src/gromacs/gmxpreprocess/nm2type.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "nm2type.h"
  41
  42 #include <string.h>
  43
  44 #include <algorithm>
  45
  46 #include "gromacs/fileio/confio.h"
  47 #include "gromacs/gmxpreprocess/fflibutil.h"
  48 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
  49 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
  50 #include "gromacs/gmxpreprocess/notset.h"
  51 #include "gromacs/gmxpreprocess/pdb2top.h"
  52 #include "gromacs/gmxpreprocess/toppush.h"
  53 #include "gromacs/math/utilities.h"
  54 #include "gromacs/math/vec.h"
  55 #include "gromacs/mdtypes/md_enums.h"
  56 #include "gromacs/utility/cstringutil.h"
  57 #include "gromacs/utility/fatalerror.h"
  58 #include "gromacs/utility/futil.h"
  59 #include "gromacs/utility/smalloc.h"
  60
  61 static void rd_nm2type_file(const char *fn, int *nnm, t_nm2type **nmp)
  62 {
  63     FILE         *fp;
  64     gmx_bool      bCont;
  65     char          libfilename[128];
  66     char          format[128], f1[128];
  67     char          buf[1024], elem[16], type[16], nbbuf[16], **newbuf;
  68     int           i, nb, nnnm, line = 1;
  69     double        qq, mm;
  70     t_nm2type    *nm2t = nullptr;
  71
  72     fp = fflib_open(fn);
  73     if (nullptr == fp)
  74     {
  75         gmx_fatal(FARGS, "Can not find %s in library directory", fn);
  76     }
  77
  78     nnnm = *nnm;
  79     nm2t = *nmp;
  80     do
  81     {
  82         /* Read a line from the file */
  83         bCont = (fgets2(buf, 1023, fp) != nullptr);
  84
  85         if (bCont)
  86         {
  87             /* Remove comment */
  88             strip_comment(buf);
  89             if (sscanf(buf, "%s%s%lf%lf%d", elem, type, &qq, &mm, &nb) == 5)
  90             {
  91                 /* If we can read the first four, there probably is more */
  92                 srenew(nm2t, nnnm+1);
  93                 snew(nm2t[nnnm].blen, nb);
  94                 if (nb > 0)
  95                 {
  96                     snew(newbuf, nb);
  97                     strcpy(format, "%*s%*s%*s%*s%*s");
  98                     for (i = 0; (i < nb); i++)
  99                     {
 100                         /* Complicated format statement */
 101                         strcpy(f1, format);
 102                         strcat(f1, "%s%lf");
 103                         if (sscanf(buf, f1, nbbuf, &(nm2t[nnnm].blen[i])) != 2)
 104                         {
 105                             gmx_fatal(FARGS, "Error on line %d of %s", line, libfilename);
 106                         }
 107                         newbuf[i] = gmx_strdup(nbbuf);
 108                         strcat(format, "%*s%*s");
 109                     }
 110                 }
 111                 else
 112                 {
 113                     newbuf = nullptr;
 114                 }
 115                 nm2t[nnnm].elem   = gmx_strdup(elem);
 116                 nm2t[nnnm].type   = gmx_strdup(type);
 117                 nm2t[nnnm].q      = qq;
 118                 nm2t[nnnm].m      = mm;
 119                 nm2t[nnnm].nbonds = nb;
 120                 nm2t[nnnm].bond   = newbuf;
 121                 nnnm++;
 122             }
 123             line++;
 124         }
 125     }
 126     while (bCont);
 127     gmx_ffclose(fp);
 128
 129     *nnm = nnnm;
 130     *nmp = nm2t;
 131 }
 132
 133 t_nm2type *rd_nm2type(const char *ffdir, int *nnm)
 134 {
 135     int        nff, f;
 136     char     **ff;
 137     t_nm2type *nm;
 138
 139     nff  = fflib_search_file_end(ffdir, ".n2t", FALSE, &ff);
 140     *nnm = 0;
 141     nm   = nullptr;
 142     for (f = 0; f < nff; f++)
 143     {
 144         rd_nm2type_file(ff[f], nnm, &nm);
 145         sfree(ff[f]);
 146     }
 147     sfree(ff);
 148
 149     return nm;
 150 }
 151
 152 void dump_nm2type(FILE *fp, int nnm, t_nm2type nm2t[])
 153 {
 154     int i, j;
 155
 156     fprintf(fp, "; nm2type database\n");
 157     for (i = 0; (i < nnm); i++)
 158     {
 159         fprintf(fp, "%-8s %-8s %8.4f %8.4f %-4d",
 160                 nm2t[i].elem, nm2t[i].type,
 161                 nm2t[i].q, nm2t[i].m, nm2t[i].nbonds);
 162         for (j = 0; (j < nm2t[i].nbonds); j++)
 163         {
 164             fprintf(fp, " %-5s %6.4f", nm2t[i].bond[j], nm2t[i].blen[j]);
 165         }
 166         fprintf(fp, "\n");
 167     }
 168 }
 169
 170 enum {
 171     ematchNone, ematchWild, ematchElem, ematchExact, ematchNR
 172 };
 173
 174 static int match_str(const char *atom, const char *template_string)
 175 {
 176     if (!atom || !template_string)
 177     {
 178         return ematchNone;
 179     }
 180     else if (gmx_strcasecmp(atom, template_string) == 0)
 181     {
 182         return ematchExact;
 183     }
 184     else if (atom[0] == template_string[0])
 185     {
 186         return ematchElem;
 187     }
 188     else if (strcmp(template_string, "*") == 0)
 189     {
 190         return ematchWild;
 191     }
 192     else
 193     {
 194         return ematchNone;
 195     }
 196 }
 197
 198 int nm2type(int nnm, t_nm2type nm2t[], struct t_symtab *tab, t_atoms *atoms,
 199             gpp_atomtype_t atype, int *nbonds, t_params *bonds)
 200 {
 201     int      cur = 0;
 202 #define prev (1-cur)
 203     int      i, j, k, m, n, nresolved, nb, maxbond, ai, aj, best, im, nqual[2][ematchNR];
 204     int     *bbb, *n_mask, *m_mask, **match;
 205     char    *aname_i, *aname_m, *aname_n, *type;
 206     double   qq, mm;
 207     t_param *param;
 208
 209     snew(param, 1);
 210     maxbond = 0;
 211     for (i = 0; (i < atoms->nr); i++)
 212     {
 213         maxbond = std::max(maxbond, nbonds[i]);
 214     }
 215     if (debug)
 216     {
 217         fprintf(debug, "Max number of bonds per atom is %d\n", maxbond);
 218     }
 219     snew(bbb, maxbond);
 220     snew(n_mask, maxbond);
 221     snew(m_mask, maxbond);
 222     snew(match, maxbond);
 223     for (i = 0; (i < maxbond); i++)
 224     {
 225         snew(match[i], maxbond);
 226     }
 227
 228     nresolved = 0;
 229     for (i = 0; (i < atoms->nr); i++)
 230     {
 231         aname_i = *atoms->atomname[i];
 232         nb      = 0;
 233         for (j = 0; (j < bonds->nr); j++)
 234         {
 235             ai = bonds->param[j].ai();
 236             aj = bonds->param[j].aj();
 237             if (ai == i)
 238             {
 239                 bbb[nb++] = aj;
 240             }
 241             else if (aj == i)
 242             {
 243                 bbb[nb++] = ai;
 244             }
 245         }
 246         if (nb != nbonds[i])
 247         {
 248             gmx_fatal(FARGS, "Counting number of bonds nb = %d, nbonds[%d] = %d",
 249                       nb, i, nbonds[i]);
 250         }
 251         if (debug)
 252         {
 253             fprintf(debug, "%4s has bonds to", aname_i);
 254             for (j = 0; (j < nb); j++)
 255             {
 256                 fprintf(debug, " %4s", *atoms->atomname[bbb[j]]);
 257             }
 258             fprintf(debug, "\n");
 259         }
 260         best = -1;
 261         for (k = 0; (k < ematchNR); k++)
 262         {
 263             nqual[prev][k] = 0;
 264         }
 265
 266         /* First check for names */
 267         for (k = 0; (k < nnm); k++)
 268         {
 269             if (nm2t[k].nbonds == nb)
 270             {
 271                 im = match_str(*atoms->atomname[i], nm2t[k].elem);
 272                 if (im > ematchWild)
 273                 {
 274                     for (j = 0; (j < ematchNR); j++)
 275                     {
 276                         nqual[cur][j] = 0;
 277                     }
 278
 279                     /* Fill a matrix with matching quality */
 280                     for (m = 0; (m < nb); m++)
 281                     {
 282                         aname_m = *atoms->atomname[bbb[m]];
 283                         for (n = 0; (n < nb); n++)
 284                         {
 285                             aname_n     = nm2t[k].bond[n];
 286                             match[m][n] = match_str(aname_m, aname_n);
 287                         }
 288                     }
 289                     /* Now pick the best matches */
 290                     for (m = 0; (m < nb); m++)
 291                     {
 292                         n_mask[m] = 0;
 293                         m_mask[m] = 0;
 294                     }
 295                     for (j = ematchNR-1; (j > 0); j--)
 296                     {
 297                         for (m = 0; (m < nb); m++)
 298                         {
 299                             for (n = 0; (n < nb); n++)
 300                             {
 301                                 if ((n_mask[n] == 0) &&
 302                                     (m_mask[m] == 0) &&
 303                                     (match[m][n] == j))
 304                                 {
 305                                     n_mask[n] = 1;
 306                                     m_mask[m] = 1;
 307                                     nqual[cur][j]++;
 308                                 }
 309                             }
 310                         }
 311                     }
 312                     if ((nqual[cur][ematchExact]+
 313                          nqual[cur][ematchElem]+
 314                          nqual[cur][ematchWild]) == nb)
 315                     {
 316                         if ((nqual[cur][ematchExact] > nqual[prev][ematchExact]) ||
 317
 318                             ((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
 319                              (nqual[cur][ematchElem] > nqual[prev][ematchElem])) ||
 320
 321                             ((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
 322                              (nqual[cur][ematchElem] == nqual[prev][ematchElem]) &&
 323                              (nqual[cur][ematchWild] > nqual[prev][ematchWild])))
 324                         {
 325                             best = k;
 326                             cur  = prev;
 327                         }
 328                     }
 329                 }
 330             }
 331         }
 332         if (best != -1)
 333         {
 334             int  atomnr = 0;
 335             real alpha  = 0;
 336
 337             qq   = nm2t[best].q;
 338             mm   = nm2t[best].m;
 339             type = nm2t[best].type;
 340
 341             if ((k = get_atomtype_type(type, atype)) == NOTSET)
 342             {
 343                 atoms->atom[i].qB = alpha;
 344                 atoms->atom[i].m  = atoms->atom[i].mB = mm;
 345                 k                 = add_atomtype(atype, tab, &(atoms->atom[i]), type, param,
 346                                                  atoms->atom[i].type, 0, 0, 0, atomnr, 0, 0);
 347             }
 348             atoms->atom[i].type  = k;
 349             atoms->atom[i].typeB = k;
 350             atoms->atom[i].q     = qq;
 351             atoms->atom[i].qB    = qq;
 352             atoms->atom[i].m     = mm;
 353             atoms->atom[i].mB    = mm;
 354             nresolved++;
 355         }
 356         else
 357         {
 358             fprintf(stderr, "Can not find forcefield for atom %s-%d with %d bonds\n",
 359                     *atoms->atomname[i], i+1, nb);
 360         }
 361     }
 362     sfree(bbb);
 363     sfree(n_mask);
 364     sfree(m_mask);
 365     sfree(param);
 366
 367     return nresolved;
 368 }