src/gromacs/gmxpreprocess/nm2type.cpp

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  38 /* This file is completely threadsafe - keep it that way! */
  39 #include "gmxpre.h"
  40
  41 #include "nm2type.h"
  42
  43 #include <cstring>
  44
  45 #include <algorithm>
  46 #include <string>
  47 #include <vector>
  48
  49 #include "gromacs/fileio/confio.h"
  50 #include "gromacs/gmxpreprocess/fflibutil.h"
  51 #include "gromacs/gmxpreprocess/gpp_atomtype.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     } while (bCont);
 129     gmx_ffclose(fp);
 130
 131     *nnm = nnnm;
 132     *nmp = nm2t;
 133 }
 134
 135 t_nm2type* rd_nm2type(const char* ffdir, int* nnm)
 136 {
 137     std::vector<std::string> ff = fflib_search_file_end(ffdir, ".n2t", FALSE);
 138     *nnm                        = 0;
 139     t_nm2type* nm               = nullptr;
 140     for (const auto& filename : ff)
 141     {
 142         rd_nm2type_file(filename, nnm, &nm);
 143     }
 144     return nm;
 145 }
 146
 147 void dump_nm2type(FILE* fp, int nnm, t_nm2type nm2t[])
 148 {
 149     int i, j;
 150
 151     fprintf(fp, "; nm2type database\n");
 152     for (i = 0; (i < nnm); i++)
 153     {
 154         fprintf(fp, "%-8s %-8s %8.4f %8.4f %-4d", nm2t[i].elem, nm2t[i].type, nm2t[i].q, nm2t[i].m,
 155                 nm2t[i].nbonds);
 156         for (j = 0; (j < nm2t[i].nbonds); j++)
 157         {
 158             fprintf(fp, " %-5s %6.4f", nm2t[i].bond[j], nm2t[i].blen[j]);
 159         }
 160         fprintf(fp, "\n");
 161     }
 162 }
 163
 164 enum
 165 {
 166     ematchNone,
 167     ematchWild,
 168     ematchElem,
 169     ematchExact,
 170     ematchNR
 171 };
 172
 173 static int match_str(const char* atom, const char* template_string)
 174 {
 175     if (!atom || !template_string)
 176     { // NOLINT bugprone-branch-clone
 177         return ematchNone;
 178     }
 179     else if (gmx_strcasecmp(atom, template_string) == 0)
 180     {
 181         return ematchExact;
 182     }
 183     else if (atom[0] == template_string[0])
 184     {
 185         return ematchElem;
 186     }
 187     else if (strcmp(template_string, "*") == 0)
 188     {
 189         return ematchWild;
 190     }
 191     else
 192     {
 193         return ematchNone;
 194     }
 195 }
 196
 197 int nm2type(int                     nnm,
 198             t_nm2type               nm2t[],
 199             t_symtab*               tab,
 200             t_atoms*                atoms,
 201             PreprocessingAtomTypes* atype,
 202             int*                    nbonds,
 203             InteractionsOfType*     bonds)
 204 {
 205     int cur = 0;
 206 #define prev (1 - cur)
 207     int   nresolved, nb, maxbond, nqual[2][ematchNR];
 208     int * bbb, *n_mask, *m_mask, **match;
 209     char *aname_i, *aname_n;
 210
 211     maxbond = 0;
 212     for (int 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 (int i = 0; (i < maxbond); i++)
 225     {
 226         snew(match[i], maxbond);
 227     }
 228
 229     nresolved = 0;
 230     for (int i = 0; (i < atoms->nr); i++)
 231     {
 232         aname_i = *atoms->atomname[i];
 233         nb      = 0;
 234         for (const auto& bond : bonds->interactionTypes)
 235         {
 236             int ai = bond.ai();
 237             int aj = bond.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", nb, i, nbonds[i]);
 250         }
 251         if (debug)
 252         {
 253             fprintf(debug, "%4s has bonds to", aname_i);
 254             for (int j = 0; (j < nb); j++)
 255             {
 256                 fprintf(debug, " %4s", *atoms->atomname[bbb[j]]);
 257             }
 258             fprintf(debug, "\n");
 259         }
 260         int best = -1;
 261         for (int k = 0; (k < ematchNR); k++)
 262         {
 263             nqual[prev][k] = 0;
 264         }
 265
 266         /* First check for names */
 267         for (int k = 0; (k < nnm); k++)
 268         {
 269             if (nm2t[k].nbonds == nb)
 270             {
 271                 int im = match_str(*atoms->atomname[i], nm2t[k].elem);
 272                 if (im > ematchWild)
 273                 {
 274                     for (int j = 0; (j < ematchNR); j++)
 275                     {
 276                         nqual[cur][j] = 0;
 277                     }
 278
 279                     /* Fill a matrix with matching quality */
 280                     for (int m = 0; (m < nb); m++)
 281                     {
 282                         const char* aname_m = *atoms->atomname[bbb[m]];
 283                         for (int 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 (int m = 0; (m < nb); m++)
 291                     {
 292                         n_mask[m] = 0;
 293                         m_mask[m] = 0;
 294                     }
 295                     for (int j = ematchNR - 1; (j > 0); j--)
 296                     {
 297                         for (int m = 0; (m < nb); m++)
 298                         {
 299                             for (int n = 0; (n < nb); n++)
 300                             {
 301                                 if ((n_mask[n] == 0) && (m_mask[m] == 0) && (match[m][n] == j))
 302                                 {
 303                                     n_mask[n] = 1;
 304                                     m_mask[m] = 1;
 305                                     nqual[cur][j]++;
 306                                 }
 307                             }
 308                         }
 309                     }
 310                     if ((nqual[cur][ematchExact] + nqual[cur][ematchElem] + nqual[cur][ematchWild]) == nb)
 311                     {
 312                         if ((nqual[cur][ematchExact] > nqual[prev][ematchExact]) ||
 313
 314                             ((nqual[cur][ematchExact] == nqual[prev][ematchExact])
 315                              && (nqual[cur][ematchElem] > nqual[prev][ematchElem]))
 316                             ||
 317
 318                             ((nqual[cur][ematchExact] == nqual[prev][ematchExact])
 319                              && (nqual[cur][ematchElem] == nqual[prev][ematchElem])
 320                              && (nqual[cur][ematchWild] > nqual[prev][ematchWild])))
 321                         {
 322                             best = k;
 323                             cur  = prev;
 324                         }
 325                     }
 326                 }
 327             }
 328         }
 329         if (best != -1)
 330         {
 331             int  atomnr = 0;
 332             real alpha  = 0;
 333
 334             double      qq   = nm2t[best].q;
 335             double      mm   = nm2t[best].m;
 336             const char* type = nm2t[best].type;
 337
 338             int k;
 339             if ((k = atype->atomTypeFromName(type)) == NOTSET)
 340             {
 341                 atoms->atom[i].qB = alpha;
 342                 atoms->atom[i].m = atoms->atom[i].mB = mm;
 343                 k = atype->addType(tab, atoms->atom[i], type, InteractionOfType({}, {}),
 344                                    atoms->atom[i].type, atomnr);
 345             }
 346             atoms->atom[i].type  = k;
 347             atoms->atom[i].typeB = k;
 348             atoms->atom[i].q     = qq;
 349             atoms->atom[i].qB    = qq;
 350             atoms->atom[i].m     = mm;
 351             atoms->atom[i].mB    = mm;
 352             nresolved++;
 353         }
 354         else
 355         {
 356             fprintf(stderr, "Can not find forcefield for atom %s-%d with %d bonds\n",
 357                     *atoms->atomname[i], i + 1, nb);
 358         }
 359     }
 360     sfree(bbb);
 361     sfree(n_mask);
 362     sfree(m_mask);
 363
 364     return nresolved;
 365 }