src/gromacs/fileio/espio.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "espio.h"
  40
  41 #include <cstdio>
  42 #include <cstdlib>
  43 #include <cstring>
  44
  45 #include "gromacs/fileio/gmxfio.h"
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/pbcutil/pbc.h"
  48 #include "gromacs/topology/atoms.h"
  49 #include "gromacs/topology/symtab.h"
  50 #include "gromacs/topology/topology.h"
  51 #include "gromacs/utility/cstringutil.h"
  52 #include "gromacs/utility/fatalerror.h"
  53 #include "gromacs/utility/smalloc.h"
  54
  55 static int get_espresso_word(FILE* fp, char word[])
  56 {
  57     int ret, nc, i;
  58
  59     ret = 0;
  60     nc  = 0;
  61
  62     do
  63     {
  64         i = fgetc(fp);
  65         if (i != EOF)
  66         {
  67             if (i == ' ' || i == '\n' || i == '\t')
  68             {
  69                 if (nc > 0)
  70                 {
  71                     ret = 1;
  72                 }
  73             }
  74             else if (i == '{')
  75             {
  76                 if (nc == 0)
  77                 {
  78                     word[nc++] = '{';
  79                 }
  80                 ret = 2;
  81             }
  82             else if (i == '}')
  83             {
  84                 if (nc == 0)
  85                 {
  86                     word[nc++] = '}';
  87                 }
  88                 ret = 3;
  89             }
  90             else
  91             {
  92                 word[nc++] = static_cast<char>(i);
  93             }
  94         }
  95     } while (i != EOF && ret == 0);
  96
  97     word[nc] = '\0';
  98
  99     return ret;
 100 }
 101
 102 static int check_open_parenthesis(FILE* fp, int r, const char* infile, const char* keyword)
 103 {
 104     int  level_inc;
 105     char word[STRLEN];
 106
 107     level_inc = 0;
 108     if (r == 2)
 109     {
 110         level_inc++;
 111     }
 112     else
 113     {
 114         r = get_espresso_word(fp, word);
 115         if (r == 2)
 116         {
 117             level_inc++;
 118         }
 119         else
 120         {
 121             gmx_fatal(FARGS, "Expected '{' after '%s' in file '%s'", keyword, infile);
 122         }
 123     }
 124
 125     return level_inc;
 126 }
 127
 128 static int check_close_parenthesis(FILE* fp, int r, const char* infile, const char* keyword)
 129 {
 130     int  level_inc;
 131     char word[STRLEN];
 132
 133     level_inc = 0;
 134     if (r == 3)
 135     {
 136         level_inc--;
 137     }
 138     else
 139     {
 140         r = get_espresso_word(fp, word);
 141         if (r == 3)
 142         {
 143             level_inc--;
 144         }
 145         else
 146         {
 147             gmx_fatal(FARGS, "Expected '}' after section '%s' in file '%s'", keyword, infile);
 148         }
 149     }
 150
 151     return level_inc;
 152 }
 153
 154 enum
 155 {
 156     espID,
 157     espPOS,
 158     espTYPE,
 159     espQ,
 160     espV,
 161     espF,
 162     espMOLECULE,
 163     espNR
 164 };
 165 static const char* const esp_prop[espNR] = { "id", "pos", "type", "q", "v", "f", "molecule" };
 166
 167 void gmx_espresso_read_conf(const char* infile, t_symtab* symtab, char** name, t_atoms* atoms, rvec x[], rvec* v, matrix box)
 168 {
 169     FILE*    fp;
 170     char     word[STRLEN], buf[STRLEN];
 171     int      level, r, nprop, p, i, m, molnr;
 172     int      prop[32];
 173     double   d;
 174     gmx_bool bFoundParticles, bFoundProp, bFoundVariable, bMol;
 175
 176     if (name != nullptr)
 177     {
 178         // No title reading implemented for espresso files
 179         *name = gmx_strdup("");
 180     }
 181
 182     clear_mat(box);
 183
 184     atoms->haveMass    = FALSE;
 185     atoms->haveCharge  = FALSE;
 186     atoms->haveType    = FALSE;
 187     atoms->haveBState  = FALSE;
 188     atoms->havePdbInfo = FALSE;
 189
 190     fp = gmx_fio_fopen(infile, "r");
 191
 192     bFoundParticles = FALSE;
 193     bFoundVariable  = FALSE;
 194     bMol            = FALSE;
 195     level           = 0;
 196     while ((r = get_espresso_word(fp, word)))
 197     {
 198         if (level == 1 && std::strcmp(word, "particles") == 0 && !bFoundParticles)
 199         {
 200             bFoundParticles = TRUE;
 201             level += check_open_parenthesis(fp, r, infile, "particles");
 202             nprop = 0;
 203             while (level == 2 && (r = get_espresso_word(fp, word)))
 204             {
 205                 bFoundProp = FALSE;
 206                 for (p = 0; p < espNR; p++)
 207                 {
 208                     if (strcmp(word, esp_prop[p]) == 0)
 209                     {
 210                         bFoundProp    = TRUE;
 211                         prop[nprop++] = p;
 212                         if (p == espQ)
 213                         {
 214                             atoms->haveCharge = TRUE;
 215                         }
 216
 217                         if (debug)
 218                         {
 219                             fprintf(debug, "  prop[%d] = %s\n", nprop - 1, esp_prop[prop[nprop - 1]]);
 220                         }
 221                     }
 222                 }
 223                 if (!bFoundProp && word[0] != '}')
 224                 {
 225                     gmx_fatal(FARGS, "Can not read Espresso files with particle property '%s'", word);
 226                 }
 227                 if (bFoundProp && p == espMOLECULE)
 228                 {
 229                     bMol = TRUE;
 230                 }
 231                 if (r == 3)
 232                 {
 233                     level--;
 234                 }
 235             }
 236
 237             i = 0;
 238             while (level > 0 && (r = get_espresso_word(fp, word)))
 239             {
 240                 if (r == 2)
 241                 {
 242                     level++;
 243                 }
 244                 else if (r == 3)
 245                 {
 246                     level--;
 247                 }
 248                 if (level == 2)
 249                 {
 250                     for (p = 0; p < nprop; p++)
 251                     {
 252                         switch (prop[p])
 253                         {
 254                             case espID:
 255                                 r = get_espresso_word(fp, word);
 256                                 /* Not used */
 257                                 break;
 258                             case espPOS:
 259                                 for (m = 0; m < 3; m++)
 260                                 {
 261                                     r = get_espresso_word(fp, word);
 262                                     sscanf(word, "%lf", &d);
 263                                     x[i][m] = d;
 264                                 }
 265                                 break;
 266                             case espTYPE:
 267                                 r                   = get_espresso_word(fp, word);
 268                                 atoms->atom[i].type = std::strtol(word, nullptr, 10);
 269                                 break;
 270                             case espQ:
 271                                 r = get_espresso_word(fp, word);
 272                                 sscanf(word, "%lf", &d);
 273                                 atoms->atom[i].q = d;
 274                                 break;
 275                             case espV:
 276                                 for (m = 0; m < 3; m++)
 277                                 {
 278                                     r = get_espresso_word(fp, word);
 279                                     sscanf(word, "%lf", &d);
 280                                     v[i][m] = d;
 281                                 }
 282                                 break;
 283                             case espF:
 284                                 for (m = 0; m < 3; m++)
 285                                 {
 286                                     r = get_espresso_word(fp, word);
 287                                     /* not used */
 288                                 }
 289                                 break;
 290                             case espMOLECULE:
 291                                 r     = get_espresso_word(fp, word);
 292                                 molnr = std::strtol(word, nullptr, 10);
 293                                 if (i == 0 || atoms->resinfo[atoms->atom[i - 1].resind].nr != molnr)
 294                                 {
 295                                     atoms->atom[i].resind = (i == 0 ? 0 : atoms->atom[i - 1].resind + 1);
 296                                     atoms->resinfo[atoms->atom[i].resind].nr      = molnr;
 297                                     atoms->resinfo[atoms->atom[i].resind].ic      = ' ';
 298                                     atoms->resinfo[atoms->atom[i].resind].chainid = ' ';
 299                                     atoms->resinfo[atoms->atom[i].resind].chainnum =
 300                                             molnr; /* Not sure if this is right? */
 301                                 }
 302                                 else
 303                                 {
 304                                     atoms->atom[i].resind = atoms->atom[i - 1].resind;
 305                                 }
 306                                 break;
 307                         }
 308                     }
 309                     /* Generate an atom name from the particle type */
 310                     sprintf(buf, "T%hu", atoms->atom[i].type);
 311                     atoms->atomname[i] = put_symtab(symtab, buf);
 312                     if (bMol)
 313                     {
 314                         if (i == 0 || atoms->atom[i].resind != atoms->atom[i - 1].resind)
 315                         {
 316                             atoms->resinfo[atoms->atom[i].resind].name = put_symtab(symtab, "MOL");
 317                         }
 318                     }
 319                     else
 320                     {
 321                         /* Residue number is the atom number */
 322                         atoms->atom[i].resind = i;
 323                         /* Generate an residue name from the particle type */
 324                         if (atoms->atom[i].type < 26)
 325                         {
 326                             sprintf(buf, "T%c", 'A' + atoms->atom[i].type);
 327                         }
 328                         else
 329                         {
 330                             sprintf(buf, "T%c%c", 'A' + atoms->atom[i].type / 26,
 331                                     'A' + atoms->atom[i].type % 26);
 332                         }
 333                         t_atoms_set_resinfo(atoms, i, symtab, buf, i, ' ', 0, ' ');
 334                     }
 335
 336                     if (r == 3)
 337                     {
 338                         level--;
 339                     }
 340                     i++;
 341                 }
 342             }
 343             atoms->nres = atoms->nr;
 344
 345             if (i != atoms->nr)
 346             {
 347                 gmx_fatal(FARGS,
 348                           "Internal inconsistency in Espresso routines, read %d atoms, expected %d "
 349                           "atoms",
 350                           i, atoms->nr);
 351             }
 352         }
 353         else if (level == 1 && std::strcmp(word, "variable") == 0 && !bFoundVariable)
 354         {
 355             bFoundVariable = TRUE;
 356             level += check_open_parenthesis(fp, r, infile, "variable");
 357             while (level == 2 && (r = get_espresso_word(fp, word)))
 358             {
 359                 if (level == 2 && std::strcmp(word, "box_l") == 0)
 360                 {
 361                     for (m = 0; m < 3; m++)
 362                     {
 363                         r = get_espresso_word(fp, word);
 364                         sscanf(word, "%lf", &d);
 365                         box[m][m] = d;
 366                     }
 367                     level += check_close_parenthesis(fp, r, infile, "box_l");
 368                 }
 369             }
 370         }
 371         else if (r == 2)
 372         {
 373             level++;
 374         }
 375         else if (r == 3)
 376         {
 377             level--;
 378         }
 379     }
 380
 381     if (!bFoundParticles)
 382     {
 383         fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n", infile);
 384     }
 385
 386     gmx_fio_fclose(fp);
 387 }
 388
 389 int get_espresso_coordnum(const char* infile)
 390 {
 391     FILE*    fp;
 392     char     word[STRLEN];
 393     int      natoms, level, r;
 394     gmx_bool bFoundParticles;
 395
 396     natoms = 0;
 397
 398     fp = gmx_fio_fopen(infile, "r");
 399
 400     bFoundParticles = FALSE;
 401     level           = 0;
 402     while ((r = get_espresso_word(fp, word)) && !bFoundParticles)
 403     {
 404         if (level == 1 && strcmp(word, "particles") == 0 && !bFoundParticles)
 405         {
 406             bFoundParticles = TRUE;
 407             level += check_open_parenthesis(fp, r, infile, "particles");
 408             while (level > 0 && (r = get_espresso_word(fp, word)))
 409             {
 410                 if (r == 2)
 411                 {
 412                     level++;
 413                     if (level == 2)
 414                     {
 415                         natoms++;
 416                     }
 417                 }
 418                 else if (r == 3)
 419                 {
 420                     level--;
 421                 }
 422             }
 423         }
 424         else if (r == 2)
 425         {
 426             level++;
 427         }
 428         else if (r == 3)
 429         {
 430             level--;
 431         }
 432     }
 433     if (!bFoundParticles)
 434     {
 435         fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n", infile);
 436     }
 437
 438     gmx_fio_fclose(fp);
 439
 440     return natoms;
 441 }
 442
 443 void write_espresso_conf_indexed(FILE*          out,
 444                                  const char*    title,
 445                                  const t_atoms* atoms,
 446                                  int            nx,
 447                                  const int*     index,
 448                                  const rvec*    x,
 449                                  const rvec*    v,
 450                                  const matrix   box)
 451 {
 452     int i, j;
 453
 454     fprintf(out, "# %s\n", title);
 455     if (TRICLINIC(box))
 456     {
 457         gmx_warning("The Espresso format does not support triclinic unit-cells");
 458     }
 459     fprintf(out, "{variable {box_l %f %f %f}}\n", box[0][0], box[1][1], box[2][2]);
 460
 461     fprintf(out, "{particles {id pos type q%s}\n", v ? " v" : "");
 462     for (i = 0; i < nx; i++)
 463     {
 464         if (index)
 465         {
 466             j = index[i];
 467         }
 468         else
 469         {
 470             j = i;
 471         }
 472         fprintf(out, "\t{%d %f %f %f %hu %g", j, x[j][XX], x[j][YY], x[j][ZZ], atoms->atom[j].type,
 473                 atoms->atom[j].q);
 474         if (v)
 475         {
 476             fprintf(out, " %f %f %f", v[j][XX], v[j][YY], v[j][ZZ]);
 477         }
 478         fprintf(out, "}\n");
 479     }
 480     fprintf(out, "}\n");
 481 }