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Remove all unnecessary HAVE_CONFIG_H
[gromacs.git] / src / gromacs / fileio / tpxio.c
blob96c948f9a6d7a803b5a59690924f0bfe1938f50f
1 /*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
10 *
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
15 *
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
20 *
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
25 *
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
33 *
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
36 */
37 #include "config.h"
38
39 /* This file is completely threadsafe - keep it that way! */
40
41 #include <stdlib.h>
42 #include <string.h>
43
44 #include "macros.h"
45 #include "names.h"
46 #include "gromacs/utility/futil.h"
47 #include "filenm.h"
48 #include "gmxfio.h"
49 #include "tpxio.h"
50 #include "txtdump.h"
51 #include "confio.h"
52 #include "copyrite.h"
53
54 #include "gromacs/math/vec.h"
55 #include "gromacs/topology/atomprop.h"
56 #include "gromacs/topology/block.h"
57 #include "gromacs/topology/mtop_util.h"
58 #include "gromacs/topology/symtab.h"
59 #include "gromacs/topology/topology.h"
60 #include "gromacs/utility/cstringutil.h"
61 #include "gromacs/utility/fatalerror.h"
62 #include "gromacs/utility/smalloc.h"
63
64 #define TPX_TAG_RELEASE "release"
65
66 /*! \brief Tag string for the file format written to run input files
67 * written by this version of the code.
68 *
69 * Change this if you want to change the run input format in a feature
70 * branch. This ensures that there will not be different run input
71 * formats around which cannot be distinguished, while not causing
72 * problems rebasing the feature branch onto upstream changes. When
73 * merging with mainstream GROMACS, set this tag string back to
74 * TPX_TAG_RELEASE, and instead add an element to tpxv and set
75 * tpx_version to that.
76 */
77 static const char *tpx_tag = TPX_TAG_RELEASE;
78
79 /*! \brief Enum of values that describe the contents of a tpr file
80 * whose format matches a version number
81 *
82 * The enum helps the code be more self-documenting and ensure merges
83 * do not silently resolve when two patches make the same bump. When
84 * adding new functionality, add a new element to the end of this
85 * enumeration, change the definition of tpx_version, and write code
86 * below that does the right thing according to the value of
87 * file_version. */
88 enum tpxv {
89 tpxv_ComputationalElectrophysiology = 96, /**< support for ion/water position swaps (computational electrophysiology) */
90 tpxv_Use64BitRandomSeed, /**< change ld_seed from int to gmx_int64_t */
91 tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, /**< potentials for supporting coarse-grained force fields */
92 tpxv_InteractiveMolecularDynamics, /**< interactive molecular dynamics (IMD) */
93 tpxv_RemoveObsoleteParameters1 /**< remove optimize_fft, dihre_fc, nstcheckpoint */
94 };
95
96 /*! \brief Version number of the file format written to run input
97 * files by this version of the code.
98 *
99 * The tpx_version number should be increased whenever the file format
100 * in the main development branch changes, generally to the highest
101 * value present in tpxv. Backward compatibility for reading old run
102 * input files is maintained by checking this version number against
103 * that of the file and then using the correct code path.
104 *
105 * When developing a feature branch that needs to change the run input
106 * file format, change tpx_tag instead. */
107 static const int tpx_version = tpxv_RemoveObsoleteParameters1;
108
109
110 /* This number should only be increased when you edit the TOPOLOGY section
111 * or the HEADER of the tpx format.
112 * This way we can maintain forward compatibility too for all analysis tools
113 * and/or external programs that only need to know the atom/residue names,
114 * charges, and bond connectivity.
115 *
116 * It first appeared in tpx version 26, when I also moved the inputrecord
117 * to the end of the tpx file, so we can just skip it if we only
118 * want the topology.
119 *
120 * In particular, it must be increased when adding new elements to
121 * ftupd, so that old code can read new .tpr files.
122 */
123 static const int tpx_generation = 26;
124
125 /* This number should be the most recent backwards incompatible version
126 * I.e., if this number is 9, we cannot read tpx version 9 with this code.
127 */
128 static const int tpx_incompatible_version = 9;
129
130
131
132 /* Struct used to maintain tpx compatibility when function types are added */
133 typedef struct {
134 int fvnr; /* file version number in which the function type first appeared */
135 int ftype; /* function type */
136 } t_ftupd;
137
138 /*
139 * The entries should be ordered in:
140 * 1. ascending file version number
141 * 2. ascending function type number
142 */
143 /*static const t_ftupd ftupd[] = {
144 { 20, F_CUBICBONDS },
145 { 20, F_CONNBONDS },
146 { 20, F_HARMONIC },
147 { 20, F_EQM, },
148 { 22, F_DISRESVIOL },
149 { 22, F_ORIRES },
150 { 22, F_ORIRESDEV },
151 { 26, F_FOURDIHS },
152 { 26, F_PIDIHS },
153 { 26, F_DIHRES },
154 { 26, F_DIHRESVIOL },
155 { 30, F_CROSS_BOND_BONDS },
156 { 30, F_CROSS_BOND_ANGLES },
157 { 30, F_UREY_BRADLEY },
158 { 30, F_POLARIZATION },
159 { 54, F_DHDL_CON },
160 };*/
161 /*
162 * The entries should be ordered in:
163 * 1. ascending function type number
164 * 2. ascending file version number
165 */
166 /* question; what is the purpose of the commented code above? */
167 static const t_ftupd ftupd[] = {
168 { 20, F_CUBICBONDS },
169 { 20, F_CONNBONDS },
170 { 20, F_HARMONIC },
171 { 34, F_FENEBONDS },
172 { 43, F_TABBONDS },
173 { 43, F_TABBONDSNC },
174 { 70, F_RESTRBONDS },
175 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
176 { 76, F_LINEAR_ANGLES },
177 { 30, F_CROSS_BOND_BONDS },
178 { 30, F_CROSS_BOND_ANGLES },
179 { 30, F_UREY_BRADLEY },
180 { 34, F_QUARTIC_ANGLES },
181 { 43, F_TABANGLES },
182 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
183 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
184 { 26, F_FOURDIHS },
185 { 26, F_PIDIHS },
186 { 43, F_TABDIHS },
187 { 65, F_CMAP },
188 { 60, F_GB12 },
189 { 61, F_GB13 },
190 { 61, F_GB14 },
191 { 72, F_GBPOL },
192 { 72, F_NPSOLVATION },
193 { 41, F_LJC14_Q },
194 { 41, F_LJC_PAIRS_NB },
195 { 32, F_BHAM_LR },
196 { 32, F_RF_EXCL },
197 { 32, F_COUL_RECIP },
198 { 93, F_LJ_RECIP },
199 { 46, F_DPD },
200 { 30, F_POLARIZATION },
201 { 36, F_THOLE_POL },
202 { 90, F_FBPOSRES },
203 { 22, F_DISRESVIOL },
204 { 22, F_ORIRES },
205 { 22, F_ORIRESDEV },
206 { 26, F_DIHRES },
207 { 26, F_DIHRESVIOL },
208 { 49, F_VSITE4FDN },
209 { 50, F_VSITEN },
210 { 46, F_COM_PULL },
211 { 20, F_EQM },
212 { 46, F_ECONSERVED },
213 { 69, F_VTEMP_NOLONGERUSED},
214 { 66, F_PDISPCORR },
215 { 54, F_DVDL_CONSTR },
216 { 76, F_ANHARM_POL },
217 { 79, F_DVDL_COUL },
218 { 79, F_DVDL_VDW, },
219 { 79, F_DVDL_BONDED, },
220 { 79, F_DVDL_RESTRAINT },
221 { 79, F_DVDL_TEMPERATURE },
222 };
223 #define NFTUPD asize(ftupd)
224
225 /* Needed for backward compatibility */
226 #define MAXNODES 256
227
228 static void _do_section(t_fileio *fio, int key, gmx_bool bRead, const char *src,
229 int line)
230 {
231 char buf[STRLEN];
232 gmx_bool bDbg;
233
234 if (gmx_fio_getftp(fio) == efTPA)
235 {
236 if (!bRead)
237 {
238 gmx_fio_write_string(fio, itemstr[key]);
239 bDbg = gmx_fio_getdebug(fio);
240 gmx_fio_setdebug(fio, FALSE);
241 gmx_fio_write_string(fio, comment_str[key]);
242 gmx_fio_setdebug(fio, bDbg);
243 }
244 else
245 {
246 if (gmx_fio_getdebug(fio))
247 {
248 fprintf(stderr, "Looking for section %s (%s, %d)",
249 itemstr[key], src, line);
250 }
251
252 do
253 {
254 gmx_fio_do_string(fio, buf);
255 }
256 while ((gmx_strcasecmp(buf, itemstr[key]) != 0));
257
258 if (gmx_strcasecmp(buf, itemstr[key]) != 0)
259 {
260 gmx_fatal(FARGS, "\nCould not find section heading %s", itemstr[key]);
261 }
262 else if (gmx_fio_getdebug(fio))
263 {
264 fprintf(stderr, " and found it\n");
265 }
266 }
267 }
268 }
269
270 #define do_section(fio, key, bRead) _do_section(fio, key, bRead, __FILE__, __LINE__)
271
272 /**************************************************************
273 *
274 * Now the higer level routines that do io of the structures and arrays
275 *
276 **************************************************************/
277 static void do_pullgrp_tpx_pre95(t_fileio *fio,
278 t_pull_group *pgrp,
279 t_pull_coord *pcrd,
280 gmx_bool bRead,
281 int file_version)
282 {
283 int i;
284 rvec tmp;
285
286 gmx_fio_do_int(fio, pgrp->nat);
287 if (bRead)
288 {
289 snew(pgrp->ind, pgrp->nat);
290 }
291 gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
292 gmx_fio_do_int(fio, pgrp->nweight);
293 if (bRead)
294 {
295 snew(pgrp->weight, pgrp->nweight);
296 }
297 gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight);
298 gmx_fio_do_int(fio, pgrp->pbcatom);
299 gmx_fio_do_rvec(fio, pcrd->vec);
300 clear_rvec(pcrd->origin);
301 gmx_fio_do_rvec(fio, tmp);
302 pcrd->init = tmp[0];
303 gmx_fio_do_real(fio, pcrd->rate);
304 gmx_fio_do_real(fio, pcrd->k);
305 if (file_version >= 56)
306 {
307 gmx_fio_do_real(fio, pcrd->kB);
308 }
309 else
310 {
311 pcrd->kB = pcrd->k;
312 }
313 }
314
315 static void do_pull_group(t_fileio *fio, t_pull_group *pgrp, gmx_bool bRead)
316 {
317 int i;
318
319 gmx_fio_do_int(fio, pgrp->nat);
320 if (bRead)
321 {
322 snew(pgrp->ind, pgrp->nat);
323 }
324 gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
325 gmx_fio_do_int(fio, pgrp->nweight);
326 if (bRead)
327 {
328 snew(pgrp->weight, pgrp->nweight);
329 }
330 gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight);
331 gmx_fio_do_int(fio, pgrp->pbcatom);
332 }
333
334 static void do_pull_coord(t_fileio *fio, t_pull_coord *pcrd)
335 {
336 int i;
337
338 gmx_fio_do_int(fio, pcrd->group[0]);
339 gmx_fio_do_int(fio, pcrd->group[1]);
340 gmx_fio_do_rvec(fio, pcrd->origin);
341 gmx_fio_do_rvec(fio, pcrd->vec);
342 gmx_fio_do_real(fio, pcrd->init);
343 gmx_fio_do_real(fio, pcrd->rate);
344 gmx_fio_do_real(fio, pcrd->k);
345 gmx_fio_do_real(fio, pcrd->kB);
346 }
347
348 static void do_expandedvals(t_fileio *fio, t_expanded *expand, t_lambda *fepvals, gmx_bool bRead, int file_version)
349 {
350 /* i is used in the ndo_double macro*/
351 int i;
352 real fv;
353 real rdum;
354 int n_lambda = fepvals->n_lambda;
355
356 /* reset the lambda calculation window */
357 fepvals->lambda_start_n = 0;
358 fepvals->lambda_stop_n = n_lambda;
359 if (file_version >= 79)
360 {
361 if (n_lambda > 0)
362 {
363 if (bRead)
364 {
365 snew(expand->init_lambda_weights, n_lambda);
366 }
367 gmx_fio_ndo_real(fio, expand->init_lambda_weights, n_lambda);
368 gmx_fio_do_gmx_bool(fio, expand->bInit_weights);
369 }
370
371 gmx_fio_do_int(fio, expand->nstexpanded);
372 gmx_fio_do_int(fio, expand->elmcmove);
373 gmx_fio_do_int(fio, expand->elamstats);
374 gmx_fio_do_int(fio, expand->lmc_repeats);
375 gmx_fio_do_int(fio, expand->gibbsdeltalam);
376 gmx_fio_do_int(fio, expand->lmc_forced_nstart);
377 gmx_fio_do_int(fio, expand->lmc_seed);
378 gmx_fio_do_real(fio, expand->mc_temp);
379 gmx_fio_do_int(fio, expand->bSymmetrizedTMatrix);
380 gmx_fio_do_int(fio, expand->nstTij);
381 gmx_fio_do_int(fio, expand->minvarmin);
382 gmx_fio_do_int(fio, expand->c_range);
383 gmx_fio_do_real(fio, expand->wl_scale);
384 gmx_fio_do_real(fio, expand->wl_ratio);
385 gmx_fio_do_real(fio, expand->init_wl_delta);
386 gmx_fio_do_gmx_bool(fio, expand->bWLoneovert);
387 gmx_fio_do_int(fio, expand->elmceq);
388 gmx_fio_do_int(fio, expand->equil_steps);
389 gmx_fio_do_int(fio, expand->equil_samples);
390 gmx_fio_do_int(fio, expand->equil_n_at_lam);
391 gmx_fio_do_real(fio, expand->equil_wl_delta);
392 gmx_fio_do_real(fio, expand->equil_ratio);
393 }
394 }
395
396 static void do_simtempvals(t_fileio *fio, t_simtemp *simtemp, int n_lambda, gmx_bool bRead,
397 int file_version)
398 {
399 if (file_version >= 79)
400 {
401 gmx_fio_do_int(fio, simtemp->eSimTempScale);
402 gmx_fio_do_real(fio, simtemp->simtemp_high);
403 gmx_fio_do_real(fio, simtemp->simtemp_low);
404 if (n_lambda > 0)
405 {
406 if (bRead)
407 {
408 snew(simtemp->temperatures, n_lambda);
409 }
410 gmx_fio_ndo_real(fio, simtemp->temperatures, n_lambda);
411 }
412 }
413 }
414
415 static void do_imd(t_fileio *fio, t_IMD *imd, gmx_bool bRead)
416 {
417 gmx_fio_do_int(fio, imd->nat);
418 if (bRead)
419 {
420 snew(imd->ind, imd->nat);
421 }
422 gmx_fio_ndo_int(fio, imd->ind, imd->nat);
423 }
424
425 static void do_fepvals(t_fileio *fio, t_lambda *fepvals, gmx_bool bRead, int file_version)
426 {
427 /* i is defined in the ndo_double macro; use g to iterate. */
428 int i, g;
429 real fv;
430 real rdum;
431
432 /* free energy values */
433
434 if (file_version >= 79)
435 {
436 gmx_fio_do_int(fio, fepvals->init_fep_state);
437 gmx_fio_do_double(fio, fepvals->init_lambda);
438 gmx_fio_do_double(fio, fepvals->delta_lambda);
439 }
440 else if (file_version >= 59)
441 {
442 gmx_fio_do_double(fio, fepvals->init_lambda);
443 gmx_fio_do_double(fio, fepvals->delta_lambda);
444 }
445 else
446 {
447 gmx_fio_do_real(fio, rdum);
448 fepvals->init_lambda = rdum;
449 gmx_fio_do_real(fio, rdum);
450 fepvals->delta_lambda = rdum;
451 }
452 if (file_version >= 79)
453 {
454 gmx_fio_do_int(fio, fepvals->n_lambda);
455 if (bRead)
456 {
457 snew(fepvals->all_lambda, efptNR);
458 }
459 for (g = 0; g < efptNR; g++)
460 {
461 if (fepvals->n_lambda > 0)
462 {
463 if (bRead)
464 {
465 snew(fepvals->all_lambda[g], fepvals->n_lambda);
466 }
467 gmx_fio_ndo_double(fio, fepvals->all_lambda[g], fepvals->n_lambda);
468 gmx_fio_ndo_int(fio, fepvals->separate_dvdl, efptNR);
469 }
470 else if (fepvals->init_lambda >= 0)
471 {
472 fepvals->separate_dvdl[efptFEP] = TRUE;
473 }
474 }
475 }
476 else if (file_version >= 64)
477 {
478 gmx_fio_do_int(fio, fepvals->n_lambda);
479 if (bRead)
480 {
481 int g;
482
483 snew(fepvals->all_lambda, efptNR);
484 /* still allocate the all_lambda array's contents. */
485 for (g = 0; g < efptNR; g++)
486 {
487 if (fepvals->n_lambda > 0)
488 {
489 snew(fepvals->all_lambda[g], fepvals->n_lambda);
490 }
491 }
492 }
493 gmx_fio_ndo_double(fio, fepvals->all_lambda[efptFEP],
494 fepvals->n_lambda);
495 if (fepvals->init_lambda >= 0)
496 {
497 int g, h;
498
499 fepvals->separate_dvdl[efptFEP] = TRUE;
500
501 if (bRead)
502 {
503 /* copy the contents of the efptFEP lambda component to all
504 the other components */
505 for (g = 0; g < efptNR; g++)
506 {
507 for (h = 0; h < fepvals->n_lambda; h++)
508 {
509 if (g != efptFEP)
510 {
511 fepvals->all_lambda[g][h] =
512 fepvals->all_lambda[efptFEP][h];
513 }
514 }
515 }
516 }
517 }
518 }
519 else
520 {
521 fepvals->n_lambda = 0;
522 fepvals->all_lambda = NULL;
523 if (fepvals->init_lambda >= 0)
524 {
525 fepvals->separate_dvdl[efptFEP] = TRUE;
526 }
527 }
528 if (file_version >= 13)
529 {
530 gmx_fio_do_real(fio, fepvals->sc_alpha);
531 }
532 else
533 {
534 fepvals->sc_alpha = 0;
535 }
536 if (file_version >= 38)
537 {
538 gmx_fio_do_int(fio, fepvals->sc_power);
539 }
540 else
541 {
542 fepvals->sc_power = 2;
543 }
544 if (file_version >= 79)
545 {
546 gmx_fio_do_real(fio, fepvals->sc_r_power);
547 }
548 else
549 {
550 fepvals->sc_r_power = 6.0;
551 }
552 if (file_version >= 15)
553 {
554 gmx_fio_do_real(fio, fepvals->sc_sigma);
555 }
556 else
557 {
558 fepvals->sc_sigma = 0.3;
559 }
560 if (bRead)
561 {
562 if (file_version >= 71)
563 {
564 fepvals->sc_sigma_min = fepvals->sc_sigma;
565 }
566 else
567 {
568 fepvals->sc_sigma_min = 0;
569 }
570 }
571 if (file_version >= 79)
572 {
573 gmx_fio_do_int(fio, fepvals->bScCoul);
574 }
575 else
576 {
577 fepvals->bScCoul = TRUE;
578 }
579 if (file_version >= 64)
580 {
581 gmx_fio_do_int(fio, fepvals->nstdhdl);
582 }
583 else
584 {
585 fepvals->nstdhdl = 1;
586 }
587
588 if (file_version >= 73)
589 {
590 gmx_fio_do_int(fio, fepvals->separate_dhdl_file);
591 gmx_fio_do_int(fio, fepvals->dhdl_derivatives);
592 }
593 else
594 {
595 fepvals->separate_dhdl_file = esepdhdlfileYES;
596 fepvals->dhdl_derivatives = edhdlderivativesYES;
597 }
598 if (file_version >= 71)
599 {
600 gmx_fio_do_int(fio, fepvals->dh_hist_size);
601 gmx_fio_do_double(fio, fepvals->dh_hist_spacing);
602 }
603 else
604 {
605 fepvals->dh_hist_size = 0;
606 fepvals->dh_hist_spacing = 0.1;
607 }
608 if (file_version >= 79)
609 {
610 gmx_fio_do_int(fio, fepvals->edHdLPrintEnergy);
611 }
612 else
613 {
614 fepvals->edHdLPrintEnergy = edHdLPrintEnergyNO;
615 }
616
617 /* handle lambda_neighbors */
618 if ((file_version >= 83 && file_version < 90) || file_version >= 92)
619 {
620 gmx_fio_do_int(fio, fepvals->lambda_neighbors);
621 if ( (fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0) &&
622 (fepvals->init_lambda < 0) )
623 {
624 fepvals->lambda_start_n = (fepvals->init_fep_state -
625 fepvals->lambda_neighbors);
626 fepvals->lambda_stop_n = (fepvals->init_fep_state +
627 fepvals->lambda_neighbors + 1);
628 if (fepvals->lambda_start_n < 0)
629 {
630 fepvals->lambda_start_n = 0;;
631 }
632 if (fepvals->lambda_stop_n >= fepvals->n_lambda)
633 {
634 fepvals->lambda_stop_n = fepvals->n_lambda;
635 }
636 }
637 else
638 {
639 fepvals->lambda_start_n = 0;
640 fepvals->lambda_stop_n = fepvals->n_lambda;
641 }
642 }
643 else
644 {
645 fepvals->lambda_start_n = 0;
646 fepvals->lambda_stop_n = fepvals->n_lambda;
647 }
648 }
649
650 static void do_pull(t_fileio *fio, t_pull *pull, gmx_bool bRead, int file_version)
651 {
652 int g;
653
654 if (file_version >= 95)
655 {
656 gmx_fio_do_int(fio, pull->ngroup);
657 }
658 gmx_fio_do_int(fio, pull->ncoord);
659 if (file_version < 95)
660 {
661 pull->ngroup = pull->ncoord + 1;
662 }
663 gmx_fio_do_int(fio, pull->eGeom);
664 gmx_fio_do_ivec(fio, pull->dim);
665 gmx_fio_do_real(fio, pull->cyl_r1);
666 gmx_fio_do_real(fio, pull->cyl_r0);
667 gmx_fio_do_real(fio, pull->constr_tol);
668 if (file_version >= 95)
669 {
670 gmx_fio_do_int(fio, pull->bPrintRef);
671 }
672 gmx_fio_do_int(fio, pull->nstxout);
673 gmx_fio_do_int(fio, pull->nstfout);
674 if (bRead)
675 {
676 snew(pull->group, pull->ngroup);
677 snew(pull->coord, pull->ncoord);
678 }
679 if (file_version < 95)
680 {
681 /* epullgPOS for position pulling, before epullgDIRPBC was removed */
682 if (pull->eGeom == epullgDIRPBC)
683 {
684 gmx_fatal(FARGS, "pull-geometry=position is no longer supported");
685 }
686 if (pull->eGeom > epullgDIRPBC)
687 {
688 pull->eGeom -= 1;
689 }
690
691 for (g = 0; g < pull->ngroup; g++)
692 {
693 /* We read and ignore a pull coordinate for group 0 */
694 do_pullgrp_tpx_pre95(fio, &pull->group[g], &pull->coord[max(g-1, 0)],
695 bRead, file_version);
696 if (g > 0)
697 {
698 pull->coord[g-1].group[0] = 0;
699 pull->coord[g-1].group[1] = g;
700 }
701 }
702
703 pull->bPrintRef = (pull->group[0].nat > 0);
704 }
705 else
706 {
707 for (g = 0; g < pull->ngroup; g++)
708 {
709 do_pull_group(fio, &pull->group[g], bRead);
710 }
711 for (g = 0; g < pull->ncoord; g++)
712 {
713 do_pull_coord(fio, &pull->coord[g]);
714 }
715 }
716 }
717
718
719 static void do_rotgrp(t_fileio *fio, t_rotgrp *rotg, gmx_bool bRead)
720 {
721 int i;
722
723 gmx_fio_do_int(fio, rotg->eType);
724 gmx_fio_do_int(fio, rotg->bMassW);
725 gmx_fio_do_int(fio, rotg->nat);
726 if (bRead)
727 {
728 snew(rotg->ind, rotg->nat);
729 }
730 gmx_fio_ndo_int(fio, rotg->ind, rotg->nat);
731 if (bRead)
732 {
733 snew(rotg->x_ref, rotg->nat);
734 }
735 gmx_fio_ndo_rvec(fio, rotg->x_ref, rotg->nat);
736 gmx_fio_do_rvec(fio, rotg->vec);
737 gmx_fio_do_rvec(fio, rotg->pivot);
738 gmx_fio_do_real(fio, rotg->rate);
739 gmx_fio_do_real(fio, rotg->k);
740 gmx_fio_do_real(fio, rotg->slab_dist);
741 gmx_fio_do_real(fio, rotg->min_gaussian);
742 gmx_fio_do_real(fio, rotg->eps);
743 gmx_fio_do_int(fio, rotg->eFittype);
744 gmx_fio_do_int(fio, rotg->PotAngle_nstep);
745 gmx_fio_do_real(fio, rotg->PotAngle_step);
746 }
747
748 static void do_rot(t_fileio *fio, t_rot *rot, gmx_bool bRead)
749 {
750 int g;
751
752 gmx_fio_do_int(fio, rot->ngrp);
753 gmx_fio_do_int(fio, rot->nstrout);
754 gmx_fio_do_int(fio, rot->nstsout);
755 if (bRead)
756 {
757 snew(rot->grp, rot->ngrp);
758 }
759 for (g = 0; g < rot->ngrp; g++)
760 {
761 do_rotgrp(fio, &rot->grp[g], bRead);
762 }
763 }
764
765
766 static void do_swapcoords(t_fileio *fio, t_swapcoords *swap, gmx_bool bRead)
767 {
768 int i, j;
769
770
771 gmx_fio_do_int(fio, swap->nat);
772 gmx_fio_do_int(fio, swap->nat_sol);
773 for (j = 0; j < 2; j++)
774 {
775 gmx_fio_do_int(fio, swap->nat_split[j]);
776 gmx_fio_do_int(fio, swap->massw_split[j]);
777 }
778 gmx_fio_do_int(fio, swap->nstswap);
779 gmx_fio_do_int(fio, swap->nAverage);
780 gmx_fio_do_real(fio, swap->threshold);
781 gmx_fio_do_real(fio, swap->cyl0r);
782 gmx_fio_do_real(fio, swap->cyl0u);
783 gmx_fio_do_real(fio, swap->cyl0l);
784 gmx_fio_do_real(fio, swap->cyl1r);
785 gmx_fio_do_real(fio, swap->cyl1u);
786 gmx_fio_do_real(fio, swap->cyl1l);
787
788 if (bRead)
789 {
790 snew(swap->ind, swap->nat);
791 snew(swap->ind_sol, swap->nat_sol);
792 for (j = 0; j < 2; j++)
793 {
794 snew(swap->ind_split[j], swap->nat_split[j]);
795 }
796 }
797
798 gmx_fio_ndo_int(fio, swap->ind, swap->nat);
799 gmx_fio_ndo_int(fio, swap->ind_sol, swap->nat_sol);
800 for (j = 0; j < 2; j++)
801 {
802 gmx_fio_ndo_int(fio, swap->ind_split[j], swap->nat_split[j]);
803 }
804
805 for (j = 0; j < eCompNR; j++)
806 {
807 gmx_fio_do_int(fio, swap->nanions[j]);
808 gmx_fio_do_int(fio, swap->ncations[j]);
809 }
810
811 }
812
813
814 static void do_inputrec(t_fileio *fio, t_inputrec *ir, gmx_bool bRead,
815 int file_version, real *fudgeQQ)
816 {
817 int i, j, k, *tmp, idum = 0;
818 real rdum, bd_temp;
819 rvec vdum;
820 gmx_bool bSimAnn, bdum = 0;
821 real zerotemptime, finish_t, init_temp, finish_temp;
822
823 if (file_version != tpx_version)
824 {
825 /* Give a warning about features that are not accessible */
826 fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n",
827 file_version, tpx_version);
828 }
829
830 if (bRead)
831 {
832 init_inputrec(ir);
833 }
834
835 if (file_version == 0)
836 {
837 return;
838 }
839
840 /* Basic inputrec stuff */
841 gmx_fio_do_int(fio, ir->eI);
842 if (file_version >= 62)
843 {
844 gmx_fio_do_int64(fio, ir->nsteps);
845 }
846 else
847 {
848 gmx_fio_do_int(fio, idum);
849 ir->nsteps = idum;
850 }
851
852 if (file_version > 25)
853 {
854 if (file_version >= 62)
855 {
856 gmx_fio_do_int64(fio, ir->init_step);
857 }
858 else
859 {
860 gmx_fio_do_int(fio, idum);
861 ir->init_step = idum;
862 }
863 }
864 else
865 {
866 ir->init_step = 0;
867 }
868
869 if (file_version >= 58)
870 {
871 gmx_fio_do_int(fio, ir->simulation_part);
872 }
873 else
874 {
875 ir->simulation_part = 1;
876 }
877
878 if (file_version >= 67)
879 {
880 gmx_fio_do_int(fio, ir->nstcalcenergy);
881 }
882 else
883 {
884 ir->nstcalcenergy = 1;
885 }
886 if (file_version < 53)
887 {
888 /* The pbc info has been moved out of do_inputrec,
889 * since we always want it, also without reading the inputrec.
890 */
891 gmx_fio_do_int(fio, ir->ePBC);
892 if ((file_version <= 15) && (ir->ePBC == 2))
893 {
894 ir->ePBC = epbcNONE;
895 }
896 if (file_version >= 45)
897 {
898 gmx_fio_do_int(fio, ir->bPeriodicMols);
899 }
900 else
901 {
902 if (ir->ePBC == 2)
903 {
904 ir->ePBC = epbcXYZ;
905 ir->bPeriodicMols = TRUE;
906 }
907 else
908 {
909 ir->bPeriodicMols = FALSE;
910 }
911 }
912 }
913 if (file_version >= 81)
914 {
915 gmx_fio_do_int(fio, ir->cutoff_scheme);
916 if (file_version < 94)
917 {
918 ir->cutoff_scheme = 1 - ir->cutoff_scheme;
919 }
920 }
921 else
922 {
923 ir->cutoff_scheme = ecutsGROUP;
924 }
925 gmx_fio_do_int(fio, ir->ns_type);
926 gmx_fio_do_int(fio, ir->nstlist);
927 gmx_fio_do_int(fio, idum); /* used to be ndelta; not used anymore */
928 if (file_version < 41)
929 {
930 gmx_fio_do_int(fio, idum);
931 gmx_fio_do_int(fio, idum);
932 }
933 if (file_version >= 45)
934 {
935 gmx_fio_do_real(fio, ir->rtpi);
936 }
937 else
938 {
939 ir->rtpi = 0.05;
940 }
941 gmx_fio_do_int(fio, ir->nstcomm);
942 if (file_version > 34)
943 {
944 gmx_fio_do_int(fio, ir->comm_mode);
945 }
946 else if (ir->nstcomm < 0)
947 {
948 ir->comm_mode = ecmANGULAR;
949 }
950 else
951 {
952 ir->comm_mode = ecmLINEAR;
953 }
954 ir->nstcomm = abs(ir->nstcomm);
955
956 /* ignore nstcheckpoint */
957 if (file_version > 25 && file_version < tpxv_RemoveObsoleteParameters1)
958 {
959 gmx_fio_do_int(fio, idum);
960 }
961
962 gmx_fio_do_int(fio, ir->nstcgsteep);
963
964 if (file_version >= 30)
965 {
966 gmx_fio_do_int(fio, ir->nbfgscorr);
967 }
968 else if (bRead)
969 {
970 ir->nbfgscorr = 10;
971 }
972
973 gmx_fio_do_int(fio, ir->nstlog);
974 gmx_fio_do_int(fio, ir->nstxout);
975 gmx_fio_do_int(fio, ir->nstvout);
976 gmx_fio_do_int(fio, ir->nstfout);
977 gmx_fio_do_int(fio, ir->nstenergy);
978 gmx_fio_do_int(fio, ir->nstxout_compressed);
979 if (file_version >= 59)
980 {
981 gmx_fio_do_double(fio, ir->init_t);
982 gmx_fio_do_double(fio, ir->delta_t);
983 }
984 else
985 {
986 gmx_fio_do_real(fio, rdum);
987 ir->init_t = rdum;
988 gmx_fio_do_real(fio, rdum);
989 ir->delta_t = rdum;
990 }
991 gmx_fio_do_real(fio, ir->x_compression_precision);
992 if (file_version < 19)
993 {
994 gmx_fio_do_int(fio, idum);
995 gmx_fio_do_int(fio, idum);
996 }
997 if (file_version < 18)
998 {
999 gmx_fio_do_int(fio, idum);
1000 }
1001 if (file_version >= 81)
1002 {
1003 gmx_fio_do_real(fio, ir->verletbuf_tol);
1004 }
1005 else
1006 {
1007 ir->verletbuf_tol = 0;
1008 }
1009 gmx_fio_do_real(fio, ir->rlist);
1010 if (file_version >= 67)
1011 {
1012 gmx_fio_do_real(fio, ir->rlistlong);
1013 }
1014 if (file_version >= 82 && file_version != 90)
1015 {
1016 gmx_fio_do_int(fio, ir->nstcalclr);
1017 }
1018 else
1019 {
1020 /* Calculate at NS steps */
1021 ir->nstcalclr = ir->nstlist;
1022 }
1023 gmx_fio_do_int(fio, ir->coulombtype);
1024 if (file_version < 32 && ir->coulombtype == eelRF)
1025 {
1026 ir->coulombtype = eelRF_NEC;
1027 }
1028 if (file_version >= 81)
1029 {
1030 gmx_fio_do_int(fio, ir->coulomb_modifier);
1031 }
1032 else
1033 {
1034 ir->coulomb_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1035 }
1036 gmx_fio_do_real(fio, ir->rcoulomb_switch);
1037 gmx_fio_do_real(fio, ir->rcoulomb);
1038 gmx_fio_do_int(fio, ir->vdwtype);
1039 if (file_version >= 81)
1040 {
1041 gmx_fio_do_int(fio, ir->vdw_modifier);
1042 }
1043 else
1044 {
1045 ir->vdw_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1046 }
1047 gmx_fio_do_real(fio, ir->rvdw_switch);
1048 gmx_fio_do_real(fio, ir->rvdw);
1049 if (file_version < 67)
1050 {
1051 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
1052 }
1053 gmx_fio_do_int(fio, ir->eDispCorr);
1054 gmx_fio_do_real(fio, ir->epsilon_r);
1055 if (file_version >= 37)
1056 {
1057 gmx_fio_do_real(fio, ir->epsilon_rf);
1058 }
1059 else
1060 {
1061 if (EEL_RF(ir->coulombtype))
1062 {
1063 ir->epsilon_rf = ir->epsilon_r;
1064 ir->epsilon_r = 1.0;
1065 }
1066 else
1067 {
1068 ir->epsilon_rf = 1.0;
1069 }
1070 }
1071 if (file_version >= 29)
1072 {
1073 gmx_fio_do_real(fio, ir->tabext);
1074 }
1075 else
1076 {
1077 ir->tabext = 1.0;
1078 }
1079
1080 if (file_version > 25)
1081 {
1082 gmx_fio_do_int(fio, ir->gb_algorithm);
1083 gmx_fio_do_int(fio, ir->nstgbradii);
1084 gmx_fio_do_real(fio, ir->rgbradii);
1085 gmx_fio_do_real(fio, ir->gb_saltconc);
1086 gmx_fio_do_int(fio, ir->implicit_solvent);
1087 }
1088 else
1089 {
1090 ir->gb_algorithm = egbSTILL;
1091 ir->nstgbradii = 1;
1092 ir->rgbradii = 1.0;
1093 ir->gb_saltconc = 0;
1094 ir->implicit_solvent = eisNO;
1095 }
1096 if (file_version >= 55)
1097 {
1098 gmx_fio_do_real(fio, ir->gb_epsilon_solvent);
1099 gmx_fio_do_real(fio, ir->gb_obc_alpha);
1100 gmx_fio_do_real(fio, ir->gb_obc_beta);
1101 gmx_fio_do_real(fio, ir->gb_obc_gamma);
1102 if (file_version >= 60)
1103 {
1104 gmx_fio_do_real(fio, ir->gb_dielectric_offset);
1105 gmx_fio_do_int(fio, ir->sa_algorithm);
1106 }
1107 else
1108 {
1109 ir->gb_dielectric_offset = 0.009;
1110 ir->sa_algorithm = esaAPPROX;
1111 }
1112 gmx_fio_do_real(fio, ir->sa_surface_tension);
1113
1114 /* Override sa_surface_tension if it is not changed in the mpd-file */
1115 if (ir->sa_surface_tension < 0)
1116 {
1117 if (ir->gb_algorithm == egbSTILL)
1118 {
1119 ir->sa_surface_tension = 0.0049 * 100 * CAL2JOULE;
1120 }
1121 else if (ir->gb_algorithm == egbHCT || ir->gb_algorithm == egbOBC)
1122 {
1123 ir->sa_surface_tension = 0.0054 * 100 * CAL2JOULE;
1124 }
1125 }
1126
1127 }
1128 else
1129 {
1130 /* Better use sensible values than insane (0.0) ones... */
1131 ir->gb_epsilon_solvent = 80;
1132 ir->gb_obc_alpha = 1.0;
1133 ir->gb_obc_beta = 0.8;
1134 ir->gb_obc_gamma = 4.85;
1135 ir->sa_surface_tension = 2.092;
1136 }
1137
1138
1139 if (file_version >= 81)
1140 {
1141 gmx_fio_do_real(fio, ir->fourier_spacing);
1142 }
1143 else
1144 {
1145 ir->fourier_spacing = 0.0;
1146 }
1147 gmx_fio_do_int(fio, ir->nkx);
1148 gmx_fio_do_int(fio, ir->nky);
1149 gmx_fio_do_int(fio, ir->nkz);
1150 gmx_fio_do_int(fio, ir->pme_order);
1151 gmx_fio_do_real(fio, ir->ewald_rtol);
1152
1153 if (file_version >= 93)
1154 {
1155 gmx_fio_do_real(fio, ir->ewald_rtol_lj);
1156 }
1157 else
1158 {
1159 ir->ewald_rtol_lj = ir->ewald_rtol;
1160 }
1161
1162 if (file_version >= 24)
1163 {
1164 gmx_fio_do_int(fio, ir->ewald_geometry);
1165 }
1166 else
1167 {
1168 ir->ewald_geometry = eewg3D;
1169 }
1170
1171 if (file_version <= 17)
1172 {
1173 ir->epsilon_surface = 0;
1174 if (file_version == 17)
1175 {
1176 gmx_fio_do_int(fio, idum);
1177 }
1178 }
1179 else
1180 {
1181 gmx_fio_do_real(fio, ir->epsilon_surface);
1182 }
1183
1184 /* ignore bOptFFT */
1185 if (file_version < tpxv_RemoveObsoleteParameters1)
1186 {
1187 gmx_fio_do_gmx_bool(fio, bdum);
1188 }
1189
1190 if (file_version >= 93)
1191 {
1192 gmx_fio_do_int(fio, ir->ljpme_combination_rule);
1193 }
1194 gmx_fio_do_gmx_bool(fio, ir->bContinuation);
1195 gmx_fio_do_int(fio, ir->etc);
1196 /* before version 18, ir->etc was a gmx_bool (ir->btc),
1197 * but the values 0 and 1 still mean no and
1198 * berendsen temperature coupling, respectively.
1199 */
1200 if (file_version >= 79)
1201 {
1202 gmx_fio_do_gmx_bool(fio, ir->bPrintNHChains);
1203 }
1204 if (file_version >= 71)
1205 {
1206 gmx_fio_do_int(fio, ir->nsttcouple);
1207 }
1208 else
1209 {
1210 ir->nsttcouple = ir->nstcalcenergy;
1211 }
1212 if (file_version <= 15)
1213 {
1214 gmx_fio_do_int(fio, idum);
1215 }
1216 if (file_version <= 17)
1217 {
1218 gmx_fio_do_int(fio, ir->epct);
1219 if (file_version <= 15)
1220 {
1221 if (ir->epct == 5)
1222 {
1223 ir->epct = epctSURFACETENSION;
1224 }
1225 gmx_fio_do_int(fio, idum);
1226 }
1227 ir->epct -= 1;
1228 /* we have removed the NO alternative at the beginning */
1229 if (ir->epct == -1)
1230 {
1231 ir->epc = epcNO;
1232 ir->epct = epctISOTROPIC;
1233 }
1234 else
1235 {
1236 ir->epc = epcBERENDSEN;
1237 }
1238 }
1239 else
1240 {
1241 gmx_fio_do_int(fio, ir->epc);
1242 gmx_fio_do_int(fio, ir->epct);
1243 }
1244 if (file_version >= 71)
1245 {
1246 gmx_fio_do_int(fio, ir->nstpcouple);
1247 }
1248 else
1249 {
1250 ir->nstpcouple = ir->nstcalcenergy;
1251 }
1252 gmx_fio_do_real(fio, ir->tau_p);
1253 if (file_version <= 15)
1254 {
1255 gmx_fio_do_rvec(fio, vdum);
1256 clear_mat(ir->ref_p);
1257 for (i = 0; i < DIM; i++)
1258 {
1259 ir->ref_p[i][i] = vdum[i];
1260 }
1261 }
1262 else
1263 {
1264 gmx_fio_do_rvec(fio, ir->ref_p[XX]);
1265 gmx_fio_do_rvec(fio, ir->ref_p[YY]);
1266 gmx_fio_do_rvec(fio, ir->ref_p[ZZ]);
1267 }
1268 if (file_version <= 15)
1269 {
1270 gmx_fio_do_rvec(fio, vdum);
1271 clear_mat(ir->compress);
1272 for (i = 0; i < DIM; i++)
1273 {
1274 ir->compress[i][i] = vdum[i];
1275 }
1276 }
1277 else
1278 {
1279 gmx_fio_do_rvec(fio, ir->compress[XX]);
1280 gmx_fio_do_rvec(fio, ir->compress[YY]);
1281 gmx_fio_do_rvec(fio, ir->compress[ZZ]);
1282 }
1283 if (file_version >= 47)
1284 {
1285 gmx_fio_do_int(fio, ir->refcoord_scaling);
1286 gmx_fio_do_rvec(fio, ir->posres_com);
1287 gmx_fio_do_rvec(fio, ir->posres_comB);
1288 }
1289 else
1290 {
1291 ir->refcoord_scaling = erscNO;
1292 clear_rvec(ir->posres_com);
1293 clear_rvec(ir->posres_comB);
1294 }
1295 if ((file_version > 25) && (file_version < 79))
1296 {
1297 gmx_fio_do_int(fio, ir->andersen_seed);
1298 }
1299 else
1300 {
1301 ir->andersen_seed = 0;
1302 }
1303 if (file_version < 26)
1304 {
1305 gmx_fio_do_gmx_bool(fio, bSimAnn);
1306 gmx_fio_do_real(fio, zerotemptime);
1307 }
1308
1309 if (file_version < 37)
1310 {
1311 gmx_fio_do_real(fio, rdum);
1312 }
1313
1314 gmx_fio_do_real(fio, ir->shake_tol);
1315 if (file_version < 54)
1316 {
1317 gmx_fio_do_real(fio, *fudgeQQ);
1318 }
1319
1320 gmx_fio_do_int(fio, ir->efep);
1321 if (file_version <= 14 && ir->efep != efepNO)
1322 {
1323 ir->efep = efepYES;
1324 }
1325 do_fepvals(fio, ir->fepvals, bRead, file_version);
1326
1327 if (file_version >= 79)
1328 {
1329 gmx_fio_do_gmx_bool(fio, ir->bSimTemp);
1330 if (ir->bSimTemp)
1331 {
1332 ir->bSimTemp = TRUE;
1333 }
1334 }
1335 else
1336 {
1337 ir->bSimTemp = FALSE;
1338 }
1339 if (ir->bSimTemp)
1340 {
1341 do_simtempvals(fio, ir->simtempvals, ir->fepvals->n_lambda, bRead, file_version);
1342 }
1343
1344 if (file_version >= 79)
1345 {
1346 gmx_fio_do_gmx_bool(fio, ir->bExpanded);
1347 if (ir->bExpanded)
1348 {
1349 ir->bExpanded = TRUE;
1350 }
1351 else
1352 {
1353 ir->bExpanded = FALSE;
1354 }
1355 }
1356 if (ir->bExpanded)
1357 {
1358 do_expandedvals(fio, ir->expandedvals, ir->fepvals, bRead, file_version);
1359 }
1360 if (file_version >= 57)
1361 {
1362 gmx_fio_do_int(fio, ir->eDisre);
1363 }
1364 gmx_fio_do_int(fio, ir->eDisreWeighting);
1365 if (file_version < 22)
1366 {
1367 if (ir->eDisreWeighting == 0)
1368 {
1369 ir->eDisreWeighting = edrwEqual;
1370 }
1371 else
1372 {
1373 ir->eDisreWeighting = edrwConservative;
1374 }
1375 }
1376 gmx_fio_do_gmx_bool(fio, ir->bDisreMixed);
1377 gmx_fio_do_real(fio, ir->dr_fc);
1378 gmx_fio_do_real(fio, ir->dr_tau);
1379 gmx_fio_do_int(fio, ir->nstdisreout);
1380 if (file_version >= 22)
1381 {
1382 gmx_fio_do_real(fio, ir->orires_fc);
1383 gmx_fio_do_real(fio, ir->orires_tau);
1384 gmx_fio_do_int(fio, ir->nstorireout);
1385 }
1386 else
1387 {
1388 ir->orires_fc = 0;
1389 ir->orires_tau = 0;
1390 ir->nstorireout = 0;
1391 }
1392
1393 /* ignore dihre_fc */
1394 if (file_version >= 26 && file_version < 79)
1395 {
1396 gmx_fio_do_real(fio, rdum);
1397 if (file_version < 56)
1398 {
1399 gmx_fio_do_real(fio, rdum);
1400 gmx_fio_do_int(fio, idum);
1401 }
1402 }
1403
1404 gmx_fio_do_real(fio, ir->em_stepsize);
1405 gmx_fio_do_real(fio, ir->em_tol);
1406 if (file_version >= 22)
1407 {
1408 gmx_fio_do_gmx_bool(fio, ir->bShakeSOR);
1409 }
1410 else if (bRead)
1411 {
1412 ir->bShakeSOR = TRUE;
1413 }
1414 if (file_version >= 11)
1415 {
1416 gmx_fio_do_int(fio, ir->niter);
1417 }
1418 else if (bRead)
1419 {
1420 ir->niter = 25;
1421 fprintf(stderr, "Note: niter not in run input file, setting it to %d\n",
1422 ir->niter);
1423 }
1424 if (file_version >= 21)
1425 {
1426 gmx_fio_do_real(fio, ir->fc_stepsize);
1427 }
1428 else
1429 {
1430 ir->fc_stepsize = 0;
1431 }
1432 gmx_fio_do_int(fio, ir->eConstrAlg);
1433 gmx_fio_do_int(fio, ir->nProjOrder);
1434 gmx_fio_do_real(fio, ir->LincsWarnAngle);
1435 if (file_version <= 14)
1436 {
1437 gmx_fio_do_int(fio, idum);
1438 }
1439 if (file_version >= 26)
1440 {
1441 gmx_fio_do_int(fio, ir->nLincsIter);
1442 }
1443 else if (bRead)
1444 {
1445 ir->nLincsIter = 1;
1446 fprintf(stderr, "Note: nLincsIter not in run input file, setting it to %d\n",
1447 ir->nLincsIter);
1448 }
1449 if (file_version < 33)
1450 {
1451 gmx_fio_do_real(fio, bd_temp);
1452 }
1453 gmx_fio_do_real(fio, ir->bd_fric);
1454 if (file_version >= tpxv_Use64BitRandomSeed)
1455 {
1456 gmx_fio_do_int64(fio, ir->ld_seed);
1457 }
1458 else
1459 {
1460 gmx_fio_do_int(fio, idum);
1461 ir->ld_seed = idum;
1462 }
1463 if (file_version >= 33)
1464 {
1465 for (i = 0; i < DIM; i++)
1466 {
1467 gmx_fio_do_rvec(fio, ir->deform[i]);
1468 }
1469 }
1470 else
1471 {
1472 for (i = 0; i < DIM; i++)
1473 {
1474 clear_rvec(ir->deform[i]);
1475 }
1476 }
1477 if (file_version >= 14)
1478 {
1479 gmx_fio_do_real(fio, ir->cos_accel);
1480 }
1481 else if (bRead)
1482 {
1483 ir->cos_accel = 0;
1484 }
1485 gmx_fio_do_int(fio, ir->userint1);
1486 gmx_fio_do_int(fio, ir->userint2);
1487 gmx_fio_do_int(fio, ir->userint3);
1488 gmx_fio_do_int(fio, ir->userint4);
1489 gmx_fio_do_real(fio, ir->userreal1);
1490 gmx_fio_do_real(fio, ir->userreal2);
1491 gmx_fio_do_real(fio, ir->userreal3);
1492 gmx_fio_do_real(fio, ir->userreal4);
1493
1494 /* AdResS stuff */
1495 if (file_version >= 77)
1496 {
1497 gmx_fio_do_gmx_bool(fio, ir->bAdress);
1498 if (ir->bAdress)
1499 {
1500 if (bRead)
1501 {
1502 snew(ir->adress, 1);
1503 }
1504 gmx_fio_do_int(fio, ir->adress->type);
1505 gmx_fio_do_real(fio, ir->adress->const_wf);
1506 gmx_fio_do_real(fio, ir->adress->ex_width);
1507 gmx_fio_do_real(fio, ir->adress->hy_width);
1508 gmx_fio_do_int(fio, ir->adress->icor);
1509 gmx_fio_do_int(fio, ir->adress->site);
1510 gmx_fio_do_rvec(fio, ir->adress->refs);
1511 gmx_fio_do_int(fio, ir->adress->n_tf_grps);
1512 gmx_fio_do_real(fio, ir->adress->ex_forcecap);
1513 gmx_fio_do_int(fio, ir->adress->n_energy_grps);
1514 gmx_fio_do_int(fio, ir->adress->do_hybridpairs);
1515
1516 if (bRead)
1517 {
1518 snew(ir->adress->tf_table_index, ir->adress->n_tf_grps);
1519 }
1520 if (ir->adress->n_tf_grps > 0)
1521 {
1522 gmx_fio_ndo_int(fio, ir->adress->tf_table_index, ir->adress->n_tf_grps);
1523 }
1524 if (bRead)
1525 {
1526 snew(ir->adress->group_explicit, ir->adress->n_energy_grps);
1527 }
1528 if (ir->adress->n_energy_grps > 0)
1529 {
1530 gmx_fio_ndo_int(fio, ir->adress->group_explicit, ir->adress->n_energy_grps);
1531 }
1532 }
1533 }
1534 else
1535 {
1536 ir->bAdress = FALSE;
1537 }
1538
1539 /* pull stuff */
1540 if (file_version >= 48)
1541 {
1542 gmx_fio_do_int(fio, ir->ePull);
1543 if (ir->ePull != epullNO)
1544 {
1545 if (bRead)
1546 {
1547 snew(ir->pull, 1);
1548 }
1549 do_pull(fio, ir->pull, bRead, file_version);
1550 }
1551 }
1552 else
1553 {
1554 ir->ePull = epullNO;
1555 }
1556
1557 /* Enforced rotation */
1558 if (file_version >= 74)
1559 {
1560 gmx_fio_do_int(fio, ir->bRot);
1561 if (ir->bRot == TRUE)
1562 {
1563 if (bRead)
1564 {
1565 snew(ir->rot, 1);
1566 }
1567 do_rot(fio, ir->rot, bRead);
1568 }
1569 }
1570 else
1571 {
1572 ir->bRot = FALSE;
1573 }
1574
1575 /* Interactive molecular dynamics */
1576 if (file_version >= tpxv_InteractiveMolecularDynamics)
1577 {
1578 gmx_fio_do_int(fio, ir->bIMD);
1579 if (TRUE == ir->bIMD)
1580 {
1581 if (bRead)
1582 {
1583 snew(ir->imd, 1);
1584 }
1585 do_imd(fio, ir->imd, bRead);
1586 }
1587 }
1588 else
1589 {
1590 /* We don't support IMD sessions for old .tpr files */
1591 ir->bIMD = FALSE;
1592 }
1593
1594 /* grpopts stuff */
1595 gmx_fio_do_int(fio, ir->opts.ngtc);
1596 if (file_version >= 69)
1597 {
1598 gmx_fio_do_int(fio, ir->opts.nhchainlength);
1599 }
1600 else
1601 {
1602 ir->opts.nhchainlength = 1;
1603 }
1604 gmx_fio_do_int(fio, ir->opts.ngacc);
1605 gmx_fio_do_int(fio, ir->opts.ngfrz);
1606 gmx_fio_do_int(fio, ir->opts.ngener);
1607
1608 if (bRead)
1609 {
1610 snew(ir->opts.nrdf, ir->opts.ngtc);
1611 snew(ir->opts.ref_t, ir->opts.ngtc);
1612 snew(ir->opts.annealing, ir->opts.ngtc);
1613 snew(ir->opts.anneal_npoints, ir->opts.ngtc);
1614 snew(ir->opts.anneal_time, ir->opts.ngtc);
1615 snew(ir->opts.anneal_temp, ir->opts.ngtc);
1616 snew(ir->opts.tau_t, ir->opts.ngtc);
1617 snew(ir->opts.nFreeze, ir->opts.ngfrz);
1618 snew(ir->opts.acc, ir->opts.ngacc);
1619 snew(ir->opts.egp_flags, ir->opts.ngener*ir->opts.ngener);
1620 }
1621 if (ir->opts.ngtc > 0)
1622 {
1623 if (bRead && file_version < 13)
1624 {
1625 snew(tmp, ir->opts.ngtc);
1626 gmx_fio_ndo_int(fio, tmp, ir->opts.ngtc);
1627 for (i = 0; i < ir->opts.ngtc; i++)
1628 {
1629 ir->opts.nrdf[i] = tmp[i];
1630 }
1631 sfree(tmp);
1632 }
1633 else
1634 {
1635 gmx_fio_ndo_real(fio, ir->opts.nrdf, ir->opts.ngtc);
1636 }
1637 gmx_fio_ndo_real(fio, ir->opts.ref_t, ir->opts.ngtc);
1638 gmx_fio_ndo_real(fio, ir->opts.tau_t, ir->opts.ngtc);
1639 if (file_version < 33 && ir->eI == eiBD)
1640 {
1641 for (i = 0; i < ir->opts.ngtc; i++)
1642 {
1643 ir->opts.tau_t[i] = bd_temp;
1644 }
1645 }
1646 }
1647 if (ir->opts.ngfrz > 0)
1648 {
1649 gmx_fio_ndo_ivec(fio, ir->opts.nFreeze, ir->opts.ngfrz);
1650 }
1651 if (ir->opts.ngacc > 0)
1652 {
1653 gmx_fio_ndo_rvec(fio, ir->opts.acc, ir->opts.ngacc);
1654 }
1655 if (file_version >= 12)
1656 {
1657 gmx_fio_ndo_int(fio, ir->opts.egp_flags,
1658 ir->opts.ngener*ir->opts.ngener);
1659 }
1660
1661 if (bRead && file_version < 26)
1662 {
1663 for (i = 0; i < ir->opts.ngtc; i++)
1664 {
1665 if (bSimAnn)
1666 {
1667 ir->opts.annealing[i] = eannSINGLE;
1668 ir->opts.anneal_npoints[i] = 2;
1669 snew(ir->opts.anneal_time[i], 2);
1670 snew(ir->opts.anneal_temp[i], 2);
1671 /* calculate the starting/ending temperatures from reft, zerotemptime, and nsteps */
1672 finish_t = ir->init_t + ir->nsteps * ir->delta_t;
1673 init_temp = ir->opts.ref_t[i]*(1-ir->init_t/zerotemptime);
1674 finish_temp = ir->opts.ref_t[i]*(1-finish_t/zerotemptime);
1675 ir->opts.anneal_time[i][0] = ir->init_t;
1676 ir->opts.anneal_time[i][1] = finish_t;
1677 ir->opts.anneal_temp[i][0] = init_temp;
1678 ir->opts.anneal_temp[i][1] = finish_temp;
1679 }
1680 else
1681 {
1682 ir->opts.annealing[i] = eannNO;
1683 ir->opts.anneal_npoints[i] = 0;
1684 }
1685 }
1686 }
1687 else
1688 {
1689 /* file version 26 or later */
1690 /* First read the lists with annealing and npoints for each group */
1691 gmx_fio_ndo_int(fio, ir->opts.annealing, ir->opts.ngtc);
1692 gmx_fio_ndo_int(fio, ir->opts.anneal_npoints, ir->opts.ngtc);
1693 for (j = 0; j < (ir->opts.ngtc); j++)
1694 {
1695 k = ir->opts.anneal_npoints[j];
1696 if (bRead)
1697 {
1698 snew(ir->opts.anneal_time[j], k);
1699 snew(ir->opts.anneal_temp[j], k);
1700 }
1701 gmx_fio_ndo_real(fio, ir->opts.anneal_time[j], k);
1702 gmx_fio_ndo_real(fio, ir->opts.anneal_temp[j], k);
1703 }
1704 }
1705 /* Walls */
1706 if (file_version >= 45)
1707 {
1708 gmx_fio_do_int(fio, ir->nwall);
1709 gmx_fio_do_int(fio, ir->wall_type);
1710 if (file_version >= 50)
1711 {
1712 gmx_fio_do_real(fio, ir->wall_r_linpot);
1713 }
1714 else
1715 {
1716 ir->wall_r_linpot = -1;
1717 }
1718 gmx_fio_do_int(fio, ir->wall_atomtype[0]);
1719 gmx_fio_do_int(fio, ir->wall_atomtype[1]);
1720 gmx_fio_do_real(fio, ir->wall_density[0]);
1721 gmx_fio_do_real(fio, ir->wall_density[1]);
1722 gmx_fio_do_real(fio, ir->wall_ewald_zfac);
1723 }
1724 else
1725 {
1726 ir->nwall = 0;
1727 ir->wall_type = 0;
1728 ir->wall_atomtype[0] = -1;
1729 ir->wall_atomtype[1] = -1;
1730 ir->wall_density[0] = 0;
1731 ir->wall_density[1] = 0;
1732 ir->wall_ewald_zfac = 3;
1733 }
1734 /* Cosine stuff for electric fields */
1735 for (j = 0; (j < DIM); j++)
1736 {
1737 gmx_fio_do_int(fio, ir->ex[j].n);
1738 gmx_fio_do_int(fio, ir->et[j].n);
1739 if (bRead)
1740 {
1741 snew(ir->ex[j].a, ir->ex[j].n);
1742 snew(ir->ex[j].phi, ir->ex[j].n);
1743 snew(ir->et[j].a, ir->et[j].n);
1744 snew(ir->et[j].phi, ir->et[j].n);
1745 }
1746 gmx_fio_ndo_real(fio, ir->ex[j].a, ir->ex[j].n);
1747 gmx_fio_ndo_real(fio, ir->ex[j].phi, ir->ex[j].n);
1748 gmx_fio_ndo_real(fio, ir->et[j].a, ir->et[j].n);
1749 gmx_fio_ndo_real(fio, ir->et[j].phi, ir->et[j].n);
1750 }
1751
1752 /* Swap ions */
1753 if (file_version >= tpxv_ComputationalElectrophysiology)
1754 {
1755 gmx_fio_do_int(fio, ir->eSwapCoords);
1756 if (ir->eSwapCoords != eswapNO)
1757 {
1758 if (bRead)
1759 {
1760 snew(ir->swap, 1);
1761 }
1762 do_swapcoords(fio, ir->swap, bRead);
1763 }
1764 }
1765
1766 /* QMMM stuff */
1767 if (file_version >= 39)
1768 {
1769 gmx_fio_do_gmx_bool(fio, ir->bQMMM);
1770 gmx_fio_do_int(fio, ir->QMMMscheme);
1771 gmx_fio_do_real(fio, ir->scalefactor);
1772 gmx_fio_do_int(fio, ir->opts.ngQM);
1773 if (bRead)
1774 {
1775 snew(ir->opts.QMmethod, ir->opts.ngQM);
1776 snew(ir->opts.QMbasis, ir->opts.ngQM);
1777 snew(ir->opts.QMcharge, ir->opts.ngQM);
1778 snew(ir->opts.QMmult, ir->opts.ngQM);
1779 snew(ir->opts.bSH, ir->opts.ngQM);
1780 snew(ir->opts.CASorbitals, ir->opts.ngQM);
1781 snew(ir->opts.CASelectrons, ir->opts.ngQM);
1782 snew(ir->opts.SAon, ir->opts.ngQM);
1783 snew(ir->opts.SAoff, ir->opts.ngQM);
1784 snew(ir->opts.SAsteps, ir->opts.ngQM);
1785 snew(ir->opts.bOPT, ir->opts.ngQM);
1786 snew(ir->opts.bTS, ir->opts.ngQM);
1787 }
1788 if (ir->opts.ngQM > 0)
1789 {
1790 gmx_fio_ndo_int(fio, ir->opts.QMmethod, ir->opts.ngQM);
1791 gmx_fio_ndo_int(fio, ir->opts.QMbasis, ir->opts.ngQM);
1792 gmx_fio_ndo_int(fio, ir->opts.QMcharge, ir->opts.ngQM);
1793 gmx_fio_ndo_int(fio, ir->opts.QMmult, ir->opts.ngQM);
1794 gmx_fio_ndo_gmx_bool(fio, ir->opts.bSH, ir->opts.ngQM);
1795 gmx_fio_ndo_int(fio, ir->opts.CASorbitals, ir->opts.ngQM);
1796 gmx_fio_ndo_int(fio, ir->opts.CASelectrons, ir->opts.ngQM);
1797 gmx_fio_ndo_real(fio, ir->opts.SAon, ir->opts.ngQM);
1798 gmx_fio_ndo_real(fio, ir->opts.SAoff, ir->opts.ngQM);
1799 gmx_fio_ndo_int(fio, ir->opts.SAsteps, ir->opts.ngQM);
1800 gmx_fio_ndo_gmx_bool(fio, ir->opts.bOPT, ir->opts.ngQM);
1801 gmx_fio_ndo_gmx_bool(fio, ir->opts.bTS, ir->opts.ngQM);
1802 }
1803 /* end of QMMM stuff */
1804 }
1805 }
1806
1807
1808 static void do_harm(t_fileio *fio, t_iparams *iparams)
1809 {
1810 gmx_fio_do_real(fio, iparams->harmonic.rA);
1811 gmx_fio_do_real(fio, iparams->harmonic.krA);
1812 gmx_fio_do_real(fio, iparams->harmonic.rB);
1813 gmx_fio_do_real(fio, iparams->harmonic.krB);
1814 }
1815
1816 void do_iparams(t_fileio *fio, t_functype ftype, t_iparams *iparams,
1817 gmx_bool bRead, int file_version)
1818 {
1819 int idum;
1820 real rdum;
1821
1822 if (!bRead)
1823 {
1824 gmx_fio_set_comment(fio, interaction_function[ftype].name);
1825 }
1826 switch (ftype)
1827 {
1828 case F_ANGLES:
1829 case F_G96ANGLES:
1830 case F_BONDS:
1831 case F_G96BONDS:
1832 case F_HARMONIC:
1833 case F_IDIHS:
1834 do_harm(fio, iparams);
1835 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && bRead)
1836 {
1837 /* Correct incorrect storage of parameters */
1838 iparams->pdihs.phiB = iparams->pdihs.phiA;
1839 iparams->pdihs.cpB = iparams->pdihs.cpA;
1840 }
1841 break;
1842 case F_RESTRANGLES:
1843 gmx_fio_do_real(fio, iparams->harmonic.rA);
1844 gmx_fio_do_real(fio, iparams->harmonic.krA);
1845 break;
1846 case F_LINEAR_ANGLES:
1847 gmx_fio_do_real(fio, iparams->linangle.klinA);
1848 gmx_fio_do_real(fio, iparams->linangle.aA);
1849 gmx_fio_do_real(fio, iparams->linangle.klinB);
1850 gmx_fio_do_real(fio, iparams->linangle.aB);
1851 break;
1852 case F_FENEBONDS:
1853 gmx_fio_do_real(fio, iparams->fene.bm);
1854 gmx_fio_do_real(fio, iparams->fene.kb);
1855 break;
1856
1857 case F_RESTRBONDS:
1858 gmx_fio_do_real(fio, iparams->restraint.lowA);
1859 gmx_fio_do_real(fio, iparams->restraint.up1A);
1860 gmx_fio_do_real(fio, iparams->restraint.up2A);
1861 gmx_fio_do_real(fio, iparams->restraint.kA);
1862 gmx_fio_do_real(fio, iparams->restraint.lowB);
1863 gmx_fio_do_real(fio, iparams->restraint.up1B);
1864 gmx_fio_do_real(fio, iparams->restraint.up2B);
1865 gmx_fio_do_real(fio, iparams->restraint.kB);
1866 break;
1867 case F_TABBONDS:
1868 case F_TABBONDSNC:
1869 case F_TABANGLES:
1870 case F_TABDIHS:
1871 gmx_fio_do_real(fio, iparams->tab.kA);
1872 gmx_fio_do_int(fio, iparams->tab.table);
1873 gmx_fio_do_real(fio, iparams->tab.kB);
1874 break;
1875 case F_CROSS_BOND_BONDS:
1876 gmx_fio_do_real(fio, iparams->cross_bb.r1e);
1877 gmx_fio_do_real(fio, iparams->cross_bb.r2e);
1878 gmx_fio_do_real(fio, iparams->cross_bb.krr);
1879 break;
1880 case F_CROSS_BOND_ANGLES:
1881 gmx_fio_do_real(fio, iparams->cross_ba.r1e);
1882 gmx_fio_do_real(fio, iparams->cross_ba.r2e);
1883 gmx_fio_do_real(fio, iparams->cross_ba.r3e);
1884 gmx_fio_do_real(fio, iparams->cross_ba.krt);
1885 break;
1886 case F_UREY_BRADLEY:
1887 gmx_fio_do_real(fio, iparams->u_b.thetaA);
1888 gmx_fio_do_real(fio, iparams->u_b.kthetaA);
1889 gmx_fio_do_real(fio, iparams->u_b.r13A);
1890 gmx_fio_do_real(fio, iparams->u_b.kUBA);
1891 if (file_version >= 79)
1892 {
1893 gmx_fio_do_real(fio, iparams->u_b.thetaB);
1894 gmx_fio_do_real(fio, iparams->u_b.kthetaB);
1895 gmx_fio_do_real(fio, iparams->u_b.r13B);
1896 gmx_fio_do_real(fio, iparams->u_b.kUBB);
1897 }
1898 else
1899 {
1900 iparams->u_b.thetaB = iparams->u_b.thetaA;
1901 iparams->u_b.kthetaB = iparams->u_b.kthetaA;
1902 iparams->u_b.r13B = iparams->u_b.r13A;
1903 iparams->u_b.kUBB = iparams->u_b.kUBA;
1904 }
1905 break;
1906 case F_QUARTIC_ANGLES:
1907 gmx_fio_do_real(fio, iparams->qangle.theta);
1908 gmx_fio_ndo_real(fio, iparams->qangle.c, 5);
1909 break;
1910 case F_BHAM:
1911 gmx_fio_do_real(fio, iparams->bham.a);
1912 gmx_fio_do_real(fio, iparams->bham.b);
1913 gmx_fio_do_real(fio, iparams->bham.c);
1914 break;
1915 case F_MORSE:
1916 gmx_fio_do_real(fio, iparams->morse.b0A);
1917 gmx_fio_do_real(fio, iparams->morse.cbA);
1918 gmx_fio_do_real(fio, iparams->morse.betaA);
1919 if (file_version >= 79)
1920 {
1921 gmx_fio_do_real(fio, iparams->morse.b0B);
1922 gmx_fio_do_real(fio, iparams->morse.cbB);
1923 gmx_fio_do_real(fio, iparams->morse.betaB);
1924 }
1925 else
1926 {
1927 iparams->morse.b0B = iparams->morse.b0A;
1928 iparams->morse.cbB = iparams->morse.cbA;
1929 iparams->morse.betaB = iparams->morse.betaA;
1930 }
1931 break;
1932 case F_CUBICBONDS:
1933 gmx_fio_do_real(fio, iparams->cubic.b0);
1934 gmx_fio_do_real(fio, iparams->cubic.kb);
1935 gmx_fio_do_real(fio, iparams->cubic.kcub);
1936 break;
1937 case F_CONNBONDS:
1938 break;
1939 case F_POLARIZATION:
1940 gmx_fio_do_real(fio, iparams->polarize.alpha);
1941 break;
1942 case F_ANHARM_POL:
1943 gmx_fio_do_real(fio, iparams->anharm_polarize.alpha);
1944 gmx_fio_do_real(fio, iparams->anharm_polarize.drcut);
1945 gmx_fio_do_real(fio, iparams->anharm_polarize.khyp);
1946 break;
1947 case F_WATER_POL:
1948 if (file_version < 31)
1949 {
1950 gmx_fatal(FARGS, "Old tpr files with water_polarization not supported. Make a new.");
1951 }
1952 gmx_fio_do_real(fio, iparams->wpol.al_x);
1953 gmx_fio_do_real(fio, iparams->wpol.al_y);
1954 gmx_fio_do_real(fio, iparams->wpol.al_z);
1955 gmx_fio_do_real(fio, iparams->wpol.rOH);
1956 gmx_fio_do_real(fio, iparams->wpol.rHH);
1957 gmx_fio_do_real(fio, iparams->wpol.rOD);
1958 break;
1959 case F_THOLE_POL:
1960 gmx_fio_do_real(fio, iparams->thole.a);
1961 gmx_fio_do_real(fio, iparams->thole.alpha1);
1962 gmx_fio_do_real(fio, iparams->thole.alpha2);
1963 gmx_fio_do_real(fio, iparams->thole.rfac);
1964 break;
1965 case F_LJ:
1966 gmx_fio_do_real(fio, iparams->lj.c6);
1967 gmx_fio_do_real(fio, iparams->lj.c12);
1968 break;
1969 case F_LJ14:
1970 gmx_fio_do_real(fio, iparams->lj14.c6A);
1971 gmx_fio_do_real(fio, iparams->lj14.c12A);
1972 gmx_fio_do_real(fio, iparams->lj14.c6B);
1973 gmx_fio_do_real(fio, iparams->lj14.c12B);
1974 break;
1975 case F_LJC14_Q:
1976 gmx_fio_do_real(fio, iparams->ljc14.fqq);
1977 gmx_fio_do_real(fio, iparams->ljc14.qi);
1978 gmx_fio_do_real(fio, iparams->ljc14.qj);
1979 gmx_fio_do_real(fio, iparams->ljc14.c6);
1980 gmx_fio_do_real(fio, iparams->ljc14.c12);
1981 break;
1982 case F_LJC_PAIRS_NB:
1983 gmx_fio_do_real(fio, iparams->ljcnb.qi);
1984 gmx_fio_do_real(fio, iparams->ljcnb.qj);
1985 gmx_fio_do_real(fio, iparams->ljcnb.c6);
1986 gmx_fio_do_real(fio, iparams->ljcnb.c12);
1987 break;
1988 case F_PDIHS:
1989 case F_PIDIHS:
1990 case F_ANGRES:
1991 case F_ANGRESZ:
1992 gmx_fio_do_real(fio, iparams->pdihs.phiA);
1993 gmx_fio_do_real(fio, iparams->pdihs.cpA);
1994 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && file_version < 42)
1995 {
1996 /* Read the incorrectly stored multiplicity */
1997 gmx_fio_do_real(fio, iparams->harmonic.rB);
1998 gmx_fio_do_real(fio, iparams->harmonic.krB);
1999 iparams->pdihs.phiB = iparams->pdihs.phiA;
2000 iparams->pdihs.cpB = iparams->pdihs.cpA;
2001 }
2002 else
2003 {
2004 gmx_fio_do_real(fio, iparams->pdihs.phiB);
2005 gmx_fio_do_real(fio, iparams->pdihs.cpB);
2006 gmx_fio_do_int(fio, iparams->pdihs.mult);
2007 }
2008 break;
2009 case F_RESTRDIHS:
2010 gmx_fio_do_real(fio, iparams->pdihs.phiA);
2011 gmx_fio_do_real(fio, iparams->pdihs.cpA);
2012 break;
2013 case F_DISRES:
2014 gmx_fio_do_int(fio, iparams->disres.label);
2015 gmx_fio_do_int(fio, iparams->disres.type);
2016 gmx_fio_do_real(fio, iparams->disres.low);
2017 gmx_fio_do_real(fio, iparams->disres.up1);
2018 gmx_fio_do_real(fio, iparams->disres.up2);
2019 gmx_fio_do_real(fio, iparams->disres.kfac);
2020 break;
2021 case F_ORIRES:
2022 gmx_fio_do_int(fio, iparams->orires.ex);
2023 gmx_fio_do_int(fio, iparams->orires.label);
2024 gmx_fio_do_int(fio, iparams->orires.power);
2025 gmx_fio_do_real(fio, iparams->orires.c);
2026 gmx_fio_do_real(fio, iparams->orires.obs);
2027 gmx_fio_do_real(fio, iparams->orires.kfac);
2028 break;
2029 case F_DIHRES:
2030 if (file_version < 82)
2031 {
2032 gmx_fio_do_int(fio, idum);
2033 gmx_fio_do_int(fio, idum);
2034 }
2035 gmx_fio_do_real(fio, iparams->dihres.phiA);
2036 gmx_fio_do_real(fio, iparams->dihres.dphiA);
2037 gmx_fio_do_real(fio, iparams->dihres.kfacA);
2038 if (file_version >= 82)
2039 {
2040 gmx_fio_do_real(fio, iparams->dihres.phiB);
2041 gmx_fio_do_real(fio, iparams->dihres.dphiB);
2042 gmx_fio_do_real(fio, iparams->dihres.kfacB);
2043 }
2044 else
2045 {
2046 iparams->dihres.phiB = iparams->dihres.phiA;
2047 iparams->dihres.dphiB = iparams->dihres.dphiA;
2048 iparams->dihres.kfacB = iparams->dihres.kfacA;
2049 }
2050 break;
2051 case F_POSRES:
2052 gmx_fio_do_rvec(fio, iparams->posres.pos0A);
2053 gmx_fio_do_rvec(fio, iparams->posres.fcA);
2054 if (bRead && file_version < 27)
2055 {
2056 copy_rvec(iparams->posres.pos0A, iparams->posres.pos0B);
2057 copy_rvec(iparams->posres.fcA, iparams->posres.fcB);
2058 }
2059 else
2060 {
2061 gmx_fio_do_rvec(fio, iparams->posres.pos0B);
2062 gmx_fio_do_rvec(fio, iparams->posres.fcB);
2063 }
2064 break;
2065 case F_FBPOSRES:
2066 gmx_fio_do_int(fio, iparams->fbposres.geom);
2067 gmx_fio_do_rvec(fio, iparams->fbposres.pos0);
2068 gmx_fio_do_real(fio, iparams->fbposres.r);
2069 gmx_fio_do_real(fio, iparams->fbposres.k);
2070 break;
2071 case F_CBTDIHS:
2072 gmx_fio_ndo_real(fio, iparams->cbtdihs.cbtcA, NR_CBTDIHS);
2073 break;
2074 case F_RBDIHS:
2075 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
2076 if (file_version >= 25)
2077 {
2078 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
2079 }
2080 break;
2081 case F_FOURDIHS:
2082 /* Fourier dihedrals are internally represented
2083 * as Ryckaert-Bellemans since those are faster to compute.
2084 */
2085 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
2086 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
2087 break;
2088 case F_CONSTR:
2089 case F_CONSTRNC:
2090 gmx_fio_do_real(fio, iparams->constr.dA);
2091 gmx_fio_do_real(fio, iparams->constr.dB);
2092 break;
2093 case F_SETTLE:
2094 gmx_fio_do_real(fio, iparams->settle.doh);
2095 gmx_fio_do_real(fio, iparams->settle.dhh);
2096 break;
2097 case F_VSITE2:
2098 gmx_fio_do_real(fio, iparams->vsite.a);
2099 break;
2100 case F_VSITE3:
2101 case F_VSITE3FD:
2102 case F_VSITE3FAD:
2103 gmx_fio_do_real(fio, iparams->vsite.a);
2104 gmx_fio_do_real(fio, iparams->vsite.b);
2105 break;
2106 case F_VSITE3OUT:
2107 case F_VSITE4FD:
2108 case F_VSITE4FDN:
2109 gmx_fio_do_real(fio, iparams->vsite.a);
2110 gmx_fio_do_real(fio, iparams->vsite.b);
2111 gmx_fio_do_real(fio, iparams->vsite.c);
2112 break;
2113 case F_VSITEN:
2114 gmx_fio_do_int(fio, iparams->vsiten.n);
2115 gmx_fio_do_real(fio, iparams->vsiten.a);
2116 break;
2117 case F_GB12:
2118 case F_GB13:
2119 case F_GB14:
2120 /* We got rid of some parameters in version 68 */
2121 if (bRead && file_version < 68)
2122 {
2123 gmx_fio_do_real(fio, rdum);
2124 gmx_fio_do_real(fio, rdum);
2125 gmx_fio_do_real(fio, rdum);
2126 gmx_fio_do_real(fio, rdum);
2127 }
2128 gmx_fio_do_real(fio, iparams->gb.sar);
2129 gmx_fio_do_real(fio, iparams->gb.st);
2130 gmx_fio_do_real(fio, iparams->gb.pi);
2131 gmx_fio_do_real(fio, iparams->gb.gbr);
2132 gmx_fio_do_real(fio, iparams->gb.bmlt);
2133 break;
2134 case F_CMAP:
2135 gmx_fio_do_int(fio, iparams->cmap.cmapA);
2136 gmx_fio_do_int(fio, iparams->cmap.cmapB);
2137 break;
2138 default:
2139 gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
2140 ftype, interaction_function[ftype].name, __FILE__, __LINE__);
2141 }
2142 if (!bRead)
2143 {
2144 gmx_fio_unset_comment(fio);
2145 }
2146 }
2147
2148 static void do_ilist(t_fileio *fio, t_ilist *ilist, gmx_bool bRead, int file_version,
2149 int ftype)
2150 {
2151 int i, k, idum;
2152
2153 if (!bRead)
2154 {
2155 gmx_fio_set_comment(fio, interaction_function[ftype].name);
2156 }
2157 if (file_version < 44)
2158 {
2159 for (i = 0; i < MAXNODES; i++)
2160 {
2161 gmx_fio_do_int(fio, idum);
2162 }
2163 }
2164 gmx_fio_do_int(fio, ilist->nr);
2165 if (bRead)
2166 {
2167 snew(ilist->iatoms, ilist->nr);
2168 }
2169 gmx_fio_ndo_int(fio, ilist->iatoms, ilist->nr);
2170 if (!bRead)
2171 {
2172 gmx_fio_unset_comment(fio);
2173 }
2174 }
2175
2176 static void do_ffparams(t_fileio *fio, gmx_ffparams_t *ffparams,
2177 gmx_bool bRead, int file_version)
2178 {
2179 int idum, i, j;
2180 unsigned int k;
2181
2182 gmx_fio_do_int(fio, ffparams->atnr);
2183 if (file_version < 57)
2184 {
2185 gmx_fio_do_int(fio, idum);
2186 }
2187 gmx_fio_do_int(fio, ffparams->ntypes);
2188 if (bRead && debug)
2189 {
2190 fprintf(debug, "ffparams->atnr = %d, ntypes = %d\n",
2191 ffparams->atnr, ffparams->ntypes);
2192 }
2193 if (bRead)
2194 {
2195 snew(ffparams->functype, ffparams->ntypes);
2196 snew(ffparams->iparams, ffparams->ntypes);
2197 }
2198 /* Read/write all the function types */
2199 gmx_fio_ndo_int(fio, ffparams->functype, ffparams->ntypes);
2200 if (bRead && debug)
2201 {
2202 pr_ivec(debug, 0, "functype", ffparams->functype, ffparams->ntypes, TRUE);
2203 }
2204
2205 if (file_version >= 66)
2206 {
2207 gmx_fio_do_double(fio, ffparams->reppow);
2208 }
2209 else
2210 {
2211 ffparams->reppow = 12.0;
2212 }
2213
2214 if (file_version >= 57)
2215 {
2216 gmx_fio_do_real(fio, ffparams->fudgeQQ);
2217 }
2218
2219 /* Check whether all these function types are supported by the code.
2220 * In practice the code is backwards compatible, which means that the
2221 * numbering may have to be altered from old numbering to new numbering
2222 */
2223 for (i = 0; (i < ffparams->ntypes); i++)
2224 {
2225 if (bRead)
2226 {
2227 /* Loop over file versions */
2228 for (k = 0; (k < NFTUPD); k++)
2229 {
2230 /* Compare the read file_version to the update table */
2231 if ((file_version < ftupd[k].fvnr) &&
2232 (ffparams->functype[i] >= ftupd[k].ftype))
2233 {
2234 ffparams->functype[i] += 1;
2235 if (debug)
2236 {
2237 fprintf(debug, "Incrementing function type %d to %d (due to %s)\n",
2238 i, ffparams->functype[i],
2239 interaction_function[ftupd[k].ftype].longname);
2240 fflush(debug);
2241 }
2242 }
2243 }
2244 }
2245
2246 do_iparams(fio, ffparams->functype[i], &ffparams->iparams[i], bRead,
2247 file_version);
2248 if (bRead && debug)
2249 {
2250 pr_iparams(debug, ffparams->functype[i], &ffparams->iparams[i]);
2251 }
2252 }
2253 }
2254
2255 static void add_settle_atoms(t_ilist *ilist)
2256 {
2257 int i;
2258
2259 /* Settle used to only store the first atom: add the other two */
2260 srenew(ilist->iatoms, 2*ilist->nr);
2261 for (i = ilist->nr/2-1; i >= 0; i--)
2262 {
2263 ilist->iatoms[4*i+0] = ilist->iatoms[2*i+0];
2264 ilist->iatoms[4*i+1] = ilist->iatoms[2*i+1];
2265 ilist->iatoms[4*i+2] = ilist->iatoms[2*i+1] + 1;
2266 ilist->iatoms[4*i+3] = ilist->iatoms[2*i+1] + 2;
2267 }
2268 ilist->nr = 2*ilist->nr;
2269 }
2270
2271 static void do_ilists(t_fileio *fio, t_ilist *ilist, gmx_bool bRead,
2272 int file_version)
2273 {
2274 int i, j, renum[F_NRE];
2275 gmx_bool bClear;
2276 unsigned int k;
2277
2278 for (j = 0; (j < F_NRE); j++)
2279 {
2280 bClear = FALSE;
2281 if (bRead)
2282 {
2283 for (k = 0; k < NFTUPD; k++)
2284 {
2285 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
2286 {
2287 bClear = TRUE;
2288 }
2289 }
2290 }
2291 if (bClear)
2292 {
2293 ilist[j].nr = 0;
2294 ilist[j].iatoms = NULL;
2295 }
2296 else
2297 {
2298 do_ilist(fio, &ilist[j], bRead, file_version, j);
2299 if (file_version < 78 && j == F_SETTLE && ilist[j].nr > 0)
2300 {
2301 add_settle_atoms(&ilist[j]);
2302 }
2303 }
2304 /*
2305 if (bRead && gmx_debug_at)
2306 pr_ilist(debug,0,interaction_function[j].longname,
2307 functype,&ilist[j],TRUE);
2308 */
2309 }
2310 }
2311
2312 static void do_idef(t_fileio *fio, gmx_ffparams_t *ffparams, gmx_moltype_t *molt,
2313 gmx_bool bRead, int file_version)
2314 {
2315 do_ffparams(fio, ffparams, bRead, file_version);
2316
2317 if (file_version >= 54)
2318 {
2319 gmx_fio_do_real(fio, ffparams->fudgeQQ);
2320 }
2321
2322 do_ilists(fio, molt->ilist, bRead, file_version);
2323 }
2324
2325 static void do_block(t_fileio *fio, t_block *block, gmx_bool bRead, int file_version)
2326 {
2327 int i, idum, dum_nra, *dum_a;
2328
2329 if (file_version < 44)
2330 {
2331 for (i = 0; i < MAXNODES; i++)
2332 {
2333 gmx_fio_do_int(fio, idum);
2334 }
2335 }
2336 gmx_fio_do_int(fio, block->nr);
2337 if (file_version < 51)
2338 {
2339 gmx_fio_do_int(fio, dum_nra);
2340 }
2341 if (bRead)
2342 {
2343 if ((block->nalloc_index > 0) && (NULL != block->index))
2344 {
2345 sfree(block->index);
2346 }
2347 block->nalloc_index = block->nr+1;
2348 snew(block->index, block->nalloc_index);
2349 }
2350 gmx_fio_ndo_int(fio, block->index, block->nr+1);
2351
2352 if (file_version < 51 && dum_nra > 0)
2353 {
2354 snew(dum_a, dum_nra);
2355 gmx_fio_ndo_int(fio, dum_a, dum_nra);
2356 sfree(dum_a);
2357 }
2358 }
2359
2360 static void do_blocka(t_fileio *fio, t_blocka *block, gmx_bool bRead,
2361 int file_version)
2362 {
2363 int i, idum;
2364
2365 if (file_version < 44)
2366 {
2367 for (i = 0; i < MAXNODES; i++)
2368 {
2369 gmx_fio_do_int(fio, idum);
2370 }
2371 }
2372 gmx_fio_do_int(fio, block->nr);
2373 gmx_fio_do_int(fio, block->nra);
2374 if (bRead)
2375 {
2376 block->nalloc_index = block->nr+1;
2377 snew(block->index, block->nalloc_index);
2378 block->nalloc_a = block->nra;
2379 snew(block->a, block->nalloc_a);
2380 }
2381 gmx_fio_ndo_int(fio, block->index, block->nr+1);
2382 gmx_fio_ndo_int(fio, block->a, block->nra);
2383 }
2384
2385 /* This is a primitive routine to make it possible to translate atomic numbers
2386 * to element names when reading TPR files, without making the Gromacs library
2387 * directory a dependency on mdrun (which is the case if we need elements.dat).
2388 */
2389 static const char *
2390 atomicnumber_to_element(int atomicnumber)
2391 {
2392 const char * p;
2393
2394 /* This does not have to be complete, so we only include elements likely
2395 * to occur in PDB files.
2396 */
2397 switch (atomicnumber)
2398 {
2399 case 1: p = "H"; break;
2400 case 5: p = "B"; break;
2401 case 6: p = "C"; break;
2402 case 7: p = "N"; break;
2403 case 8: p = "O"; break;
2404 case 9: p = "F"; break;
2405 case 11: p = "Na"; break;
2406 case 12: p = "Mg"; break;
2407 case 15: p = "P"; break;
2408 case 16: p = "S"; break;
2409 case 17: p = "Cl"; break;
2410 case 18: p = "Ar"; break;
2411 case 19: p = "K"; break;
2412 case 20: p = "Ca"; break;
2413 case 25: p = "Mn"; break;
2414 case 26: p = "Fe"; break;
2415 case 28: p = "Ni"; break;
2416 case 29: p = "Cu"; break;
2417 case 30: p = "Zn"; break;
2418 case 35: p = "Br"; break;
2419 case 47: p = "Ag"; break;
2420 default: p = ""; break;
2421 }
2422 return p;
2423 }
2424
2425
2426 static void do_atom(t_fileio *fio, t_atom *atom, int ngrp, gmx_bool bRead,
2427 int file_version, gmx_groups_t *groups, int atnr)
2428 {
2429 int i, myngrp;
2430 char * p_elem;
2431
2432 gmx_fio_do_real(fio, atom->m);
2433 gmx_fio_do_real(fio, atom->q);
2434 gmx_fio_do_real(fio, atom->mB);
2435 gmx_fio_do_real(fio, atom->qB);
2436 gmx_fio_do_ushort(fio, atom->type);
2437 gmx_fio_do_ushort(fio, atom->typeB);
2438 gmx_fio_do_int(fio, atom->ptype);
2439 gmx_fio_do_int(fio, atom->resind);
2440 if (file_version >= 52)
2441 {
2442 gmx_fio_do_int(fio, atom->atomnumber);
2443 if (bRead)
2444 {
2445 /* Set element string from atomic number if present.
2446 * This routine returns an empty string if the name is not found.
2447 */
2448 strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
2449 /* avoid warnings about potentially unterminated string */
2450 atom->elem[3] = '\0';
2451 }
2452 }
2453 else if (bRead)
2454 {
2455 atom->atomnumber = NOTSET;
2456 }
2457 if (file_version < 23)
2458 {
2459 myngrp = 8;
2460 }
2461 else if (file_version < 39)
2462 {
2463 myngrp = 9;
2464 }
2465 else
2466 {
2467 myngrp = ngrp;
2468 }
2469
2470 if (file_version < 57)
2471 {
2472 unsigned char uchar[egcNR];
2473 gmx_fio_ndo_uchar(fio, uchar, myngrp);
2474 for (i = myngrp; (i < ngrp); i++)
2475 {
2476 uchar[i] = 0;
2477 }
2478 /* Copy the old data format to the groups struct */
2479 for (i = 0; i < ngrp; i++)
2480 {
2481 groups->grpnr[i][atnr] = uchar[i];
2482 }
2483 }
2484 }
2485
2486 static void do_grps(t_fileio *fio, int ngrp, t_grps grps[], gmx_bool bRead,
2487 int file_version)
2488 {
2489 int i, j, myngrp;
2490
2491 if (file_version < 23)
2492 {
2493 myngrp = 8;
2494 }
2495 else if (file_version < 39)
2496 {
2497 myngrp = 9;
2498 }
2499 else
2500 {
2501 myngrp = ngrp;
2502 }
2503
2504 for (j = 0; (j < ngrp); j++)
2505 {
2506 if (j < myngrp)
2507 {
2508 gmx_fio_do_int(fio, grps[j].nr);
2509 if (bRead)
2510 {
2511 snew(grps[j].nm_ind, grps[j].nr);
2512 }
2513 gmx_fio_ndo_int(fio, grps[j].nm_ind, grps[j].nr);
2514 }
2515 else
2516 {
2517 grps[j].nr = 1;
2518 snew(grps[j].nm_ind, grps[j].nr);
2519 }
2520 }
2521 }
2522
2523 static void do_symstr(t_fileio *fio, char ***nm, gmx_bool bRead, t_symtab *symtab)
2524 {
2525 int ls;
2526
2527 if (bRead)
2528 {
2529 gmx_fio_do_int(fio, ls);
2530 *nm = get_symtab_handle(symtab, ls);
2531 }
2532 else
2533 {
2534 ls = lookup_symtab(symtab, *nm);
2535 gmx_fio_do_int(fio, ls);
2536 }
2537 }
2538
2539 static void do_strstr(t_fileio *fio, int nstr, char ***nm, gmx_bool bRead,
2540 t_symtab *symtab)
2541 {
2542 int j;
2543
2544 for (j = 0; (j < nstr); j++)
2545 {
2546 do_symstr(fio, &(nm[j]), bRead, symtab);
2547 }
2548 }
2549
2550 static void do_resinfo(t_fileio *fio, int n, t_resinfo *ri, gmx_bool bRead,
2551 t_symtab *symtab, int file_version)
2552 {
2553 int j;
2554
2555 for (j = 0; (j < n); j++)
2556 {
2557 do_symstr(fio, &(ri[j].name), bRead, symtab);
2558 if (file_version >= 63)
2559 {
2560 gmx_fio_do_int(fio, ri[j].nr);
2561 gmx_fio_do_uchar(fio, ri[j].ic);
2562 }
2563 else
2564 {
2565 ri[j].nr = j + 1;
2566 ri[j].ic = ' ';
2567 }
2568 }
2569 }
2570
2571 static void do_atoms(t_fileio *fio, t_atoms *atoms, gmx_bool bRead, t_symtab *symtab,
2572 int file_version,
2573 gmx_groups_t *groups)
2574 {
2575 int i;
2576
2577 gmx_fio_do_int(fio, atoms->nr);
2578 gmx_fio_do_int(fio, atoms->nres);
2579 if (file_version < 57)
2580 {
2581 gmx_fio_do_int(fio, groups->ngrpname);
2582 for (i = 0; i < egcNR; i++)
2583 {
2584 groups->ngrpnr[i] = atoms->nr;
2585 snew(groups->grpnr[i], groups->ngrpnr[i]);
2586 }
2587 }
2588 if (bRead)
2589 {
2590 snew(atoms->atom, atoms->nr);
2591 snew(atoms->atomname, atoms->nr);
2592 snew(atoms->atomtype, atoms->nr);
2593 snew(atoms->atomtypeB, atoms->nr);
2594 snew(atoms->resinfo, atoms->nres);
2595 if (file_version < 57)
2596 {
2597 snew(groups->grpname, groups->ngrpname);
2598 }
2599 atoms->pdbinfo = NULL;
2600 }
2601 for (i = 0; (i < atoms->nr); i++)
2602 {
2603 do_atom(fio, &atoms->atom[i], egcNR, bRead, file_version, groups, i);
2604 }
2605 do_strstr(fio, atoms->nr, atoms->atomname, bRead, symtab);
2606 if (bRead && (file_version <= 20))
2607 {
2608 for (i = 0; i < atoms->nr; i++)
2609 {
2610 atoms->atomtype[i] = put_symtab(symtab, "?");
2611 atoms->atomtypeB[i] = put_symtab(symtab, "?");
2612 }
2613 }
2614 else
2615 {
2616 do_strstr(fio, atoms->nr, atoms->atomtype, bRead, symtab);
2617 do_strstr(fio, atoms->nr, atoms->atomtypeB, bRead, symtab);
2618 }
2619 do_resinfo(fio, atoms->nres, atoms->resinfo, bRead, symtab, file_version);
2620
2621 if (file_version < 57)
2622 {
2623 do_strstr(fio, groups->ngrpname, groups->grpname, bRead, symtab);
2624
2625 do_grps(fio, egcNR, groups->grps, bRead, file_version);
2626 }
2627 }
2628
2629 static void do_groups(t_fileio *fio, gmx_groups_t *groups,
2630 gmx_bool bRead, t_symtab *symtab,
2631 int file_version)
2632 {
2633 int g, n, i;
2634
2635 do_grps(fio, egcNR, groups->grps, bRead, file_version);
2636 gmx_fio_do_int(fio, groups->ngrpname);
2637 if (bRead)
2638 {
2639 snew(groups->grpname, groups->ngrpname);
2640 }
2641 do_strstr(fio, groups->ngrpname, groups->grpname, bRead, symtab);
2642 for (g = 0; g < egcNR; g++)
2643 {
2644 gmx_fio_do_int(fio, groups->ngrpnr[g]);
2645 if (groups->ngrpnr[g] == 0)
2646 {
2647 if (bRead)
2648 {
2649 groups->grpnr[g] = NULL;
2650 }
2651 }
2652 else
2653 {
2654 if (bRead)
2655 {
2656 snew(groups->grpnr[g], groups->ngrpnr[g]);
2657 }
2658 gmx_fio_ndo_uchar(fio, groups->grpnr[g], groups->ngrpnr[g]);
2659 }
2660 }
2661 }
2662
2663 static void do_atomtypes(t_fileio *fio, t_atomtypes *atomtypes, gmx_bool bRead,
2664 int file_version)
2665 {
2666 int i, j;
2667
2668 if (file_version > 25)
2669 {
2670 gmx_fio_do_int(fio, atomtypes->nr);
2671 j = atomtypes->nr;
2672 if (bRead)
2673 {
2674 snew(atomtypes->radius, j);
2675 snew(atomtypes->vol, j);
2676 snew(atomtypes->surftens, j);
2677 snew(atomtypes->atomnumber, j);
2678 snew(atomtypes->gb_radius, j);
2679 snew(atomtypes->S_hct, j);
2680 }
2681 gmx_fio_ndo_real(fio, atomtypes->radius, j);
2682 gmx_fio_ndo_real(fio, atomtypes->vol, j);
2683 gmx_fio_ndo_real(fio, atomtypes->surftens, j);
2684 if (file_version >= 40)
2685 {
2686 gmx_fio_ndo_int(fio, atomtypes->atomnumber, j);
2687 }
2688 if (file_version >= 60)
2689 {
2690 gmx_fio_ndo_real(fio, atomtypes->gb_radius, j);
2691 gmx_fio_ndo_real(fio, atomtypes->S_hct, j);
2692 }
2693 }
2694 else
2695 {
2696 /* File versions prior to 26 cannot do GBSA,
2697 * so they dont use this structure
2698 */
2699 atomtypes->nr = 0;
2700 atomtypes->radius = NULL;
2701 atomtypes->vol = NULL;
2702 atomtypes->surftens = NULL;
2703 atomtypes->atomnumber = NULL;
2704 atomtypes->gb_radius = NULL;
2705 atomtypes->S_hct = NULL;
2706 }
2707 }
2708
2709 static void do_symtab(t_fileio *fio, t_symtab *symtab, gmx_bool bRead)
2710 {
2711 int i, nr;
2712 t_symbuf *symbuf;
2713 char buf[STRLEN];
2714
2715 gmx_fio_do_int(fio, symtab->nr);
2716 nr = symtab->nr;
2717 if (bRead)
2718 {
2719 snew(symtab->symbuf, 1);
2720 symbuf = symtab->symbuf;
2721 symbuf->bufsize = nr;
2722 snew(symbuf->buf, nr);
2723 for (i = 0; (i < nr); i++)
2724 {
2725 gmx_fio_do_string(fio, buf);
2726 symbuf->buf[i] = strdup(buf);
2727 }
2728 }
2729 else
2730 {
2731 symbuf = symtab->symbuf;
2732 while (symbuf != NULL)
2733 {
2734 for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
2735 {
2736 gmx_fio_do_string(fio, symbuf->buf[i]);
2737 }
2738 nr -= i;
2739 symbuf = symbuf->next;
2740 }
2741 if (nr != 0)
2742 {
2743 gmx_fatal(FARGS, "nr of symtab strings left: %d", nr);
2744 }
2745 }
2746 }
2747
2748 static void do_cmap(t_fileio *fio, gmx_cmap_t *cmap_grid, gmx_bool bRead)
2749 {
2750 int i, j, ngrid, gs, nelem;
2751
2752 gmx_fio_do_int(fio, cmap_grid->ngrid);
2753 gmx_fio_do_int(fio, cmap_grid->grid_spacing);
2754
2755 ngrid = cmap_grid->ngrid;
2756 gs = cmap_grid->grid_spacing;
2757 nelem = gs * gs;
2758
2759 if (bRead)
2760 {
2761 snew(cmap_grid->cmapdata, ngrid);
2762
2763 for (i = 0; i < cmap_grid->ngrid; i++)
2764 {
2765 snew(cmap_grid->cmapdata[i].cmap, 4*nelem);
2766 }
2767 }
2768
2769 for (i = 0; i < cmap_grid->ngrid; i++)
2770 {
2771 for (j = 0; j < nelem; j++)
2772 {
2773 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4]);
2774 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+1]);
2775 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+2]);
2776 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+3]);
2777 }
2778 }
2779 }
2780
2781
2782 void tpx_make_chain_identifiers(t_atoms *atoms, t_block *mols)
2783 {
2784 int m, a, a0, a1, r;
2785 char c, chainid;
2786 int chainnum;
2787
2788 /* We always assign a new chain number, but save the chain id characters
2789 * for larger molecules.
2790 */
2791 #define CHAIN_MIN_ATOMS 15
2792
2793 chainnum = 0;
2794 chainid = 'A';
2795 for (m = 0; m < mols->nr; m++)
2796 {
2797 a0 = mols->index[m];
2798 a1 = mols->index[m+1];
2799 if ((a1-a0 >= CHAIN_MIN_ATOMS) && (chainid <= 'Z'))
2800 {
2801 c = chainid;
2802 chainid++;
2803 }
2804 else
2805 {
2806 c = ' ';
2807 }
2808 for (a = a0; a < a1; a++)
2809 {
2810 atoms->resinfo[atoms->atom[a].resind].chainnum = chainnum;
2811 atoms->resinfo[atoms->atom[a].resind].chainid = c;
2812 }
2813 chainnum++;
2814 }
2815
2816 /* Blank out the chain id if there was only one chain */
2817 if (chainid == 'B')
2818 {
2819 for (r = 0; r < atoms->nres; r++)
2820 {
2821 atoms->resinfo[r].chainid = ' ';
2822 }
2823 }
2824 }
2825
2826 static void do_moltype(t_fileio *fio, gmx_moltype_t *molt, gmx_bool bRead,
2827 t_symtab *symtab, int file_version,
2828 gmx_groups_t *groups)
2829 {
2830 int i;
2831
2832 if (file_version >= 57)
2833 {
2834 do_symstr(fio, &(molt->name), bRead, symtab);
2835 }
2836
2837 do_atoms(fio, &molt->atoms, bRead, symtab, file_version, groups);
2838
2839 if (bRead && gmx_debug_at)
2840 {
2841 pr_atoms(debug, 0, "atoms", &molt->atoms, TRUE);
2842 }
2843
2844 if (file_version >= 57)
2845 {
2846 do_ilists(fio, molt->ilist, bRead, file_version);
2847
2848 do_block(fio, &molt->cgs, bRead, file_version);
2849 if (bRead && gmx_debug_at)
2850 {
2851 pr_block(debug, 0, "cgs", &molt->cgs, TRUE);
2852 }
2853 }
2854
2855 /* This used to be in the atoms struct */
2856 do_blocka(fio, &molt->excls, bRead, file_version);
2857 }
2858
2859 static void do_molblock(t_fileio *fio, gmx_molblock_t *molb, gmx_bool bRead)
2860 {
2861 int i;
2862
2863 gmx_fio_do_int(fio, molb->type);
2864 gmx_fio_do_int(fio, molb->nmol);
2865 gmx_fio_do_int(fio, molb->natoms_mol);
2866 /* Position restraint coordinates */
2867 gmx_fio_do_int(fio, molb->nposres_xA);
2868 if (molb->nposres_xA > 0)
2869 {
2870 if (bRead)
2871 {
2872 snew(molb->posres_xA, molb->nposres_xA);
2873 }
2874 gmx_fio_ndo_rvec(fio, molb->posres_xA, molb->nposres_xA);
2875 }
2876 gmx_fio_do_int(fio, molb->nposres_xB);
2877 if (molb->nposres_xB > 0)
2878 {
2879 if (bRead)
2880 {
2881 snew(molb->posres_xB, molb->nposres_xB);
2882 }
2883 gmx_fio_ndo_rvec(fio, molb->posres_xB, molb->nposres_xB);
2884 }
2885
2886 }
2887
2888 static t_block mtop_mols(gmx_mtop_t *mtop)
2889 {
2890 int mb, m, a, mol;
2891 t_block mols;
2892
2893 mols.nr = 0;
2894 for (mb = 0; mb < mtop->nmolblock; mb++)
2895 {
2896 mols.nr += mtop->molblock[mb].nmol;
2897 }
2898 mols.nalloc_index = mols.nr + 1;
2899 snew(mols.index, mols.nalloc_index);
2900
2901 a = 0;
2902 m = 0;
2903 mols.index[m] = a;
2904 for (mb = 0; mb < mtop->nmolblock; mb++)
2905 {
2906 for (mol = 0; mol < mtop->molblock[mb].nmol; mol++)
2907 {
2908 a += mtop->molblock[mb].natoms_mol;
2909 m++;
2910 mols.index[m] = a;
2911 }
2912 }
2913
2914 return mols;
2915 }
2916
2917 static void add_posres_molblock(gmx_mtop_t *mtop)
2918 {
2919 t_ilist *il, *ilfb;
2920 int am, i, mol, a;
2921 gmx_bool bFE;
2922 gmx_molblock_t *molb;
2923 t_iparams *ip;
2924
2925 /* posres reference positions are stored in ip->posres (if present) and
2926 in ip->fbposres (if present). If normal and flat-bottomed posres are present,
2927 posres.pos0A are identical to fbposres.pos0. */
2928 il = &mtop->moltype[0].ilist[F_POSRES];
2929 ilfb = &mtop->moltype[0].ilist[F_FBPOSRES];
2930 if (il->nr == 0 && ilfb->nr == 0)
2931 {
2932 return;
2933 }
2934 am = 0;
2935 bFE = FALSE;
2936 for (i = 0; i < il->nr; i += 2)
2937 {
2938 ip = &mtop->ffparams.iparams[il->iatoms[i]];
2939 am = max(am, il->iatoms[i+1]);
2940 if (ip->posres.pos0B[XX] != ip->posres.pos0A[XX] ||
2941 ip->posres.pos0B[YY] != ip->posres.pos0A[YY] ||
2942 ip->posres.pos0B[ZZ] != ip->posres.pos0A[ZZ])
2943 {
2944 bFE = TRUE;
2945 }
2946 }
2947 /* This loop is required if we have only flat-bottomed posres:
2948 - set am
2949 - bFE == FALSE (no B-state for flat-bottomed posres) */
2950 if (il->nr == 0)
2951 {
2952 for (i = 0; i < ilfb->nr; i += 2)
2953 {
2954 ip = &mtop->ffparams.iparams[ilfb->iatoms[i]];
2955 am = max(am, ilfb->iatoms[i+1]);
2956 }
2957 }
2958 /* Make the posres coordinate block end at a molecule end */
2959 mol = 0;
2960 while (am >= mtop->mols.index[mol+1])
2961 {
2962 mol++;
2963 }
2964 molb = &mtop->molblock[0];
2965 molb->nposres_xA = mtop->mols.index[mol+1];
2966 snew(molb->posres_xA, molb->nposres_xA);
2967 if (bFE)
2968 {
2969 molb->nposres_xB = molb->nposres_xA;
2970 snew(molb->posres_xB, molb->nposres_xB);
2971 }
2972 else
2973 {
2974 molb->nposres_xB = 0;
2975 }
2976 for (i = 0; i < il->nr; i += 2)
2977 {
2978 ip = &mtop->ffparams.iparams[il->iatoms[i]];
2979 a = il->iatoms[i+1];
2980 molb->posres_xA[a][XX] = ip->posres.pos0A[XX];
2981 molb->posres_xA[a][YY] = ip->posres.pos0A[YY];
2982 molb->posres_xA[a][ZZ] = ip->posres.pos0A[ZZ];
2983 if (bFE)
2984 {
2985 molb->posres_xB[a][XX] = ip->posres.pos0B[XX];
2986 molb->posres_xB[a][YY] = ip->posres.pos0B[YY];
2987 molb->posres_xB[a][ZZ] = ip->posres.pos0B[ZZ];
2988 }
2989 }
2990 if (il->nr == 0)
2991 {
2992 /* If only flat-bottomed posres are present, take reference pos from them.
2993 Here: bFE == FALSE */
2994 for (i = 0; i < ilfb->nr; i += 2)
2995 {
2996 ip = &mtop->ffparams.iparams[ilfb->iatoms[i]];
2997 a = ilfb->iatoms[i+1];
2998 molb->posres_xA[a][XX] = ip->fbposres.pos0[XX];
2999 molb->posres_xA[a][YY] = ip->fbposres.pos0[YY];
3000 molb->posres_xA[a][ZZ] = ip->fbposres.pos0[ZZ];
3001 }
3002 }
3003 }
3004
3005 static void set_disres_npair(gmx_mtop_t *mtop)
3006 {
3007 int mt, i, npair;
3008 t_iparams *ip;
3009 t_ilist *il;
3010 t_iatom *a;
3011
3012 ip = mtop->ffparams.iparams;
3013
3014 for (mt = 0; mt < mtop->nmoltype; mt++)
3015 {
3016 il = &mtop->moltype[mt].ilist[F_DISRES];
3017 if (il->nr > 0)
3018 {
3019 a = il->iatoms;
3020 npair = 0;
3021 for (i = 0; i < il->nr; i += 3)
3022 {
3023 npair++;
3024 if (i+3 == il->nr || ip[a[i]].disres.label != ip[a[i+3]].disres.label)
3025 {
3026 ip[a[i]].disres.npair = npair;
3027 npair = 0;
3028 }
3029 }
3030 }
3031 }
3032 }
3033
3034 static void do_mtop(t_fileio *fio, gmx_mtop_t *mtop, gmx_bool bRead,
3035 int file_version)
3036 {
3037 int mt, mb, i;
3038 t_blocka dumb;
3039
3040 if (bRead)
3041 {
3042 init_mtop(mtop);
3043 }
3044 do_symtab(fio, &(mtop->symtab), bRead);
3045 if (bRead && debug)
3046 {
3047 pr_symtab(debug, 0, "symtab", &mtop->symtab);
3048 }
3049
3050 do_symstr(fio, &(mtop->name), bRead, &(mtop->symtab));
3051
3052 if (file_version >= 57)
3053 {
3054 do_ffparams(fio, &mtop->ffparams, bRead, file_version);
3055
3056 gmx_fio_do_int(fio, mtop->nmoltype);
3057 }
3058 else
3059 {
3060 mtop->nmoltype = 1;
3061 }
3062 if (bRead)
3063 {
3064 snew(mtop->moltype, mtop->nmoltype);
3065 if (file_version < 57)
3066 {
3067 mtop->moltype[0].name = mtop->name;
3068 }
3069 }
3070 for (mt = 0; mt < mtop->nmoltype; mt++)
3071 {
3072 do_moltype(fio, &mtop->moltype[mt], bRead, &mtop->symtab, file_version,
3073 &mtop->groups);
3074 }
3075
3076 if (file_version >= 57)
3077 {
3078 gmx_fio_do_int(fio, mtop->nmolblock);
3079 }
3080 else
3081 {
3082 mtop->nmolblock = 1;
3083 }
3084 if (bRead)
3085 {
3086 snew(mtop->molblock, mtop->nmolblock);
3087 }
3088 if (file_version >= 57)
3089 {
3090 for (mb = 0; mb < mtop->nmolblock; mb++)
3091 {
3092 do_molblock(fio, &mtop->molblock[mb], bRead);
3093 }
3094 gmx_fio_do_int(fio, mtop->natoms);
3095 }
3096 else
3097 {
3098 mtop->molblock[0].type = 0;
3099 mtop->molblock[0].nmol = 1;
3100 mtop->molblock[0].natoms_mol = mtop->moltype[0].atoms.nr;
3101 mtop->molblock[0].nposres_xA = 0;
3102 mtop->molblock[0].nposres_xB = 0;
3103 }
3104
3105 do_atomtypes (fio, &(mtop->atomtypes), bRead, file_version);
3106 if (bRead && debug)
3107 {
3108 pr_atomtypes(debug, 0, "atomtypes", &mtop->atomtypes, TRUE);
3109 }
3110
3111 if (file_version < 57)
3112 {
3113 /* Debug statements are inside do_idef */
3114 do_idef (fio, &mtop->ffparams, &mtop->moltype[0], bRead, file_version);
3115 mtop->natoms = mtop->moltype[0].atoms.nr;
3116 }
3117
3118 if (file_version >= 65)
3119 {
3120 do_cmap(fio, &mtop->ffparams.cmap_grid, bRead);
3121 }
3122 else
3123 {
3124 mtop->ffparams.cmap_grid.ngrid = 0;
3125 mtop->ffparams.cmap_grid.grid_spacing = 0;
3126 mtop->ffparams.cmap_grid.cmapdata = NULL;
3127 }
3128
3129 if (file_version >= 57)
3130 {
3131 do_groups(fio, &mtop->groups, bRead, &(mtop->symtab), file_version);
3132 }
3133
3134 if (file_version < 57)
3135 {
3136 do_block(fio, &mtop->moltype[0].cgs, bRead, file_version);
3137 if (bRead && gmx_debug_at)
3138 {
3139 pr_block(debug, 0, "cgs", &mtop->moltype[0].cgs, TRUE);
3140 }
3141 do_block(fio, &mtop->mols, bRead, file_version);
3142 /* Add the posres coordinates to the molblock */
3143 add_posres_molblock(mtop);
3144 }
3145 if (bRead)
3146 {
3147 if (file_version >= 57)
3148 {
3149 done_block(&mtop->mols);
3150 mtop->mols = mtop_mols(mtop);
3151 }
3152 if (gmx_debug_at)
3153 {
3154 pr_block(debug, 0, "mols", &mtop->mols, TRUE);
3155 }
3156 }
3157
3158 if (file_version < 51)
3159 {
3160 /* Here used to be the shake blocks */
3161 do_blocka(fio, &dumb, bRead, file_version);
3162 if (dumb.nr > 0)
3163 {
3164 sfree(dumb.index);
3165 }
3166 if (dumb.nra > 0)
3167 {
3168 sfree(dumb.a);
3169 }
3170 }
3171
3172 if (bRead)
3173 {
3174 close_symtab(&(mtop->symtab));
3175 }
3176 }
3177
3178 /* If TopOnlyOK is TRUE then we can read even future versions
3179 * of tpx files, provided the file_generation hasn't changed.
3180 * If it is FALSE, we need the inputrecord too, and bail out
3181 * if the file is newer than the program.
3182 *
3183 * The version and generation if the topology (see top of this file)
3184 * are returned in the two last arguments.
3185 *
3186 * If possible, we will read the inputrec even when TopOnlyOK is TRUE.
3187 */
3188 static void do_tpxheader(t_fileio *fio, gmx_bool bRead, t_tpxheader *tpx,
3189 gmx_bool TopOnlyOK, int *file_version,
3190 int *file_generation)
3191 {
3192 char buf[STRLEN];
3193 char file_tag[STRLEN];
3194 gmx_bool bDouble;
3195 int precision;
3196 int fver, fgen;
3197 int idum = 0;
3198 real rdum = 0;
3199
3200 gmx_fio_checktype(fio);
3201 gmx_fio_setdebug(fio, bDebugMode());
3202
3203 /* NEW! XDR tpb file */
3204 precision = sizeof(real);
3205 if (bRead)
3206 {
3207 gmx_fio_do_string(fio, buf);
3208 if (strncmp(buf, "VERSION", 7))
3209 {
3210 gmx_fatal(FARGS, "Can not read file %s,\n"
3211 " this file is from a Gromacs version which is older than 2.0\n"
3212 " Make a new one with grompp or use a gro or pdb file, if possible",
3213 gmx_fio_getname(fio));
3214 }
3215 gmx_fio_do_int(fio, precision);
3216 bDouble = (precision == sizeof(double));
3217 if ((precision != sizeof(float)) && !bDouble)
3218 {
3219 gmx_fatal(FARGS, "Unknown precision in file %s: real is %d bytes "
3220 "instead of %d or %d",
3221 gmx_fio_getname(fio), precision, sizeof(float), sizeof(double));
3222 }
3223 gmx_fio_setprecision(fio, bDouble);
3224 fprintf(stderr, "Reading file %s, %s (%s precision)\n",
3225 gmx_fio_getname(fio), buf, bDouble ? "double" : "single");
3226 }
3227 else
3228 {
3229 gmx_fio_write_string(fio, GromacsVersion());
3230 bDouble = (precision == sizeof(double));
3231 gmx_fio_setprecision(fio, bDouble);
3232 gmx_fio_do_int(fio, precision);
3233 fver = tpx_version;
3234 sprintf(file_tag, "%s", tpx_tag);
3235 fgen = tpx_generation;
3236 }
3237
3238 /* Check versions! */
3239 gmx_fio_do_int(fio, fver);
3240
3241 /* This is for backward compatibility with development versions 77-79
3242 * where the tag was, mistakenly, placed before the generation,
3243 * which would cause a segv instead of a proper error message
3244 * when reading the topology only from tpx with <77 code.
3245 */
3246 if (fver >= 77 && fver <= 79)
3247 {
3248 gmx_fio_do_string(fio, file_tag);
3249 }
3250
3251 if (fver >= 26)
3252 {
3253 gmx_fio_do_int(fio, fgen);
3254 }
3255 else
3256 {
3257 fgen = 0;
3258 }
3259
3260 if (fver >= 81)
3261 {
3262 gmx_fio_do_string(fio, file_tag);
3263 }
3264 if (bRead)
3265 {
3266 if (fver < 77)
3267 {
3268 /* Versions before 77 don't have the tag, set it to release */
3269 sprintf(file_tag, "%s", TPX_TAG_RELEASE);
3270 }
3271
3272 if (strcmp(file_tag, tpx_tag) != 0)
3273 {
3274 fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n",
3275 file_tag, tpx_tag);
3276
3277 /* We only support reading tpx files with the same tag as the code
3278 * or tpx files with the release tag and with lower version number.
3279 */
3280 if (!strcmp(file_tag, TPX_TAG_RELEASE) == 0 && fver < tpx_version)
3281 {
3282 gmx_fatal(FARGS, "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
3283 gmx_fio_getname(fio), fver, file_tag,
3284 tpx_version, tpx_tag);
3285 }
3286 }
3287 }
3288
3289 if (file_version != NULL)
3290 {
3291 *file_version = fver;
3292 }
3293 if (file_generation != NULL)
3294 {
3295 *file_generation = fgen;
3296 }
3297
3298
3299 if ((fver <= tpx_incompatible_version) ||
3300 ((fver > tpx_version) && !TopOnlyOK) ||
3301 (fgen > tpx_generation) ||
3302 tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
3303 {
3304 gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program",
3305 gmx_fio_getname(fio), fver, tpx_version);
3306 }
3307
3308 do_section(fio, eitemHEADER, bRead);
3309 gmx_fio_do_int(fio, tpx->natoms);
3310 if (fver >= 28)
3311 {
3312 gmx_fio_do_int(fio, tpx->ngtc);
3313 }
3314 else
3315 {
3316 tpx->ngtc = 0;
3317 }
3318 if (fver < 62)
3319 {
3320 gmx_fio_do_int(fio, idum);
3321 gmx_fio_do_real(fio, rdum);
3322 }
3323 /*a better decision will eventually (5.0 or later) need to be made
3324 on how to treat the alchemical state of the system, which can now
3325 vary through a simulation, and cannot be completely described
3326 though a single lambda variable, or even a single state
3327 index. Eventually, should probably be a vector. MRS*/
3328 if (fver >= 79)
3329 {
3330 gmx_fio_do_int(fio, tpx->fep_state);
3331 }
3332 gmx_fio_do_real(fio, tpx->lambda);
3333 gmx_fio_do_int(fio, tpx->bIr);
3334 gmx_fio_do_int(fio, tpx->bTop);
3335 gmx_fio_do_int(fio, tpx->bX);
3336 gmx_fio_do_int(fio, tpx->bV);
3337 gmx_fio_do_int(fio, tpx->bF);
3338 gmx_fio_do_int(fio, tpx->bBox);
3339
3340 if ((fgen > tpx_generation))
3341 {
3342 /* This can only happen if TopOnlyOK=TRUE */
3343 tpx->bIr = FALSE;
3344 }
3345 }
3346
3347 static int do_tpx(t_fileio *fio, gmx_bool bRead,
3348 t_inputrec *ir, t_state *state, rvec *f, gmx_mtop_t *mtop,
3349 gmx_bool bXVallocated)
3350 {
3351 t_tpxheader tpx;
3352 t_inputrec dum_ir;
3353 gmx_mtop_t dum_top;
3354 gmx_bool TopOnlyOK;
3355 int file_version, file_generation;
3356 int i;
3357 rvec *xptr, *vptr;
3358 int ePBC;
3359 gmx_bool bPeriodicMols;
3360
3361 if (!bRead)
3362 {
3363 tpx.natoms = state->natoms;
3364 tpx.ngtc = state->ngtc; /* need to add nnhpres here? */
3365 tpx.fep_state = state->fep_state;
3366 tpx.lambda = state->lambda[efptFEP];
3367 tpx.bIr = (ir != NULL);
3368 tpx.bTop = (mtop != NULL);
3369 tpx.bX = (state->x != NULL);
3370 tpx.bV = (state->v != NULL);
3371 tpx.bF = (f != NULL);
3372 tpx.bBox = TRUE;
3373 }
3374
3375 TopOnlyOK = (ir == NULL);
3376
3377 do_tpxheader(fio, bRead, &tpx, TopOnlyOK, &file_version, &file_generation);
3378
3379 if (bRead)
3380 {
3381 state->flags = 0;
3382 /* state->lambda = tpx.lambda;*/ /*remove this eventually? */
3383 /* The init_state calls initialize the Nose-Hoover xi integrals to zero */
3384 if (bXVallocated)
3385 {
3386 xptr = state->x;
3387 vptr = state->v;
3388 init_state(state, 0, tpx.ngtc, 0, 0, 0); /* nose-hoover chains */ /* eventually, need to add nnhpres here? */
3389 state->natoms = tpx.natoms;
3390 state->nalloc = tpx.natoms;
3391 state->x = xptr;
3392 state->v = vptr;
3393 }
3394 else
3395 {
3396 init_state(state, tpx.natoms, tpx.ngtc, 0, 0, 0); /* nose-hoover chains */
3397 }
3398 }
3399
3400 #define do_test(fio, b, p) if (bRead && (p != NULL) && !b) gmx_fatal(FARGS, "No %s in %s",#p, gmx_fio_getname(fio))
3401
3402 do_test(fio, tpx.bBox, state->box);
3403 do_section(fio, eitemBOX, bRead);
3404 if (tpx.bBox)
3405 {
3406 gmx_fio_ndo_rvec(fio, state->box, DIM);
3407 if (file_version >= 51)
3408 {
3409 gmx_fio_ndo_rvec(fio, state->box_rel, DIM);
3410 }
3411 else
3412 {
3413 /* We initialize box_rel after reading the inputrec */
3414 clear_mat(state->box_rel);
3415 }
3416 if (file_version >= 28)
3417 {
3418 gmx_fio_ndo_rvec(fio, state->boxv, DIM);
3419 if (file_version < 56)
3420 {
3421 matrix mdum;
3422 gmx_fio_ndo_rvec(fio, mdum, DIM);
3423 }
3424 }
3425 }
3426
3427 if (state->ngtc > 0 && file_version >= 28)
3428 {
3429 real *dumv;
3430 /*ndo_double(state->nosehoover_xi,state->ngtc,bDum);*/
3431 /*ndo_double(state->nosehoover_vxi,state->ngtc,bDum);*/
3432 /*ndo_double(state->therm_integral,state->ngtc,bDum);*/
3433 snew(dumv, state->ngtc);
3434 if (file_version < 69)
3435 {
3436 gmx_fio_ndo_real(fio, dumv, state->ngtc);
3437 }
3438 /* These used to be the Berendsen tcoupl_lambda's */
3439 gmx_fio_ndo_real(fio, dumv, state->ngtc);
3440 sfree(dumv);
3441 }
3442
3443 /* Prior to tpx version 26, the inputrec was here.
3444 * I moved it to enable partial forward-compatibility
3445 * for analysis/viewer programs.
3446 */
3447 if (file_version < 26)
3448 {
3449 do_test(fio, tpx.bIr, ir);
3450 do_section(fio, eitemIR, bRead);
3451 if (tpx.bIr)
3452 {
3453 if (ir)
3454 {
3455 do_inputrec(fio, ir, bRead, file_version,
3456 mtop ? &mtop->ffparams.fudgeQQ : NULL);
3457 if (bRead && debug)
3458 {
3459 pr_inputrec(debug, 0, "inputrec", ir, FALSE);
3460 }
3461 }
3462 else
3463 {
3464 do_inputrec(fio, &dum_ir, bRead, file_version,
3465 mtop ? &mtop->ffparams.fudgeQQ : NULL);
3466 if (bRead && debug)
3467 {
3468 pr_inputrec(debug, 0, "inputrec", &dum_ir, FALSE);
3469 }
3470 done_inputrec(&dum_ir);
3471 }
3472
3473 }
3474 }
3475
3476 do_test(fio, tpx.bTop, mtop);
3477 do_section(fio, eitemTOP, bRead);
3478 if (tpx.bTop)
3479 {
3480 if (mtop)
3481 {
3482 do_mtop(fio, mtop, bRead, file_version);
3483 }
3484 else
3485 {
3486 do_mtop(fio, &dum_top, bRead, file_version);
3487 done_mtop(&dum_top, TRUE);
3488 }
3489 }
3490 do_test(fio, tpx.bX, state->x);
3491 do_section(fio, eitemX, bRead);
3492 if (tpx.bX)
3493 {
3494 if (bRead)
3495 {
3496 state->flags |= (1<<estX);
3497 }
3498 gmx_fio_ndo_rvec(fio, state->x, state->natoms);
3499 }
3500
3501 do_test(fio, tpx.bV, state->v);
3502 do_section(fio, eitemV, bRead);
3503 if (tpx.bV)
3504 {
3505 if (bRead)
3506 {
3507 state->flags |= (1<<estV);
3508 }
3509 gmx_fio_ndo_rvec(fio, state->v, state->natoms);
3510 }
3511
3512 do_test(fio, tpx.bF, f);
3513 do_section(fio, eitemF, bRead);
3514 if (tpx.bF)
3515 {
3516 gmx_fio_ndo_rvec(fio, f, state->natoms);
3517 }
3518
3519 /* Starting with tpx version 26, we have the inputrec
3520 * at the end of the file, so we can ignore it
3521 * if the file is never than the software (but still the
3522 * same generation - see comments at the top of this file.
3523 *
3524 *
3525 */
3526 ePBC = -1;
3527 bPeriodicMols = FALSE;
3528 if (file_version >= 26)
3529 {
3530 do_test(fio, tpx.bIr, ir);
3531 do_section(fio, eitemIR, bRead);
3532 if (tpx.bIr)
3533 {
3534 if (file_version >= 53)
3535 {
3536 /* Removed the pbc info from do_inputrec, since we always want it */
3537 if (!bRead)
3538 {
3539 ePBC = ir->ePBC;
3540 bPeriodicMols = ir->bPeriodicMols;
3541 }
3542 gmx_fio_do_int(fio, ePBC);
3543 gmx_fio_do_gmx_bool(fio, bPeriodicMols);
3544 }
3545 if (file_generation <= tpx_generation && ir)
3546 {
3547 do_inputrec(fio, ir, bRead, file_version, mtop ? &mtop->ffparams.fudgeQQ : NULL);
3548 if (bRead && debug)
3549 {
3550 pr_inputrec(debug, 0, "inputrec", ir, FALSE);
3551 }
3552 if (file_version < 51)
3553 {
3554 set_box_rel(ir, state);
3555 }
3556 if (file_version < 53)
3557 {
3558 ePBC = ir->ePBC;
3559 bPeriodicMols = ir->bPeriodicMols;
3560 }
3561 }
3562 if (bRead && ir && file_version >= 53)
3563 {
3564 /* We need to do this after do_inputrec, since that initializes ir */
3565 ir->ePBC = ePBC;
3566 ir->bPeriodicMols = bPeriodicMols;
3567 }
3568 }
3569 }
3570
3571 if (bRead)
3572 {
3573 if (tpx.bIr && ir)
3574 {
3575 if (state->ngtc == 0)
3576 {
3577 /* Reading old version without tcoupl state data: set it */
3578 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
3579 }
3580 if (tpx.bTop && mtop)
3581 {
3582 if (file_version < 57)
3583 {
3584 if (mtop->moltype[0].ilist[F_DISRES].nr > 0)
3585 {
3586 ir->eDisre = edrSimple;
3587 }
3588 else
3589 {
3590 ir->eDisre = edrNone;
3591 }
3592 }
3593 set_disres_npair(mtop);
3594 }
3595 }
3596
3597 if (tpx.bTop && mtop)
3598 {
3599 gmx_mtop_finalize(mtop);
3600 }
3601
3602 if (file_version >= 57)
3603 {
3604 char *env;
3605 int ienv;
3606 env = getenv("GMX_NOCHARGEGROUPS");
3607 if (env != NULL)
3608 {
3609 sscanf(env, "%d", &ienv);
3610 fprintf(stderr, "\nFound env.var. GMX_NOCHARGEGROUPS = %d\n",
3611 ienv);
3612 if (ienv > 0)
3613 {
3614 fprintf(stderr,
3615 "Will make single atomic charge groups in non-solvent%s\n",
3616 ienv > 1 ? " and solvent" : "");
3617 gmx_mtop_make_atomic_charge_groups(mtop, ienv == 1);
3618 }
3619 fprintf(stderr, "\n");
3620 }
3621 }
3622 }
3623
3624 return ePBC;
3625 }
3626
3627 /************************************************************
3628 *
3629 * The following routines are the exported ones
3630 *
3631 ************************************************************/
3632
3633 t_fileio *open_tpx(const char *fn, const char *mode)
3634 {
3635 return gmx_fio_open(fn, mode);
3636 }
3637
3638 void close_tpx(t_fileio *fio)
3639 {
3640 gmx_fio_close(fio);
3641 }
3642
3643 void read_tpxheader(const char *fn, t_tpxheader *tpx, gmx_bool TopOnlyOK,
3644 int *file_version, int *file_generation)
3645 {
3646 t_fileio *fio;
3647
3648 fio = open_tpx(fn, "r");
3649 do_tpxheader(fio, TRUE, tpx, TopOnlyOK, file_version, file_generation);
3650 close_tpx(fio);
3651 }
3652
3653 void write_tpx_state(const char *fn,
3654 t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
3655 {
3656 t_fileio *fio;
3657
3658 fio = open_tpx(fn, "w");
3659 do_tpx(fio, FALSE, ir, state, NULL, mtop, FALSE);
3660 close_tpx(fio);
3661 }
3662
3663 void read_tpx_state(const char *fn,
3664 t_inputrec *ir, t_state *state, rvec *f, gmx_mtop_t *mtop)
3665 {
3666 t_fileio *fio;
3667
3668 fio = open_tpx(fn, "r");
3669 do_tpx(fio, TRUE, ir, state, f, mtop, FALSE);
3670 close_tpx(fio);
3671 }
3672
3673 int read_tpx(const char *fn,
3674 t_inputrec *ir, matrix box, int *natoms,
3675 rvec *x, rvec *v, rvec *f, gmx_mtop_t *mtop)
3676 {
3677 t_fileio *fio;
3678 t_state state;
3679 int ePBC;
3680
3681 state.x = x;
3682 state.v = v;
3683 fio = open_tpx(fn, "r");
3684 ePBC = do_tpx(fio, TRUE, ir, &state, f, mtop, TRUE);
3685 close_tpx(fio);
3686 *natoms = state.natoms;
3687 if (box)
3688 {
3689 copy_mat(state.box, box);
3690 }
3691 state.x = NULL;
3692 state.v = NULL;
3693 done_state(&state);
3694
3695 return ePBC;
3696 }
3697
3698 int read_tpx_top(const char *fn,
3699 t_inputrec *ir, matrix box, int *natoms,
3700 rvec *x, rvec *v, rvec *f, t_topology *top)
3701 {
3702 gmx_mtop_t mtop;
3703 t_topology *ltop;
3704 int ePBC;
3705
3706 ePBC = read_tpx(fn, ir, box, natoms, x, v, f, &mtop);
3707
3708 *top = gmx_mtop_t_to_t_topology(&mtop);
3709
3710 return ePBC;
3711 }
3712
3713 gmx_bool fn2bTPX(const char *file)
3714 {
3715 switch (fn2ftp(file))
3716 {
3717 case efTPR:
3718 case efTPB:
3719 case efTPA:
3720 return TRUE;
3721 default:
3722 return FALSE;
3723 }
3724 }
3725
3726 static void done_gmx_groups_t(gmx_groups_t *g)
3727 {
3728 int i;
3729
3730 for (i = 0; (i < egcNR); i++)
3731 {
3732 if (NULL != g->grps[i].nm_ind)
3733 {
3734 sfree(g->grps[i].nm_ind);
3735 g->grps[i].nm_ind = NULL;
3736 }
3737 if (NULL != g->grpnr[i])
3738 {
3739 sfree(g->grpnr[i]);
3740 g->grpnr[i] = NULL;
3741 }
3742 }
3743 /* The contents of this array is in symtab, don't free it here */
3744 sfree(g->grpname);
3745 }
3746
3747 gmx_bool read_tps_conf(const char *infile, char *title, t_topology *top, int *ePBC,
3748 rvec **x, rvec **v, matrix box, gmx_bool bMass)
3749 {
3750 t_tpxheader header;
3751 int natoms, i, version, generation;
3752 gmx_bool bTop, bXNULL = FALSE;
3753 gmx_mtop_t *mtop;
3754 t_topology *topconv;
3755 gmx_atomprop_t aps;
3756
3757 bTop = fn2bTPX(infile);
3758 *ePBC = -1;
3759 if (bTop)
3760 {
3761 read_tpxheader(infile, &header, TRUE, &version, &generation);
3762 if (x)
3763 {
3764 snew(*x, header.natoms);
3765 }
3766 if (v)
3767 {
3768 snew(*v, header.natoms);
3769 }
3770 snew(mtop, 1);
3771 *ePBC = read_tpx(infile, NULL, box, &natoms,
3772 (x == NULL) ? NULL : *x, (v == NULL) ? NULL : *v, NULL, mtop);
3773 *top = gmx_mtop_t_to_t_topology(mtop);
3774 /* In this case we need to throw away the group data too */
3775 done_gmx_groups_t(&mtop->groups);
3776 sfree(mtop);
3777 strcpy(title, *top->name);
3778 tpx_make_chain_identifiers(&top->atoms, &top->mols);
3779 }
3780 else
3781 {
3782 get_stx_coordnum(infile, &natoms);
3783 init_t_atoms(&top->atoms, natoms, (fn2ftp(infile) == efPDB));
3784 if (x == NULL)
3785 {
3786 snew(x, 1);
3787 bXNULL = TRUE;
3788 }
3789 snew(*x, natoms);
3790 if (v)
3791 {
3792 snew(*v, natoms);
3793 }
3794 read_stx_conf(infile, title, &top->atoms, *x, (v == NULL) ? NULL : *v, ePBC, box);
3795 if (bXNULL)
3796 {
3797 sfree(*x);
3798 sfree(x);
3799 }
3800 if (bMass)
3801 {
3802 aps = gmx_atomprop_init();
3803 for (i = 0; (i < natoms); i++)
3804 {
3805 if (!gmx_atomprop_query(aps, epropMass,
3806 *top->atoms.resinfo[top->atoms.atom[i].resind].name,
3807 *top->atoms.atomname[i],
3808 &(top->atoms.atom[i].m)))
3809 {
3810 if (debug)
3811 {
3812 fprintf(debug, "Can not find mass for atom %s %d %s, setting to 1\n",
3813 *top->atoms.resinfo[top->atoms.atom[i].resind].name,
3814 top->atoms.resinfo[top->atoms.atom[i].resind].nr,
3815 *top->atoms.atomname[i]);
3816 }
3817 }
3818 }
3819 gmx_atomprop_destroy(aps);
3820 }
3821 top->idef.ntypes = -1;
3822 }
3823
3824 return bTop;
3825 }
The ultimate molecular dynamics simulation package