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Moved copyrite.* to fileio from gmxlib and legacyheaders.
[gromacs.git] / src / gromacs / fileio / tpxio.cpp
blob371d73c6b0847ed35fbccf77e29e9f3066599452
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) 2013,2014,2015, 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,
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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
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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 "gmxpre.h"
38
39 /* This file is completely threadsafe - keep it that way! */
40
41 #include "tpxio.h"
42
43 #include <cstdlib>
44 #include <cstring>
45
46 #include <algorithm>
47
48 #include "gromacs/fileio/filenm.h"
49 #include "gromacs/fileio/gmxfio.h"
50 #include "gromacs/fileio/gmxfio-xdr.h"
51 #include "gromacs/legacyheaders/names.h"
52 #include "gromacs/legacyheaders/types/ifunc.h"
53 #include "gromacs/math/vec.h"
54 #include "gromacs/mdtypes/inputrec.h"
55 #include "gromacs/mdtypes/state.h"
56 #include "gromacs/pbcutil/boxutilities.h"
57 #include "gromacs/pbcutil/pbc.h"
58 #include "gromacs/topology/block.h"
59 #include "gromacs/topology/mtop_util.h"
60 #include "gromacs/topology/symtab.h"
61 #include "gromacs/topology/topology.h"
62 #include "gromacs/utility/arraysize.h"
63 #include "gromacs/utility/baseversion.h"
64 #include "gromacs/utility/cstringutil.h"
65 #include "gromacs/utility/fatalerror.h"
66 #include "gromacs/utility/futil.h"
67 #include "gromacs/utility/smalloc.h"
68
69 #define TPX_TAG_RELEASE "release"
70
71 /*! \brief Tag string for the file format written to run input files
72 * written by this version of the code.
73 *
74 * Change this if you want to change the run input format in a feature
75 * branch. This ensures that there will not be different run input
76 * formats around which cannot be distinguished, while not causing
77 * problems rebasing the feature branch onto upstream changes. When
78 * merging with mainstream GROMACS, set this tag string back to
79 * TPX_TAG_RELEASE, and instead add an element to tpxv.
80 */
81 static const char *tpx_tag = TPX_TAG_RELEASE;
82
83 /*! \brief Enum of values that describe the contents of a tpr file
84 * whose format matches a version number
85 *
86 * The enum helps the code be more self-documenting and ensure merges
87 * do not silently resolve when two patches make the same bump. When
88 * adding new functionality, add a new element just above tpxv_Count
89 * in this enumeration, and write code below that does the right thing
90 * according to the value of file_version.
91 */
92 enum tpxv {
93 tpxv_ComputationalElectrophysiology = 96, /**< support for ion/water position swaps (computational electrophysiology) */
94 tpxv_Use64BitRandomSeed, /**< change ld_seed from int to gmx_int64_t */
95 tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, /**< potentials for supporting coarse-grained force fields */
96 tpxv_InteractiveMolecularDynamics, /**< interactive molecular dynamics (IMD) */
97 tpxv_RemoveObsoleteParameters1, /**< remove optimize_fft, dihre_fc, nstcheckpoint */
98 tpxv_PullCoordTypeGeom, /**< add pull type and geometry per group and flat-bottom */
99 tpxv_PullGeomDirRel, /**< add pull geometry direction-relative */
100 tpxv_IntermolecularBondeds, /**< permit inter-molecular bonded interactions in the topology */
101 tpxv_CompElWithSwapLayerOffset, /**< added parameters for improved CompEl setups */
102 tpxv_Count /**< the total number of tpxv versions */
103 };
104
105 /*! \brief Version number of the file format written to run input
106 * files by this version of the code.
107 *
108 * The tpx_version increases whenever the file format in the main
109 * development branch changes, due to an extension of the tpxv enum above.
110 * Backward compatibility for reading old run input files is maintained
111 * by checking this version number against that of the file and then using
112 * the correct code path.
113 *
114 * When developing a feature branch that needs to change the run input
115 * file format, change tpx_tag instead. */
116 static const int tpx_version = tpxv_Count - 1;
117
118
119 /* This number should only be increased when you edit the TOPOLOGY section
120 * or the HEADER of the tpx format.
121 * This way we can maintain forward compatibility too for all analysis tools
122 * and/or external programs that only need to know the atom/residue names,
123 * charges, and bond connectivity.
124 *
125 * It first appeared in tpx version 26, when I also moved the inputrecord
126 * to the end of the tpx file, so we can just skip it if we only
127 * want the topology.
128 *
129 * In particular, it must be increased when adding new elements to
130 * ftupd, so that old code can read new .tpr files.
131 */
132 static const int tpx_generation = 26;
133
134 /* This number should be the most recent backwards incompatible version
135 * I.e., if this number is 9, we cannot read tpx version 9 with this code.
136 */
137 static const int tpx_incompatible_version = 9;
138
139
140
141 /* Struct used to maintain tpx compatibility when function types are added */
142 typedef struct {
143 int fvnr; /* file version number in which the function type first appeared */
144 int ftype; /* function type */
145 } t_ftupd;
146
147 /*
148 * The entries should be ordered in:
149 * 1. ascending function type number
150 * 2. ascending file version number
151 */
152 static const t_ftupd ftupd[] = {
153 { 20, F_CUBICBONDS },
154 { 20, F_CONNBONDS },
155 { 20, F_HARMONIC },
156 { 34, F_FENEBONDS },
157 { 43, F_TABBONDS },
158 { 43, F_TABBONDSNC },
159 { 70, F_RESTRBONDS },
160 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
161 { 76, F_LINEAR_ANGLES },
162 { 30, F_CROSS_BOND_BONDS },
163 { 30, F_CROSS_BOND_ANGLES },
164 { 30, F_UREY_BRADLEY },
165 { 34, F_QUARTIC_ANGLES },
166 { 43, F_TABANGLES },
167 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
168 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
169 { 26, F_FOURDIHS },
170 { 26, F_PIDIHS },
171 { 43, F_TABDIHS },
172 { 65, F_CMAP },
173 { 60, F_GB12 },
174 { 61, F_GB13 },
175 { 61, F_GB14 },
176 { 72, F_GBPOL },
177 { 72, F_NPSOLVATION },
178 { 41, F_LJC14_Q },
179 { 41, F_LJC_PAIRS_NB },
180 { 32, F_BHAM_LR },
181 { 32, F_RF_EXCL },
182 { 32, F_COUL_RECIP },
183 { 93, F_LJ_RECIP },
184 { 46, F_DPD },
185 { 30, F_POLARIZATION },
186 { 36, F_THOLE_POL },
187 { 90, F_FBPOSRES },
188 { 22, F_DISRESVIOL },
189 { 22, F_ORIRES },
190 { 22, F_ORIRESDEV },
191 { 26, F_DIHRES },
192 { 26, F_DIHRESVIOL },
193 { 49, F_VSITE4FDN },
194 { 50, F_VSITEN },
195 { 46, F_COM_PULL },
196 { 20, F_EQM },
197 { 46, F_ECONSERVED },
198 { 69, F_VTEMP_NOLONGERUSED},
199 { 66, F_PDISPCORR },
200 { 54, F_DVDL_CONSTR },
201 { 76, F_ANHARM_POL },
202 { 79, F_DVDL_COUL },
203 { 79, F_DVDL_VDW, },
204 { 79, F_DVDL_BONDED, },
205 { 79, F_DVDL_RESTRAINT },
206 { 79, F_DVDL_TEMPERATURE },
207 };
208 #define NFTUPD asize(ftupd)
209
210 /* Needed for backward compatibility */
211 #define MAXNODES 256
212
213 /**************************************************************
214 *
215 * Now the higer level routines that do io of the structures and arrays
216 *
217 **************************************************************/
218 static void do_pullgrp_tpx_pre95(t_fileio *fio,
219 t_pull_group *pgrp,
220 t_pull_coord *pcrd,
221 gmx_bool bRead,
222 int file_version)
223 {
224 rvec tmp;
225
226 gmx_fio_do_int(fio, pgrp->nat);
227 if (bRead)
228 {
229 snew(pgrp->ind, pgrp->nat);
230 }
231 gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
232 gmx_fio_do_int(fio, pgrp->nweight);
233 if (bRead)
234 {
235 snew(pgrp->weight, pgrp->nweight);
236 }
237 gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight);
238 gmx_fio_do_int(fio, pgrp->pbcatom);
239 gmx_fio_do_rvec(fio, pcrd->vec);
240 clear_rvec(pcrd->origin);
241 gmx_fio_do_rvec(fio, tmp);
242 pcrd->init = tmp[0];
243 gmx_fio_do_real(fio, pcrd->rate);
244 gmx_fio_do_real(fio, pcrd->k);
245 if (file_version >= 56)
246 {
247 gmx_fio_do_real(fio, pcrd->kB);
248 }
249 else
250 {
251 pcrd->kB = pcrd->k;
252 }
253 }
254
255 static void do_pull_group(t_fileio *fio, t_pull_group *pgrp, gmx_bool bRead)
256 {
257 gmx_fio_do_int(fio, pgrp->nat);
258 if (bRead)
259 {
260 snew(pgrp->ind, pgrp->nat);
261 }
262 gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
263 gmx_fio_do_int(fio, pgrp->nweight);
264 if (bRead)
265 {
266 snew(pgrp->weight, pgrp->nweight);
267 }
268 gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight);
269 gmx_fio_do_int(fio, pgrp->pbcatom);
270 }
271
272 static void do_pull_coord(t_fileio *fio, t_pull_coord *pcrd, int file_version,
273 int ePullOld, int eGeomOld, ivec dimOld)
274 {
275 gmx_fio_do_int(fio, pcrd->group[0]);
276 gmx_fio_do_int(fio, pcrd->group[1]);
277 if (file_version >= tpxv_PullCoordTypeGeom)
278 {
279 gmx_fio_do_int(fio, pcrd->eType);
280 gmx_fio_do_int(fio, pcrd->eGeom);
281 if (pcrd->eGeom == epullgDIRRELATIVE)
282 {
283 gmx_fio_do_int(fio, pcrd->group[2]);
284 gmx_fio_do_int(fio, pcrd->group[3]);
285 }
286 gmx_fio_do_ivec(fio, pcrd->dim);
287 }
288 else
289 {
290 pcrd->eType = ePullOld;
291 pcrd->eGeom = eGeomOld;
292 copy_ivec(dimOld, pcrd->dim);
293 }
294 gmx_fio_do_rvec(fio, pcrd->origin);
295 gmx_fio_do_rvec(fio, pcrd->vec);
296 if (file_version >= tpxv_PullCoordTypeGeom)
297 {
298 gmx_fio_do_gmx_bool(fio, pcrd->bStart);
299 }
300 else
301 {
302 /* This parameter is only printed, but not actually used by mdrun */
303 pcrd->bStart = FALSE;
304 }
305 gmx_fio_do_real(fio, pcrd->init);
306 gmx_fio_do_real(fio, pcrd->rate);
307 gmx_fio_do_real(fio, pcrd->k);
308 gmx_fio_do_real(fio, pcrd->kB);
309 }
310
311 static void do_expandedvals(t_fileio *fio, t_expanded *expand, t_lambda *fepvals, gmx_bool bRead, int file_version)
312 {
313 int n_lambda = fepvals->n_lambda;
314
315 /* reset the lambda calculation window */
316 fepvals->lambda_start_n = 0;
317 fepvals->lambda_stop_n = n_lambda;
318 if (file_version >= 79)
319 {
320 if (n_lambda > 0)
321 {
322 if (bRead)
323 {
324 snew(expand->init_lambda_weights, n_lambda);
325 }
326 gmx_fio_ndo_real(fio, expand->init_lambda_weights, n_lambda);
327 gmx_fio_do_gmx_bool(fio, expand->bInit_weights);
328 }
329
330 gmx_fio_do_int(fio, expand->nstexpanded);
331 gmx_fio_do_int(fio, expand->elmcmove);
332 gmx_fio_do_int(fio, expand->elamstats);
333 gmx_fio_do_int(fio, expand->lmc_repeats);
334 gmx_fio_do_int(fio, expand->gibbsdeltalam);
335 gmx_fio_do_int(fio, expand->lmc_forced_nstart);
336 gmx_fio_do_int(fio, expand->lmc_seed);
337 gmx_fio_do_real(fio, expand->mc_temp);
338 gmx_fio_do_int(fio, expand->bSymmetrizedTMatrix);
339 gmx_fio_do_int(fio, expand->nstTij);
340 gmx_fio_do_int(fio, expand->minvarmin);
341 gmx_fio_do_int(fio, expand->c_range);
342 gmx_fio_do_real(fio, expand->wl_scale);
343 gmx_fio_do_real(fio, expand->wl_ratio);
344 gmx_fio_do_real(fio, expand->init_wl_delta);
345 gmx_fio_do_gmx_bool(fio, expand->bWLoneovert);
346 gmx_fio_do_int(fio, expand->elmceq);
347 gmx_fio_do_int(fio, expand->equil_steps);
348 gmx_fio_do_int(fio, expand->equil_samples);
349 gmx_fio_do_int(fio, expand->equil_n_at_lam);
350 gmx_fio_do_real(fio, expand->equil_wl_delta);
351 gmx_fio_do_real(fio, expand->equil_ratio);
352 }
353 }
354
355 static void do_simtempvals(t_fileio *fio, t_simtemp *simtemp, int n_lambda, gmx_bool bRead,
356 int file_version)
357 {
358 if (file_version >= 79)
359 {
360 gmx_fio_do_int(fio, simtemp->eSimTempScale);
361 gmx_fio_do_real(fio, simtemp->simtemp_high);
362 gmx_fio_do_real(fio, simtemp->simtemp_low);
363 if (n_lambda > 0)
364 {
365 if (bRead)
366 {
367 snew(simtemp->temperatures, n_lambda);
368 }
369 gmx_fio_ndo_real(fio, simtemp->temperatures, n_lambda);
370 }
371 }
372 }
373
374 static void do_imd(t_fileio *fio, t_IMD *imd, gmx_bool bRead)
375 {
376 gmx_fio_do_int(fio, imd->nat);
377 if (bRead)
378 {
379 snew(imd->ind, imd->nat);
380 }
381 gmx_fio_ndo_int(fio, imd->ind, imd->nat);
382 }
383
384 static void do_fepvals(t_fileio *fio, t_lambda *fepvals, gmx_bool bRead, int file_version)
385 {
386 /* i is defined in the ndo_double macro; use g to iterate. */
387 int g;
388 real rdum;
389
390 /* free energy values */
391
392 if (file_version >= 79)
393 {
394 gmx_fio_do_int(fio, fepvals->init_fep_state);
395 gmx_fio_do_double(fio, fepvals->init_lambda);
396 gmx_fio_do_double(fio, fepvals->delta_lambda);
397 }
398 else if (file_version >= 59)
399 {
400 gmx_fio_do_double(fio, fepvals->init_lambda);
401 gmx_fio_do_double(fio, fepvals->delta_lambda);
402 }
403 else
404 {
405 gmx_fio_do_real(fio, rdum);
406 fepvals->init_lambda = rdum;
407 gmx_fio_do_real(fio, rdum);
408 fepvals->delta_lambda = rdum;
409 }
410 if (file_version >= 79)
411 {
412 gmx_fio_do_int(fio, fepvals->n_lambda);
413 if (bRead)
414 {
415 snew(fepvals->all_lambda, efptNR);
416 }
417 for (g = 0; g < efptNR; g++)
418 {
419 if (fepvals->n_lambda > 0)
420 {
421 if (bRead)
422 {
423 snew(fepvals->all_lambda[g], fepvals->n_lambda);
424 }
425 gmx_fio_ndo_double(fio, fepvals->all_lambda[g], fepvals->n_lambda);
426 gmx_fio_ndo_int(fio, fepvals->separate_dvdl, efptNR);
427 }
428 else if (fepvals->init_lambda >= 0)
429 {
430 fepvals->separate_dvdl[efptFEP] = TRUE;
431 }
432 }
433 }
434 else if (file_version >= 64)
435 {
436 gmx_fio_do_int(fio, fepvals->n_lambda);
437 if (bRead)
438 {
439 int g;
440
441 snew(fepvals->all_lambda, efptNR);
442 /* still allocate the all_lambda array's contents. */
443 for (g = 0; g < efptNR; g++)
444 {
445 if (fepvals->n_lambda > 0)
446 {
447 snew(fepvals->all_lambda[g], fepvals->n_lambda);
448 }
449 }
450 }
451 gmx_fio_ndo_double(fio, fepvals->all_lambda[efptFEP],
452 fepvals->n_lambda);
453 if (fepvals->init_lambda >= 0)
454 {
455 int g, h;
456
457 fepvals->separate_dvdl[efptFEP] = TRUE;
458
459 if (bRead)
460 {
461 /* copy the contents of the efptFEP lambda component to all
462 the other components */
463 for (g = 0; g < efptNR; g++)
464 {
465 for (h = 0; h < fepvals->n_lambda; h++)
466 {
467 if (g != efptFEP)
468 {
469 fepvals->all_lambda[g][h] =
470 fepvals->all_lambda[efptFEP][h];
471 }
472 }
473 }
474 }
475 }
476 }
477 else
478 {
479 fepvals->n_lambda = 0;
480 fepvals->all_lambda = NULL;
481 if (fepvals->init_lambda >= 0)
482 {
483 fepvals->separate_dvdl[efptFEP] = TRUE;
484 }
485 }
486 if (file_version >= 13)
487 {
488 gmx_fio_do_real(fio, fepvals->sc_alpha);
489 }
490 else
491 {
492 fepvals->sc_alpha = 0;
493 }
494 if (file_version >= 38)
495 {
496 gmx_fio_do_int(fio, fepvals->sc_power);
497 }
498 else
499 {
500 fepvals->sc_power = 2;
501 }
502 if (file_version >= 79)
503 {
504 gmx_fio_do_real(fio, fepvals->sc_r_power);
505 }
506 else
507 {
508 fepvals->sc_r_power = 6.0;
509 }
510 if (file_version >= 15)
511 {
512 gmx_fio_do_real(fio, fepvals->sc_sigma);
513 }
514 else
515 {
516 fepvals->sc_sigma = 0.3;
517 }
518 if (bRead)
519 {
520 if (file_version >= 71)
521 {
522 fepvals->sc_sigma_min = fepvals->sc_sigma;
523 }
524 else
525 {
526 fepvals->sc_sigma_min = 0;
527 }
528 }
529 if (file_version >= 79)
530 {
531 gmx_fio_do_int(fio, fepvals->bScCoul);
532 }
533 else
534 {
535 fepvals->bScCoul = TRUE;
536 }
537 if (file_version >= 64)
538 {
539 gmx_fio_do_int(fio, fepvals->nstdhdl);
540 }
541 else
542 {
543 fepvals->nstdhdl = 1;
544 }
545
546 if (file_version >= 73)
547 {
548 gmx_fio_do_int(fio, fepvals->separate_dhdl_file);
549 gmx_fio_do_int(fio, fepvals->dhdl_derivatives);
550 }
551 else
552 {
553 fepvals->separate_dhdl_file = esepdhdlfileYES;
554 fepvals->dhdl_derivatives = edhdlderivativesYES;
555 }
556 if (file_version >= 71)
557 {
558 gmx_fio_do_int(fio, fepvals->dh_hist_size);
559 gmx_fio_do_double(fio, fepvals->dh_hist_spacing);
560 }
561 else
562 {
563 fepvals->dh_hist_size = 0;
564 fepvals->dh_hist_spacing = 0.1;
565 }
566 if (file_version >= 79)
567 {
568 gmx_fio_do_int(fio, fepvals->edHdLPrintEnergy);
569 }
570 else
571 {
572 fepvals->edHdLPrintEnergy = edHdLPrintEnergyNO;
573 }
574
575 /* handle lambda_neighbors */
576 if ((file_version >= 83 && file_version < 90) || file_version >= 92)
577 {
578 gmx_fio_do_int(fio, fepvals->lambda_neighbors);
579 if ( (fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0) &&
580 (fepvals->init_lambda < 0) )
581 {
582 fepvals->lambda_start_n = (fepvals->init_fep_state -
583 fepvals->lambda_neighbors);
584 fepvals->lambda_stop_n = (fepvals->init_fep_state +
585 fepvals->lambda_neighbors + 1);
586 if (fepvals->lambda_start_n < 0)
587 {
588 fepvals->lambda_start_n = 0;;
589 }
590 if (fepvals->lambda_stop_n >= fepvals->n_lambda)
591 {
592 fepvals->lambda_stop_n = fepvals->n_lambda;
593 }
594 }
595 else
596 {
597 fepvals->lambda_start_n = 0;
598 fepvals->lambda_stop_n = fepvals->n_lambda;
599 }
600 }
601 else
602 {
603 fepvals->lambda_start_n = 0;
604 fepvals->lambda_stop_n = fepvals->n_lambda;
605 }
606 }
607
608 static void do_pull(t_fileio *fio, pull_params_t *pull, gmx_bool bRead,
609 int file_version, int ePullOld)
610 {
611 int eGeomOld = -1;
612 ivec dimOld;
613 int g;
614
615 if (file_version >= 95)
616 {
617 gmx_fio_do_int(fio, pull->ngroup);
618 }
619 gmx_fio_do_int(fio, pull->ncoord);
620 if (file_version < 95)
621 {
622 pull->ngroup = pull->ncoord + 1;
623 }
624 if (file_version < tpxv_PullCoordTypeGeom)
625 {
626 real dum;
627
628 gmx_fio_do_int(fio, eGeomOld);
629 gmx_fio_do_ivec(fio, dimOld);
630 /* The inner cylinder radius, now removed */
631 gmx_fio_do_real(fio, dum);
632 }
633 gmx_fio_do_real(fio, pull->cylinder_r);
634 gmx_fio_do_real(fio, pull->constr_tol);
635 if (file_version >= 95)
636 {
637 gmx_fio_do_int(fio, pull->bPrintCOM1);
638 /* With file_version < 95 this value is set below */
639 }
640 if (file_version >= tpxv_PullCoordTypeGeom)
641 {
642 gmx_fio_do_int(fio, pull->bPrintCOM2);
643 gmx_fio_do_int(fio, pull->bPrintRefValue);
644 gmx_fio_do_int(fio, pull->bPrintComp);
645 }
646 else
647 {
648 pull->bPrintCOM2 = FALSE;
649 pull->bPrintRefValue = FALSE;
650 pull->bPrintComp = TRUE;
651 }
652 gmx_fio_do_int(fio, pull->nstxout);
653 gmx_fio_do_int(fio, pull->nstfout);
654 if (bRead)
655 {
656 snew(pull->group, pull->ngroup);
657 snew(pull->coord, pull->ncoord);
658 }
659 if (file_version < 95)
660 {
661 /* epullgPOS for position pulling, before epullgDIRPBC was removed */
662 if (eGeomOld == epullgDIRPBC)
663 {
664 gmx_fatal(FARGS, "pull-geometry=position is no longer supported");
665 }
666 if (eGeomOld > epullgDIRPBC)
667 {
668 eGeomOld -= 1;
669 }
670
671 for (g = 0; g < pull->ngroup; g++)
672 {
673 /* We read and ignore a pull coordinate for group 0 */
674 do_pullgrp_tpx_pre95(fio, &pull->group[g], &pull->coord[std::max(g-1, 0)],
675 bRead, file_version);
676 if (g > 0)
677 {
678 pull->coord[g-1].group[0] = 0;
679 pull->coord[g-1].group[1] = g;
680 }
681 }
682
683 pull->bPrintCOM1 = (pull->group[0].nat > 0);
684 }
685 else
686 {
687 for (g = 0; g < pull->ngroup; g++)
688 {
689 do_pull_group(fio, &pull->group[g], bRead);
690 }
691 for (g = 0; g < pull->ncoord; g++)
692 {
693 do_pull_coord(fio, &pull->coord[g],
694 file_version, ePullOld, eGeomOld, dimOld);
695 }
696 }
697 }
698
699
700 static void do_rotgrp(t_fileio *fio, t_rotgrp *rotg, gmx_bool bRead)
701 {
702 gmx_fio_do_int(fio, rotg->eType);
703 gmx_fio_do_int(fio, rotg->bMassW);
704 gmx_fio_do_int(fio, rotg->nat);
705 if (bRead)
706 {
707 snew(rotg->ind, rotg->nat);
708 }
709 gmx_fio_ndo_int(fio, rotg->ind, rotg->nat);
710 if (bRead)
711 {
712 snew(rotg->x_ref, rotg->nat);
713 }
714 gmx_fio_ndo_rvec(fio, rotg->x_ref, rotg->nat);
715 gmx_fio_do_rvec(fio, rotg->vec);
716 gmx_fio_do_rvec(fio, rotg->pivot);
717 gmx_fio_do_real(fio, rotg->rate);
718 gmx_fio_do_real(fio, rotg->k);
719 gmx_fio_do_real(fio, rotg->slab_dist);
720 gmx_fio_do_real(fio, rotg->min_gaussian);
721 gmx_fio_do_real(fio, rotg->eps);
722 gmx_fio_do_int(fio, rotg->eFittype);
723 gmx_fio_do_int(fio, rotg->PotAngle_nstep);
724 gmx_fio_do_real(fio, rotg->PotAngle_step);
725 }
726
727 static void do_rot(t_fileio *fio, t_rot *rot, gmx_bool bRead)
728 {
729 int g;
730
731 gmx_fio_do_int(fio, rot->ngrp);
732 gmx_fio_do_int(fio, rot->nstrout);
733 gmx_fio_do_int(fio, rot->nstsout);
734 if (bRead)
735 {
736 snew(rot->grp, rot->ngrp);
737 }
738 for (g = 0; g < rot->ngrp; g++)
739 {
740 do_rotgrp(fio, &rot->grp[g], bRead);
741 }
742 }
743
744
745 static void do_swapcoords(t_fileio *fio, t_swapcoords *swap, gmx_bool bRead, int file_version)
746 {
747 int j;
748
749 gmx_fio_do_int(fio, swap->nat);
750 gmx_fio_do_int(fio, swap->nat_sol);
751 for (j = 0; j < 2; j++)
752 {
753 gmx_fio_do_int(fio, swap->nat_split[j]);
754 gmx_fio_do_int(fio, swap->massw_split[j]);
755 }
756 gmx_fio_do_int(fio, swap->nstswap);
757 gmx_fio_do_int(fio, swap->nAverage);
758 gmx_fio_do_real(fio, swap->threshold);
759 gmx_fio_do_real(fio, swap->cyl0r);
760 gmx_fio_do_real(fio, swap->cyl0u);
761 gmx_fio_do_real(fio, swap->cyl0l);
762 gmx_fio_do_real(fio, swap->cyl1r);
763 gmx_fio_do_real(fio, swap->cyl1u);
764 gmx_fio_do_real(fio, swap->cyl1l);
765
766 if (bRead)
767 {
768 snew(swap->ind, swap->nat);
769 snew(swap->ind_sol, swap->nat_sol);
770 for (j = 0; j < 2; j++)
771 {
772 snew(swap->ind_split[j], swap->nat_split[j]);
773 }
774 }
775
776 gmx_fio_ndo_int(fio, swap->ind, swap->nat);
777 gmx_fio_ndo_int(fio, swap->ind_sol, swap->nat_sol);
778 for (j = 0; j < 2; j++)
779 {
780 gmx_fio_ndo_int(fio, swap->ind_split[j], swap->nat_split[j]);
781 }
782
783 for (j = 0; j < eCompNR; j++)
784 {
785 gmx_fio_do_int(fio, swap->nanions[j]);
786 gmx_fio_do_int(fio, swap->ncations[j]);
787 }
788
789 if (file_version >= tpxv_CompElWithSwapLayerOffset)
790 {
791 for (j = 0; j < eCompNR; j++)
792 {
793 gmx_fio_do_real(fio, swap->bulkOffset[j]);
794 }
795 }
796
797 }
798
799
800 static void do_inputrec(t_fileio *fio, t_inputrec *ir, gmx_bool bRead,
801 int file_version, real *fudgeQQ)
802 {
803 int i, j, k, *tmp, idum = 0;
804 real rdum, bd_temp;
805 rvec vdum;
806 gmx_bool bSimAnn, bdum = 0;
807 real zerotemptime, finish_t, init_temp, finish_temp;
808
809 if (file_version != tpx_version)
810 {
811 /* Give a warning about features that are not accessible */
812 fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n",
813 file_version, tpx_version);
814 }
815
816 if (bRead)
817 {
818 init_inputrec(ir);
819 }
820
821 if (file_version == 0)
822 {
823 return;
824 }
825
826 /* Basic inputrec stuff */
827 gmx_fio_do_int(fio, ir->eI);
828 if (file_version >= 62)
829 {
830 gmx_fio_do_int64(fio, ir->nsteps);
831 }
832 else
833 {
834 gmx_fio_do_int(fio, idum);
835 ir->nsteps = idum;
836 }
837
838 if (file_version > 25)
839 {
840 if (file_version >= 62)
841 {
842 gmx_fio_do_int64(fio, ir->init_step);
843 }
844 else
845 {
846 gmx_fio_do_int(fio, idum);
847 ir->init_step = idum;
848 }
849 }
850 else
851 {
852 ir->init_step = 0;
853 }
854
855 if (file_version >= 58)
856 {
857 gmx_fio_do_int(fio, ir->simulation_part);
858 }
859 else
860 {
861 ir->simulation_part = 1;
862 }
863
864 if (file_version >= 67)
865 {
866 gmx_fio_do_int(fio, ir->nstcalcenergy);
867 }
868 else
869 {
870 ir->nstcalcenergy = 1;
871 }
872 if (file_version < 53)
873 {
874 /* The pbc info has been moved out of do_inputrec,
875 * since we always want it, also without reading the inputrec.
876 */
877 gmx_fio_do_int(fio, ir->ePBC);
878 if ((file_version <= 15) && (ir->ePBC == 2))
879 {
880 ir->ePBC = epbcNONE;
881 }
882 if (file_version >= 45)
883 {
884 gmx_fio_do_int(fio, ir->bPeriodicMols);
885 }
886 else
887 {
888 if (ir->ePBC == 2)
889 {
890 ir->ePBC = epbcXYZ;
891 ir->bPeriodicMols = TRUE;
892 }
893 else
894 {
895 ir->bPeriodicMols = FALSE;
896 }
897 }
898 }
899 if (file_version >= 81)
900 {
901 gmx_fio_do_int(fio, ir->cutoff_scheme);
902 if (file_version < 94)
903 {
904 ir->cutoff_scheme = 1 - ir->cutoff_scheme;
905 }
906 }
907 else
908 {
909 ir->cutoff_scheme = ecutsGROUP;
910 }
911 gmx_fio_do_int(fio, ir->ns_type);
912 gmx_fio_do_int(fio, ir->nstlist);
913 gmx_fio_do_int(fio, idum); /* used to be ndelta; not used anymore */
914 if (file_version < 41)
915 {
916 gmx_fio_do_int(fio, idum);
917 gmx_fio_do_int(fio, idum);
918 }
919 if (file_version >= 45)
920 {
921 gmx_fio_do_real(fio, ir->rtpi);
922 }
923 else
924 {
925 ir->rtpi = 0.05;
926 }
927 gmx_fio_do_int(fio, ir->nstcomm);
928 if (file_version > 34)
929 {
930 gmx_fio_do_int(fio, ir->comm_mode);
931 }
932 else if (ir->nstcomm < 0)
933 {
934 ir->comm_mode = ecmANGULAR;
935 }
936 else
937 {
938 ir->comm_mode = ecmLINEAR;
939 }
940 ir->nstcomm = abs(ir->nstcomm);
941
942 /* ignore nstcheckpoint */
943 if (file_version > 25 && file_version < tpxv_RemoveObsoleteParameters1)
944 {
945 gmx_fio_do_int(fio, idum);
946 }
947
948 gmx_fio_do_int(fio, ir->nstcgsteep);
949
950 if (file_version >= 30)
951 {
952 gmx_fio_do_int(fio, ir->nbfgscorr);
953 }
954 else if (bRead)
955 {
956 ir->nbfgscorr = 10;
957 }
958
959 gmx_fio_do_int(fio, ir->nstlog);
960 gmx_fio_do_int(fio, ir->nstxout);
961 gmx_fio_do_int(fio, ir->nstvout);
962 gmx_fio_do_int(fio, ir->nstfout);
963 gmx_fio_do_int(fio, ir->nstenergy);
964 gmx_fio_do_int(fio, ir->nstxout_compressed);
965 if (file_version >= 59)
966 {
967 gmx_fio_do_double(fio, ir->init_t);
968 gmx_fio_do_double(fio, ir->delta_t);
969 }
970 else
971 {
972 gmx_fio_do_real(fio, rdum);
973 ir->init_t = rdum;
974 gmx_fio_do_real(fio, rdum);
975 ir->delta_t = rdum;
976 }
977 gmx_fio_do_real(fio, ir->x_compression_precision);
978 if (file_version < 19)
979 {
980 gmx_fio_do_int(fio, idum);
981 gmx_fio_do_int(fio, idum);
982 }
983 if (file_version < 18)
984 {
985 gmx_fio_do_int(fio, idum);
986 }
987 if (file_version >= 81)
988 {
989 gmx_fio_do_real(fio, ir->verletbuf_tol);
990 }
991 else
992 {
993 ir->verletbuf_tol = 0;
994 }
995 gmx_fio_do_real(fio, ir->rlist);
996 if (file_version >= 67)
997 {
998 gmx_fio_do_real(fio, ir->rlistlong);
999 }
1000 if (file_version >= 82 && file_version != 90)
1001 {
1002 gmx_fio_do_int(fio, ir->nstcalclr);
1003 }
1004 else
1005 {
1006 /* Calculate at NS steps */
1007 ir->nstcalclr = ir->nstlist;
1008 }
1009 gmx_fio_do_int(fio, ir->coulombtype);
1010 if (file_version < 32 && ir->coulombtype == eelRF)
1011 {
1012 ir->coulombtype = eelRF_NEC;
1013 }
1014 if (file_version >= 81)
1015 {
1016 gmx_fio_do_int(fio, ir->coulomb_modifier);
1017 }
1018 else
1019 {
1020 ir->coulomb_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1021 }
1022 gmx_fio_do_real(fio, ir->rcoulomb_switch);
1023 gmx_fio_do_real(fio, ir->rcoulomb);
1024 gmx_fio_do_int(fio, ir->vdwtype);
1025 if (file_version >= 81)
1026 {
1027 gmx_fio_do_int(fio, ir->vdw_modifier);
1028 }
1029 else
1030 {
1031 ir->vdw_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1032 }
1033 gmx_fio_do_real(fio, ir->rvdw_switch);
1034 gmx_fio_do_real(fio, ir->rvdw);
1035 if (file_version < 67)
1036 {
1037 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
1038 }
1039 gmx_fio_do_int(fio, ir->eDispCorr);
1040 gmx_fio_do_real(fio, ir->epsilon_r);
1041 if (file_version >= 37)
1042 {
1043 gmx_fio_do_real(fio, ir->epsilon_rf);
1044 }
1045 else
1046 {
1047 if (EEL_RF(ir->coulombtype))
1048 {
1049 ir->epsilon_rf = ir->epsilon_r;
1050 ir->epsilon_r = 1.0;
1051 }
1052 else
1053 {
1054 ir->epsilon_rf = 1.0;
1055 }
1056 }
1057 if (file_version >= 29)
1058 {
1059 gmx_fio_do_real(fio, ir->tabext);
1060 }
1061 else
1062 {
1063 ir->tabext = 1.0;
1064 }
1065
1066 if (file_version > 25)
1067 {
1068 gmx_fio_do_int(fio, ir->gb_algorithm);
1069 gmx_fio_do_int(fio, ir->nstgbradii);
1070 gmx_fio_do_real(fio, ir->rgbradii);
1071 gmx_fio_do_real(fio, ir->gb_saltconc);
1072 gmx_fio_do_int(fio, ir->implicit_solvent);
1073 }
1074 else
1075 {
1076 ir->gb_algorithm = egbSTILL;
1077 ir->nstgbradii = 1;
1078 ir->rgbradii = 1.0;
1079 ir->gb_saltconc = 0;
1080 ir->implicit_solvent = eisNO;
1081 }
1082 if (file_version >= 55)
1083 {
1084 gmx_fio_do_real(fio, ir->gb_epsilon_solvent);
1085 gmx_fio_do_real(fio, ir->gb_obc_alpha);
1086 gmx_fio_do_real(fio, ir->gb_obc_beta);
1087 gmx_fio_do_real(fio, ir->gb_obc_gamma);
1088 if (file_version >= 60)
1089 {
1090 gmx_fio_do_real(fio, ir->gb_dielectric_offset);
1091 gmx_fio_do_int(fio, ir->sa_algorithm);
1092 }
1093 else
1094 {
1095 ir->gb_dielectric_offset = 0.009;
1096 ir->sa_algorithm = esaAPPROX;
1097 }
1098 gmx_fio_do_real(fio, ir->sa_surface_tension);
1099
1100 /* Override sa_surface_tension if it is not changed in the mpd-file */
1101 if (ir->sa_surface_tension < 0)
1102 {
1103 if (ir->gb_algorithm == egbSTILL)
1104 {
1105 ir->sa_surface_tension = 0.0049 * 100 * CAL2JOULE;
1106 }
1107 else if (ir->gb_algorithm == egbHCT || ir->gb_algorithm == egbOBC)
1108 {
1109 ir->sa_surface_tension = 0.0054 * 100 * CAL2JOULE;
1110 }
1111 }
1112
1113 }
1114 else
1115 {
1116 /* Better use sensible values than insane (0.0) ones... */
1117 ir->gb_epsilon_solvent = 80;
1118 ir->gb_obc_alpha = 1.0;
1119 ir->gb_obc_beta = 0.8;
1120 ir->gb_obc_gamma = 4.85;
1121 ir->sa_surface_tension = 2.092;
1122 }
1123
1124
1125 if (file_version >= 81)
1126 {
1127 gmx_fio_do_real(fio, ir->fourier_spacing);
1128 }
1129 else
1130 {
1131 ir->fourier_spacing = 0.0;
1132 }
1133 gmx_fio_do_int(fio, ir->nkx);
1134 gmx_fio_do_int(fio, ir->nky);
1135 gmx_fio_do_int(fio, ir->nkz);
1136 gmx_fio_do_int(fio, ir->pme_order);
1137 gmx_fio_do_real(fio, ir->ewald_rtol);
1138
1139 if (file_version >= 93)
1140 {
1141 gmx_fio_do_real(fio, ir->ewald_rtol_lj);
1142 }
1143 else
1144 {
1145 ir->ewald_rtol_lj = ir->ewald_rtol;
1146 }
1147
1148 if (file_version >= 24)
1149 {
1150 gmx_fio_do_int(fio, ir->ewald_geometry);
1151 }
1152 else
1153 {
1154 ir->ewald_geometry = eewg3D;
1155 }
1156
1157 if (file_version <= 17)
1158 {
1159 ir->epsilon_surface = 0;
1160 if (file_version == 17)
1161 {
1162 gmx_fio_do_int(fio, idum);
1163 }
1164 }
1165 else
1166 {
1167 gmx_fio_do_real(fio, ir->epsilon_surface);
1168 }
1169
1170 /* ignore bOptFFT */
1171 if (file_version < tpxv_RemoveObsoleteParameters1)
1172 {
1173 gmx_fio_do_gmx_bool(fio, bdum);
1174 }
1175
1176 if (file_version >= 93)
1177 {
1178 gmx_fio_do_int(fio, ir->ljpme_combination_rule);
1179 }
1180 gmx_fio_do_gmx_bool(fio, ir->bContinuation);
1181 gmx_fio_do_int(fio, ir->etc);
1182 /* before version 18, ir->etc was a gmx_bool (ir->btc),
1183 * but the values 0 and 1 still mean no and
1184 * berendsen temperature coupling, respectively.
1185 */
1186 if (file_version >= 79)
1187 {
1188 gmx_fio_do_gmx_bool(fio, ir->bPrintNHChains);
1189 }
1190 if (file_version >= 71)
1191 {
1192 gmx_fio_do_int(fio, ir->nsttcouple);
1193 }
1194 else
1195 {
1196 ir->nsttcouple = ir->nstcalcenergy;
1197 }
1198 if (file_version <= 15)
1199 {
1200 gmx_fio_do_int(fio, idum);
1201 }
1202 if (file_version <= 17)
1203 {
1204 gmx_fio_do_int(fio, ir->epct);
1205 if (file_version <= 15)
1206 {
1207 if (ir->epct == 5)
1208 {
1209 ir->epct = epctSURFACETENSION;
1210 }
1211 gmx_fio_do_int(fio, idum);
1212 }
1213 ir->epct -= 1;
1214 /* we have removed the NO alternative at the beginning */
1215 if (ir->epct == -1)
1216 {
1217 ir->epc = epcNO;
1218 ir->epct = epctISOTROPIC;
1219 }
1220 else
1221 {
1222 ir->epc = epcBERENDSEN;
1223 }
1224 }
1225 else
1226 {
1227 gmx_fio_do_int(fio, ir->epc);
1228 gmx_fio_do_int(fio, ir->epct);
1229 }
1230 if (file_version >= 71)
1231 {
1232 gmx_fio_do_int(fio, ir->nstpcouple);
1233 }
1234 else
1235 {
1236 ir->nstpcouple = ir->nstcalcenergy;
1237 }
1238 gmx_fio_do_real(fio, ir->tau_p);
1239 if (file_version <= 15)
1240 {
1241 gmx_fio_do_rvec(fio, vdum);
1242 clear_mat(ir->ref_p);
1243 for (i = 0; i < DIM; i++)
1244 {
1245 ir->ref_p[i][i] = vdum[i];
1246 }
1247 }
1248 else
1249 {
1250 gmx_fio_do_rvec(fio, ir->ref_p[XX]);
1251 gmx_fio_do_rvec(fio, ir->ref_p[YY]);
1252 gmx_fio_do_rvec(fio, ir->ref_p[ZZ]);
1253 }
1254 if (file_version <= 15)
1255 {
1256 gmx_fio_do_rvec(fio, vdum);
1257 clear_mat(ir->compress);
1258 for (i = 0; i < DIM; i++)
1259 {
1260 ir->compress[i][i] = vdum[i];
1261 }
1262 }
1263 else
1264 {
1265 gmx_fio_do_rvec(fio, ir->compress[XX]);
1266 gmx_fio_do_rvec(fio, ir->compress[YY]);
1267 gmx_fio_do_rvec(fio, ir->compress[ZZ]);
1268 }
1269 if (file_version >= 47)
1270 {
1271 gmx_fio_do_int(fio, ir->refcoord_scaling);
1272 gmx_fio_do_rvec(fio, ir->posres_com);
1273 gmx_fio_do_rvec(fio, ir->posres_comB);
1274 }
1275 else
1276 {
1277 ir->refcoord_scaling = erscNO;
1278 clear_rvec(ir->posres_com);
1279 clear_rvec(ir->posres_comB);
1280 }
1281 if ((file_version > 25) && (file_version < 79))
1282 {
1283 gmx_fio_do_int(fio, ir->andersen_seed);
1284 }
1285 else
1286 {
1287 ir->andersen_seed = 0;
1288 }
1289 if (file_version < 26)
1290 {
1291 gmx_fio_do_gmx_bool(fio, bSimAnn);
1292 gmx_fio_do_real(fio, zerotemptime);
1293 }
1294
1295 if (file_version < 37)
1296 {
1297 gmx_fio_do_real(fio, rdum);
1298 }
1299
1300 gmx_fio_do_real(fio, ir->shake_tol);
1301 if (file_version < 54)
1302 {
1303 gmx_fio_do_real(fio, *fudgeQQ);
1304 }
1305
1306 gmx_fio_do_int(fio, ir->efep);
1307 if (file_version <= 14 && ir->efep != efepNO)
1308 {
1309 ir->efep = efepYES;
1310 }
1311 do_fepvals(fio, ir->fepvals, bRead, file_version);
1312
1313 if (file_version >= 79)
1314 {
1315 gmx_fio_do_gmx_bool(fio, ir->bSimTemp);
1316 if (ir->bSimTemp)
1317 {
1318 ir->bSimTemp = TRUE;
1319 }
1320 }
1321 else
1322 {
1323 ir->bSimTemp = FALSE;
1324 }
1325 if (ir->bSimTemp)
1326 {
1327 do_simtempvals(fio, ir->simtempvals, ir->fepvals->n_lambda, bRead, file_version);
1328 }
1329
1330 if (file_version >= 79)
1331 {
1332 gmx_fio_do_gmx_bool(fio, ir->bExpanded);
1333 if (ir->bExpanded)
1334 {
1335 ir->bExpanded = TRUE;
1336 }
1337 else
1338 {
1339 ir->bExpanded = FALSE;
1340 }
1341 }
1342 if (ir->bExpanded)
1343 {
1344 do_expandedvals(fio, ir->expandedvals, ir->fepvals, bRead, file_version);
1345 }
1346 if (file_version >= 57)
1347 {
1348 gmx_fio_do_int(fio, ir->eDisre);
1349 }
1350 gmx_fio_do_int(fio, ir->eDisreWeighting);
1351 if (file_version < 22)
1352 {
1353 if (ir->eDisreWeighting == 0)
1354 {
1355 ir->eDisreWeighting = edrwEqual;
1356 }
1357 else
1358 {
1359 ir->eDisreWeighting = edrwConservative;
1360 }
1361 }
1362 gmx_fio_do_gmx_bool(fio, ir->bDisreMixed);
1363 gmx_fio_do_real(fio, ir->dr_fc);
1364 gmx_fio_do_real(fio, ir->dr_tau);
1365 gmx_fio_do_int(fio, ir->nstdisreout);
1366 if (file_version >= 22)
1367 {
1368 gmx_fio_do_real(fio, ir->orires_fc);
1369 gmx_fio_do_real(fio, ir->orires_tau);
1370 gmx_fio_do_int(fio, ir->nstorireout);
1371 }
1372 else
1373 {
1374 ir->orires_fc = 0;
1375 ir->orires_tau = 0;
1376 ir->nstorireout = 0;
1377 }
1378
1379 /* ignore dihre_fc */
1380 if (file_version >= 26 && file_version < 79)
1381 {
1382 gmx_fio_do_real(fio, rdum);
1383 if (file_version < 56)
1384 {
1385 gmx_fio_do_real(fio, rdum);
1386 gmx_fio_do_int(fio, idum);
1387 }
1388 }
1389
1390 gmx_fio_do_real(fio, ir->em_stepsize);
1391 gmx_fio_do_real(fio, ir->em_tol);
1392 if (file_version >= 22)
1393 {
1394 gmx_fio_do_gmx_bool(fio, ir->bShakeSOR);
1395 }
1396 else if (bRead)
1397 {
1398 ir->bShakeSOR = TRUE;
1399 }
1400 if (file_version >= 11)
1401 {
1402 gmx_fio_do_int(fio, ir->niter);
1403 }
1404 else if (bRead)
1405 {
1406 ir->niter = 25;
1407 fprintf(stderr, "Note: niter not in run input file, setting it to %d\n",
1408 ir->niter);
1409 }
1410 if (file_version >= 21)
1411 {
1412 gmx_fio_do_real(fio, ir->fc_stepsize);
1413 }
1414 else
1415 {
1416 ir->fc_stepsize = 0;
1417 }
1418 gmx_fio_do_int(fio, ir->eConstrAlg);
1419 gmx_fio_do_int(fio, ir->nProjOrder);
1420 gmx_fio_do_real(fio, ir->LincsWarnAngle);
1421 if (file_version <= 14)
1422 {
1423 gmx_fio_do_int(fio, idum);
1424 }
1425 if (file_version >= 26)
1426 {
1427 gmx_fio_do_int(fio, ir->nLincsIter);
1428 }
1429 else if (bRead)
1430 {
1431 ir->nLincsIter = 1;
1432 fprintf(stderr, "Note: nLincsIter not in run input file, setting it to %d\n",
1433 ir->nLincsIter);
1434 }
1435 if (file_version < 33)
1436 {
1437 gmx_fio_do_real(fio, bd_temp);
1438 }
1439 gmx_fio_do_real(fio, ir->bd_fric);
1440 if (file_version >= tpxv_Use64BitRandomSeed)
1441 {
1442 gmx_fio_do_int64(fio, ir->ld_seed);
1443 }
1444 else
1445 {
1446 gmx_fio_do_int(fio, idum);
1447 ir->ld_seed = idum;
1448 }
1449 if (file_version >= 33)
1450 {
1451 for (i = 0; i < DIM; i++)
1452 {
1453 gmx_fio_do_rvec(fio, ir->deform[i]);
1454 }
1455 }
1456 else
1457 {
1458 for (i = 0; i < DIM; i++)
1459 {
1460 clear_rvec(ir->deform[i]);
1461 }
1462 }
1463 if (file_version >= 14)
1464 {
1465 gmx_fio_do_real(fio, ir->cos_accel);
1466 }
1467 else if (bRead)
1468 {
1469 ir->cos_accel = 0;
1470 }
1471 gmx_fio_do_int(fio, ir->userint1);
1472 gmx_fio_do_int(fio, ir->userint2);
1473 gmx_fio_do_int(fio, ir->userint3);
1474 gmx_fio_do_int(fio, ir->userint4);
1475 gmx_fio_do_real(fio, ir->userreal1);
1476 gmx_fio_do_real(fio, ir->userreal2);
1477 gmx_fio_do_real(fio, ir->userreal3);
1478 gmx_fio_do_real(fio, ir->userreal4);
1479
1480 /* AdResS stuff */
1481 if (file_version >= 77)
1482 {
1483 gmx_fio_do_gmx_bool(fio, ir->bAdress);
1484 if (ir->bAdress)
1485 {
1486 if (bRead)
1487 {
1488 snew(ir->adress, 1);
1489 }
1490 gmx_fio_do_int(fio, ir->adress->type);
1491 gmx_fio_do_real(fio, ir->adress->const_wf);
1492 gmx_fio_do_real(fio, ir->adress->ex_width);
1493 gmx_fio_do_real(fio, ir->adress->hy_width);
1494 gmx_fio_do_int(fio, ir->adress->icor);
1495 gmx_fio_do_int(fio, ir->adress->site);
1496 gmx_fio_do_rvec(fio, ir->adress->refs);
1497 gmx_fio_do_int(fio, ir->adress->n_tf_grps);
1498 gmx_fio_do_real(fio, ir->adress->ex_forcecap);
1499 gmx_fio_do_int(fio, ir->adress->n_energy_grps);
1500 gmx_fio_do_int(fio, ir->adress->do_hybridpairs);
1501
1502 if (bRead)
1503 {
1504 snew(ir->adress->tf_table_index, ir->adress->n_tf_grps);
1505 }
1506 if (ir->adress->n_tf_grps > 0)
1507 {
1508 gmx_fio_ndo_int(fio, ir->adress->tf_table_index, ir->adress->n_tf_grps);
1509 }
1510 if (bRead)
1511 {
1512 snew(ir->adress->group_explicit, ir->adress->n_energy_grps);
1513 }
1514 if (ir->adress->n_energy_grps > 0)
1515 {
1516 gmx_fio_ndo_int(fio, ir->adress->group_explicit, ir->adress->n_energy_grps);
1517 }
1518 }
1519 }
1520 else
1521 {
1522 ir->bAdress = FALSE;
1523 }
1524
1525 /* pull stuff */
1526 if (file_version >= 48)
1527 {
1528 int ePullOld = 0;
1529
1530 if (file_version >= tpxv_PullCoordTypeGeom)
1531 {
1532 gmx_fio_do_gmx_bool(fio, ir->bPull);
1533 }
1534 else
1535 {
1536 gmx_fio_do_int(fio, ePullOld);
1537 ir->bPull = (ePullOld > 0);
1538 /* We removed the first ePull=ePullNo for the enum */
1539 ePullOld -= 1;
1540 }
1541 if (ir->bPull)
1542 {
1543 if (bRead)
1544 {
1545 snew(ir->pull, 1);
1546 }
1547 do_pull(fio, ir->pull, bRead, file_version, ePullOld);
1548 }
1549 }
1550 else
1551 {
1552 ir->bPull = FALSE;
1553 }
1554
1555 /* Enforced rotation */
1556 if (file_version >= 74)
1557 {
1558 gmx_fio_do_int(fio, ir->bRot);
1559 if (ir->bRot == TRUE)
1560 {
1561 if (bRead)
1562 {
1563 snew(ir->rot, 1);
1564 }
1565 do_rot(fio, ir->rot, bRead);
1566 }
1567 }
1568 else
1569 {
1570 ir->bRot = FALSE;
1571 }
1572
1573 /* Interactive molecular dynamics */
1574 if (file_version >= tpxv_InteractiveMolecularDynamics)
1575 {
1576 gmx_fio_do_int(fio, ir->bIMD);
1577 if (TRUE == ir->bIMD)
1578 {
1579 if (bRead)
1580 {
1581 snew(ir->imd, 1);
1582 }
1583 do_imd(fio, ir->imd, bRead);
1584 }
1585 }
1586 else
1587 {
1588 /* We don't support IMD sessions for old .tpr files */
1589 ir->bIMD = FALSE;
1590 }
1591
1592 /* grpopts stuff */
1593 gmx_fio_do_int(fio, ir->opts.ngtc);
1594 if (file_version >= 69)
1595 {
1596 gmx_fio_do_int(fio, ir->opts.nhchainlength);
1597 }
1598 else
1599 {
1600 ir->opts.nhchainlength = 1;
1601 }
1602 gmx_fio_do_int(fio, ir->opts.ngacc);
1603 gmx_fio_do_int(fio, ir->opts.ngfrz);
1604 gmx_fio_do_int(fio, ir->opts.ngener);
1605
1606 if (bRead)
1607 {
1608 snew(ir->opts.nrdf, ir->opts.ngtc);
1609 snew(ir->opts.ref_t, ir->opts.ngtc);
1610 snew(ir->opts.annealing, ir->opts.ngtc);
1611 snew(ir->opts.anneal_npoints, ir->opts.ngtc);
1612 snew(ir->opts.anneal_time, ir->opts.ngtc);
1613 snew(ir->opts.anneal_temp, ir->opts.ngtc);
1614 snew(ir->opts.tau_t, ir->opts.ngtc);
1615 snew(ir->opts.nFreeze, ir->opts.ngfrz);
1616 snew(ir->opts.acc, ir->opts.ngacc);
1617 snew(ir->opts.egp_flags, ir->opts.ngener*ir->opts.ngener);
1618 }
1619 if (ir->opts.ngtc > 0)
1620 {
1621 if (bRead && file_version < 13)
1622 {
1623 snew(tmp, ir->opts.ngtc);
1624 gmx_fio_ndo_int(fio, tmp, ir->opts.ngtc);
1625 for (i = 0; i < ir->opts.ngtc; i++)
1626 {
1627 ir->opts.nrdf[i] = tmp[i];
1628 }
1629 sfree(tmp);
1630 }
1631 else
1632 {
1633 gmx_fio_ndo_real(fio, ir->opts.nrdf, ir->opts.ngtc);
1634 }
1635 gmx_fio_ndo_real(fio, ir->opts.ref_t, ir->opts.ngtc);
1636 gmx_fio_ndo_real(fio, ir->opts.tau_t, ir->opts.ngtc);
1637 if (file_version < 33 && ir->eI == eiBD)
1638 {
1639 for (i = 0; i < ir->opts.ngtc; i++)
1640 {
1641 ir->opts.tau_t[i] = bd_temp;
1642 }
1643 }
1644 }
1645 if (ir->opts.ngfrz > 0)
1646 {
1647 gmx_fio_ndo_ivec(fio, ir->opts.nFreeze, ir->opts.ngfrz);
1648 }
1649 if (ir->opts.ngacc > 0)
1650 {
1651 gmx_fio_ndo_rvec(fio, ir->opts.acc, ir->opts.ngacc);
1652 }
1653 if (file_version >= 12)
1654 {
1655 gmx_fio_ndo_int(fio, ir->opts.egp_flags,
1656 ir->opts.ngener*ir->opts.ngener);
1657 }
1658
1659 if (bRead && file_version < 26)
1660 {
1661 for (i = 0; i < ir->opts.ngtc; i++)
1662 {
1663 if (bSimAnn)
1664 {
1665 ir->opts.annealing[i] = eannSINGLE;
1666 ir->opts.anneal_npoints[i] = 2;
1667 snew(ir->opts.anneal_time[i], 2);
1668 snew(ir->opts.anneal_temp[i], 2);
1669 /* calculate the starting/ending temperatures from reft, zerotemptime, and nsteps */
1670 finish_t = ir->init_t + ir->nsteps * ir->delta_t;
1671 init_temp = ir->opts.ref_t[i]*(1-ir->init_t/zerotemptime);
1672 finish_temp = ir->opts.ref_t[i]*(1-finish_t/zerotemptime);
1673 ir->opts.anneal_time[i][0] = ir->init_t;
1674 ir->opts.anneal_time[i][1] = finish_t;
1675 ir->opts.anneal_temp[i][0] = init_temp;
1676 ir->opts.anneal_temp[i][1] = finish_temp;
1677 }
1678 else
1679 {
1680 ir->opts.annealing[i] = eannNO;
1681 ir->opts.anneal_npoints[i] = 0;
1682 }
1683 }
1684 }
1685 else
1686 {
1687 /* file version 26 or later */
1688 /* First read the lists with annealing and npoints for each group */
1689 gmx_fio_ndo_int(fio, ir->opts.annealing, ir->opts.ngtc);
1690 gmx_fio_ndo_int(fio, ir->opts.anneal_npoints, ir->opts.ngtc);
1691 for (j = 0; j < (ir->opts.ngtc); j++)
1692 {
1693 k = ir->opts.anneal_npoints[j];
1694 if (bRead)
1695 {
1696 snew(ir->opts.anneal_time[j], k);
1697 snew(ir->opts.anneal_temp[j], k);
1698 }
1699 gmx_fio_ndo_real(fio, ir->opts.anneal_time[j], k);
1700 gmx_fio_ndo_real(fio, ir->opts.anneal_temp[j], k);
1701 }
1702 }
1703 /* Walls */
1704 if (file_version >= 45)
1705 {
1706 gmx_fio_do_int(fio, ir->nwall);
1707 gmx_fio_do_int(fio, ir->wall_type);
1708 if (file_version >= 50)
1709 {
1710 gmx_fio_do_real(fio, ir->wall_r_linpot);
1711 }
1712 else
1713 {
1714 ir->wall_r_linpot = -1;
1715 }
1716 gmx_fio_do_int(fio, ir->wall_atomtype[0]);
1717 gmx_fio_do_int(fio, ir->wall_atomtype[1]);
1718 gmx_fio_do_real(fio, ir->wall_density[0]);
1719 gmx_fio_do_real(fio, ir->wall_density[1]);
1720 gmx_fio_do_real(fio, ir->wall_ewald_zfac);
1721 }
1722 else
1723 {
1724 ir->nwall = 0;
1725 ir->wall_type = 0;
1726 ir->wall_atomtype[0] = -1;
1727 ir->wall_atomtype[1] = -1;
1728 ir->wall_density[0] = 0;
1729 ir->wall_density[1] = 0;
1730 ir->wall_ewald_zfac = 3;
1731 }
1732 /* Cosine stuff for electric fields */
1733 for (j = 0; (j < DIM); j++)
1734 {
1735 gmx_fio_do_int(fio, ir->ex[j].n);
1736 gmx_fio_do_int(fio, ir->et[j].n);
1737 if (bRead)
1738 {
1739 snew(ir->ex[j].a, ir->ex[j].n);
1740 snew(ir->ex[j].phi, ir->ex[j].n);
1741 snew(ir->et[j].a, ir->et[j].n);
1742 snew(ir->et[j].phi, ir->et[j].n);
1743 }
1744 gmx_fio_ndo_real(fio, ir->ex[j].a, ir->ex[j].n);
1745 gmx_fio_ndo_real(fio, ir->ex[j].phi, ir->ex[j].n);
1746 gmx_fio_ndo_real(fio, ir->et[j].a, ir->et[j].n);
1747 gmx_fio_ndo_real(fio, ir->et[j].phi, ir->et[j].n);
1748 }
1749
1750 /* Swap ions */
1751 if (file_version >= tpxv_ComputationalElectrophysiology)
1752 {
1753 gmx_fio_do_int(fio, ir->eSwapCoords);
1754 if (ir->eSwapCoords != eswapNO)
1755 {
1756 if (bRead)
1757 {
1758 snew(ir->swap, 1);
1759 }
1760 do_swapcoords(fio, ir->swap, bRead, file_version);
1761 }
1762 }
1763
1764 /* QMMM stuff */
1765 if (file_version >= 39)
1766 {
1767 gmx_fio_do_gmx_bool(fio, ir->bQMMM);
1768 gmx_fio_do_int(fio, ir->QMMMscheme);
1769 gmx_fio_do_real(fio, ir->scalefactor);
1770 gmx_fio_do_int(fio, ir->opts.ngQM);
1771 if (bRead)
1772 {
1773 snew(ir->opts.QMmethod, ir->opts.ngQM);
1774 snew(ir->opts.QMbasis, ir->opts.ngQM);
1775 snew(ir->opts.QMcharge, ir->opts.ngQM);
1776 snew(ir->opts.QMmult, ir->opts.ngQM);
1777 snew(ir->opts.bSH, ir->opts.ngQM);
1778 snew(ir->opts.CASorbitals, ir->opts.ngQM);
1779 snew(ir->opts.CASelectrons, ir->opts.ngQM);
1780 snew(ir->opts.SAon, ir->opts.ngQM);
1781 snew(ir->opts.SAoff, ir->opts.ngQM);
1782 snew(ir->opts.SAsteps, ir->opts.ngQM);
1783 snew(ir->opts.bOPT, ir->opts.ngQM);
1784 snew(ir->opts.bTS, ir->opts.ngQM);
1785 }
1786 if (ir->opts.ngQM > 0)
1787 {
1788 gmx_fio_ndo_int(fio, ir->opts.QMmethod, ir->opts.ngQM);
1789 gmx_fio_ndo_int(fio, ir->opts.QMbasis, ir->opts.ngQM);
1790 gmx_fio_ndo_int(fio, ir->opts.QMcharge, ir->opts.ngQM);
1791 gmx_fio_ndo_int(fio, ir->opts.QMmult, ir->opts.ngQM);
1792 gmx_fio_ndo_gmx_bool(fio, ir->opts.bSH, ir->opts.ngQM);
1793 gmx_fio_ndo_int(fio, ir->opts.CASorbitals, ir->opts.ngQM);
1794 gmx_fio_ndo_int(fio, ir->opts.CASelectrons, ir->opts.ngQM);
1795 gmx_fio_ndo_real(fio, ir->opts.SAon, ir->opts.ngQM);
1796 gmx_fio_ndo_real(fio, ir->opts.SAoff, ir->opts.ngQM);
1797 gmx_fio_ndo_int(fio, ir->opts.SAsteps, ir->opts.ngQM);
1798 gmx_fio_ndo_gmx_bool(fio, ir->opts.bOPT, ir->opts.ngQM);
1799 gmx_fio_ndo_gmx_bool(fio, ir->opts.bTS, ir->opts.ngQM);
1800 }
1801 /* end of QMMM stuff */
1802 }
1803 }
1804
1805
1806 static void do_harm(t_fileio *fio, t_iparams *iparams)
1807 {
1808 gmx_fio_do_real(fio, iparams->harmonic.rA);
1809 gmx_fio_do_real(fio, iparams->harmonic.krA);
1810 gmx_fio_do_real(fio, iparams->harmonic.rB);
1811 gmx_fio_do_real(fio, iparams->harmonic.krB);
1812 }
1813
1814 void do_iparams(t_fileio *fio, t_functype ftype, t_iparams *iparams,
1815 gmx_bool bRead, int file_version)
1816 {
1817 int idum;
1818 real rdum;
1819
1820 switch (ftype)
1821 {
1822 case F_ANGLES:
1823 case F_G96ANGLES:
1824 case F_BONDS:
1825 case F_G96BONDS:
1826 case F_HARMONIC:
1827 case F_IDIHS:
1828 do_harm(fio, iparams);
1829 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && bRead)
1830 {
1831 /* Correct incorrect storage of parameters */
1832 iparams->pdihs.phiB = iparams->pdihs.phiA;
1833 iparams->pdihs.cpB = iparams->pdihs.cpA;
1834 }
1835 break;
1836 case F_RESTRANGLES:
1837 gmx_fio_do_real(fio, iparams->harmonic.rA);
1838 gmx_fio_do_real(fio, iparams->harmonic.krA);
1839 break;
1840 case F_LINEAR_ANGLES:
1841 gmx_fio_do_real(fio, iparams->linangle.klinA);
1842 gmx_fio_do_real(fio, iparams->linangle.aA);
1843 gmx_fio_do_real(fio, iparams->linangle.klinB);
1844 gmx_fio_do_real(fio, iparams->linangle.aB);
1845 break;
1846 case F_FENEBONDS:
1847 gmx_fio_do_real(fio, iparams->fene.bm);
1848 gmx_fio_do_real(fio, iparams->fene.kb);
1849 break;
1850
1851 case F_RESTRBONDS:
1852 gmx_fio_do_real(fio, iparams->restraint.lowA);
1853 gmx_fio_do_real(fio, iparams->restraint.up1A);
1854 gmx_fio_do_real(fio, iparams->restraint.up2A);
1855 gmx_fio_do_real(fio, iparams->restraint.kA);
1856 gmx_fio_do_real(fio, iparams->restraint.lowB);
1857 gmx_fio_do_real(fio, iparams->restraint.up1B);
1858 gmx_fio_do_real(fio, iparams->restraint.up2B);
1859 gmx_fio_do_real(fio, iparams->restraint.kB);
1860 break;
1861 case F_TABBONDS:
1862 case F_TABBONDSNC:
1863 case F_TABANGLES:
1864 case F_TABDIHS:
1865 gmx_fio_do_real(fio, iparams->tab.kA);
1866 gmx_fio_do_int(fio, iparams->tab.table);
1867 gmx_fio_do_real(fio, iparams->tab.kB);
1868 break;
1869 case F_CROSS_BOND_BONDS:
1870 gmx_fio_do_real(fio, iparams->cross_bb.r1e);
1871 gmx_fio_do_real(fio, iparams->cross_bb.r2e);
1872 gmx_fio_do_real(fio, iparams->cross_bb.krr);
1873 break;
1874 case F_CROSS_BOND_ANGLES:
1875 gmx_fio_do_real(fio, iparams->cross_ba.r1e);
1876 gmx_fio_do_real(fio, iparams->cross_ba.r2e);
1877 gmx_fio_do_real(fio, iparams->cross_ba.r3e);
1878 gmx_fio_do_real(fio, iparams->cross_ba.krt);
1879 break;
1880 case F_UREY_BRADLEY:
1881 gmx_fio_do_real(fio, iparams->u_b.thetaA);
1882 gmx_fio_do_real(fio, iparams->u_b.kthetaA);
1883 gmx_fio_do_real(fio, iparams->u_b.r13A);
1884 gmx_fio_do_real(fio, iparams->u_b.kUBA);
1885 if (file_version >= 79)
1886 {
1887 gmx_fio_do_real(fio, iparams->u_b.thetaB);
1888 gmx_fio_do_real(fio, iparams->u_b.kthetaB);
1889 gmx_fio_do_real(fio, iparams->u_b.r13B);
1890 gmx_fio_do_real(fio, iparams->u_b.kUBB);
1891 }
1892 else
1893 {
1894 iparams->u_b.thetaB = iparams->u_b.thetaA;
1895 iparams->u_b.kthetaB = iparams->u_b.kthetaA;
1896 iparams->u_b.r13B = iparams->u_b.r13A;
1897 iparams->u_b.kUBB = iparams->u_b.kUBA;
1898 }
1899 break;
1900 case F_QUARTIC_ANGLES:
1901 gmx_fio_do_real(fio, iparams->qangle.theta);
1902 gmx_fio_ndo_real(fio, iparams->qangle.c, 5);
1903 break;
1904 case F_BHAM:
1905 gmx_fio_do_real(fio, iparams->bham.a);
1906 gmx_fio_do_real(fio, iparams->bham.b);
1907 gmx_fio_do_real(fio, iparams->bham.c);
1908 break;
1909 case F_MORSE:
1910 gmx_fio_do_real(fio, iparams->morse.b0A);
1911 gmx_fio_do_real(fio, iparams->morse.cbA);
1912 gmx_fio_do_real(fio, iparams->morse.betaA);
1913 if (file_version >= 79)
1914 {
1915 gmx_fio_do_real(fio, iparams->morse.b0B);
1916 gmx_fio_do_real(fio, iparams->morse.cbB);
1917 gmx_fio_do_real(fio, iparams->morse.betaB);
1918 }
1919 else
1920 {
1921 iparams->morse.b0B = iparams->morse.b0A;
1922 iparams->morse.cbB = iparams->morse.cbA;
1923 iparams->morse.betaB = iparams->morse.betaA;
1924 }
1925 break;
1926 case F_CUBICBONDS:
1927 gmx_fio_do_real(fio, iparams->cubic.b0);
1928 gmx_fio_do_real(fio, iparams->cubic.kb);
1929 gmx_fio_do_real(fio, iparams->cubic.kcub);
1930 break;
1931 case F_CONNBONDS:
1932 break;
1933 case F_POLARIZATION:
1934 gmx_fio_do_real(fio, iparams->polarize.alpha);
1935 break;
1936 case F_ANHARM_POL:
1937 gmx_fio_do_real(fio, iparams->anharm_polarize.alpha);
1938 gmx_fio_do_real(fio, iparams->anharm_polarize.drcut);
1939 gmx_fio_do_real(fio, iparams->anharm_polarize.khyp);
1940 break;
1941 case F_WATER_POL:
1942 if (file_version < 31)
1943 {
1944 gmx_fatal(FARGS, "Old tpr files with water_polarization not supported. Make a new.");
1945 }
1946 gmx_fio_do_real(fio, iparams->wpol.al_x);
1947 gmx_fio_do_real(fio, iparams->wpol.al_y);
1948 gmx_fio_do_real(fio, iparams->wpol.al_z);
1949 gmx_fio_do_real(fio, iparams->wpol.rOH);
1950 gmx_fio_do_real(fio, iparams->wpol.rHH);
1951 gmx_fio_do_real(fio, iparams->wpol.rOD);
1952 break;
1953 case F_THOLE_POL:
1954 gmx_fio_do_real(fio, iparams->thole.a);
1955 gmx_fio_do_real(fio, iparams->thole.alpha1);
1956 gmx_fio_do_real(fio, iparams->thole.alpha2);
1957 gmx_fio_do_real(fio, iparams->thole.rfac);
1958 break;
1959 case F_LJ:
1960 gmx_fio_do_real(fio, iparams->lj.c6);
1961 gmx_fio_do_real(fio, iparams->lj.c12);
1962 break;
1963 case F_LJ14:
1964 gmx_fio_do_real(fio, iparams->lj14.c6A);
1965 gmx_fio_do_real(fio, iparams->lj14.c12A);
1966 gmx_fio_do_real(fio, iparams->lj14.c6B);
1967 gmx_fio_do_real(fio, iparams->lj14.c12B);
1968 break;
1969 case F_LJC14_Q:
1970 gmx_fio_do_real(fio, iparams->ljc14.fqq);
1971 gmx_fio_do_real(fio, iparams->ljc14.qi);
1972 gmx_fio_do_real(fio, iparams->ljc14.qj);
1973 gmx_fio_do_real(fio, iparams->ljc14.c6);
1974 gmx_fio_do_real(fio, iparams->ljc14.c12);
1975 break;
1976 case F_LJC_PAIRS_NB:
1977 gmx_fio_do_real(fio, iparams->ljcnb.qi);
1978 gmx_fio_do_real(fio, iparams->ljcnb.qj);
1979 gmx_fio_do_real(fio, iparams->ljcnb.c6);
1980 gmx_fio_do_real(fio, iparams->ljcnb.c12);
1981 break;
1982 case F_PDIHS:
1983 case F_PIDIHS:
1984 case F_ANGRES:
1985 case F_ANGRESZ:
1986 gmx_fio_do_real(fio, iparams->pdihs.phiA);
1987 gmx_fio_do_real(fio, iparams->pdihs.cpA);
1988 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && file_version < 42)
1989 {
1990 /* Read the incorrectly stored multiplicity */
1991 gmx_fio_do_real(fio, iparams->harmonic.rB);
1992 gmx_fio_do_real(fio, iparams->harmonic.krB);
1993 iparams->pdihs.phiB = iparams->pdihs.phiA;
1994 iparams->pdihs.cpB = iparams->pdihs.cpA;
1995 }
1996 else
1997 {
1998 gmx_fio_do_real(fio, iparams->pdihs.phiB);
1999 gmx_fio_do_real(fio, iparams->pdihs.cpB);
2000 gmx_fio_do_int(fio, iparams->pdihs.mult);
2001 }
2002 break;
2003 case F_RESTRDIHS:
2004 gmx_fio_do_real(fio, iparams->pdihs.phiA);
2005 gmx_fio_do_real(fio, iparams->pdihs.cpA);
2006 break;
2007 case F_DISRES:
2008 gmx_fio_do_int(fio, iparams->disres.label);
2009 gmx_fio_do_int(fio, iparams->disres.type);
2010 gmx_fio_do_real(fio, iparams->disres.low);
2011 gmx_fio_do_real(fio, iparams->disres.up1);
2012 gmx_fio_do_real(fio, iparams->disres.up2);
2013 gmx_fio_do_real(fio, iparams->disres.kfac);
2014 break;
2015 case F_ORIRES:
2016 gmx_fio_do_int(fio, iparams->orires.ex);
2017 gmx_fio_do_int(fio, iparams->orires.label);
2018 gmx_fio_do_int(fio, iparams->orires.power);
2019 gmx_fio_do_real(fio, iparams->orires.c);
2020 gmx_fio_do_real(fio, iparams->orires.obs);
2021 gmx_fio_do_real(fio, iparams->orires.kfac);
2022 break;
2023 case F_DIHRES:
2024 if (file_version < 82)
2025 {
2026 gmx_fio_do_int(fio, idum);
2027 gmx_fio_do_int(fio, idum);
2028 }
2029 gmx_fio_do_real(fio, iparams->dihres.phiA);
2030 gmx_fio_do_real(fio, iparams->dihres.dphiA);
2031 gmx_fio_do_real(fio, iparams->dihres.kfacA);
2032 if (file_version >= 82)
2033 {
2034 gmx_fio_do_real(fio, iparams->dihres.phiB);
2035 gmx_fio_do_real(fio, iparams->dihres.dphiB);
2036 gmx_fio_do_real(fio, iparams->dihres.kfacB);
2037 }
2038 else
2039 {
2040 iparams->dihres.phiB = iparams->dihres.phiA;
2041 iparams->dihres.dphiB = iparams->dihres.dphiA;
2042 iparams->dihres.kfacB = iparams->dihres.kfacA;
2043 }
2044 break;
2045 case F_POSRES:
2046 gmx_fio_do_rvec(fio, iparams->posres.pos0A);
2047 gmx_fio_do_rvec(fio, iparams->posres.fcA);
2048 if (bRead && file_version < 27)
2049 {
2050 copy_rvec(iparams->posres.pos0A, iparams->posres.pos0B);
2051 copy_rvec(iparams->posres.fcA, iparams->posres.fcB);
2052 }
2053 else
2054 {
2055 gmx_fio_do_rvec(fio, iparams->posres.pos0B);
2056 gmx_fio_do_rvec(fio, iparams->posres.fcB);
2057 }
2058 break;
2059 case F_FBPOSRES:
2060 gmx_fio_do_int(fio, iparams->fbposres.geom);
2061 gmx_fio_do_rvec(fio, iparams->fbposres.pos0);
2062 gmx_fio_do_real(fio, iparams->fbposres.r);
2063 gmx_fio_do_real(fio, iparams->fbposres.k);
2064 break;
2065 case F_CBTDIHS:
2066 gmx_fio_ndo_real(fio, iparams->cbtdihs.cbtcA, NR_CBTDIHS);
2067 break;
2068 case F_RBDIHS:
2069 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
2070 if (file_version >= 25)
2071 {
2072 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
2073 }
2074 break;
2075 case F_FOURDIHS:
2076 /* Fourier dihedrals are internally represented
2077 * as Ryckaert-Bellemans since those are faster to compute.
2078 */
2079 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
2080 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
2081 break;
2082 case F_CONSTR:
2083 case F_CONSTRNC:
2084 gmx_fio_do_real(fio, iparams->constr.dA);
2085 gmx_fio_do_real(fio, iparams->constr.dB);
2086 break;
2087 case F_SETTLE:
2088 gmx_fio_do_real(fio, iparams->settle.doh);
2089 gmx_fio_do_real(fio, iparams->settle.dhh);
2090 break;
2091 case F_VSITE2:
2092 gmx_fio_do_real(fio, iparams->vsite.a);
2093 break;
2094 case F_VSITE3:
2095 case F_VSITE3FD:
2096 case F_VSITE3FAD:
2097 gmx_fio_do_real(fio, iparams->vsite.a);
2098 gmx_fio_do_real(fio, iparams->vsite.b);
2099 break;
2100 case F_VSITE3OUT:
2101 case F_VSITE4FD:
2102 case F_VSITE4FDN:
2103 gmx_fio_do_real(fio, iparams->vsite.a);
2104 gmx_fio_do_real(fio, iparams->vsite.b);
2105 gmx_fio_do_real(fio, iparams->vsite.c);
2106 break;
2107 case F_VSITEN:
2108 gmx_fio_do_int(fio, iparams->vsiten.n);
2109 gmx_fio_do_real(fio, iparams->vsiten.a);
2110 break;
2111 case F_GB12:
2112 case F_GB13:
2113 case F_GB14:
2114 /* We got rid of some parameters in version 68 */
2115 if (bRead && file_version < 68)
2116 {
2117 gmx_fio_do_real(fio, rdum);
2118 gmx_fio_do_real(fio, rdum);
2119 gmx_fio_do_real(fio, rdum);
2120 gmx_fio_do_real(fio, rdum);
2121 }
2122 gmx_fio_do_real(fio, iparams->gb.sar);
2123 gmx_fio_do_real(fio, iparams->gb.st);
2124 gmx_fio_do_real(fio, iparams->gb.pi);
2125 gmx_fio_do_real(fio, iparams->gb.gbr);
2126 gmx_fio_do_real(fio, iparams->gb.bmlt);
2127 break;
2128 case F_CMAP:
2129 gmx_fio_do_int(fio, iparams->cmap.cmapA);
2130 gmx_fio_do_int(fio, iparams->cmap.cmapB);
2131 break;
2132 default:
2133 gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
2134 ftype, interaction_function[ftype].name, __FILE__, __LINE__);
2135 }
2136 }
2137
2138 static void do_ilist(t_fileio *fio, t_ilist *ilist, gmx_bool bRead, int file_version)
2139 {
2140 int i, idum;
2141
2142 if (file_version < 44)
2143 {
2144 for (i = 0; i < MAXNODES; i++)
2145 {
2146 gmx_fio_do_int(fio, idum);
2147 }
2148 }
2149 gmx_fio_do_int(fio, ilist->nr);
2150 if (bRead)
2151 {
2152 snew(ilist->iatoms, ilist->nr);
2153 }
2154 gmx_fio_ndo_int(fio, ilist->iatoms, ilist->nr);
2155 }
2156
2157 static void do_ffparams(t_fileio *fio, gmx_ffparams_t *ffparams,
2158 gmx_bool bRead, int file_version)
2159 {
2160 int idum, i;
2161 unsigned int k;
2162
2163 gmx_fio_do_int(fio, ffparams->atnr);
2164 if (file_version < 57)
2165 {
2166 gmx_fio_do_int(fio, idum);
2167 }
2168 gmx_fio_do_int(fio, ffparams->ntypes);
2169 if (bRead)
2170 {
2171 snew(ffparams->functype, ffparams->ntypes);
2172 snew(ffparams->iparams, ffparams->ntypes);
2173 }
2174 /* Read/write all the function types */
2175 gmx_fio_ndo_int(fio, ffparams->functype, ffparams->ntypes);
2176
2177 if (file_version >= 66)
2178 {
2179 gmx_fio_do_double(fio, ffparams->reppow);
2180 }
2181 else
2182 {
2183 ffparams->reppow = 12.0;
2184 }
2185
2186 if (file_version >= 57)
2187 {
2188 gmx_fio_do_real(fio, ffparams->fudgeQQ);
2189 }
2190
2191 /* Check whether all these function types are supported by the code.
2192 * In practice the code is backwards compatible, which means that the
2193 * numbering may have to be altered from old numbering to new numbering
2194 */
2195 for (i = 0; (i < ffparams->ntypes); i++)
2196 {
2197 if (bRead)
2198 {
2199 /* Loop over file versions */
2200 for (k = 0; (k < NFTUPD); k++)
2201 {
2202 /* Compare the read file_version to the update table */
2203 if ((file_version < ftupd[k].fvnr) &&
2204 (ffparams->functype[i] >= ftupd[k].ftype))
2205 {
2206 ffparams->functype[i] += 1;
2207 }
2208 }
2209 }
2210
2211 do_iparams(fio, ffparams->functype[i], &ffparams->iparams[i], bRead,
2212 file_version);
2213 }
2214 }
2215
2216 static void add_settle_atoms(t_ilist *ilist)
2217 {
2218 int i;
2219
2220 /* Settle used to only store the first atom: add the other two */
2221 srenew(ilist->iatoms, 2*ilist->nr);
2222 for (i = ilist->nr/2-1; i >= 0; i--)
2223 {
2224 ilist->iatoms[4*i+0] = ilist->iatoms[2*i+0];
2225 ilist->iatoms[4*i+1] = ilist->iatoms[2*i+1];
2226 ilist->iatoms[4*i+2] = ilist->iatoms[2*i+1] + 1;
2227 ilist->iatoms[4*i+3] = ilist->iatoms[2*i+1] + 2;
2228 }
2229 ilist->nr = 2*ilist->nr;
2230 }
2231
2232 static void do_ilists(t_fileio *fio, t_ilist *ilist, gmx_bool bRead,
2233 int file_version)
2234 {
2235 int j;
2236 gmx_bool bClear;
2237 unsigned int k;
2238
2239 for (j = 0; (j < F_NRE); j++)
2240 {
2241 bClear = FALSE;
2242 if (bRead)
2243 {
2244 for (k = 0; k < NFTUPD; k++)
2245 {
2246 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
2247 {
2248 bClear = TRUE;
2249 }
2250 }
2251 }
2252 if (bClear)
2253 {
2254 ilist[j].nr = 0;
2255 ilist[j].iatoms = NULL;
2256 }
2257 else
2258 {
2259 do_ilist(fio, &ilist[j], bRead, file_version);
2260 if (file_version < 78 && j == F_SETTLE && ilist[j].nr > 0)
2261 {
2262 add_settle_atoms(&ilist[j]);
2263 }
2264 }
2265 }
2266 }
2267
2268 static void do_idef(t_fileio *fio, gmx_ffparams_t *ffparams, gmx_moltype_t *molt,
2269 gmx_bool bRead, int file_version)
2270 {
2271 do_ffparams(fio, ffparams, bRead, file_version);
2272
2273 if (file_version >= 54)
2274 {
2275 gmx_fio_do_real(fio, ffparams->fudgeQQ);
2276 }
2277
2278 do_ilists(fio, molt->ilist, bRead, file_version);
2279 }
2280
2281 static void do_block(t_fileio *fio, t_block *block, gmx_bool bRead, int file_version)
2282 {
2283 int i, idum, dum_nra, *dum_a;
2284
2285 if (file_version < 44)
2286 {
2287 for (i = 0; i < MAXNODES; i++)
2288 {
2289 gmx_fio_do_int(fio, idum);
2290 }
2291 }
2292 gmx_fio_do_int(fio, block->nr);
2293 if (file_version < 51)
2294 {
2295 gmx_fio_do_int(fio, dum_nra);
2296 }
2297 if (bRead)
2298 {
2299 if ((block->nalloc_index > 0) && (NULL != block->index))
2300 {
2301 sfree(block->index);
2302 }
2303 block->nalloc_index = block->nr+1;
2304 snew(block->index, block->nalloc_index);
2305 }
2306 gmx_fio_ndo_int(fio, block->index, block->nr+1);
2307
2308 if (file_version < 51 && dum_nra > 0)
2309 {
2310 snew(dum_a, dum_nra);
2311 gmx_fio_ndo_int(fio, dum_a, dum_nra);
2312 sfree(dum_a);
2313 }
2314 }
2315
2316 static void do_blocka(t_fileio *fio, t_blocka *block, gmx_bool bRead,
2317 int file_version)
2318 {
2319 int i, idum;
2320
2321 if (file_version < 44)
2322 {
2323 for (i = 0; i < MAXNODES; i++)
2324 {
2325 gmx_fio_do_int(fio, idum);
2326 }
2327 }
2328 gmx_fio_do_int(fio, block->nr);
2329 gmx_fio_do_int(fio, block->nra);
2330 if (bRead)
2331 {
2332 block->nalloc_index = block->nr+1;
2333 snew(block->index, block->nalloc_index);
2334 block->nalloc_a = block->nra;
2335 snew(block->a, block->nalloc_a);
2336 }
2337 gmx_fio_ndo_int(fio, block->index, block->nr+1);
2338 gmx_fio_ndo_int(fio, block->a, block->nra);
2339 }
2340
2341 /* This is a primitive routine to make it possible to translate atomic numbers
2342 * to element names when reading TPR files, without making the Gromacs library
2343 * directory a dependency on mdrun (which is the case if we need elements.dat).
2344 */
2345 static const char *
2346 atomicnumber_to_element(int atomicnumber)
2347 {
2348 const char * p;
2349
2350 /* This does not have to be complete, so we only include elements likely
2351 * to occur in PDB files.
2352 */
2353 switch (atomicnumber)
2354 {
2355 case 1: p = "H"; break;
2356 case 5: p = "B"; break;
2357 case 6: p = "C"; break;
2358 case 7: p = "N"; break;
2359 case 8: p = "O"; break;
2360 case 9: p = "F"; break;
2361 case 11: p = "Na"; break;
2362 case 12: p = "Mg"; break;
2363 case 15: p = "P"; break;
2364 case 16: p = "S"; break;
2365 case 17: p = "Cl"; break;
2366 case 18: p = "Ar"; break;
2367 case 19: p = "K"; break;
2368 case 20: p = "Ca"; break;
2369 case 25: p = "Mn"; break;
2370 case 26: p = "Fe"; break;
2371 case 28: p = "Ni"; break;
2372 case 29: p = "Cu"; break;
2373 case 30: p = "Zn"; break;
2374 case 35: p = "Br"; break;
2375 case 47: p = "Ag"; break;
2376 default: p = ""; break;
2377 }
2378 return p;
2379 }
2380
2381
2382 static void do_atom(t_fileio *fio, t_atom *atom, int ngrp, gmx_bool bRead,
2383 int file_version, gmx_groups_t *groups, int atnr)
2384 {
2385 int i, myngrp;
2386
2387 gmx_fio_do_real(fio, atom->m);
2388 gmx_fio_do_real(fio, atom->q);
2389 gmx_fio_do_real(fio, atom->mB);
2390 gmx_fio_do_real(fio, atom->qB);
2391 gmx_fio_do_ushort(fio, atom->type);
2392 gmx_fio_do_ushort(fio, atom->typeB);
2393 gmx_fio_do_int(fio, atom->ptype);
2394 gmx_fio_do_int(fio, atom->resind);
2395 if (file_version >= 52)
2396 {
2397 gmx_fio_do_int(fio, atom->atomnumber);
2398 if (bRead)
2399 {
2400 /* Set element string from atomic number if present.
2401 * This routine returns an empty string if the name is not found.
2402 */
2403 std::strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
2404 /* avoid warnings about potentially unterminated string */
2405 atom->elem[3] = '\0';
2406 }
2407 }
2408 else if (bRead)
2409 {
2410 atom->atomnumber = 0;
2411 }
2412 if (file_version < 23)
2413 {
2414 myngrp = 8;
2415 }
2416 else if (file_version < 39)
2417 {
2418 myngrp = 9;
2419 }
2420 else
2421 {
2422 myngrp = ngrp;
2423 }
2424
2425 if (file_version < 57)
2426 {
2427 unsigned char uchar[egcNR];
2428 gmx_fio_ndo_uchar(fio, uchar, myngrp);
2429 for (i = myngrp; (i < ngrp); i++)
2430 {
2431 uchar[i] = 0;
2432 }
2433 /* Copy the old data format to the groups struct */
2434 for (i = 0; i < ngrp; i++)
2435 {
2436 groups->grpnr[i][atnr] = uchar[i];
2437 }
2438 }
2439 }
2440
2441 static void do_grps(t_fileio *fio, int ngrp, t_grps grps[], gmx_bool bRead,
2442 int file_version)
2443 {
2444 int j, myngrp;
2445
2446 if (file_version < 23)
2447 {
2448 myngrp = 8;
2449 }
2450 else if (file_version < 39)
2451 {
2452 myngrp = 9;
2453 }
2454 else
2455 {
2456 myngrp = ngrp;
2457 }
2458
2459 for (j = 0; (j < ngrp); j++)
2460 {
2461 if (j < myngrp)
2462 {
2463 gmx_fio_do_int(fio, grps[j].nr);
2464 if (bRead)
2465 {
2466 snew(grps[j].nm_ind, grps[j].nr);
2467 }
2468 gmx_fio_ndo_int(fio, grps[j].nm_ind, grps[j].nr);
2469 }
2470 else
2471 {
2472 grps[j].nr = 1;
2473 snew(grps[j].nm_ind, grps[j].nr);
2474 }
2475 }
2476 }
2477
2478 static void do_symstr(t_fileio *fio, char ***nm, gmx_bool bRead, t_symtab *symtab)
2479 {
2480 int ls;
2481
2482 if (bRead)
2483 {
2484 gmx_fio_do_int(fio, ls);
2485 *nm = get_symtab_handle(symtab, ls);
2486 }
2487 else
2488 {
2489 ls = lookup_symtab(symtab, *nm);
2490 gmx_fio_do_int(fio, ls);
2491 }
2492 }
2493
2494 static void do_strstr(t_fileio *fio, int nstr, char ***nm, gmx_bool bRead,
2495 t_symtab *symtab)
2496 {
2497 int j;
2498
2499 for (j = 0; (j < nstr); j++)
2500 {
2501 do_symstr(fio, &(nm[j]), bRead, symtab);
2502 }
2503 }
2504
2505 static void do_resinfo(t_fileio *fio, int n, t_resinfo *ri, gmx_bool bRead,
2506 t_symtab *symtab, int file_version)
2507 {
2508 int j;
2509
2510 for (j = 0; (j < n); j++)
2511 {
2512 do_symstr(fio, &(ri[j].name), bRead, symtab);
2513 if (file_version >= 63)
2514 {
2515 gmx_fio_do_int(fio, ri[j].nr);
2516 gmx_fio_do_uchar(fio, ri[j].ic);
2517 }
2518 else
2519 {
2520 ri[j].nr = j + 1;
2521 ri[j].ic = ' ';
2522 }
2523 }
2524 }
2525
2526 static void do_atoms(t_fileio *fio, t_atoms *atoms, gmx_bool bRead, t_symtab *symtab,
2527 int file_version,
2528 gmx_groups_t *groups)
2529 {
2530 int i;
2531
2532 gmx_fio_do_int(fio, atoms->nr);
2533 gmx_fio_do_int(fio, atoms->nres);
2534 if (file_version < 57)
2535 {
2536 gmx_fio_do_int(fio, groups->ngrpname);
2537 for (i = 0; i < egcNR; i++)
2538 {
2539 groups->ngrpnr[i] = atoms->nr;
2540 snew(groups->grpnr[i], groups->ngrpnr[i]);
2541 }
2542 }
2543 if (bRead)
2544 {
2545 snew(atoms->atom, atoms->nr);
2546 snew(atoms->atomname, atoms->nr);
2547 snew(atoms->atomtype, atoms->nr);
2548 snew(atoms->atomtypeB, atoms->nr);
2549 snew(atoms->resinfo, atoms->nres);
2550 if (file_version < 57)
2551 {
2552 snew(groups->grpname, groups->ngrpname);
2553 }
2554 atoms->pdbinfo = NULL;
2555 }
2556 for (i = 0; (i < atoms->nr); i++)
2557 {
2558 do_atom(fio, &atoms->atom[i], egcNR, bRead, file_version, groups, i);
2559 }
2560 do_strstr(fio, atoms->nr, atoms->atomname, bRead, symtab);
2561 if (bRead && (file_version <= 20))
2562 {
2563 for (i = 0; i < atoms->nr; i++)
2564 {
2565 atoms->atomtype[i] = put_symtab(symtab, "?");
2566 atoms->atomtypeB[i] = put_symtab(symtab, "?");
2567 }
2568 }
2569 else
2570 {
2571 do_strstr(fio, atoms->nr, atoms->atomtype, bRead, symtab);
2572 do_strstr(fio, atoms->nr, atoms->atomtypeB, bRead, symtab);
2573 }
2574 do_resinfo(fio, atoms->nres, atoms->resinfo, bRead, symtab, file_version);
2575
2576 if (file_version < 57)
2577 {
2578 do_strstr(fio, groups->ngrpname, groups->grpname, bRead, symtab);
2579
2580 do_grps(fio, egcNR, groups->grps, bRead, file_version);
2581 }
2582 }
2583
2584 static void do_groups(t_fileio *fio, gmx_groups_t *groups,
2585 gmx_bool bRead, t_symtab *symtab,
2586 int file_version)
2587 {
2588 int g;
2589
2590 do_grps(fio, egcNR, groups->grps, bRead, file_version);
2591 gmx_fio_do_int(fio, groups->ngrpname);
2592 if (bRead)
2593 {
2594 snew(groups->grpname, groups->ngrpname);
2595 }
2596 do_strstr(fio, groups->ngrpname, groups->grpname, bRead, symtab);
2597 for (g = 0; g < egcNR; g++)
2598 {
2599 gmx_fio_do_int(fio, groups->ngrpnr[g]);
2600 if (groups->ngrpnr[g] == 0)
2601 {
2602 if (bRead)
2603 {
2604 groups->grpnr[g] = NULL;
2605 }
2606 }
2607 else
2608 {
2609 if (bRead)
2610 {
2611 snew(groups->grpnr[g], groups->ngrpnr[g]);
2612 }
2613 gmx_fio_ndo_uchar(fio, groups->grpnr[g], groups->ngrpnr[g]);
2614 }
2615 }
2616 }
2617
2618 static void do_atomtypes(t_fileio *fio, t_atomtypes *atomtypes, gmx_bool bRead,
2619 int file_version)
2620 {
2621 int j;
2622
2623 if (file_version > 25)
2624 {
2625 gmx_fio_do_int(fio, atomtypes->nr);
2626 j = atomtypes->nr;
2627 if (bRead)
2628 {
2629 snew(atomtypes->radius, j);
2630 snew(atomtypes->vol, j);
2631 snew(atomtypes->surftens, j);
2632 snew(atomtypes->atomnumber, j);
2633 snew(atomtypes->gb_radius, j);
2634 snew(atomtypes->S_hct, j);
2635 }
2636 gmx_fio_ndo_real(fio, atomtypes->radius, j);
2637 gmx_fio_ndo_real(fio, atomtypes->vol, j);
2638 gmx_fio_ndo_real(fio, atomtypes->surftens, j);
2639 if (file_version >= 40)
2640 {
2641 gmx_fio_ndo_int(fio, atomtypes->atomnumber, j);
2642 }
2643 if (file_version >= 60)
2644 {
2645 gmx_fio_ndo_real(fio, atomtypes->gb_radius, j);
2646 gmx_fio_ndo_real(fio, atomtypes->S_hct, j);
2647 }
2648 }
2649 else
2650 {
2651 /* File versions prior to 26 cannot do GBSA,
2652 * so they dont use this structure
2653 */
2654 atomtypes->nr = 0;
2655 atomtypes->radius = NULL;
2656 atomtypes->vol = NULL;
2657 atomtypes->surftens = NULL;
2658 atomtypes->atomnumber = NULL;
2659 atomtypes->gb_radius = NULL;
2660 atomtypes->S_hct = NULL;
2661 }
2662 }
2663
2664 static void do_symtab(t_fileio *fio, t_symtab *symtab, gmx_bool bRead)
2665 {
2666 int i, nr;
2667 t_symbuf *symbuf;
2668 char buf[STRLEN];
2669
2670 gmx_fio_do_int(fio, symtab->nr);
2671 nr = symtab->nr;
2672 if (bRead)
2673 {
2674 snew(symtab->symbuf, 1);
2675 symbuf = symtab->symbuf;
2676 symbuf->bufsize = nr;
2677 snew(symbuf->buf, nr);
2678 for (i = 0; (i < nr); i++)
2679 {
2680 gmx_fio_do_string(fio, buf);
2681 symbuf->buf[i] = gmx_strdup(buf);
2682 }
2683 }
2684 else
2685 {
2686 symbuf = symtab->symbuf;
2687 while (symbuf != NULL)
2688 {
2689 for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
2690 {
2691 gmx_fio_do_string(fio, symbuf->buf[i]);
2692 }
2693 nr -= i;
2694 symbuf = symbuf->next;
2695 }
2696 if (nr != 0)
2697 {
2698 gmx_fatal(FARGS, "nr of symtab strings left: %d", nr);
2699 }
2700 }
2701 }
2702
2703 static void do_cmap(t_fileio *fio, gmx_cmap_t *cmap_grid, gmx_bool bRead)
2704 {
2705 int i, j, ngrid, gs, nelem;
2706
2707 gmx_fio_do_int(fio, cmap_grid->ngrid);
2708 gmx_fio_do_int(fio, cmap_grid->grid_spacing);
2709
2710 ngrid = cmap_grid->ngrid;
2711 gs = cmap_grid->grid_spacing;
2712 nelem = gs * gs;
2713
2714 if (bRead)
2715 {
2716 snew(cmap_grid->cmapdata, ngrid);
2717
2718 for (i = 0; i < cmap_grid->ngrid; i++)
2719 {
2720 snew(cmap_grid->cmapdata[i].cmap, 4*nelem);
2721 }
2722 }
2723
2724 for (i = 0; i < cmap_grid->ngrid; i++)
2725 {
2726 for (j = 0; j < nelem; j++)
2727 {
2728 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4]);
2729 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+1]);
2730 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+2]);
2731 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+3]);
2732 }
2733 }
2734 }
2735
2736
2737 static void do_moltype(t_fileio *fio, gmx_moltype_t *molt, gmx_bool bRead,
2738 t_symtab *symtab, int file_version,
2739 gmx_groups_t *groups)
2740 {
2741 if (file_version >= 57)
2742 {
2743 do_symstr(fio, &(molt->name), bRead, symtab);
2744 }
2745
2746 do_atoms(fio, &molt->atoms, bRead, symtab, file_version, groups);
2747
2748 if (file_version >= 57)
2749 {
2750 do_ilists(fio, molt->ilist, bRead, file_version);
2751
2752 do_block(fio, &molt->cgs, bRead, file_version);
2753 }
2754
2755 /* This used to be in the atoms struct */
2756 do_blocka(fio, &molt->excls, bRead, file_version);
2757 }
2758
2759 static void do_molblock(t_fileio *fio, gmx_molblock_t *molb, gmx_bool bRead)
2760 {
2761 gmx_fio_do_int(fio, molb->type);
2762 gmx_fio_do_int(fio, molb->nmol);
2763 gmx_fio_do_int(fio, molb->natoms_mol);
2764 /* Position restraint coordinates */
2765 gmx_fio_do_int(fio, molb->nposres_xA);
2766 if (molb->nposres_xA > 0)
2767 {
2768 if (bRead)
2769 {
2770 snew(molb->posres_xA, molb->nposres_xA);
2771 }
2772 gmx_fio_ndo_rvec(fio, molb->posres_xA, molb->nposres_xA);
2773 }
2774 gmx_fio_do_int(fio, molb->nposres_xB);
2775 if (molb->nposres_xB > 0)
2776 {
2777 if (bRead)
2778 {
2779 snew(molb->posres_xB, molb->nposres_xB);
2780 }
2781 gmx_fio_ndo_rvec(fio, molb->posres_xB, molb->nposres_xB);
2782 }
2783
2784 }
2785
2786 static t_block mtop_mols(gmx_mtop_t *mtop)
2787 {
2788 int mb, m, a, mol;
2789 t_block mols;
2790
2791 mols.nr = 0;
2792 for (mb = 0; mb < mtop->nmolblock; mb++)
2793 {
2794 mols.nr += mtop->molblock[mb].nmol;
2795 }
2796 mols.nalloc_index = mols.nr + 1;
2797 snew(mols.index, mols.nalloc_index);
2798
2799 a = 0;
2800 m = 0;
2801 mols.index[m] = a;
2802 for (mb = 0; mb < mtop->nmolblock; mb++)
2803 {
2804 for (mol = 0; mol < mtop->molblock[mb].nmol; mol++)
2805 {
2806 a += mtop->molblock[mb].natoms_mol;
2807 m++;
2808 mols.index[m] = a;
2809 }
2810 }
2811
2812 return mols;
2813 }
2814
2815 static void add_posres_molblock(gmx_mtop_t *mtop)
2816 {
2817 t_ilist *il, *ilfb;
2818 int am, i, mol, a;
2819 gmx_bool bFE;
2820 gmx_molblock_t *molb;
2821 t_iparams *ip;
2822
2823 /* posres reference positions are stored in ip->posres (if present) and
2824 in ip->fbposres (if present). If normal and flat-bottomed posres are present,
2825 posres.pos0A are identical to fbposres.pos0. */
2826 il = &mtop->moltype[0].ilist[F_POSRES];
2827 ilfb = &mtop->moltype[0].ilist[F_FBPOSRES];
2828 if (il->nr == 0 && ilfb->nr == 0)
2829 {
2830 return;
2831 }
2832 am = 0;
2833 bFE = FALSE;
2834 for (i = 0; i < il->nr; i += 2)
2835 {
2836 ip = &mtop->ffparams.iparams[il->iatoms[i]];
2837 am = std::max(am, il->iatoms[i+1]);
2838 if (ip->posres.pos0B[XX] != ip->posres.pos0A[XX] ||
2839 ip->posres.pos0B[YY] != ip->posres.pos0A[YY] ||
2840 ip->posres.pos0B[ZZ] != ip->posres.pos0A[ZZ])
2841 {
2842 bFE = TRUE;
2843 }
2844 }
2845 /* This loop is required if we have only flat-bottomed posres:
2846 - set am
2847 - bFE == FALSE (no B-state for flat-bottomed posres) */
2848 if (il->nr == 0)
2849 {
2850 for (i = 0; i < ilfb->nr; i += 2)
2851 {
2852 am = std::max(am, ilfb->iatoms[i+1]);
2853 }
2854 }
2855 /* Make the posres coordinate block end at a molecule end */
2856 mol = 0;
2857 while (am >= mtop->mols.index[mol+1])
2858 {
2859 mol++;
2860 }
2861 molb = &mtop->molblock[0];
2862 molb->nposres_xA = mtop->mols.index[mol+1];
2863 snew(molb->posres_xA, molb->nposres_xA);
2864 if (bFE)
2865 {
2866 molb->nposres_xB = molb->nposres_xA;
2867 snew(molb->posres_xB, molb->nposres_xB);
2868 }
2869 else
2870 {
2871 molb->nposres_xB = 0;
2872 }
2873 for (i = 0; i < il->nr; i += 2)
2874 {
2875 ip = &mtop->ffparams.iparams[il->iatoms[i]];
2876 a = il->iatoms[i+1];
2877 molb->posres_xA[a][XX] = ip->posres.pos0A[XX];
2878 molb->posres_xA[a][YY] = ip->posres.pos0A[YY];
2879 molb->posres_xA[a][ZZ] = ip->posres.pos0A[ZZ];
2880 if (bFE)
2881 {
2882 molb->posres_xB[a][XX] = ip->posres.pos0B[XX];
2883 molb->posres_xB[a][YY] = ip->posres.pos0B[YY];
2884 molb->posres_xB[a][ZZ] = ip->posres.pos0B[ZZ];
2885 }
2886 }
2887 if (il->nr == 0)
2888 {
2889 /* If only flat-bottomed posres are present, take reference pos from them.
2890 Here: bFE == FALSE */
2891 for (i = 0; i < ilfb->nr; i += 2)
2892 {
2893 ip = &mtop->ffparams.iparams[ilfb->iatoms[i]];
2894 a = ilfb->iatoms[i+1];
2895 molb->posres_xA[a][XX] = ip->fbposres.pos0[XX];
2896 molb->posres_xA[a][YY] = ip->fbposres.pos0[YY];
2897 molb->posres_xA[a][ZZ] = ip->fbposres.pos0[ZZ];
2898 }
2899 }
2900 }
2901
2902 static void set_disres_npair(gmx_mtop_t *mtop)
2903 {
2904 t_iparams *ip;
2905 gmx_mtop_ilistloop_t iloop;
2906 t_ilist *ilist, *il;
2907 int nmol, i, npair;
2908 t_iatom *a;
2909
2910 ip = mtop->ffparams.iparams;
2911
2912 iloop = gmx_mtop_ilistloop_init(mtop);
2913 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
2914 {
2915 il = &ilist[F_DISRES];
2916
2917 if (il->nr > 0)
2918 {
2919 a = il->iatoms;
2920 npair = 0;
2921 for (i = 0; i < il->nr; i += 3)
2922 {
2923 npair++;
2924 if (i+3 == il->nr || ip[a[i]].disres.label != ip[a[i+3]].disres.label)
2925 {
2926 ip[a[i]].disres.npair = npair;
2927 npair = 0;
2928 }
2929 }
2930 }
2931 }
2932 }
2933
2934 static void do_mtop(t_fileio *fio, gmx_mtop_t *mtop, gmx_bool bRead,
2935 int file_version)
2936 {
2937 int mt, mb;
2938 t_blocka dumb;
2939
2940 if (bRead)
2941 {
2942 init_mtop(mtop);
2943 }
2944 do_symtab(fio, &(mtop->symtab), bRead);
2945
2946 do_symstr(fio, &(mtop->name), bRead, &(mtop->symtab));
2947
2948 if (file_version >= 57)
2949 {
2950 do_ffparams(fio, &mtop->ffparams, bRead, file_version);
2951
2952 gmx_fio_do_int(fio, mtop->nmoltype);
2953 }
2954 else
2955 {
2956 mtop->nmoltype = 1;
2957 }
2958 if (bRead)
2959 {
2960 snew(mtop->moltype, mtop->nmoltype);
2961 if (file_version < 57)
2962 {
2963 mtop->moltype[0].name = mtop->name;
2964 }
2965 }
2966 for (mt = 0; mt < mtop->nmoltype; mt++)
2967 {
2968 do_moltype(fio, &mtop->moltype[mt], bRead, &mtop->symtab, file_version,
2969 &mtop->groups);
2970 }
2971
2972 if (file_version >= 57)
2973 {
2974 gmx_fio_do_int(fio, mtop->nmolblock);
2975 }
2976 else
2977 {
2978 mtop->nmolblock = 1;
2979 }
2980 if (bRead)
2981 {
2982 snew(mtop->molblock, mtop->nmolblock);
2983 }
2984 if (file_version >= 57)
2985 {
2986 for (mb = 0; mb < mtop->nmolblock; mb++)
2987 {
2988 do_molblock(fio, &mtop->molblock[mb], bRead);
2989 }
2990 gmx_fio_do_int(fio, mtop->natoms);
2991 }
2992 else
2993 {
2994 mtop->molblock[0].type = 0;
2995 mtop->molblock[0].nmol = 1;
2996 mtop->molblock[0].natoms_mol = mtop->moltype[0].atoms.nr;
2997 mtop->molblock[0].nposres_xA = 0;
2998 mtop->molblock[0].nposres_xB = 0;
2999 }
3000
3001 if (file_version >= tpxv_IntermolecularBondeds)
3002 {
3003 gmx_fio_do_gmx_bool(fio, mtop->bIntermolecularInteractions);
3004 if (mtop->bIntermolecularInteractions)
3005 {
3006 if (bRead)
3007 {
3008 snew(mtop->intermolecular_ilist, F_NRE);
3009 }
3010 do_ilists(fio, mtop->intermolecular_ilist, bRead, file_version);
3011 }
3012 }
3013 else
3014 {
3015 mtop->bIntermolecularInteractions = FALSE;
3016 }
3017
3018 do_atomtypes (fio, &(mtop->atomtypes), bRead, file_version);
3019
3020 if (file_version < 57)
3021 {
3022 do_idef (fio, &mtop->ffparams, &mtop->moltype[0], bRead, file_version);
3023 mtop->natoms = mtop->moltype[0].atoms.nr;
3024 }
3025
3026 if (file_version >= 65)
3027 {
3028 do_cmap(fio, &mtop->ffparams.cmap_grid, bRead);
3029 }
3030 else
3031 {
3032 mtop->ffparams.cmap_grid.ngrid = 0;
3033 mtop->ffparams.cmap_grid.grid_spacing = 0;
3034 mtop->ffparams.cmap_grid.cmapdata = NULL;
3035 }
3036
3037 if (file_version >= 57)
3038 {
3039 do_groups(fio, &mtop->groups, bRead, &(mtop->symtab), file_version);
3040 }
3041
3042 if (file_version < 57)
3043 {
3044 do_block(fio, &mtop->moltype[0].cgs, bRead, file_version);
3045 do_block(fio, &mtop->mols, bRead, file_version);
3046 /* Add the posres coordinates to the molblock */
3047 add_posres_molblock(mtop);
3048 }
3049 if (bRead)
3050 {
3051 if (file_version >= 57)
3052 {
3053 done_block(&mtop->mols);
3054 mtop->mols = mtop_mols(mtop);
3055 }
3056 }
3057
3058 if (file_version < 51)
3059 {
3060 /* Here used to be the shake blocks */
3061 do_blocka(fio, &dumb, bRead, file_version);
3062 if (dumb.nr > 0)
3063 {
3064 sfree(dumb.index);
3065 }
3066 if (dumb.nra > 0)
3067 {
3068 sfree(dumb.a);
3069 }
3070 }
3071
3072 if (bRead)
3073 {
3074 close_symtab(&(mtop->symtab));
3075 }
3076 }
3077
3078 /* If TopOnlyOK is TRUE then we can read even future versions
3079 * of tpx files, provided the file_generation hasn't changed.
3080 * If it is FALSE, we need the inputrecord too, and bail out
3081 * if the file is newer than the program.
3082 *
3083 * The version and generation if the topology (see top of this file)
3084 * are returned in the two last arguments.
3085 *
3086 * If possible, we will read the inputrec even when TopOnlyOK is TRUE.
3087 */
3088 static void do_tpxheader(t_fileio *fio, gmx_bool bRead, t_tpxheader *tpx,
3089 gmx_bool TopOnlyOK, int *file_version,
3090 int *file_generation)
3091 {
3092 char buf[STRLEN];
3093 char file_tag[STRLEN];
3094 gmx_bool bDouble;
3095 int precision;
3096 int fver, fgen;
3097 int idum = 0;
3098 real rdum = 0;
3099
3100 /* XDR binary topology file */
3101 precision = sizeof(real);
3102 if (bRead)
3103 {
3104 gmx_fio_do_string(fio, buf);
3105 if (std::strncmp(buf, "VERSION", 7))
3106 {
3107 gmx_fatal(FARGS, "Can not read file %s,\n"
3108 " this file is from a GROMACS version which is older than 2.0\n"
3109 " Make a new one with grompp or use a gro or pdb file, if possible",
3110 gmx_fio_getname(fio));
3111 }
3112 gmx_fio_do_int(fio, precision);
3113 bDouble = (precision == sizeof(double));
3114 if ((precision != sizeof(float)) && !bDouble)
3115 {
3116 gmx_fatal(FARGS, "Unknown precision in file %s: real is %d bytes "
3117 "instead of %d or %d",
3118 gmx_fio_getname(fio), precision, sizeof(float), sizeof(double));
3119 }
3120 gmx_fio_setprecision(fio, bDouble);
3121 fprintf(stderr, "Reading file %s, %s (%s precision)\n",
3122 gmx_fio_getname(fio), buf, bDouble ? "double" : "single");
3123 }
3124 else
3125 {
3126 gmx_fio_write_string(fio, gmx_version());
3127 bDouble = (precision == sizeof(double));
3128 gmx_fio_setprecision(fio, bDouble);
3129 gmx_fio_do_int(fio, precision);
3130 fver = tpx_version;
3131 sprintf(file_tag, "%s", tpx_tag);
3132 fgen = tpx_generation;
3133 }
3134
3135 /* Check versions! */
3136 gmx_fio_do_int(fio, fver);
3137
3138 /* This is for backward compatibility with development versions 77-79
3139 * where the tag was, mistakenly, placed before the generation,
3140 * which would cause a segv instead of a proper error message
3141 * when reading the topology only from tpx with <77 code.
3142 */
3143 if (fver >= 77 && fver <= 79)
3144 {
3145 gmx_fio_do_string(fio, file_tag);
3146 }
3147
3148 if (fver >= 26)
3149 {
3150 gmx_fio_do_int(fio, fgen);
3151 }
3152 else
3153 {
3154 fgen = 0;
3155 }
3156
3157 if (fver >= 81)
3158 {
3159 gmx_fio_do_string(fio, file_tag);
3160 }
3161 if (bRead)
3162 {
3163 if (fver < 77)
3164 {
3165 /* Versions before 77 don't have the tag, set it to release */
3166 sprintf(file_tag, "%s", TPX_TAG_RELEASE);
3167 }
3168
3169 if (std::strcmp(file_tag, tpx_tag) != 0)
3170 {
3171 fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n",
3172 file_tag, tpx_tag);
3173
3174 /* We only support reading tpx files with the same tag as the code
3175 * or tpx files with the release tag and with lower version number.
3176 */
3177 if (std::strcmp(file_tag, TPX_TAG_RELEASE) != 0 && fver < tpx_version)
3178 {
3179 gmx_fatal(FARGS, "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
3180 gmx_fio_getname(fio), fver, file_tag,
3181 tpx_version, tpx_tag);
3182 }
3183 }
3184 }
3185
3186 if (file_version != NULL)
3187 {
3188 *file_version = fver;
3189 }
3190 if (file_generation != NULL)
3191 {
3192 *file_generation = fgen;
3193 }
3194
3195
3196 if ((fver <= tpx_incompatible_version) ||
3197 ((fver > tpx_version) && !TopOnlyOK) ||
3198 (fgen > tpx_generation) ||
3199 tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
3200 {
3201 gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program",
3202 gmx_fio_getname(fio), fver, tpx_version);
3203 }
3204
3205 gmx_fio_do_int(fio, tpx->natoms);
3206 if (fver >= 28)
3207 {
3208 gmx_fio_do_int(fio, tpx->ngtc);
3209 }
3210 else
3211 {
3212 tpx->ngtc = 0;
3213 }
3214 if (fver < 62)
3215 {
3216 gmx_fio_do_int(fio, idum);
3217 gmx_fio_do_real(fio, rdum);
3218 }
3219 if (fver >= 79)
3220 {
3221 gmx_fio_do_int(fio, tpx->fep_state);
3222 }
3223 gmx_fio_do_real(fio, tpx->lambda);
3224 gmx_fio_do_int(fio, tpx->bIr);
3225 gmx_fio_do_int(fio, tpx->bTop);
3226 gmx_fio_do_int(fio, tpx->bX);
3227 gmx_fio_do_int(fio, tpx->bV);
3228 gmx_fio_do_int(fio, tpx->bF);
3229 gmx_fio_do_int(fio, tpx->bBox);
3230
3231 if ((fgen > tpx_generation))
3232 {
3233 /* This can only happen if TopOnlyOK=TRUE */
3234 tpx->bIr = FALSE;
3235 }
3236 }
3237
3238 static int do_tpx(t_fileio *fio, gmx_bool bRead,
3239 t_inputrec *ir, t_state *state, gmx_mtop_t *mtop,
3240 gmx_bool bXVallocated)
3241 {
3242 t_tpxheader tpx;
3243 t_inputrec dum_ir;
3244 gmx_mtop_t dum_top;
3245 gmx_bool TopOnlyOK;
3246 int file_version, file_generation;
3247 rvec *xptr, *vptr;
3248 int ePBC;
3249 gmx_bool bPeriodicMols;
3250
3251 if (!bRead)
3252 {
3253 tpx.natoms = state->natoms;
3254 tpx.ngtc = state->ngtc;
3255 tpx.fep_state = state->fep_state;
3256 tpx.lambda = state->lambda[efptFEP];
3257 tpx.bIr = (ir != NULL);
3258 tpx.bTop = (mtop != NULL);
3259 tpx.bX = (state->x != NULL);
3260 tpx.bV = (state->v != NULL);
3261 tpx.bF = FALSE;
3262 tpx.bBox = TRUE;
3263 }
3264
3265 TopOnlyOK = (ir == NULL);
3266
3267 do_tpxheader(fio, bRead, &tpx, TopOnlyOK, &file_version, &file_generation);
3268
3269 if (bRead)
3270 {
3271 state->flags = 0;
3272 if (bXVallocated)
3273 {
3274 xptr = state->x;
3275 vptr = state->v;
3276 init_state(state, 0, tpx.ngtc, 0, 0, 0);
3277 state->natoms = tpx.natoms;
3278 state->nalloc = tpx.natoms;
3279 state->x = xptr;
3280 state->v = vptr;
3281 }
3282 else
3283 {
3284 init_state(state, tpx.natoms, tpx.ngtc, 0, 0, 0);
3285 }
3286 }
3287
3288 #define do_test(fio, b, p) if (bRead && (p != NULL) && !b) gmx_fatal(FARGS, "No %s in %s",#p, gmx_fio_getname(fio))
3289
3290 do_test(fio, tpx.bBox, state->box);
3291 if (tpx.bBox)
3292 {
3293 gmx_fio_ndo_rvec(fio, state->box, DIM);
3294 if (file_version >= 51)
3295 {
3296 gmx_fio_ndo_rvec(fio, state->box_rel, DIM);
3297 }
3298 else
3299 {
3300 /* We initialize box_rel after reading the inputrec */
3301 clear_mat(state->box_rel);
3302 }
3303 if (file_version >= 28)
3304 {
3305 gmx_fio_ndo_rvec(fio, state->boxv, DIM);
3306 if (file_version < 56)
3307 {
3308 matrix mdum;
3309 gmx_fio_ndo_rvec(fio, mdum, DIM);
3310 }
3311 }
3312 }
3313
3314 if (state->ngtc > 0 && file_version >= 28)
3315 {
3316 real *dumv;
3317 snew(dumv, state->ngtc);
3318 if (file_version < 69)
3319 {
3320 gmx_fio_ndo_real(fio, dumv, state->ngtc);
3321 }
3322 /* These used to be the Berendsen tcoupl_lambda's */
3323 gmx_fio_ndo_real(fio, dumv, state->ngtc);
3324 sfree(dumv);
3325 }
3326
3327 /* Prior to tpx version 26, the inputrec was here.
3328 * I moved it to enable partial forward-compatibility
3329 * for analysis/viewer programs.
3330 */
3331 if (file_version < 26)
3332 {
3333 do_test(fio, tpx.bIr, ir);
3334 if (tpx.bIr)
3335 {
3336 if (ir)
3337 {
3338 do_inputrec(fio, ir, bRead, file_version,
3339 mtop ? &mtop->ffparams.fudgeQQ : NULL);
3340 }
3341 else
3342 {
3343 do_inputrec(fio, &dum_ir, bRead, file_version,
3344 mtop ? &mtop->ffparams.fudgeQQ : NULL);
3345 done_inputrec(&dum_ir);
3346 }
3347
3348 }
3349 }
3350
3351 do_test(fio, tpx.bTop, mtop);
3352 if (tpx.bTop)
3353 {
3354 if (mtop)
3355 {
3356 do_mtop(fio, mtop, bRead, file_version);
3357 }
3358 else
3359 {
3360 do_mtop(fio, &dum_top, bRead, file_version);
3361 done_mtop(&dum_top, TRUE);
3362 }
3363 }
3364 do_test(fio, tpx.bX, state->x);
3365 if (tpx.bX)
3366 {
3367 if (bRead)
3368 {
3369 state->flags |= (1<<estX);
3370 }
3371 gmx_fio_ndo_rvec(fio, state->x, state->natoms);
3372 }
3373
3374 do_test(fio, tpx.bV, state->v);
3375 if (tpx.bV)
3376 {
3377 if (bRead)
3378 {
3379 state->flags |= (1<<estV);
3380 }
3381 gmx_fio_ndo_rvec(fio, state->v, state->natoms);
3382 }
3383
3384 // No need to run do_test when the last argument is NULL
3385 if (tpx.bF)
3386 {
3387 rvec *dummyForces;
3388 snew(dummyForces, state->natoms);
3389 gmx_fio_ndo_rvec(fio, dummyForces, state->natoms);
3390 sfree(dummyForces);
3391 }
3392
3393 /* Starting with tpx version 26, we have the inputrec
3394 * at the end of the file, so we can ignore it
3395 * if the file is never than the software (but still the
3396 * same generation - see comments at the top of this file.
3397 *
3398 *
3399 */
3400 ePBC = -1;
3401 bPeriodicMols = FALSE;
3402 if (file_version >= 26)
3403 {
3404 do_test(fio, tpx.bIr, ir);
3405 if (tpx.bIr)
3406 {
3407 if (file_version >= 53)
3408 {
3409 /* Removed the pbc info from do_inputrec, since we always want it */
3410 if (!bRead)
3411 {
3412 ePBC = ir->ePBC;
3413 bPeriodicMols = ir->bPeriodicMols;
3414 }
3415 gmx_fio_do_int(fio, ePBC);
3416 gmx_fio_do_gmx_bool(fio, bPeriodicMols);
3417 }
3418 if (file_generation <= tpx_generation && ir)
3419 {
3420 do_inputrec(fio, ir, bRead, file_version, mtop ? &mtop->ffparams.fudgeQQ : NULL);
3421 if (file_version < 51)
3422 {
3423 set_box_rel(ir, state);
3424 }
3425 if (file_version < 53)
3426 {
3427 ePBC = ir->ePBC;
3428 bPeriodicMols = ir->bPeriodicMols;
3429 }
3430 }
3431 if (bRead && ir && file_version >= 53)
3432 {
3433 /* We need to do this after do_inputrec, since that initializes ir */
3434 ir->ePBC = ePBC;
3435 ir->bPeriodicMols = bPeriodicMols;
3436 }
3437 }
3438 }
3439
3440 if (bRead)
3441 {
3442 if (tpx.bIr && ir)
3443 {
3444 if (state->ngtc == 0)
3445 {
3446 /* Reading old version without tcoupl state data: set it */
3447 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
3448 }
3449 if (tpx.bTop && mtop)
3450 {
3451 if (file_version < 57)
3452 {
3453 if (mtop->moltype[0].ilist[F_DISRES].nr > 0)
3454 {
3455 ir->eDisre = edrSimple;
3456 }
3457 else
3458 {
3459 ir->eDisre = edrNone;
3460 }
3461 }
3462 set_disres_npair(mtop);
3463 }
3464 }
3465
3466 if (tpx.bTop && mtop)
3467 {
3468 gmx_mtop_finalize(mtop);
3469 }
3470 }
3471
3472 return ePBC;
3473 }
3474
3475 static t_fileio *open_tpx(const char *fn, const char *mode)
3476 {
3477 return gmx_fio_open(fn, mode);
3478 }
3479
3480 static void close_tpx(t_fileio *fio)
3481 {
3482 gmx_fio_close(fio);
3483 }
3484
3485 /************************************************************
3486 *
3487 * The following routines are the exported ones
3488 *
3489 ************************************************************/
3490
3491 void read_tpxheader(const char *fn, t_tpxheader *tpx, gmx_bool TopOnlyOK,
3492 int *file_version, int *file_generation)
3493 {
3494 t_fileio *fio;
3495
3496 fio = open_tpx(fn, "r");
3497 do_tpxheader(fio, TRUE, tpx, TopOnlyOK, file_version, file_generation);
3498 close_tpx(fio);
3499 }
3500
3501 void write_tpx_state(const char *fn,
3502 t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
3503 {
3504 t_fileio *fio;
3505
3506 fio = open_tpx(fn, "w");
3507 do_tpx(fio, FALSE, ir, state, mtop, FALSE);
3508 close_tpx(fio);
3509 }
3510
3511 void read_tpx_state(const char *fn,
3512 t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
3513 {
3514 t_fileio *fio;
3515
3516 fio = open_tpx(fn, "r");
3517 do_tpx(fio, TRUE, ir, state, mtop, FALSE);
3518 close_tpx(fio);
3519 }
3520
3521 int read_tpx(const char *fn,
3522 t_inputrec *ir, matrix box, int *natoms,
3523 rvec *x, rvec *v, gmx_mtop_t *mtop)
3524 {
3525 t_fileio *fio;
3526 t_state state;
3527 int ePBC;
3528
3529 state.x = x;
3530 state.v = v;
3531 fio = open_tpx(fn, "r");
3532 ePBC = do_tpx(fio, TRUE, ir, &state, mtop, TRUE);
3533 close_tpx(fio);
3534 *natoms = state.natoms;
3535 if (box)
3536 {
3537 copy_mat(state.box, box);
3538 }
3539 state.x = NULL;
3540 state.v = NULL;
3541 done_state(&state);
3542
3543 return ePBC;
3544 }
3545
3546 int read_tpx_top(const char *fn,
3547 t_inputrec *ir, matrix box, int *natoms,
3548 rvec *x, rvec *v, t_topology *top)
3549 {
3550 gmx_mtop_t mtop;
3551 int ePBC;
3552
3553 ePBC = read_tpx(fn, ir, box, natoms, x, v, &mtop);
3554
3555 *top = gmx_mtop_t_to_t_topology(&mtop);
3556
3557 return ePBC;
3558 }
3559
3560 gmx_bool fn2bTPX(const char *file)
3561 {
3562 return (efTPR == fn2ftp(file));
3563 }
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