src/gromacs/gmxpreprocess/gpp_atomtype.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "gpp_atomtype.h"
  40
  41 #include <string.h>
  42
  43 #include <climits>
  44 #include <cmath>
  45
  46 #include "gromacs/gmxpreprocess/notset.h"
  47 #include "gromacs/gmxpreprocess/topdirs.h"
  48 #include "gromacs/gmxpreprocess/toputil.h"
  49 #include "gromacs/legacyheaders/txtdump.h"
  50 #include "gromacs/legacyheaders/types/ifunc.h"
  51 #include "gromacs/topology/symtab.h"
  52 #include "gromacs/utility/fatalerror.h"
  53 #include "gromacs/utility/smalloc.h"
  54
  55 typedef struct gpp_atomtype {
  56     int              nr;           /* The number of atomtypes           */
  57     t_atom          *atom;         /* Array of atoms                    */
  58     char          ***atomname;     /* Names of the atomtypes            */
  59     t_param         *nb;           /* Nonbonded force default params    */
  60     int             *bondatomtype; /* The bond_atomtype for each atomtype  */
  61     real            *radius;       /* Radius for GBSA stuff                */
  62     real            *vol;          /* Effective volume for GBSA            */
  63     real            *surftens;     /* Surface tension with water, for GBSA */
  64     real            *gb_radius;    /* Radius for Still model               */
  65     real            *S_hct;        /* Overlap factor for HCT model         */
  66     int             *atomnumber;   /* Atomic number, used for QM/MM        */
  67 } t_gpp_atomtype;
  68
  69 int get_atomtype_type(const char *str, gpp_atomtype_t ga)
  70 {
  71     int i;
  72
  73     /* Atom types are always case sensitive */
  74     for (i = 0; (i < ga->nr); i++)
  75     {
  76         if (strcmp(str, *(ga->atomname[i])) == 0)
  77         {
  78             return i;
  79         }
  80     }
  81
  82     return NOTSET;
  83 }
  84
  85 int get_atomtype_ntypes(gpp_atomtype_t ga)
  86 {
  87     return ga->nr;
  88 }
  89
  90 char *get_atomtype_name(int nt, gpp_atomtype_t ga)
  91 {
  92     if ((nt < 0) || (nt >= ga->nr))
  93     {
  94         return NULL;
  95     }
  96
  97     return *(ga->atomname[nt]);
  98 }
  99
 100 real get_atomtype_massA(int nt, gpp_atomtype_t ga)
 101 {
 102     if ((nt < 0) || (nt >= ga->nr))
 103     {
 104         return NOTSET;
 105     }
 106
 107     return ga->atom[nt].m;
 108 }
 109
 110 real get_atomtype_massB(int nt, gpp_atomtype_t ga)
 111 {
 112     if ((nt < 0) || (nt >= ga->nr))
 113     {
 114         return NOTSET;
 115     }
 116
 117     return ga->atom[nt].mB;
 118 }
 119
 120 real get_atomtype_qA(int nt, gpp_atomtype_t ga)
 121 {
 122     if ((nt < 0) || (nt >= ga->nr))
 123     {
 124         return NOTSET;
 125     }
 126
 127     return ga->atom[nt].q;
 128 }
 129
 130 real get_atomtype_qB(int nt, gpp_atomtype_t ga)
 131 {
 132     if ((nt < 0) || (nt >= ga->nr))
 133     {
 134         return NOTSET;
 135     }
 136
 137     return ga->atom[nt].qB;
 138 }
 139
 140 int get_atomtype_ptype(int nt, gpp_atomtype_t ga)
 141 {
 142     if ((nt < 0) || (nt >= ga->nr))
 143     {
 144         return NOTSET;
 145     }
 146
 147     return ga->atom[nt].ptype;
 148 }
 149
 150 int get_atomtype_batype(int nt, gpp_atomtype_t ga)
 151 {
 152     if ((nt < 0) || (nt >= ga->nr))
 153     {
 154         return NOTSET;
 155     }
 156
 157     return ga->bondatomtype[nt];
 158 }
 159
 160 int get_atomtype_atomnumber(int nt, gpp_atomtype_t ga)
 161 {
 162     if ((nt < 0) || (nt >= ga->nr))
 163     {
 164         return NOTSET;
 165     }
 166
 167     return ga->atomnumber[nt];
 168 }
 169
 170 real get_atomtype_radius(int nt, gpp_atomtype_t ga)
 171 {
 172     if ((nt < 0) || (nt >= ga->nr))
 173     {
 174         return NOTSET;
 175     }
 176
 177     return ga->radius[nt];
 178 }
 179
 180 real get_atomtype_vol(int nt, gpp_atomtype_t ga)
 181 {
 182     if ((nt < 0) || (nt >= ga->nr))
 183     {
 184         return NOTSET;
 185     }
 186
 187     return ga->vol[nt];
 188 }
 189
 190 real get_atomtype_surftens(int nt, gpp_atomtype_t ga)
 191 {
 192     if ((nt < 0) || (nt >= ga->nr))
 193     {
 194         return NOTSET;
 195     }
 196
 197     return ga->surftens[nt];
 198 }
 199
 200 real get_atomtype_gb_radius(int nt, gpp_atomtype_t ga)
 201 {
 202     if ((nt < 0) || (nt >= ga->nr))
 203     {
 204         return NOTSET;
 205     }
 206
 207     return ga->gb_radius[nt];
 208 }
 209
 210 real get_atomtype_S_hct(int nt, gpp_atomtype_t ga)
 211 {
 212     if ((nt < 0) || (nt >= ga->nr))
 213     {
 214         return NOTSET;
 215     }
 216
 217     return ga->S_hct[nt];
 218 }
 219
 220 real get_atomtype_nbparam(int nt, int param, gpp_atomtype_t ga)
 221 {
 222     if ((nt < 0) || (nt >= ga->nr))
 223     {
 224         return NOTSET;
 225     }
 226     if ((param < 0) || (param >= MAXFORCEPARAM))
 227     {
 228         return NOTSET;
 229     }
 230     return ga->nb[nt].c[param];
 231 }
 232
 233 gpp_atomtype_t init_atomtype(void)
 234 {
 235     gpp_atomtype_t ga;
 236
 237     snew(ga, 1);
 238
 239     ga->nr           = 0;
 240     ga->atom         = NULL;
 241     ga->atomname     = NULL;
 242     ga->nb           = NULL;
 243     ga->bondatomtype = NULL;
 244     ga->radius       = NULL;
 245     ga->vol          = NULL;
 246     ga->surftens     = NULL;
 247     ga->atomnumber   = NULL;
 248     ga->gb_radius    = NULL;
 249     ga->S_hct        = NULL;
 250
 251     return ga;
 252 }
 253
 254 int
 255 set_atomtype_gbparam(gpp_atomtype_t ga, int i,
 256                      real radius, real vol, real surftens,
 257                      real gb_radius, real S_hct)
 258 {
 259     if ( (i < 0) || (i >= ga->nr))
 260     {
 261         return NOTSET;
 262     }
 263
 264     ga->radius[i]    = radius;
 265     ga->vol[i]       = vol;
 266     ga->surftens[i]  = surftens;
 267     ga->gb_radius[i] = gb_radius;
 268     ga->S_hct[i]     = S_hct;
 269
 270     return i;
 271 }
 272
 273
 274 int set_atomtype(int nt, gpp_atomtype_t ga, t_symtab *tab,
 275                  t_atom *a, const char *name, t_param *nb,
 276                  int bondatomtype,
 277                  real radius, real vol, real surftens, int atomnumber,
 278                  real gb_radius, real S_hct)
 279 {
 280     if ((nt < 0) || (nt >= ga->nr))
 281     {
 282         return NOTSET;
 283     }
 284
 285     ga->atom[nt]         = *a;
 286     ga->atomname[nt]     = put_symtab(tab, name);
 287     ga->nb[nt]           = *nb;
 288     ga->bondatomtype[nt] = bondatomtype;
 289     ga->radius[nt]       = radius;
 290     ga->vol[nt]          = vol;
 291     ga->surftens[nt]     = surftens;
 292     ga->atomnumber[nt]   = atomnumber;
 293     ga->gb_radius[nt]    = gb_radius;
 294     ga->S_hct[nt]        = S_hct;
 295
 296     return nt;
 297 }
 298
 299 int add_atomtype(gpp_atomtype_t ga, t_symtab *tab,
 300                  t_atom *a, const char *name, t_param *nb,
 301                  int bondatomtype,
 302                  real radius, real vol, real surftens, int atomnumber,
 303                  real gb_radius, real S_hct)
 304 {
 305     int i;
 306
 307     for (i = 0; (i < ga->nr); i++)
 308     {
 309         if (strcmp(*ga->atomname[i], name) == 0)
 310         {
 311             if (NULL != debug)
 312             {
 313                 fprintf(debug, "Trying to add atomtype %s again. Skipping it.\n", name);
 314             }
 315             break;
 316         }
 317     }
 318     if (i == ga->nr)
 319     {
 320         ga->nr++;
 321         srenew(ga->atom, ga->nr);
 322         srenew(ga->atomname, ga->nr);
 323         srenew(ga->nb, ga->nr);
 324         srenew(ga->bondatomtype, ga->nr);
 325         srenew(ga->radius, ga->nr);
 326         srenew(ga->vol, ga->nr);
 327         srenew(ga->surftens, ga->nr);
 328         srenew(ga->atomnumber, ga->nr);
 329         srenew(ga->gb_radius, ga->nr);
 330         srenew(ga->S_hct, ga->nr);
 331
 332         return set_atomtype(ga->nr-1, ga, tab, a, name, nb, bondatomtype, radius,
 333                             vol, surftens, atomnumber, gb_radius, S_hct);
 334     }
 335     else
 336     {
 337         return i;
 338     }
 339 }
 340
 341 void print_at (FILE * out, gpp_atomtype_t ga)
 342 {
 343     int         i;
 344     t_atom     *atom = ga->atom;
 345     t_param    *nb   = ga->nb;
 346
 347     fprintf (out, "[ %s ]\n", dir2str(d_atomtypes));
 348     fprintf (out, "; %6s  %8s  %8s  %8s  %12s  %12s\n",
 349              "type", "mass", "charge", "particle", "c6", "c12");
 350     for (i = 0; (i < ga->nr); i++)
 351     {
 352         fprintf(out, "%8s  %8.3f  %8.3f  %8s  %12e  %12e\n",
 353                 *(ga->atomname[i]), atom[i].m, atom[i].q, "A",
 354                 nb[i].c0(), nb[i].c1());
 355     }
 356
 357     fprintf (out, "\n");
 358 }
 359
 360 void done_atomtype(gpp_atomtype_t ga)
 361 {
 362     sfree(ga->atom);
 363     sfree(ga->atomname);
 364     sfree(ga->nb);
 365     sfree(ga->bondatomtype);
 366     sfree(ga->radius);
 367     sfree(ga->vol);
 368     sfree(ga->gb_radius);
 369     sfree(ga->S_hct);
 370     sfree(ga->surftens);
 371     sfree(ga->atomnumber);
 372     ga->nr = 0;
 373     sfree(ga);
 374 }
 375
 376 static int search_atomtypes(gpp_atomtype_t ga, int *n, int typelist[],
 377                             int thistype,
 378                             t_param param[], int ftype)
 379 {
 380     int      i, nn, nrfp, j, k, ntype, tli;
 381     gmx_bool bFound = FALSE;
 382
 383     nn    = *n;
 384     nrfp  = NRFP(ftype);
 385     ntype = get_atomtype_ntypes(ga);
 386
 387     for (i = 0; (i < nn); i++)
 388     {
 389         if (typelist[i] == thistype)
 390         {
 391             /* This type number has already been added */
 392             break;
 393         }
 394
 395         /* Otherwise, check if the parameters are identical to any previously added type */
 396
 397         bFound = TRUE;
 398         for (j = 0; j < ntype && bFound; j++)
 399         {
 400             /* Check nonbonded parameters */
 401             for (k = 0; k < nrfp && bFound; k++)
 402             {
 403                 bFound = (param[ntype*typelist[i]+j].c[k] == param[ntype*thistype+j].c[k]);
 404             }
 405
 406             /* Check radius, volume, surftens */
 407             tli    = typelist[i];
 408             bFound = bFound &&
 409                 (get_atomtype_radius(tli, ga) == get_atomtype_radius(thistype, ga)) &&
 410                 (get_atomtype_vol(tli, ga) == get_atomtype_vol(thistype, ga)) &&
 411                 (get_atomtype_surftens(tli, ga) == get_atomtype_surftens(thistype, ga)) &&
 412                 (get_atomtype_atomnumber(tli, ga) == get_atomtype_atomnumber(thistype, ga)) &&
 413                 (get_atomtype_gb_radius(tli, ga) == get_atomtype_gb_radius(thistype, ga)) &&
 414                 (get_atomtype_S_hct(tli, ga) == get_atomtype_S_hct(thistype, ga));
 415         }
 416         if (bFound)
 417         {
 418             break;
 419         }
 420     }
 421
 422     if (i == nn)
 423     {
 424         if (debug)
 425         {
 426             fprintf(debug, "Renumbering atomtype %d to %d\n", thistype, nn);
 427         }
 428         if (nn == ntype)
 429         {
 430             gmx_fatal(FARGS, "Atomtype horror n = %d, %s, %d", nn, __FILE__, __LINE__);
 431         }
 432         typelist[nn] = thistype;
 433         nn++;
 434     }
 435     *n = nn;
 436
 437     return i;
 438 }
 439
 440 void renum_atype(t_params plist[], gmx_mtop_t *mtop,
 441                  int *wall_atomtype,
 442                  gpp_atomtype_t ga, gmx_bool bVerbose)
 443 {
 444     int         i, j, k, l, molt, mi, mj, nat, nrfp, ftype, ntype;
 445     t_atoms    *atoms;
 446     t_param    *nbsnew;
 447     int        *typelist;
 448     real       *new_radius;
 449     real       *new_vol;
 450     real       *new_surftens;
 451     real       *new_gb_radius;
 452     real       *new_S_hct;
 453     int        *new_atomnumber;
 454     char     ***new_atomname;
 455
 456     ntype = get_atomtype_ntypes(ga);
 457     snew(typelist, ntype);
 458
 459     if (bVerbose)
 460     {
 461         fprintf(stderr, "renumbering atomtypes...\n");
 462     }
 463
 464     /* Since the bonded interactions have been assigned now,
 465      * we want to reduce the number of atom types by merging
 466      * ones with identical nonbonded interactions, in addition
 467      * to removing unused ones.
 468      *
 469      * With Generalized-Born electrostatics, or implicit solvent
 470      * we also check that the atomtype radius, effective_volume
 471      * and surface tension match.
 472      *
 473      * With QM/MM we also check that the atom numbers match
 474      */
 475
 476     /* Get nonbonded interaction type */
 477     if (plist[F_LJ].nr > 0)
 478     {
 479         ftype = F_LJ;
 480     }
 481     else
 482     {
 483         ftype = F_BHAM;
 484     }
 485
 486     /* Renumber atomtypes by first making a list of which ones are actually used.
 487      * We provide the list of nonbonded parameters so search_atomtypes
 488      * can determine if two types should be merged.
 489      */
 490     nat = 0;
 491     for (molt = 0; molt < mtop->nmoltype; molt++)
 492     {
 493         atoms = &mtop->moltype[molt].atoms;
 494         for (i = 0; (i < atoms->nr); i++)
 495         {
 496             atoms->atom[i].type =
 497                 search_atomtypes(ga, &nat, typelist, atoms->atom[i].type,
 498                                  plist[ftype].param, ftype);
 499             atoms->atom[i].typeB =
 500                 search_atomtypes(ga, &nat, typelist, atoms->atom[i].typeB,
 501                                  plist[ftype].param, ftype);
 502         }
 503     }
 504
 505     for (i = 0; i < 2; i++)
 506     {
 507         if (wall_atomtype[i] >= 0)
 508         {
 509             wall_atomtype[i] = search_atomtypes(ga, &nat, typelist, wall_atomtype[i],
 510                                                 plist[ftype].param, ftype);
 511         }
 512     }
 513
 514     snew(new_radius, nat);
 515     snew(new_vol, nat);
 516     snew(new_surftens, nat);
 517     snew(new_atomnumber, nat);
 518     snew(new_gb_radius, nat);
 519     snew(new_S_hct, nat);
 520     snew(new_atomname, nat);
 521
 522     /* We now have a list of unique atomtypes in typelist */
 523
 524     if (debug)
 525     {
 526         pr_ivec(debug, 0, "typelist", typelist, nat, TRUE);
 527     }
 528
 529     /* Renumber nlist */
 530     nbsnew = NULL;
 531     snew(nbsnew, plist[ftype].nr);
 532
 533     nrfp  = NRFP(ftype);
 534
 535     for (i = k = 0; (i < nat); i++)
 536     {
 537         mi = typelist[i];
 538         for (j = 0; (j < nat); j++, k++)
 539         {
 540             mj = typelist[j];
 541             for (l = 0; (l < nrfp); l++)
 542             {
 543                 nbsnew[k].c[l] = plist[ftype].param[ntype*mi+mj].c[l];
 544             }
 545         }
 546         new_radius[i]     = get_atomtype_radius(mi, ga);
 547         new_vol[i]        = get_atomtype_vol(mi, ga);
 548         new_surftens[i]   = get_atomtype_surftens(mi, ga);
 549         new_atomnumber[i] = get_atomtype_atomnumber(mi, ga);
 550         new_gb_radius[i]  = get_atomtype_gb_radius(mi, ga);
 551         new_S_hct[i]      = get_atomtype_S_hct(mi, ga);
 552         new_atomname[i]   = ga->atomname[mi];
 553     }
 554
 555     for (i = 0; (i < nat*nat); i++)
 556     {
 557         for (l = 0; (l < nrfp); l++)
 558         {
 559             plist[ftype].param[i].c[l] = nbsnew[i].c[l];
 560         }
 561     }
 562     plist[ftype].nr     = i;
 563     mtop->ffparams.atnr = nat;
 564
 565     sfree(ga->radius);
 566     sfree(ga->vol);
 567     sfree(ga->surftens);
 568     sfree(ga->atomnumber);
 569     sfree(ga->gb_radius);
 570     sfree(ga->S_hct);
 571     /* Dangling atomname pointers ? */
 572     sfree(ga->atomname);
 573
 574     ga->radius     = new_radius;
 575     ga->vol        = new_vol;
 576     ga->surftens   = new_surftens;
 577     ga->atomnumber = new_atomnumber;
 578     ga->gb_radius  = new_gb_radius;
 579     ga->S_hct      = new_S_hct;
 580     ga->atomname   = new_atomname;
 581
 582     ga->nr = nat;
 583
 584     sfree(nbsnew);
 585     sfree(typelist);
 586 }
 587
 588 void copy_atomtype_atomtypes(gpp_atomtype_t ga, t_atomtypes *atomtypes)
 589 {
 590     int i, ntype;
 591
 592     /* Copy the atomtype data to the topology atomtype list */
 593     ntype         = get_atomtype_ntypes(ga);
 594     atomtypes->nr = ntype;
 595     snew(atomtypes->radius, ntype);
 596     snew(atomtypes->vol, ntype);
 597     snew(atomtypes->surftens, ntype);
 598     snew(atomtypes->atomnumber, ntype);
 599     snew(atomtypes->gb_radius, ntype);
 600     snew(atomtypes->S_hct, ntype);
 601
 602     for (i = 0; i < ntype; i++)
 603     {
 604         atomtypes->radius[i]     = ga->radius[i];
 605         atomtypes->vol[i]        = ga->vol[i];
 606         atomtypes->surftens[i]   = ga->surftens[i];
 607         atomtypes->atomnumber[i] = ga->atomnumber[i];
 608         atomtypes->gb_radius[i]  = ga->gb_radius[i];
 609         atomtypes->S_hct[i]      = ga->S_hct[i];
 610     }
 611 }