src/gmxlib/mtop_util.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   3  *
   4  * This file is part of Gromacs        Copyright (c) 1991-2008
   5  * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
   6  *
   7  * This program is free software; you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation; either version 2
  10  * of the License, or (at your option) any later version.
  11  *
  12  * To help us fund GROMACS development, we humbly ask that you cite
  13  * the research papers on the package. Check out http://www.gromacs.org
  14  *
  15  * And Hey:
  16  * Gnomes, ROck Monsters And Chili Sauce
  17  */
  18
  19 #ifdef HAVE_CONFIG_H
  20 #include <config.h>
  21 #endif
  22
  23 #include <string.h>
  24 #include "smalloc.h"
  25 #include "typedefs.h"
  26 #include "mtop_util.h"
  27 #include "topsort.h"
  28 #include "symtab.h"
  29 #include "gmx_fatal.h"
  30
  31 static int gmx_mtop_maxresnr(const gmx_mtop_t *mtop,int maxres_renum)
  32 {
  33     int maxresnr,mt,r;
  34     const t_atoms *atoms;
  35
  36     maxresnr = 0;
  37
  38     for(mt=0; mt<mtop->nmoltype; mt++)
  39     {
  40         atoms = &mtop->moltype[mt].atoms;
  41         if (atoms->nres > maxres_renum)
  42         {
  43             for(r=0; r<atoms->nres; r++)
  44             {
  45                 if (atoms->resinfo[r].nr > maxresnr)
  46                 {
  47                     maxresnr = atoms->resinfo[r].nr;
  48                 }
  49             }
  50         }
  51     }
  52
  53     return maxresnr;
  54 }
  55
  56 void gmx_mtop_finalize(gmx_mtop_t *mtop)
  57 {
  58     char *env;
  59
  60     mtop->maxres_renum = 1;
  61
  62     env = getenv("GMX_MAXRESRENUM");
  63     if (env != NULL)
  64     {
  65         sscanf(env,"%d",&mtop->maxres_renum);
  66     }
  67     if (mtop->maxres_renum == -1)
  68     {
  69         /* -1 signals renumber residues in all molecules */
  70         mtop->maxres_renum = INT_MAX;
  71     }
  72
  73     mtop->maxresnr = gmx_mtop_maxresnr(mtop,mtop->maxres_renum);
  74 }
  75
  76 int ncg_mtop(const gmx_mtop_t *mtop)
  77 {
  78     int ncg;
  79     int mb;
  80
  81     ncg = 0;
  82     for(mb=0; mb<mtop->nmolblock; mb++)
  83     {
  84         ncg +=
  85             mtop->molblock[mb].nmol*
  86             mtop->moltype[mtop->molblock[mb].type].cgs.nr;
  87     }
  88
  89     return ncg;
  90 }
  91
  92 void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop)
  93 {
  94     int mt;
  95     t_block *cgs;
  96     int i;
  97
  98     for(mt=0; mt<mtop->nmoltype; mt++)
  99     {
 100         cgs = &mtop->moltype[mt].cgs;
 101         if (cgs->nr < mtop->moltype[mt].atoms.nr)
 102         {
 103             cgs->nr = mtop->moltype[mt].atoms.nr;
 104             srenew(cgs->index,cgs->nr+1);
 105             for(i=0; i<cgs->nr+1; i++)
 106             {
 107                 cgs->index[i] = i;
 108             }
 109         }
 110     }
 111 }
 112
 113
 114 typedef struct
 115 {
 116     int a_start;
 117     int a_end;
 118     int na_mol;
 119 } mb_at_t;
 120
 121 typedef struct gmx_mtop_atomlookup
 122 {
 123     const gmx_mtop_t *mtop;
 124     int     nmb;
 125     int     mb_start;
 126     mb_at_t *mba;
 127 } t_gmx_mtop_atomlookup;
 128
 129
 130 gmx_mtop_atomlookup_t
 131 gmx_mtop_atomlookup_init(const gmx_mtop_t *mtop)
 132 {
 133     t_gmx_mtop_atomlookup *alook;
 134     int mb;
 135     int a_start,a_end,na,na_start=-1;
 136
 137     snew(alook,1);
 138
 139     alook->mtop     = mtop;
 140     alook->nmb      = mtop->nmolblock;
 141     alook->mb_start = 0;
 142     snew(alook->mba,alook->nmb);
 143
 144     a_start = 0;
 145     for(mb=0; mb<mtop->nmolblock; mb++)
 146     {
 147         na    = mtop->molblock[mb].nmol*mtop->molblock[mb].natoms_mol;
 148         a_end = a_start + na;
 149
 150         alook->mba[mb].a_start = a_start;
 151         alook->mba[mb].a_end   = a_end;
 152         alook->mba[mb].na_mol  = mtop->molblock[mb].natoms_mol;
 153
 154         /* We start the binary search with the largest block */
 155         if (mb == 0 || na > na_start)
 156         {
 157             alook->mb_start = mb;
 158             na_start        = na;
 159         }
 160
 161         a_start = a_end;
 162     }
 163
 164     return alook;
 165 }
 166
 167 gmx_mtop_atomlookup_t
 168 gmx_mtop_atomlookup_settle_init(const gmx_mtop_t *mtop)
 169 {
 170      t_gmx_mtop_atomlookup *alook;
 171      int mb;
 172      int na,na_start=-1;
 173
 174      alook = gmx_mtop_atomlookup_init(mtop);
 175
 176      /* Check if the starting molblock has settle */
 177      if (mtop->moltype[mtop->molblock[alook->mb_start].type].ilist[F_SETTLE].nr  == 0)
 178      {
 179          /* Search the largest molblock with settle */
 180          alook->mb_start = -1;
 181          for(mb=0; mb<mtop->nmolblock; mb++)
 182          {
 183              if (mtop->moltype[mtop->molblock[mb].type].ilist[F_SETTLE].nr > 0)
 184              {
 185                  na = alook->mba[mb].a_end - alook->mba[mb].a_start;
 186                  if (alook->mb_start == -1 || na > na_start)
 187                  {
 188                      alook->mb_start = mb;
 189                      na_start        = na;
 190                  }
 191              }
 192          }
 193
 194          if (alook->mb_start == -1)
 195          {
 196              gmx_incons("gmx_mtop_atomlookup_settle_init called without settles");
 197          }
 198      }
 199
 200      return alook;
 201 }
 202
 203 void
 204 gmx_mtop_atomlookup_destroy(gmx_mtop_atomlookup_t alook)
 205 {
 206     sfree(alook->mba);
 207     sfree(alook);
 208 }
 209
 210 void gmx_mtop_atomnr_to_atom(const gmx_mtop_atomlookup_t alook,
 211                              int atnr_global,
 212                              t_atom **atom)
 213 {
 214     int mb0,mb1,mb;
 215     int a_start,atnr_mol;
 216
 217 #ifdef DEBUG_MTOP
 218     if (atnr_global < 0 || atnr_global >= mtop->natoms)
 219     {
 220         gmx_fatal(FARGS,"gmx_mtop_atomnr_to_moltype was called with atnr_global=%d which is not in the atom range of this system (%d-%d)",
 221                   atnr_global,0,mtop->natoms-1);
 222     }
 223 #endif
 224
 225     mb0 = -1;
 226     mb1 = alook->nmb;
 227     mb  = alook->mb_start;
 228
 229     while (TRUE)
 230     {
 231         a_start = alook->mba[mb].a_start;
 232         if (atnr_global < a_start)
 233         {
 234             mb1 = mb;
 235         }
 236         else if (atnr_global >= alook->mba[mb].a_end)
 237         {
 238             mb0 = mb;
 239         }
 240         else
 241         {
 242             break;
 243         }
 244         mb = ((mb0 + mb1 + 1)>>1);
 245     }
 246
 247     atnr_mol = (atnr_global - a_start) % alook->mba[mb].na_mol;
 248
 249     *atom = &alook->mtop->moltype[alook->mtop->molblock[mb].type].atoms.atom[atnr_mol];
 250 }
 251
 252 void gmx_mtop_atomnr_to_ilist(const gmx_mtop_atomlookup_t alook,
 253                               int atnr_global,
 254                               t_ilist **ilist_mol,int *atnr_offset)
 255 {
 256     int mb0,mb1,mb;
 257     int a_start,atnr_local;
 258
 259 #ifdef DEBUG_MTOP
 260     if (atnr_global < 0 || atnr_global >= mtop->natoms)
 261     {
 262         gmx_fatal(FARGS,"gmx_mtop_atomnr_to_moltype was called with atnr_global=%d which is not in the atom range of this system (%d-%d)",
 263                   atnr_global,0,mtop->natoms-1);
 264     }
 265 #endif
 266
 267     mb0 = -1;
 268     mb1 = alook->nmb;
 269     mb  = alook->mb_start;
 270
 271     while (TRUE)
 272     {
 273         a_start = alook->mba[mb].a_start;
 274         if (atnr_global < a_start)
 275         {
 276             mb1 = mb;
 277         }
 278         else if (atnr_global >= alook->mba[mb].a_end)
 279         {
 280             mb0 = mb;
 281         }
 282         else
 283         {
 284             break;
 285         }
 286         mb = ((mb0 + mb1 + 1)>>1);
 287     }
 288
 289     *ilist_mol = alook->mtop->moltype[alook->mtop->molblock[mb].type].ilist;
 290
 291     atnr_local = (atnr_global - a_start) % alook->mba[mb].na_mol;
 292
 293     *atnr_offset = atnr_global - atnr_local;
 294 }
 295
 296 void gmx_mtop_atomnr_to_molblock_ind(const gmx_mtop_atomlookup_t alook,
 297                                      int atnr_global,
 298                                      int *molb,int *molnr,int *atnr_mol)
 299 {
 300     int mb0,mb1,mb;
 301     int a_start;
 302
 303 #ifdef DEBUG_MTOP
 304     if (atnr_global < 0 || atnr_global >= mtop->natoms)
 305     {
 306         gmx_fatal(FARGS,"gmx_mtop_atomnr_to_moltype was called with atnr_global=%d which is not in the atom range of this system (%d-%d)",
 307                   atnr_global,0,mtop->natoms-1);
 308     }
 309 #endif
 310
 311     mb0 = -1;
 312     mb1 = alook->nmb;
 313     mb  = alook->mb_start;
 314
 315     while (TRUE)
 316     {
 317         a_start = alook->mba[mb].a_start;
 318         if (atnr_global < a_start)
 319         {
 320             mb1 = mb;
 321         }
 322         else if (atnr_global >= alook->mba[mb].a_end)
 323         {
 324             mb0 = mb;
 325         }
 326         else
 327         {
 328             break;
 329         }
 330         mb = ((mb0 + mb1 + 1)>>1);
 331     }
 332
 333     *molb  = mb;
 334     *molnr = (atnr_global - a_start) / alook->mba[mb].na_mol;
 335     *atnr_mol = atnr_global - a_start - (*molnr)*alook->mba[mb].na_mol;
 336 }
 337
 338 void gmx_mtop_atominfo_global(const gmx_mtop_t *mtop,int atnr_global,
 339                               char **atomname,int *resnr,char **resname)
 340 {
 341     int mb,a_start,a_end,maxresnr,at_loc;
 342     gmx_molblock_t *molb;
 343     t_atoms *atoms=NULL;
 344
 345     if (atnr_global < 0 || atnr_global >= mtop->natoms)
 346     {
 347         gmx_fatal(FARGS,"gmx_mtop_atominfo_global was called with atnr_global=%d which is not in the atom range of this system (%d-%d)",
 348                   atnr_global,0,mtop->natoms-1);
 349     }
 350
 351     mb = -1;
 352     a_end = 0;
 353     maxresnr = mtop->maxresnr;
 354     do
 355     {
 356         if (mb >= 0)
 357         {
 358             if (atoms->nres <= mtop->maxres_renum)
 359             {
 360                 /* Single residue molecule, keep counting */
 361                 maxresnr += mtop->molblock[mb].nmol*atoms->nres;
 362             }
 363         }
 364         mb++;
 365         atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
 366         a_start = a_end;
 367         a_end = a_start + mtop->molblock[mb].nmol*atoms->nr;
 368     }
 369     while (atnr_global >= a_end);
 370
 371     at_loc = (atnr_global - a_start) % atoms->nr;
 372     *atomname = *(atoms->atomname[at_loc]);
 373     if (atoms->nres > mtop->maxres_renum)
 374     {
 375         *resnr = atoms->resinfo[atoms->atom[at_loc].resind].nr;
 376     }
 377     else
 378     {
 379         /* Single residue molecule, keep counting */
 380         *resnr = maxresnr + 1 + (atnr_global - a_start)/atoms->nr*atoms->nres + atoms->atom[at_loc].resind;
 381     }
 382     *resname  = *(atoms->resinfo[atoms->atom[at_loc].resind].name);
 383 }
 384
 385 typedef struct gmx_mtop_atomloop_all
 386 {
 387     const gmx_mtop_t *mtop;
 388     int        mblock;
 389     t_atoms    *atoms;
 390     int        mol;
 391     int        maxresnr;
 392     int        at_local;
 393     int        at_global;
 394 } t_gmx_mtop_atomloop_all;
 395
 396 gmx_mtop_atomloop_all_t
 397 gmx_mtop_atomloop_all_init(const gmx_mtop_t *mtop)
 398 {
 399     struct gmx_mtop_atomloop_all *aloop;
 400
 401     snew(aloop,1);
 402
 403     aloop->mtop         = mtop;
 404     aloop->mblock       = 0;
 405     aloop->atoms        =
 406         &mtop->moltype[mtop->molblock[aloop->mblock].type].atoms;
 407     aloop->mol          = 0;
 408     aloop->maxresnr     = mtop->maxresnr;
 409     aloop->at_local     = -1;
 410     aloop->at_global    = -1;
 411
 412     return aloop;
 413 }
 414
 415 static void gmx_mtop_atomloop_all_destroy(gmx_mtop_atomloop_all_t aloop)
 416 {
 417     sfree(aloop);
 418 }
 419
 420 gmx_bool gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
 421                                 int *at_global,t_atom **atom)
 422 {
 423     if (aloop == NULL)
 424     {
 425         gmx_incons("gmx_mtop_atomloop_all_next called without calling gmx_mtop_atomloop_all_init");
 426     }
 427
 428     aloop->at_local++;
 429     aloop->at_global++;
 430
 431     if (aloop->at_local >= aloop->atoms->nr)
 432     {
 433         if (aloop->atoms->nres <= aloop->mtop->maxres_renum)
 434         {
 435             /* Single residue molecule, increase the count with one */
 436             aloop->maxresnr += aloop->atoms->nres;
 437         }
 438         aloop->mol++;
 439         aloop->at_local = 0;
 440         if (aloop->mol >= aloop->mtop->molblock[aloop->mblock].nmol)
 441         {
 442             aloop->mblock++;
 443             if (aloop->mblock >= aloop->mtop->nmolblock)
 444             {
 445                 gmx_mtop_atomloop_all_destroy(aloop);
 446                 return FALSE;
 447             }
 448             aloop->atoms = &aloop->mtop->moltype[aloop->mtop->molblock[aloop->mblock].type].atoms;
 449             aloop->mol = 0;
 450         }
 451     }
 452
 453     *at_global = aloop->at_global;
 454     *atom      = &aloop->atoms->atom[aloop->at_local];
 455
 456     return TRUE;
 457 }
 458
 459 void gmx_mtop_atomloop_all_names(gmx_mtop_atomloop_all_t aloop,
 460                                  char **atomname,int *resnr,char **resname)
 461 {
 462     int resind_mol;
 463
 464     *atomname = *(aloop->atoms->atomname[aloop->at_local]);
 465     resind_mol = aloop->atoms->atom[aloop->at_local].resind;
 466     *resnr = aloop->atoms->resinfo[resind_mol].nr;
 467     if (aloop->atoms->nres <= aloop->mtop->maxres_renum)
 468     {
 469         *resnr = aloop->maxresnr + 1 + resind_mol;
 470     }
 471     *resname  = *(aloop->atoms->resinfo[resind_mol].name);
 472 }
 473
 474 void gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
 475                                    gmx_moltype_t **moltype,int *at_mol)
 476 {
 477     *moltype = &aloop->mtop->moltype[aloop->mtop->molblock[aloop->mblock].type];
 478     *at_mol  = aloop->at_local;
 479 }
 480
 481 typedef struct gmx_mtop_atomloop_block
 482 {
 483     const gmx_mtop_t *mtop;
 484     int        mblock;
 485     t_atoms    *atoms;
 486     int        at_local;
 487 } t_gmx_mtop_atomloop_block;
 488
 489 gmx_mtop_atomloop_block_t
 490 gmx_mtop_atomloop_block_init(const gmx_mtop_t *mtop)
 491 {
 492     struct gmx_mtop_atomloop_block *aloop;
 493
 494     snew(aloop,1);
 495
 496     aloop->mtop      = mtop;
 497     aloop->mblock    = 0;
 498     aloop->atoms     = &mtop->moltype[mtop->molblock[aloop->mblock].type].atoms;
 499     aloop->at_local  = -1;
 500
 501     return aloop;
 502 }
 503
 504 static void gmx_mtop_atomloop_block_destroy(gmx_mtop_atomloop_block_t aloop)
 505 {
 506     sfree(aloop);
 507 }
 508
 509 gmx_bool gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
 510                                   t_atom **atom,int *nmol)
 511 {
 512     if (aloop == NULL)
 513     {
 514         gmx_incons("gmx_mtop_atomloop_all_next called without calling gmx_mtop_atomloop_all_init");
 515     }
 516
 517     aloop->at_local++;
 518
 519     if (aloop->at_local >= aloop->atoms->nr)
 520     {
 521         aloop->mblock++;
 522         if (aloop->mblock >= aloop->mtop->nmolblock)
 523         {
 524             gmx_mtop_atomloop_block_destroy(aloop);
 525             return FALSE;
 526         }
 527         aloop->atoms = &aloop->mtop->moltype[aloop->mtop->molblock[aloop->mblock].type].atoms;
 528         aloop->at_local = 0;
 529     }
 530
 531     *atom = &aloop->atoms->atom[aloop->at_local];
 532     *nmol = aloop->mtop->molblock[aloop->mblock].nmol;
 533
 534     return TRUE;
 535 }
 536
 537 typedef struct gmx_mtop_ilistloop
 538 {
 539     const gmx_mtop_t *mtop;
 540     int           mblock;
 541 } t_gmx_mtop_ilist;
 542
 543 gmx_mtop_ilistloop_t
 544 gmx_mtop_ilistloop_init(const gmx_mtop_t *mtop)
 545 {
 546     struct gmx_mtop_ilistloop *iloop;
 547
 548     snew(iloop,1);
 549
 550     iloop->mtop      = mtop;
 551     iloop->mblock    = -1;
 552
 553     return iloop;
 554 }
 555
 556 static void gmx_mtop_ilistloop_destroy(gmx_mtop_ilistloop_t iloop)
 557 {
 558     sfree(iloop);
 559 }
 560
 561 gmx_bool gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
 562                              t_ilist **ilist_mol,int *nmol)
 563 {
 564     if (iloop == NULL)
 565     {
 566         gmx_incons("gmx_mtop_ilistloop_next called without calling gmx_mtop_ilistloop_init");
 567     }
 568
 569     iloop->mblock++;
 570     if (iloop->mblock == iloop->mtop->nmolblock)
 571     {
 572         gmx_mtop_ilistloop_destroy(iloop);
 573         return FALSE;
 574     }
 575
 576     *ilist_mol =
 577         iloop->mtop->moltype[iloop->mtop->molblock[iloop->mblock].type].ilist;
 578
 579     *nmol = iloop->mtop->molblock[iloop->mblock].nmol;
 580
 581     return TRUE;
 582 }
 583 typedef struct gmx_mtop_ilistloop_all
 584 {
 585     const gmx_mtop_t *mtop;
 586     int           mblock;
 587     int           mol;
 588     int           a_offset;
 589 } t_gmx_mtop_ilist_all;
 590
 591 gmx_mtop_ilistloop_all_t
 592 gmx_mtop_ilistloop_all_init(const gmx_mtop_t *mtop)
 593 {
 594     struct gmx_mtop_ilistloop_all *iloop;
 595
 596     snew(iloop,1);
 597
 598     iloop->mtop      = mtop;
 599     iloop->mblock    = 0;
 600     iloop->mol       = -1;
 601     iloop->a_offset  = 0;
 602
 603     return iloop;
 604 }
 605
 606 static void gmx_mtop_ilistloop_all_destroy(gmx_mtop_ilistloop_all_t iloop)
 607 {
 608     sfree(iloop);
 609 }
 610
 611 gmx_bool gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
 612                                  t_ilist **ilist_mol,int *atnr_offset)
 613 {
 614     gmx_molblock_t *molb;
 615
 616     if (iloop == NULL)
 617     {
 618         gmx_incons("gmx_mtop_ilistloop_all_next called without calling gmx_mtop_ilistloop_all_init");
 619     }
 620
 621     if (iloop->mol >= 0)
 622     {
 623         iloop->a_offset += iloop->mtop->molblock[iloop->mblock].natoms_mol;
 624     }
 625
 626     iloop->mol++;
 627
 628     if (iloop->mol >= iloop->mtop->molblock[iloop->mblock].nmol) {
 629         iloop->mblock++;
 630         iloop->mol = 0;
 631         if (iloop->mblock == iloop->mtop->nmolblock)
 632         {
 633             gmx_mtop_ilistloop_all_destroy(iloop);
 634             return FALSE;
 635         }
 636     }
 637
 638     *ilist_mol =
 639         iloop->mtop->moltype[iloop->mtop->molblock[iloop->mblock].type].ilist;
 640
 641     *atnr_offset = iloop->a_offset;
 642
 643     return TRUE;
 644 }
 645
 646 int gmx_mtop_ftype_count(const gmx_mtop_t *mtop,int ftype)
 647 {
 648     gmx_mtop_ilistloop_t iloop;
 649     t_ilist *il;
 650     int n,nmol;
 651
 652     n = 0;
 653
 654     iloop = gmx_mtop_ilistloop_init(mtop);
 655     while (gmx_mtop_ilistloop_next(iloop,&il,&nmol))
 656     {
 657         n += nmol*il[ftype].nr/(1+NRAL(ftype));
 658     }
 659
 660     return n;
 661 }
 662
 663 t_block gmx_mtop_global_cgs(const gmx_mtop_t *mtop)
 664 {
 665     t_block cgs_gl,*cgs_mol;
 666     int mb,mol,cg;
 667     gmx_molblock_t *molb;
 668     t_atoms *atoms;
 669
 670     /* In most cases this is too much, but we realloc at the end */
 671     snew(cgs_gl.index,mtop->natoms+1);
 672
 673     cgs_gl.nr       = 0;
 674     cgs_gl.index[0] = 0;
 675     for(mb=0; mb<mtop->nmolblock; mb++)
 676     {
 677         molb    = &mtop->molblock[mb];
 678         cgs_mol = &mtop->moltype[molb->type].cgs;
 679         for(mol=0; mol<molb->nmol; mol++)
 680         {
 681             for(cg=0; cg<cgs_mol->nr; cg++)
 682             {
 683                 cgs_gl.index[cgs_gl.nr+1] =
 684                     cgs_gl.index[cgs_gl.nr] +
 685                     cgs_mol->index[cg+1] - cgs_mol->index[cg];
 686                 cgs_gl.nr++;
 687             }
 688         }
 689     }
 690     cgs_gl.nalloc_index = cgs_gl.nr + 1;
 691     srenew(cgs_gl.index,cgs_gl.nalloc_index);
 692
 693     return cgs_gl;
 694 }
 695
 696 static void atomcat(t_atoms *dest, t_atoms *src, int copies,
 697                     int maxres_renum, int *maxresnr)
 698 {
 699     int i,j,l,size;
 700     int srcnr=src->nr;
 701     int destnr=dest->nr;
 702
 703     if (srcnr)
 704     {
 705         size=destnr+copies*srcnr;
 706         srenew(dest->atom,size);
 707         srenew(dest->atomname,size);
 708         srenew(dest->atomtype,size);
 709         srenew(dest->atomtypeB,size);
 710     }
 711     if (src->nres)
 712     {
 713         size=dest->nres+copies*src->nres;
 714         srenew(dest->resinfo,size);
 715     }
 716
 717     /* residue information */
 718     for (l=dest->nres,j=0; (j<copies); j++,l+=src->nres)
 719     {
 720         memcpy((char *) &(dest->resinfo[l]),(char *) &(src->resinfo[0]),
 721                (size_t)(src->nres*sizeof(src->resinfo[0])));
 722     }
 723
 724     for (l=destnr,j=0; (j<copies); j++,l+=srcnr)
 725     {
 726         memcpy((char *) &(dest->atomname[l]),(char *) &(src->atomname[0]),
 727                (size_t)(srcnr*sizeof(src->atomname[0])));
 728         memcpy((char *) &(dest->atomtype[l]),(char *) &(src->atomtype[0]),
 729                (size_t)(srcnr*sizeof(src->atomtype[0])));
 730         memcpy((char *) &(dest->atomtypeB[l]),(char *) &(src->atomtypeB[0]),
 731                (size_t)(srcnr*sizeof(src->atomtypeB[0])));
 732         memcpy((char *) &(dest->atom[l]),(char *) &(src->atom[0]),
 733                (size_t)(srcnr*sizeof(src->atom[0])));
 734     }
 735
 736     /* Increment residue indices */
 737     for (l=destnr,j=0; (j<copies); j++)
 738     {
 739         for (i=0; (i<srcnr); i++,l++)
 740         {
 741             dest->atom[l].resind = dest->nres+j*src->nres+src->atom[i].resind;
 742         }
 743     }
 744
 745     if (src->nres <= maxres_renum)
 746     {
 747         /* Single residue molecule, continue counting residues */
 748         for (j=0; (j<copies); j++)
 749         {
 750             for (l=0; l<src->nres; l++)
 751             {
 752                 (*maxresnr)++;
 753                 dest->resinfo[dest->nres+j*src->nres+l].nr = *maxresnr;
 754             }
 755         }
 756     }
 757
 758     dest->nres += copies*src->nres;
 759     dest->nr   += copies*src->nr;
 760 }
 761
 762 t_atoms gmx_mtop_global_atoms(const gmx_mtop_t *mtop)
 763 {
 764     t_atoms atoms;
 765     int maxresnr,mb;
 766     gmx_molblock_t *molb;
 767
 768     init_t_atoms(&atoms,0,FALSE);
 769
 770     maxresnr = mtop->maxresnr;
 771     for(mb=0; mb<mtop->nmolblock; mb++)
 772     {
 773         molb = &mtop->molblock[mb];
 774         atomcat(&atoms,&mtop->moltype[molb->type].atoms,molb->nmol,
 775                 mtop->maxres_renum,&maxresnr);
 776     }
 777
 778     return atoms;
 779 }
 780
 781 void gmx_mtop_make_atomic_charge_groups(gmx_mtop_t *mtop,
 782                                         gmx_bool bKeepSingleMolCG)
 783 {
 784     int     mb,cg;
 785     t_block *cgs_mol;
 786
 787     for(mb=0; mb<mtop->nmolblock; mb++)
 788     {
 789         cgs_mol = &mtop->moltype[mtop->molblock[mb].type].cgs;
 790         if (!(bKeepSingleMolCG && cgs_mol->nr == 1))
 791         {
 792             cgs_mol->nr           = mtop->molblock[mb].natoms_mol;
 793             cgs_mol->nalloc_index = cgs_mol->nr + 1;
 794             srenew(cgs_mol->index,cgs_mol->nalloc_index);
 795             for(cg=0; cg<cgs_mol->nr+1; cg++)
 796             {
 797                 cgs_mol->index[cg] = cg;
 798             }
 799         }
 800     }
 801 }
 802
 803 /*
 804  * The cat routines below are old code from src/kernel/topcat.c
 805  */
 806
 807 static void blockcat(t_block *dest,t_block *src,int copies,
 808                      int dnum,int snum)
 809 {
 810     int i,j,l,nra,size;
 811
 812     if (src->nr)
 813     {
 814         size=(dest->nr+copies*src->nr+1);
 815         srenew(dest->index,size);
 816     }
 817
 818     nra = dest->index[dest->nr];
 819     for (l=dest->nr,j=0; (j<copies); j++)
 820     {
 821         for (i=0; (i<src->nr); i++)
 822         {
 823             dest->index[l++] = nra + src->index[i];
 824         }
 825         nra += src->index[src->nr];
 826     }
 827     dest->nr += copies*src->nr;
 828     dest->index[dest->nr] = nra;
 829 }
 830
 831 static void blockacat(t_blocka *dest,t_blocka *src,int copies,
 832                       int dnum,int snum)
 833 {
 834     int i,j,l,size;
 835     int destnr  = dest->nr;
 836     int destnra = dest->nra;
 837
 838     if (src->nr)
 839     {
 840         size=(dest->nr+copies*src->nr+1);
 841         srenew(dest->index,size);
 842     }
 843     if (src->nra)
 844     {
 845         size=(dest->nra+copies*src->nra);
 846         srenew(dest->a,size);
 847     }
 848
 849     for (l=destnr,j=0; (j<copies); j++)
 850     {
 851         for (i=0; (i<src->nr); i++)
 852         {
 853             dest->index[l++] = dest->nra+src->index[i];
 854         }
 855         dest->nra += src->nra;
 856     }
 857     for (l=destnra,j=0; (j<copies); j++)
 858     {
 859         for (i=0; (i<src->nra); i++)
 860         {
 861             dest->a[l++] = dnum+src->a[i];
 862         }
 863         dnum+=snum;
 864         dest->nr += src->nr;
 865     }
 866     dest->index[dest->nr] = dest->nra;
 867 }
 868
 869 static void ilistcat(int ftype,t_ilist *dest,t_ilist *src,int copies,
 870                      int dnum,int snum)
 871 {
 872     int nral,c,i,a;
 873
 874     nral = NRAL(ftype);
 875
 876     dest->nalloc = dest->nr + copies*src->nr;
 877     srenew(dest->iatoms,dest->nalloc);
 878
 879     for(c=0; c<copies; c++)
 880     {
 881         for(i=0; i<src->nr; )
 882         {
 883             dest->iatoms[dest->nr++] = src->iatoms[i++];
 884             for(a=0; a<nral; a++)
 885             {
 886                 dest->iatoms[dest->nr++] = dnum + src->iatoms[i++];
 887             }
 888         }
 889         dnum += snum;
 890     }
 891 }
 892
 893 static void set_posres_params(t_idef *idef,gmx_molblock_t *molb,
 894                               int i0,int a_offset)
 895 {
 896     t_ilist *il;
 897     int i1,i,a_molb;
 898     t_iparams *ip;
 899
 900     il = &idef->il[F_POSRES];
 901     i1 = il->nr/2;
 902     idef->iparams_posres_nalloc = i1;
 903     srenew(idef->iparams_posres,idef->iparams_posres_nalloc);
 904     for(i=i0; i<i1; i++)
 905     {
 906         ip = &idef->iparams_posres[i];
 907         /* Copy the force constants */
 908         *ip    = idef->iparams[il->iatoms[i*2]];
 909         a_molb = il->iatoms[i*2+1] - a_offset;
 910         if (molb->nposres_xA == 0)
 911         {
 912             gmx_incons("Position restraint coordinates are missing");
 913         }
 914         ip->posres.pos0A[XX] = molb->posres_xA[a_molb][XX];
 915         ip->posres.pos0A[YY] = molb->posres_xA[a_molb][YY];
 916         ip->posres.pos0A[ZZ] = molb->posres_xA[a_molb][ZZ];
 917         if (molb->nposres_xB > 0)
 918         {
 919             ip->posres.pos0B[XX] = molb->posres_xB[a_molb][XX];
 920             ip->posres.pos0B[YY] = molb->posres_xB[a_molb][YY];
 921             ip->posres.pos0B[ZZ] = molb->posres_xB[a_molb][ZZ];
 922         }
 923         else
 924         {
 925             ip->posres.pos0B[XX] = ip->posres.pos0A[XX];
 926             ip->posres.pos0B[YY] = ip->posres.pos0A[YY];
 927             ip->posres.pos0B[ZZ] = ip->posres.pos0A[ZZ];
 928         }
 929         /* Set the parameter index for idef->iparams_posre */
 930         il->iatoms[i*2] = i;
 931     }
 932 }
 933
 934 static void gen_local_top(const gmx_mtop_t *mtop,const t_inputrec *ir,
 935                           gmx_bool bMergeConstr,
 936                           gmx_localtop_t *top)
 937 {
 938     int mb,srcnr,destnr,ftype,ftype_dest,mt,natoms,mol,nposre_old;
 939     gmx_molblock_t *molb;
 940     gmx_moltype_t *molt;
 941     const gmx_ffparams_t *ffp;
 942     t_idef *idef;
 943     real   *qA,*qB;
 944     gmx_mtop_atomloop_all_t aloop;
 945     int    ag;
 946     t_atom *atom;
 947
 948     top->atomtypes = mtop->atomtypes;
 949
 950     ffp = &mtop->ffparams;
 951
 952     idef = &top->idef;
 953     idef->ntypes   = ffp->ntypes;
 954     idef->atnr     = ffp->atnr;
 955     idef->functype = ffp->functype;
 956     idef->iparams  = ffp->iparams;
 957     idef->iparams_posres = NULL;
 958     idef->iparams_posres_nalloc = 0;
 959     idef->fudgeQQ  = ffp->fudgeQQ;
 960     idef->cmap_grid = ffp->cmap_grid;
 961     idef->ilsort   = ilsortUNKNOWN;
 962
 963     init_block(&top->cgs);
 964     init_blocka(&top->excls);
 965     for(ftype=0; ftype<F_NRE; ftype++)
 966     {
 967         idef->il[ftype].nr     = 0;
 968         idef->il[ftype].nalloc = 0;
 969         idef->il[ftype].iatoms = NULL;
 970     }
 971
 972     natoms = 0;
 973     for(mb=0; mb<mtop->nmolblock; mb++)
 974     {
 975         molb = &mtop->molblock[mb];
 976         molt = &mtop->moltype[molb->type];
 977
 978         srcnr  = molt->atoms.nr;
 979         destnr = natoms;
 980
 981         blockcat(&top->cgs,&molt->cgs,molb->nmol,destnr,srcnr);
 982
 983         blockacat(&top->excls,&molt->excls,molb->nmol,destnr,srcnr);
 984
 985         nposre_old = idef->il[F_POSRES].nr;
 986         for(ftype=0; ftype<F_NRE; ftype++)
 987         {
 988             if (bMergeConstr &&
 989                 ftype == F_CONSTR && molt->ilist[F_CONSTRNC].nr > 0)
 990             {
 991                 /* Merge all constrains into one ilist.
 992                  * This simplifies the constraint code.
 993                  */
 994                 for(mol=0; mol<molb->nmol; mol++) {
 995                     ilistcat(ftype,&idef->il[F_CONSTR],&molt->ilist[F_CONSTR],
 996                              1,destnr+mol*srcnr,srcnr);
 997                     ilistcat(ftype,&idef->il[F_CONSTR],&molt->ilist[F_CONSTRNC],
 998                              1,destnr+mol*srcnr,srcnr);
 999                 }
1000             }
1001             else if (!(bMergeConstr && ftype == F_CONSTRNC))
1002             {
1003                 ilistcat(ftype,&idef->il[ftype],&molt->ilist[ftype],
1004                          molb->nmol,destnr,srcnr);
1005             }
1006         }
1007         if (idef->il[F_POSRES].nr > nposre_old)
1008         {
1009             set_posres_params(idef,molb,nposre_old/2,natoms);
1010         }
1011
1012         natoms += molb->nmol*srcnr;
1013     }
1014
1015     if (ir == NULL)
1016     {
1017         top->idef.ilsort = ilsortUNKNOWN;
1018     }
1019     else
1020     {
1021         if (ir->efep != efepNO && gmx_mtop_bondeds_free_energy(mtop))
1022         {
1023             snew(qA,mtop->natoms);
1024             snew(qB,mtop->natoms);
1025             aloop = gmx_mtop_atomloop_all_init(mtop);
1026             while (gmx_mtop_atomloop_all_next(aloop,&ag,&atom))
1027             {
1028                 qA[ag] = atom->q;
1029                 qB[ag] = atom->qB;
1030             }
1031             gmx_sort_ilist_fe(&top->idef,qA,qB);
1032             sfree(qA);
1033             sfree(qB);
1034         }
1035         else
1036         {
1037             top->idef.ilsort = ilsortNO_FE;
1038         }
1039     }
1040 }
1041
1042 gmx_localtop_t *gmx_mtop_generate_local_top(const gmx_mtop_t *mtop,
1043                                             const t_inputrec *ir)
1044 {
1045     gmx_localtop_t *top;
1046
1047     snew(top,1);
1048
1049     gen_local_top(mtop,ir,TRUE,top);
1050
1051     return top;
1052 }
1053
1054 t_topology gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop)
1055 {
1056     int mt,mb;
1057     gmx_localtop_t ltop;
1058     t_topology top;
1059
1060     gen_local_top(mtop,NULL,FALSE,&ltop);
1061
1062     top.name      = mtop->name;
1063     top.idef      = ltop.idef;
1064     top.atomtypes = ltop.atomtypes;
1065     top.cgs       = ltop.cgs;
1066     top.excls     = ltop.excls;
1067     top.atoms     = gmx_mtop_global_atoms(mtop);
1068     top.mols      = mtop->mols;
1069     top.symtab    = mtop->symtab;
1070
1071     /* We only need to free the moltype and molblock data,
1072      * all other pointers have been copied to top.
1073      *
1074      * Well, except for the group data, but we can't free those, because they
1075      * are used somewhere even after a call to this function.
1076      */
1077     for(mt=0; mt<mtop->nmoltype; mt++)
1078     {
1079         done_moltype(&mtop->moltype[mt]);
1080     }
1081     sfree(mtop->moltype);
1082
1083     for(mb=0; mb<mtop->nmolblock; mb++)
1084     {
1085         done_molblock(&mtop->molblock[mb]);
1086     }
1087     sfree(mtop->molblock);
1088
1089     return top;
1090 }