-/* -*- 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.
- *
+ *
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+ * Lesser General Public License for more details.
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+ * You should have received a copy of the GNU Lesser General Public
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+ * 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
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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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- *
- * And Hey:
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+ * 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
{
{
gmx_global_stat_t gs;
- snew(gs,1);
-
+ snew(gs, 1);
+
gs->rb = mk_bin();
- snew(gs->itc0,ir->opts.ngtc);
- snew(gs->itc1,ir->opts.ngtc);
+ snew(gs->itc0, ir->opts.ngtc);
+ snew(gs->itc1, ir->opts.ngtc);
return gs;
}
}
static int filter_enerdterm(real *afrom, gmx_bool bToBuffer, real *ato,
- gmx_bool bTemp, gmx_bool bPres, gmx_bool bEner) {
- int i,to,from;
+ gmx_bool bTemp, gmx_bool bPres, gmx_bool bEner)
+{
+ int i, to, from;
from = 0;
to = 0;
- for (i=0;i<F_NRE;i++)
+ for (i = 0; i < F_NRE; i++)
{
if (bToBuffer)
{
{
to = i;
}
- switch (i) {
- case F_EKIN:
- case F_TEMP:
- case F_DKDL:
- if (bTemp)
- {
- ato[to++] = afrom[from++];
- }
- break;
- case F_PRES:
- case F_PDISPCORR:
- case F_VTEMP:
- if (bPres)
- {
- ato[to++] = afrom[from++];
- }
- break;
- default:
- if (bEner)
- {
- ato[to++] = afrom[from++];
- }
- break;
+ switch (i)
+ {
+ case F_EKIN:
+ case F_TEMP:
+ case F_DKDL:
+ if (bTemp)
+ {
+ ato[to++] = afrom[from++];
+ }
+ break;
+ case F_PRES:
+ case F_PDISPCORR:
+ if (bPres)
+ {
+ ato[to++] = afrom[from++];
+ }
+ break;
+ default:
+ if (bEner)
+ {
+ ato[to++] = afrom[from++];
+ }
+ break;
}
}
return to;
}
-void global_stat(FILE *fplog,gmx_global_stat_t gs,
- t_commrec *cr,gmx_enerdata_t *enerd,
- tensor fvir,tensor svir,rvec mu_tot,
+void global_stat(FILE *fplog, gmx_global_stat_t gs,
+ t_commrec *cr, gmx_enerdata_t *enerd,
+ tensor fvir, tensor svir, rvec mu_tot,
t_inputrec *inputrec,
- gmx_ekindata_t *ekind,gmx_constr_t constr,
+ gmx_ekindata_t *ekind, gmx_constr_t constr,
t_vcm *vcm,
- int nsig,real *sig,
- gmx_mtop_t *top_global, t_state *state_local,
+ int nsig, real *sig,
+ gmx_mtop_t *top_global, t_state *state_local,
gmx_bool bSumEkinhOld, int flags)
/* instead of current system, gmx_booleans for summing virial, kinetic energy, and other terms */
{
- t_bin *rb;
- int *itc0,*itc1;
- int ie=0,ifv=0,isv=0,irmsd=0,imu=0;
- int idedl=0,idvdll=0,idvdlnl=0,iepl=0,icm=0,imass=0,ica=0,inb=0;
- int isig=-1;
- int icj=-1,ici=-1,icx=-1;
- int inn[egNR];
- real copyenerd[F_NRE];
- int nener,j;
- real *rmsd_data=NULL;
- double nb;
- gmx_bool bVV,bTemp,bEner,bPres,bConstrVir,bEkinAveVel,bFirstIterate,bReadEkin;
-
- bVV = EI_VV(inputrec->eI);
- bTemp = flags & CGLO_TEMPERATURE;
- bEner = flags & CGLO_ENERGY;
- bPres = (flags & CGLO_PRESSURE);
- bConstrVir = (flags & CGLO_CONSTRAINT);
- bFirstIterate = (flags & CGLO_FIRSTITERATE);
- bEkinAveVel = (inputrec->eI==eiVV || (inputrec->eI==eiVVAK && bPres));
- bReadEkin = (flags & CGLO_READEKIN);
-
- rb = gs->rb;
- itc0 = gs->itc0;
- itc1 = gs->itc1;
-
-
- reset_bin(rb);
- /* This routine copies all the data to be summed to one big buffer
- * using the t_bin struct.
- */
-
- /* First, we neeed to identify which enerd->term should be
- communicated. Temperature and pressure terms should only be
- communicated and summed when they need to be, to avoid repeating
- the sums and overcounting. */
-
- nener = filter_enerdterm(enerd->term,TRUE,copyenerd,bTemp,bPres,bEner);
-
- /* First, the data that needs to be communicated with velocity verlet every time
- This is just the constraint virial.*/
- if (bConstrVir) {
- isv = add_binr(rb,DIM*DIM,svir[0]);
- where();
- }
-
-/* We need the force virial and the kinetic energy for the first time through with velocity verlet */
- if (bTemp || !bVV)
- {
- if (ekind)
- {
- for(j=0; (j<inputrec->opts.ngtc); j++)
- {
- if (bSumEkinhOld)
- {
- itc0[j]=add_binr(rb,DIM*DIM,ekind->tcstat[j].ekinh_old[0]);
- }
- if (bEkinAveVel && !bReadEkin)
- {
- itc1[j]=add_binr(rb,DIM*DIM,ekind->tcstat[j].ekinf[0]);
- }
- else if (!bReadEkin)
- {
- itc1[j]=add_binr(rb,DIM*DIM,ekind->tcstat[j].ekinh[0]);
- }
- }
- /* these probably need to be put into one of these categories */
- where();
- idedl = add_binr(rb,1,&(ekind->dekindl));
- where();
- ica = add_binr(rb,1,&(ekind->cosacc.mvcos));
- where();
- }
- }
- where();
-
- if ((bPres || !bVV) && bFirstIterate)
- {
- ifv = add_binr(rb,DIM*DIM,fvir[0]);
- }
-
-
- if (bEner)
- {
- where();
- if (bFirstIterate)
- {
- ie = add_binr(rb,nener,copyenerd);
- }
- where();
- if (constr)
- {
- rmsd_data = constr_rmsd_data(constr);
- if (rmsd_data)
- {
- irmsd = add_binr(rb,inputrec->eI==eiSD2 ? 3 : 2,rmsd_data);
- }
- }
- if (!NEED_MUTOT(*inputrec))
- {
- imu = add_binr(rb,DIM,mu_tot);
- where();
- }
-
- if (bFirstIterate)
- {
- for(j=0; (j<egNR); j++)
- {
- inn[j]=add_binr(rb,enerd->grpp.nener,enerd->grpp.ener[j]);
- }
- where();
- if (inputrec->efep != efepNO)
- {
- idvdll = add_bind(rb,efptNR,enerd->dvdl_lin);
- idvdlnl = add_bind(rb,efptNR,enerd->dvdl_nonlin);
- if (enerd->n_lambda > 0)
- {
- iepl = add_bind(rb,enerd->n_lambda,enerd->enerpart_lambda);
- }
- }
- }
- }
-
- if (vcm)
- {
- icm = add_binr(rb,DIM*vcm->nr,vcm->group_p[0]);
- where();
- imass = add_binr(rb,vcm->nr,vcm->group_mass);
- where();
- if (vcm->mode == ecmANGULAR)
- {
- icj = add_binr(rb,DIM*vcm->nr,vcm->group_j[0]);
- where();
- icx = add_binr(rb,DIM*vcm->nr,vcm->group_x[0]);
- where();
- ici = add_binr(rb,DIM*DIM*vcm->nr,vcm->group_i[0][0]);
- where();
- }
- }
-
- if (DOMAINDECOMP(cr))
- {
- nb = cr->dd->nbonded_local;
- inb = add_bind(rb,1,&nb);
- }
- where();
- if (nsig > 0)
- {
- isig = add_binr(rb,nsig,sig);
- }
-
- /* Global sum it all */
- if (debug)
- {
- fprintf(debug,"Summing %d energies\n",rb->maxreal);
- }
- sum_bin(rb,cr);
- where();
-
- /* Extract all the data locally */
-
- if (bConstrVir)
- {
- extract_binr(rb,isv ,DIM*DIM,svir[0]);
- }
-
- /* We need the force virial and the kinetic energy for the first time through with velocity verlet */
- if (bTemp || !bVV)
- {
- if (ekind)
- {
- for(j=0; (j<inputrec->opts.ngtc); j++)
- {
- if (bSumEkinhOld)
- {
- extract_binr(rb,itc0[j],DIM*DIM,ekind->tcstat[j].ekinh_old[0]);
- }
- if (bEkinAveVel && !bReadEkin) {
- extract_binr(rb,itc1[j],DIM*DIM,ekind->tcstat[j].ekinf[0]);
- }
- else if (!bReadEkin)
- {
- extract_binr(rb,itc1[j],DIM*DIM,ekind->tcstat[j].ekinh[0]);
- }
- }
- extract_binr(rb,idedl,1,&(ekind->dekindl));
- extract_binr(rb,ica,1,&(ekind->cosacc.mvcos));
- where();
- }
- }
- if ((bPres || !bVV) && bFirstIterate)
- {
- extract_binr(rb,ifv ,DIM*DIM,fvir[0]);
- }
-
- if (bEner)
- {
- if (bFirstIterate)
- {
- extract_binr(rb,ie,nener,copyenerd);
- if (rmsd_data)
- {
- extract_binr(rb,irmsd,inputrec->eI==eiSD2 ? 3 : 2,rmsd_data);
- }
- if (!NEED_MUTOT(*inputrec))
- {
- extract_binr(rb,imu,DIM,mu_tot);
- }
-
- for(j=0; (j<egNR); j++)
- {
- extract_binr(rb,inn[j],enerd->grpp.nener,enerd->grpp.ener[j]);
- }
- if (inputrec->efep != efepNO)
- {
- extract_bind(rb,idvdll ,efptNR,enerd->dvdl_lin);
- extract_bind(rb,idvdlnl,efptNR,enerd->dvdl_nonlin);
- if (enerd->n_lambda > 0)
- {
- extract_bind(rb,iepl,enerd->n_lambda,enerd->enerpart_lambda);
- }
- }
- if (DOMAINDECOMP(cr))
- {
- extract_bind(rb,inb,1,&nb);
- if ((int)(nb + 0.5) != cr->dd->nbonded_global)
- {
- dd_print_missing_interactions(fplog,cr,(int)(nb + 0.5),top_global,state_local);
- }
- }
- where();
-
- filter_enerdterm(copyenerd,FALSE,enerd->term,bTemp,bPres,bEner);
- }
- }
-
- if (vcm)
- {
- extract_binr(rb,icm,DIM*vcm->nr,vcm->group_p[0]);
- where();
- extract_binr(rb,imass,vcm->nr,vcm->group_mass);
- where();
- if (vcm->mode == ecmANGULAR)
- {
- extract_binr(rb,icj,DIM*vcm->nr,vcm->group_j[0]);
- where();
- extract_binr(rb,icx,DIM*vcm->nr,vcm->group_x[0]);
- where();
- extract_binr(rb,ici,DIM*DIM*vcm->nr,vcm->group_i[0][0]);
- where();
- }
- }
-
- if (nsig > 0)
- {
- extract_binr(rb,isig,nsig,sig);
- }
- where();
-}
+ t_bin *rb;
+ int *itc0, *itc1;
+ int ie = 0, ifv = 0, isv = 0, irmsd = 0, imu = 0;
+ int idedl = 0, idvdll = 0, idvdlnl = 0, iepl = 0, icm = 0, imass = 0, ica = 0, inb = 0;
+ int isig = -1;
+ int icj = -1, ici = -1, icx = -1;
+ int inn[egNR];
+ real copyenerd[F_NRE];
+ int nener, j;
+ real *rmsd_data = NULL;
+ double nb;
+ gmx_bool bVV, bTemp, bEner, bPres, bConstrVir, bEkinAveVel, bFirstIterate, bReadEkin;
+
+ bVV = EI_VV(inputrec->eI);
+ bTemp = flags & CGLO_TEMPERATURE;
+ bEner = flags & CGLO_ENERGY;
+ bPres = (flags & CGLO_PRESSURE);
+ bConstrVir = (flags & CGLO_CONSTRAINT);
+ bFirstIterate = (flags & CGLO_FIRSTITERATE);
+ bEkinAveVel = (inputrec->eI == eiVV || (inputrec->eI == eiVVAK && bPres));
+ bReadEkin = (flags & CGLO_READEKIN);
+
+ rb = gs->rb;
+ itc0 = gs->itc0;
+ itc1 = gs->itc1;
+
+
+ reset_bin(rb);
+ /* This routine copies all the data to be summed to one big buffer
+ * using the t_bin struct.
+ */
+
+ /* First, we neeed to identify which enerd->term should be
+ communicated. Temperature and pressure terms should only be
+ communicated and summed when they need to be, to avoid repeating
+ the sums and overcounting. */
+
+ nener = filter_enerdterm(enerd->term, TRUE, copyenerd, bTemp, bPres, bEner);
+
+ /* First, the data that needs to be communicated with velocity verlet every time
+ This is just the constraint virial.*/
+ if (bConstrVir)
+ {
+ isv = add_binr(rb, DIM*DIM, svir[0]);
+ where();
+ }
-int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep)
-{
- if (nstep != 0)
- return ((step % nstep)==0);
- else
- return 0;
-}
+/* We need the force virial and the kinetic energy for the first time through with velocity verlet */
+ if (bTemp || !bVV)
+ {
+ if (ekind)
+ {
+ for (j = 0; (j < inputrec->opts.ngtc); j++)
+ {
+ if (bSumEkinhOld)
+ {
+ itc0[j] = add_binr(rb, DIM*DIM, ekind->tcstat[j].ekinh_old[0]);
+ }
+ if (bEkinAveVel && !bReadEkin)
+ {
+ itc1[j] = add_binr(rb, DIM*DIM, ekind->tcstat[j].ekinf[0]);
+ }
+ else if (!bReadEkin)
+ {
+ itc1[j] = add_binr(rb, DIM*DIM, ekind->tcstat[j].ekinh[0]);
+ }
+ }
+ /* these probably need to be put into one of these categories */
+ where();
+ idedl = add_binr(rb, 1, &(ekind->dekindl));
+ where();
+ ica = add_binr(rb, 1, &(ekind->cosacc.mvcos));
+ where();
+ }
+ }
+ where();
-static void moveit(t_commrec *cr,
- int left,int right,const char *s,rvec xx[])
-{
- if (!xx)
- return;
+ if ((bPres || !bVV) && bFirstIterate)
+ {
+ ifv = add_binr(rb, DIM*DIM, fvir[0]);
+ }
- 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))
+ if (bEner)
{
- 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
- )
+ where();
+ if (bFirstIterate)
{
- of->fp_trn = open_trn(ftp2fn(efTRN,nfile,fnm), filemode);
+ ie = add_binr(rb, nener, copyenerd);
}
- if (EI_DYNAMICS(ir->eI) &&
- ir->nstxtcout > 0)
+ where();
+ if (constr)
{
- of->fp_xtc = open_xtc(ftp2fn(efXTC,nfile,fnm), filemode);
- of->xtc_prec = ir->xtcprec;
+ rmsd_data = constr_rmsd_data(constr);
+ if (rmsd_data)
+ {
+ irmsd = add_binr(rb, inputrec->eI == eiSD2 ? 3 : 2, rmsd_data);
+ }
}
- if (EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
+ if (!NEED_MUTOT(*inputrec))
{
- of->fp_ene = open_enx(ftp2fn(efEDR,nfile,fnm), filemode);
+ imu = add_binr(rb, DIM, mu_tot);
+ where();
}
- 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 (bFirstIterate)
{
- if (bAppendFiles)
- {
- of->fp_dhdl = gmx_fio_fopen(opt2fn("-dhdl",nfile,fnm),filemode);
- }
- else
+ for (j = 0; (j < egNR); j++)
{
- of->fp_dhdl = open_dhdl(opt2fn("-dhdl",nfile,fnm),ir,oenv);
+ inn[j] = add_binr(rb, enerd->grpp.nener, enerd->grpp.ener[j]);
}
- }
-
- if (opt2bSet("-field",nfile,fnm) &&
- (ir->ex[XX].n || ir->ex[YY].n || ir->ex[ZZ].n))
- {
- if (bAppendFiles)
+ where();
+ if (inputrec->efep != efepNO)
{
- 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);
+ idvdll = add_bind(rb, efptNR, enerd->dvdl_lin);
+ idvdlnl = add_bind(rb, efptNR, enerd->dvdl_nonlin);
+ if (enerd->n_lambda > 0)
+ {
+ iepl = add_bind(rb, enerd->n_lambda, enerd->enerpart_lambda);
+ }
}
}
}
- return of;
-}
-
-void done_mdoutf(gmx_mdoutf_t *of)
-{
- if (of->fp_ene != NULL)
+ if (vcm)
{
- close_enx(of->fp_ene);
+ icm = add_binr(rb, DIM*vcm->nr, vcm->group_p[0]);
+ where();
+ imass = add_binr(rb, vcm->nr, vcm->group_mass);
+ where();
+ if (vcm->mode == ecmANGULAR)
+ {
+ icj = add_binr(rb, DIM*vcm->nr, vcm->group_j[0]);
+ where();
+ icx = add_binr(rb, DIM*vcm->nr, vcm->group_x[0]);
+ where();
+ ici = add_binr(rb, DIM*DIM*vcm->nr, vcm->group_i[0][0]);
+ where();
+ }
}
- if (of->fp_xtc)
+
+ if (DOMAINDECOMP(cr))
{
- close_xtc(of->fp_xtc);
+ nb = cr->dd->nbonded_local;
+ inb = add_bind(rb, 1, &nb);
}
- if (of->fp_trn)
+ where();
+ if (nsig > 0)
{
- close_trn(of->fp_trn);
+ isig = add_binr(rb, nsig, sig);
}
- if (of->fp_dhdl != NULL)
+
+ /* Global sum it all */
+ if (debug)
{
- gmx_fio_fclose(of->fp_dhdl);
+ fprintf(debug, "Summing %d energies\n", rb->maxreal);
}
- if (of->fp_field != NULL)
+ sum_bin(rb, cr);
+ where();
+
+ /* Extract all the data locally */
+
+ if (bConstrVir)
{
- gmx_fio_fclose(of->fp_field);
+ extract_binr(rb, isv, DIM*DIM, svir[0]);
}
- 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))
+ /* We need the force virial and the kinetic energy for the first time through with velocity verlet */
+ if (bTemp || !bVV)
{
- if (mdof_flags & MDOF_CPT)
- {
- dd_collect_state(cr->dd,state_local,state_global);
- }
- else
+ if (ekind)
{
- 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)
+ for (j = 0; (j < inputrec->opts.ngtc); j++)
{
- dd_collect_vec(cr->dd,state_local,local_v,
- global_v);
+ if (bSumEkinhOld)
+ {
+ extract_binr(rb, itc0[j], DIM*DIM, ekind->tcstat[j].ekinh_old[0]);
+ }
+ if (bEkinAveVel && !bReadEkin)
+ {
+ extract_binr(rb, itc1[j], DIM*DIM, ekind->tcstat[j].ekinf[0]);
+ }
+ else if (!bReadEkin)
+ {
+ extract_binr(rb, itc1[j], DIM*DIM, ekind->tcstat[j].ekinh[0]);
+ }
}
- }
- if (mdof_flags & MDOF_F)
- {
- dd_collect_vec(cr->dd,state_local,f_local,f_global);
+ extract_binr(rb, idedl, 1, &(ekind->dekindl));
+ extract_binr(rb, ica, 1, &(ekind->cosacc.mvcos));
+ where();
}
}
- else
+ if ((bPres || !bVV) && bFirstIterate)
{
- 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)
+ extract_binr(rb, ifv, DIM*DIM, fvir[0]);
+ }
+
+ if (bEner)
+ {
+ if (bFirstIterate)
{
- /* Particle decomposition, collect the data on the master node */
- if (mdof_flags & MDOF_CPT)
+ extract_binr(rb, ie, nener, copyenerd);
+ if (rmsd_data)
{
- 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
- }
- }
+ extract_binr(rb, irmsd, inputrec->eI == eiSD2 ? 3 : 2, rmsd_data);
}
- else
+ if (!NEED_MUTOT(*inputrec))
{
- if (mdof_flags & (MDOF_X | MDOF_XTC)) MX(state_global->x);
- if (mdof_flags & MDOF_V) MX(global_v);
+ extract_binr(rb, imu, DIM, mu_tot);
}
- 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)
+
+ for (j = 0; (j < egNR); j++)
{
- gmx_file("Cannot write trajectory; maybe you are out of disk space?");
+ extract_binr(rb, inn[j], enerd->grpp.nener, enerd->grpp.ener[j]);
}
- gmx_fio_check_file_position(of->fp_trn);
- }
- if (mdof_flags & MDOF_XTC) {
- groups = &top_global->groups;
- if (*n_xtc == -1)
+ if (inputrec->efep != efepNO)
{
- *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)
+ extract_bind(rb, idvdll, efptNR, enerd->dvdl_lin);
+ extract_bind(rb, idvdlnl, efptNR, enerd->dvdl_nonlin);
+ if (enerd->n_lambda > 0)
{
- snew(*x_xtc,*n_xtc);
+ extract_bind(rb, iepl, enerd->n_lambda, enerd->enerpart_lambda);
}
}
- if (*n_xtc == top_global->natoms)
- {
- xxtc = state_global->x;
- }
- else
+ if (DOMAINDECOMP(cr))
{
- xxtc = *x_xtc;
- j = 0;
- for(i=0; (i<top_global->natoms); i++)
+ extract_bind(rb, inb, 1, &nb);
+ if ((int)(nb + 0.5) != cr->dd->nbonded_global)
{
- if (ggrpnr(groups,egcXTC,i) == 0)
- {
- copy_rvec(state_global->x[i],xxtc[j++]);
- }
+ dd_print_missing_interactions(fplog, cr, (int)(nb + 0.5), top_global, state_local);
}
}
- 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);
+ where();
+
+ filter_enerdterm(copyenerd, FALSE, enerd->term, bTemp, bPres, bEner);
+ }
+ }
+
+ if (vcm)
+ {
+ extract_binr(rb, icm, DIM*vcm->nr, vcm->group_p[0]);
+ where();
+ extract_binr(rb, imass, vcm->nr, vcm->group_mass);
+ where();
+ if (vcm->mode == ecmANGULAR)
+ {
+ extract_binr(rb, icj, DIM*vcm->nr, vcm->group_j[0]);
+ where();
+ extract_binr(rb, icx, DIM*vcm->nr, vcm->group_x[0]);
+ where();
+ extract_binr(rb, ici, DIM*DIM*vcm->nr, vcm->group_i[0][0]);
+ where();
}
}
+
+ if (nsig > 0)
+ {
+ extract_binr(rb, isig, nsig, sig);
+ }
+ where();
}
+int do_per_step(gmx_int64_t step, gmx_int64_t nstep)
+{
+ if (nstep != 0)
+ {
+ return ((step % nstep) == 0);
+ }
+ else
+ {
+ return 0;
+ }
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff