src/kernel/nm2type.c

   1 /*
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   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.3.3
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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  12  * Copyright (c) 2001-2008, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
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  15  * This program is free software; you can redistribute it and/or
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  35 /* This file is completely threadsafe - keep it that way! */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include "assert.h"
  41 #include "maths.h"
  42 #include "macros.h"
  43 #include "copyrite.h"
  44 #include "bondf.h"
  45 #include "string2.h"
  46 #include "smalloc.h"
  47 #include "sysstuff.h"
  48 #include "confio.h"
  49 #include "physics.h"
  50 #include "statutil.h"
  51 #include "vec.h"
  52 #include "random.h"
  53 #include "3dview.h"
  54 #include "txtdump.h"
  55 #include "readinp.h"
  56 #include "names.h"
  57 #include "toppush.h"
  58 #include "pdb2top.h"
  59 #include "gpp_nextnb.h"
  60 #include "gpp_atomtype.h"
  61 #include "g_x2top.h"
  62 #include "fflibutil.h"
  63
  64 static void rd_nm2type_file(const char *fn,int *nnm,t_nm2type **nmp)
  65 {
  66   FILE      *fp;
  67   gmx_bool      bCont;
  68   char      libfilename[128];
  69   char      format[128],f1[128];
  70   char      buf[1024],elem[16],type[16],nbbuf[16],**newbuf;
  71   int       i,nb,nnnm,line=1;
  72   double    qq,mm,*blen;
  73   t_nm2type *nm2t=NULL;
  74
  75   fp = fflib_open(fn);
  76   if (NULL == fp)
  77     gmx_fatal(FARGS,"Can not find %s in library directory",fn);
  78
  79   nnnm = *nnm;
  80   nm2t = *nmp;
  81   do {
  82     /* Read a line from the file */
  83     bCont = (fgets2(buf,1023,fp) != NULL);
  84
  85     if (bCont) {
  86       /* Remove comment */
  87       strip_comment(buf);
  88       if (sscanf(buf,"%s%s%lf%lf%d",elem,type,&qq,&mm,&nb) == 5) {
  89         /* If we can read the first four, there probably is more */
  90         srenew(nm2t,nnnm+1);
  91         snew(nm2t[nnnm].blen,nb);
  92         if (nb > 0) {
  93           snew(newbuf,nb);
  94           strcpy(format,"%*s%*s%*s%*s%*s");
  95           for(i=0; (i<nb); i++) {
  96             /* Complicated format statement */
  97             strcpy(f1,format);
  98             strcat(f1,"%s%lf");
  99             if (sscanf(buf,f1,nbbuf,&(nm2t[nnnm].blen[i])) != 2)
 100               gmx_fatal(FARGS,"Error on line %d of %s",line,libfilename);
 101             newbuf[i] = strdup(nbbuf);
 102             strcat(format,"%*s%*s");
 103           }
 104         }
 105         else
 106           newbuf = NULL;
 107         nm2t[nnnm].elem   = strdup(elem);
 108         nm2t[nnnm].type   = strdup(type);
 109         nm2t[nnnm].q      = qq;
 110         nm2t[nnnm].m      = mm;
 111         nm2t[nnnm].nbonds = nb;
 112         nm2t[nnnm].bond   = newbuf;
 113         nnnm++;
 114       }
 115       line++;
 116     }
 117   } while(bCont);
 118   ffclose(fp);
 119
 120   *nnm = nnnm;
 121   *nmp = nm2t;
 122 }
 123
 124 t_nm2type *rd_nm2type(const char *ffdir,int *nnm)
 125 {
 126   int  nff,f;
 127   char **ff;
 128   t_nm2type *nm;
 129
 130   nff = fflib_search_file_end(ffdir,".n2t",FALSE,&ff);
 131   *nnm = 0;
 132   nm   = NULL;
 133   for(f=0; f<nff; f++) {
 134     rd_nm2type_file(ff[f],nnm,&nm);
 135     sfree(ff[f]);
 136   }
 137   sfree(ff);
 138
 139   return nm;
 140 }
 141
 142 void dump_nm2type(FILE *fp,int nnm,t_nm2type nm2t[])
 143 {
 144   int i,j;
 145
 146   fprintf(fp,"; nm2type database\n");
 147   for(i=0; (i<nnm); i++) {
 148     fprintf(fp,"%-8s %-8s %8.4f %8.4f %-4d",
 149             nm2t[i].elem,nm2t[i].type,
 150             nm2t[i].q,nm2t[i].m,nm2t[i].nbonds);
 151     for(j=0; (j<nm2t[i].nbonds); j++)
 152       fprintf(fp," %-5s %6.4f",nm2t[i].bond[j],nm2t[i].blen[j]);
 153     fprintf(fp,"\n");
 154   }
 155 }
 156
 157 enum { ematchNone, ematchWild, ematchElem, ematchExact, ematchNR };
 158
 159 static int match_str(const char *atom,const char *template_string)
 160 {
 161   if (!atom || !template_string)
 162     return ematchNone;
 163   else if (gmx_strcasecmp(atom,template_string) == 0)
 164     return ematchExact;
 165   else if (atom[0] == template_string[0])
 166     return ematchElem;
 167   else if (strcmp(template_string,"*") == 0)
 168     return ematchWild;
 169   else
 170     return ematchNone;
 171 }
 172
 173 int nm2type(int nnm,t_nm2type nm2t[],t_symtab *tab,t_atoms *atoms,
 174             gpp_atomtype_t atype,int *nbonds,t_params *bonds)
 175 {
 176   int cur = 0;
 177 #define prev (1-cur)
 178   int i,j,k,m,n,nresolved,nb,maxbond,ai,aj,best,im,nqual[2][ematchNR];
 179   int *bbb,*n_mask,*m_mask,**match,**quality;
 180   char *aname_i,*aname_m,*aname_n,*type;
 181   double qq,mm;
 182   t_param *param;
 183
 184   snew(param,1);
 185   maxbond = 0;
 186   for(i=0; (i<atoms->nr); i++)
 187     maxbond = max(maxbond,nbonds[i]);
 188   if (debug)
 189     fprintf(debug,"Max number of bonds per atom is %d\n",maxbond);
 190   snew(bbb,maxbond);
 191   snew(n_mask,maxbond);
 192   snew(m_mask,maxbond);
 193   snew(match,maxbond);
 194   for(i=0; (i<maxbond); i++)
 195     snew(match[i],maxbond);
 196
 197   nresolved = 0;
 198   for(i=0; (i<atoms->nr); i++) {
 199     aname_i = *atoms->atomname[i];
 200     nb = 0;
 201     for(j=0; (j<bonds->nr); j++) {
 202       ai = bonds->param[j].AI;
 203       aj = bonds->param[j].AJ;
 204       if (ai == i)
 205         bbb[nb++] = aj;
 206       else if (aj == i)
 207         bbb[nb++] = ai;
 208     }
 209     if (nb != nbonds[i])
 210       gmx_fatal(FARGS,"Counting number of bonds nb = %d, nbonds[%d] = %d",
 211                 nb,i,nbonds[i]);
 212     if(debug) {
 213       fprintf(debug,"%4s has bonds to",aname_i);
 214       for(j=0; (j<nb); j++)
 215         fprintf(debug," %4s",*atoms->atomname[bbb[j]]);
 216       fprintf(debug,"\n");
 217     }
 218     best = -1;
 219     for(k=0; (k<ematchNR); k++)
 220       nqual[prev][k] = 0;
 221
 222     /* First check for names */
 223     for(k=0; (k<nnm); k++) {
 224       if (nm2t[k].nbonds == nb) {
 225         im = match_str(*atoms->atomname[i],nm2t[k].elem);
 226         if (im > ematchWild) {
 227           for(j=0; (j<ematchNR); j++)
 228             nqual[cur][j] = 0;
 229
 230           /* Fill a matrix with matching quality */
 231           for(m=0; (m<nb); m++) {
 232             aname_m = *atoms->atomname[bbb[m]];
 233             for(n=0; (n<nb); n++) {
 234               aname_n = nm2t[k].bond[n];
 235               match[m][n] = match_str(aname_m,aname_n);
 236             }
 237           }
 238           /* Now pick the best matches */
 239           for(m=0; (m<nb); m++) {
 240             n_mask[m] = 0;
 241             m_mask[m] = 0;
 242           }
 243           for(j=ematchNR-1; (j>0); j--) {
 244             for(m=0; (m<nb); m++) {
 245               for(n=0; (n<nb); n++) {
 246                 if ((n_mask[n] == 0) &&
 247                     (m_mask[m] == 0) &&
 248                     (match[m][n] == j)) {
 249                   n_mask[n] = 1;
 250                   m_mask[m] = 1;
 251                   nqual[cur][j]++;
 252                 }
 253               }
 254             }
 255           }
 256           if ((nqual[cur][ematchExact]+
 257                nqual[cur][ematchElem]+
 258                nqual[cur][ematchWild]) == nb) {
 259             if ((nqual[cur][ematchExact] > nqual[prev][ematchExact]) ||
 260
 261                 ((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
 262                  (nqual[cur][ematchElem] > nqual[prev][ematchElem])) ||
 263
 264                 ((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
 265                  (nqual[cur][ematchElem] == nqual[prev][ematchElem]) &&
 266                  (nqual[cur][ematchWild] > nqual[prev][ematchWild]))) {
 267               best = k;
 268               cur  = prev;
 269             }
 270           }
 271         }
 272       }
 273     }
 274     if (best != -1) {
 275       int  atomnr=0;
 276       real alpha=0;
 277
 278       qq   = nm2t[best].q;
 279       mm   = nm2t[best].m;
 280       type = nm2t[best].type;
 281
 282       if ((k = get_atomtype_type(type,atype)) == NOTSET) {
 283         atoms->atom[i].qB = alpha;
 284         atoms->atom[i].m = atoms->atom[i].mB = mm;
 285         k = add_atomtype(atype,tab,&(atoms->atom[i]),type,param,
 286                          atoms->atom[i].type,0,0,0,atomnr,0,0);
 287       }
 288       atoms->atom[i].type  = k;
 289       atoms->atom[i].typeB = k;
 290       atoms->atom[i].q  = qq;
 291       atoms->atom[i].qB = qq;
 292       atoms->atom[i].m  = mm;
 293       atoms->atom[i].mB = mm;
 294       nresolved++;
 295     }
 296     else {
 297       fprintf(stderr,"Can not find forcefield for atom %s-%d with %d bonds\n",
 298               *atoms->atomname[i],i+1,nb);
 299     }
 300   }
 301   sfree(bbb);
 302   sfree(n_mask);
 303   sfree(m_mask);
 304   sfree(param);
 305
 306   return nresolved;
 307 }
 308