/*
- *
- * 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) 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.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
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+ * 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
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- * GROwing Monsters And Cloning Shrimps
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <stdio.h>
#include <string.h>
-#include "string2.h"
-#include "force.h"
-#include "smalloc.h"
-#include "ns.h"
-#include "nrnb.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "futil.h"
-#include "names.h"
-#include "domdec.h"
-#include "gmxfio.h"
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define header "Neighborlist:"
-static void write_nblist(FILE *out,gmx_domdec_t *dd,t_nblist *nblist,int nDNL)
+static void write_nblist(FILE *out, gmx_domdec_t *dd, t_nblist *nblist, int nDNL)
{
- int i,nii,ii,j,zi,zj0,zj1,aj,zj,nj;
- int ca1[DD_MAXZONE],np[DD_MAXZONE];
- gmx_domdec_zones_t *dd_zones;
-
- if (nblist->nri > 0) {
- fprintf(out,"il_name: %s Solvent opt: %s\n",
- nrnb_str(nblist->il_code),
- enlist_names[nblist->enlist]);
- fprintf(out,"nri: %d npair: %d\n",nblist->nri,nblist->nrj);
- if (dd) {
- dd_zones = domdec_zones(dd);
-
- for(zi=0; zi<dd_zones->n; zi++)
- ca1[zi] = dd->cgindex[dd_zones->cg_range[zi+1]];
- i = 0;
- for(zi=0; zi<dd_zones->nizone; zi++) {
- zj0 = dd_zones->izone[zi].j0;
- zj1 = dd_zones->izone[zi].j1;
- for(zj=zj0; zj<zj1; zj++)
- np[zj] = 0;
- while(i < nblist->nri && nblist->iinr[i] < ca1[zi]) {
- for(j=nblist->jindex[i]; (j<nblist->jindex[i+1]); j++) {
- aj = nblist->jjnr[j];
- zj = zj0;
- while (aj >= ca1[zj])
- zj++;
- np[zj]++;
- }
- i++;
- }
- fprintf(out,"DD zone %d:",zi);
- for(zj=zj0; zj<zj1; zj++)
- fprintf(out," %d %d",zj,np[zj]);
- fprintf(out,"\n");
- }
- }
- if (nDNL >= 2) {
- for(i=0; i<nblist->nri; i++) {
- nii = 1;
- if (nDNL >= 3 && nblist->enlist != enlistATOM_ATOM)
- nii = 3;
- nj = nblist->jindex[i+1] - nblist->jindex[i];
- fprintf(out,"i: %d shift: %d gid: %d nj: %d\n",
- ddglatnr(dd,nblist->iinr[i]),
- nblist->shift[i],nblist->gid[i],nj);
- for(ii=0; ii<nii; ii++) {
- for(j=nblist->jindex[i]; (j<nblist->jindex[i+1]); j++) {
- fprintf(out," i: %5d j: %5d\n",
- ddglatnr(dd,nblist->iinr[i]+ii),
- ddglatnr(dd,nblist->jjnr[j]));
- }
- }
- }
- }
- fflush(out);
- }
-}
+ int i, nii, ii, j, zi, zj0, zj1, aj, zj, nj;
+ int ca1[DD_MAXZONE], np[DD_MAXZONE];
+ gmx_domdec_zones_t *dd_zones;
-static void set_mat(FILE *fp,int **mat,int i0,int ni,int j0,int nj,
- gmx_bool bSymm,int shift)
-{
- int i,j;
-
- for(i=i0; (i<i0+ni); i++) {
- for(j=j0; (j<j0+nj); j++) {
- if (mat[i][j] != 0)
- fprintf(fp,"mat[%d][%d] changing from %d to %d\n",
- i,j,mat[i][j],shift+1);
- mat[i][j] = shift+1;
- if (bSymm)
- mat[j][i] = 27-shift;
+ if (nblist->nri > 0)
+ {
+ fprintf(out, "ielec: %d, ivdw: %d, type: %d, Solvent opt: %s\n",
+ nblist->ielec, nblist->ivdw, nblist->type,
+ gmx_nblist_geometry_names[nblist->igeometry]);
+ fprintf(out, "nri: %d npair: %d\n", nblist->nri, nblist->nrj);
+ if (dd)
+ {
+ dd_zones = domdec_zones(dd);
+
+ for (zi = 0; zi < dd_zones->n; zi++)
+ {
+ ca1[zi] = dd->cgindex[dd_zones->cg_range[zi+1]];
+ }
+ i = 0;
+ for (zi = 0; zi < dd_zones->nizone; zi++)
+ {
+ zj0 = dd_zones->izone[zi].j0;
+ zj1 = dd_zones->izone[zi].j1;
+ for (zj = zj0; zj < zj1; zj++)
+ {
+ np[zj] = 0;
+ }
+ while (i < nblist->nri && nblist->iinr[i] < ca1[zi])
+ {
+ for (j = nblist->jindex[i]; (j < nblist->jindex[i+1]); j++)
+ {
+ aj = nblist->jjnr[j];
+ zj = zj0;
+ while (aj >= ca1[zj])
+ {
+ zj++;
+ }
+ np[zj]++;
+ }
+ i++;
+ }
+ fprintf(out, "DD zone %d:", zi);
+ for (zj = zj0; zj < zj1; zj++)
+ {
+ fprintf(out, " %d %d", zj, np[zj]);
+ }
+ fprintf(out, "\n");
+ }
+ }
+ if (nDNL >= 2)
+ {
+ for (i = 0; i < nblist->nri; i++)
+ {
+ nii = 1;
+ if (nDNL >= 3 && nblist->igeometry != GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE)
+ {
+ nii = 3;
+ }
+ nj = nblist->jindex[i+1] - nblist->jindex[i];
+ fprintf(out, "i: %d shift: %d gid: %d nj: %d\n",
+ ddglatnr(dd, nblist->iinr[i]),
+ nblist->shift[i], nblist->gid[i], nj);
+ for (ii = 0; ii < nii; ii++)
+ {
+ for (j = nblist->jindex[i]; (j < nblist->jindex[i+1]); j++)
+ {
+ fprintf(out, " i: %5d j: %5d\n",
+ ddglatnr(dd, nblist->iinr[i]+ii),
+ ddglatnr(dd, nblist->jjnr[j]));
+ }
+ }
+ }
+ }
+ fflush(out);
}
- }
}
-int read_nblist(FILE *in,FILE *fp,int **mat,int natoms,gmx_bool bSymm)
+static void set_mat(FILE *fp, int **mat, int i0, int ni, int j0, int nj,
+ gmx_bool bSymm, int shift)
{
- gmx_bool bNL;
- char buf[256],b1[32],b2[32],solv[256],il_code[256];
- int i,ii,j,nnbl,full,icmp,nri,isolv;
- int iatom,nrj,nj,shift,gid,nargs,njtot=0;
-
- do {
- if (fgets2(buf,255,in) == NULL)
- gmx_fatal(FARGS,"EOF when looking for '%s' in logfile",header);
- } while (strstr(buf,header) == NULL);
-
- do {
- do {
- if (fgets2(buf,255,in) == NULL)
- return njtot;
- } while (strstr(buf,"nri:") == NULL);
-
- if (0) {
- if ((nargs = sscanf(buf,"%*s%s%*s%s",il_code,solv)) != 2) {
- fprintf(stderr,"Can not find the right il_code\n");
- return njtot;
- }
- for(isolv=0; (isolv<esolNR); isolv++)
- if (strstr(esol_names[isolv],solv) != NULL)
- break;
-
- if (isolv == esolNR) {
- fprintf(stderr,"Can not read il_code or solv (nargs=%d)\n",nargs);
- return njtot;
+ int i, j;
+
+ for (i = i0; (i < i0+ni); i++)
+ {
+ for (j = j0; (j < j0+nj); j++)
+ {
+ if (mat[i][j] != 0)
+ {
+ fprintf(fp, "mat[%d][%d] changing from %d to %d\n",
+ i, j, mat[i][j], shift+1);
+ }
+ mat[i][j] = shift+1;
+ if (bSymm)
+ {
+ mat[j][i] = 27-shift;
+ }
}
- }
- else
- isolv = enlistATOM_ATOM;
-
- /* gmx_fatal(FARGS,"Can not read il_code or solv (nargs=%d)",nargs);*/
- if ((nargs = sscanf(buf,"%*s%d%*s%d",&nri,&nrj)) != 2)
- gmx_fatal(FARGS,"Can not read nri or nrj (nargs=%d)",nargs);
- for(ii=0; (ii<nri); ii++) {
- if ((nargs = fscanf(in,"%*s%d%*s%d%*s%d%*s%d",
- &iatom,&shift,&gid,&nj)) != 4)
- gmx_fatal(FARGS,"Can not read iatom, shift gid or nj (nargs=%d)",nargs);
- /* Number shifts from 1 to 27 iso 0 to 26 to distinguish uninitialized
- * matrix elements.
- */
- range_check(iatom,0,natoms);
- for(i=0; (i<nj); i++) {
- if ((nargs = fscanf(in,"%*s%d",&j)) != 1)
- gmx_fatal(FARGS,"Can not read j");
- range_check(j,0,natoms);
- switch (isolv) {
- case enlistATOM_ATOM:
- set_mat(fp,mat,iatom,1,j,1,bSymm,shift);
- njtot++;
- break;
- case enlistSPC_ATOM:
- set_mat(fp,mat,iatom,3,j,1,bSymm,shift);
- njtot+=3;
- break;
- case enlistSPC_SPC:
- set_mat(fp,mat,iatom,3,j,3,bSymm,shift);
- njtot+=9;
- break;
- case enlistTIP4P_ATOM:
- set_mat(fp,mat,iatom,4,j,1,bSymm,shift);
- njtot+=4;
- break;
- case enlistTIP4P_TIP4P:
- set_mat(fp,mat,iatom,4,j,4,bSymm,shift);
- njtot+=16;
- break;
- default:
- gmx_incons("non-existing solvent type");
- }
- }
- }
- fprintf(fp,"nri = %d nrj = %d\n",nri,nrj);
- } while (TRUE);
- return -1;
+ }
}
-void dump_nblist(FILE *out,t_commrec *cr,t_forcerec *fr,int nDNL)
+
+
+void dump_nblist(FILE *out, t_commrec *cr, t_forcerec *fr, int nDNL)
{
#if 0
- static FILE *fp=NULL;
- char buf[STRLEN];
- int n,i;
-
- if (fp == NULL) {
- if (PAR(cr)) {
- sprintf(buf,"nlist_n%d.txt",cr->nodeid);
- } else {
- sprintf(buf,"nlist.txt");
+ static FILE *fp = NULL;
+ char buf[STRLEN];
+ int n, i;
+
+ if (fp == NULL)
+ {
+ if (PAR(cr))
+ {
+ sprintf(buf, "nlist_n%d.txt", cr->nodeid);
+ }
+ else
+ {
+ sprintf(buf, "nlist.txt");
+ }
+ fp = gmx_fio_fopen(buf, "w");
}
- fp = gmx_fio_fopen(buf,"w");
- }
- fprintf(fp,"%s\n",header);
+ fprintf(fp, "%s\n", header);
- for(n=0; (n<fr->nnblists); n++)
- for(i=0; (i<eNL_NR); i++)
- write_nblist(fp,cr->dd,&fr->nblists[n].nlist_sr[i],nDNL);
+ for (n = 0; (n < fr->nnblists); n++)
+ {
+ for (i = 0; (i < eNL_NR); i++)
+ {
+ write_nblist(fp, cr->dd, &fr->nblists[n].nlist_sr[i], nDNL);
+ }
+ }
#endif
- char buf[STRLEN];
- int n,i;
+ char buf[STRLEN];
+ int n, i;
- fprintf(out,"%s\n",header);
+ fprintf(out, "%s\n", header);
- for(n=0; (n<fr->nnblists); n++)
- for(i=0; (i<eNL_NR); i++)
- write_nblist(out,cr->dd,&fr->nblists[n].nlist_sr[i],nDNL);
+ for (n = 0; (n < fr->nnblists); n++)
+ {
+ for (i = 0; (i < eNL_NR); i++)
+ {
+ write_nblist(out, cr->dd, &fr->nblists[n].nlist_sr[i], nDNL);
+ }
+ }
}
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff