin(md->ebin,md->iconrmsd,md->nCrmsd,crmsd,FALSE);
+ add_ebin(md->ebin, md->iconrmsd, md->nCrmsd, crmsd, FALSE);
}
if (md->bDynBox)
{
int nboxs;
- if(md->bTricl)
+ if (md->bTricl)
{
bs[0] = box[XX][XX];
bs[1] = box[YY][YY];
bs[3] = box[YY][XX];
bs[4] = box[ZZ][XX];
bs[5] = box[ZZ][YY];
- nboxs=NTRICLBOXS;
+ nboxs = NTRICLBOXS;
}
else
{
bs[0] = box[XX][XX];
bs[1] = box[YY][YY];
bs[2] = box[ZZ][ZZ];
- nboxs=NBOXS;
+ nboxs = NBOXS;
}
vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
- add_ebin(md->ebin,md->ib ,nboxs,bs ,bSum);
- add_ebin(md->ebin,md->ivol ,1 ,&vol ,bSum);
- add_ebin(md->ebin,md->idens,1 ,&dens,bSum);
+ add_ebin(md->ebin, md->ib, nboxs, bs, bSum);
+ add_ebin(md->ebin, md->ivol, 1, &vol, bSum);
+ add_ebin(md->ebin, md->idens, 1, &dens, bSum);
if (md->bDiagPres)
{
not the instantaneous pressure */
pv = vol*md->ref_p/PRESFAC;
- add_ebin(md->ebin,md->ipv ,1 ,&pv ,bSum);
+ add_ebin(md->ebin, md->ipv, 1, &pv, bSum);
enthalpy = pv + enerd->term[F_ETOT];
- add_ebin(md->ebin,md->ienthalpy ,1 ,&enthalpy ,bSum);
+ add_ebin(md->ebin, md->ienthalpy, 1, &enthalpy, bSum);
}
}
if (md->bConstrVir)
{
- add_ebin(md->ebin,md->isvir,9,svir[0],bSum);
- add_ebin(md->ebin,md->ifvir,9,fvir[0],bSum);
+ add_ebin(md->ebin, md->isvir, 9, svir[0], bSum);
+ add_ebin(md->ebin, md->ifvir, 9, fvir[0], bSum);
}
if (md->bVir)
- add_ebin(md->ebin,md->ivir,9,vir[0],bSum);
+ {
+ add_ebin(md->ebin, md->ivir, 9, vir[0], bSum);
+ }
if (md->bPress)
- add_ebin(md->ebin,md->ipres,9,pres[0],bSum);
- if (md->bSurft){
+ {
+ add_ebin(md->ebin, md->ipres, 9, pres[0], bSum);
+ }
+ if (md->bSurft)
+ {
tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
- add_ebin(md->ebin,md->isurft,1,&tmp,bSum);
+ add_ebin(md->ebin, md->isurft, 1, &tmp, bSum);
}
if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
{
tmp6[3] = state->boxv[YY][XX];
tmp6[4] = state->boxv[ZZ][XX];
tmp6[5] = state->boxv[ZZ][YY];
- add_ebin(md->ebin,md->ipc,md->bTricl ? 6 : 3,tmp6,bSum);
+ add_ebin(md->ebin, md->ipc, md->bTricl ? 6 : 3, tmp6, bSum);
+ }
+ if (md->bMu)
+ {
+ add_ebin(md->ebin, md->imu, 3, mu_tot, bSum);
}
- if(md->bMu)
- add_ebin(md->ebin,md->imu,3,mu_tot,bSum);
if (ekind && ekind->cosacc.cos_accel != 0)
{
vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
- add_ebin(md->ebin,md->ivcos,1,&(ekind->cosacc.vcos),bSum);
+ add_ebin(md->ebin, md->ivcos, 1, &(ekind->cosacc.vcos), bSum);
/* 1/viscosity, unit 1/(kg m^-1 s^-1) */
tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
- *dens*vol*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
- add_ebin(md->ebin,md->ivisc,1,&tmp,bSum);
+ *dens*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
+ add_ebin(md->ebin, md->ivisc, 1, &tmp, bSum);
}
if (md->nE > 1)
{
- n=0;
- for(i=0; (i<md->nEg); i++)
+ n = 0;
+ for (i = 0; (i < md->nEg); i++)
{
- for(j=i; (j<md->nEg); j++)
+ for (j = i; (j < md->nEg); j++)
{
- gid=GID(i,j,md->nEg);
- for(k=kk=0; (k<egNR); k++)
+ gid = GID(i, j, md->nEg);
+ for (k = kk = 0; (k < egNR); k++)
{
if (md->bEInd[k])
{
eee[kk++] = enerd->grpp.ener[k][gid];
}
}
- add_ebin(md->ebin,md->igrp[n],md->nEc,eee,bSum);
+ add_ebin(md->ebin, md->igrp[n], md->nEc, eee, bSum);
n++;
}
}
if (ekind)
{
- for(i=0; (i<md->nTC); i++)
+ for (i = 0; (i < md->nTC); i++)
{
md->tmp_r[i] = ekind->tcstat[i].T;
}
- add_ebin(md->ebin,md->itemp,md->nTC,md->tmp_r,bSum);
+ add_ebin(md->ebin, md->itemp, md->nTC, md->tmp_r, bSum);
if (md->etc == etcNOSEHOOVER)
{
{
if (md->bNHC_trotter)
{
- for(i=0; (i<md->nTC); i++)
+ for (i = 0; (i < md->nTC); i++)
{
- for (j=0;j<md->nNHC;j++)
+ for (j = 0; j < md->nNHC; j++)
{
- k = i*md->nNHC+j;
- md->tmp_r[2*k] = state->nosehoover_xi[k];
+ k = i*md->nNHC+j;
+ md->tmp_r[2*k] = state->nosehoover_xi[k];
md->tmp_r[2*k+1] = state->nosehoover_vxi[k];
}
}
- add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
+ add_ebin(md->ebin, md->itc, md->mde_n, md->tmp_r, bSum);
- if (md->bMTTK) {
- for(i=0; (i<md->nTCP); i++)
+ if (md->bMTTK)
+ {
+ for (i = 0; (i < md->nTCP); i++)
{
- for (j=0;j<md->nNHC;j++)
+ for (j = 0; j < md->nNHC; j++)
{
- k = i*md->nNHC+j;
- md->tmp_r[2*k] = state->nhpres_xi[k];
+ k = i*md->nNHC+j;
+ md->tmp_r[2*k] = state->nhpres_xi[k];
md->tmp_r[2*k+1] = state->nhpres_vxi[k];
}
}
- add_ebin(md->ebin,md->itcb,md->mdeb_n,md->tmp_r,bSum);
+ add_ebin(md->ebin, md->itcb, md->mdeb_n, md->tmp_r, bSum);
}
}
else
{
- for(i=0; (i<md->nTC); i++)
+ for (i = 0; (i < md->nTC); i++)
{
- md->tmp_r[2*i] = state->nosehoover_xi[i];
+ md->tmp_r[2*i] = state->nosehoover_xi[i];
md->tmp_r[2*i+1] = state->nosehoover_vxi[i];
}
- add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
+ add_ebin(md->ebin, md->itc, md->mde_n, md->tmp_r, bSum);
}
}
}
else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
md->etc == etcVRESCALE)
{
- for(i=0; (i<md->nTC); i++)
+ for (i = 0; (i < md->nTC); i++)
{
md->tmp_r[i] = ekind->tcstat[i].lambda;
}
- add_ebin(md->ebin,md->itc,md->nTC,md->tmp_r,bSum);
+ add_ebin(md->ebin, md->itc, md->nTC, md->tmp_r, bSum);
}
}
if (ekind && md->nU > 1)
{
- for(i=0; (i<md->nU); i++)
+ for (i = 0; (i < md->nU); i++)
{
- copy_rvec(ekind->grpstat[i].u,md->tmp_v[i]);
+ copy_rvec(ekind->grpstat[i].u, md->tmp_v[i]);
}
- add_ebin(md->ebin,md->iu,3*md->nU,md->tmp_v[0],bSum);
+ add_ebin(md->ebin, md->iu, 3*md->nU, md->tmp_v[0], bSum);
}
- ebin_increase_count(md->ebin,bSum);
+ ebin_increase_count(md->ebin, bSum);
/* BAR + thermodynamic integration values */
- if ((md->fp_dhdl || md->dhc) && bDoDHDL && (enerd->n_lambda > 0))
+ if ((md->fp_dhdl || md->dhc) && bDoDHDL)
{
- snew(dE,enerd->n_lambda-1);
- for(i=0; i<enerd->n_lambda-1; i++) {
- dE[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0]; /* zero for simulated tempering */
- if (md->temperatures!=NULL)
+ for (i = 0; i < enerd->n_lambda-1; i++)
+ {
+ /* zero for simulated tempering */
+ md->dE[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0];
+ if (md->temperatures != NULL)
{
/* MRS: is this right, given the way we have defined the exchange probabilities? */
/* is this even useful to have at all? */
- dE[i] += (md->temperatures[i]/md->temperatures[state->fep_state]-1.0)*enerd->term[F_EKIN];
+ md->dE[i] += (md->temperatures[i]/
+ md->temperatures[state->fep_state]-1.0)*
+ enerd->term[F_EKIN];
}
}
- }
-
- if (md->fp_dhdl && bDoDHDL)
- {
- fprintf(md->fp_dhdl,"%.4f",time);
- /* the current free energy state */
- /* print the current state if we are doing expanded ensemble */
- if (expand->elmcmove > elmcmoveNO) {
- fprintf(md->fp_dhdl," %4d",state->fep_state);
- }
- /* total energy (for if the temperature changes */
- if (fep->bPrintEnergy)
+ if (md->fp_dhdl)
{
- store_energy = enerd->term[F_ETOT];
- fprintf(md->fp_dhdl," %#.8g",store_energy);
- }
+ fprintf(md->fp_dhdl, "%.4f", time);
+ /* the current free energy state */
- for (i=0;i<efptNR;i++)
- {
- if (fep->separate_dvdl[i])
+ /* print the current state if we are doing expanded ensemble */
+ if (expand->elmcmove > elmcmoveNO)
{
- fprintf(md->fp_dhdl," %#.8g",enerd->term[F_DVDL+i]); /* assumes F_DVDL is first */
+ fprintf(md->fp_dhdl, " %4d", state->fep_state);
}
- }
- for(i=1; i<enerd->n_lambda; i++)
- {
- fprintf(md->fp_dhdl," %#.8g",dE[i-1]);
+ /* total energy (for if the temperature changes */
+ if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ {
+ 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);
+ }
+
+ if (fep->dhdl_derivatives == edhdlderivativesYES)
+ {
+ for (i = 0; i < efptNR; i++)
+ {
+ if (fep->separate_dvdl[i])
+ {
+ /* assumes F_DVDL is first */
+ fprintf(md->fp_dhdl, " %#.8g", enerd->term[F_DVDL+i]);
+ }
+ }
+ }
+ for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
+ {
+ fprintf(md->fp_dhdl, " %#.8g", md->dE[i]);
+ }
+ if ((md->epc != epcNO) &&
+ (enerd->n_lambda > 0) &&
+ (fep->init_lambda < 0))
+ {
+ fprintf(md->fp_dhdl, " %#.8g", pv); /* PV term only needed when
+ there are alternate state
+ lambda and we're not in
+ compatibility mode */
+ }
+ fprintf(md->fp_dhdl, "\n");
+ /* and the binary free energy output */
}
- if ((md->epc!=epcNO) && (enerd->n_lambda > 0))
- {
- fprintf(md->fp_dhdl," %#.8g",pv); /* PV term only needed when there are alternate state lambda */
- }
- fprintf(md->fp_dhdl,"\n");
- /* and the binary free energy output */
- }
- if (md->dhc && bDoDHDL)
- {
- int idhdl = 0;
- for (i=0;i<efptNR;i++)
+ if (md->dhc && bDoDHDL)
{
- if (fep->separate_dvdl[i])
+ int idhdl = 0;
+ for (i = 0; i < efptNR; i++)
{
- store_dhdl[idhdl] = enerd->term[F_DVDL+i]; /* assumes F_DVDL is first */
- idhdl+=1;
+ if (fep->separate_dvdl[i])
+ {
+ /* assumes F_DVDL is first */
+ store_dhdl[idhdl] = enerd->term[F_DVDL+i];
+ idhdl += 1;
+ }
}
+ store_energy = enerd->term[F_ETOT];
+ /* store_dh is dE */
+ mde_delta_h_coll_add_dh(md->dhc,
+ (double)state->fep_state,
+ store_energy,
+ pv,
+ store_dhdl,
+ md->dE + fep->lambda_start_n,
+ time);
}
- /* store_dh is dE */
- mde_delta_h_coll_add_dh(md->dhc,
- (double)state->fep_state,
- store_energy,
- pv,
- (expand->elamstats>elamstatsNO),
- (fep->bPrintEnergy),
- (md->epc!=epcNO),
- idhdl,
- fep->n_lambda,
- store_dhdl,
- dE,
- time);
- }
- if ((md->fp_dhdl || md->dhc) && bDoDHDL && (enerd->n_lambda >0))
- {
- sfree(dE);
}
}
void upd_mdebin_step(t_mdebin *md)
{
- ebin_increase_count(md->ebin,FALSE);
+ ebin_increase_count(md->ebin, FALSE);
}
-static void npr(FILE *log,int n,char c)
+static void npr(FILE *log, int n, char c)
{
- for(; (n>0); n--) fprintf(log,"%c",c);
+ for (; (n > 0); n--)
+ {
+ fprintf(log, "%c", c);
+ }
}
-static void pprint(FILE *log,const char *s,t_mdebin *md)
+static void pprint(FILE *log, const char *s, t_mdebin *md)
{
- char CHAR='#';
+ char CHAR = '#';
int slen;
- char buf1[22],buf2[22];
+ char buf1[22], buf2[22];
slen = strlen(s);
- fprintf(log,"\t<====== ");
- npr(log,slen,CHAR);
- fprintf(log," ==>\n");
- fprintf(log,"\t<==== %s ====>\n",s);
- fprintf(log,"\t<== ");
- npr(log,slen,CHAR);
- fprintf(log," ======>\n\n");
-
- fprintf(log,"\tStatistics over %s steps using %s frames\n",
- gmx_step_str(md->ebin->nsteps_sim,buf1),
- gmx_step_str(md->ebin->nsum_sim,buf2));
- fprintf(log,"\n");
+ fprintf(log, "\t<====== ");
+ npr(log, slen, CHAR);
+ fprintf(log, " ==>\n");
+ fprintf(log, "\t<==== %s ====>\n", s);
+ fprintf(log, "\t<== ");
+ npr(log, slen, CHAR);
+ fprintf(log, " ======>\n\n");
+
+ fprintf(log, "\tStatistics over %s steps using %s frames\n",
+ gmx_step_str(md->ebin->nsteps_sim, buf1),
+ gmx_step_str(md->ebin->nsum_sim, buf2));
+ 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];
- fprintf(log," %12s %12s %12s\n"
+ fprintf(log, " %12s %12s %12s\n"
" %12s %12.5f %12.5f\n\n",
- "Step","Time","Lambda",gmx_step_str(steps,buf),time,lambda);
+ "Step", "Time", "Lambda", gmx_step_str(steps, buf), time, lambda);
}
-void print_ebin(ener_file_t fp_ene,gmx_bool bEne,gmx_bool bDR,gmx_bool bOR,
+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,
- int mode,gmx_bool bCompact,
- t_mdebin *md,t_fcdata *fcd,
- gmx_groups_t *groups,t_grpopts *opts)
+ gmx_int64_t step, double time,
+ int mode, gmx_bool bCompact,
+ t_mdebin *md, t_fcdata *fcd,
+ gmx_groups_t *groups, t_grpopts *opts)
{
/*static char **grpnms=NULL;*/
- char buf[246];
- int i,j,n,ni,nj,ndr,nor,b;
- int ndisre=0;
+ char buf[246];
+ int i, j, n, ni, nj, ndr, nor, b;
+ int ndisre = 0;
real *disre_rm3tav, *disre_rt;
/* these are for the old-style blocks (1 subblock, only reals), because
there can be only one per ID for these */
- int nr[enxNR];
- int id[enxNR];
+ int nr[enxNR];
+ int id[enxNR];
real *block[enxNR];
/* temporary arrays for the lambda values to write out */
disre_rm3tav = fcd->disres.rm3tav;
disre_rt = fcd->disres.rt;
/* Optional additional old-style (real-only) blocks. */
- for(i=0; i<enxNR; i++)
+ for (i = 0; i < enxNR; i++)
{
nr[i] = 0;
}
block[enxOR] = fcd->orires.otav;
id[enxOR] = enxOR;
nr[enxORI] = (fcd->orires.oinsl != fcd->orires.otav) ?
- fcd->orires.nr : 0;
+ fcd->orires.nr : 0;
block[enxORI] = fcd->orires.oinsl;
id[enxORI] = enxORI;
nr[enxORT] = fcd->orires.nex*12;
/* the old-style blocks go first */
fr.nblock = 0;
- for(i=0; i<enxNR; i++)
+ for (i = 0; i < enxNR; i++)
{
if (nr[i] > 0)
{
}
}
add_blocks_enxframe(&fr, fr.nblock);
- for(b=0;b<fr.nblock;b++)
+ for (b = 0; b < fr.nblock; b++)
{
add_subblocks_enxblock(&(fr.block[b]), 1);
- fr.block[b].id=id[b];
+ fr.block[b].id = id[b];
fr.block[b].sub[0].nr = nr[b];
#ifndef GMX_DOUBLE
fr.block[b].sub[0].type = xdr_datatype_float;
}
/* check for disre block & fill it. */
- if (ndisre>0)
+ if (ndisre > 0)
{
int db = fr.nblock;
- fr.nblock+=1;
+ fr.nblock += 1;
add_blocks_enxframe(&fr, fr.nblock);
add_subblocks_enxblock(&(fr.block[db]), 2);
- fr.block[db].id=enxDISRE;
- fr.block[db].sub[0].nr=ndisre;
- fr.block[db].sub[1].nr=ndisre;
+ fr.block[db].id = enxDISRE;
+ fr.block[db].sub[0].nr = ndisre;
+ fr.block[db].sub[1].nr = ndisre;
#ifndef GMX_DOUBLE
- fr.block[db].sub[0].type=xdr_datatype_float;
- fr.block[db].sub[1].type=xdr_datatype_float;
- fr.block[db].sub[0].fval=disre_rt;
- fr.block[db].sub[1].fval=disre_rm3tav;
+ fr.block[db].sub[0].type = xdr_datatype_float;
+ fr.block[db].sub[1].type = xdr_datatype_float;
+ fr.block[db].sub[0].fval = disre_rt;
+ fr.block[db].sub[1].fval = disre_rm3tav;
#else
- fr.block[db].sub[0].type=xdr_datatype_double;
- fr.block[db].sub[1].type=xdr_datatype_double;
- fr.block[db].sub[0].dval=disre_rt;
- fr.block[db].sub[1].dval=disre_rm3tav;
+ fr.block[db].sub[0].type = xdr_datatype_double;
+ fr.block[db].sub[1].type = xdr_datatype_double;
+ fr.block[db].sub[0].dval = disre_rt;
+ fr.block[db].sub[1].dval = disre_rm3tav;
#endif
}
/* here we can put new-style blocks */
}
/* do the actual I/O */
- do_enx(fp_ene,&fr);
- gmx_fio_check_file_position(enx_file_pointer(fp_ene));
+ do_enx(fp_ene, &fr);
if (fr.nre)
{
/* We have stored the sums, so reset the sum history */
case eprAVER:
if (log)
{
- pprint(log,"A V E R A G E S",md);
+ pprint(log, "A V E R A G E S", md);
}
break;
case eprRMS:
if (log)
{
- pprint(log,"R M S - F L U C T U A T I O N S",md);
+ pprint(log, "R M S - F L U C T U A T I O N S", md);
}
break;
default:
- gmx_fatal(FARGS,"Invalid print mode (%d)",mode);
+ gmx_fatal(FARGS, "Invalid print mode (%d)", mode);
}
if (log)
{
- for(i=0;i<opts->ngtc;i++)
+ for (i = 0; i < opts->ngtc; i++)
{
- if(opts->annealing[i]!=eannNO)
+ if (opts->annealing[i] != eannNO)
{
- fprintf(log,"Current ref_t for group %s: %8.1f\n",
+ fprintf(log, "Current ref_t for group %s: %8.1f\n",
*(groups->grpname[groups->grps[egcTC].nm_ind[i]]),
opts->ref_t[i]);
}
}
- if (mode==eprNORMAL && fcd->orires.nr>0)
+ if (mode == eprNORMAL && fcd->orires.nr > 0)
{
- print_orires_log(log,&(fcd->orires));
+ print_orires_log(log, &(fcd->orires));
}
- fprintf(log," Energies (%s)\n",unit_energy);
- pr_ebin(log,md->ebin,md->ie,md->f_nre+md->nCrmsd,5,mode,TRUE);
- fprintf(log,"\n");
+ fprintf(log, " Energies (%s)\n", unit_energy);
+ pr_ebin(log, md->ebin, md->ie, md->f_nre+md->nCrmsd, 5, mode, TRUE);
+ fprintf(log, "\n");
if (!bCompact)
{
if (md->bDynBox)
{
- pr_ebin(log,md->ebin,md->ib, md->bTricl ? NTRICLBOXS : NBOXS,5,
- mode,TRUE);
- fprintf(log,"\n");
+ pr_ebin(log, md->ebin, md->ib, md->bTricl ? NTRICLBOXS : NBOXS, 5,
+ mode, TRUE);
+ fprintf(log, "\n");
}
if (md->bConstrVir)
{
- fprintf(log," Constraint Virial (%s)\n",unit_energy);
- pr_ebin(log,md->ebin,md->isvir,9,3,mode,FALSE);
- fprintf(log,"\n");
- fprintf(log," Force Virial (%s)\n",unit_energy);
- pr_ebin(log,md->ebin,md->ifvir,9,3,mode,FALSE);
- fprintf(log,"\n");
+ fprintf(log, " Constraint Virial (%s)\n", unit_energy);
+ pr_ebin(log, md->ebin, md->isvir, 9, 3, mode, FALSE);
+ fprintf(log, "\n");
+ fprintf(log, " Force Virial (%s)\n", unit_energy);
+ pr_ebin(log, md->ebin, md->ifvir, 9, 3, mode, FALSE);
+ fprintf(log, "\n");
}
if (md->bVir)
{
- fprintf(log," Total Virial (%s)\n",unit_energy);
- pr_ebin(log,md->ebin,md->ivir,9,3,mode,FALSE);
- fprintf(log,"\n");
+ fprintf(log, " Total Virial (%s)\n", unit_energy);
+ pr_ebin(log, md->ebin, md->ivir, 9, 3, mode, FALSE);
+ fprintf(log, "\n");
}
if (md->bPress)
{
- fprintf(log," Pressure (%s)\n",unit_pres_bar);
- pr_ebin(log,md->ebin,md->ipres,9,3,mode,FALSE);
- fprintf(log,"\n");
+ fprintf(log, " Pressure (%s)\n", unit_pres_bar);
+ pr_ebin(log, md->ebin, md->ipres, 9, 3, mode, FALSE);
+ fprintf(log, "\n");
+ }
+ if (md->bMu)
+ {
+ fprintf(log, " Total Dipole (%s)\n", unit_dipole_D);
+ pr_ebin(log, md->ebin, md->imu, 3, 3, mode, FALSE);
+ fprintf(log, "\n");
}
- fprintf(log," Total Dipole (%s)\n",unit_dipole_D);
- pr_ebin(log,md->ebin,md->imu,3,3,mode,FALSE);
- fprintf(log,"\n");
if (md->nE > 1)
{
- if (md->print_grpnms==NULL)
+ if (md->print_grpnms == NULL)
{
- snew(md->print_grpnms,md->nE);
- n=0;
- for(i=0; (i<md->nEg); i++)
+ snew(md->print_grpnms, md->nE);
+ n = 0;
+ for (i = 0; (i < md->nEg); i++)
{
- ni=groups->grps[egcENER].nm_ind[i];
- for(j=i; (j<md->nEg); j++)
+ ni = groups->grps[egcENER].nm_ind[i];
+ for (j = i; (j < md->nEg); j++)
{
- nj=groups->grps[egcENER].nm_ind[j];
- sprintf(buf,"%s-%s",*(groups->grpname[ni]),
+ 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);
}
}
}
- sprintf(buf,"Epot (%s)",unit_energy);
- fprintf(log,"%15s ",buf);
- for(i=0; (i<egNR); i++)
+ sprintf(buf, "Epot (%s)", unit_energy);
+ fprintf(log, "%15s ", buf);
+ for (i = 0; (i < egNR); i++)
{
if (md->bEInd[i])
{
- fprintf(log,"%12s ",egrp_nm[i]);
+ fprintf(log, "%12s ", egrp_nm[i]);
}
}
- fprintf(log,"\n");
- for(i=0; (i<md->nE); i++)
+ fprintf(log, "\n");
+ for (i = 0; (i < md->nE); i++)
{
- fprintf(log,"%15s",md->print_grpnms[i]);
- pr_ebin(log,md->ebin,md->igrp[i],md->nEc,md->nEc,mode,
+ fprintf(log, "%15s", md->print_grpnms[i]);
+ pr_ebin(log, md->ebin, md->igrp[i], md->nEc, md->nEc, mode,
FALSE);
}
- fprintf(log,"\n");
+ fprintf(log, "\n");
}
if (md->nTC > 1)
{
- pr_ebin(log,md->ebin,md->itemp,md->nTC,4,mode,TRUE);
- fprintf(log,"\n");
+ pr_ebin(log, md->ebin, md->itemp, md->nTC, 4, mode, TRUE);
+ fprintf(log, "\n");
}
if (md->nU > 1)
{
- fprintf(log,"%15s %12s %12s %12s\n",
- "Group","Ux","Uy","Uz");
- for(i=0; (i<md->nU); i++)
+ fprintf(log, "%15s %12s %12s %12s\n",
+ "Group", "Ux", "Uy", "Uz");
+ for (i = 0; (i < md->nU); i++)
{
- ni=groups->grps[egcACC].nm_ind[i];
- fprintf(log,"%15s",*groups->grpname[ni]);
- pr_ebin(log,md->ebin,md->iu+3*i,3,3,mode,FALSE);
+ ni = groups->grps[egcACC].nm_ind[i];
+ fprintf(log, "%15s", *groups->grpname[ni]);
+ pr_ebin(log, md->ebin, md->iu+3*i, 3, 3, mode, FALSE);
}
- fprintf(log,"\n");
+ fprintf(log, "\n");
}
}
}
}
-void update_energyhistory(energyhistory_t * enerhist,t_mdebin * mdebin)
+void update_energyhistory(energyhistory_t * enerhist, t_mdebin * mdebin)
{
int i;
if (mdebin->ebin->nsum > 0)
{
/* Check if we need to allocate first */
- if(enerhist->ener_ave == NULL)
+ if (enerhist->ener_ave == NULL)
{
- snew(enerhist->ener_ave,enerhist->nener);
- snew(enerhist->ener_sum,enerhist->nener);
+ snew(enerhist->ener_ave, enerhist->nener);
+ snew(enerhist->ener_sum, enerhist->nener);
}
- for(i=0;i<enerhist->nener;i++)
+ for (i = 0; i < enerhist->nener; i++)
{
enerhist->ener_ave[i] = mdebin->ebin->e[i].eav;
enerhist->ener_sum[i] = mdebin->ebin->e[i].esum;
if (mdebin->ebin->nsum_sim > 0)
{
/* Check if we need to allocate first */
- if(enerhist->ener_sum_sim == NULL)
+ if (enerhist->ener_sum_sim == NULL)
{
- snew(enerhist->ener_sum_sim,enerhist->nener);
+ snew(enerhist->ener_sum_sim, enerhist->nener);
}
- for(i=0;i<enerhist->nener;i++)
+ for (i = 0; i < enerhist->nener; i++)
{
enerhist->ener_sum_sim[i] = mdebin->ebin->e_sim[i].esum;
}
}
}
-void restore_energyhistory_from_state(t_mdebin * mdebin,
+void restore_energyhistory_from_state(t_mdebin * mdebin,
energyhistory_t * enerhist)
{
int i;
if ((enerhist->nsum > 0 || enerhist->nsum_sim > 0) &&
mdebin->ebin->nener != enerhist->nener)
{
- gmx_fatal(FARGS,"Mismatch between number of energies in run input (%d) and checkpoint file (%d).",
- mdebin->ebin->nener,enerhist->nener);
+ gmx_fatal(FARGS, "Mismatch between number of energies in run input (%d) and checkpoint file (%d).",
+ mdebin->ebin->nener, enerhist->nener);
}
mdebin->ebin->nsteps = enerhist->nsteps;
mdebin->ebin->nsteps_sim = enerhist->nsteps_sim;
mdebin->ebin->nsum_sim = enerhist->nsum_sim;
- for(i=0; i<mdebin->ebin->nener; i++)
+ for (i = 0; i < mdebin->ebin->nener; i++)
{
mdebin->ebin->e[i].eav =
- (enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
+ (enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
mdebin->ebin->e[i].esum =
- (enerhist->nsum > 0 ? enerhist->ener_sum[i] : 0);
+ (enerhist->nsum > 0 ? enerhist->ener_sum[i] : 0);
mdebin->ebin->e_sim[i].esum =
- (enerhist->nsum_sim > 0 ? enerhist->ener_sum_sim[i] : 0);
+ (enerhist->nsum_sim > 0 ? enerhist->ener_sum_sim[i] : 0);
}
if (mdebin->dhc)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff