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/gmxlib/readinp.h"
  48 #include "gromacs/gmxpreprocess/fflibutil.h"
  49 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
  50 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
  51 #include "gromacs/gmxpreprocess/notset.h"
  52 #include "gromacs/gmxpreprocess/pdb2top.h"
  53 #include "gromacs/gmxpreprocess/toppush.h"
  54 #include "gromacs/math/utilities.h"
  55 #include "gromacs/math/vec.h"
  56 #include "gromacs/mdtypes/md_enums.h"
  57 #include "gromacs/utility/cstringutil.h"
  58 #include "gromacs/utility/fatalerror.h"
  59 #include "gromacs/utility/futil.h"
  60 #include "gromacs/utility/smalloc.h"
  61
  62 static void rd_nm2type_file(const char *fn, int *nnm, t_nm2type **nmp)
  63 {
  64     FILE         *fp;
  65     gmx_bool      bCont;
  66     char          libfilename[128];
  67     char          format[128], f1[128];
  68     char          buf[1024], elem[16], type[16], nbbuf[16], **newbuf;
  69     int           i, nb, nnnm, line = 1;
  70     double        qq, mm;
  71     t_nm2type    *nm2t = NULL;
  72
  73     fp = fflib_open(fn);
  74     if (NULL == fp)
  75     {
  76         gmx_fatal(FARGS, "Can not find %s in library directory", fn);
  77     }
  78
  79     nnnm = *nnm;
  80     nm2t = *nmp;
  81     do
  82     {
  83         /* Read a line from the file */
  84         bCont = (fgets2(buf, 1023, fp) != NULL);
  85
  86         if (bCont)
  87         {
  88             /* Remove comment */
  89             strip_comment(buf);
  90             if (sscanf(buf, "%s%s%lf%lf%d", elem, type, &qq, &mm, &nb) == 5)
  91             {
  92                 /* If we can read the first four, there probably is more */
  93                 srenew(nm2t, nnnm+1);
  94                 snew(nm2t[nnnm].blen, nb);
  95                 if (nb > 0)
  96                 {
  97                     snew(newbuf, nb);
  98                     strcpy(format, "%*s%*s%*s%*s%*s");
  99                     for (i = 0; (i < nb); i++)
 100                     {
 101                         /* Complicated format statement */
 102                         strcpy(f1, format);
 103                         strcat(f1, "%s%lf");
 104                         if (sscanf(buf, f1, nbbuf, &(nm2t[nnnm].blen[i])) != 2)
 105                         {
 106                             gmx_fatal(FARGS, "Error on line %d of %s", line, libfilename);
 107                         }
 108                         newbuf[i] = gmx_strdup(nbbuf);
 109                         strcat(format, "%*s%*s");
 110                     }
 111                 }
 112                 else
 113                 {
 114                     newbuf = NULL;
 115                 }
 116                 nm2t[nnnm].elem   = gmx_strdup(elem);
 117                 nm2t[nnnm].type   = gmx_strdup(type);
 118                 nm2t[nnnm].q      = qq;
 119                 nm2t[nnnm].m      = mm;
 120                 nm2t[nnnm].nbonds = nb;
 121                 nm2t[nnnm].bond   = newbuf;
 122                 nnnm++;
 123             }
 124             line++;
 125         }
 126     }
 127     while (bCont);
 128     gmx_ffclose(fp);
 129
 130     *nnm = nnnm;
 131     *nmp = nm2t;
 132 }
 133
 134 t_nm2type *rd_nm2type(const char *ffdir, int *nnm)
 135 {
 136     int        nff, f;
 137     char     **ff;
 138     t_nm2type *nm;
 139
 140     nff  = fflib_search_file_end(ffdir, ".n2t", FALSE, &ff);
 141     *nnm = 0;
 142     nm   = NULL;
 143     for (f = 0; f < nff; f++)
 144     {
 145         rd_nm2type_file(ff[f], nnm, &nm);
 146         sfree(ff[f]);
 147     }
 148     sfree(ff);
 149
 150     return nm;
 151 }
 152
 153 void dump_nm2type(FILE *fp, int nnm, t_nm2type nm2t[])
 154 {
 155     int i, j;
 156
 157     fprintf(fp, "; nm2type database\n");
 158     for (i = 0; (i < nnm); i++)
 159     {
 160         fprintf(fp, "%-8s %-8s %8.4f %8.4f %-4d",
 161                 nm2t[i].elem, nm2t[i].type,
 162                 nm2t[i].q, nm2t[i].m, nm2t[i].nbonds);
 163         for (j = 0; (j < nm2t[i].nbonds); j++)
 164         {
 165             fprintf(fp, " %-5s %6.4f", nm2t[i].bond[j], nm2t[i].blen[j]);
 166         }
 167         fprintf(fp, "\n");
 168     }
 169 }
 170
 171 enum {
 172     ematchNone, ematchWild, ematchElem, ematchExact, ematchNR
 173 };
 174
 175 static int match_str(const char *atom, const char *template_string)
 176 {
 177     if (!atom || !template_string)
 178     {
 179         return ematchNone;
 180     }
 181     else if (gmx_strcasecmp(atom, template_string) == 0)
 182     {
 183         return ematchExact;
 184     }
 185     else if (atom[0] == template_string[0])
 186     {
 187         return ematchElem;
 188     }
 189     else if (strcmp(template_string, "*") == 0)
 190     {
 191         return ematchWild;
 192     }
 193     else
 194     {
 195         return ematchNone;
 196     }
 197 }
 198
 199 int nm2type(int nnm, t_nm2type nm2t[], struct t_symtab *tab, t_atoms *atoms,
 200             gpp_atomtype_t atype, int *nbonds, t_params *bonds)
 201 {
 202     int      cur = 0;
 203 #define prev (1-cur)
 204     int      i, j, k, m, n, nresolved, nb, maxbond, ai, aj, best, im, nqual[2][ematchNR];
 205     int     *bbb, *n_mask, *m_mask, **match;
 206     char    *aname_i, *aname_m, *aname_n, *type;
 207     double   qq, mm;
 208     t_param *param;
 209
 210     snew(param, 1);
 211     maxbond = 0;
 212     for (i = 0; (i < atoms->nr); i++)
 213     {
 214         maxbond = std::max(maxbond, nbonds[i]);
 215     }
 216     if (debug)
 217     {
 218         fprintf(debug, "Max number of bonds per atom is %d\n", maxbond);
 219     }
 220     snew(bbb, maxbond);
 221     snew(n_mask, maxbond);
 222     snew(m_mask, maxbond);
 223     snew(match, maxbond);
 224     for (i = 0; (i < maxbond); i++)
 225     {
 226         snew(match[i], maxbond);
 227     }
 228
 229     nresolved = 0;
 230     for (i = 0; (i < atoms->nr); i++)
 231     {
 232         aname_i = *atoms->atomname[i];
 233         nb      = 0;
 234         for (j = 0; (j < bonds->nr); j++)
 235         {
 236             ai = bonds->param[j].ai();
 237             aj = bonds->param[j].aj();
 238             if (ai == i)
 239             {
 240                 bbb[nb++] = aj;
 241             }
 242             else if (aj == i)
 243             {
 244                 bbb[nb++] = ai;
 245             }
 246         }
 247         if (nb != nbonds[i])
 248         {
 249             gmx_fatal(FARGS, "Counting number of bonds nb = %d, nbonds[%d] = %d",
 250                       nb, i, nbonds[i]);
 251         }
 252         if (debug)
 253         {
 254             fprintf(debug, "%4s has bonds to", aname_i);
 255             for (j = 0; (j < nb); j++)
 256             {
 257                 fprintf(debug, " %4s", *atoms->atomname[bbb[j]]);
 258             }
 259             fprintf(debug, "\n");
 260         }
 261         best = -1;
 262         for (k = 0; (k < ematchNR); k++)
 263         {
 264             nqual[prev][k] = 0;
 265         }
 266
 267         /* First check for names */
 268         for (k = 0; (k < nnm); k++)
 269         {
 270             if (nm2t[k].nbonds == nb)
 271             {
 272                 im = match_str(*atoms->atomname[i], nm2t[k].elem);
 273                 if (im > ematchWild)
 274                 {
 275                     for (j = 0; (j < ematchNR); j++)
 276                     {
 277                         nqual[cur][j] = 0;
 278                     }
 279
 280                     /* Fill a matrix with matching quality */
 281                     for (m = 0; (m < nb); m++)
 282                     {
 283                         aname_m = *atoms->atomname[bbb[m]];
 284                         for (n = 0; (n < nb); n++)
 285                         {
 286                             aname_n     = nm2t[k].bond[n];
 287                             match[m][n] = match_str(aname_m, aname_n);
 288                         }
 289                     }
 290                     /* Now pick the best matches */
 291                     for (m = 0; (m < nb); m++)
 292                     {
 293                         n_mask[m] = 0;
 294                         m_mask[m] = 0;
 295                     }
 296                     for (j = ematchNR-1; (j > 0); j--)
 297                     {
 298                         for (m = 0; (m < nb); m++)
 299                         {
 300                             for (n = 0; (n < nb); n++)
 301                             {
 302                                 if ((n_mask[n] == 0) &&
 303                                     (m_mask[m] == 0) &&
 304                                     (match[m][n] == j))
 305                                 {
 306                                     n_mask[n] = 1;
 307                                     m_mask[m] = 1;
 308                                     nqual[cur][j]++;
 309                                 }
 310                             }
 311                         }
 312                     }
 313                     if ((nqual[cur][ematchExact]+
 314                          nqual[cur][ematchElem]+
 315                          nqual[cur][ematchWild]) == nb)
 316                     {
 317                         if ((nqual[cur][ematchExact] > nqual[prev][ematchExact]) ||
 318
 319                             ((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
 320                              (nqual[cur][ematchElem] > nqual[prev][ematchElem])) ||
 321
 322                             ((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
 323                              (nqual[cur][ematchElem] == nqual[prev][ematchElem]) &&
 324                              (nqual[cur][ematchWild] > nqual[prev][ematchWild])))
 325                         {
 326                             best = k;
 327                             cur  = prev;
 328                         }
 329                     }
 330                 }
 331             }
 332         }
 333         if (best != -1)
 334         {
 335             int  atomnr = 0;
 336             real alpha  = 0;
 337
 338             qq   = nm2t[best].q;
 339             mm   = nm2t[best].m;
 340             type = nm2t[best].type;
 341
 342             if ((k = get_atomtype_type(type, atype)) == NOTSET)
 343             {
 344                 atoms->atom[i].qB = alpha;
 345                 atoms->atom[i].m  = atoms->atom[i].mB = mm;
 346                 k                 = add_atomtype(atype, tab, &(atoms->atom[i]), type, param,
 347                                                  atoms->atom[i].type, 0, 0, 0, atomnr, 0, 0);
 348             }
 349             atoms->atom[i].type  = k;
 350             atoms->atom[i].typeB = k;
 351             atoms->atom[i].q     = qq;
 352             atoms->atom[i].qB    = qq;
 353             atoms->atom[i].m     = mm;
 354             atoms->atom[i].mB    = mm;
 355             nresolved++;
 356         }
 357         else
 358         {
 359             fprintf(stderr, "Can not find forcefield for atom %s-%d with %d bonds\n",
 360                     *atoms->atomname[i], i+1, nb);
 361         }
 362     }
 363     sfree(bbb);
 364     sfree(n_mask);
 365     sfree(m_mask);
 366     sfree(param);
 367
 368     return nresolved;
 369 }