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Code cleanup to avoid name collisions
[gromacs.git] / src / gmxlib / typedefs.c
blob897d2f82a78598ddeb3fe2ed14f7d7a51b6a207a
1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
2 *
3 *
4 * This source code is part of
5 *
6 * G R O M A C S
7 *
8 * GROningen MAchine for Chemical Simulations
9 *
10 * VERSION 3.2.0
11 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
12 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
13 * Copyright (c) 2001-2004, The GROMACS development team,
14 * check out http://www.gromacs.org for more information.
15
16 * This program is free software; you can redistribute it and/or
17 * modify it under the terms of the GNU General Public License
18 * as published by the Free Software Foundation; either version 2
19 * of the License, or (at your option) any later version.
20 *
21 * If you want to redistribute modifications, please consider that
22 * scientific software is very special. Version control is crucial -
23 * bugs must be traceable. We will be happy to consider code for
24 * inclusion in the official distribution, but derived work must not
25 * be called official GROMACS. Details are found in the README & COPYING
26 * files - if they are missing, get the official version at www.gromacs.org.
27 *
28 * To help us fund GROMACS development, we humbly ask that you cite
29 * the papers on the package - you can find them in the top README file.
30 *
31 * For more info, check our website at http://www.gromacs.org
32 *
33 * And Hey:
34 * GROningen Mixture of Alchemy and Childrens' Stories
35 */
36 /* This file is completely threadsafe - keep it that way! */
37 #ifdef HAVE_CONFIG_H
38 #include <config.h>
39 #endif
40
41 #include "smalloc.h"
42 #include "symtab.h"
43 #include "vec.h"
44 #include "pbc.h"
45 #include <string.h>
46
47 #ifdef GMX_THREAD_MPI
48 #include "thread_mpi.h"
49 #endif
50
51 /* The source code in this file should be thread-safe.
52 Please keep it that way. */
53
54
55
56 static gmx_bool bOverAllocDD=FALSE;
57 #ifdef GMX_THREAD_MPI
58 static tMPI_Thread_mutex_t over_alloc_mutex=TMPI_THREAD_MUTEX_INITIALIZER;
59 #endif
60
61
62 void set_over_alloc_dd(gmx_bool set)
63 {
64 #ifdef GMX_THREAD_MPI
65 tMPI_Thread_mutex_lock(&over_alloc_mutex);
66 /* we just make sure that we don't set this at the same time.
67 We don't worry too much about reading this rarely-set variable */
68 #endif
69 bOverAllocDD = set;
70 #ifdef GMX_THREAD_MPI
71 tMPI_Thread_mutex_unlock(&over_alloc_mutex);
72 #endif
73 }
74
75 int over_alloc_dd(int n)
76 {
77 if (bOverAllocDD)
78 return OVER_ALLOC_FAC*n + 100;
79 else
80 return n;
81 }
82
83 int gmx_large_int_to_int(gmx_large_int_t step,const char *warn)
84 {
85 int i;
86
87 i = (int)step;
88
89 if (warn != NULL && (step < INT_MIN || step > INT_MAX)) {
90 fprintf(stderr,"\nWARNING during %s:\n",warn);
91 fprintf(stderr,"step value ");
92 fprintf(stderr,gmx_large_int_pfmt,step);
93 fprintf(stderr," does not fit in int, converted to %d\n\n",i);
94 }
95
96 return i;
97 }
98
99 char *gmx_step_str(gmx_large_int_t i,char *buf)
100 {
101 sprintf(buf,gmx_large_int_pfmt,i);
102
103 return buf;
104 }
105
106 void init_block(t_block *block)
107 {
108 int i;
109
110 block->nr = 0;
111 block->nalloc_index = 1;
112 snew(block->index,block->nalloc_index);
113 block->index[0] = 0;
114 }
115
116 void init_blocka(t_blocka *block)
117 {
118 int i;
119
120 block->nr = 0;
121 block->nra = 0;
122 block->nalloc_index = 1;
123 snew(block->index,block->nalloc_index);
124 block->index[0] = 0;
125 block->nalloc_a = 0;
126 block->a = NULL;
127 }
128
129 void init_atom(t_atoms *at)
130 {
131 int i;
132
133 at->nr = 0;
134 at->nres = 0;
135 at->atom = NULL;
136 at->resinfo = NULL;
137 at->atomname = NULL;
138 at->atomtype = NULL;
139 at->atomtypeB= NULL;
140 at->pdbinfo = NULL;
141 }
142
143 void init_atomtypes(t_atomtypes *at)
144 {
145 at->nr = 0;
146 at->radius = NULL;
147 at->vol = NULL;
148 at->atomnumber = NULL;
149 at->gb_radius = NULL;
150 at->S_hct = NULL;
151 }
152
153 void init_groups(gmx_groups_t *groups)
154 {
155 int g;
156
157 groups->ngrpname = 0;
158 groups->grpname = NULL;
159 for(g=0; (g<egcNR); g++) {
160 groups->grps[g].nm_ind = NULL;
161 groups->ngrpnr[g] = 0;
162 groups->grpnr[g] = NULL;
163 }
164
165 }
166
167 void init_mtop(gmx_mtop_t *mtop)
168 {
169 mtop->name = NULL;
170 mtop->nmoltype = 0;
171 mtop->moltype = NULL;
172 mtop->nmolblock = 0;
173 mtop->molblock = NULL;
174 mtop->maxres_renum = 0;
175 mtop->maxresnr = -1;
176 init_groups(&mtop->groups);
177 init_block(&mtop->mols);
178 open_symtab(&mtop->symtab);
179 }
180
181 void init_top (t_topology *top)
182 {
183 int i;
184
185 top->name = NULL;
186 init_atom (&(top->atoms));
187 init_atomtypes(&(top->atomtypes));
188 init_block(&top->cgs);
189 init_block(&top->mols);
190 init_blocka(&top->excls);
191 open_symtab(&top->symtab);
192 }
193
194 void init_inputrec(t_inputrec *ir)
195 {
196 memset(ir,0,(size_t)sizeof(*ir));
197 }
198
199 void stupid_fill_block(t_block *grp,int natom,gmx_bool bOneIndexGroup)
200 {
201 int i;
202
203 if (bOneIndexGroup) {
204 grp->nalloc_index = 2;
205 snew(grp->index,grp->nalloc_index);
206 grp->index[0]=0;
207 grp->index[1]=natom;
208 grp->nr=1;
209 }
210 else {
211 grp->nalloc_index = natom+1;
212 snew(grp->index,grp->nalloc_index);
213 snew(grp->index,natom+1);
214 for(i=0; (i<=natom); i++)
215 grp->index[i]=i;
216 grp->nr=natom;
217 }
218 }
219
220 void stupid_fill_blocka(t_blocka *grp,int natom)
221 {
222 int i;
223
224 grp->nalloc_a = natom;
225 snew(grp->a,grp->nalloc_a);
226 for(i=0; (i<natom); i++)
227 grp->a[i]=i;
228 grp->nra=natom;
229
230 grp->nalloc_index = natom + 1;
231 snew(grp->index,grp->nalloc_index);
232 for(i=0; (i<=natom); i++)
233 grp->index[i]=i;
234 grp->nr=natom;
235 }
236
237 void copy_blocka(const t_blocka *src,t_blocka *dest)
238 {
239 int i;
240
241 dest->nr = src->nr;
242 dest->nalloc_index = dest->nr + 1;
243 snew(dest->index,dest->nalloc_index);
244 for(i=0; i<dest->nr+1; i++) {
245 dest->index[i] = src->index[i];
246 }
247 dest->nra = src->nra;
248 dest->nalloc_a = dest->nra + 1;
249 snew(dest->a,dest->nalloc_a);
250 for(i=0; i<dest->nra+1; i++) {
251 dest->a[i] = src->a[i];
252 }
253 }
254
255 void done_block(t_block *block)
256 {
257 block->nr = 0;
258 sfree(block->index);
259 block->nalloc_index = 0;
260 }
261
262 void done_blocka(t_blocka *block)
263 {
264 block->nr = 0;
265 block->nra = 0;
266 sfree(block->index);
267 if (block->a)
268 sfree(block->a);
269 block->nalloc_index = 0;
270 block->nalloc_a = 0;
271 }
272
273 void done_atom (t_atoms *at)
274 {
275 at->nr = 0;
276 at->nres = 0;
277 sfree(at->atom);
278 sfree(at->resinfo);
279 sfree(at->atomname);
280 sfree(at->atomtype);
281 sfree(at->atomtypeB);
282 }
283
284 void done_atomtypes(t_atomtypes *atype)
285 {
286 atype->nr = 0;
287 sfree(atype->radius);
288 sfree(atype->vol);
289 sfree(atype->surftens);
290 sfree(atype->atomnumber);
291 sfree(atype->gb_radius);
292 sfree(atype->S_hct);
293 }
294
295 void done_moltype(gmx_moltype_t *molt)
296 {
297 int f;
298
299 done_atom(&molt->atoms);
300 done_block(&molt->cgs);
301 done_blocka(&molt->excls);
302
303 for(f=0; f<F_NRE; f++) {
304 sfree(molt->ilist[f].iatoms);
305 molt->ilist[f].nalloc = 0;
306 }
307 }
308
309 void done_molblock(gmx_molblock_t *molb)
310 {
311 if (molb->nposres_xA > 0) {
312 molb->nposres_xA = 0;
313 free(molb->posres_xA);
314 }
315 if (molb->nposres_xB > 0) {
316 molb->nposres_xB = 0;
317 free(molb->posres_xB);
318 }
319 }
320
321 void done_mtop(gmx_mtop_t *mtop,gmx_bool bDoneSymtab)
322 {
323 int i;
324
325 if (bDoneSymtab) {
326 done_symtab(&mtop->symtab);
327 }
328
329 sfree(mtop->ffparams.functype);
330 sfree(mtop->ffparams.iparams);
331
332 for(i=0; i<mtop->nmoltype; i++) {
333 done_moltype(&mtop->moltype[i]);
334 }
335 sfree(mtop->moltype);
336 for(i=0; i<mtop->nmolblock; i++) {
337 done_molblock(&mtop->molblock[i]);
338 }
339 sfree(mtop->molblock);
340 done_block(&mtop->mols);
341 }
342
343 void done_top(t_topology *top)
344 {
345 int f;
346
347 sfree(top->idef.functype);
348 sfree(top->idef.iparams);
349 for (f = 0; f < F_NRE; ++f)
350 {
351 sfree(top->idef.il[f].iatoms);
352 top->idef.il[f].iatoms = NULL;
353 top->idef.il[f].nalloc = 0;
354 }
355
356 done_atom (&(top->atoms));
357
358 /* For GB */
359 done_atomtypes(&(top->atomtypes));
360
361 done_symtab(&(top->symtab));
362 done_block(&(top->cgs));
363 done_block(&(top->mols));
364 done_blocka(&(top->excls));
365 }
366
367 static void done_pullgrp(t_pullgrp *pgrp)
368 {
369 sfree(pgrp->ind);
370 sfree(pgrp->ind_loc);
371 sfree(pgrp->weight);
372 sfree(pgrp->weight_loc);
373 }
374
375 static void done_pull(t_pull *pull)
376 {
377 int i;
378
379 for(i=0; i<pull->ngrp+1; i++) {
380 done_pullgrp(pull->grp);
381 done_pullgrp(pull->dyna);
382 }
383 }
384
385 void done_inputrec(t_inputrec *ir)
386 {
387 int m;
388
389 for(m=0; (m<DIM); m++) {
390 if (ir->ex[m].a) sfree(ir->ex[m].a);
391 if (ir->ex[m].phi) sfree(ir->ex[m].phi);
392 if (ir->et[m].a) sfree(ir->et[m].a);
393 if (ir->et[m].phi) sfree(ir->et[m].phi);
394 }
395
396 sfree(ir->opts.nrdf);
397 sfree(ir->opts.ref_t);
398 sfree(ir->opts.annealing);
399 sfree(ir->opts.anneal_npoints);
400 sfree(ir->opts.anneal_time);
401 sfree(ir->opts.anneal_temp);
402 sfree(ir->opts.tau_t);
403 sfree(ir->opts.acc);
404 sfree(ir->opts.nFreeze);
405 sfree(ir->opts.QMmethod);
406 sfree(ir->opts.QMbasis);
407 sfree(ir->opts.QMcharge);
408 sfree(ir->opts.QMmult);
409 sfree(ir->opts.bSH);
410 sfree(ir->opts.CASorbitals);
411 sfree(ir->opts.CASelectrons);
412 sfree(ir->opts.SAon);
413 sfree(ir->opts.SAoff);
414 sfree(ir->opts.SAsteps);
415 sfree(ir->opts.bOPT);
416 sfree(ir->opts.bTS);
417
418 if (ir->pull) {
419 done_pull(ir->pull);
420 sfree(ir->pull);
421 }
422 }
423
424 static void zero_ekinstate(ekinstate_t *eks)
425 {
426 eks->ekin_n = 0;
427 eks->ekinh = NULL;
428 eks->ekinf = NULL;
429 eks->ekinh_old = NULL;
430 eks->ekinscalef_nhc = NULL;
431 eks->ekinscaleh_nhc = NULL;
432 eks->vscale_nhc = NULL;
433 eks->dekindl = 0;
434 eks->mvcos = 0;
435 }
436
437 void init_energyhistory(energyhistory_t * enerhist)
438 {
439 enerhist->nener = 0;
440
441 enerhist->ener_ave = NULL;
442 enerhist->ener_sum = NULL;
443 enerhist->ener_sum_sim = NULL;
444 enerhist->dht = NULL;
445
446 enerhist->nsteps = 0;
447 enerhist->nsum = 0;
448 enerhist->nsteps_sim = 0;
449 enerhist->nsum_sim = 0;
450
451 enerhist->dht = NULL;
452 }
453
454 static void done_delta_h_history(delta_h_history_t *dht)
455 {
456 int i;
457
458 for(i=0; i<dht->nndh; i++)
459 {
460 sfree(dht->dh[i]);
461 }
462 sfree(dht->dh);
463 sfree(dht->ndh);
464 }
465
466 void done_energyhistory(energyhistory_t * enerhist)
467 {
468 sfree(enerhist->ener_ave);
469 sfree(enerhist->ener_sum);
470 sfree(enerhist->ener_sum_sim);
471
472 if (enerhist->dht != NULL)
473 {
474 done_delta_h_history(enerhist->dht);
475 sfree(enerhist->dht);
476 }
477 }
478
479 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength)
480 {
481 int i,j;
482
483 state->ngtc = ngtc;
484 state->nnhpres = nnhpres;
485 state->nhchainlength = nhchainlength;
486 if (state->ngtc > 0)
487 {
488 snew(state->nosehoover_xi,state->nhchainlength*state->ngtc);
489 snew(state->nosehoover_vxi,state->nhchainlength*state->ngtc);
490 snew(state->therm_integral,state->ngtc);
491 for(i=0; i<state->ngtc; i++)
492 {
493 for (j=0;j<state->nhchainlength;j++)
494 {
495 state->nosehoover_xi[i*state->nhchainlength + j] = 0.0;
496 state->nosehoover_vxi[i*state->nhchainlength + j] = 0.0;
497 }
498 }
499 for(i=0; i<state->ngtc; i++) {
500 state->therm_integral[i] = 0.0;
501 }
502 }
503 else
504 {
505 state->nosehoover_xi = NULL;
506 state->nosehoover_vxi = NULL;
507 state->therm_integral = NULL;
508 }
509
510 if (state->nnhpres > 0)
511 {
512 snew(state->nhpres_xi,state->nhchainlength*nnhpres);
513 snew(state->nhpres_vxi,state->nhchainlength*nnhpres);
514 for(i=0; i<nnhpres; i++)
515 {
516 for (j=0;j<state->nhchainlength;j++)
517 {
518 state->nhpres_xi[i*nhchainlength + j] = 0.0;
519 state->nhpres_vxi[i*nhchainlength + j] = 0.0;
520 }
521 }
522 }
523 else
524 {
525 state->nhpres_xi = NULL;
526 state->nhpres_vxi = NULL;
527 }
528 }
529
530
531 void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength)
532 {
533 int i;
534
535 state->natoms = natoms;
536 state->nrng = 0;
537 state->flags = 0;
538 state->lambda = 0;
539 state->veta = 0;
540 clear_mat(state->box);
541 clear_mat(state->box_rel);
542 clear_mat(state->boxv);
543 clear_mat(state->pres_prev);
544 clear_mat(state->svir_prev);
545 clear_mat(state->fvir_prev);
546 init_gtc_state(state,ngtc,nnhpres,nhchainlength);
547 state->nalloc = state->natoms;
548 if (state->nalloc > 0) {
549 snew(state->x,state->nalloc);
550 snew(state->v,state->nalloc);
551 } else {
552 state->x = NULL;
553 state->v = NULL;
554 }
555 state->sd_X = NULL;
556 state->cg_p = NULL;
557
558 zero_ekinstate(&state->ekinstate);
559
560 init_energyhistory(&state->enerhist);
561
562 state->ddp_count = 0;
563 state->ddp_count_cg_gl = 0;
564 state->cg_gl = NULL;
565 state->cg_gl_nalloc = 0;
566 }
567
568 void done_state(t_state *state)
569 {
570 if (state->nosehoover_xi) sfree(state->nosehoover_xi);
571 if (state->x) sfree(state->x);
572 if (state->v) sfree(state->v);
573 if (state->sd_X) sfree(state->sd_X);
574 if (state->cg_p) sfree(state->cg_p);
575 state->nalloc = 0;
576 if (state->cg_gl) sfree(state->cg_gl);
577 state->cg_gl_nalloc = 0;
578 }
579
580 static void do_box_rel(t_inputrec *ir,matrix box_rel,matrix b,gmx_bool bInit)
581 {
582 int d,d2;
583
584 for(d=YY; d<=ZZ; d++) {
585 for(d2=XX; d2<=(ir->epct==epctSEMIISOTROPIC ? YY : ZZ); d2++) {
586 /* We need to check if this box component is deformed
587 * or if deformation of another component might cause
588 * changes in this component due to box corrections.
589 */
590 if (ir->deform[d][d2] == 0 &&
591 !(d == ZZ && d2 == XX && ir->deform[d][YY] != 0 &&
592 (b[YY][d2] != 0 || ir->deform[YY][d2] != 0))) {
593 if (bInit) {
594 box_rel[d][d2] = b[d][d2]/b[XX][XX];
595 } else {
596 b[d][d2] = b[XX][XX]*box_rel[d][d2];
597 }
598 }
599 }
600 }
601 }
602
603 void set_box_rel(t_inputrec *ir,t_state *state)
604 {
605 /* Make sure the box obeys the restrictions before we fix the ratios */
606 correct_box(NULL,0,state->box,NULL);
607
608 clear_mat(state->box_rel);
609
610 if (PRESERVE_SHAPE(*ir))
611 do_box_rel(ir,state->box_rel,state->box,TRUE);
612 }
613
614 void preserve_box_shape(t_inputrec *ir,matrix box_rel,matrix b)
615 {
616 if (PRESERVE_SHAPE(*ir))
617 do_box_rel(ir,box_rel,b,FALSE);
618 }
619
620 void add_t_atoms(t_atoms *atoms,int natom_extra,int nres_extra)
621 {
622 int i;
623
624 if (natom_extra > 0)
625 {
626 srenew(atoms->atomname,atoms->nr+natom_extra);
627 srenew(atoms->atom,atoms->nr+natom_extra);
628 if (NULL != atoms->pdbinfo)
629 srenew(atoms->pdbinfo,atoms->nr+natom_extra);
630 if (NULL != atoms->atomtype)
631 srenew(atoms->atomtype,atoms->nr+natom_extra);
632 if (NULL != atoms->atomtypeB)
633 srenew(atoms->atomtypeB,atoms->nr+natom_extra);
634 for(i=atoms->nr; (i<atoms->nr+natom_extra); i++) {
635 atoms->atomname[i] = NULL;
636 memset(&atoms->atom[i],0,sizeof(atoms->atom[i]));
637 if (NULL != atoms->pdbinfo)
638 memset(&atoms->pdbinfo[i],0,sizeof(atoms->pdbinfo[i]));
639 if (NULL != atoms->atomtype)
640 atoms->atomtype[i] = NULL;
641 if (NULL != atoms->atomtypeB)
642 atoms->atomtypeB[i] = NULL;
643 }
644 atoms->nr += natom_extra;
645 }
646 if (nres_extra > 0)
647 {
648 srenew(atoms->resinfo,atoms->nres+nres_extra);
649 for(i=atoms->nres; (i<atoms->nres+nres_extra); i++) {
650 memset(&atoms->resinfo[i],0,sizeof(atoms->resinfo[i]));
651 }
652 atoms->nres += nres_extra;
653 }
654 }
655
656 void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo)
657 {
658 atoms->nr=natoms;
659 atoms->nres=0;
660 snew(atoms->atomname,natoms);
661 atoms->atomtype=NULL;
662 atoms->atomtypeB=NULL;
663 snew(atoms->resinfo,natoms);
664 snew(atoms->atom,natoms);
665 if (bPdbinfo)
666 snew(atoms->pdbinfo,natoms);
667 else
668 atoms->pdbinfo=NULL;
669 }
670
671 t_atoms *copy_t_atoms(t_atoms *src)
672 {
673 t_atoms *dst;
674 int i;
675
676 snew(dst,1);
677 init_t_atoms(dst,src->nr,(NULL != src->pdbinfo));
678 dst->nr = src->nr;
679 if (NULL != src->atomname)
680 snew(dst->atomname,src->nr);
681 if (NULL != src->atomtype)
682 snew(dst->atomtype,src->nr);
683 if (NULL != src->atomtypeB)
684 snew(dst->atomtypeB,src->nr);
685 for(i=0; (i<src->nr); i++) {
686 dst->atom[i] = src->atom[i];
687 if (NULL != src->pdbinfo)
688 dst->pdbinfo[i] = src->pdbinfo[i];
689 if (NULL != src->atomname)
690 dst->atomname[i] = src->atomname[i];
691 if (NULL != src->atomtype)
692 dst->atomtype[i] = src->atomtype[i];
693 if (NULL != src->atomtypeB)
694 dst->atomtypeB[i] = src->atomtypeB[i];
695 }
696 dst->nres = src->nres;
697 for(i=0; (i<src->nres); i++) {
698 dst->resinfo[i] = src->resinfo[i];
699 }
700 return dst;
701 }
702
703 void t_atoms_set_resinfo(t_atoms *atoms,int atom_ind,t_symtab *symtab,
704 const char *resname,int resnr,unsigned char ic,
705 int chainnum, char chainid)
706 {
707 t_resinfo *ri;
708
709 ri = &atoms->resinfo[atoms->atom[atom_ind].resind];
710 ri->name = put_symtab(symtab,resname);
711 ri->rtp = NULL;
712 ri->nr = resnr;
713 ri->ic = ic;
714 ri->chainnum = chainnum;
715 ri->chainid = chainid;
716 }
717
718 void free_t_atoms(t_atoms *atoms,gmx_bool bFreeNames)
719 {
720 int i;
721
722 if (bFreeNames) {
723 for(i=0; i<atoms->nr; i++) {
724 sfree(*atoms->atomname[i]);
725 *atoms->atomname[i]=NULL;
726 }
727 for(i=0; i<atoms->nres; i++) {
728 sfree(*atoms->resinfo[i].name);
729 *atoms->resinfo[i].name=NULL;
730 }
731 }
732 sfree(atoms->atomname);
733 /* Do we need to free atomtype and atomtypeB as well ? */
734 sfree(atoms->resinfo);
735 sfree(atoms->atom);
736 if (atoms->pdbinfo)
737 sfree(atoms->pdbinfo);
738 atoms->nr=0;
739 atoms->nres=0;
740 }
741
742 real max_cutoff(real cutoff1,real cutoff2)
743 {
744 if (cutoff1 == 0 || cutoff2 == 0)
745 {
746 return 0;
747 }
748 else
749 {
750 return max(cutoff1,cutoff2);
751 }
752 }
The ultimate molecular dynamics simulation package