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