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added Verlet scheme and NxN non-bonded functionality
[gromacs.git] / src / gmxlib / tpxio.c
blob96df62a49386a0da496377d7d681b62ac41be1be
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 #ifdef HAVE_CONFIG_H
37 #include <config.h>
38 #endif
39
40 /* This file is completely threadsafe - keep it that way! */
41 #ifdef GMX_THREAD_MPI
42 #include <thread_mpi.h>
43 #endif
44
45
46 #include <ctype.h>
47 #include "sysstuff.h"
48 #include "smalloc.h"
49 #include "string2.h"
50 #include "gmx_fatal.h"
51 #include "macros.h"
52 #include "names.h"
53 #include "symtab.h"
54 #include "futil.h"
55 #include "filenm.h"
56 #include "gmxfio.h"
57 #include "topsort.h"
58 #include "tpxio.h"
59 #include "txtdump.h"
60 #include "confio.h"
61 #include "atomprop.h"
62 #include "copyrite.h"
63 #include "vec.h"
64 #include "mtop_util.h"
65
66 #define TPX_TAG_RELEASE "release"
67
68 /* This is the tag string which is stored in the tpx file.
69 * Change this if you want to change the tpx format in a feature branch.
70 * This ensures that there will not be different tpx formats around which
71 * can not be distinguished.
72 */
73 static const char *tpx_tag = TPX_TAG_RELEASE;
74
75 /* This number should be increased whenever the file format changes! */
76 static const int tpx_version = 80;
77
78 /* This number should only be increased when you edit the TOPOLOGY section
79 * or the HEADER of the tpx format.
80 * This way we can maintain forward compatibility too for all analysis tools
81 * and/or external programs that only need to know the atom/residue names,
82 * charges, and bond connectivity.
83 *
84 * It first appeared in tpx version 26, when I also moved the inputrecord
85 * to the end of the tpx file, so we can just skip it if we only
86 * want the topology.
87 */
88 static const int tpx_generation = 24;
89
90 /* This number should be the most recent backwards incompatible version
91 * I.e., if this number is 9, we cannot read tpx version 9 with this code.
92 */
93 static const int tpx_incompatible_version = 9;
94
95
96
97 /* Struct used to maintain tpx compatibility when function types are added */
98 typedef struct {
99 int fvnr; /* file version number in which the function type first appeared */
100 int ftype; /* function type */
101 } t_ftupd;
102
103 /*
104 *The entries should be ordered in:
105 * 1. ascending file version number
106 * 2. ascending function type number
107 */
108 /*static const t_ftupd ftupd[] = {
109 { 20, F_CUBICBONDS },
110 { 20, F_CONNBONDS },
111 { 20, F_HARMONIC },
112 { 20, F_EQM, },
113 { 22, F_DISRESVIOL },
114 { 22, F_ORIRES },
115 { 22, F_ORIRESDEV },
116 { 26, F_FOURDIHS },
117 { 26, F_PIDIHS },
118 { 26, F_DIHRES },
119 { 26, F_DIHRESVIOL },
120 { 30, F_CROSS_BOND_BONDS },
121 { 30, F_CROSS_BOND_ANGLES },
122 { 30, F_UREY_BRADLEY },
123 { 30, F_POLARIZATION },
124 { 54, F_DHDL_CON },
125 };*/
126 /*
127 *The entries should be ordered in:
128 * 1. ascending function type number
129 * 2. ascending file version number
130 */
131 /* question; what is the purpose of the commented code above? */
132 static const t_ftupd ftupd[] = {
133 { 20, F_CUBICBONDS },
134 { 20, F_CONNBONDS },
135 { 20, F_HARMONIC },
136 { 34, F_FENEBONDS },
137 { 43, F_TABBONDS },
138 { 43, F_TABBONDSNC },
139 { 70, F_RESTRBONDS },
140 { 76, F_LINEAR_ANGLES },
141 { 30, F_CROSS_BOND_BONDS },
142 { 30, F_CROSS_BOND_ANGLES },
143 { 30, F_UREY_BRADLEY },
144 { 34, F_QUARTIC_ANGLES },
145 { 43, F_TABANGLES },
146 { 26, F_FOURDIHS },
147 { 26, F_PIDIHS },
148 { 43, F_TABDIHS },
149 { 65, F_CMAP },
150 { 60, F_GB12 },
151 { 61, F_GB13 },
152 { 61, F_GB14 },
153 { 72, F_GBPOL },
154 { 72, F_NPSOLVATION },
155 { 41, F_LJC14_Q },
156 { 41, F_LJC_PAIRS_NB },
157 { 32, F_BHAM_LR },
158 { 32, F_RF_EXCL },
159 { 32, F_COUL_RECIP },
160 { 46, F_DPD },
161 { 30, F_POLARIZATION },
162 { 36, F_THOLE_POL },
163 { 22, F_DISRESVIOL },
164 { 22, F_ORIRES },
165 { 22, F_ORIRESDEV },
166 { 26, F_DIHRES },
167 { 26, F_DIHRESVIOL },
168 { 49, F_VSITE4FDN },
169 { 50, F_VSITEN },
170 { 46, F_COM_PULL },
171 { 20, F_EQM },
172 { 46, F_ECONSERVED },
173 { 69, F_VTEMP },
174 { 66, F_PDISPCORR },
175 { 54, F_DHDL_CON },
176 { 76, F_ANHARM_POL },
177 { 79, F_DVDL_COUL },
178 { 79, F_DVDL_VDW, },
179 { 79, F_DVDL_BONDED, },
180 { 79, F_DVDL_RESTRAINT },
181 { 79, F_DVDL_TEMPERATURE },
182 { 54, F_DHDL_CON }
183 };
184 #define NFTUPD asize(ftupd)
185
186 /* Needed for backward compatibility */
187 #define MAXNODES 256
188
189 static void _do_section(t_fileio *fio,int key,gmx_bool bRead,const char *src,
190 int line)
191 {
192 char buf[STRLEN];
193 gmx_bool bDbg;
194
195 if (gmx_fio_getftp(fio) == efTPA) {
196 if (!bRead) {
197 gmx_fio_write_string(fio,itemstr[key]);
198 bDbg = gmx_fio_getdebug(fio);
199 gmx_fio_setdebug(fio,FALSE);
200 gmx_fio_write_string(fio,comment_str[key]);
201 gmx_fio_setdebug(fio,bDbg);
202 }
203 else {
204 if (gmx_fio_getdebug(fio))
205 fprintf(stderr,"Looking for section %s (%s, %d)",
206 itemstr[key],src,line);
207
208 do {
209 gmx_fio_do_string(fio,buf);
210 } while ((gmx_strcasecmp(buf,itemstr[key]) != 0));
211
212 if (gmx_strcasecmp(buf,itemstr[key]) != 0)
213 gmx_fatal(FARGS,"\nCould not find section heading %s",itemstr[key]);
214 else if (gmx_fio_getdebug(fio))
215 fprintf(stderr," and found it\n");
216 }
217 }
218 }
219
220 #define do_section(fio,key,bRead) _do_section(fio,key,bRead,__FILE__,__LINE__)
221
222 /**************************************************************
223 *
224 * Now the higer level routines that do io of the structures and arrays
225 *
226 **************************************************************/
227 static void do_pullgrp(t_fileio *fio, t_pullgrp *pgrp, gmx_bool bRead,
228 int file_version)
229 {
230 gmx_bool bDum=TRUE;
231 int i;
232
233 gmx_fio_do_int(fio,pgrp->nat);
234 if (bRead)
235 snew(pgrp->ind,pgrp->nat);
236 bDum=gmx_fio_ndo_int(fio,pgrp->ind,pgrp->nat);
237 gmx_fio_do_int(fio,pgrp->nweight);
238 if (bRead)
239 snew(pgrp->weight,pgrp->nweight);
240 bDum=gmx_fio_ndo_real(fio,pgrp->weight,pgrp->nweight);
241 gmx_fio_do_int(fio,pgrp->pbcatom);
242 gmx_fio_do_rvec(fio,pgrp->vec);
243 gmx_fio_do_rvec(fio,pgrp->init);
244 gmx_fio_do_real(fio,pgrp->rate);
245 gmx_fio_do_real(fio,pgrp->k);
246 if (file_version >= 56) {
247 gmx_fio_do_real(fio,pgrp->kB);
248 } else {
249 pgrp->kB = pgrp->k;
250 }
251 }
252
253 static void do_expandedvals(t_fileio *fio,t_expanded *expand,int n_lambda, gmx_bool bRead, int file_version)
254 {
255 /* i is used in the ndo_double macro*/
256 int i;
257 real fv;
258 gmx_bool bDum=TRUE;
259 real rdum;
260
261 if (file_version >= 79)
262 {
263 if (n_lambda>0)
264 {
265 if (bRead)
266 {
267 snew(expand->init_lambda_weights,n_lambda);
268 }
269 bDum=gmx_fio_ndo_real(fio,expand->init_lambda_weights,n_lambda);
270 gmx_fio_do_gmx_bool(fio,expand->bInit_weights);
271 }
272
273 gmx_fio_do_int(fio,expand->nstexpanded);
274 gmx_fio_do_int(fio,expand->elmcmove);
275 gmx_fio_do_int(fio,expand->elamstats);
276 gmx_fio_do_int(fio,expand->lmc_repeats);
277 gmx_fio_do_int(fio,expand->gibbsdeltalam);
278 gmx_fio_do_int(fio,expand->lmc_forced_nstart);
279 gmx_fio_do_int(fio,expand->lmc_seed);
280 gmx_fio_do_real(fio,expand->mc_temp);
281 gmx_fio_do_int(fio,expand->bSymmetrizedTMatrix);
282 gmx_fio_do_int(fio,expand->nstTij);
283 gmx_fio_do_int(fio,expand->minvarmin);
284 gmx_fio_do_int(fio,expand->c_range);
285 gmx_fio_do_real(fio,expand->wl_scale);
286 gmx_fio_do_real(fio,expand->wl_ratio);
287 gmx_fio_do_real(fio,expand->init_wl_delta);
288 gmx_fio_do_gmx_bool(fio,expand->bWLoneovert);
289 gmx_fio_do_int(fio,expand->elmceq);
290 gmx_fio_do_int(fio,expand->equil_steps);
291 gmx_fio_do_int(fio,expand->equil_samples);
292 gmx_fio_do_int(fio,expand->equil_n_at_lam);
293 gmx_fio_do_real(fio,expand->equil_wl_delta);
294 gmx_fio_do_real(fio,expand->equil_ratio);
295 }
296 }
297
298 static void do_simtempvals(t_fileio *fio,t_simtemp *simtemp, int n_lambda, gmx_bool bRead,
299 int file_version)
300 {
301 gmx_bool bDum=TRUE;
302
303 if (file_version >= 79)
304 {
305 gmx_fio_do_int(fio,simtemp->eSimTempScale);
306 gmx_fio_do_real(fio,simtemp->simtemp_high);
307 gmx_fio_do_real(fio,simtemp->simtemp_low);
308 if (n_lambda>0)
309 {
310 if (bRead)
311 {
312 snew(simtemp->temperatures,n_lambda);
313 }
314 bDum=gmx_fio_ndo_real(fio,simtemp->temperatures,n_lambda);
315 }
316 }
317 }
318
319 static void do_fepvals(t_fileio *fio,t_lambda *fepvals,gmx_bool bRead, int file_version)
320 {
321 /* i is defined in the ndo_double macro; use g to iterate. */
322 int i,g;
323 real fv;
324 gmx_bool bDum=TRUE;
325 real rdum;
326
327 /* free energy values */
328 if (file_version >= 79)
329 {
330 gmx_fio_do_int(fio,fepvals->init_fep_state);
331 gmx_fio_do_double(fio,fepvals->init_lambda);
332 gmx_fio_do_double(fio,fepvals->delta_lambda);
333 }
334 else if (file_version >= 59) {
335 gmx_fio_do_double(fio,fepvals->init_lambda);
336 gmx_fio_do_double(fio,fepvals->delta_lambda);
337 } else {
338 gmx_fio_do_real(fio,rdum);
339 fepvals->init_lambda = rdum;
340 gmx_fio_do_real(fio,rdum);
341 fepvals->delta_lambda = rdum;
342 }
343 if (file_version >= 79)
344 {
345 gmx_fio_do_int(fio,fepvals->n_lambda);
346 if (bRead)
347 {
348 snew(fepvals->all_lambda,efptNR);
349 }
350 for (g=0;g<efptNR;g++)
351 {
352 if (fepvals->n_lambda > 0) {
353 if (bRead)
354 {
355 snew(fepvals->all_lambda[g],fepvals->n_lambda);
356 }
357 bDum=gmx_fio_ndo_double(fio,fepvals->all_lambda[g],fepvals->n_lambda);
358 bDum=gmx_fio_ndo_int(fio,fepvals->separate_dvdl,efptNR);
359 }
360 else if (fepvals->init_lambda >= 0)
361 {
362 fepvals->separate_dvdl[efptFEP] = TRUE;
363 }
364 }
365 }
366 else if (file_version >= 64)
367 {
368 gmx_fio_do_int(fio,fepvals->n_lambda);
369 snew(fepvals->all_lambda,efptNR);
370 if (bRead)
371 {
372 snew(fepvals->all_lambda[efptFEP],fepvals->n_lambda);
373 }
374 bDum=gmx_fio_ndo_double(fio,fepvals->all_lambda[efptFEP],fepvals->n_lambda);
375 if (fepvals->init_lambda >= 0)
376 {
377 fepvals->separate_dvdl[efptFEP] = TRUE;
378 }
379 /* still allocate the all_lambda array's contents. */
380 for (g=0;g<efptNR;g++)
381 {
382 if (fepvals->n_lambda > 0) {
383 if (bRead)
384 {
385 snew(fepvals->all_lambda[g],fepvals->n_lambda);
386 }
387 }
388 }
389 }
390 else
391 {
392 fepvals->n_lambda = 0;
393 fepvals->all_lambda = NULL;
394 if (fepvals->init_lambda >= 0)
395 {
396 fepvals->separate_dvdl[efptFEP] = TRUE;
397 }
398 }
399 if (file_version >= 13)
400 {
401 gmx_fio_do_real(fio,fepvals->sc_alpha);
402 }
403 else
404 {
405 fepvals->sc_alpha = 0;
406 }
407 if (file_version >= 38)
408 {
409 gmx_fio_do_int(fio,fepvals->sc_power);
410 }
411 else
412 {
413 fepvals->sc_power = 2;
414 }
415 if (file_version >= 79)
416 {
417 gmx_fio_do_real(fio,fepvals->sc_r_power);
418 }
419 else
420 {
421 fepvals->sc_r_power = 6.0;
422 }
423 if (file_version >= 15)
424 {
425 gmx_fio_do_real(fio,fepvals->sc_sigma);
426 }
427 else
428 {
429 fepvals->sc_sigma = 0.3;
430 }
431 if (bRead)
432 {
433 if (file_version >= 71)
434 {
435 fepvals->sc_sigma_min = fepvals->sc_sigma;
436 }
437 else
438 {
439 fepvals->sc_sigma_min = 0;
440 }
441 }
442 if (file_version >= 79)
443 {
444 gmx_fio_do_int(fio,fepvals->bScCoul);
445 }
446 else
447 {
448 fepvals->bScCoul = TRUE;
449 }
450 if (file_version >= 64) {
451 gmx_fio_do_int(fio,fepvals->nstdhdl);
452 } else {
453 fepvals->nstdhdl = 1;
454 }
455
456 if (file_version >= 73)
457 {
458 gmx_fio_do_int(fio, fepvals->separate_dhdl_file);
459 gmx_fio_do_int(fio, fepvals->dhdl_derivatives);
460 }
461 else
462 {
463 fepvals->separate_dhdl_file = esepdhdlfileYES;
464 fepvals->dhdl_derivatives = edhdlderivativesYES;
465 }
466 if (file_version >= 71)
467 {
468 gmx_fio_do_int(fio,fepvals->dh_hist_size);
469 gmx_fio_do_double(fio,fepvals->dh_hist_spacing);
470 }
471 else
472 {
473 fepvals->dh_hist_size = 0;
474 fepvals->dh_hist_spacing = 0.1;
475 }
476 if (file_version >= 79)
477 {
478 gmx_fio_do_int(fio,fepvals->bPrintEnergy);
479 }
480 else
481 {
482 fepvals->bPrintEnergy = FALSE;
483 }
484 }
485
486 static void do_pull(t_fileio *fio, t_pull *pull,gmx_bool bRead, int file_version)
487 {
488 int g;
489
490 gmx_fio_do_int(fio,pull->ngrp);
491 gmx_fio_do_int(fio,pull->eGeom);
492 gmx_fio_do_ivec(fio,pull->dim);
493 gmx_fio_do_real(fio,pull->cyl_r1);
494 gmx_fio_do_real(fio,pull->cyl_r0);
495 gmx_fio_do_real(fio,pull->constr_tol);
496 gmx_fio_do_int(fio,pull->nstxout);
497 gmx_fio_do_int(fio,pull->nstfout);
498 if (bRead)
499 snew(pull->grp,pull->ngrp+1);
500 for(g=0; g<pull->ngrp+1; g++)
501 do_pullgrp(fio,&pull->grp[g],bRead,file_version);
502 }
503
504
505 static void do_rotgrp(t_fileio *fio, t_rotgrp *rotg,gmx_bool bRead, int file_version)
506 {
507 gmx_bool bDum=TRUE;
508 int i;
509
510 gmx_fio_do_int(fio,rotg->eType);
511 gmx_fio_do_int(fio,rotg->bMassW);
512 gmx_fio_do_int(fio,rotg->nat);
513 if (bRead)
514 snew(rotg->ind,rotg->nat);
515 gmx_fio_ndo_int(fio,rotg->ind,rotg->nat);
516 if (bRead)
517 snew(rotg->x_ref,rotg->nat);
518 gmx_fio_ndo_rvec(fio,rotg->x_ref,rotg->nat);
519 gmx_fio_do_rvec(fio,rotg->vec);
520 gmx_fio_do_rvec(fio,rotg->pivot);
521 gmx_fio_do_real(fio,rotg->rate);
522 gmx_fio_do_real(fio,rotg->k);
523 gmx_fio_do_real(fio,rotg->slab_dist);
524 gmx_fio_do_real(fio,rotg->min_gaussian);
525 gmx_fio_do_real(fio,rotg->eps);
526 gmx_fio_do_int(fio,rotg->eFittype);
527 gmx_fio_do_int(fio,rotg->PotAngle_nstep);
528 gmx_fio_do_real(fio,rotg->PotAngle_step);
529 }
530
531 static void do_rot(t_fileio *fio, t_rot *rot,gmx_bool bRead, int file_version)
532 {
533 int g;
534
535 gmx_fio_do_int(fio,rot->ngrp);
536 gmx_fio_do_int(fio,rot->nstrout);
537 gmx_fio_do_int(fio,rot->nstsout);
538 if (bRead)
539 snew(rot->grp,rot->ngrp);
540 for(g=0; g<rot->ngrp; g++)
541 do_rotgrp(fio, &rot->grp[g],bRead,file_version);
542 }
543
544
545 static void do_inputrec(t_fileio *fio, t_inputrec *ir,gmx_bool bRead,
546 int file_version, real *fudgeQQ)
547 {
548 int i,j,k,*tmp,idum=0;
549 gmx_bool bDum=TRUE;
550 real rdum,bd_temp;
551 rvec vdum;
552 gmx_bool bSimAnn;
553 real zerotemptime,finish_t,init_temp,finish_temp;
554
555 if (file_version != tpx_version)
556 {
557 /* Give a warning about features that are not accessible */
558 fprintf(stderr,"Note: file tpx version %d, software tpx version %d\n",
559 file_version,tpx_version);
560 }
561
562 if (bRead)
563 {
564 init_inputrec(ir);
565 }
566
567 if (file_version == 0)
568 {
569 return;
570 }
571
572 /* Basic inputrec stuff */
573 gmx_fio_do_int(fio,ir->eI);
574 if (file_version >= 62) {
575 gmx_fio_do_gmx_large_int(fio, ir->nsteps);
576 } else {
577 gmx_fio_do_int(fio,idum);
578 ir->nsteps = idum;
579 }
580 if(file_version > 25) {
581 if (file_version >= 62) {
582 gmx_fio_do_gmx_large_int(fio, ir->init_step);
583 } else {
584 gmx_fio_do_int(fio,idum);
585 ir->init_step = idum;
586 }
587 } else {
588 ir->init_step=0;
589 }
590
591 if(file_version >= 58)
592 gmx_fio_do_int(fio,ir->simulation_part);
593 else
594 ir->simulation_part=1;
595
596 if (file_version >= 67) {
597 gmx_fio_do_int(fio,ir->nstcalcenergy);
598 } else {
599 ir->nstcalcenergy = 1;
600 }
601 if (file_version < 53) {
602 /* The pbc info has been moved out of do_inputrec,
603 * since we always want it, also without reading the inputrec.
604 */
605 gmx_fio_do_int(fio,ir->ePBC);
606 if ((file_version <= 15) && (ir->ePBC == 2))
607 ir->ePBC = epbcNONE;
608 if (file_version >= 45) {
609 gmx_fio_do_int(fio,ir->bPeriodicMols);
610 } else {
611 if (ir->ePBC == 2) {
612 ir->ePBC = epbcXYZ;
613 ir->bPeriodicMols = TRUE;
614 } else {
615 ir->bPeriodicMols = FALSE;
616 }
617 }
618 }
619 if (file_version >= 80)
620 {
621 gmx_fio_do_int(fio,ir->cutoff_scheme);
622 }
623 else
624 {
625 ir->cutoff_scheme = ecutsGROUP;
626 }
627 gmx_fio_do_int(fio,ir->ns_type);
628 gmx_fio_do_int(fio,ir->nstlist);
629 gmx_fio_do_int(fio,ir->ndelta);
630 if (file_version < 41) {
631 gmx_fio_do_int(fio,idum);
632 gmx_fio_do_int(fio,idum);
633 }
634 if (file_version >= 45)
635 gmx_fio_do_real(fio,ir->rtpi);
636 else
637 ir->rtpi = 0.05;
638 gmx_fio_do_int(fio,ir->nstcomm);
639 if (file_version > 34)
640 gmx_fio_do_int(fio,ir->comm_mode);
641 else if (ir->nstcomm < 0)
642 ir->comm_mode = ecmANGULAR;
643 else
644 ir->comm_mode = ecmLINEAR;
645 ir->nstcomm = abs(ir->nstcomm);
646
647 if(file_version > 25)
648 gmx_fio_do_int(fio,ir->nstcheckpoint);
649 else
650 ir->nstcheckpoint=0;
651
652 gmx_fio_do_int(fio,ir->nstcgsteep);
653
654 if(file_version>=30)
655 gmx_fio_do_int(fio,ir->nbfgscorr);
656 else if (bRead)
657 ir->nbfgscorr = 10;
658
659 gmx_fio_do_int(fio,ir->nstlog);
660 gmx_fio_do_int(fio,ir->nstxout);
661 gmx_fio_do_int(fio,ir->nstvout);
662 gmx_fio_do_int(fio,ir->nstfout);
663 gmx_fio_do_int(fio,ir->nstenergy);
664 gmx_fio_do_int(fio,ir->nstxtcout);
665 if (file_version >= 59) {
666 gmx_fio_do_double(fio,ir->init_t);
667 gmx_fio_do_double(fio,ir->delta_t);
668 } else {
669 gmx_fio_do_real(fio,rdum);
670 ir->init_t = rdum;
671 gmx_fio_do_real(fio,rdum);
672 ir->delta_t = rdum;
673 }
674 gmx_fio_do_real(fio,ir->xtcprec);
675 if (file_version < 19) {
676 gmx_fio_do_int(fio,idum);
677 gmx_fio_do_int(fio,idum);
678 }
679 if(file_version < 18)
680 gmx_fio_do_int(fio,idum);
681 if (file_version >= 80) {
682 gmx_fio_do_real(fio,ir->verletbuf_drift);
683 } else {
684 ir->verletbuf_drift = 0;
685 }
686 gmx_fio_do_real(fio,ir->rlist);
687 if (file_version >= 67) {
688 gmx_fio_do_real(fio,ir->rlistlong);
689 }
690 gmx_fio_do_int(fio,ir->coulombtype);
691 if (file_version < 32 && ir->coulombtype == eelRF)
692 ir->coulombtype = eelRF_NEC;
693 gmx_fio_do_real(fio,ir->rcoulomb_switch);
694 gmx_fio_do_real(fio,ir->rcoulomb);
695 gmx_fio_do_int(fio,ir->vdwtype);
696 gmx_fio_do_real(fio,ir->rvdw_switch);
697 gmx_fio_do_real(fio,ir->rvdw);
698 if (file_version < 67) {
699 ir->rlistlong = max_cutoff(ir->rlist,max_cutoff(ir->rvdw,ir->rcoulomb));
700 }
701 gmx_fio_do_int(fio,ir->eDispCorr);
702 gmx_fio_do_real(fio,ir->epsilon_r);
703 if (file_version >= 37) {
704 gmx_fio_do_real(fio,ir->epsilon_rf);
705 } else {
706 if (EEL_RF(ir->coulombtype)) {
707 ir->epsilon_rf = ir->epsilon_r;
708 ir->epsilon_r = 1.0;
709 } else {
710 ir->epsilon_rf = 1.0;
711 }
712 }
713 if (file_version >= 29)
714 gmx_fio_do_real(fio,ir->tabext);
715 else
716 ir->tabext=1.0;
717
718 if(file_version > 25) {
719 gmx_fio_do_int(fio,ir->gb_algorithm);
720 gmx_fio_do_int(fio,ir->nstgbradii);
721 gmx_fio_do_real(fio,ir->rgbradii);
722 gmx_fio_do_real(fio,ir->gb_saltconc);
723 gmx_fio_do_int(fio,ir->implicit_solvent);
724 } else {
725 ir->gb_algorithm=egbSTILL;
726 ir->nstgbradii=1;
727 ir->rgbradii=1.0;
728 ir->gb_saltconc=0;
729 ir->implicit_solvent=eisNO;
730 }
731 if(file_version>=55)
732 {
733 gmx_fio_do_real(fio,ir->gb_epsilon_solvent);
734 gmx_fio_do_real(fio,ir->gb_obc_alpha);
735 gmx_fio_do_real(fio,ir->gb_obc_beta);
736 gmx_fio_do_real(fio,ir->gb_obc_gamma);
737 if(file_version>=60)
738 {
739 gmx_fio_do_real(fio,ir->gb_dielectric_offset);
740 gmx_fio_do_int(fio,ir->sa_algorithm);
741 }
742 else
743 {
744 ir->gb_dielectric_offset = 0.009;
745 ir->sa_algorithm = esaAPPROX;
746 }
747 gmx_fio_do_real(fio,ir->sa_surface_tension);
748
749 /* Override sa_surface_tension if it is not changed in the mpd-file */
750 if(ir->sa_surface_tension<0)
751 {
752 if(ir->gb_algorithm==egbSTILL)
753 {
754 ir->sa_surface_tension = 0.0049 * 100 * CAL2JOULE;
755 }
756 else if(ir->gb_algorithm==egbHCT || ir->gb_algorithm==egbOBC)
757 {
758 ir->sa_surface_tension = 0.0054 * 100 * CAL2JOULE;
759 }
760 }
761
762 }
763 else
764 {
765 /* Better use sensible values than insane (0.0) ones... */
766 ir->gb_epsilon_solvent = 80;
767 ir->gb_obc_alpha = 1.0;
768 ir->gb_obc_beta = 0.8;
769 ir->gb_obc_gamma = 4.85;
770 ir->sa_surface_tension = 2.092;
771 }
772
773
774 if (file_version >= 80)
775 {
776 gmx_fio_do_real(fio,ir->fourier_spacing);
777 }
778 else
779 {
780 ir->fourier_spacing = 0.0;
781 }
782 gmx_fio_do_int(fio,ir->nkx);
783 gmx_fio_do_int(fio,ir->nky);
784 gmx_fio_do_int(fio,ir->nkz);
785 gmx_fio_do_int(fio,ir->pme_order);
786 gmx_fio_do_real(fio,ir->ewald_rtol);
787
788 if (file_version >=24)
789 gmx_fio_do_int(fio,ir->ewald_geometry);
790 else
791 ir->ewald_geometry=eewg3D;
792
793 if (file_version <=17) {
794 ir->epsilon_surface=0;
795 if (file_version==17)
796 gmx_fio_do_int(fio,idum);
797 }
798 else
799 gmx_fio_do_real(fio,ir->epsilon_surface);
800
801 gmx_fio_do_gmx_bool(fio,ir->bOptFFT);
802
803 gmx_fio_do_gmx_bool(fio,ir->bContinuation);
804 gmx_fio_do_int(fio,ir->etc);
805 /* before version 18, ir->etc was a gmx_bool (ir->btc),
806 * but the values 0 and 1 still mean no and
807 * berendsen temperature coupling, respectively.
808 */
809 if (file_version >= 79) {
810 gmx_fio_do_gmx_bool(fio,ir->bPrintNHChains);
811 }
812 if (file_version >= 71)
813 {
814 gmx_fio_do_int(fio,ir->nsttcouple);
815 }
816 else
817 {
818 ir->nsttcouple = ir->nstcalcenergy;
819 }
820 if (file_version <= 15)
821 {
822 gmx_fio_do_int(fio,idum);
823 }
824 if (file_version <=17)
825 {
826 gmx_fio_do_int(fio,ir->epct);
827 if (file_version <= 15)
828 {
829 if (ir->epct == 5)
830 {
831 ir->epct = epctSURFACETENSION;
832 }
833 gmx_fio_do_int(fio,idum);
834 }
835 ir->epct -= 1;
836 /* we have removed the NO alternative at the beginning */
837 if(ir->epct==-1)
838 {
839 ir->epc=epcNO;
840 ir->epct=epctISOTROPIC;
841 }
842 else
843 {
844 ir->epc=epcBERENDSEN;
845 }
846 }
847 else
848 {
849 gmx_fio_do_int(fio,ir->epc);
850 gmx_fio_do_int(fio,ir->epct);
851 }
852 if (file_version >= 71)
853 {
854 gmx_fio_do_int(fio,ir->nstpcouple);
855 }
856 else
857 {
858 ir->nstpcouple = ir->nstcalcenergy;
859 }
860 gmx_fio_do_real(fio,ir->tau_p);
861 if (file_version <= 15) {
862 gmx_fio_do_rvec(fio,vdum);
863 clear_mat(ir->ref_p);
864 for(i=0; i<DIM; i++)
865 ir->ref_p[i][i] = vdum[i];
866 } else {
867 gmx_fio_do_rvec(fio,ir->ref_p[XX]);
868 gmx_fio_do_rvec(fio,ir->ref_p[YY]);
869 gmx_fio_do_rvec(fio,ir->ref_p[ZZ]);
870 }
871 if (file_version <= 15) {
872 gmx_fio_do_rvec(fio,vdum);
873 clear_mat(ir->compress);
874 for(i=0; i<DIM; i++)
875 ir->compress[i][i] = vdum[i];
876 }
877 else {
878 gmx_fio_do_rvec(fio,ir->compress[XX]);
879 gmx_fio_do_rvec(fio,ir->compress[YY]);
880 gmx_fio_do_rvec(fio,ir->compress[ZZ]);
881 }
882 if (file_version >= 47) {
883 gmx_fio_do_int(fio,ir->refcoord_scaling);
884 gmx_fio_do_rvec(fio,ir->posres_com);
885 gmx_fio_do_rvec(fio,ir->posres_comB);
886 } else {
887 ir->refcoord_scaling = erscNO;
888 clear_rvec(ir->posres_com);
889 clear_rvec(ir->posres_comB);
890 }
891 if((file_version > 25) && (file_version < 79))
892 gmx_fio_do_int(fio,ir->andersen_seed);
893 else
894 ir->andersen_seed=0;
895 if(file_version < 26) {
896 gmx_fio_do_gmx_bool(fio,bSimAnn);
897 gmx_fio_do_real(fio,zerotemptime);
898 }
899
900 if (file_version < 37)
901 gmx_fio_do_real(fio,rdum);
902
903 gmx_fio_do_real(fio,ir->shake_tol);
904 if (file_version < 54)
905 gmx_fio_do_real(fio,*fudgeQQ);
906
907 gmx_fio_do_int(fio,ir->efep);
908 if (file_version <= 14 && ir->efep != efepNO)
909 {
910 ir->efep = efepYES;
911 }
912 do_fepvals(fio,ir->fepvals,bRead,file_version);
913
914 if (file_version >= 79)
915 {
916 gmx_fio_do_gmx_bool(fio,ir->bSimTemp);
917 if (ir->bSimTemp)
918 {
919 ir->bSimTemp = TRUE;
920 }
921 }
922 else
923 {
924 ir->bSimTemp = FALSE;
925 }
926 if (ir->bSimTemp)
927 {
928 do_simtempvals(fio,ir->simtempvals,ir->fepvals->n_lambda,bRead,file_version);
929 }
930
931 if (file_version >= 79)
932 {
933 gmx_fio_do_gmx_bool(fio,ir->bExpanded);
934 if (ir->bExpanded)
935 {
936 ir->bExpanded = TRUE;
937 }
938 else
939 {
940 ir->bExpanded = FALSE;
941 }
942 }
943 if (ir->bExpanded)
944 {
945 do_expandedvals(fio,ir->expandedvals,ir->fepvals->n_lambda,bRead,file_version);
946 }
947 if (file_version >= 57) {
948 gmx_fio_do_int(fio,ir->eDisre);
949 }
950 gmx_fio_do_int(fio,ir->eDisreWeighting);
951 if (file_version < 22) {
952 if (ir->eDisreWeighting == 0)
953 ir->eDisreWeighting = edrwEqual;
954 else
955 ir->eDisreWeighting = edrwConservative;
956 }
957 gmx_fio_do_gmx_bool(fio,ir->bDisreMixed);
958 gmx_fio_do_real(fio,ir->dr_fc);
959 gmx_fio_do_real(fio,ir->dr_tau);
960 gmx_fio_do_int(fio,ir->nstdisreout);
961 if (file_version >= 22) {
962 gmx_fio_do_real(fio,ir->orires_fc);
963 gmx_fio_do_real(fio,ir->orires_tau);
964 gmx_fio_do_int(fio,ir->nstorireout);
965 } else {
966 ir->orires_fc = 0;
967 ir->orires_tau = 0;
968 ir->nstorireout = 0;
969 }
970 if(file_version >= 26 && file_version < 79) {
971 gmx_fio_do_real(fio,ir->dihre_fc);
972 if (file_version < 56)
973 {
974 gmx_fio_do_real(fio,rdum);
975 gmx_fio_do_int(fio,idum);
976 }
977 } else {
978 ir->dihre_fc=0;
979 }
980
981 gmx_fio_do_real(fio,ir->em_stepsize);
982 gmx_fio_do_real(fio,ir->em_tol);
983 if (file_version >= 22)
984 gmx_fio_do_gmx_bool(fio,ir->bShakeSOR);
985 else if (bRead)
986 ir->bShakeSOR = TRUE;
987 if (file_version >= 11)
988 gmx_fio_do_int(fio,ir->niter);
989 else if (bRead) {
990 ir->niter = 25;
991 fprintf(stderr,"Note: niter not in run input file, setting it to %d\n",
992 ir->niter);
993 }
994 if (file_version >= 21)
995 gmx_fio_do_real(fio,ir->fc_stepsize);
996 else
997 ir->fc_stepsize = 0;
998 gmx_fio_do_int(fio,ir->eConstrAlg);
999 gmx_fio_do_int(fio,ir->nProjOrder);
1000 gmx_fio_do_real(fio,ir->LincsWarnAngle);
1001 if (file_version <= 14)
1002 gmx_fio_do_int(fio,idum);
1003 if (file_version >=26)
1004 gmx_fio_do_int(fio,ir->nLincsIter);
1005 else if (bRead) {
1006 ir->nLincsIter = 1;
1007 fprintf(stderr,"Note: nLincsIter not in run input file, setting it to %d\n",
1008 ir->nLincsIter);
1009 }
1010 if (file_version < 33)
1011 gmx_fio_do_real(fio,bd_temp);
1012 gmx_fio_do_real(fio,ir->bd_fric);
1013 gmx_fio_do_int(fio,ir->ld_seed);
1014 if (file_version >= 33) {
1015 for(i=0; i<DIM; i++)
1016 gmx_fio_do_rvec(fio,ir->deform[i]);
1017 } else {
1018 for(i=0; i<DIM; i++)
1019 clear_rvec(ir->deform[i]);
1020 }
1021 if (file_version >= 14)
1022 gmx_fio_do_real(fio,ir->cos_accel);
1023 else if (bRead)
1024 ir->cos_accel = 0;
1025 gmx_fio_do_int(fio,ir->userint1);
1026 gmx_fio_do_int(fio,ir->userint2);
1027 gmx_fio_do_int(fio,ir->userint3);
1028 gmx_fio_do_int(fio,ir->userint4);
1029 gmx_fio_do_real(fio,ir->userreal1);
1030 gmx_fio_do_real(fio,ir->userreal2);
1031 gmx_fio_do_real(fio,ir->userreal3);
1032 gmx_fio_do_real(fio,ir->userreal4);
1033
1034 /* AdResS stuff */
1035 if (file_version >= 77) {
1036 gmx_fio_do_gmx_bool(fio,ir->bAdress);
1037 if(ir->bAdress){
1038 if (bRead) snew(ir->adress, 1);
1039 gmx_fio_do_int(fio,ir->adress->type);
1040 gmx_fio_do_real(fio,ir->adress->const_wf);
1041 gmx_fio_do_real(fio,ir->adress->ex_width);
1042 gmx_fio_do_real(fio,ir->adress->hy_width);
1043 gmx_fio_do_int(fio,ir->adress->icor);
1044 gmx_fio_do_int(fio,ir->adress->site);
1045 gmx_fio_do_rvec(fio,ir->adress->refs);
1046 gmx_fio_do_int(fio,ir->adress->n_tf_grps);
1047 gmx_fio_do_real(fio, ir->adress->ex_forcecap);
1048 gmx_fio_do_int(fio, ir->adress->n_energy_grps);
1049 gmx_fio_do_int(fio,ir->adress->do_hybridpairs);
1050
1051 if (bRead)snew(ir->adress->tf_table_index,ir->adress->n_tf_grps);
1052 if (ir->adress->n_tf_grps > 0) {
1053 bDum=gmx_fio_ndo_int(fio,ir->adress->tf_table_index,ir->adress->n_tf_grps);
1054 }
1055 if (bRead)snew(ir->adress->group_explicit,ir->adress->n_energy_grps);
1056 if (ir->adress->n_energy_grps > 0) {
1057 bDum=gmx_fio_ndo_int(fio, ir->adress->group_explicit,ir->adress->n_energy_grps);
1058 }
1059 }
1060 } else {
1061 ir->bAdress = FALSE;
1062 }
1063
1064 /* pull stuff */
1065 if (file_version >= 48) {
1066 gmx_fio_do_int(fio,ir->ePull);
1067 if (ir->ePull != epullNO) {
1068 if (bRead)
1069 snew(ir->pull,1);
1070 do_pull(fio, ir->pull,bRead,file_version);
1071 }
1072 } else {
1073 ir->ePull = epullNO;
1074 }
1075
1076 /* Enforced rotation */
1077 if (file_version >= 74) {
1078 gmx_fio_do_int(fio,ir->bRot);
1079 if (ir->bRot == TRUE) {
1080 if (bRead)
1081 snew(ir->rot,1);
1082 do_rot(fio, ir->rot,bRead,file_version);
1083 }
1084 } else {
1085 ir->bRot = FALSE;
1086 }
1087
1088 /* grpopts stuff */
1089 gmx_fio_do_int(fio,ir->opts.ngtc);
1090 if (file_version >= 69) {
1091 gmx_fio_do_int(fio,ir->opts.nhchainlength);
1092 } else {
1093 ir->opts.nhchainlength = 1;
1094 }
1095 gmx_fio_do_int(fio,ir->opts.ngacc);
1096 gmx_fio_do_int(fio,ir->opts.ngfrz);
1097 gmx_fio_do_int(fio,ir->opts.ngener);
1098
1099 if (bRead) {
1100 snew(ir->opts.nrdf, ir->opts.ngtc);
1101 snew(ir->opts.ref_t, ir->opts.ngtc);
1102 snew(ir->opts.annealing, ir->opts.ngtc);
1103 snew(ir->opts.anneal_npoints, ir->opts.ngtc);
1104 snew(ir->opts.anneal_time, ir->opts.ngtc);
1105 snew(ir->opts.anneal_temp, ir->opts.ngtc);
1106 snew(ir->opts.tau_t, ir->opts.ngtc);
1107 snew(ir->opts.nFreeze,ir->opts.ngfrz);
1108 snew(ir->opts.acc, ir->opts.ngacc);
1109 snew(ir->opts.egp_flags,ir->opts.ngener*ir->opts.ngener);
1110 }
1111 if (ir->opts.ngtc > 0) {
1112 if (bRead && file_version<13) {
1113 snew(tmp,ir->opts.ngtc);
1114 bDum=gmx_fio_ndo_int(fio,tmp, ir->opts.ngtc);
1115 for(i=0; i<ir->opts.ngtc; i++)
1116 ir->opts.nrdf[i] = tmp[i];
1117 sfree(tmp);
1118 } else {
1119 bDum=gmx_fio_ndo_real(fio,ir->opts.nrdf, ir->opts.ngtc);
1120 }
1121 bDum=gmx_fio_ndo_real(fio,ir->opts.ref_t,ir->opts.ngtc);
1122 bDum=gmx_fio_ndo_real(fio,ir->opts.tau_t,ir->opts.ngtc);
1123 if (file_version<33 && ir->eI==eiBD) {
1124 for(i=0; i<ir->opts.ngtc; i++)
1125 ir->opts.tau_t[i] = bd_temp;
1126 }
1127 }
1128 if (ir->opts.ngfrz > 0)
1129 bDum=gmx_fio_ndo_ivec(fio,ir->opts.nFreeze,ir->opts.ngfrz);
1130 if (ir->opts.ngacc > 0)
1131 gmx_fio_ndo_rvec(fio,ir->opts.acc,ir->opts.ngacc);
1132 if (file_version >= 12)
1133 bDum=gmx_fio_ndo_int(fio,ir->opts.egp_flags,
1134 ir->opts.ngener*ir->opts.ngener);
1135
1136 if(bRead && file_version < 26) {
1137 for(i=0;i<ir->opts.ngtc;i++) {
1138 if(bSimAnn) {
1139 ir->opts.annealing[i] = eannSINGLE;
1140 ir->opts.anneal_npoints[i] = 2;
1141 snew(ir->opts.anneal_time[i],2);
1142 snew(ir->opts.anneal_temp[i],2);
1143 /* calculate the starting/ending temperatures from reft, zerotemptime, and nsteps */
1144 finish_t = ir->init_t + ir->nsteps * ir->delta_t;
1145 init_temp = ir->opts.ref_t[i]*(1-ir->init_t/zerotemptime);
1146 finish_temp = ir->opts.ref_t[i]*(1-finish_t/zerotemptime);
1147 ir->opts.anneal_time[i][0] = ir->init_t;
1148 ir->opts.anneal_time[i][1] = finish_t;
1149 ir->opts.anneal_temp[i][0] = init_temp;
1150 ir->opts.anneal_temp[i][1] = finish_temp;
1151 } else {
1152 ir->opts.annealing[i] = eannNO;
1153 ir->opts.anneal_npoints[i] = 0;
1154 }
1155 }
1156 } else {
1157 /* file version 26 or later */
1158 /* First read the lists with annealing and npoints for each group */
1159 bDum=gmx_fio_ndo_int(fio,ir->opts.annealing,ir->opts.ngtc);
1160 bDum=gmx_fio_ndo_int(fio,ir->opts.anneal_npoints,ir->opts.ngtc);
1161 for(j=0;j<(ir->opts.ngtc);j++) {
1162 k=ir->opts.anneal_npoints[j];
1163 if(bRead) {
1164 snew(ir->opts.anneal_time[j],k);
1165 snew(ir->opts.anneal_temp[j],k);
1166 }
1167 bDum=gmx_fio_ndo_real(fio,ir->opts.anneal_time[j],k);
1168 bDum=gmx_fio_ndo_real(fio,ir->opts.anneal_temp[j],k);
1169 }
1170 }
1171 /* Walls */
1172 if (file_version >= 45) {
1173 gmx_fio_do_int(fio,ir->nwall);
1174 gmx_fio_do_int(fio,ir->wall_type);
1175 if (file_version >= 50)
1176 gmx_fio_do_real(fio,ir->wall_r_linpot);
1177 else
1178 ir->wall_r_linpot = -1;
1179 gmx_fio_do_int(fio,ir->wall_atomtype[0]);
1180 gmx_fio_do_int(fio,ir->wall_atomtype[1]);
1181 gmx_fio_do_real(fio,ir->wall_density[0]);
1182 gmx_fio_do_real(fio,ir->wall_density[1]);
1183 gmx_fio_do_real(fio,ir->wall_ewald_zfac);
1184 } else {
1185 ir->nwall = 0;
1186 ir->wall_type = 0;
1187 ir->wall_atomtype[0] = -1;
1188 ir->wall_atomtype[1] = -1;
1189 ir->wall_density[0] = 0;
1190 ir->wall_density[1] = 0;
1191 ir->wall_ewald_zfac = 3;
1192 }
1193 /* Cosine stuff for electric fields */
1194 for(j=0; (j<DIM); j++) {
1195 gmx_fio_do_int(fio,ir->ex[j].n);
1196 gmx_fio_do_int(fio,ir->et[j].n);
1197 if (bRead) {
1198 snew(ir->ex[j].a, ir->ex[j].n);
1199 snew(ir->ex[j].phi,ir->ex[j].n);
1200 snew(ir->et[j].a, ir->et[j].n);
1201 snew(ir->et[j].phi,ir->et[j].n);
1202 }
1203 bDum=gmx_fio_ndo_real(fio,ir->ex[j].a, ir->ex[j].n);
1204 bDum=gmx_fio_ndo_real(fio,ir->ex[j].phi,ir->ex[j].n);
1205 bDum=gmx_fio_ndo_real(fio,ir->et[j].a, ir->et[j].n);
1206 bDum=gmx_fio_ndo_real(fio,ir->et[j].phi,ir->et[j].n);
1207 }
1208
1209 /* QMMM stuff */
1210 if(file_version>=39){
1211 gmx_fio_do_gmx_bool(fio,ir->bQMMM);
1212 gmx_fio_do_int(fio,ir->QMMMscheme);
1213 gmx_fio_do_real(fio,ir->scalefactor);
1214 gmx_fio_do_int(fio,ir->opts.ngQM);
1215 if (bRead) {
1216 snew(ir->opts.QMmethod, ir->opts.ngQM);
1217 snew(ir->opts.QMbasis, ir->opts.ngQM);
1218 snew(ir->opts.QMcharge, ir->opts.ngQM);
1219 snew(ir->opts.QMmult, ir->opts.ngQM);
1220 snew(ir->opts.bSH, ir->opts.ngQM);
1221 snew(ir->opts.CASorbitals, ir->opts.ngQM);
1222 snew(ir->opts.CASelectrons,ir->opts.ngQM);
1223 snew(ir->opts.SAon, ir->opts.ngQM);
1224 snew(ir->opts.SAoff, ir->opts.ngQM);
1225 snew(ir->opts.SAsteps, ir->opts.ngQM);
1226 snew(ir->opts.bOPT, ir->opts.ngQM);
1227 snew(ir->opts.bTS, ir->opts.ngQM);
1228 }
1229 if (ir->opts.ngQM > 0) {
1230 bDum=gmx_fio_ndo_int(fio,ir->opts.QMmethod,ir->opts.ngQM);
1231 bDum=gmx_fio_ndo_int(fio,ir->opts.QMbasis,ir->opts.ngQM);
1232 bDum=gmx_fio_ndo_int(fio,ir->opts.QMcharge,ir->opts.ngQM);
1233 bDum=gmx_fio_ndo_int(fio,ir->opts.QMmult,ir->opts.ngQM);
1234 bDum=gmx_fio_ndo_gmx_bool(fio,ir->opts.bSH,ir->opts.ngQM);
1235 bDum=gmx_fio_ndo_int(fio,ir->opts.CASorbitals,ir->opts.ngQM);
1236 bDum=gmx_fio_ndo_int(fio,ir->opts.CASelectrons,ir->opts.ngQM);
1237 bDum=gmx_fio_ndo_real(fio,ir->opts.SAon,ir->opts.ngQM);
1238 bDum=gmx_fio_ndo_real(fio,ir->opts.SAoff,ir->opts.ngQM);
1239 bDum=gmx_fio_ndo_int(fio,ir->opts.SAsteps,ir->opts.ngQM);
1240 bDum=gmx_fio_ndo_gmx_bool(fio,ir->opts.bOPT,ir->opts.ngQM);
1241 bDum=gmx_fio_ndo_gmx_bool(fio,ir->opts.bTS,ir->opts.ngQM);
1242 }
1243 /* end of QMMM stuff */
1244 }
1245 }
1246
1247
1248 static void do_harm(t_fileio *fio, t_iparams *iparams,gmx_bool bRead)
1249 {
1250 gmx_fio_do_real(fio,iparams->harmonic.rA);
1251 gmx_fio_do_real(fio,iparams->harmonic.krA);
1252 gmx_fio_do_real(fio,iparams->harmonic.rB);
1253 gmx_fio_do_real(fio,iparams->harmonic.krB);
1254 }
1255
1256 void do_iparams(t_fileio *fio, t_functype ftype,t_iparams *iparams,
1257 gmx_bool bRead, int file_version)
1258 {
1259 int i;
1260 gmx_bool bDum;
1261 real rdum;
1262
1263 if (!bRead)
1264 gmx_fio_set_comment(fio, interaction_function[ftype].name);
1265 switch (ftype) {
1266 case F_ANGLES:
1267 case F_G96ANGLES:
1268 case F_BONDS:
1269 case F_G96BONDS:
1270 case F_HARMONIC:
1271 case F_IDIHS:
1272 do_harm(fio, iparams,bRead);
1273 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && bRead) {
1274 /* Correct incorrect storage of parameters */
1275 iparams->pdihs.phiB = iparams->pdihs.phiA;
1276 iparams->pdihs.cpB = iparams->pdihs.cpA;
1277 }
1278 break;
1279 case F_LINEAR_ANGLES:
1280 gmx_fio_do_real(fio,iparams->linangle.klinA);
1281 gmx_fio_do_real(fio,iparams->linangle.aA);
1282 gmx_fio_do_real(fio,iparams->linangle.klinB);
1283 gmx_fio_do_real(fio,iparams->linangle.aB);
1284 break;
1285 case F_FENEBONDS:
1286 gmx_fio_do_real(fio,iparams->fene.bm);
1287 gmx_fio_do_real(fio,iparams->fene.kb);
1288 break;
1289 case F_RESTRBONDS:
1290 gmx_fio_do_real(fio,iparams->restraint.lowA);
1291 gmx_fio_do_real(fio,iparams->restraint.up1A);
1292 gmx_fio_do_real(fio,iparams->restraint.up2A);
1293 gmx_fio_do_real(fio,iparams->restraint.kA);
1294 gmx_fio_do_real(fio,iparams->restraint.lowB);
1295 gmx_fio_do_real(fio,iparams->restraint.up1B);
1296 gmx_fio_do_real(fio,iparams->restraint.up2B);
1297 gmx_fio_do_real(fio,iparams->restraint.kB);
1298 break;
1299 case F_TABBONDS:
1300 case F_TABBONDSNC:
1301 case F_TABANGLES:
1302 case F_TABDIHS:
1303 gmx_fio_do_real(fio,iparams->tab.kA);
1304 gmx_fio_do_int(fio,iparams->tab.table);
1305 gmx_fio_do_real(fio,iparams->tab.kB);
1306 break;
1307 case F_CROSS_BOND_BONDS:
1308 gmx_fio_do_real(fio,iparams->cross_bb.r1e);
1309 gmx_fio_do_real(fio,iparams->cross_bb.r2e);
1310 gmx_fio_do_real(fio,iparams->cross_bb.krr);
1311 break;
1312 case F_CROSS_BOND_ANGLES:
1313 gmx_fio_do_real(fio,iparams->cross_ba.r1e);
1314 gmx_fio_do_real(fio,iparams->cross_ba.r2e);
1315 gmx_fio_do_real(fio,iparams->cross_ba.r3e);
1316 gmx_fio_do_real(fio,iparams->cross_ba.krt);
1317 break;
1318 case F_UREY_BRADLEY:
1319 gmx_fio_do_real(fio,iparams->u_b.thetaA);
1320 gmx_fio_do_real(fio,iparams->u_b.kthetaA);
1321 gmx_fio_do_real(fio,iparams->u_b.r13A);
1322 gmx_fio_do_real(fio,iparams->u_b.kUBA);
1323 if (file_version >= 79) {
1324 gmx_fio_do_real(fio,iparams->u_b.thetaB);
1325 gmx_fio_do_real(fio,iparams->u_b.kthetaB);
1326 gmx_fio_do_real(fio,iparams->u_b.r13B);
1327 gmx_fio_do_real(fio,iparams->u_b.kUBB);
1328 } else {
1329 iparams->u_b.thetaB=iparams->u_b.thetaA;
1330 iparams->u_b.kthetaB=iparams->u_b.kthetaA;
1331 iparams->u_b.r13B=iparams->u_b.r13A;
1332 iparams->u_b.kUBB=iparams->u_b.kUBA;
1333 }
1334 break;
1335 case F_QUARTIC_ANGLES:
1336 gmx_fio_do_real(fio,iparams->qangle.theta);
1337 bDum=gmx_fio_ndo_real(fio,iparams->qangle.c,5);
1338 break;
1339 case F_BHAM:
1340 gmx_fio_do_real(fio,iparams->bham.a);
1341 gmx_fio_do_real(fio,iparams->bham.b);
1342 gmx_fio_do_real(fio,iparams->bham.c);
1343 break;
1344 case F_MORSE:
1345 gmx_fio_do_real(fio,iparams->morse.b0A);
1346 gmx_fio_do_real(fio,iparams->morse.cbA);
1347 gmx_fio_do_real(fio,iparams->morse.betaA);
1348 if (file_version >= 79) {
1349 gmx_fio_do_real(fio,iparams->morse.b0B);
1350 gmx_fio_do_real(fio,iparams->morse.cbB);
1351 gmx_fio_do_real(fio,iparams->morse.betaB);
1352 } else {
1353 iparams->morse.b0B = iparams->morse.b0A;
1354 iparams->morse.cbB = iparams->morse.cbA;
1355 iparams->morse.betaB = iparams->morse.betaA;
1356 }
1357 break;
1358 case F_CUBICBONDS:
1359 gmx_fio_do_real(fio,iparams->cubic.b0);
1360 gmx_fio_do_real(fio,iparams->cubic.kb);
1361 gmx_fio_do_real(fio,iparams->cubic.kcub);
1362 break;
1363 case F_CONNBONDS:
1364 break;
1365 case F_POLARIZATION:
1366 gmx_fio_do_real(fio,iparams->polarize.alpha);
1367 break;
1368 case F_ANHARM_POL:
1369 gmx_fio_do_real(fio,iparams->anharm_polarize.alpha);
1370 gmx_fio_do_real(fio,iparams->anharm_polarize.drcut);
1371 gmx_fio_do_real(fio,iparams->anharm_polarize.khyp);
1372 break;
1373 case F_WATER_POL:
1374 if (file_version < 31)
1375 gmx_fatal(FARGS,"Old tpr files with water_polarization not supported. Make a new.");
1376 gmx_fio_do_real(fio,iparams->wpol.al_x);
1377 gmx_fio_do_real(fio,iparams->wpol.al_y);
1378 gmx_fio_do_real(fio,iparams->wpol.al_z);
1379 gmx_fio_do_real(fio,iparams->wpol.rOH);
1380 gmx_fio_do_real(fio,iparams->wpol.rHH);
1381 gmx_fio_do_real(fio,iparams->wpol.rOD);
1382 break;
1383 case F_THOLE_POL:
1384 gmx_fio_do_real(fio,iparams->thole.a);
1385 gmx_fio_do_real(fio,iparams->thole.alpha1);
1386 gmx_fio_do_real(fio,iparams->thole.alpha2);
1387 gmx_fio_do_real(fio,iparams->thole.rfac);
1388 break;
1389 case F_LJ:
1390 gmx_fio_do_real(fio,iparams->lj.c6);
1391 gmx_fio_do_real(fio,iparams->lj.c12);
1392 break;
1393 case F_LJ14:
1394 gmx_fio_do_real(fio,iparams->lj14.c6A);
1395 gmx_fio_do_real(fio,iparams->lj14.c12A);
1396 gmx_fio_do_real(fio,iparams->lj14.c6B);
1397 gmx_fio_do_real(fio,iparams->lj14.c12B);
1398 break;
1399 case F_LJC14_Q:
1400 gmx_fio_do_real(fio,iparams->ljc14.fqq);
1401 gmx_fio_do_real(fio,iparams->ljc14.qi);
1402 gmx_fio_do_real(fio,iparams->ljc14.qj);
1403 gmx_fio_do_real(fio,iparams->ljc14.c6);
1404 gmx_fio_do_real(fio,iparams->ljc14.c12);
1405 break;
1406 case F_LJC_PAIRS_NB:
1407 gmx_fio_do_real(fio,iparams->ljcnb.qi);
1408 gmx_fio_do_real(fio,iparams->ljcnb.qj);
1409 gmx_fio_do_real(fio,iparams->ljcnb.c6);
1410 gmx_fio_do_real(fio,iparams->ljcnb.c12);
1411 break;
1412 case F_PDIHS:
1413 case F_PIDIHS:
1414 case F_ANGRES:
1415 case F_ANGRESZ:
1416 gmx_fio_do_real(fio,iparams->pdihs.phiA);
1417 gmx_fio_do_real(fio,iparams->pdihs.cpA);
1418 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && file_version < 42) {
1419 /* Read the incorrectly stored multiplicity */
1420 gmx_fio_do_real(fio,iparams->harmonic.rB);
1421 gmx_fio_do_real(fio,iparams->harmonic.krB);
1422 iparams->pdihs.phiB = iparams->pdihs.phiA;
1423 iparams->pdihs.cpB = iparams->pdihs.cpA;
1424 } else {
1425 gmx_fio_do_real(fio,iparams->pdihs.phiB);
1426 gmx_fio_do_real(fio,iparams->pdihs.cpB);
1427 gmx_fio_do_int(fio,iparams->pdihs.mult);
1428 }
1429 break;
1430 case F_DISRES:
1431 gmx_fio_do_int(fio,iparams->disres.label);
1432 gmx_fio_do_int(fio,iparams->disres.type);
1433 gmx_fio_do_real(fio,iparams->disres.low);
1434 gmx_fio_do_real(fio,iparams->disres.up1);
1435 gmx_fio_do_real(fio,iparams->disres.up2);
1436 gmx_fio_do_real(fio,iparams->disres.kfac);
1437 break;
1438 case F_ORIRES:
1439 gmx_fio_do_int(fio,iparams->orires.ex);
1440 gmx_fio_do_int(fio,iparams->orires.label);
1441 gmx_fio_do_int(fio,iparams->orires.power);
1442 gmx_fio_do_real(fio,iparams->orires.c);
1443 gmx_fio_do_real(fio,iparams->orires.obs);
1444 gmx_fio_do_real(fio,iparams->orires.kfac);
1445 break;
1446 case F_DIHRES:
1447 gmx_fio_do_real(fio,iparams->dihres.phiA);
1448 gmx_fio_do_real(fio,iparams->dihres.dphiA);
1449 gmx_fio_do_real(fio,iparams->dihres.kfacA);
1450 if (file_version >= 72) {
1451 gmx_fio_do_real(fio,iparams->dihres.phiB);
1452 gmx_fio_do_real(fio,iparams->dihres.dphiB);
1453 gmx_fio_do_real(fio,iparams->dihres.kfacB);
1454 } else {
1455 iparams->dihres.phiB=iparams->dihres.phiA;
1456 iparams->dihres.dphiB=iparams->dihres.dphiA;
1457 iparams->dihres.kfacB=iparams->dihres.kfacA;
1458 }
1459 break;
1460 case F_POSRES:
1461 gmx_fio_do_rvec(fio,iparams->posres.pos0A);
1462 gmx_fio_do_rvec(fio,iparams->posres.fcA);
1463 if (bRead && file_version < 27) {
1464 copy_rvec(iparams->posres.pos0A,iparams->posres.pos0B);
1465 copy_rvec(iparams->posres.fcA,iparams->posres.fcB);
1466 } else {
1467 gmx_fio_do_rvec(fio,iparams->posres.pos0B);
1468 gmx_fio_do_rvec(fio,iparams->posres.fcB);
1469 }
1470 break;
1471 case F_RBDIHS:
1472 bDum=gmx_fio_ndo_real(fio,iparams->rbdihs.rbcA,NR_RBDIHS);
1473 if(file_version>=25)
1474 bDum=gmx_fio_ndo_real(fio,iparams->rbdihs.rbcB,NR_RBDIHS);
1475 break;
1476 case F_FOURDIHS:
1477 /* Fourier dihedrals are internally represented
1478 * as Ryckaert-Bellemans since those are faster to compute.
1479 */
1480 bDum=gmx_fio_ndo_real(fio,iparams->rbdihs.rbcA, NR_RBDIHS);
1481 bDum=gmx_fio_ndo_real(fio,iparams->rbdihs.rbcB, NR_RBDIHS);
1482 break;
1483 case F_CONSTR:
1484 case F_CONSTRNC:
1485 gmx_fio_do_real(fio,iparams->constr.dA);
1486 gmx_fio_do_real(fio,iparams->constr.dB);
1487 break;
1488 case F_SETTLE:
1489 gmx_fio_do_real(fio,iparams->settle.doh);
1490 gmx_fio_do_real(fio,iparams->settle.dhh);
1491 break;
1492 case F_VSITE2:
1493 gmx_fio_do_real(fio,iparams->vsite.a);
1494 break;
1495 case F_VSITE3:
1496 case F_VSITE3FD:
1497 case F_VSITE3FAD:
1498 gmx_fio_do_real(fio,iparams->vsite.a);
1499 gmx_fio_do_real(fio,iparams->vsite.b);
1500 break;
1501 case F_VSITE3OUT:
1502 case F_VSITE4FD:
1503 case F_VSITE4FDN:
1504 gmx_fio_do_real(fio,iparams->vsite.a);
1505 gmx_fio_do_real(fio,iparams->vsite.b);
1506 gmx_fio_do_real(fio,iparams->vsite.c);
1507 break;
1508 case F_VSITEN:
1509 gmx_fio_do_int(fio,iparams->vsiten.n);
1510 gmx_fio_do_real(fio,iparams->vsiten.a);
1511 break;
1512 case F_GB12:
1513 case F_GB13:
1514 case F_GB14:
1515 /* We got rid of some parameters in version 68 */
1516 if(bRead && file_version<68)
1517 {
1518 gmx_fio_do_real(fio,rdum);
1519 gmx_fio_do_real(fio,rdum);
1520 gmx_fio_do_real(fio,rdum);
1521 gmx_fio_do_real(fio,rdum);
1522 }
1523 gmx_fio_do_real(fio,iparams->gb.sar);
1524 gmx_fio_do_real(fio,iparams->gb.st);
1525 gmx_fio_do_real(fio,iparams->gb.pi);
1526 gmx_fio_do_real(fio,iparams->gb.gbr);
1527 gmx_fio_do_real(fio,iparams->gb.bmlt);
1528 break;
1529 case F_CMAP:
1530 gmx_fio_do_int(fio,iparams->cmap.cmapA);
1531 gmx_fio_do_int(fio,iparams->cmap.cmapB);
1532 break;
1533 default:
1534 gmx_fatal(FARGS,"unknown function type %d (%s) in %s line %d",
1535 ftype,interaction_function[ftype].name,__FILE__,__LINE__);
1536 }
1537 if (!bRead)
1538 gmx_fio_unset_comment(fio);
1539 }
1540
1541 static void do_ilist(t_fileio *fio, t_ilist *ilist,gmx_bool bRead,int file_version,
1542 int ftype)
1543 {
1544 int i,k,idum;
1545 gmx_bool bDum=TRUE;
1546
1547 if (!bRead) {
1548 gmx_fio_set_comment(fio, interaction_function[ftype].name);
1549 }
1550 if (file_version < 44) {
1551 for(i=0; i<MAXNODES; i++)
1552 gmx_fio_do_int(fio,idum);
1553 }
1554 gmx_fio_do_int(fio,ilist->nr);
1555 if (bRead)
1556 snew(ilist->iatoms,ilist->nr);
1557 bDum=gmx_fio_ndo_int(fio,ilist->iatoms,ilist->nr);
1558 if (!bRead)
1559 gmx_fio_unset_comment(fio);
1560 }
1561
1562 static void do_ffparams(t_fileio *fio, gmx_ffparams_t *ffparams,
1563 gmx_bool bRead, int file_version)
1564 {
1565 int idum,i,j;
1566 gmx_bool bDum=TRUE;
1567 unsigned int k;
1568
1569 gmx_fio_do_int(fio,ffparams->atnr);
1570 if (file_version < 57) {
1571 gmx_fio_do_int(fio,idum);
1572 }
1573 gmx_fio_do_int(fio,ffparams->ntypes);
1574 if (bRead && debug)
1575 fprintf(debug,"ffparams->atnr = %d, ntypes = %d\n",
1576 ffparams->atnr,ffparams->ntypes);
1577 if (bRead) {
1578 snew(ffparams->functype,ffparams->ntypes);
1579 snew(ffparams->iparams,ffparams->ntypes);
1580 }
1581 /* Read/write all the function types */
1582 bDum=gmx_fio_ndo_int(fio,ffparams->functype,ffparams->ntypes);
1583 if (bRead && debug)
1584 pr_ivec(debug,0,"functype",ffparams->functype,ffparams->ntypes,TRUE);
1585
1586 if (file_version >= 66) {
1587 gmx_fio_do_double(fio,ffparams->reppow);
1588 } else {
1589 ffparams->reppow = 12.0;
1590 }
1591
1592 if (file_version >= 57) {
1593 gmx_fio_do_real(fio,ffparams->fudgeQQ);
1594 }
1595
1596 /* Check whether all these function types are supported by the code.
1597 * In practice the code is backwards compatible, which means that the
1598 * numbering may have to be altered from old numbering to new numbering
1599 */
1600 for (i=0; (i<ffparams->ntypes); i++) {
1601 if (bRead)
1602 /* Loop over file versions */
1603 for (k=0; (k<NFTUPD); k++)
1604 /* Compare the read file_version to the update table */
1605 if ((file_version < ftupd[k].fvnr) &&
1606 (ffparams->functype[i] >= ftupd[k].ftype)) {
1607 ffparams->functype[i] += 1;
1608 if (debug) {
1609 fprintf(debug,"Incrementing function type %d to %d (due to %s)\n",
1610 i,ffparams->functype[i],
1611 interaction_function[ftupd[k].ftype].longname);
1612 fflush(debug);
1613 }
1614 }
1615
1616 do_iparams(fio, ffparams->functype[i],&ffparams->iparams[i],bRead,
1617 file_version);
1618 if (bRead && debug)
1619 pr_iparams(debug,ffparams->functype[i],&ffparams->iparams[i]);
1620 }
1621 }
1622
1623 static void add_settle_atoms(t_ilist *ilist)
1624 {
1625 int i;
1626
1627 /* Settle used to only store the first atom: add the other two */
1628 srenew(ilist->iatoms,2*ilist->nr);
1629 for(i=ilist->nr/2-1; i>=0; i--)
1630 {
1631 ilist->iatoms[4*i+0] = ilist->iatoms[2*i+0];
1632 ilist->iatoms[4*i+1] = ilist->iatoms[2*i+1];
1633 ilist->iatoms[4*i+2] = ilist->iatoms[2*i+1] + 1;
1634 ilist->iatoms[4*i+3] = ilist->iatoms[2*i+1] + 2;
1635 }
1636 ilist->nr = 2*ilist->nr;
1637 }
1638
1639 static void do_ilists(t_fileio *fio, t_ilist *ilist,gmx_bool bRead,
1640 int file_version)
1641 {
1642 int i,j,renum[F_NRE];
1643 gmx_bool bDum=TRUE,bClear;
1644 unsigned int k;
1645
1646 for(j=0; (j<F_NRE); j++) {
1647 bClear = FALSE;
1648 if (bRead)
1649 for (k=0; k<NFTUPD; k++)
1650 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
1651 bClear = TRUE;
1652 if (bClear) {
1653 ilist[j].nr = 0;
1654 ilist[j].iatoms = NULL;
1655 } else {
1656 do_ilist(fio, &ilist[j],bRead,file_version,j);
1657 if (file_version < 78 && j == F_SETTLE && ilist[j].nr > 0)
1658 {
1659 add_settle_atoms(&ilist[j]);
1660 }
1661 }
1662 /*
1663 if (bRead && gmx_debug_at)
1664 pr_ilist(debug,0,interaction_function[j].longname,
1665 functype,&ilist[j],TRUE);
1666 */
1667 }
1668 }
1669
1670 static void do_idef(t_fileio *fio, gmx_ffparams_t *ffparams,gmx_moltype_t *molt,
1671 gmx_bool bRead, int file_version)
1672 {
1673 do_ffparams(fio, ffparams,bRead,file_version);
1674
1675 if (file_version >= 54) {
1676 gmx_fio_do_real(fio,ffparams->fudgeQQ);
1677 }
1678
1679 do_ilists(fio, molt->ilist,bRead,file_version);
1680 }
1681
1682 static void do_block(t_fileio *fio, t_block *block,gmx_bool bRead,int file_version)
1683 {
1684 int i,idum,dum_nra,*dum_a;
1685 gmx_bool bDum=TRUE;
1686
1687 if (file_version < 44)
1688 for(i=0; i<MAXNODES; i++)
1689 gmx_fio_do_int(fio,idum);
1690 gmx_fio_do_int(fio,block->nr);
1691 if (file_version < 51)
1692 gmx_fio_do_int(fio,dum_nra);
1693 if (bRead) {
1694 block->nalloc_index = block->nr+1;
1695 snew(block->index,block->nalloc_index);
1696 }
1697 bDum=gmx_fio_ndo_int(fio,block->index,block->nr+1);
1698
1699 if (file_version < 51 && dum_nra > 0) {
1700 snew(dum_a,dum_nra);
1701 bDum=gmx_fio_ndo_int(fio,dum_a,dum_nra);
1702 sfree(dum_a);
1703 }
1704 }
1705
1706 static void do_blocka(t_fileio *fio, t_blocka *block,gmx_bool bRead,
1707 int file_version)
1708 {
1709 int i,idum;
1710 gmx_bool bDum=TRUE;
1711
1712 if (file_version < 44)
1713 for(i=0; i<MAXNODES; i++)
1714 gmx_fio_do_int(fio,idum);
1715 gmx_fio_do_int(fio,block->nr);
1716 gmx_fio_do_int(fio,block->nra);
1717 if (bRead) {
1718 block->nalloc_index = block->nr+1;
1719 snew(block->index,block->nalloc_index);
1720 block->nalloc_a = block->nra;
1721 snew(block->a,block->nalloc_a);
1722 }
1723 bDum=gmx_fio_ndo_int(fio,block->index,block->nr+1);
1724 bDum=gmx_fio_ndo_int(fio,block->a,block->nra);
1725 }
1726
1727 static void do_atom(t_fileio *fio, t_atom *atom,int ngrp,gmx_bool bRead,
1728 int file_version, gmx_groups_t *groups,int atnr)
1729 {
1730 int i,myngrp;
1731
1732 gmx_fio_do_real(fio,atom->m);
1733 gmx_fio_do_real(fio,atom->q);
1734 gmx_fio_do_real(fio,atom->mB);
1735 gmx_fio_do_real(fio,atom->qB);
1736 gmx_fio_do_ushort(fio, atom->type);
1737 gmx_fio_do_ushort(fio, atom->typeB);
1738 gmx_fio_do_int(fio,atom->ptype);
1739 gmx_fio_do_int(fio,atom->resind);
1740 if (file_version >= 52)
1741 gmx_fio_do_int(fio,atom->atomnumber);
1742 else if (bRead)
1743 atom->atomnumber = NOTSET;
1744 if (file_version < 23)
1745 myngrp = 8;
1746 else if (file_version < 39)
1747 myngrp = 9;
1748 else
1749 myngrp = ngrp;
1750
1751 if (file_version < 57) {
1752 unsigned char uchar[egcNR];
1753 gmx_fio_ndo_uchar(fio,uchar,myngrp);
1754 for(i=myngrp; (i<ngrp); i++) {
1755 uchar[i] = 0;
1756 }
1757 /* Copy the old data format to the groups struct */
1758 for(i=0; i<ngrp; i++) {
1759 groups->grpnr[i][atnr] = uchar[i];
1760 }
1761 }
1762 }
1763
1764 static void do_grps(t_fileio *fio, int ngrp,t_grps grps[],gmx_bool bRead,
1765 int file_version)
1766 {
1767 int i,j,myngrp;
1768 gmx_bool bDum=TRUE;
1769
1770 if (file_version < 23)
1771 myngrp = 8;
1772 else if (file_version < 39)
1773 myngrp = 9;
1774 else
1775 myngrp = ngrp;
1776
1777 for(j=0; (j<ngrp); j++) {
1778 if (j<myngrp) {
1779 gmx_fio_do_int(fio,grps[j].nr);
1780 if (bRead)
1781 snew(grps[j].nm_ind,grps[j].nr);
1782 bDum=gmx_fio_ndo_int(fio,grps[j].nm_ind,grps[j].nr);
1783 }
1784 else {
1785 grps[j].nr = 1;
1786 snew(grps[j].nm_ind,grps[j].nr);
1787 }
1788 }
1789 }
1790
1791 static void do_symstr(t_fileio *fio, char ***nm,gmx_bool bRead,t_symtab *symtab)
1792 {
1793 int ls;
1794
1795 if (bRead) {
1796 gmx_fio_do_int(fio,ls);
1797 *nm = get_symtab_handle(symtab,ls);
1798 }
1799 else {
1800 ls = lookup_symtab(symtab,*nm);
1801 gmx_fio_do_int(fio,ls);
1802 }
1803 }
1804
1805 static void do_strstr(t_fileio *fio, int nstr,char ***nm,gmx_bool bRead,
1806 t_symtab *symtab)
1807 {
1808 int j;
1809
1810 for (j=0; (j<nstr); j++)
1811 do_symstr(fio, &(nm[j]),bRead,symtab);
1812 }
1813
1814 static void do_resinfo(t_fileio *fio, int n,t_resinfo *ri,gmx_bool bRead,
1815 t_symtab *symtab, int file_version)
1816 {
1817 int j;
1818
1819 for (j=0; (j<n); j++) {
1820 do_symstr(fio, &(ri[j].name),bRead,symtab);
1821 if (file_version >= 63) {
1822 gmx_fio_do_int(fio,ri[j].nr);
1823 gmx_fio_do_uchar(fio, ri[j].ic);
1824 } else {
1825 ri[j].nr = j + 1;
1826 ri[j].ic = ' ';
1827 }
1828 }
1829 }
1830
1831 static void do_atoms(t_fileio *fio, t_atoms *atoms,gmx_bool bRead,t_symtab *symtab,
1832 int file_version,
1833 gmx_groups_t *groups)
1834 {
1835 int i;
1836
1837 gmx_fio_do_int(fio,atoms->nr);
1838 gmx_fio_do_int(fio,atoms->nres);
1839 if (file_version < 57) {
1840 gmx_fio_do_int(fio,groups->ngrpname);
1841 for(i=0; i<egcNR; i++) {
1842 groups->ngrpnr[i] = atoms->nr;
1843 snew(groups->grpnr[i],groups->ngrpnr[i]);
1844 }
1845 }
1846 if (bRead) {
1847 snew(atoms->atom,atoms->nr);
1848 snew(atoms->atomname,atoms->nr);
1849 snew(atoms->atomtype,atoms->nr);
1850 snew(atoms->atomtypeB,atoms->nr);
1851 snew(atoms->resinfo,atoms->nres);
1852 if (file_version < 57) {
1853 snew(groups->grpname,groups->ngrpname);
1854 }
1855 atoms->pdbinfo = NULL;
1856 }
1857 for(i=0; (i<atoms->nr); i++) {
1858 do_atom(fio, &atoms->atom[i],egcNR,bRead, file_version,groups,i);
1859 }
1860 do_strstr(fio, atoms->nr,atoms->atomname,bRead,symtab);
1861 if (bRead && (file_version <= 20)) {
1862 for(i=0; i<atoms->nr; i++) {
1863 atoms->atomtype[i] = put_symtab(symtab,"?");
1864 atoms->atomtypeB[i] = put_symtab(symtab,"?");
1865 }
1866 } else {
1867 do_strstr(fio, atoms->nr,atoms->atomtype,bRead,symtab);
1868 do_strstr(fio, atoms->nr,atoms->atomtypeB,bRead,symtab);
1869 }
1870 do_resinfo(fio, atoms->nres,atoms->resinfo,bRead,symtab,file_version);
1871
1872 if (file_version < 57) {
1873 do_strstr(fio, groups->ngrpname,groups->grpname,bRead,symtab);
1874
1875 do_grps(fio, egcNR,groups->grps,bRead,file_version);
1876 }
1877 }
1878
1879 static void do_groups(t_fileio *fio, gmx_groups_t *groups,
1880 gmx_bool bRead,t_symtab *symtab,
1881 int file_version)
1882 {
1883 int g,n,i;
1884 gmx_bool bDum=TRUE;
1885
1886 do_grps(fio, egcNR,groups->grps,bRead,file_version);
1887 gmx_fio_do_int(fio,groups->ngrpname);
1888 if (bRead) {
1889 snew(groups->grpname,groups->ngrpname);
1890 }
1891 do_strstr(fio, groups->ngrpname,groups->grpname,bRead,symtab);
1892 for(g=0; g<egcNR; g++) {
1893 gmx_fio_do_int(fio,groups->ngrpnr[g]);
1894 if (groups->ngrpnr[g] == 0) {
1895 if (bRead) {
1896 groups->grpnr[g] = NULL;
1897 }
1898 } else {
1899 if (bRead) {
1900 snew(groups->grpnr[g],groups->ngrpnr[g]);
1901 }
1902 bDum=gmx_fio_ndo_uchar(fio, groups->grpnr[g],groups->ngrpnr[g]);
1903 }
1904 }
1905 }
1906
1907 static void do_atomtypes(t_fileio *fio, t_atomtypes *atomtypes,gmx_bool bRead,
1908 t_symtab *symtab,int file_version)
1909 {
1910 int i,j;
1911 gmx_bool bDum = TRUE;
1912
1913 if (file_version > 25) {
1914 gmx_fio_do_int(fio,atomtypes->nr);
1915 j=atomtypes->nr;
1916 if (bRead) {
1917 snew(atomtypes->radius,j);
1918 snew(atomtypes->vol,j);
1919 snew(atomtypes->surftens,j);
1920 snew(atomtypes->atomnumber,j);
1921 snew(atomtypes->gb_radius,j);
1922 snew(atomtypes->S_hct,j);
1923 }
1924 bDum=gmx_fio_ndo_real(fio,atomtypes->radius,j);
1925 bDum=gmx_fio_ndo_real(fio,atomtypes->vol,j);
1926 bDum=gmx_fio_ndo_real(fio,atomtypes->surftens,j);
1927 if(file_version >= 40)
1928 {
1929 bDum=gmx_fio_ndo_int(fio,atomtypes->atomnumber,j);
1930 }
1931 if(file_version >= 60)
1932 {
1933 bDum=gmx_fio_ndo_real(fio,atomtypes->gb_radius,j);
1934 bDum=gmx_fio_ndo_real(fio,atomtypes->S_hct,j);
1935 }
1936 } else {
1937 /* File versions prior to 26 cannot do GBSA,
1938 * so they dont use this structure
1939 */
1940 atomtypes->nr = 0;
1941 atomtypes->radius = NULL;
1942 atomtypes->vol = NULL;
1943 atomtypes->surftens = NULL;
1944 atomtypes->atomnumber = NULL;
1945 atomtypes->gb_radius = NULL;
1946 atomtypes->S_hct = NULL;
1947 }
1948 }
1949
1950 static void do_symtab(t_fileio *fio, t_symtab *symtab,gmx_bool bRead)
1951 {
1952 int i,nr;
1953 t_symbuf *symbuf;
1954 char buf[STRLEN];
1955
1956 gmx_fio_do_int(fio,symtab->nr);
1957 nr = symtab->nr;
1958 if (bRead) {
1959 snew(symtab->symbuf,1);
1960 symbuf = symtab->symbuf;
1961 symbuf->bufsize = nr;
1962 snew(symbuf->buf,nr);
1963 for (i=0; (i<nr); i++) {
1964 gmx_fio_do_string(fio,buf);
1965 symbuf->buf[i]=strdup(buf);
1966 }
1967 }
1968 else {
1969 symbuf = symtab->symbuf;
1970 while (symbuf!=NULL) {
1971 for (i=0; (i<symbuf->bufsize) && (i<nr); i++)
1972 gmx_fio_do_string(fio,symbuf->buf[i]);
1973 nr-=i;
1974 symbuf=symbuf->next;
1975 }
1976 if (nr != 0)
1977 gmx_fatal(FARGS,"nr of symtab strings left: %d",nr);
1978 }
1979 }
1980
1981 static void do_cmap(t_fileio *fio, gmx_cmap_t *cmap_grid, gmx_bool bRead)
1982 {
1983 int i,j,ngrid,gs,nelem;
1984
1985 gmx_fio_do_int(fio,cmap_grid->ngrid);
1986 gmx_fio_do_int(fio,cmap_grid->grid_spacing);
1987
1988 ngrid = cmap_grid->ngrid;
1989 gs = cmap_grid->grid_spacing;
1990 nelem = gs * gs;
1991
1992 if(bRead)
1993 {
1994 snew(cmap_grid->cmapdata,ngrid);
1995
1996 for(i=0;i<cmap_grid->ngrid;i++)
1997 {
1998 snew(cmap_grid->cmapdata[i].cmap,4*nelem);
1999 }
2000 }
2001
2002 for(i=0;i<cmap_grid->ngrid;i++)
2003 {
2004 for(j=0;j<nelem;j++)
2005 {
2006 gmx_fio_do_real(fio,cmap_grid->cmapdata[i].cmap[j*4]);
2007 gmx_fio_do_real(fio,cmap_grid->cmapdata[i].cmap[j*4+1]);
2008 gmx_fio_do_real(fio,cmap_grid->cmapdata[i].cmap[j*4+2]);
2009 gmx_fio_do_real(fio,cmap_grid->cmapdata[i].cmap[j*4+3]);
2010 }
2011 }
2012 }
2013
2014
2015 void tpx_make_chain_identifiers(t_atoms *atoms,t_block *mols)
2016 {
2017 int m,a,a0,a1,r;
2018 char c,chainid;
2019 int chainnum;
2020
2021 /* We always assign a new chain number, but save the chain id characters
2022 * for larger molecules.
2023 */
2024 #define CHAIN_MIN_ATOMS 15
2025
2026 chainnum=0;
2027 chainid='A';
2028 for(m=0; m<mols->nr; m++)
2029 {
2030 a0=mols->index[m];
2031 a1=mols->index[m+1];
2032 if ((a1-a0 >= CHAIN_MIN_ATOMS) && (chainid <= 'Z'))
2033 {
2034 c=chainid;
2035 chainid++;
2036 }
2037 else
2038 {
2039 c=' ';
2040 }
2041 for(a=a0; a<a1; a++)
2042 {
2043 atoms->resinfo[atoms->atom[a].resind].chainnum = chainnum;
2044 atoms->resinfo[atoms->atom[a].resind].chainid = c;
2045 }
2046 chainnum++;
2047 }
2048
2049 /* Blank out the chain id if there was only one chain */
2050 if (chainid == 'B')
2051 {
2052 for(r=0; r<atoms->nres; r++)
2053 {
2054 atoms->resinfo[r].chainid = ' ';
2055 }
2056 }
2057 }
2058
2059 static void do_moltype(t_fileio *fio, gmx_moltype_t *molt,gmx_bool bRead,
2060 t_symtab *symtab, int file_version,
2061 gmx_groups_t *groups)
2062 {
2063 int i;
2064
2065 if (file_version >= 57) {
2066 do_symstr(fio, &(molt->name),bRead,symtab);
2067 }
2068
2069 do_atoms(fio, &molt->atoms, bRead, symtab, file_version, groups);
2070
2071 if (bRead && gmx_debug_at) {
2072 pr_atoms(debug,0,"atoms",&molt->atoms,TRUE);
2073 }
2074
2075 if (file_version >= 57) {
2076 do_ilists(fio, molt->ilist,bRead,file_version);
2077
2078 do_block(fio, &molt->cgs,bRead,file_version);
2079 if (bRead && gmx_debug_at) {
2080 pr_block(debug,0,"cgs",&molt->cgs,TRUE);
2081 }
2082 }
2083
2084 /* This used to be in the atoms struct */
2085 do_blocka(fio, &molt->excls, bRead, file_version);
2086 }
2087
2088 static void do_molblock(t_fileio *fio, gmx_molblock_t *molb,gmx_bool bRead,
2089 int file_version)
2090 {
2091 int i;
2092
2093 gmx_fio_do_int(fio,molb->type);
2094 gmx_fio_do_int(fio,molb->nmol);
2095 gmx_fio_do_int(fio,molb->natoms_mol);
2096 /* Position restraint coordinates */
2097 gmx_fio_do_int(fio,molb->nposres_xA);
2098 if (molb->nposres_xA > 0) {
2099 if (bRead) {
2100 snew(molb->posres_xA,molb->nposres_xA);
2101 }
2102 gmx_fio_ndo_rvec(fio,molb->posres_xA,molb->nposres_xA);
2103 }
2104 gmx_fio_do_int(fio,molb->nposres_xB);
2105 if (molb->nposres_xB > 0) {
2106 if (bRead) {
2107 snew(molb->posres_xB,molb->nposres_xB);
2108 }
2109 gmx_fio_ndo_rvec(fio,molb->posres_xB,molb->nposres_xB);
2110 }
2111
2112 }
2113
2114 static t_block mtop_mols(gmx_mtop_t *mtop)
2115 {
2116 int mb,m,a,mol;
2117 t_block mols;
2118
2119 mols.nr = 0;
2120 for(mb=0; mb<mtop->nmolblock; mb++) {
2121 mols.nr += mtop->molblock[mb].nmol;
2122 }
2123 mols.nalloc_index = mols.nr + 1;
2124 snew(mols.index,mols.nalloc_index);
2125
2126 a = 0;
2127 m = 0;
2128 mols.index[m] = a;
2129 for(mb=0; mb<mtop->nmolblock; mb++) {
2130 for(mol=0; mol<mtop->molblock[mb].nmol; mol++) {
2131 a += mtop->molblock[mb].natoms_mol;
2132 m++;
2133 mols.index[m] = a;
2134 }
2135 }
2136
2137 return mols;
2138 }
2139
2140 static void add_posres_molblock(gmx_mtop_t *mtop)
2141 {
2142 t_ilist *il;
2143 int am,i,mol,a;
2144 gmx_bool bFE;
2145 gmx_molblock_t *molb;
2146 t_iparams *ip;
2147
2148 il = &mtop->moltype[0].ilist[F_POSRES];
2149 if (il->nr == 0) {
2150 return;
2151 }
2152 am = 0;
2153 bFE = FALSE;
2154 for(i=0; i<il->nr; i+=2) {
2155 ip = &mtop->ffparams.iparams[il->iatoms[i]];
2156 am = max(am,il->iatoms[i+1]);
2157 if (ip->posres.pos0B[XX] != ip->posres.pos0A[XX] ||
2158 ip->posres.pos0B[YY] != ip->posres.pos0A[YY] ||
2159 ip->posres.pos0B[ZZ] != ip->posres.pos0A[ZZ]) {
2160 bFE = TRUE;
2161 }
2162 }
2163 /* Make the posres coordinate block end at a molecule end */
2164 mol = 0;
2165 while(am >= mtop->mols.index[mol+1]) {
2166 mol++;
2167 }
2168 molb = &mtop->molblock[0];
2169 molb->nposres_xA = mtop->mols.index[mol+1];
2170 snew(molb->posres_xA,molb->nposres_xA);
2171 if (bFE) {
2172 molb->nposres_xB = molb->nposres_xA;
2173 snew(molb->posres_xB,molb->nposres_xB);
2174 } else {
2175 molb->nposres_xB = 0;
2176 }
2177 for(i=0; i<il->nr; i+=2) {
2178 ip = &mtop->ffparams.iparams[il->iatoms[i]];
2179 a = il->iatoms[i+1];
2180 molb->posres_xA[a][XX] = ip->posres.pos0A[XX];
2181 molb->posres_xA[a][YY] = ip->posres.pos0A[YY];
2182 molb->posres_xA[a][ZZ] = ip->posres.pos0A[ZZ];
2183 if (bFE) {
2184 molb->posres_xB[a][XX] = ip->posres.pos0B[XX];
2185 molb->posres_xB[a][YY] = ip->posres.pos0B[YY];
2186 molb->posres_xB[a][ZZ] = ip->posres.pos0B[ZZ];
2187 }
2188 }
2189 }
2190
2191 static void set_disres_npair(gmx_mtop_t *mtop)
2192 {
2193 int mt,i,npair;
2194 t_iparams *ip;
2195 t_ilist *il;
2196 t_iatom *a;
2197
2198 ip = mtop->ffparams.iparams;
2199
2200 for(mt=0; mt<mtop->nmoltype; mt++) {
2201 il = &mtop->moltype[mt].ilist[F_DISRES];
2202 if (il->nr > 0) {
2203 a = il->iatoms;
2204 npair = 0;
2205 for(i=0; i<il->nr; i+=3) {
2206 npair++;
2207 if (i+3 == il->nr || ip[a[i]].disres.label != ip[a[i+3]].disres.label) {
2208 ip[a[i]].disres.npair = npair;
2209 npair = 0;
2210 }
2211 }
2212 }
2213 }
2214 }
2215
2216 static void do_mtop(t_fileio *fio, gmx_mtop_t *mtop,gmx_bool bRead,
2217 int file_version)
2218 {
2219 int mt,mb,i;
2220 t_blocka dumb;
2221
2222 if (bRead)
2223 init_mtop(mtop);
2224 do_symtab(fio, &(mtop->symtab),bRead);
2225 if (bRead && debug)
2226 pr_symtab(debug,0,"symtab",&mtop->symtab);
2227
2228 do_symstr(fio, &(mtop->name),bRead,&(mtop->symtab));
2229
2230 if (file_version >= 57) {
2231 do_ffparams(fio, &mtop->ffparams,bRead,file_version);
2232
2233 gmx_fio_do_int(fio,mtop->nmoltype);
2234 } else {
2235 mtop->nmoltype = 1;
2236 }
2237 if (bRead) {
2238 snew(mtop->moltype,mtop->nmoltype);
2239 if (file_version < 57) {
2240 mtop->moltype[0].name = mtop->name;
2241 }
2242 }
2243 for(mt=0; mt<mtop->nmoltype; mt++) {
2244 do_moltype(fio, &mtop->moltype[mt],bRead,&mtop->symtab,file_version,
2245 &mtop->groups);
2246 }
2247
2248 if (file_version >= 57) {
2249 gmx_fio_do_int(fio,mtop->nmolblock);
2250 } else {
2251 mtop->nmolblock = 1;
2252 }
2253 if (bRead) {
2254 snew(mtop->molblock,mtop->nmolblock);
2255 }
2256 if (file_version >= 57) {
2257 for(mb=0; mb<mtop->nmolblock; mb++) {
2258 do_molblock(fio, &mtop->molblock[mb],bRead,file_version);
2259 }
2260 gmx_fio_do_int(fio,mtop->natoms);
2261 } else {
2262 mtop->molblock[0].type = 0;
2263 mtop->molblock[0].nmol = 1;
2264 mtop->molblock[0].natoms_mol = mtop->moltype[0].atoms.nr;
2265 mtop->molblock[0].nposres_xA = 0;
2266 mtop->molblock[0].nposres_xB = 0;
2267 }
2268
2269 do_atomtypes (fio, &(mtop->atomtypes),bRead,&(mtop->symtab), file_version);
2270 if (bRead && debug)
2271 pr_atomtypes(debug,0,"atomtypes",&mtop->atomtypes,TRUE);
2272
2273 if (file_version < 57) {
2274 /* Debug statements are inside do_idef */
2275 do_idef (fio, &mtop->ffparams,&mtop->moltype[0],bRead,file_version);
2276 mtop->natoms = mtop->moltype[0].atoms.nr;
2277 }
2278
2279 if(file_version >= 65)
2280 {
2281 do_cmap(fio, &mtop->ffparams.cmap_grid,bRead);
2282 }
2283 else
2284 {
2285 mtop->ffparams.cmap_grid.ngrid = 0;
2286 mtop->ffparams.cmap_grid.grid_spacing = 0;
2287 mtop->ffparams.cmap_grid.cmapdata = NULL;
2288 }
2289
2290 if (file_version >= 57) {
2291 do_groups(fio, &mtop->groups,bRead,&(mtop->symtab),file_version);
2292 }
2293
2294 if (file_version < 57) {
2295 do_block(fio, &mtop->moltype[0].cgs,bRead,file_version);
2296 if (bRead && gmx_debug_at) {
2297 pr_block(debug,0,"cgs",&mtop->moltype[0].cgs,TRUE);
2298 }
2299 do_block(fio, &mtop->mols,bRead,file_version);
2300 /* Add the posres coordinates to the molblock */
2301 add_posres_molblock(mtop);
2302 }
2303 if (bRead) {
2304 if (file_version >= 57) {
2305 mtop->mols = mtop_mols(mtop);
2306 }
2307 if (gmx_debug_at) {
2308 pr_block(debug,0,"mols",&mtop->mols,TRUE);
2309 }
2310 }
2311
2312 if (file_version < 51) {
2313 /* Here used to be the shake blocks */
2314 do_blocka(fio, &dumb,bRead,file_version);
2315 if (dumb.nr > 0)
2316 sfree(dumb.index);
2317 if (dumb.nra > 0)
2318 sfree(dumb.a);
2319 }
2320
2321 if (bRead) {
2322 close_symtab(&(mtop->symtab));
2323 }
2324 }
2325
2326 /* If TopOnlyOK is TRUE then we can read even future versions
2327 * of tpx files, provided the file_generation hasn't changed.
2328 * If it is FALSE, we need the inputrecord too, and bail out
2329 * if the file is newer than the program.
2330 *
2331 * The version and generation if the topology (see top of this file)
2332 * are returned in the two last arguments.
2333 *
2334 * If possible, we will read the inputrec even when TopOnlyOK is TRUE.
2335 */
2336 static void do_tpxheader(t_fileio *fio,gmx_bool bRead,t_tpxheader *tpx,
2337 gmx_bool TopOnlyOK, int *file_version,
2338 int *file_generation)
2339 {
2340 char buf[STRLEN];
2341 char file_tag[STRLEN];
2342 gmx_bool bDouble;
2343 int precision;
2344 int fver,fgen;
2345 int idum=0;
2346 real rdum=0;
2347
2348 gmx_fio_checktype(fio);
2349 gmx_fio_setdebug(fio,bDebugMode());
2350
2351 /* NEW! XDR tpb file */
2352 precision = sizeof(real);
2353 if (bRead) {
2354 gmx_fio_do_string(fio,buf);
2355 if (strncmp(buf,"VERSION",7))
2356 gmx_fatal(FARGS,"Can not read file %s,\n"
2357 " this file is from a Gromacs version which is older than 2.0\n"
2358 " Make a new one with grompp or use a gro or pdb file, if possible",
2359 gmx_fio_getname(fio));
2360 gmx_fio_do_int(fio,precision);
2361 bDouble = (precision == sizeof(double));
2362 if ((precision != sizeof(float)) && !bDouble)
2363 gmx_fatal(FARGS,"Unknown precision in file %s: real is %d bytes "
2364 "instead of %d or %d",
2365 gmx_fio_getname(fio),precision,sizeof(float),sizeof(double));
2366 gmx_fio_setprecision(fio,bDouble);
2367 fprintf(stderr,"Reading file %s, %s (%s precision)\n",
2368 gmx_fio_getname(fio),buf,bDouble ? "double" : "single");
2369 }
2370 else {
2371 gmx_fio_write_string(fio,GromacsVersion());
2372 bDouble = (precision == sizeof(double));
2373 gmx_fio_setprecision(fio,bDouble);
2374 gmx_fio_do_int(fio,precision);
2375 fver = tpx_version;
2376 sprintf(file_tag,"%s",tpx_tag);
2377 fgen = tpx_generation;
2378 }
2379
2380 /* Check versions! */
2381 gmx_fio_do_int(fio,fver);
2382
2383 /* This is for backward compatibility with development versions 77-79
2384 * where the tag was, mistakenly, placed before the generation,
2385 * which would cause a segv instead of a proper error message
2386 * when reading the topology only from tpx with <77 code.
2387 */
2388 if (fver >= 77 && fver <= 79)
2389 {
2390 gmx_fio_do_string(fio,file_tag);
2391 }
2392
2393 if (fver >= 26)
2394 {
2395 gmx_fio_do_int(fio,fgen);
2396 }
2397 else
2398 {
2399 fgen = 0;
2400 }
2401
2402 if (fver >= 80)
2403 {
2404 gmx_fio_do_string(fio,file_tag);
2405 }
2406 if (bRead)
2407 {
2408 if (fver < 77)
2409 {
2410 /* Versions before 77 don't have the tag, set it to release */
2411 sprintf(file_tag,"%s",TPX_TAG_RELEASE);
2412 }
2413
2414 if (strcmp(file_tag,tpx_tag) != 0)
2415 {
2416 fprintf(stderr,"Note: file tpx tag '%s', software tpx tag '%s'\n",
2417 file_tag,tpx_tag);
2418
2419 /* We only support reading tpx files with the same tag as the code
2420 * or tpx files with the release tag and with lower version number.
2421 */
2422 if (!strcmp(file_tag,TPX_TAG_RELEASE) == 0 && fver < tpx_version)
2423 {
2424 gmx_fatal(FARGS,"tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
2425 gmx_fio_getname(fio),fver,file_tag,
2426 tpx_version,tpx_tag);
2427 }
2428 }
2429 }
2430
2431 if (file_version != NULL)
2432 {
2433 *file_version = fver;
2434 }
2435 if (file_generation != NULL)
2436 {
2437 *file_generation = fgen;
2438 }
2439
2440
2441 if ((fver <= tpx_incompatible_version) ||
2442 ((fver > tpx_version) && !TopOnlyOK) ||
2443 (fgen > tpx_generation))
2444 gmx_fatal(FARGS,"reading tpx file (%s) version %d with version %d program",
2445 gmx_fio_getname(fio),fver,tpx_version);
2446
2447 do_section(fio,eitemHEADER,bRead);
2448 gmx_fio_do_int(fio,tpx->natoms);
2449 if (fver >= 28)
2450 gmx_fio_do_int(fio,tpx->ngtc);
2451 else
2452 tpx->ngtc = 0;
2453 if (fver < 62) {
2454 gmx_fio_do_int(fio,idum);
2455 gmx_fio_do_real(fio,rdum);
2456 }
2457 /*a better decision will eventually (5.0 or later) need to be made
2458 on how to treat the alchemical state of the system, which can now
2459 vary through a simulation, and cannot be completely described
2460 though a single lambda variable, or even a single state
2461 index. Eventually, should probably be a vector. MRS*/
2462 if (fver >= 79)
2463 {
2464 gmx_fio_do_int(fio,tpx->fep_state);
2465 }
2466 gmx_fio_do_real(fio,tpx->lambda);
2467 gmx_fio_do_int(fio,tpx->bIr);
2468 gmx_fio_do_int(fio,tpx->bTop);
2469 gmx_fio_do_int(fio,tpx->bX);
2470 gmx_fio_do_int(fio,tpx->bV);
2471 gmx_fio_do_int(fio,tpx->bF);
2472 gmx_fio_do_int(fio,tpx->bBox);
2473
2474 if((fgen > tpx_generation)) {
2475 /* This can only happen if TopOnlyOK=TRUE */
2476 tpx->bIr=FALSE;
2477 }
2478 }
2479
2480 static int do_tpx(t_fileio *fio, gmx_bool bRead,
2481 t_inputrec *ir,t_state *state,rvec *f,gmx_mtop_t *mtop,
2482 gmx_bool bXVallocated)
2483 {
2484 t_tpxheader tpx;
2485 t_inputrec dum_ir;
2486 gmx_mtop_t dum_top;
2487 gmx_bool TopOnlyOK,bDum=TRUE;
2488 int file_version,file_generation;
2489 int i;
2490 rvec *xptr,*vptr;
2491 int ePBC;
2492 gmx_bool bPeriodicMols;
2493
2494 if (!bRead) {
2495 tpx.natoms = state->natoms;
2496 tpx.ngtc = state->ngtc; /* need to add nnhpres here? */
2497 tpx.fep_state = state->fep_state;
2498 tpx.lambda = state->lambda[efptFEP];
2499 tpx.bIr = (ir != NULL);
2500 tpx.bTop = (mtop != NULL);
2501 tpx.bX = (state->x != NULL);
2502 tpx.bV = (state->v != NULL);
2503 tpx.bF = (f != NULL);
2504 tpx.bBox = TRUE;
2505 }
2506
2507 TopOnlyOK = (ir==NULL);
2508
2509 do_tpxheader(fio,bRead,&tpx,TopOnlyOK,&file_version,&file_generation);
2510
2511 if (bRead) {
2512 state->flags = 0;
2513 /* state->lambda = tpx.lambda;*/ /*remove this eventually? */
2514 /* The init_state calls initialize the Nose-Hoover xi integrals to zero */
2515 if (bXVallocated) {
2516 xptr = state->x;
2517 vptr = state->v;
2518 init_state(state,0,tpx.ngtc,0,0,0); /* nose-hoover chains */ /* eventually, need to add nnhpres here? */
2519 state->natoms = tpx.natoms;
2520 state->nalloc = tpx.natoms;
2521 state->x = xptr;
2522 state->v = vptr;
2523 } else {
2524 init_state(state,tpx.natoms,tpx.ngtc,0,0,0); /* nose-hoover chains */
2525 }
2526 }
2527
2528 #define do_test(fio,b,p) if (bRead && (p!=NULL) && !b) gmx_fatal(FARGS,"No %s in %s",#p,gmx_fio_getname(fio))
2529
2530 do_test(fio,tpx.bBox,state->box);
2531 do_section(fio,eitemBOX,bRead);
2532 if (tpx.bBox) {
2533 gmx_fio_ndo_rvec(fio,state->box,DIM);
2534 if (file_version >= 51) {
2535 gmx_fio_ndo_rvec(fio,state->box_rel,DIM);
2536 } else {
2537 /* We initialize box_rel after reading the inputrec */
2538 clear_mat(state->box_rel);
2539 }
2540 if (file_version >= 28) {
2541 gmx_fio_ndo_rvec(fio,state->boxv,DIM);
2542 if (file_version < 56) {
2543 matrix mdum;
2544 gmx_fio_ndo_rvec(fio,mdum,DIM);
2545 }
2546 }
2547 }
2548
2549 if (state->ngtc > 0 && file_version >= 28) {
2550 real *dumv;
2551 /*ndo_double(state->nosehoover_xi,state->ngtc,bDum);*/
2552 /*ndo_double(state->nosehoover_vxi,state->ngtc,bDum);*/
2553 /*ndo_double(state->therm_integral,state->ngtc,bDum);*/
2554 snew(dumv,state->ngtc);
2555 if (file_version < 69) {
2556 bDum=gmx_fio_ndo_real(fio,dumv,state->ngtc);
2557 }
2558 /* These used to be the Berendsen tcoupl_lambda's */
2559 bDum=gmx_fio_ndo_real(fio,dumv,state->ngtc);
2560 sfree(dumv);
2561 }
2562
2563 /* Prior to tpx version 26, the inputrec was here.
2564 * I moved it to enable partial forward-compatibility
2565 * for analysis/viewer programs.
2566 */
2567 if(file_version<26) {
2568 do_test(fio,tpx.bIr,ir);
2569 do_section(fio,eitemIR,bRead);
2570 if (tpx.bIr) {
2571 if (ir) {
2572 do_inputrec(fio, ir,bRead,file_version,
2573 mtop ? &mtop->ffparams.fudgeQQ : NULL);
2574 if (bRead && debug)
2575 pr_inputrec(debug,0,"inputrec",ir,FALSE);
2576 }
2577 else {
2578 do_inputrec(fio, &dum_ir,bRead,file_version,
2579 mtop ? &mtop->ffparams.fudgeQQ :NULL);
2580 if (bRead && debug)
2581 pr_inputrec(debug,0,"inputrec",&dum_ir,FALSE);
2582 done_inputrec(&dum_ir);
2583 }
2584
2585 }
2586 }
2587
2588 do_test(fio,tpx.bTop,mtop);
2589 do_section(fio,eitemTOP,bRead);
2590 if (tpx.bTop) {
2591 if (mtop) {
2592 do_mtop(fio,mtop,bRead, file_version);
2593 } else {
2594 do_mtop(fio,&dum_top,bRead,file_version);
2595 done_mtop(&dum_top,TRUE);
2596 }
2597 }
2598 do_test(fio,tpx.bX,state->x);
2599 do_section(fio,eitemX,bRead);
2600 if (tpx.bX) {
2601 if (bRead) {
2602 state->flags |= (1<<estX);
2603 }
2604 gmx_fio_ndo_rvec(fio,state->x,state->natoms);
2605 }
2606
2607 do_test(fio,tpx.bV,state->v);
2608 do_section(fio,eitemV,bRead);
2609 if (tpx.bV) {
2610 if (bRead) {
2611 state->flags |= (1<<estV);
2612 }
2613 gmx_fio_ndo_rvec(fio,state->v,state->natoms);
2614 }
2615
2616 do_test(fio,tpx.bF,f);
2617 do_section(fio,eitemF,bRead);
2618 if (tpx.bF) gmx_fio_ndo_rvec(fio,f,state->natoms);
2619
2620 /* Starting with tpx version 26, we have the inputrec
2621 * at the end of the file, so we can ignore it
2622 * if the file is never than the software (but still the
2623 * same generation - see comments at the top of this file.
2624 *
2625 *
2626 */
2627 ePBC = -1;
2628 bPeriodicMols = FALSE;
2629 if (file_version >= 26) {
2630 do_test(fio,tpx.bIr,ir);
2631 do_section(fio,eitemIR,bRead);
2632 if (tpx.bIr) {
2633 if (file_version >= 53) {
2634 /* Removed the pbc info from do_inputrec, since we always want it */
2635 if (!bRead) {
2636 ePBC = ir->ePBC;
2637 bPeriodicMols = ir->bPeriodicMols;
2638 }
2639 gmx_fio_do_int(fio,ePBC);
2640 gmx_fio_do_gmx_bool(fio,bPeriodicMols);
2641 }
2642 if (file_generation <= tpx_generation && ir) {
2643 do_inputrec(fio, ir,bRead,file_version,mtop ? &mtop->ffparams.fudgeQQ : NULL);
2644 if (bRead && debug)
2645 pr_inputrec(debug,0,"inputrec",ir,FALSE);
2646 if (file_version < 51)
2647 set_box_rel(ir,state);
2648 if (file_version < 53) {
2649 ePBC = ir->ePBC;
2650 bPeriodicMols = ir->bPeriodicMols;
2651 }
2652 }
2653 if (bRead && ir && file_version >= 53) {
2654 /* We need to do this after do_inputrec, since that initializes ir */
2655 ir->ePBC = ePBC;
2656 ir->bPeriodicMols = bPeriodicMols;
2657 }
2658 }
2659 }
2660
2661 if (bRead)
2662 {
2663 if (tpx.bIr && ir)
2664 {
2665 if (state->ngtc == 0)
2666 {
2667 /* Reading old version without tcoupl state data: set it */
2668 init_gtc_state(state,ir->opts.ngtc,0,ir->opts.nhchainlength);
2669 }
2670 if (tpx.bTop && mtop)
2671 {
2672 if (file_version < 57)
2673 {
2674 if (mtop->moltype[0].ilist[F_DISRES].nr > 0)
2675 {
2676 ir->eDisre = edrSimple;
2677 }
2678 else
2679 {
2680 ir->eDisre = edrNone;
2681 }
2682 }
2683 set_disres_npair(mtop);
2684 }
2685 }
2686
2687 if (tpx.bTop && mtop)
2688 {
2689 gmx_mtop_finalize(mtop);
2690 }
2691
2692 if (file_version >= 57)
2693 {
2694 char *env;
2695 int ienv;
2696 env = getenv("GMX_NOCHARGEGROUPS");
2697 if (env != NULL)
2698 {
2699 sscanf(env,"%d",&ienv);
2700 fprintf(stderr,"\nFound env.var. GMX_NOCHARGEGROUPS = %d\n",
2701 ienv);
2702 if (ienv > 0)
2703 {
2704 fprintf(stderr,
2705 "Will make single atomic charge groups in non-solvent%s\n",
2706 ienv > 1 ? " and solvent" : "");
2707 gmx_mtop_make_atomic_charge_groups(mtop,ienv==1);
2708 }
2709 fprintf(stderr,"\n");
2710 }
2711 }
2712 }
2713
2714 return ePBC;
2715 }
2716
2717 /************************************************************
2718 *
2719 * The following routines are the exported ones
2720 *
2721 ************************************************************/
2722
2723 t_fileio *open_tpx(const char *fn,const char *mode)
2724 {
2725 return gmx_fio_open(fn,mode);
2726 }
2727
2728 void close_tpx(t_fileio *fio)
2729 {
2730 gmx_fio_close(fio);
2731 }
2732
2733 void read_tpxheader(const char *fn, t_tpxheader *tpx, gmx_bool TopOnlyOK,
2734 int *file_version, int *file_generation)
2735 {
2736 t_fileio *fio;
2737
2738 fio = open_tpx(fn,"r");
2739 do_tpxheader(fio,TRUE,tpx,TopOnlyOK,file_version,file_generation);
2740 close_tpx(fio);
2741 }
2742
2743 void write_tpx_state(const char *fn,
2744 t_inputrec *ir,t_state *state,gmx_mtop_t *mtop)
2745 {
2746 t_fileio *fio;
2747
2748 fio = open_tpx(fn,"w");
2749 do_tpx(fio,FALSE,ir,state,NULL,mtop,FALSE);
2750 close_tpx(fio);
2751 }
2752
2753 void read_tpx_state(const char *fn,
2754 t_inputrec *ir,t_state *state,rvec *f,gmx_mtop_t *mtop)
2755 {
2756 t_fileio *fio;
2757
2758 fio = open_tpx(fn,"r");
2759 do_tpx(fio,TRUE,ir,state,f,mtop,FALSE);
2760 close_tpx(fio);
2761 }
2762
2763 int read_tpx(const char *fn,
2764 t_inputrec *ir, matrix box,int *natoms,
2765 rvec *x,rvec *v,rvec *f,gmx_mtop_t *mtop)
2766 {
2767 t_fileio *fio;
2768 t_state state;
2769 int ePBC;
2770
2771 state.x = x;
2772 state.v = v;
2773 fio = open_tpx(fn,"r");
2774 ePBC = do_tpx(fio,TRUE,ir,&state,f,mtop,TRUE);
2775 close_tpx(fio);
2776 *natoms = state.natoms;
2777 if (box)
2778 copy_mat(state.box,box);
2779 state.x = NULL;
2780 state.v = NULL;
2781 done_state(&state);
2782
2783 return ePBC;
2784 }
2785
2786 int read_tpx_top(const char *fn,
2787 t_inputrec *ir, matrix box,int *natoms,
2788 rvec *x,rvec *v,rvec *f,t_topology *top)
2789 {
2790 gmx_mtop_t mtop;
2791 t_topology *ltop;
2792 int ePBC;
2793
2794 ePBC = read_tpx(fn,ir,box,natoms,x,v,f,&mtop);
2795
2796 *top = gmx_mtop_t_to_t_topology(&mtop);
2797
2798 return ePBC;
2799 }
2800
2801 gmx_bool fn2bTPX(const char *file)
2802 {
2803 switch (fn2ftp(file)) {
2804 case efTPR:
2805 case efTPB:
2806 case efTPA:
2807 return TRUE;
2808 default:
2809 return FALSE;
2810 }
2811 }
2812
2813 gmx_bool read_tps_conf(const char *infile,char *title,t_topology *top,int *ePBC,
2814 rvec **x,rvec **v,matrix box,gmx_bool bMass)
2815 {
2816 t_tpxheader header;
2817 int natoms,i,version,generation;
2818 gmx_bool bTop,bXNULL=FALSE;
2819 gmx_mtop_t *mtop;
2820 t_topology *topconv;
2821 gmx_atomprop_t aps;
2822
2823 bTop = fn2bTPX(infile);
2824 *ePBC = -1;
2825 if (bTop) {
2826 read_tpxheader(infile,&header,TRUE,&version,&generation);
2827 if (x)
2828 snew(*x,header.natoms);
2829 if (v)
2830 snew(*v,header.natoms);
2831 snew(mtop,1);
2832 *ePBC = read_tpx(infile,NULL,box,&natoms,
2833 (x==NULL) ? NULL : *x,(v==NULL) ? NULL : *v,NULL,mtop);
2834 *top = gmx_mtop_t_to_t_topology(mtop);
2835 sfree(mtop);
2836 strcpy(title,*top->name);
2837 tpx_make_chain_identifiers(&top->atoms,&top->mols);
2838 }
2839 else {
2840 get_stx_coordnum(infile,&natoms);
2841 init_t_atoms(&top->atoms,natoms,(fn2ftp(infile) == efPDB));
2842 if (x == NULL)
2843 {
2844 snew(x,1);
2845 bXNULL = TRUE;
2846 }
2847 snew(*x,natoms);
2848 if (v)
2849 snew(*v,natoms);
2850 read_stx_conf(infile,title,&top->atoms,*x,(v==NULL) ? NULL : *v,ePBC,box);
2851 if (bXNULL)
2852 {
2853 sfree(*x);
2854 sfree(x);
2855 }
2856 if (bMass) {
2857 aps = gmx_atomprop_init();
2858 for(i=0; (i<natoms); i++)
2859 if (!gmx_atomprop_query(aps,epropMass,
2860 *top->atoms.resinfo[top->atoms.atom[i].resind].name,
2861 *top->atoms.atomname[i],
2862 &(top->atoms.atom[i].m))) {
2863 if (debug)
2864 fprintf(debug,"Can not find mass for atom %s %d %s, setting to 1\n",
2865 *top->atoms.resinfo[top->atoms.atom[i].resind].name,
2866 top->atoms.resinfo[top->atoms.atom[i].resind].nr,
2867 *top->atoms.atomname[i]);
2868 }
2869 gmx_atomprop_destroy(aps);
2870 }
2871 top->idef.ntypes=-1;
2872 }
2873
2874 return bTop;
2875 }
The ultimate molecular dynamics simulation package