?  search:
summary | log | graphiclog1 | graphiclog2 | commit | commitdiff | tree | refs | edit | fork
blame | history | raw | HEAD
Revised wording in pdb2gmx.c, hopefully clearer now.
[gromacs/rigid-bodies.git] / src / gmxlib / tpxio.c
blobfd30a89e0dc0c2c3e6b9a63b5b6f15d35528b21a
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_THREADS
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 /* This number should be increased whenever the file format changes! */
67 static const int tpx_version = 73;
68
69 /* This number should only be increased when you edit the TOPOLOGY section
70 * of the tpx format. This way we can maintain forward compatibility too
71 * for all analysis tools and/or external programs that only need to
72 * know the atom/residue names, charges, and bond connectivity.
73 *
74 * It first appeared in tpx version 26, when I also moved the inputrecord
75 * to the end of the tpx file, so we can just skip it if we only
76 * want the topology.
77 */
78 static const int tpx_generation = 23;
79
80 /* This number should be the most recent backwards incompatible version
81 * I.e., if this number is 9, we cannot read tpx version 9 with this code.
82 */
83 static const int tpx_incompatible_version = 9;
84
85
86
87 /* Struct used to maintain tpx compatibility when function types are added */
88 typedef struct {
89 int fvnr; /* file version number in which the function type first appeared */
90 int ftype; /* function type */
91 } t_ftupd;
92
93 /*
94 *The entries should be ordered in:
95 * 1. ascending file version number
96 * 2. ascending function type number
97 */
98 /*static const t_ftupd ftupd[] = {
99 { 20, F_CUBICBONDS },
100 { 20, F_CONNBONDS },
101 { 20, F_HARMONIC },
102 { 20, F_EQM, },
103 { 22, F_DISRESVIOL },
104 { 22, F_ORIRES },
105 { 22, F_ORIRESDEV },
106 { 26, F_FOURDIHS },
107 { 26, F_PIDIHS },
108 { 26, F_DIHRES },
109 { 26, F_DIHRESVIOL },
110 { 30, F_CROSS_BOND_BONDS },
111 { 30, F_CROSS_BOND_ANGLES },
112 { 30, F_UREY_BRADLEY },
113 { 30, F_POLARIZATION }
114 };*/
115
116 /*
117 *The entries should be ordered in:
118 * 1. ascending function type number
119 * 2. ascending file version number
120 */
121 static const t_ftupd ftupd[] = {
122 { 20, F_CUBICBONDS },
123 { 20, F_CONNBONDS },
124 { 20, F_HARMONIC },
125 { 34, F_FENEBONDS },
126 { 43, F_TABBONDS },
127 { 43, F_TABBONDSNC },
128 { 70, F_RESTRBONDS },
129 { 30, F_CROSS_BOND_BONDS },
130 { 30, F_CROSS_BOND_ANGLES },
131 { 30, F_UREY_BRADLEY },
132 { 34, F_QUARTIC_ANGLES },
133 { 43, F_TABANGLES },
134 { 26, F_FOURDIHS },
135 { 26, F_PIDIHS },
136 { 43, F_TABDIHS },
137 { 65, F_CMAP },
138 { 60, F_GB12 },
139 { 61, F_GB13 },
140 { 61, F_GB14 },
141 { 72, F_GBPOL },
142 { 72, F_NPSOLVATION },
143 { 41, F_LJC14_Q },
144 { 41, F_LJC_PAIRS_NB },
145 { 32, F_BHAM_LR },
146 { 32, F_RF_EXCL },
147 { 32, F_COUL_RECIP },
148 { 46, F_DPD },
149 { 30, F_POLARIZATION },
150 { 36, F_THOLE_POL },
151 { 22, F_DISRESVIOL },
152 { 22, F_ORIRES },
153 { 22, F_ORIRESDEV },
154 { 26, F_DIHRES },
155 { 26, F_DIHRESVIOL },
156 { 49, F_VSITE4FDN },
157 { 50, F_VSITEN },
158 { 46, F_COM_PULL },
159 { 20, F_EQM },
160 { 46, F_ECONSERVED },
161 { 69, F_VTEMP },
162 { 66, F_PDISPCORR },
163 { 54, F_DHDL_CON },
164 };
165 #define NFTUPD asize(ftupd)
166
167 /* Needed for backward compatibility */
168 #define MAXNODES 256
169
170 static void _do_section(t_fileio *fio,int key,gmx_bool bRead,const char *src,
171 int line)
172 {
173 char buf[STRLEN];
174 gmx_bool bDbg;
175
176 if (gmx_fio_getftp(fio) == efTPA) {
177 if (!bRead) {
178 gmx_fio_write_string(fio,itemstr[key]);
179 bDbg = gmx_fio_getdebug(fio);
180 gmx_fio_setdebug(fio,FALSE);
181 gmx_fio_write_string(fio,comment_str[key]);
182 gmx_fio_setdebug(fio,bDbg);
183 }
184 else {
185 if (gmx_fio_getdebug(fio))
186 fprintf(stderr,"Looking for section %s (%s, %d)",
187 itemstr[key],src,line);
188
189 do {
190 gmx_fio_do_string(fio,buf);
191 } while ((gmx_strcasecmp(buf,itemstr[key]) != 0));
192
193 if (gmx_strcasecmp(buf,itemstr[key]) != 0)
194 gmx_fatal(FARGS,"\nCould not find section heading %s",itemstr[key]);
195 else if (gmx_fio_getdebug(fio))
196 fprintf(stderr," and found it\n");
197 }
198 }
199 }
200
201 #define do_section(fio,key,bRead) _do_section(fio,key,bRead,__FILE__,__LINE__)
202
203 /**************************************************************
204 *
205 * Now the higer level routines that do io of the structures and arrays
206 *
207 **************************************************************/
208 static void do_pullgrp(t_fileio *fio, t_pullgrp *pgrp, gmx_bool bRead,
209 int file_version)
210 {
211 gmx_bool bDum=TRUE;
212 int i;
213
214 gmx_fio_do_int(fio,pgrp->nat);
215 if (bRead)
216 snew(pgrp->ind,pgrp->nat);
217 bDum=gmx_fio_ndo_int(fio,pgrp->ind,pgrp->nat);
218 gmx_fio_do_int(fio,pgrp->nweight);
219 if (bRead)
220 snew(pgrp->weight,pgrp->nweight);
221 bDum=gmx_fio_ndo_real(fio,pgrp->weight,pgrp->nweight);
222 gmx_fio_do_int(fio,pgrp->pbcatom);
223 gmx_fio_do_rvec(fio,pgrp->vec);
224 gmx_fio_do_rvec(fio,pgrp->init);
225 gmx_fio_do_real(fio,pgrp->rate);
226 gmx_fio_do_real(fio,pgrp->k);
227 if (file_version >= 56) {
228 gmx_fio_do_real(fio,pgrp->kB);
229 } else {
230 pgrp->kB = pgrp->k;
231 }
232 }
233
234 static void do_pull(t_fileio *fio, t_pull *pull,gmx_bool bRead, int file_version)
235 {
236 int g;
237
238 gmx_fio_do_int(fio,pull->ngrp);
239 gmx_fio_do_int(fio,pull->eGeom);
240 gmx_fio_do_ivec(fio,pull->dim);
241 gmx_fio_do_real(fio,pull->cyl_r1);
242 gmx_fio_do_real(fio,pull->cyl_r0);
243 gmx_fio_do_real(fio,pull->constr_tol);
244 gmx_fio_do_int(fio,pull->nstxout);
245 gmx_fio_do_int(fio,pull->nstfout);
246 if (bRead)
247 snew(pull->grp,pull->ngrp+1);
248 for(g=0; g<pull->ngrp+1; g++)
249 do_pullgrp(fio,&pull->grp[g],bRead,file_version);
250 }
251
252 static void do_inputrec(t_fileio *fio, t_inputrec *ir,gmx_bool bRead,
253 int file_version, real *fudgeQQ)
254 {
255 int i,j,k,*tmp,idum=0;
256 gmx_bool bDum=TRUE;
257 real rdum,bd_temp;
258 rvec vdum;
259 gmx_bool bSimAnn;
260 real zerotemptime,finish_t,init_temp,finish_temp;
261
262 if (file_version != tpx_version)
263 {
264 /* Give a warning about features that are not accessible */
265 fprintf(stderr,"Note: tpx file_version %d, software version %d\n",
266 file_version,tpx_version);
267 }
268
269 if (bRead)
270 {
271 init_inputrec(ir);
272 }
273
274 if (file_version == 0)
275 {
276 return;
277 }
278
279 /* Basic inputrec stuff */
280 gmx_fio_do_int(fio,ir->eI);
281 if (file_version >= 62) {
282 gmx_fio_do_gmx_large_int(fio, ir->nsteps);
283 } else {
284 gmx_fio_do_int(fio,idum);
285 ir->nsteps = idum;
286 }
287 if(file_version > 25) {
288 if (file_version >= 62) {
289 gmx_fio_do_gmx_large_int(fio, ir->init_step);
290 } else {
291 gmx_fio_do_int(fio,idum);
292 ir->init_step = idum;
293 }
294 } else {
295 ir->init_step=0;
296 }
297
298 if(file_version >= 58)
299 gmx_fio_do_int(fio,ir->simulation_part);
300 else
301 ir->simulation_part=1;
302
303 if (file_version >= 67) {
304 gmx_fio_do_int(fio,ir->nstcalcenergy);
305 } else {
306 ir->nstcalcenergy = 1;
307 }
308 if (file_version < 53) {
309 /* The pbc info has been moved out of do_inputrec,
310 * since we always want it, also without reading the inputrec.
311 */
312 gmx_fio_do_int(fio,ir->ePBC);
313 if ((file_version <= 15) && (ir->ePBC == 2))
314 ir->ePBC = epbcNONE;
315 if (file_version >= 45) {
316 gmx_fio_do_int(fio,ir->bPeriodicMols);
317 } else {
318 if (ir->ePBC == 2) {
319 ir->ePBC = epbcXYZ;
320 ir->bPeriodicMols = TRUE;
321 } else {
322 ir->bPeriodicMols = FALSE;
323 }
324 }
325 }
326 gmx_fio_do_int(fio,ir->ns_type);
327 gmx_fio_do_int(fio,ir->nstlist);
328 gmx_fio_do_int(fio,ir->ndelta);
329 if (file_version < 41) {
330 gmx_fio_do_int(fio,idum);
331 gmx_fio_do_int(fio,idum);
332 }
333 if (file_version >= 45)
334 gmx_fio_do_real(fio,ir->rtpi);
335 else
336 ir->rtpi = 0.05;
337 gmx_fio_do_int(fio,ir->nstcomm);
338 if (file_version > 34)
339 gmx_fio_do_int(fio,ir->comm_mode);
340 else if (ir->nstcomm < 0)
341 ir->comm_mode = ecmANGULAR;
342 else
343 ir->comm_mode = ecmLINEAR;
344 ir->nstcomm = abs(ir->nstcomm);
345
346 if(file_version > 25)
347 gmx_fio_do_int(fio,ir->nstcheckpoint);
348 else
349 ir->nstcheckpoint=0;
350
351 gmx_fio_do_int(fio,ir->nstcgsteep);
352
353 if(file_version>=30)
354 gmx_fio_do_int(fio,ir->nbfgscorr);
355 else if (bRead)
356 ir->nbfgscorr = 10;
357
358 gmx_fio_do_int(fio,ir->nstlog);
359 gmx_fio_do_int(fio,ir->nstxout);
360 gmx_fio_do_int(fio,ir->nstvout);
361 gmx_fio_do_int(fio,ir->nstfout);
362 gmx_fio_do_int(fio,ir->nstenergy);
363 gmx_fio_do_int(fio,ir->nstxtcout);
364 if (file_version >= 59) {
365 gmx_fio_do_double(fio,ir->init_t);
366 gmx_fio_do_double(fio,ir->delta_t);
367 } else {
368 gmx_fio_do_real(fio,rdum);
369 ir->init_t = rdum;
370 gmx_fio_do_real(fio,rdum);
371 ir->delta_t = rdum;
372 }
373 gmx_fio_do_real(fio,ir->xtcprec);
374 if (file_version < 19) {
375 gmx_fio_do_int(fio,idum);
376 gmx_fio_do_int(fio,idum);
377 }
378 if(file_version < 18)
379 gmx_fio_do_int(fio,idum);
380 gmx_fio_do_real(fio,ir->rlist);
381 if (file_version >= 67) {
382 gmx_fio_do_real(fio,ir->rlistlong);
383 }
384 gmx_fio_do_int(fio,ir->coulombtype);
385 if (file_version < 32 && ir->coulombtype == eelRF)
386 ir->coulombtype = eelRF_NEC;
387 gmx_fio_do_real(fio,ir->rcoulomb_switch);
388 gmx_fio_do_real(fio,ir->rcoulomb);
389 gmx_fio_do_int(fio,ir->vdwtype);
390 gmx_fio_do_real(fio,ir->rvdw_switch);
391 gmx_fio_do_real(fio,ir->rvdw);
392 if (file_version < 67) {
393 ir->rlistlong = max_cutoff(ir->rlist,max_cutoff(ir->rvdw,ir->rcoulomb));
394 }
395 gmx_fio_do_int(fio,ir->eDispCorr);
396 gmx_fio_do_real(fio,ir->epsilon_r);
397 if (file_version >= 37) {
398 gmx_fio_do_real(fio,ir->epsilon_rf);
399 } else {
400 if (EEL_RF(ir->coulombtype)) {
401 ir->epsilon_rf = ir->epsilon_r;
402 ir->epsilon_r = 1.0;
403 } else {
404 ir->epsilon_rf = 1.0;
405 }
406 }
407 if (file_version >= 29)
408 gmx_fio_do_real(fio,ir->tabext);
409 else
410 ir->tabext=1.0;
411
412 if(file_version > 25) {
413 gmx_fio_do_int(fio,ir->gb_algorithm);
414 gmx_fio_do_int(fio,ir->nstgbradii);
415 gmx_fio_do_real(fio,ir->rgbradii);
416 gmx_fio_do_real(fio,ir->gb_saltconc);
417 gmx_fio_do_int(fio,ir->implicit_solvent);
418 } else {
419 ir->gb_algorithm=egbSTILL;
420 ir->nstgbradii=1;
421 ir->rgbradii=1.0;
422 ir->gb_saltconc=0;
423 ir->implicit_solvent=eisNO;
424 }
425 if(file_version>=55)
426 {
427 gmx_fio_do_real(fio,ir->gb_epsilon_solvent);
428 gmx_fio_do_real(fio,ir->gb_obc_alpha);
429 gmx_fio_do_real(fio,ir->gb_obc_beta);
430 gmx_fio_do_real(fio,ir->gb_obc_gamma);
431 if(file_version>=60)
432 {
433 gmx_fio_do_real(fio,ir->gb_dielectric_offset);
434 gmx_fio_do_int(fio,ir->sa_algorithm);
435 }
436 else
437 {
438 ir->gb_dielectric_offset = 0.009;
439 ir->sa_algorithm = esaAPPROX;
440 }
441 gmx_fio_do_real(fio,ir->sa_surface_tension);
442
443 /* Override sa_surface_tension if it is not changed in the mpd-file */
444 if(ir->sa_surface_tension<0)
445 {
446 if(ir->gb_algorithm==egbSTILL)
447 {
448 ir->sa_surface_tension = 0.0049 * 100 * CAL2JOULE;
449 }
450 else if(ir->gb_algorithm==egbHCT || ir->gb_algorithm==egbOBC)
451 {
452 ir->sa_surface_tension = 0.0054 * 100 * CAL2JOULE;
453 }
454 }
455
456 }
457 else
458 {
459 /* Better use sensible values than insane (0.0) ones... */
460 ir->gb_epsilon_solvent = 80;
461 ir->gb_obc_alpha = 1.0;
462 ir->gb_obc_beta = 0.8;
463 ir->gb_obc_gamma = 4.85;
464 ir->sa_surface_tension = 2.092;
465 }
466
467
468 gmx_fio_do_int(fio,ir->nkx);
469 gmx_fio_do_int(fio,ir->nky);
470 gmx_fio_do_int(fio,ir->nkz);
471 gmx_fio_do_int(fio,ir->pme_order);
472 gmx_fio_do_real(fio,ir->ewald_rtol);
473
474 if (file_version >=24)
475 gmx_fio_do_int(fio,ir->ewald_geometry);
476 else
477 ir->ewald_geometry=eewg3D;
478
479 if (file_version <=17) {
480 ir->epsilon_surface=0;
481 if (file_version==17)
482 gmx_fio_do_int(fio,idum);
483 }
484 else
485 gmx_fio_do_real(fio,ir->epsilon_surface);
486
487 gmx_fio_do_gmx_bool(fio,ir->bOptFFT);
488
489 gmx_fio_do_gmx_bool(fio,ir->bContinuation);
490 gmx_fio_do_int(fio,ir->etc);
491 /* before version 18, ir->etc was a gmx_bool (ir->btc),
492 * but the values 0 and 1 still mean no and
493 * berendsen temperature coupling, respectively.
494 */
495 if (file_version >= 71)
496 {
497 gmx_fio_do_int(fio,ir->nsttcouple);
498 }
499 else
500 {
501 ir->nsttcouple = ir->nstcalcenergy;
502 }
503 if (file_version <= 15)
504 {
505 gmx_fio_do_int(fio,idum);
506 }
507 if (file_version <=17)
508 {
509 gmx_fio_do_int(fio,ir->epct);
510 if (file_version <= 15)
511 {
512 if (ir->epct == 5)
513 {
514 ir->epct = epctSURFACETENSION;
515 }
516 gmx_fio_do_int(fio,idum);
517 }
518 ir->epct -= 1;
519 /* we have removed the NO alternative at the beginning */
520 if(ir->epct==-1)
521 {
522 ir->epc=epcNO;
523 ir->epct=epctISOTROPIC;
524 }
525 else
526 {
527 ir->epc=epcBERENDSEN;
528 }
529 }
530 else
531 {
532 gmx_fio_do_int(fio,ir->epc);
533 gmx_fio_do_int(fio,ir->epct);
534 }
535 if (file_version >= 71)
536 {
537 gmx_fio_do_int(fio,ir->nstpcouple);
538 }
539 else
540 {
541 ir->nstpcouple = ir->nstcalcenergy;
542 }
543 gmx_fio_do_real(fio,ir->tau_p);
544 if (file_version <= 15) {
545 gmx_fio_do_rvec(fio,vdum);
546 clear_mat(ir->ref_p);
547 for(i=0; i<DIM; i++)
548 ir->ref_p[i][i] = vdum[i];
549 } else {
550 gmx_fio_do_rvec(fio,ir->ref_p[XX]);
551 gmx_fio_do_rvec(fio,ir->ref_p[YY]);
552 gmx_fio_do_rvec(fio,ir->ref_p[ZZ]);
553 }
554 if (file_version <= 15) {
555 gmx_fio_do_rvec(fio,vdum);
556 clear_mat(ir->compress);
557 for(i=0; i<DIM; i++)
558 ir->compress[i][i] = vdum[i];
559 }
560 else {
561 gmx_fio_do_rvec(fio,ir->compress[XX]);
562 gmx_fio_do_rvec(fio,ir->compress[YY]);
563 gmx_fio_do_rvec(fio,ir->compress[ZZ]);
564 }
565 if (file_version >= 47) {
566 gmx_fio_do_int(fio,ir->refcoord_scaling);
567 gmx_fio_do_rvec(fio,ir->posres_com);
568 gmx_fio_do_rvec(fio,ir->posres_comB);
569 } else {
570 ir->refcoord_scaling = erscNO;
571 clear_rvec(ir->posres_com);
572 clear_rvec(ir->posres_comB);
573 }
574 if(file_version > 25)
575 gmx_fio_do_int(fio,ir->andersen_seed);
576 else
577 ir->andersen_seed=0;
578
579 if(file_version < 26) {
580 gmx_fio_do_gmx_bool(fio,bSimAnn);
581 gmx_fio_do_real(fio,zerotemptime);
582 }
583
584 if (file_version < 37)
585 gmx_fio_do_real(fio,rdum);
586
587 gmx_fio_do_real(fio,ir->shake_tol);
588 if (file_version < 54)
589 gmx_fio_do_real(fio,*fudgeQQ);
590 gmx_fio_do_int(fio,ir->efep);
591 if (file_version <= 14 && ir->efep > efepNO)
592 ir->efep = efepYES;
593 if (file_version >= 59) {
594 gmx_fio_do_double(fio, ir->init_lambda);
595 gmx_fio_do_double(fio, ir->delta_lambda);
596 } else {
597 gmx_fio_do_real(fio,rdum);
598 ir->init_lambda = rdum;
599 gmx_fio_do_real(fio,rdum);
600 ir->delta_lambda = rdum;
601 }
602 if (file_version >= 64) {
603 gmx_fio_do_int(fio,ir->n_flambda);
604 if (bRead) {
605 snew(ir->flambda,ir->n_flambda);
606 }
607 bDum=gmx_fio_ndo_double(fio,ir->flambda,ir->n_flambda);
608 } else {
609 ir->n_flambda = 0;
610 ir->flambda = NULL;
611 }
612 if (file_version >= 13)
613 gmx_fio_do_real(fio,ir->sc_alpha);
614 else
615 ir->sc_alpha = 0;
616 if (file_version >= 38)
617 gmx_fio_do_int(fio,ir->sc_power);
618 else
619 ir->sc_power = 2;
620 if (file_version >= 15)
621 gmx_fio_do_real(fio,ir->sc_sigma);
622 else
623 ir->sc_sigma = 0.3;
624 if (bRead)
625 {
626 if (file_version >= 71)
627 {
628 ir->sc_sigma_min = ir->sc_sigma;
629 }
630 else
631 {
632 ir->sc_sigma_min = 0;
633 }
634 }
635 if (file_version >= 64) {
636 gmx_fio_do_int(fio,ir->nstdhdl);
637 } else {
638 ir->nstdhdl = 1;
639 }
640
641 if (file_version >= 73)
642 {
643 gmx_fio_do_int(fio, ir->separate_dhdl_file);
644 gmx_fio_do_int(fio, ir->dhdl_derivatives);
645 }
646 else
647 {
648 ir->separate_dhdl_file = sepdhdlfileYES;
649 ir->dhdl_derivatives = dhdlderivativesYES;
650 }
651
652 if (file_version >= 71)
653 {
654 gmx_fio_do_int(fio,ir->dh_hist_size);
655 gmx_fio_do_double(fio,ir->dh_hist_spacing);
656 }
657 else
658 {
659 ir->dh_hist_size = 0;
660 ir->dh_hist_spacing = 0.1;
661 }
662 if (file_version >= 57) {
663 gmx_fio_do_int(fio,ir->eDisre);
664 }
665 gmx_fio_do_int(fio,ir->eDisreWeighting);
666 if (file_version < 22) {
667 if (ir->eDisreWeighting == 0)
668 ir->eDisreWeighting = edrwEqual;
669 else
670 ir->eDisreWeighting = edrwConservative;
671 }
672 gmx_fio_do_gmx_bool(fio,ir->bDisreMixed);
673 gmx_fio_do_real(fio,ir->dr_fc);
674 gmx_fio_do_real(fio,ir->dr_tau);
675 gmx_fio_do_int(fio,ir->nstdisreout);
676 if (file_version >= 22) {
677 gmx_fio_do_real(fio,ir->orires_fc);
678 gmx_fio_do_real(fio,ir->orires_tau);
679 gmx_fio_do_int(fio,ir->nstorireout);
680 } else {
681 ir->orires_fc = 0;
682 ir->orires_tau = 0;
683 ir->nstorireout = 0;
684 }
685 if(file_version >= 26) {
686 gmx_fio_do_real(fio,ir->dihre_fc);
687 if (file_version < 56) {
688 gmx_fio_do_real(fio,rdum);
689 gmx_fio_do_int(fio,idum);
690 }
691 } else {
692 ir->dihre_fc=0;
693 }
694
695 gmx_fio_do_real(fio,ir->em_stepsize);
696 gmx_fio_do_real(fio,ir->em_tol);
697 if (file_version >= 22)
698 gmx_fio_do_gmx_bool(fio,ir->bShakeSOR);
699 else if (bRead)
700 ir->bShakeSOR = TRUE;
701 if (file_version >= 11)
702 gmx_fio_do_int(fio,ir->niter);
703 else if (bRead) {
704 ir->niter = 25;
705 fprintf(stderr,"Note: niter not in run input file, setting it to %d\n",
706 ir->niter);
707 }
708 if (file_version >= 21)
709 gmx_fio_do_real(fio,ir->fc_stepsize);
710 else
711 ir->fc_stepsize = 0;
712 gmx_fio_do_int(fio,ir->eConstrAlg);
713 gmx_fio_do_int(fio,ir->nProjOrder);
714 gmx_fio_do_real(fio,ir->LincsWarnAngle);
715 if (file_version <= 14)
716 gmx_fio_do_int(fio,idum);
717 if (file_version >=26)
718 gmx_fio_do_int(fio,ir->nLincsIter);
719 else if (bRead) {
720 ir->nLincsIter = 1;
721 fprintf(stderr,"Note: nLincsIter not in run input file, setting it to %d\n",
722 ir->nLincsIter);
723 }
724 if (file_version < 33)
725 gmx_fio_do_real(fio,bd_temp);
726 gmx_fio_do_real(fio,ir->bd_fric);
727 gmx_fio_do_int(fio,ir->ld_seed);
728 if (file_version >= 33) {
729 for(i=0; i<DIM; i++)
730 gmx_fio_do_rvec(fio,ir->deform[i]);
731 } else {
732 for(i=0; i<DIM; i++)
733 clear_rvec(ir->deform[i]);
734 }
735 if (file_version >= 14)
736 gmx_fio_do_real(fio,ir->cos_accel);
737 else if (bRead)
738 ir->cos_accel = 0;
739 gmx_fio_do_int(fio,ir->userint1);
740 gmx_fio_do_int(fio,ir->userint2);
741 gmx_fio_do_int(fio,ir->userint3);
742 gmx_fio_do_int(fio,ir->userint4);
743 gmx_fio_do_real(fio,ir->userreal1);
744 gmx_fio_do_real(fio,ir->userreal2);
745 gmx_fio_do_real(fio,ir->userreal3);
746 gmx_fio_do_real(fio,ir->userreal4);
747
748 /* pull stuff */
749 if (file_version >= 48) {
750 gmx_fio_do_int(fio,ir->ePull);
751 if (ir->ePull != epullNO) {
752 if (bRead)
753 snew(ir->pull,1);
754 do_pull(fio, ir->pull,bRead,file_version);
755 }
756 } else {
757 ir->ePull = epullNO;
758 }
759
760 /* grpopts stuff */
761 gmx_fio_do_int(fio,ir->opts.ngtc);
762 if (file_version >= 69) {
763 gmx_fio_do_int(fio,ir->opts.nhchainlength);
764 } else {
765 ir->opts.nhchainlength = 1;
766 }
767 gmx_fio_do_int(fio,ir->opts.ngacc);
768 gmx_fio_do_int(fio,ir->opts.ngfrz);
769 gmx_fio_do_int(fio,ir->opts.ngener);
770
771 if (bRead) {
772 snew(ir->opts.nrdf, ir->opts.ngtc);
773 snew(ir->opts.ref_t, ir->opts.ngtc);
774 snew(ir->opts.annealing, ir->opts.ngtc);
775 snew(ir->opts.anneal_npoints, ir->opts.ngtc);
776 snew(ir->opts.anneal_time, ir->opts.ngtc);
777 snew(ir->opts.anneal_temp, ir->opts.ngtc);
778 snew(ir->opts.tau_t, ir->opts.ngtc);
779 snew(ir->opts.nFreeze,ir->opts.ngfrz);
780 snew(ir->opts.acc, ir->opts.ngacc);
781 snew(ir->opts.egp_flags,ir->opts.ngener*ir->opts.ngener);
782 }
783 if (ir->opts.ngtc > 0) {
784 if (bRead && file_version<13) {
785 snew(tmp,ir->opts.ngtc);
786 bDum=gmx_fio_ndo_int(fio,tmp, ir->opts.ngtc);
787 for(i=0; i<ir->opts.ngtc; i++)
788 ir->opts.nrdf[i] = tmp[i];
789 sfree(tmp);
790 } else {
791 bDum=gmx_fio_ndo_real(fio,ir->opts.nrdf, ir->opts.ngtc);
792 }
793 bDum=gmx_fio_ndo_real(fio,ir->opts.ref_t,ir->opts.ngtc);
794 bDum=gmx_fio_ndo_real(fio,ir->opts.tau_t,ir->opts.ngtc);
795 if (file_version<33 && ir->eI==eiBD) {
796 for(i=0; i<ir->opts.ngtc; i++)
797 ir->opts.tau_t[i] = bd_temp;
798 }
799 }
800 if (ir->opts.ngfrz > 0)
801 bDum=gmx_fio_ndo_ivec(fio,ir->opts.nFreeze,ir->opts.ngfrz);
802 if (ir->opts.ngacc > 0)
803 gmx_fio_ndo_rvec(fio,ir->opts.acc,ir->opts.ngacc);
804 if (file_version >= 12)
805 bDum=gmx_fio_ndo_int(fio,ir->opts.egp_flags,
806 ir->opts.ngener*ir->opts.ngener);
807
808 if(bRead && file_version < 26) {
809 for(i=0;i<ir->opts.ngtc;i++) {
810 if(bSimAnn) {
811 ir->opts.annealing[i] = eannSINGLE;
812 ir->opts.anneal_npoints[i] = 2;
813 snew(ir->opts.anneal_time[i],2);
814 snew(ir->opts.anneal_temp[i],2);
815 /* calculate the starting/ending temperatures from reft, zerotemptime, and nsteps */
816 finish_t = ir->init_t + ir->nsteps * ir->delta_t;
817 init_temp = ir->opts.ref_t[i]*(1-ir->init_t/zerotemptime);
818 finish_temp = ir->opts.ref_t[i]*(1-finish_t/zerotemptime);
819 ir->opts.anneal_time[i][0] = ir->init_t;
820 ir->opts.anneal_time[i][1] = finish_t;
821 ir->opts.anneal_temp[i][0] = init_temp;
822 ir->opts.anneal_temp[i][1] = finish_temp;
823 } else {
824 ir->opts.annealing[i] = eannNO;
825 ir->opts.anneal_npoints[i] = 0;
826 }
827 }
828 } else {
829 /* file version 26 or later */
830 /* First read the lists with annealing and npoints for each group */
831 bDum=gmx_fio_ndo_int(fio,ir->opts.annealing,ir->opts.ngtc);
832 bDum=gmx_fio_ndo_int(fio,ir->opts.anneal_npoints,ir->opts.ngtc);
833 for(j=0;j<(ir->opts.ngtc);j++) {
834 k=ir->opts.anneal_npoints[j];
835 if(bRead) {
836 snew(ir->opts.anneal_time[j],k);
837 snew(ir->opts.anneal_temp[j],k);
838 }
839 bDum=gmx_fio_ndo_real(fio,ir->opts.anneal_time[j],k);
840 bDum=gmx_fio_ndo_real(fio,ir->opts.anneal_temp[j],k);
841 }
842 }
843 /* Walls */
844 if (file_version >= 45) {
845 gmx_fio_do_int(fio,ir->nwall);
846 gmx_fio_do_int(fio,ir->wall_type);
847 if (file_version >= 50)
848 gmx_fio_do_real(fio,ir->wall_r_linpot);
849 else
850 ir->wall_r_linpot = -1;
851 gmx_fio_do_int(fio,ir->wall_atomtype[0]);
852 gmx_fio_do_int(fio,ir->wall_atomtype[1]);
853 gmx_fio_do_real(fio,ir->wall_density[0]);
854 gmx_fio_do_real(fio,ir->wall_density[1]);
855 gmx_fio_do_real(fio,ir->wall_ewald_zfac);
856 } else {
857 ir->nwall = 0;
858 ir->wall_type = 0;
859 ir->wall_atomtype[0] = -1;
860 ir->wall_atomtype[1] = -1;
861 ir->wall_density[0] = 0;
862 ir->wall_density[1] = 0;
863 ir->wall_ewald_zfac = 3;
864 }
865 /* Cosine stuff for electric fields */
866 for(j=0; (j<DIM); j++) {
867 gmx_fio_do_int(fio,ir->ex[j].n);
868 gmx_fio_do_int(fio,ir->et[j].n);
869 if (bRead) {
870 snew(ir->ex[j].a, ir->ex[j].n);
871 snew(ir->ex[j].phi,ir->ex[j].n);
872 snew(ir->et[j].a, ir->et[j].n);
873 snew(ir->et[j].phi,ir->et[j].n);
874 }
875 bDum=gmx_fio_ndo_real(fio,ir->ex[j].a, ir->ex[j].n);
876 bDum=gmx_fio_ndo_real(fio,ir->ex[j].phi,ir->ex[j].n);
877 bDum=gmx_fio_ndo_real(fio,ir->et[j].a, ir->et[j].n);
878 bDum=gmx_fio_ndo_real(fio,ir->et[j].phi,ir->et[j].n);
879 }
880
881 /* QMMM stuff */
882 if(file_version>=39){
883 gmx_fio_do_gmx_bool(fio,ir->bQMMM);
884 gmx_fio_do_int(fio,ir->QMMMscheme);
885 gmx_fio_do_real(fio,ir->scalefactor);
886 gmx_fio_do_int(fio,ir->opts.ngQM);
887 if (bRead) {
888 snew(ir->opts.QMmethod, ir->opts.ngQM);
889 snew(ir->opts.QMbasis, ir->opts.ngQM);
890 snew(ir->opts.QMcharge, ir->opts.ngQM);
891 snew(ir->opts.QMmult, ir->opts.ngQM);
892 snew(ir->opts.bSH, ir->opts.ngQM);
893 snew(ir->opts.CASorbitals, ir->opts.ngQM);
894 snew(ir->opts.CASelectrons,ir->opts.ngQM);
895 snew(ir->opts.SAon, ir->opts.ngQM);
896 snew(ir->opts.SAoff, ir->opts.ngQM);
897 snew(ir->opts.SAsteps, ir->opts.ngQM);
898 snew(ir->opts.bOPT, ir->opts.ngQM);
899 snew(ir->opts.bTS, ir->opts.ngQM);
900 }
901 if (ir->opts.ngQM > 0) {
902 bDum=gmx_fio_ndo_int(fio,ir->opts.QMmethod,ir->opts.ngQM);
903 bDum=gmx_fio_ndo_int(fio,ir->opts.QMbasis,ir->opts.ngQM);
904 bDum=gmx_fio_ndo_int(fio,ir->opts.QMcharge,ir->opts.ngQM);
905 bDum=gmx_fio_ndo_int(fio,ir->opts.QMmult,ir->opts.ngQM);
906 bDum=gmx_fio_ndo_gmx_bool(fio,ir->opts.bSH,ir->opts.ngQM);
907 bDum=gmx_fio_ndo_int(fio,ir->opts.CASorbitals,ir->opts.ngQM);
908 bDum=gmx_fio_ndo_int(fio,ir->opts.CASelectrons,ir->opts.ngQM);
909 bDum=gmx_fio_ndo_real(fio,ir->opts.SAon,ir->opts.ngQM);
910 bDum=gmx_fio_ndo_real(fio,ir->opts.SAoff,ir->opts.ngQM);
911 bDum=gmx_fio_ndo_int(fio,ir->opts.SAsteps,ir->opts.ngQM);
912 bDum=gmx_fio_ndo_gmx_bool(fio,ir->opts.bOPT,ir->opts.ngQM);
913 bDum=gmx_fio_ndo_gmx_bool(fio,ir->opts.bTS,ir->opts.ngQM);
914 }
915 /* end of QMMM stuff */
916 }
917 }
918
919
920 static void do_harm(t_fileio *fio, t_iparams *iparams,gmx_bool bRead)
921 {
922 gmx_fio_do_real(fio,iparams->harmonic.rA);
923 gmx_fio_do_real(fio,iparams->harmonic.krA);
924 gmx_fio_do_real(fio,iparams->harmonic.rB);
925 gmx_fio_do_real(fio,iparams->harmonic.krB);
926 }
927
928 void do_iparams(t_fileio *fio, t_functype ftype,t_iparams *iparams,
929 gmx_bool bRead, int file_version)
930 {
931 int i;
932 gmx_bool bDum;
933 real rdum;
934
935 if (!bRead)
936 gmx_fio_set_comment(fio, interaction_function[ftype].name);
937 switch (ftype) {
938 case F_ANGLES:
939 case F_G96ANGLES:
940 case F_BONDS:
941 case F_G96BONDS:
942 case F_HARMONIC:
943 case F_IDIHS:
944 do_harm(fio, iparams,bRead);
945 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && bRead) {
946 /* Correct incorrect storage of parameters */
947 iparams->pdihs.phiB = iparams->pdihs.phiA;
948 iparams->pdihs.cpB = iparams->pdihs.cpA;
949 }
950 break;
951 case F_FENEBONDS:
952 gmx_fio_do_real(fio,iparams->fene.bm);
953 gmx_fio_do_real(fio,iparams->fene.kb);
954 break;
955 case F_RESTRBONDS:
956 gmx_fio_do_real(fio,iparams->restraint.lowA);
957 gmx_fio_do_real(fio,iparams->restraint.up1A);
958 gmx_fio_do_real(fio,iparams->restraint.up2A);
959 gmx_fio_do_real(fio,iparams->restraint.kA);
960 gmx_fio_do_real(fio,iparams->restraint.lowB);
961 gmx_fio_do_real(fio,iparams->restraint.up1B);
962 gmx_fio_do_real(fio,iparams->restraint.up2B);
963 gmx_fio_do_real(fio,iparams->restraint.kB);
964 break;
965 case F_TABBONDS:
966 case F_TABBONDSNC:
967 case F_TABANGLES:
968 case F_TABDIHS:
969 gmx_fio_do_real(fio,iparams->tab.kA);
970 gmx_fio_do_int(fio,iparams->tab.table);
971 gmx_fio_do_real(fio,iparams->tab.kB);
972 break;
973 case F_CROSS_BOND_BONDS:
974 gmx_fio_do_real(fio,iparams->cross_bb.r1e);
975 gmx_fio_do_real(fio,iparams->cross_bb.r2e);
976 gmx_fio_do_real(fio,iparams->cross_bb.krr);
977 break;
978 case F_CROSS_BOND_ANGLES:
979 gmx_fio_do_real(fio,iparams->cross_ba.r1e);
980 gmx_fio_do_real(fio,iparams->cross_ba.r2e);
981 gmx_fio_do_real(fio,iparams->cross_ba.r3e);
982 gmx_fio_do_real(fio,iparams->cross_ba.krt);
983 break;
984 case F_UREY_BRADLEY:
985 gmx_fio_do_real(fio,iparams->u_b.theta);
986 gmx_fio_do_real(fio,iparams->u_b.ktheta);
987 gmx_fio_do_real(fio,iparams->u_b.r13);
988 gmx_fio_do_real(fio,iparams->u_b.kUB);
989 break;
990 case F_QUARTIC_ANGLES:
991 gmx_fio_do_real(fio,iparams->qangle.theta);
992 bDum=gmx_fio_ndo_real(fio,iparams->qangle.c,5);
993 break;
994 case F_BHAM:
995 gmx_fio_do_real(fio,iparams->bham.a);
996 gmx_fio_do_real(fio,iparams->bham.b);
997 gmx_fio_do_real(fio,iparams->bham.c);
998 break;
999 case F_MORSE:
1000 gmx_fio_do_real(fio,iparams->morse.b0);
1001 gmx_fio_do_real(fio,iparams->morse.cb);
1002 gmx_fio_do_real(fio,iparams->morse.beta);
1003 break;
1004 case F_CUBICBONDS:
1005 gmx_fio_do_real(fio,iparams->cubic.b0);
1006 gmx_fio_do_real(fio,iparams->cubic.kb);
1007 gmx_fio_do_real(fio,iparams->cubic.kcub);
1008 break;
1009 case F_CONNBONDS:
1010 break;
1011 case F_POLARIZATION:
1012 gmx_fio_do_real(fio,iparams->polarize.alpha);
1013 break;
1014 case F_WATER_POL:
1015 if (file_version < 31)
1016 gmx_fatal(FARGS,"Old tpr files with water_polarization not supported. Make a new.");
1017 gmx_fio_do_real(fio,iparams->wpol.al_x);
1018 gmx_fio_do_real(fio,iparams->wpol.al_y);
1019 gmx_fio_do_real(fio,iparams->wpol.al_z);
1020 gmx_fio_do_real(fio,iparams->wpol.rOH);
1021 gmx_fio_do_real(fio,iparams->wpol.rHH);
1022 gmx_fio_do_real(fio,iparams->wpol.rOD);
1023 break;
1024 case F_THOLE_POL:
1025 gmx_fio_do_real(fio,iparams->thole.a);
1026 gmx_fio_do_real(fio,iparams->thole.alpha1);
1027 gmx_fio_do_real(fio,iparams->thole.alpha2);
1028 gmx_fio_do_real(fio,iparams->thole.rfac);
1029 break;
1030 case F_LJ:
1031 gmx_fio_do_real(fio,iparams->lj.c6);
1032 gmx_fio_do_real(fio,iparams->lj.c12);
1033 break;
1034 case F_LJ14:
1035 gmx_fio_do_real(fio,iparams->lj14.c6A);
1036 gmx_fio_do_real(fio,iparams->lj14.c12A);
1037 gmx_fio_do_real(fio,iparams->lj14.c6B);
1038 gmx_fio_do_real(fio,iparams->lj14.c12B);
1039 break;
1040 case F_LJC14_Q:
1041 gmx_fio_do_real(fio,iparams->ljc14.fqq);
1042 gmx_fio_do_real(fio,iparams->ljc14.qi);
1043 gmx_fio_do_real(fio,iparams->ljc14.qj);
1044 gmx_fio_do_real(fio,iparams->ljc14.c6);
1045 gmx_fio_do_real(fio,iparams->ljc14.c12);
1046 break;
1047 case F_LJC_PAIRS_NB:
1048 gmx_fio_do_real(fio,iparams->ljcnb.qi);
1049 gmx_fio_do_real(fio,iparams->ljcnb.qj);
1050 gmx_fio_do_real(fio,iparams->ljcnb.c6);
1051 gmx_fio_do_real(fio,iparams->ljcnb.c12);
1052 break;
1053 case F_PDIHS:
1054 case F_PIDIHS:
1055 case F_ANGRES:
1056 case F_ANGRESZ:
1057 gmx_fio_do_real(fio,iparams->pdihs.phiA);
1058 gmx_fio_do_real(fio,iparams->pdihs.cpA);
1059 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && file_version < 42) {
1060 /* Read the incorrectly stored multiplicity */
1061 gmx_fio_do_real(fio,iparams->harmonic.rB);
1062 gmx_fio_do_real(fio,iparams->harmonic.krB);
1063 iparams->pdihs.phiB = iparams->pdihs.phiA;
1064 iparams->pdihs.cpB = iparams->pdihs.cpA;
1065 } else {
1066 gmx_fio_do_real(fio,iparams->pdihs.phiB);
1067 gmx_fio_do_real(fio,iparams->pdihs.cpB);
1068 gmx_fio_do_int(fio,iparams->pdihs.mult);
1069 }
1070 break;
1071 case F_DISRES:
1072 gmx_fio_do_int(fio,iparams->disres.label);
1073 gmx_fio_do_int(fio,iparams->disres.type);
1074 gmx_fio_do_real(fio,iparams->disres.low);
1075 gmx_fio_do_real(fio,iparams->disres.up1);
1076 gmx_fio_do_real(fio,iparams->disres.up2);
1077 gmx_fio_do_real(fio,iparams->disres.kfac);
1078 break;
1079 case F_ORIRES:
1080 gmx_fio_do_int(fio,iparams->orires.ex);
1081 gmx_fio_do_int(fio,iparams->orires.label);
1082 gmx_fio_do_int(fio,iparams->orires.power);
1083 gmx_fio_do_real(fio,iparams->orires.c);
1084 gmx_fio_do_real(fio,iparams->orires.obs);
1085 gmx_fio_do_real(fio,iparams->orires.kfac);
1086 break;
1087 case F_DIHRES:
1088 gmx_fio_do_int(fio,iparams->dihres.power);
1089 gmx_fio_do_int(fio,iparams->dihres.label);
1090 gmx_fio_do_real(fio,iparams->dihres.phi);
1091 gmx_fio_do_real(fio,iparams->dihres.dphi);
1092 gmx_fio_do_real(fio,iparams->dihres.kfac);
1093 break;
1094 case F_POSRES:
1095 gmx_fio_do_rvec(fio,iparams->posres.pos0A);
1096 gmx_fio_do_rvec(fio,iparams->posres.fcA);
1097 if (bRead && file_version < 27) {
1098 copy_rvec(iparams->posres.pos0A,iparams->posres.pos0B);
1099 copy_rvec(iparams->posres.fcA,iparams->posres.fcB);
1100 } else {
1101 gmx_fio_do_rvec(fio,iparams->posres.pos0B);
1102 gmx_fio_do_rvec(fio,iparams->posres.fcB);
1103 }
1104 break;
1105 case F_RBDIHS:
1106 bDum=gmx_fio_ndo_real(fio,iparams->rbdihs.rbcA,NR_RBDIHS);
1107 if(file_version>=25)
1108 bDum=gmx_fio_ndo_real(fio,iparams->rbdihs.rbcB,NR_RBDIHS);
1109 break;
1110 case F_FOURDIHS:
1111 /* Fourier dihedrals are internally represented
1112 * as Ryckaert-Bellemans since those are faster to compute.
1113 */
1114 bDum=gmx_fio_ndo_real(fio,iparams->rbdihs.rbcA, NR_RBDIHS);
1115 bDum=gmx_fio_ndo_real(fio,iparams->rbdihs.rbcB, NR_RBDIHS);
1116 break;
1117 case F_CONSTR:
1118 case F_CONSTRNC:
1119 gmx_fio_do_real(fio,iparams->constr.dA);
1120 gmx_fio_do_real(fio,iparams->constr.dB);
1121 break;
1122 case F_SETTLE:
1123 gmx_fio_do_real(fio,iparams->settle.doh);
1124 gmx_fio_do_real(fio,iparams->settle.dhh);
1125 break;
1126 case F_VSITE2:
1127 gmx_fio_do_real(fio,iparams->vsite.a);
1128 break;
1129 case F_VSITE3:
1130 case F_VSITE3FD:
1131 case F_VSITE3FAD:
1132 gmx_fio_do_real(fio,iparams->vsite.a);
1133 gmx_fio_do_real(fio,iparams->vsite.b);
1134 break;
1135 case F_VSITE3OUT:
1136 case F_VSITE4FD:
1137 case F_VSITE4FDN:
1138 gmx_fio_do_real(fio,iparams->vsite.a);
1139 gmx_fio_do_real(fio,iparams->vsite.b);
1140 gmx_fio_do_real(fio,iparams->vsite.c);
1141 break;
1142 case F_VSITEN:
1143 gmx_fio_do_int(fio,iparams->vsiten.n);
1144 gmx_fio_do_real(fio,iparams->vsiten.a);
1145 break;
1146 case F_GB12:
1147 case F_GB13:
1148 case F_GB14:
1149 /* We got rid of some parameters in version 68 */
1150 if(bRead && file_version<68)
1151 {
1152 gmx_fio_do_real(fio,rdum);
1153 gmx_fio_do_real(fio,rdum);
1154 gmx_fio_do_real(fio,rdum);
1155 gmx_fio_do_real(fio,rdum);
1156 }
1157 gmx_fio_do_real(fio,iparams->gb.sar);
1158 gmx_fio_do_real(fio,iparams->gb.st);
1159 gmx_fio_do_real(fio,iparams->gb.pi);
1160 gmx_fio_do_real(fio,iparams->gb.gbr);
1161 gmx_fio_do_real(fio,iparams->gb.bmlt);
1162 break;
1163 case F_CMAP:
1164 gmx_fio_do_int(fio,iparams->cmap.cmapA);
1165 gmx_fio_do_int(fio,iparams->cmap.cmapB);
1166 break;
1167 default:
1168 gmx_fatal(FARGS,"unknown function type %d (%s) in %s line %d",
1169
1170 ftype,interaction_function[ftype].name,__FILE__,__LINE__);
1171 }
1172 if (!bRead)
1173 gmx_fio_unset_comment(fio);
1174 }
1175
1176 static void do_ilist(t_fileio *fio, t_ilist *ilist,gmx_bool bRead,int file_version,
1177 int ftype)
1178 {
1179 int i,k,idum;
1180 gmx_bool bDum=TRUE;
1181
1182 if (!bRead) {
1183 gmx_fio_set_comment(fio, interaction_function[ftype].name);
1184 }
1185 if (file_version < 44) {
1186 for(i=0; i<MAXNODES; i++)
1187 gmx_fio_do_int(fio,idum);
1188 }
1189 gmx_fio_do_int(fio,ilist->nr);
1190 if (bRead)
1191 snew(ilist->iatoms,ilist->nr);
1192 bDum=gmx_fio_ndo_int(fio,ilist->iatoms,ilist->nr);
1193 if (!bRead)
1194 gmx_fio_unset_comment(fio);
1195 }
1196
1197 static void do_ffparams(t_fileio *fio, gmx_ffparams_t *ffparams,
1198 gmx_bool bRead, int file_version)
1199 {
1200 int idum,i,j;
1201 gmx_bool bDum=TRUE;
1202 unsigned int k;
1203
1204 gmx_fio_do_int(fio,ffparams->atnr);
1205 if (file_version < 57) {
1206 gmx_fio_do_int(fio,idum);
1207 }
1208 gmx_fio_do_int(fio,ffparams->ntypes);
1209 if (bRead && debug)
1210 fprintf(debug,"ffparams->atnr = %d, ntypes = %d\n",
1211 ffparams->atnr,ffparams->ntypes);
1212 if (bRead) {
1213 snew(ffparams->functype,ffparams->ntypes);
1214 snew(ffparams->iparams,ffparams->ntypes);
1215 }
1216 /* Read/write all the function types */
1217 bDum=gmx_fio_ndo_int(fio,ffparams->functype,ffparams->ntypes);
1218 if (bRead && debug)
1219 pr_ivec(debug,0,"functype",ffparams->functype,ffparams->ntypes,TRUE);
1220
1221 if (file_version >= 66) {
1222 gmx_fio_do_double(fio,ffparams->reppow);
1223 } else {
1224 ffparams->reppow = 12.0;
1225 }
1226
1227 if (file_version >= 57) {
1228 gmx_fio_do_real(fio,ffparams->fudgeQQ);
1229 }
1230
1231 /* Check whether all these function types are supported by the code.
1232 * In practice the code is backwards compatible, which means that the
1233 * numbering may have to be altered from old numbering to new numbering
1234 */
1235 for (i=0; (i<ffparams->ntypes); i++) {
1236 if (bRead)
1237 /* Loop over file versions */
1238 for (k=0; (k<NFTUPD); k++)
1239 /* Compare the read file_version to the update table */
1240 if ((file_version < ftupd[k].fvnr) &&
1241 (ffparams->functype[i] >= ftupd[k].ftype)) {
1242 ffparams->functype[i] += 1;
1243 if (debug) {
1244 fprintf(debug,"Incrementing function type %d to %d (due to %s)\n",
1245 i,ffparams->functype[i],
1246 interaction_function[ftupd[k].ftype].longname);
1247 fflush(debug);
1248 }
1249 }
1250
1251 do_iparams(fio, ffparams->functype[i],&ffparams->iparams[i],bRead,
1252 file_version);
1253 if (bRead && debug)
1254 pr_iparams(debug,ffparams->functype[i],&ffparams->iparams[i]);
1255 }
1256 }
1257
1258 static void do_ilists(t_fileio *fio, t_ilist *ilist,gmx_bool bRead,
1259 int file_version)
1260 {
1261 int i,j,renum[F_NRE];
1262 gmx_bool bDum=TRUE,bClear;
1263 unsigned int k;
1264
1265 for(j=0; (j<F_NRE); j++) {
1266 bClear = FALSE;
1267 if (bRead)
1268 for (k=0; k<NFTUPD; k++)
1269 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
1270 bClear = TRUE;
1271 if (bClear) {
1272 ilist[j].nr = 0;
1273 ilist[j].iatoms = NULL;
1274 } else {
1275 do_ilist(fio, &ilist[j],bRead,file_version,j);
1276 }
1277 /*
1278 if (bRead && gmx_debug_at)
1279 pr_ilist(debug,0,interaction_function[j].longname,
1280 functype,&ilist[j],TRUE);
1281 */
1282 }
1283 }
1284
1285 static void do_idef(t_fileio *fio, gmx_ffparams_t *ffparams,gmx_moltype_t *molt,
1286 gmx_bool bRead, int file_version)
1287 {
1288 do_ffparams(fio, ffparams,bRead,file_version);
1289
1290 if (file_version >= 54) {
1291 gmx_fio_do_real(fio,ffparams->fudgeQQ);
1292 }
1293
1294 do_ilists(fio, molt->ilist,bRead,file_version);
1295 }
1296
1297 static void do_block(t_fileio *fio, t_block *block,gmx_bool bRead,int file_version)
1298 {
1299 int i,idum,dum_nra,*dum_a;
1300 gmx_bool bDum=TRUE;
1301
1302 if (file_version < 44)
1303 for(i=0; i<MAXNODES; i++)
1304 gmx_fio_do_int(fio,idum);
1305 gmx_fio_do_int(fio,block->nr);
1306 if (file_version < 51)
1307 gmx_fio_do_int(fio,dum_nra);
1308 if (bRead) {
1309 block->nalloc_index = block->nr+1;
1310 snew(block->index,block->nalloc_index);
1311 }
1312 bDum=gmx_fio_ndo_int(fio,block->index,block->nr+1);
1313
1314 if (file_version < 51 && dum_nra > 0) {
1315 snew(dum_a,dum_nra);
1316 bDum=gmx_fio_ndo_int(fio,dum_a,dum_nra);
1317 sfree(dum_a);
1318 }
1319 }
1320
1321 static void do_blocka(t_fileio *fio, t_blocka *block,gmx_bool bRead,
1322 int file_version)
1323 {
1324 int i,idum;
1325 gmx_bool bDum=TRUE;
1326
1327 if (file_version < 44)
1328 for(i=0; i<MAXNODES; i++)
1329 gmx_fio_do_int(fio,idum);
1330 gmx_fio_do_int(fio,block->nr);
1331 gmx_fio_do_int(fio,block->nra);
1332 if (bRead) {
1333 block->nalloc_index = block->nr+1;
1334 snew(block->index,block->nalloc_index);
1335 block->nalloc_a = block->nra;
1336 snew(block->a,block->nalloc_a);
1337 }
1338 bDum=gmx_fio_ndo_int(fio,block->index,block->nr+1);
1339 bDum=gmx_fio_ndo_int(fio,block->a,block->nra);
1340 }
1341
1342 static void do_atom(t_fileio *fio, t_atom *atom,int ngrp,gmx_bool bRead,
1343 int file_version, gmx_groups_t *groups,int atnr)
1344 {
1345 int i,myngrp;
1346
1347 gmx_fio_do_real(fio,atom->m);
1348 gmx_fio_do_real(fio,atom->q);
1349 gmx_fio_do_real(fio,atom->mB);
1350 gmx_fio_do_real(fio,atom->qB);
1351 gmx_fio_do_ushort(fio, atom->type);
1352 gmx_fio_do_ushort(fio, atom->typeB);
1353 gmx_fio_do_int(fio,atom->ptype);
1354 gmx_fio_do_int(fio,atom->resind);
1355 if (file_version >= 52)
1356 gmx_fio_do_int(fio,atom->atomnumber);
1357 else if (bRead)
1358 atom->atomnumber = NOTSET;
1359 if (file_version < 23)
1360 myngrp = 8;
1361 else if (file_version < 39)
1362 myngrp = 9;
1363 else
1364 myngrp = ngrp;
1365
1366 if (file_version < 57) {
1367 unsigned char uchar[egcNR];
1368 gmx_fio_ndo_uchar(fio,uchar,myngrp);
1369 for(i=myngrp; (i<ngrp); i++) {
1370 uchar[i] = 0;
1371 }
1372 /* Copy the old data format to the groups struct */
1373 for(i=0; i<ngrp; i++) {
1374 groups->grpnr[i][atnr] = uchar[i];
1375 }
1376 }
1377 }
1378
1379 static void do_grps(t_fileio *fio, int ngrp,t_grps grps[],gmx_bool bRead,
1380 int file_version)
1381 {
1382 int i,j,myngrp;
1383 gmx_bool bDum=TRUE;
1384
1385 if (file_version < 23)
1386 myngrp = 8;
1387 else if (file_version < 39)
1388 myngrp = 9;
1389 else
1390 myngrp = ngrp;
1391
1392 for(j=0; (j<ngrp); j++) {
1393 if (j<myngrp) {
1394 gmx_fio_do_int(fio,grps[j].nr);
1395 if (bRead)
1396 snew(grps[j].nm_ind,grps[j].nr);
1397 bDum=gmx_fio_ndo_int(fio,grps[j].nm_ind,grps[j].nr);
1398 }
1399 else {
1400 grps[j].nr = 1;
1401 snew(grps[j].nm_ind,grps[j].nr);
1402 }
1403 }
1404 }
1405
1406 static void do_symstr(t_fileio *fio, char ***nm,gmx_bool bRead,t_symtab *symtab)
1407 {
1408 int ls;
1409
1410 if (bRead) {
1411 gmx_fio_do_int(fio,ls);
1412 *nm = get_symtab_handle(symtab,ls);
1413 }
1414 else {
1415 ls = lookup_symtab(symtab,*nm);
1416 gmx_fio_do_int(fio,ls);
1417 }
1418 }
1419
1420 static void do_strstr(t_fileio *fio, int nstr,char ***nm,gmx_bool bRead,
1421 t_symtab *symtab)
1422 {
1423 int j;
1424
1425 for (j=0; (j<nstr); j++)
1426 do_symstr(fio, &(nm[j]),bRead,symtab);
1427 }
1428
1429 static void do_resinfo(t_fileio *fio, int n,t_resinfo *ri,gmx_bool bRead,
1430 t_symtab *symtab, int file_version)
1431 {
1432 int j;
1433
1434 for (j=0; (j<n); j++) {
1435 do_symstr(fio, &(ri[j].name),bRead,symtab);
1436 if (file_version >= 63) {
1437 gmx_fio_do_int(fio,ri[j].nr);
1438 gmx_fio_do_uchar(fio, ri[j].ic);
1439 } else {
1440 ri[j].nr = j + 1;
1441 ri[j].ic = ' ';
1442 }
1443 }
1444 }
1445
1446 static void do_atoms(t_fileio *fio, t_atoms *atoms,gmx_bool bRead,t_symtab *symtab,
1447 int file_version,
1448 gmx_groups_t *groups)
1449 {
1450 int i;
1451
1452 gmx_fio_do_int(fio,atoms->nr);
1453 gmx_fio_do_int(fio,atoms->nres);
1454 if (file_version < 57) {
1455 gmx_fio_do_int(fio,groups->ngrpname);
1456 for(i=0; i<egcNR; i++) {
1457 groups->ngrpnr[i] = atoms->nr;
1458 snew(groups->grpnr[i],groups->ngrpnr[i]);
1459 }
1460 }
1461 if (bRead) {
1462 snew(atoms->atom,atoms->nr);
1463 snew(atoms->atomname,atoms->nr);
1464 snew(atoms->atomtype,atoms->nr);
1465 snew(atoms->atomtypeB,atoms->nr);
1466 snew(atoms->resinfo,atoms->nres);
1467 if (file_version < 57) {
1468 snew(groups->grpname,groups->ngrpname);
1469 }
1470 atoms->pdbinfo = NULL;
1471 }
1472 for(i=0; (i<atoms->nr); i++) {
1473 do_atom(fio, &atoms->atom[i],egcNR,bRead, file_version,groups,i);
1474 }
1475 do_strstr(fio, atoms->nr,atoms->atomname,bRead,symtab);
1476 if (bRead && (file_version <= 20)) {
1477 for(i=0; i<atoms->nr; i++) {
1478 atoms->atomtype[i] = put_symtab(symtab,"?");
1479 atoms->atomtypeB[i] = put_symtab(symtab,"?");
1480 }
1481 } else {
1482 do_strstr(fio, atoms->nr,atoms->atomtype,bRead,symtab);
1483 do_strstr(fio, atoms->nr,atoms->atomtypeB,bRead,symtab);
1484 }
1485 do_resinfo(fio, atoms->nres,atoms->resinfo,bRead,symtab,file_version);
1486
1487 if (file_version < 57) {
1488 do_strstr(fio, groups->ngrpname,groups->grpname,bRead,symtab);
1489
1490 do_grps(fio, egcNR,groups->grps,bRead,file_version);
1491 }
1492 }
1493
1494 static void do_groups(t_fileio *fio, gmx_groups_t *groups,
1495 gmx_bool bRead,t_symtab *symtab,
1496 int file_version)
1497 {
1498 int g,n,i;
1499 gmx_bool bDum=TRUE;
1500
1501 do_grps(fio, egcNR,groups->grps,bRead,file_version);
1502 gmx_fio_do_int(fio,groups->ngrpname);
1503 if (bRead) {
1504 snew(groups->grpname,groups->ngrpname);
1505 }
1506 do_strstr(fio, groups->ngrpname,groups->grpname,bRead,symtab);
1507 for(g=0; g<egcNR; g++) {
1508 gmx_fio_do_int(fio,groups->ngrpnr[g]);
1509 if (groups->ngrpnr[g] == 0) {
1510 if (bRead) {
1511 groups->grpnr[g] = NULL;
1512 }
1513 } else {
1514 if (bRead) {
1515 snew(groups->grpnr[g],groups->ngrpnr[g]);
1516 }
1517 bDum=gmx_fio_ndo_uchar(fio, groups->grpnr[g],groups->ngrpnr[g]);
1518 }
1519 }
1520 }
1521
1522 static void do_atomtypes(t_fileio *fio, t_atomtypes *atomtypes,gmx_bool bRead,
1523 t_symtab *symtab,int file_version)
1524 {
1525 int i,j;
1526 gmx_bool bDum = TRUE;
1527
1528 if (file_version > 25) {
1529 gmx_fio_do_int(fio,atomtypes->nr);
1530 j=atomtypes->nr;
1531 if (bRead) {
1532 snew(atomtypes->radius,j);
1533 snew(atomtypes->vol,j);
1534 snew(atomtypes->surftens,j);
1535 snew(atomtypes->atomnumber,j);
1536 snew(atomtypes->gb_radius,j);
1537 snew(atomtypes->S_hct,j);
1538 }
1539 bDum=gmx_fio_ndo_real(fio,atomtypes->radius,j);
1540 bDum=gmx_fio_ndo_real(fio,atomtypes->vol,j);
1541 bDum=gmx_fio_ndo_real(fio,atomtypes->surftens,j);
1542 if(file_version >= 40)
1543 {
1544 bDum=gmx_fio_ndo_int(fio,atomtypes->atomnumber,j);
1545 }
1546 if(file_version >= 60)
1547 {
1548 bDum=gmx_fio_ndo_real(fio,atomtypes->gb_radius,j);
1549 bDum=gmx_fio_ndo_real(fio,atomtypes->S_hct,j);
1550 }
1551 } else {
1552 /* File versions prior to 26 cannot do GBSA,
1553 * so they dont use this structure
1554 */
1555 atomtypes->nr = 0;
1556 atomtypes->radius = NULL;
1557 atomtypes->vol = NULL;
1558 atomtypes->surftens = NULL;
1559 atomtypes->atomnumber = NULL;
1560 atomtypes->gb_radius = NULL;
1561 atomtypes->S_hct = NULL;
1562 }
1563 }
1564
1565 static void do_symtab(t_fileio *fio, t_symtab *symtab,gmx_bool bRead)
1566 {
1567 int i,nr;
1568 t_symbuf *symbuf;
1569 char buf[STRLEN];
1570
1571 gmx_fio_do_int(fio,symtab->nr);
1572 nr = symtab->nr;
1573 if (bRead) {
1574 snew(symtab->symbuf,1);
1575 symbuf = symtab->symbuf;
1576 symbuf->bufsize = nr;
1577 snew(symbuf->buf,nr);
1578 for (i=0; (i<nr); i++) {
1579 gmx_fio_do_string(fio,buf);
1580 symbuf->buf[i]=strdup(buf);
1581 }
1582 }
1583 else {
1584 symbuf = symtab->symbuf;
1585 while (symbuf!=NULL) {
1586 for (i=0; (i<symbuf->bufsize) && (i<nr); i++)
1587 gmx_fio_do_string(fio,symbuf->buf[i]);
1588 nr-=i;
1589 symbuf=symbuf->next;
1590 }
1591 if (nr != 0)
1592 gmx_fatal(FARGS,"nr of symtab strings left: %d",nr);
1593 }
1594 }
1595
1596 static void do_cmap(t_fileio *fio, gmx_cmap_t *cmap_grid, gmx_bool bRead)
1597 {
1598 int i,j,ngrid,gs,nelem;
1599
1600 gmx_fio_do_int(fio,cmap_grid->ngrid);
1601 gmx_fio_do_int(fio,cmap_grid->grid_spacing);
1602
1603 ngrid = cmap_grid->ngrid;
1604 gs = cmap_grid->grid_spacing;
1605 nelem = gs * gs;
1606
1607 if(bRead)
1608 {
1609 snew(cmap_grid->cmapdata,ngrid);
1610
1611 for(i=0;i<cmap_grid->ngrid;i++)
1612 {
1613 snew(cmap_grid->cmapdata[i].cmap,4*nelem);
1614 }
1615 }
1616
1617 for(i=0;i<cmap_grid->ngrid;i++)
1618 {
1619 for(j=0;j<nelem;j++)
1620 {
1621 gmx_fio_do_real(fio,cmap_grid->cmapdata[i].cmap[j*4]);
1622 gmx_fio_do_real(fio,cmap_grid->cmapdata[i].cmap[j*4+1]);
1623 gmx_fio_do_real(fio,cmap_grid->cmapdata[i].cmap[j*4+2]);
1624 gmx_fio_do_real(fio,cmap_grid->cmapdata[i].cmap[j*4+3]);
1625 }
1626 }
1627 }
1628
1629
1630 void tpx_make_chain_identifiers(t_atoms *atoms,t_block *mols)
1631 {
1632 int m,a,a0,a1,r;
1633 char c,chainid;
1634 int chainnum;
1635
1636 /* We always assign a new chain number, but save the chain id characters
1637 * for larger molecules.
1638 */
1639 #define CHAIN_MIN_ATOMS 15
1640
1641 chainnum=0;
1642 chainid='A';
1643 for(m=0; m<mols->nr; m++)
1644 {
1645 a0=mols->index[m];
1646 a1=mols->index[m+1];
1647 if ((a1-a0 >= CHAIN_MIN_ATOMS) && (chainid <= 'Z'))
1648 {
1649 c=chainid;
1650 chainid++;
1651 }
1652 else
1653 {
1654 c=' ';
1655 }
1656 for(a=a0; a<a1; a++)
1657 {
1658 atoms->resinfo[atoms->atom[a].resind].chainnum = chainnum;
1659 atoms->resinfo[atoms->atom[a].resind].chainid = c;
1660 }
1661 chainnum++;
1662 }
1663
1664 /* Blank out the chain id if there was only one chain */
1665 if (chainid == 'B')
1666 {
1667 for(r=0; r<atoms->nres; r++)
1668 {
1669 atoms->resinfo[r].chainid = ' ';
1670 }
1671 }
1672 }
1673
1674 static void do_moltype(t_fileio *fio, gmx_moltype_t *molt,gmx_bool bRead,
1675 t_symtab *symtab, int file_version,
1676 gmx_groups_t *groups)
1677 {
1678 int i;
1679
1680 if (file_version >= 57) {
1681 do_symstr(fio, &(molt->name),bRead,symtab);
1682 }
1683
1684 do_atoms(fio, &molt->atoms, bRead, symtab, file_version, groups);
1685
1686 if (bRead && gmx_debug_at) {
1687 pr_atoms(debug,0,"atoms",&molt->atoms,TRUE);
1688 }
1689
1690 if (file_version >= 57) {
1691 do_ilists(fio, molt->ilist,bRead,file_version);
1692
1693 do_block(fio, &molt->cgs,bRead,file_version);
1694 if (bRead && gmx_debug_at) {
1695 pr_block(debug,0,"cgs",&molt->cgs,TRUE);
1696 }
1697 }
1698
1699 /* This used to be in the atoms struct */
1700 do_blocka(fio, &molt->excls, bRead, file_version);
1701 }
1702
1703 static void do_molblock(t_fileio *fio, gmx_molblock_t *molb,gmx_bool bRead,
1704 int file_version)
1705 {
1706 int i;
1707
1708 gmx_fio_do_int(fio,molb->type);
1709 gmx_fio_do_int(fio,molb->nmol);
1710 gmx_fio_do_int(fio,molb->natoms_mol);
1711 /* Position restraint coordinates */
1712 gmx_fio_do_int(fio,molb->nposres_xA);
1713 if (molb->nposres_xA > 0) {
1714 if (bRead) {
1715 snew(molb->posres_xA,molb->nposres_xA);
1716 }
1717 gmx_fio_ndo_rvec(fio,molb->posres_xA,molb->nposres_xA);
1718 }
1719 gmx_fio_do_int(fio,molb->nposres_xB);
1720 if (molb->nposres_xB > 0) {
1721 if (bRead) {
1722 snew(molb->posres_xB,molb->nposres_xB);
1723 }
1724 gmx_fio_ndo_rvec(fio,molb->posres_xB,molb->nposres_xB);
1725 }
1726
1727 }
1728
1729 static t_block mtop_mols(gmx_mtop_t *mtop)
1730 {
1731 int mb,m,a,mol;
1732 t_block mols;
1733
1734 mols.nr = 0;
1735 for(mb=0; mb<mtop->nmolblock; mb++) {
1736 mols.nr += mtop->molblock[mb].nmol;
1737 }
1738 mols.nalloc_index = mols.nr + 1;
1739 snew(mols.index,mols.nalloc_index);
1740
1741 a = 0;
1742 m = 0;
1743 mols.index[m] = a;
1744 for(mb=0; mb<mtop->nmolblock; mb++) {
1745 for(mol=0; mol<mtop->molblock[mb].nmol; mol++) {
1746 a += mtop->molblock[mb].natoms_mol;
1747 m++;
1748 mols.index[m] = a;
1749 }
1750 }
1751
1752 return mols;
1753 }
1754
1755 static void add_posres_molblock(gmx_mtop_t *mtop)
1756 {
1757 t_ilist *il;
1758 int am,i,mol,a;
1759 gmx_bool bFE;
1760 gmx_molblock_t *molb;
1761 t_iparams *ip;
1762
1763 il = &mtop->moltype[0].ilist[F_POSRES];
1764 if (il->nr == 0) {
1765 return;
1766 }
1767 am = 0;
1768 bFE = FALSE;
1769 for(i=0; i<il->nr; i+=2) {
1770 ip = &mtop->ffparams.iparams[il->iatoms[i]];
1771 am = max(am,il->iatoms[i+1]);
1772 if (ip->posres.pos0B[XX] != ip->posres.pos0A[XX] ||
1773 ip->posres.pos0B[YY] != ip->posres.pos0A[YY] ||
1774 ip->posres.pos0B[ZZ] != ip->posres.pos0A[ZZ]) {
1775 bFE = TRUE;
1776 }
1777 }
1778 /* Make the posres coordinate block end at a molecule end */
1779 mol = 0;
1780 while(am >= mtop->mols.index[mol+1]) {
1781 mol++;
1782 }
1783 molb = &mtop->molblock[0];
1784 molb->nposres_xA = mtop->mols.index[mol+1];
1785 snew(molb->posres_xA,molb->nposres_xA);
1786 if (bFE) {
1787 molb->nposres_xB = molb->nposres_xA;
1788 snew(molb->posres_xB,molb->nposres_xB);
1789 } else {
1790 molb->nposres_xB = 0;
1791 }
1792 for(i=0; i<il->nr; i+=2) {
1793 ip = &mtop->ffparams.iparams[il->iatoms[i]];
1794 a = il->iatoms[i+1];
1795 molb->posres_xA[a][XX] = ip->posres.pos0A[XX];
1796 molb->posres_xA[a][YY] = ip->posres.pos0A[YY];
1797 molb->posres_xA[a][ZZ] = ip->posres.pos0A[ZZ];
1798 if (bFE) {
1799 molb->posres_xB[a][XX] = ip->posres.pos0B[XX];
1800 molb->posres_xB[a][YY] = ip->posres.pos0B[YY];
1801 molb->posres_xB[a][ZZ] = ip->posres.pos0B[ZZ];
1802 }
1803 }
1804 }
1805
1806 static void set_disres_npair(gmx_mtop_t *mtop)
1807 {
1808 int mt,i,npair;
1809 t_iparams *ip;
1810 t_ilist *il;
1811 t_iatom *a;
1812
1813 ip = mtop->ffparams.iparams;
1814
1815 for(mt=0; mt<mtop->nmoltype; mt++) {
1816 il = &mtop->moltype[mt].ilist[F_DISRES];
1817 if (il->nr > 0) {
1818 a = il->iatoms;
1819 npair = 0;
1820 for(i=0; i<il->nr; i+=3) {
1821 npair++;
1822 if (i+3 == il->nr || ip[a[i]].disres.label != ip[a[i+3]].disres.label) {
1823 ip[a[i]].disres.npair = npair;
1824 npair = 0;
1825 }
1826 }
1827 }
1828 }
1829 }
1830
1831 static void do_mtop(t_fileio *fio, gmx_mtop_t *mtop,gmx_bool bRead,
1832 int file_version)
1833 {
1834 int mt,mb,i;
1835 t_blocka dumb;
1836
1837 if (bRead)
1838 init_mtop(mtop);
1839 do_symtab(fio, &(mtop->symtab),bRead);
1840 if (bRead && debug)
1841 pr_symtab(debug,0,"symtab",&mtop->symtab);
1842
1843 do_symstr(fio, &(mtop->name),bRead,&(mtop->symtab));
1844
1845 if (file_version >= 57) {
1846 do_ffparams(fio, &mtop->ffparams,bRead,file_version);
1847
1848 gmx_fio_do_int(fio,mtop->nmoltype);
1849 } else {
1850 mtop->nmoltype = 1;
1851 }
1852 if (bRead) {
1853 snew(mtop->moltype,mtop->nmoltype);
1854 if (file_version < 57) {
1855 mtop->moltype[0].name = mtop->name;
1856 }
1857 }
1858 for(mt=0; mt<mtop->nmoltype; mt++) {
1859 do_moltype(fio, &mtop->moltype[mt],bRead,&mtop->symtab,file_version,
1860 &mtop->groups);
1861 }
1862
1863 if (file_version >= 57) {
1864 gmx_fio_do_int(fio,mtop->nmolblock);
1865 } else {
1866 mtop->nmolblock = 1;
1867 }
1868 if (bRead) {
1869 snew(mtop->molblock,mtop->nmolblock);
1870 }
1871 if (file_version >= 57) {
1872 for(mb=0; mb<mtop->nmolblock; mb++) {
1873 do_molblock(fio, &mtop->molblock[mb],bRead,file_version);
1874 }
1875 gmx_fio_do_int(fio,mtop->natoms);
1876 } else {
1877 mtop->molblock[0].type = 0;
1878 mtop->molblock[0].nmol = 1;
1879 mtop->molblock[0].natoms_mol = mtop->moltype[0].atoms.nr;
1880 mtop->molblock[0].nposres_xA = 0;
1881 mtop->molblock[0].nposres_xB = 0;
1882 }
1883
1884 do_atomtypes (fio, &(mtop->atomtypes),bRead,&(mtop->symtab), file_version);
1885 if (bRead && debug)
1886 pr_atomtypes(debug,0,"atomtypes",&mtop->atomtypes,TRUE);
1887
1888 if (file_version < 57) {
1889 /* Debug statements are inside do_idef */
1890 do_idef (fio, &mtop->ffparams,&mtop->moltype[0],bRead,file_version);
1891 mtop->natoms = mtop->moltype[0].atoms.nr;
1892 }
1893
1894 if(file_version >= 65)
1895 {
1896 do_cmap(fio, &mtop->ffparams.cmap_grid,bRead);
1897 }
1898 else
1899 {
1900 mtop->ffparams.cmap_grid.ngrid = 0;
1901 mtop->ffparams.cmap_grid.grid_spacing = 0.1;
1902 mtop->ffparams.cmap_grid.cmapdata = NULL;
1903 }
1904
1905 if (file_version >= 57) {
1906 do_groups(fio, &mtop->groups,bRead,&(mtop->symtab),file_version);
1907 }
1908
1909 if (file_version < 57) {
1910 do_block(fio, &mtop->moltype[0].cgs,bRead,file_version);
1911 if (bRead && gmx_debug_at) {
1912 pr_block(debug,0,"cgs",&mtop->moltype[0].cgs,TRUE);
1913 }
1914 do_block(fio, &mtop->mols,bRead,file_version);
1915 /* Add the posres coordinates to the molblock */
1916 add_posres_molblock(mtop);
1917 }
1918 if (bRead) {
1919 if (file_version >= 57) {
1920 mtop->mols = mtop_mols(mtop);
1921 }
1922 if (gmx_debug_at) {
1923 pr_block(debug,0,"mols",&mtop->mols,TRUE);
1924 }
1925 }
1926
1927 if (file_version < 51) {
1928 /* Here used to be the shake blocks */
1929 do_blocka(fio, &dumb,bRead,file_version);
1930 if (dumb.nr > 0)
1931 sfree(dumb.index);
1932 if (dumb.nra > 0)
1933 sfree(dumb.a);
1934 }
1935
1936 if (bRead) {
1937 close_symtab(&(mtop->symtab));
1938 }
1939 }
1940
1941 /* If TopOnlyOK is TRUE then we can read even future versions
1942 * of tpx files, provided the file_generation hasn't changed.
1943 * If it is FALSE, we need the inputrecord too, and bail out
1944 * if the file is newer than the program.
1945 *
1946 * The version and generation if the topology (see top of this file)
1947 * are returned in the two last arguments.
1948 *
1949 * If possible, we will read the inputrec even when TopOnlyOK is TRUE.
1950 */
1951 static void do_tpxheader(t_fileio *fio,gmx_bool bRead,t_tpxheader *tpx,
1952 gmx_bool TopOnlyOK, int *file_version,
1953 int *file_generation)
1954 {
1955 char buf[STRLEN];
1956 gmx_bool bDouble;
1957 int precision;
1958 int fver,fgen;
1959 int idum=0;
1960 real rdum=0;
1961
1962 gmx_fio_checktype(fio);
1963 gmx_fio_setdebug(fio,bDebugMode());
1964
1965 /* NEW! XDR tpb file */
1966 precision = sizeof(real);
1967 if (bRead) {
1968 gmx_fio_do_string(fio,buf);
1969 if (strncmp(buf,"VERSION",7))
1970 gmx_fatal(FARGS,"Can not read file %s,\n"
1971 " this file is from a Gromacs version which is older than 2.0\n"
1972 " Make a new one with grompp or use a gro or pdb file, if possible",
1973 gmx_fio_getname(fio));
1974 gmx_fio_do_int(fio,precision);
1975 bDouble = (precision == sizeof(double));
1976 if ((precision != sizeof(float)) && !bDouble)
1977 gmx_fatal(FARGS,"Unknown precision in file %s: real is %d bytes "
1978 "instead of %d or %d",
1979 gmx_fio_getname(fio),precision,sizeof(float),sizeof(double));
1980 gmx_fio_setprecision(fio,bDouble);
1981 fprintf(stderr,"Reading file %s, %s (%s precision)\n",
1982 gmx_fio_getname(fio),buf,bDouble ? "double" : "single");
1983 }
1984 else {
1985 gmx_fio_write_string(fio,GromacsVersion());
1986 bDouble = (precision == sizeof(double));
1987 gmx_fio_setprecision(fio,bDouble);
1988 gmx_fio_do_int(fio,precision);
1989 fver = tpx_version;
1990 fgen = tpx_generation;
1991 }
1992
1993 /* Check versions! */
1994 gmx_fio_do_int(fio,fver);
1995
1996 if(fver>=26)
1997 gmx_fio_do_int(fio,fgen);
1998 else
1999 fgen=0;
2000
2001 if(file_version!=NULL)
2002 *file_version = fver;
2003 if(file_generation!=NULL)
2004 *file_generation = fgen;
2005
2006
2007 if ((fver <= tpx_incompatible_version) ||
2008 ((fver > tpx_version) && !TopOnlyOK) ||
2009 (fgen > tpx_generation))
2010 gmx_fatal(FARGS,"reading tpx file (%s) version %d with version %d program",
2011 gmx_fio_getname(fio),fver,tpx_version);
2012
2013 do_section(fio,eitemHEADER,bRead);
2014 gmx_fio_do_int(fio,tpx->natoms);
2015 if (fver >= 28)
2016 gmx_fio_do_int(fio,tpx->ngtc);
2017 else
2018 tpx->ngtc = 0;
2019 if (fver < 62) {
2020 gmx_fio_do_int(fio,idum);
2021 gmx_fio_do_real(fio,rdum);
2022 }
2023 gmx_fio_do_real(fio,tpx->lambda);
2024 gmx_fio_do_int(fio,tpx->bIr);
2025 gmx_fio_do_int(fio,tpx->bTop);
2026 gmx_fio_do_int(fio,tpx->bX);
2027 gmx_fio_do_int(fio,tpx->bV);
2028 gmx_fio_do_int(fio,tpx->bF);
2029 gmx_fio_do_int(fio,tpx->bBox);
2030
2031 if((fgen > tpx_generation)) {
2032 /* This can only happen if TopOnlyOK=TRUE */
2033 tpx->bIr=FALSE;
2034 }
2035 }
2036
2037 static int do_tpx(t_fileio *fio, gmx_bool bRead,
2038 t_inputrec *ir,t_state *state,rvec *f,gmx_mtop_t *mtop,
2039 gmx_bool bXVallocated)
2040 {
2041 t_tpxheader tpx;
2042 t_inputrec dum_ir;
2043 gmx_mtop_t dum_top;
2044 gmx_bool TopOnlyOK,bDum=TRUE;
2045 int file_version,file_generation;
2046 int i;
2047 rvec *xptr,*vptr;
2048 int ePBC;
2049 gmx_bool bPeriodicMols;
2050
2051 if (!bRead) {
2052 tpx.natoms = state->natoms;
2053 tpx.ngtc = state->ngtc;
2054 tpx.lambda = state->lambda;
2055 tpx.bIr = (ir != NULL);
2056 tpx.bTop = (mtop != NULL);
2057 tpx.bX = (state->x != NULL);
2058 tpx.bV = (state->v != NULL);
2059 tpx.bF = (f != NULL);
2060 tpx.bBox = TRUE;
2061 }
2062
2063 TopOnlyOK = (ir==NULL);
2064
2065 do_tpxheader(fio,bRead,&tpx,TopOnlyOK,&file_version,&file_generation);
2066
2067 if (bRead) {
2068 state->flags = 0;
2069 state->lambda = tpx.lambda;
2070 /* The init_state calls initialize the Nose-Hoover xi integrals to zero */
2071 if (bXVallocated) {
2072 xptr = state->x;
2073 vptr = state->v;
2074 init_state(state,0,tpx.ngtc,0,0); /* nose-hoover chains */ /* eventually, need to add nnhpres here? */
2075 state->natoms = tpx.natoms;
2076 state->nalloc = tpx.natoms;
2077 state->x = xptr;
2078 state->v = vptr;
2079 } else {
2080 init_state(state,tpx.natoms,tpx.ngtc,0,0); /* nose-hoover chains */
2081 }
2082 }
2083
2084 #define do_test(fio,b,p) if (bRead && (p!=NULL) && !b) gmx_fatal(FARGS,"No %s in %s",#p,gmx_fio_getname(fio))
2085
2086 do_test(fio,tpx.bBox,state->box);
2087 do_section(fio,eitemBOX,bRead);
2088 if (tpx.bBox) {
2089 gmx_fio_ndo_rvec(fio,state->box,DIM);
2090 if (file_version >= 51) {
2091 gmx_fio_ndo_rvec(fio,state->box_rel,DIM);
2092 } else {
2093 /* We initialize box_rel after reading the inputrec */
2094 clear_mat(state->box_rel);
2095 }
2096 if (file_version >= 28) {
2097 gmx_fio_ndo_rvec(fio,state->boxv,DIM);
2098 if (file_version < 56) {
2099 matrix mdum;
2100 gmx_fio_ndo_rvec(fio,mdum,DIM);
2101 }
2102 }
2103 }
2104
2105 if (state->ngtc > 0 && file_version >= 28) {
2106 real *dumv;
2107 /*ndo_double(state->nosehoover_xi,state->ngtc,bDum);*/
2108 /*ndo_double(state->nosehoover_vxi,state->ngtc,bDum);*/
2109 /*ndo_double(state->therm_integral,state->ngtc,bDum);*/
2110 snew(dumv,state->ngtc);
2111 if (file_version < 69) {
2112 bDum=gmx_fio_ndo_real(fio,dumv,state->ngtc);
2113 }
2114 /* These used to be the Berendsen tcoupl_lambda's */
2115 bDum=gmx_fio_ndo_real(fio,dumv,state->ngtc);
2116 sfree(dumv);
2117 }
2118
2119 /* Prior to tpx version 26, the inputrec was here.
2120 * I moved it to enable partial forward-compatibility
2121 * for analysis/viewer programs.
2122 */
2123 if(file_version<26) {
2124 do_test(fio,tpx.bIr,ir);
2125 do_section(fio,eitemIR,bRead);
2126 if (tpx.bIr) {
2127 if (ir) {
2128 do_inputrec(fio, ir,bRead,file_version,
2129 mtop ? &mtop->ffparams.fudgeQQ : NULL);
2130 if (bRead && debug)
2131 pr_inputrec(debug,0,"inputrec",ir,FALSE);
2132 }
2133 else {
2134 do_inputrec(fio, &dum_ir,bRead,file_version,
2135 mtop ? &mtop->ffparams.fudgeQQ :NULL);
2136 if (bRead && debug)
2137 pr_inputrec(debug,0,"inputrec",&dum_ir,FALSE);
2138 done_inputrec(&dum_ir);
2139 }
2140
2141 }
2142 }
2143
2144 do_test(fio,tpx.bTop,mtop);
2145 do_section(fio,eitemTOP,bRead);
2146 if (tpx.bTop) {
2147 if (mtop) {
2148 do_mtop(fio,mtop,bRead, file_version);
2149 } else {
2150 do_mtop(fio,&dum_top,bRead,file_version);
2151 done_mtop(&dum_top,TRUE);
2152 }
2153 }
2154 do_test(fio,tpx.bX,state->x);
2155 do_section(fio,eitemX,bRead);
2156 if (tpx.bX) {
2157 if (bRead) {
2158 state->flags |= (1<<estX);
2159 }
2160 gmx_fio_ndo_rvec(fio,state->x,state->natoms);
2161 }
2162
2163 do_test(fio,tpx.bV,state->v);
2164 do_section(fio,eitemV,bRead);
2165 if (tpx.bV) {
2166 if (bRead) {
2167 state->flags |= (1<<estV);
2168 }
2169 gmx_fio_ndo_rvec(fio,state->v,state->natoms);
2170 }
2171
2172 do_test(fio,tpx.bF,f);
2173 do_section(fio,eitemF,bRead);
2174 if (tpx.bF) gmx_fio_ndo_rvec(fio,f,state->natoms);
2175
2176 /* Starting with tpx version 26, we have the inputrec
2177 * at the end of the file, so we can ignore it
2178 * if the file is never than the software (but still the
2179 * same generation - see comments at the top of this file.
2180 *
2181 *
2182 */
2183 ePBC = -1;
2184 bPeriodicMols = FALSE;
2185 if (file_version >= 26) {
2186 do_test(fio,tpx.bIr,ir);
2187 do_section(fio,eitemIR,bRead);
2188 if (tpx.bIr) {
2189 if (file_version >= 53) {
2190 /* Removed the pbc info from do_inputrec, since we always want it */
2191 if (!bRead) {
2192 ePBC = ir->ePBC;
2193 bPeriodicMols = ir->bPeriodicMols;
2194 }
2195 gmx_fio_do_int(fio,ePBC);
2196 gmx_fio_do_gmx_bool(fio,bPeriodicMols);
2197 }
2198 if (file_generation <= tpx_generation && ir) {
2199 do_inputrec(fio, ir,bRead,file_version,mtop ? &mtop->ffparams.fudgeQQ : NULL);
2200 if (bRead && debug)
2201 pr_inputrec(debug,0,"inputrec",ir,FALSE);
2202 if (file_version < 51)
2203 set_box_rel(ir,state);
2204 if (file_version < 53) {
2205 ePBC = ir->ePBC;
2206 bPeriodicMols = ir->bPeriodicMols;
2207 }
2208 }
2209 if (bRead && ir && file_version >= 53) {
2210 /* We need to do this after do_inputrec, since that initializes ir */
2211 ir->ePBC = ePBC;
2212 ir->bPeriodicMols = bPeriodicMols;
2213 }
2214 }
2215 }
2216
2217 if (bRead)
2218 {
2219 if (tpx.bIr && ir)
2220 {
2221 if (state->ngtc == 0)
2222 {
2223 /* Reading old version without tcoupl state data: set it */
2224 init_gtc_state(state,ir->opts.ngtc,0,ir->opts.nhchainlength);
2225 }
2226 if (tpx.bTop && mtop)
2227 {
2228 if (file_version < 57)
2229 {
2230 if (mtop->moltype[0].ilist[F_DISRES].nr > 0)
2231 {
2232 ir->eDisre = edrSimple;
2233 }
2234 else
2235 {
2236 ir->eDisre = edrNone;
2237 }
2238 }
2239 set_disres_npair(mtop);
2240 }
2241 }
2242
2243 if (tpx.bTop && mtop)
2244 {
2245 gmx_mtop_finalize(mtop);
2246 }
2247
2248 if (file_version >= 57)
2249 {
2250 char *env;
2251 int ienv;
2252 env = getenv("GMX_NOCHARGEGROUPS");
2253 if (env != NULL)
2254 {
2255 sscanf(env,"%d",&ienv);
2256 fprintf(stderr,"\nFound env.var. GMX_NOCHARGEGROUPS = %d\n",
2257 ienv);
2258 if (ienv > 0)
2259 {
2260 fprintf(stderr,
2261 "Will make single atomic charge groups in non-solvent%s\n",
2262 ienv > 1 ? " and solvent" : "");
2263 gmx_mtop_make_atomic_charge_groups(mtop,ienv==1);
2264 }
2265 fprintf(stderr,"\n");
2266 }
2267 }
2268 }
2269
2270 return ePBC;
2271 }
2272
2273 /************************************************************
2274 *
2275 * The following routines are the exported ones
2276 *
2277 ************************************************************/
2278
2279 t_fileio *open_tpx(const char *fn,const char *mode)
2280 {
2281 return gmx_fio_open(fn,mode);
2282 }
2283
2284 void close_tpx(t_fileio *fio)
2285 {
2286 gmx_fio_close(fio);
2287 }
2288
2289 void read_tpxheader(const char *fn, t_tpxheader *tpx, gmx_bool TopOnlyOK,
2290 int *file_version, int *file_generation)
2291 {
2292 t_fileio *fio;
2293
2294 fio = open_tpx(fn,"r");
2295 do_tpxheader(fio,TRUE,tpx,TopOnlyOK,file_version,file_generation);
2296 close_tpx(fio);
2297 }
2298
2299 void write_tpx_state(const char *fn,
2300 t_inputrec *ir,t_state *state,gmx_mtop_t *mtop)
2301 {
2302 t_fileio *fio;
2303
2304 fio = open_tpx(fn,"w");
2305 do_tpx(fio,FALSE,ir,state,NULL,mtop,FALSE);
2306 close_tpx(fio);
2307 }
2308
2309 void read_tpx_state(const char *fn,
2310 t_inputrec *ir,t_state *state,rvec *f,gmx_mtop_t *mtop)
2311 {
2312 t_fileio *fio;
2313
2314 fio = open_tpx(fn,"r");
2315 do_tpx(fio,TRUE,ir,state,f,mtop,FALSE);
2316 close_tpx(fio);
2317 }
2318
2319 int read_tpx(const char *fn,
2320 t_inputrec *ir, matrix box,int *natoms,
2321 rvec *x,rvec *v,rvec *f,gmx_mtop_t *mtop)
2322 {
2323 t_fileio *fio;
2324 t_state state;
2325 int ePBC;
2326
2327 state.x = x;
2328 state.v = v;
2329 fio = open_tpx(fn,"r");
2330 ePBC = do_tpx(fio,TRUE,ir,&state,f,mtop,TRUE);
2331 close_tpx(fio);
2332 *natoms = state.natoms;
2333 if (box)
2334 copy_mat(state.box,box);
2335 state.x = NULL;
2336 state.v = NULL;
2337 done_state(&state);
2338
2339 return ePBC;
2340 }
2341
2342 int read_tpx_top(const char *fn,
2343 t_inputrec *ir, matrix box,int *natoms,
2344 rvec *x,rvec *v,rvec *f,t_topology *top)
2345 {
2346 gmx_mtop_t mtop;
2347 t_topology *ltop;
2348 int ePBC;
2349
2350 ePBC = read_tpx(fn,ir,box,natoms,x,v,f,&mtop);
2351
2352 *top = gmx_mtop_t_to_t_topology(&mtop);
2353
2354 return ePBC;
2355 }
2356
2357 gmx_bool fn2bTPX(const char *file)
2358 {
2359 switch (fn2ftp(file)) {
2360 case efTPR:
2361 case efTPB:
2362 case efTPA:
2363 return TRUE;
2364 default:
2365 return FALSE;
2366 }
2367 }
2368
2369 gmx_bool read_tps_conf(const char *infile,char *title,t_topology *top,int *ePBC,
2370 rvec **x,rvec **v,matrix box,gmx_bool bMass)
2371 {
2372 t_tpxheader header;
2373 int natoms,i,version,generation;
2374 gmx_bool bTop,bXNULL;
2375 gmx_mtop_t *mtop;
2376 t_topology *topconv;
2377 gmx_atomprop_t aps;
2378
2379 bTop = fn2bTPX(infile);
2380 *ePBC = -1;
2381 if (bTop) {
2382 read_tpxheader(infile,&header,TRUE,&version,&generation);
2383 if (x)
2384 snew(*x,header.natoms);
2385 if (v)
2386 snew(*v,header.natoms);
2387 snew(mtop,1);
2388 *ePBC = read_tpx(infile,NULL,box,&natoms,
2389 (x==NULL) ? NULL : *x,(v==NULL) ? NULL : *v,NULL,mtop);
2390 *top = gmx_mtop_t_to_t_topology(mtop);
2391 sfree(mtop);
2392 strcpy(title,*top->name);
2393 tpx_make_chain_identifiers(&top->atoms,&top->mols);
2394 }
2395 else {
2396 get_stx_coordnum(infile,&natoms);
2397 init_t_atoms(&top->atoms,natoms,FALSE);
2398 bXNULL = (x == NULL);
2399 snew(*x,natoms);
2400 if (v)
2401 snew(*v,natoms);
2402 read_stx_conf(infile,title,&top->atoms,*x,(v==NULL) ? NULL : *v,ePBC,box);
2403 if (bXNULL) {
2404 sfree(*x);
2405 x = NULL;
2406 }
2407 if (bMass) {
2408 aps = gmx_atomprop_init();
2409 for(i=0; (i<natoms); i++)
2410 if (!gmx_atomprop_query(aps,epropMass,
2411 *top->atoms.resinfo[top->atoms.atom[i].resind].name,
2412 *top->atoms.atomname[i],
2413 &(top->atoms.atom[i].m))) {
2414 if (debug)
2415 fprintf(debug,"Can not find mass for atom %s %d %s, setting to 1\n",
2416 *top->atoms.resinfo[top->atoms.atom[i].resind].name,
2417 top->atoms.resinfo[top->atoms.atom[i].resind].nr,
2418 *top->atoms.atomname[i]);
2419 }
2420 gmx_atomprop_destroy(aps);
2421 }
2422 top->idef.ntypes=-1;
2423 }
2424
2425 return bTop;
2426 }