src/mdlib/wnblist.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
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  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
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  29  *
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  34  */
  35 /* This file is completely threadsafe - keep it that way! */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <stdio.h>
  41 #include <string.h>
  42 #include "string2.h"
  43 #include "force.h"
  44 #include "smalloc.h"
  45 #include "ns.h"
  46 #include "nrnb.h"
  47 #include "gmx_fatal.h"
  48 #include "macros.h"
  49 #include "futil.h"
  50 #include "names.h"
  51 #include "domdec.h"
  52 #include "gmxfio.h"
  53
  54 #define header "Neighborlist:"
  55
  56 static void write_nblist(FILE *out,gmx_domdec_t *dd,t_nblist *nblist,int nDNL)
  57 {
  58   int i,nii,ii,j,zi,zj0,zj1,aj,zj,nj;
  59   int ca1[DD_MAXZONE],np[DD_MAXZONE];
  60   gmx_domdec_zones_t *dd_zones;
  61
  62   if (nblist->nri > 0) {
  63     fprintf(out,"il_name: %s  Solvent opt: %s\n",
  64             nrnb_str(nblist->il_code),
  65             enlist_names[nblist->enlist]);
  66     fprintf(out,"nri: %d  npair: %d\n",nblist->nri,nblist->nrj);
  67     if (dd) {
  68       dd_zones = domdec_zones(dd);
  69
  70       for(zi=0; zi<dd_zones->n; zi++)
  71         ca1[zi] = dd->cgindex[dd_zones->cg_range[zi+1]];
  72       i = 0;
  73       for(zi=0; zi<dd_zones->nizone; zi++) {
  74         zj0 = dd_zones->izone[zi].j0;
  75         zj1 = dd_zones->izone[zi].j1;
  76         for(zj=zj0; zj<zj1; zj++)
  77           np[zj] = 0;
  78         while(i < nblist->nri && nblist->iinr[i] < ca1[zi]) {
  79           for(j=nblist->jindex[i]; (j<nblist->jindex[i+1]); j++) {
  80             aj = nblist->jjnr[j];
  81             zj = zj0;
  82             while (aj >= ca1[zj])
  83               zj++;
  84             np[zj]++;
  85           }
  86           i++;
  87         }
  88         fprintf(out,"DD zone %d:",zi);
  89         for(zj=zj0; zj<zj1; zj++)
  90           fprintf(out," %d %d",zj,np[zj]);
  91         fprintf(out,"\n");
  92       }
  93     }
  94     if (nDNL >= 2) {
  95       for(i=0; i<nblist->nri; i++) {
  96         nii = 1;
  97         if (nDNL >= 3 && nblist->enlist != enlistATOM_ATOM)
  98           nii = 3;
  99         nj = nblist->jindex[i+1] - nblist->jindex[i];
 100         fprintf(out,"i: %d shift: %d gid: %d nj: %d\n",
 101                 ddglatnr(dd,nblist->iinr[i]),
 102                 nblist->shift[i],nblist->gid[i],nj);
 103         for(ii=0; ii<nii; ii++) {
 104           for(j=nblist->jindex[i]; (j<nblist->jindex[i+1]); j++) {
 105             fprintf(out,"  i: %5d  j: %5d\n",
 106                     ddglatnr(dd,nblist->iinr[i]+ii),
 107                     ddglatnr(dd,nblist->jjnr[j]));
 108           }
 109         }
 110       }
 111     }
 112     fflush(out);
 113   }
 114 }
 115
 116 static void set_mat(FILE *fp,int **mat,int i0,int ni,int j0,int nj,
 117                     gmx_bool bSymm,int shift)
 118 {
 119   int i,j;
 120
 121   for(i=i0; (i<i0+ni); i++) {
 122     for(j=j0; (j<j0+nj); j++) {
 123       if (mat[i][j] != 0)
 124         fprintf(fp,"mat[%d][%d] changing from %d to %d\n",
 125                 i,j,mat[i][j],shift+1);
 126       mat[i][j] = shift+1;
 127       if (bSymm)
 128         mat[j][i] = 27-shift;
 129     }
 130   }
 131 }
 132
 133 int read_nblist(FILE *in,FILE *fp,int **mat,int natoms,gmx_bool bSymm)
 134 {
 135     gmx_bool bNL;
 136     char buf[256],b1[32],b2[32],solv[256],il_code[256];
 137     int  i,ii,j,nnbl,full,icmp,nri,isolv;
 138     int  iatom,nrj,nj,shift,gid,nargs,njtot=0;
 139
 140     do {
 141         if (fgets2(buf,255,in) == NULL)
 142             gmx_fatal(FARGS,"EOF when looking for '%s' in logfile",header);
 143     } while (strstr(buf,header) == NULL);
 144
 145     do {
 146       do {
 147         if (fgets2(buf,255,in) == NULL)
 148           return njtot;
 149       } while (strstr(buf,"nri:") == NULL);
 150
 151       if (0) {
 152         if ((nargs = sscanf(buf,"%*s%s%*s%s",il_code,solv)) != 2) {
 153           fprintf(stderr,"Can not find the right il_code\n");
 154           return njtot;
 155         }
 156         for(isolv=0; (isolv<esolNR); isolv++)
 157           if (strstr(esol_names[isolv],solv) != NULL)
 158             break;
 159
 160         if (isolv == esolNR) {
 161           fprintf(stderr,"Can not read il_code or solv (nargs=%d)\n",nargs);
 162           return njtot;
 163         }
 164       }
 165       else
 166         isolv = enlistATOM_ATOM;
 167
 168       /* gmx_fatal(FARGS,"Can not read il_code or solv (nargs=%d)",nargs);*/
 169       if ((nargs = sscanf(buf,"%*s%d%*s%d",&nri,&nrj)) != 2)
 170         gmx_fatal(FARGS,"Can not read nri or nrj (nargs=%d)",nargs);
 171       for(ii=0; (ii<nri); ii++) {
 172         if ((nargs = fscanf(in,"%*s%d%*s%d%*s%d%*s%d",
 173                             &iatom,&shift,&gid,&nj)) != 4)
 174           gmx_fatal(FARGS,"Can not read iatom, shift gid or nj (nargs=%d)",nargs);
 175         /* Number shifts from 1 to 27 iso 0 to 26 to distinguish uninitialized
 176          * matrix elements.
 177          */
 178         range_check(iatom,0,natoms);
 179         for(i=0; (i<nj); i++) {
 180           if ((nargs = fscanf(in,"%*s%d",&j)) != 1)
 181             gmx_fatal(FARGS,"Can not read j");
 182           range_check(j,0,natoms);
 183           switch (isolv) {
 184           case enlistATOM_ATOM:
 185             set_mat(fp,mat,iatom,1,j,1,bSymm,shift);
 186             njtot++;
 187             break;
 188           case enlistSPC_ATOM:
 189             set_mat(fp,mat,iatom,3,j,1,bSymm,shift);
 190             njtot+=3;
 191             break;
 192           case enlistSPC_SPC:
 193             set_mat(fp,mat,iatom,3,j,3,bSymm,shift);
 194             njtot+=9;
 195             break;
 196           case enlistTIP4P_ATOM:
 197             set_mat(fp,mat,iatom,4,j,1,bSymm,shift);
 198             njtot+=4;
 199             break;
 200           case enlistTIP4P_TIP4P:
 201             set_mat(fp,mat,iatom,4,j,4,bSymm,shift);
 202             njtot+=16;
 203             break;
 204             gmx_incons("non-existing solvent type");
 205           }
 206         }
 207       }
 208       fprintf(fp,"nri = %d  nrj = %d\n",nri,nrj);
 209     } while (TRUE);
 210     return -1;
 211 }
 212
 213 void dump_nblist(FILE *out,t_commrec *cr,t_forcerec *fr,int nDNL)
 214 {
 215 #if 0
 216   static FILE *fp=NULL;
 217   char buf[STRLEN];
 218   int  n,i;
 219
 220   if (fp == NULL) {
 221     if (PAR(cr)) {
 222       sprintf(buf,"nlist_n%d.txt",cr->nodeid);
 223     } else {
 224       sprintf(buf,"nlist.txt");
 225     }
 226     fp = gmx_fio_fopen(buf,"w");
 227   }
 228   fprintf(fp,"%s\n",header);
 229
 230   for(n=0; (n<fr->nnblists); n++)
 231     for(i=0; (i<eNL_NR); i++)
 232       write_nblist(fp,cr->dd,&fr->nblists[n].nlist_sr[i],nDNL);
 233 #endif
 234   char buf[STRLEN];
 235   int  n,i;
 236
 237   fprintf(out,"%s\n",header);
 238
 239   for(n=0; (n<fr->nnblists); n++)
 240     for(i=0; (i<eNL_NR); i++)
 241       write_nblist(out,cr->dd,&fr->nblists[n].nlist_sr[i],nDNL);
 242
 243 }
 244