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Split txtdump.*, part 1
[gromacs.git] / src / gromacs / fileio / tpxio.cpp
blob37b8b6056def7e8edd7547708e949c35cf5fb921
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,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
20 *
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
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25 *
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
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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 <cstdio>
44 #include <cstdlib>
45 #include <cstring>
46
47 #include <algorithm>
48 #include <vector>
49
50 #include "gromacs/fileio/filetypes.h"
51 #include "gromacs/fileio/gmxfio.h"
52 #include "gromacs/fileio/gmxfio-xdr.h"
53 #include "gromacs/fileio/txtdump.h"
54 #include "gromacs/gmxlib/ifunc.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/mdtypes/inputrec.h"
57 #include "gromacs/mdtypes/md_enums.h"
58 #include "gromacs/mdtypes/pull-params.h"
59 #include "gromacs/mdtypes/state.h"
60 #include "gromacs/pbcutil/boxutilities.h"
61 #include "gromacs/pbcutil/pbc.h"
62 #include "gromacs/topology/block.h"
63 #include "gromacs/topology/mtop_util.h"
64 #include "gromacs/topology/symtab.h"
65 #include "gromacs/topology/topology.h"
66 #include "gromacs/utility/arraysize.h"
67 #include "gromacs/utility/baseversion.h"
68 #include "gromacs/utility/cstringutil.h"
69 #include "gromacs/utility/fatalerror.h"
70 #include "gromacs/utility/futil.h"
71 #include "gromacs/utility/smalloc.h"
72
73 #define TPX_TAG_RELEASE "release"
74
75 /*! \brief Tag string for the file format written to run input files
76 * written by this version of the code.
77 *
78 * Change this if you want to change the run input format in a feature
79 * branch. This ensures that there will not be different run input
80 * formats around which cannot be distinguished, while not causing
81 * problems rebasing the feature branch onto upstream changes. When
82 * merging with mainstream GROMACS, set this tag string back to
83 * TPX_TAG_RELEASE, and instead add an element to tpxv.
84 */
85 static const char *tpx_tag = TPX_TAG_RELEASE;
86
87 /*! \brief Enum of values that describe the contents of a tpr file
88 * whose format matches a version number
89 *
90 * The enum helps the code be more self-documenting and ensure merges
91 * do not silently resolve when two patches make the same bump. When
92 * adding new functionality, add a new element just above tpxv_Count
93 * in this enumeration, and write code below that does the right thing
94 * according to the value of file_version.
95 */
96 enum tpxv {
97 tpxv_ComputationalElectrophysiology = 96, /**< support for ion/water position swaps (computational electrophysiology) */
98 tpxv_Use64BitRandomSeed, /**< change ld_seed from int to gmx_int64_t */
99 tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, /**< potentials for supporting coarse-grained force fields */
100 tpxv_InteractiveMolecularDynamics, /**< interactive molecular dynamics (IMD) */
101 tpxv_RemoveObsoleteParameters1, /**< remove optimize_fft, dihre_fc, nstcheckpoint */
102 tpxv_PullCoordTypeGeom, /**< add pull type and geometry per group and flat-bottom */
103 tpxv_PullGeomDirRel, /**< add pull geometry direction-relative */
104 tpxv_IntermolecularBondeds, /**< permit inter-molecular bonded interactions in the topology */
105 tpxv_CompElWithSwapLayerOffset, /**< added parameters for improved CompEl setups */
106 tpxv_CompElPolyatomicIonsAndMultipleIonTypes, /**< CompEl now can handle polyatomic ions and more than two types of ions */
107 tpxv_RemoveAdress, /**< removed support for AdResS */
108 tpxv_PullCoordNGroup, /**< add ngroup to pull coord */
109 tpxv_RemoveTwinRange, /**< removed support for twin-range interactions */
110 tpxv_Count /**< the total number of tpxv versions */
111 };
112
113 /*! \brief Version number of the file format written to run input
114 * files by this version of the code.
115 *
116 * The tpx_version increases whenever the file format in the main
117 * development branch changes, due to an extension of the tpxv enum above.
118 * Backward compatibility for reading old run input files is maintained
119 * by checking this version number against that of the file and then using
120 * the correct code path.
121 *
122 * When developing a feature branch that needs to change the run input
123 * file format, change tpx_tag instead. */
124 static const int tpx_version = tpxv_Count - 1;
125
126
127 /* This number should only be increased when you edit the TOPOLOGY section
128 * or the HEADER of the tpx format.
129 * This way we can maintain forward compatibility too for all analysis tools
130 * and/or external programs that only need to know the atom/residue names,
131 * charges, and bond connectivity.
132 *
133 * It first appeared in tpx version 26, when I also moved the inputrecord
134 * to the end of the tpx file, so we can just skip it if we only
135 * want the topology.
136 *
137 * In particular, it must be increased when adding new elements to
138 * ftupd, so that old code can read new .tpr files.
139 */
140 static const int tpx_generation = 26;
141
142 /* This number should be the most recent backwards incompatible version
143 * I.e., if this number is 9, we cannot read tpx version 9 with this code.
144 */
145 static const int tpx_incompatible_version = 9;
146
147
148
149 /* Struct used to maintain tpx compatibility when function types are added */
150 typedef struct {
151 int fvnr; /* file version number in which the function type first appeared */
152 int ftype; /* function type */
153 } t_ftupd;
154
155 /*
156 * The entries should be ordered in:
157 * 1. ascending function type number
158 * 2. ascending file version number
159 */
160 static const t_ftupd ftupd[] = {
161 { 20, F_CUBICBONDS },
162 { 20, F_CONNBONDS },
163 { 20, F_HARMONIC },
164 { 34, F_FENEBONDS },
165 { 43, F_TABBONDS },
166 { 43, F_TABBONDSNC },
167 { 70, F_RESTRBONDS },
168 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
169 { 76, F_LINEAR_ANGLES },
170 { 30, F_CROSS_BOND_BONDS },
171 { 30, F_CROSS_BOND_ANGLES },
172 { 30, F_UREY_BRADLEY },
173 { 34, F_QUARTIC_ANGLES },
174 { 43, F_TABANGLES },
175 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
176 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
177 { 26, F_FOURDIHS },
178 { 26, F_PIDIHS },
179 { 43, F_TABDIHS },
180 { 65, F_CMAP },
181 { 60, F_GB12 },
182 { 61, F_GB13 },
183 { 61, F_GB14 },
184 { 72, F_GBPOL },
185 { 72, F_NPSOLVATION },
186 { 41, F_LJC14_Q },
187 { 41, F_LJC_PAIRS_NB },
188 { 32, F_BHAM_LR_NOLONGERUSED },
189 { 32, F_RF_EXCL },
190 { 32, F_COUL_RECIP },
191 { 93, F_LJ_RECIP },
192 { 46, F_DPD },
193 { 30, F_POLARIZATION },
194 { 36, F_THOLE_POL },
195 { 90, F_FBPOSRES },
196 { 22, F_DISRESVIOL },
197 { 22, F_ORIRES },
198 { 22, F_ORIRESDEV },
199 { 26, F_DIHRES },
200 { 26, F_DIHRESVIOL },
201 { 49, F_VSITE4FDN },
202 { 50, F_VSITEN },
203 { 46, F_COM_PULL },
204 { 20, F_EQM },
205 { 46, F_ECONSERVED },
206 { 69, F_VTEMP_NOLONGERUSED},
207 { 66, F_PDISPCORR },
208 { 54, F_DVDL_CONSTR },
209 { 76, F_ANHARM_POL },
210 { 79, F_DVDL_COUL },
211 { 79, F_DVDL_VDW, },
212 { 79, F_DVDL_BONDED, },
213 { 79, F_DVDL_RESTRAINT },
214 { 79, F_DVDL_TEMPERATURE },
215 };
216 #define NFTUPD asize(ftupd)
217
218 /* Needed for backward compatibility */
219 #define MAXNODES 256
220
221 /**************************************************************
222 *
223 * Now the higer level routines that do io of the structures and arrays
224 *
225 **************************************************************/
226 static void do_pullgrp_tpx_pre95(t_fileio *fio,
227 t_pull_group *pgrp,
228 t_pull_coord *pcrd,
229 gmx_bool bRead,
230 int file_version)
231 {
232 rvec tmp;
233
234 gmx_fio_do_int(fio, pgrp->nat);
235 if (bRead)
236 {
237 snew(pgrp->ind, pgrp->nat);
238 }
239 gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
240 gmx_fio_do_int(fio, pgrp->nweight);
241 if (bRead)
242 {
243 snew(pgrp->weight, pgrp->nweight);
244 }
245 gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight);
246 gmx_fio_do_int(fio, pgrp->pbcatom);
247 gmx_fio_do_rvec(fio, pcrd->vec);
248 clear_rvec(pcrd->origin);
249 gmx_fio_do_rvec(fio, tmp);
250 pcrd->init = tmp[0];
251 gmx_fio_do_real(fio, pcrd->rate);
252 gmx_fio_do_real(fio, pcrd->k);
253 if (file_version >= 56)
254 {
255 gmx_fio_do_real(fio, pcrd->kB);
256 }
257 else
258 {
259 pcrd->kB = pcrd->k;
260 }
261 }
262
263 static void do_pull_group(t_fileio *fio, t_pull_group *pgrp, gmx_bool bRead)
264 {
265 gmx_fio_do_int(fio, pgrp->nat);
266 if (bRead)
267 {
268 snew(pgrp->ind, pgrp->nat);
269 }
270 gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
271 gmx_fio_do_int(fio, pgrp->nweight);
272 if (bRead)
273 {
274 snew(pgrp->weight, pgrp->nweight);
275 }
276 gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight);
277 gmx_fio_do_int(fio, pgrp->pbcatom);
278 }
279
280 static void do_pull_coord(t_fileio *fio, t_pull_coord *pcrd, int file_version,
281 int ePullOld, int eGeomOld, ivec dimOld)
282 {
283 if (file_version >= tpxv_PullCoordNGroup)
284 {
285 gmx_fio_do_int(fio, pcrd->eType);
286 /* Note that we try to support adding new geometries without
287 * changing the tpx version. This requires checks when printing the
288 * geometry string and a check and fatal_error in init_pull.
289 */
290 gmx_fio_do_int(fio, pcrd->eGeom);
291 gmx_fio_do_int(fio, pcrd->ngroup);
292 if (pcrd->ngroup <= PULL_COORD_NGROUP_MAX)
293 {
294 gmx_fio_ndo_int(fio, pcrd->group, pcrd->ngroup);
295 }
296 else
297 {
298 /* More groups in file than supported, this must be a new geometry
299 * that is not supported by our current code. Since we will not
300 * use the groups for this coord (checks in the pull and WHAM code
301 * ensure this), we can ignore the groups and set ngroup=0.
302 */
303 int *dum;
304 snew(dum, pcrd->ngroup);
305 gmx_fio_ndo_int(fio, dum, pcrd->ngroup);
306 sfree(dum);
307
308 pcrd->ngroup = 0;
309 }
310 gmx_fio_do_ivec(fio, pcrd->dim);
311 }
312 else
313 {
314 pcrd->ngroup = 2;
315 gmx_fio_do_int(fio, pcrd->group[0]);
316 gmx_fio_do_int(fio, pcrd->group[1]);
317 if (file_version >= tpxv_PullCoordTypeGeom)
318 {
319 pcrd->ngroup = (pcrd->eGeom == epullgDIRRELATIVE ? 4 : 2);
320 gmx_fio_do_int(fio, pcrd->eType);
321 gmx_fio_do_int(fio, pcrd->eGeom);
322 if (pcrd->ngroup == 4)
323 {
324 gmx_fio_do_int(fio, pcrd->group[2]);
325 gmx_fio_do_int(fio, pcrd->group[3]);
326 }
327 gmx_fio_do_ivec(fio, pcrd->dim);
328 }
329 else
330 {
331 pcrd->eType = ePullOld;
332 pcrd->eGeom = eGeomOld;
333 copy_ivec(dimOld, pcrd->dim);
334 }
335 }
336 gmx_fio_do_rvec(fio, pcrd->origin);
337 gmx_fio_do_rvec(fio, pcrd->vec);
338 if (file_version >= tpxv_PullCoordTypeGeom)
339 {
340 gmx_fio_do_gmx_bool(fio, pcrd->bStart);
341 }
342 else
343 {
344 /* This parameter is only printed, but not actually used by mdrun */
345 pcrd->bStart = FALSE;
346 }
347 gmx_fio_do_real(fio, pcrd->init);
348 gmx_fio_do_real(fio, pcrd->rate);
349 gmx_fio_do_real(fio, pcrd->k);
350 gmx_fio_do_real(fio, pcrd->kB);
351 }
352
353 static void do_expandedvals(t_fileio *fio, t_expanded *expand, t_lambda *fepvals, gmx_bool bRead, int file_version)
354 {
355 int n_lambda = fepvals->n_lambda;
356
357 /* reset the lambda calculation window */
358 fepvals->lambda_start_n = 0;
359 fepvals->lambda_stop_n = n_lambda;
360 if (file_version >= 79)
361 {
362 if (n_lambda > 0)
363 {
364 if (bRead)
365 {
366 snew(expand->init_lambda_weights, n_lambda);
367 }
368 gmx_fio_ndo_real(fio, expand->init_lambda_weights, n_lambda);
369 gmx_fio_do_gmx_bool(fio, expand->bInit_weights);
370 }
371
372 gmx_fio_do_int(fio, expand->nstexpanded);
373 gmx_fio_do_int(fio, expand->elmcmove);
374 gmx_fio_do_int(fio, expand->elamstats);
375 gmx_fio_do_int(fio, expand->lmc_repeats);
376 gmx_fio_do_int(fio, expand->gibbsdeltalam);
377 gmx_fio_do_int(fio, expand->lmc_forced_nstart);
378 gmx_fio_do_int(fio, expand->lmc_seed);
379 gmx_fio_do_real(fio, expand->mc_temp);
380 gmx_fio_do_int(fio, expand->bSymmetrizedTMatrix);
381 gmx_fio_do_int(fio, expand->nstTij);
382 gmx_fio_do_int(fio, expand->minvarmin);
383 gmx_fio_do_int(fio, expand->c_range);
384 gmx_fio_do_real(fio, expand->wl_scale);
385 gmx_fio_do_real(fio, expand->wl_ratio);
386 gmx_fio_do_real(fio, expand->init_wl_delta);
387 gmx_fio_do_gmx_bool(fio, expand->bWLoneovert);
388 gmx_fio_do_int(fio, expand->elmceq);
389 gmx_fio_do_int(fio, expand->equil_steps);
390 gmx_fio_do_int(fio, expand->equil_samples);
391 gmx_fio_do_int(fio, expand->equil_n_at_lam);
392 gmx_fio_do_real(fio, expand->equil_wl_delta);
393 gmx_fio_do_real(fio, expand->equil_ratio);
394 }
395 }
396
397 static void do_simtempvals(t_fileio *fio, t_simtemp *simtemp, int n_lambda, gmx_bool bRead,
398 int file_version)
399 {
400 if (file_version >= 79)
401 {
402 gmx_fio_do_int(fio, simtemp->eSimTempScale);
403 gmx_fio_do_real(fio, simtemp->simtemp_high);
404 gmx_fio_do_real(fio, simtemp->simtemp_low);
405 if (n_lambda > 0)
406 {
407 if (bRead)
408 {
409 snew(simtemp->temperatures, n_lambda);
410 }
411 gmx_fio_ndo_real(fio, simtemp->temperatures, n_lambda);
412 }
413 }
414 }
415
416 static void do_imd(t_fileio *fio, t_IMD *imd, gmx_bool bRead)
417 {
418 gmx_fio_do_int(fio, imd->nat);
419 if (bRead)
420 {
421 snew(imd->ind, imd->nat);
422 }
423 gmx_fio_ndo_int(fio, imd->ind, imd->nat);
424 }
425
426 static void do_fepvals(t_fileio *fio, t_lambda *fepvals, gmx_bool bRead, int file_version)
427 {
428 /* i is defined in the ndo_double macro; use g to iterate. */
429 int g;
430 real rdum;
431
432 /* free energy values */
433
434 if (file_version >= 79)
435 {
436 gmx_fio_do_int(fio, fepvals->init_fep_state);
437 gmx_fio_do_double(fio, fepvals->init_lambda);
438 gmx_fio_do_double(fio, fepvals->delta_lambda);
439 }
440 else if (file_version >= 59)
441 {
442 gmx_fio_do_double(fio, fepvals->init_lambda);
443 gmx_fio_do_double(fio, fepvals->delta_lambda);
444 }
445 else
446 {
447 gmx_fio_do_real(fio, rdum);
448 fepvals->init_lambda = rdum;
449 gmx_fio_do_real(fio, rdum);
450 fepvals->delta_lambda = rdum;
451 }
452 if (file_version >= 79)
453 {
454 gmx_fio_do_int(fio, fepvals->n_lambda);
455 if (bRead)
456 {
457 snew(fepvals->all_lambda, efptNR);
458 }
459 for (g = 0; g < efptNR; g++)
460 {
461 if (fepvals->n_lambda > 0)
462 {
463 if (bRead)
464 {
465 snew(fepvals->all_lambda[g], fepvals->n_lambda);
466 }
467 gmx_fio_ndo_double(fio, fepvals->all_lambda[g], fepvals->n_lambda);
468 gmx_fio_ndo_int(fio, fepvals->separate_dvdl, efptNR);
469 }
470 else if (fepvals->init_lambda >= 0)
471 {
472 fepvals->separate_dvdl[efptFEP] = TRUE;
473 }
474 }
475 }
476 else if (file_version >= 64)
477 {
478 gmx_fio_do_int(fio, fepvals->n_lambda);
479 if (bRead)
480 {
481 int g;
482
483 snew(fepvals->all_lambda, efptNR);
484 /* still allocate the all_lambda array's contents. */
485 for (g = 0; g < efptNR; g++)
486 {
487 if (fepvals->n_lambda > 0)
488 {
489 snew(fepvals->all_lambda[g], fepvals->n_lambda);
490 }
491 }
492 }
493 gmx_fio_ndo_double(fio, fepvals->all_lambda[efptFEP],
494 fepvals->n_lambda);
495 if (fepvals->init_lambda >= 0)
496 {
497 int g, h;
498
499 fepvals->separate_dvdl[efptFEP] = TRUE;
500
501 if (bRead)
502 {
503 /* copy the contents of the efptFEP lambda component to all
504 the other components */
505 for (g = 0; g < efptNR; g++)
506 {
507 for (h = 0; h < fepvals->n_lambda; h++)
508 {
509 if (g != efptFEP)
510 {
511 fepvals->all_lambda[g][h] =
512 fepvals->all_lambda[efptFEP][h];
513 }
514 }
515 }
516 }
517 }
518 }
519 else
520 {
521 fepvals->n_lambda = 0;
522 fepvals->all_lambda = NULL;
523 if (fepvals->init_lambda >= 0)
524 {
525 fepvals->separate_dvdl[efptFEP] = TRUE;
526 }
527 }
528 if (file_version >= 13)
529 {
530 gmx_fio_do_real(fio, fepvals->sc_alpha);
531 }
532 else
533 {
534 fepvals->sc_alpha = 0;
535 }
536 if (file_version >= 38)
537 {
538 gmx_fio_do_int(fio, fepvals->sc_power);
539 }
540 else
541 {
542 fepvals->sc_power = 2;
543 }
544 if (file_version >= 79)
545 {
546 gmx_fio_do_real(fio, fepvals->sc_r_power);
547 }
548 else
549 {
550 fepvals->sc_r_power = 6.0;
551 }
552 if (file_version >= 15)
553 {
554 gmx_fio_do_real(fio, fepvals->sc_sigma);
555 }
556 else
557 {
558 fepvals->sc_sigma = 0.3;
559 }
560 if (bRead)
561 {
562 if (file_version >= 71)
563 {
564 fepvals->sc_sigma_min = fepvals->sc_sigma;
565 }
566 else
567 {
568 fepvals->sc_sigma_min = 0;
569 }
570 }
571 if (file_version >= 79)
572 {
573 gmx_fio_do_int(fio, fepvals->bScCoul);
574 }
575 else
576 {
577 fepvals->bScCoul = TRUE;
578 }
579 if (file_version >= 64)
580 {
581 gmx_fio_do_int(fio, fepvals->nstdhdl);
582 }
583 else
584 {
585 fepvals->nstdhdl = 1;
586 }
587
588 if (file_version >= 73)
589 {
590 gmx_fio_do_int(fio, fepvals->separate_dhdl_file);
591 gmx_fio_do_int(fio, fepvals->dhdl_derivatives);
592 }
593 else
594 {
595 fepvals->separate_dhdl_file = esepdhdlfileYES;
596 fepvals->dhdl_derivatives = edhdlderivativesYES;
597 }
598 if (file_version >= 71)
599 {
600 gmx_fio_do_int(fio, fepvals->dh_hist_size);
601 gmx_fio_do_double(fio, fepvals->dh_hist_spacing);
602 }
603 else
604 {
605 fepvals->dh_hist_size = 0;
606 fepvals->dh_hist_spacing = 0.1;
607 }
608 if (file_version >= 79)
609 {
610 gmx_fio_do_int(fio, fepvals->edHdLPrintEnergy);
611 }
612 else
613 {
614 fepvals->edHdLPrintEnergy = edHdLPrintEnergyNO;
615 }
616
617 /* handle lambda_neighbors */
618 if ((file_version >= 83 && file_version < 90) || file_version >= 92)
619 {
620 gmx_fio_do_int(fio, fepvals->lambda_neighbors);
621 if ( (fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0) &&
622 (fepvals->init_lambda < 0) )
623 {
624 fepvals->lambda_start_n = (fepvals->init_fep_state -
625 fepvals->lambda_neighbors);
626 fepvals->lambda_stop_n = (fepvals->init_fep_state +
627 fepvals->lambda_neighbors + 1);
628 if (fepvals->lambda_start_n < 0)
629 {
630 fepvals->lambda_start_n = 0;;
631 }
632 if (fepvals->lambda_stop_n >= fepvals->n_lambda)
633 {
634 fepvals->lambda_stop_n = fepvals->n_lambda;
635 }
636 }
637 else
638 {
639 fepvals->lambda_start_n = 0;
640 fepvals->lambda_stop_n = fepvals->n_lambda;
641 }
642 }
643 else
644 {
645 fepvals->lambda_start_n = 0;
646 fepvals->lambda_stop_n = fepvals->n_lambda;
647 }
648 }
649
650 static void do_pull(t_fileio *fio, pull_params_t *pull, gmx_bool bRead,
651 int file_version, int ePullOld)
652 {
653 int eGeomOld = -1;
654 ivec dimOld;
655 int g;
656
657 if (file_version >= 95)
658 {
659 gmx_fio_do_int(fio, pull->ngroup);
660 }
661 gmx_fio_do_int(fio, pull->ncoord);
662 if (file_version < 95)
663 {
664 pull->ngroup = pull->ncoord + 1;
665 }
666 if (file_version < tpxv_PullCoordTypeGeom)
667 {
668 real dum;
669
670 gmx_fio_do_int(fio, eGeomOld);
671 gmx_fio_do_ivec(fio, dimOld);
672 /* The inner cylinder radius, now removed */
673 gmx_fio_do_real(fio, dum);
674 }
675 gmx_fio_do_real(fio, pull->cylinder_r);
676 gmx_fio_do_real(fio, pull->constr_tol);
677 if (file_version >= 95)
678 {
679 gmx_fio_do_int(fio, pull->bPrintCOM1);
680 /* With file_version < 95 this value is set below */
681 }
682 if (file_version >= tpxv_PullCoordTypeGeom)
683 {
684 gmx_fio_do_int(fio, pull->bPrintCOM2);
685 gmx_fio_do_int(fio, pull->bPrintRefValue);
686 gmx_fio_do_int(fio, pull->bPrintComp);
687 }
688 else
689 {
690 pull->bPrintCOM2 = FALSE;
691 pull->bPrintRefValue = FALSE;
692 pull->bPrintComp = TRUE;
693 }
694 gmx_fio_do_int(fio, pull->nstxout);
695 gmx_fio_do_int(fio, pull->nstfout);
696 if (bRead)
697 {
698 snew(pull->group, pull->ngroup);
699 snew(pull->coord, pull->ncoord);
700 }
701 if (file_version < 95)
702 {
703 /* epullgPOS for position pulling, before epullgDIRPBC was removed */
704 if (eGeomOld == epullgDIRPBC)
705 {
706 gmx_fatal(FARGS, "pull-geometry=position is no longer supported");
707 }
708 if (eGeomOld > epullgDIRPBC)
709 {
710 eGeomOld -= 1;
711 }
712
713 for (g = 0; g < pull->ngroup; g++)
714 {
715 /* We read and ignore a pull coordinate for group 0 */
716 do_pullgrp_tpx_pre95(fio, &pull->group[g], &pull->coord[std::max(g-1, 0)],
717 bRead, file_version);
718 if (g > 0)
719 {
720 pull->coord[g-1].group[0] = 0;
721 pull->coord[g-1].group[1] = g;
722 }
723 }
724
725 pull->bPrintCOM1 = (pull->group[0].nat > 0);
726 }
727 else
728 {
729 for (g = 0; g < pull->ngroup; g++)
730 {
731 do_pull_group(fio, &pull->group[g], bRead);
732 }
733 for (g = 0; g < pull->ncoord; g++)
734 {
735 do_pull_coord(fio, &pull->coord[g],
736 file_version, ePullOld, eGeomOld, dimOld);
737 }
738 }
739 }
740
741
742 static void do_rotgrp(t_fileio *fio, t_rotgrp *rotg, gmx_bool bRead)
743 {
744 gmx_fio_do_int(fio, rotg->eType);
745 gmx_fio_do_int(fio, rotg->bMassW);
746 gmx_fio_do_int(fio, rotg->nat);
747 if (bRead)
748 {
749 snew(rotg->ind, rotg->nat);
750 }
751 gmx_fio_ndo_int(fio, rotg->ind, rotg->nat);
752 if (bRead)
753 {
754 snew(rotg->x_ref, rotg->nat);
755 }
756 gmx_fio_ndo_rvec(fio, rotg->x_ref, rotg->nat);
757 gmx_fio_do_rvec(fio, rotg->vec);
758 gmx_fio_do_rvec(fio, rotg->pivot);
759 gmx_fio_do_real(fio, rotg->rate);
760 gmx_fio_do_real(fio, rotg->k);
761 gmx_fio_do_real(fio, rotg->slab_dist);
762 gmx_fio_do_real(fio, rotg->min_gaussian);
763 gmx_fio_do_real(fio, rotg->eps);
764 gmx_fio_do_int(fio, rotg->eFittype);
765 gmx_fio_do_int(fio, rotg->PotAngle_nstep);
766 gmx_fio_do_real(fio, rotg->PotAngle_step);
767 }
768
769 static void do_rot(t_fileio *fio, t_rot *rot, gmx_bool bRead)
770 {
771 int g;
772
773 gmx_fio_do_int(fio, rot->ngrp);
774 gmx_fio_do_int(fio, rot->nstrout);
775 gmx_fio_do_int(fio, rot->nstsout);
776 if (bRead)
777 {
778 snew(rot->grp, rot->ngrp);
779 }
780 for (g = 0; g < rot->ngrp; g++)
781 {
782 do_rotgrp(fio, &rot->grp[g], bRead);
783 }
784 }
785
786
787 static void do_swapgroup(t_fileio *fio, t_swapGroup *g, gmx_bool bRead)
788 {
789
790 /* Name of the group or molecule */
791 if (bRead)
792 {
793 char buf[STRLEN];
794
795 gmx_fio_do_string(fio, buf);
796 g->molname = gmx_strdup(buf);
797 }
798 else
799 {
800 gmx_fio_do_string(fio, g->molname);
801 }
802
803 /* Number of atoms in the group */
804 gmx_fio_do_int(fio, g->nat);
805
806 /* The group's atom indices */
807 if (bRead)
808 {
809 snew(g->ind, g->nat);
810 }
811 gmx_fio_ndo_int(fio, g->ind, g->nat);
812
813 /* Requested counts for compartments A and B */
814 gmx_fio_ndo_int(fio, g->nmolReq, eCompNR);
815 }
816
817 static void do_swapcoords_tpx(t_fileio *fio, t_swapcoords *swap, gmx_bool bRead, int file_version)
818 {
819 /* Enums for better readability of the code */
820 enum {
821 eCompA = 0, eCompB
822 };
823 enum {
824 eChannel0 = 0, eChannel1
825 };
826
827
828 if (file_version >= tpxv_CompElPolyatomicIonsAndMultipleIonTypes)
829 {
830 /* The total number of swap groups is the sum of the fixed groups
831 * (split0, split1, solvent), and the user-defined groups (2+ types of ions)
832 */
833 gmx_fio_do_int(fio, swap->ngrp);
834 if (bRead)
835 {
836 snew(swap->grp, swap->ngrp);
837 }
838 for (int ig = 0; ig < swap->ngrp; ig++)
839 {
840 do_swapgroup(fio, &swap->grp[ig], bRead);
841 }
842 gmx_fio_do_int(fio, swap->massw_split[eChannel0]);
843 gmx_fio_do_int(fio, swap->massw_split[eChannel1]);
844 gmx_fio_do_int(fio, swap->nstswap);
845 gmx_fio_do_int(fio, swap->nAverage);
846 gmx_fio_do_real(fio, swap->threshold);
847 gmx_fio_do_real(fio, swap->cyl0r);
848 gmx_fio_do_real(fio, swap->cyl0u);
849 gmx_fio_do_real(fio, swap->cyl0l);
850 gmx_fio_do_real(fio, swap->cyl1r);
851 gmx_fio_do_real(fio, swap->cyl1u);
852 gmx_fio_do_real(fio, swap->cyl1l);
853 }
854 else
855 {
856 /*** Support reading older CompEl .tpr files ***/
857
858 /* In the original CompEl .tpr files, we always have 5 groups: */
859 swap->ngrp = 5;
860 snew(swap->grp, swap->ngrp);
861
862 swap->grp[eGrpSplit0 ].molname = gmx_strdup("split0" ); // group 0: split0
863 swap->grp[eGrpSplit1 ].molname = gmx_strdup("split1" ); // group 1: split1
864 swap->grp[eGrpSolvent].molname = gmx_strdup("solvent"); // group 2: solvent
865 swap->grp[3 ].molname = gmx_strdup("anions" ); // group 3: anions
866 swap->grp[4 ].molname = gmx_strdup("cations"); // group 4: cations
867
868 gmx_fio_do_int(fio, swap->grp[3].nat);
869 gmx_fio_do_int(fio, swap->grp[eGrpSolvent].nat);
870 gmx_fio_do_int(fio, swap->grp[eGrpSplit0].nat);
871 gmx_fio_do_int(fio, swap->massw_split[eChannel0]);
872 gmx_fio_do_int(fio, swap->grp[eGrpSplit1].nat);
873 gmx_fio_do_int(fio, swap->massw_split[eChannel1]);
874 gmx_fio_do_int(fio, swap->nstswap);
875 gmx_fio_do_int(fio, swap->nAverage);
876 gmx_fio_do_real(fio, swap->threshold);
877 gmx_fio_do_real(fio, swap->cyl0r);
878 gmx_fio_do_real(fio, swap->cyl0u);
879 gmx_fio_do_real(fio, swap->cyl0l);
880 gmx_fio_do_real(fio, swap->cyl1r);
881 gmx_fio_do_real(fio, swap->cyl1u);
882 gmx_fio_do_real(fio, swap->cyl1l);
883
884 // The order[] array keeps compatibility with older .tpr files
885 // by reading in the groups in the classic order
886 {
887 const int order[4] = {3, eGrpSolvent, eGrpSplit0, eGrpSplit1 };
888
889 for (int ig = 0; ig < 4; ig++)
890 {
891 int g = order[ig];
892 snew(swap->grp[g].ind, swap->grp[g].nat);
893 gmx_fio_ndo_int(fio, swap->grp[g].ind, swap->grp[g].nat);
894 }
895 }
896
897 for (int j = eCompA; j <= eCompB; j++)
898 {
899 gmx_fio_do_int(fio, swap->grp[3].nmolReq[j]); // group 3 = anions
900 gmx_fio_do_int(fio, swap->grp[4].nmolReq[j]); // group 4 = cations
901 }
902 } /* End support reading older CompEl .tpr files */
903
904 if (file_version >= tpxv_CompElWithSwapLayerOffset)
905 {
906 gmx_fio_do_real(fio, swap->bulkOffset[eCompA]);
907 gmx_fio_do_real(fio, swap->bulkOffset[eCompB]);
908 }
909
910 }
911
912
913 static void do_inputrec(t_fileio *fio, t_inputrec *ir, gmx_bool bRead,
914 int file_version, real *fudgeQQ)
915 {
916 int i, j, k, *tmp, idum = 0;
917 real rdum, bd_temp;
918 rvec vdum;
919 gmx_bool bSimAnn, bdum = 0;
920 real zerotemptime, finish_t, init_temp, finish_temp;
921
922 if (file_version != tpx_version)
923 {
924 /* Give a warning about features that are not accessible */
925 fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n",
926 file_version, tpx_version);
927 }
928
929 if (bRead)
930 {
931 init_inputrec(ir);
932 }
933
934 if (file_version == 0)
935 {
936 return;
937 }
938
939 /* Basic inputrec stuff */
940 gmx_fio_do_int(fio, ir->eI);
941 if (file_version >= 62)
942 {
943 gmx_fio_do_int64(fio, ir->nsteps);
944 }
945 else
946 {
947 gmx_fio_do_int(fio, idum);
948 ir->nsteps = idum;
949 }
950
951 if (file_version > 25)
952 {
953 if (file_version >= 62)
954 {
955 gmx_fio_do_int64(fio, ir->init_step);
956 }
957 else
958 {
959 gmx_fio_do_int(fio, idum);
960 ir->init_step = idum;
961 }
962 }
963 else
964 {
965 ir->init_step = 0;
966 }
967
968 if (file_version >= 58)
969 {
970 gmx_fio_do_int(fio, ir->simulation_part);
971 }
972 else
973 {
974 ir->simulation_part = 1;
975 }
976
977 if (file_version >= 67)
978 {
979 gmx_fio_do_int(fio, ir->nstcalcenergy);
980 }
981 else
982 {
983 ir->nstcalcenergy = 1;
984 }
985 if (file_version < 53)
986 {
987 /* The pbc info has been moved out of do_inputrec,
988 * since we always want it, also without reading the inputrec.
989 */
990 gmx_fio_do_int(fio, ir->ePBC);
991 if ((file_version <= 15) && (ir->ePBC == 2))
992 {
993 ir->ePBC = epbcNONE;
994 }
995 if (file_version >= 45)
996 {
997 gmx_fio_do_int(fio, ir->bPeriodicMols);
998 }
999 else
1000 {
1001 if (ir->ePBC == 2)
1002 {
1003 ir->ePBC = epbcXYZ;
1004 ir->bPeriodicMols = TRUE;
1005 }
1006 else
1007 {
1008 ir->bPeriodicMols = FALSE;
1009 }
1010 }
1011 }
1012 if (file_version >= 81)
1013 {
1014 gmx_fio_do_int(fio, ir->cutoff_scheme);
1015 if (file_version < 94)
1016 {
1017 ir->cutoff_scheme = 1 - ir->cutoff_scheme;
1018 }
1019 }
1020 else
1021 {
1022 ir->cutoff_scheme = ecutsGROUP;
1023 }
1024 gmx_fio_do_int(fio, ir->ns_type);
1025 gmx_fio_do_int(fio, ir->nstlist);
1026 gmx_fio_do_int(fio, idum); /* used to be ndelta; not used anymore */
1027 if (file_version < 41)
1028 {
1029 gmx_fio_do_int(fio, idum);
1030 gmx_fio_do_int(fio, idum);
1031 }
1032 if (file_version >= 45)
1033 {
1034 gmx_fio_do_real(fio, ir->rtpi);
1035 }
1036 else
1037 {
1038 ir->rtpi = 0.05;
1039 }
1040 gmx_fio_do_int(fio, ir->nstcomm);
1041 if (file_version > 34)
1042 {
1043 gmx_fio_do_int(fio, ir->comm_mode);
1044 }
1045 else if (ir->nstcomm < 0)
1046 {
1047 ir->comm_mode = ecmANGULAR;
1048 }
1049 else
1050 {
1051 ir->comm_mode = ecmLINEAR;
1052 }
1053 ir->nstcomm = abs(ir->nstcomm);
1054
1055 /* ignore nstcheckpoint */
1056 if (file_version > 25 && file_version < tpxv_RemoveObsoleteParameters1)
1057 {
1058 gmx_fio_do_int(fio, idum);
1059 }
1060
1061 gmx_fio_do_int(fio, ir->nstcgsteep);
1062
1063 if (file_version >= 30)
1064 {
1065 gmx_fio_do_int(fio, ir->nbfgscorr);
1066 }
1067 else if (bRead)
1068 {
1069 ir->nbfgscorr = 10;
1070 }
1071
1072 gmx_fio_do_int(fio, ir->nstlog);
1073 gmx_fio_do_int(fio, ir->nstxout);
1074 gmx_fio_do_int(fio, ir->nstvout);
1075 gmx_fio_do_int(fio, ir->nstfout);
1076 gmx_fio_do_int(fio, ir->nstenergy);
1077 gmx_fio_do_int(fio, ir->nstxout_compressed);
1078 if (file_version >= 59)
1079 {
1080 gmx_fio_do_double(fio, ir->init_t);
1081 gmx_fio_do_double(fio, ir->delta_t);
1082 }
1083 else
1084 {
1085 gmx_fio_do_real(fio, rdum);
1086 ir->init_t = rdum;
1087 gmx_fio_do_real(fio, rdum);
1088 ir->delta_t = rdum;
1089 }
1090 gmx_fio_do_real(fio, ir->x_compression_precision);
1091 if (file_version < 19)
1092 {
1093 gmx_fio_do_int(fio, idum);
1094 gmx_fio_do_int(fio, idum);
1095 }
1096 if (file_version < 18)
1097 {
1098 gmx_fio_do_int(fio, idum);
1099 }
1100 if (file_version >= 81)
1101 {
1102 gmx_fio_do_real(fio, ir->verletbuf_tol);
1103 }
1104 else
1105 {
1106 ir->verletbuf_tol = 0;
1107 }
1108 gmx_fio_do_real(fio, ir->rlist);
1109 if (file_version >= 67 && file_version < tpxv_RemoveTwinRange)
1110 {
1111 if (bRead)
1112 {
1113 // Reading such a file version could invoke the twin-range
1114 // scheme, about which mdrun should give a fatal error.
1115 real dummy_rlistlong = -1;
1116 gmx_fio_do_real(fio, dummy_rlistlong);
1117
1118 if (ir->rlist > 0 && (dummy_rlistlong == 0 || dummy_rlistlong > ir->rlist))
1119 {
1120 // Get mdrun to issue an error (regardless of
1121 // ir->cutoff_scheme).
1122 ir->useTwinRange = true;
1123 }
1124 else
1125 {
1126 // grompp used to set rlistlong actively. Users were
1127 // probably also confused and set rlistlong == rlist.
1128 // However, in all remaining cases, it is safe to let
1129 // mdrun proceed normally.
1130 ir->useTwinRange = false;
1131 }
1132 }
1133 }
1134 else
1135 {
1136 // No need to read or write anything
1137 ir->useTwinRange = false;
1138 }
1139 if (file_version >= 82 && file_version != 90)
1140 {
1141 // Multiple time-stepping is no longer enabled, but the old
1142 // support required the twin-range scheme, for which mdrun
1143 // already emits a fatal error.
1144 int dummy_nstcalclr = -1;
1145 gmx_fio_do_int(fio, dummy_nstcalclr);
1146 }
1147 gmx_fio_do_int(fio, ir->coulombtype);
1148 if (file_version < 32 && ir->coulombtype == eelRF)
1149 {
1150 ir->coulombtype = eelRF_NEC_UNSUPPORTED;
1151 }
1152 if (file_version >= 81)
1153 {
1154 gmx_fio_do_int(fio, ir->coulomb_modifier);
1155 }
1156 else
1157 {
1158 ir->coulomb_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1159 }
1160 gmx_fio_do_real(fio, ir->rcoulomb_switch);
1161 gmx_fio_do_real(fio, ir->rcoulomb);
1162 gmx_fio_do_int(fio, ir->vdwtype);
1163 if (file_version >= 81)
1164 {
1165 gmx_fio_do_int(fio, ir->vdw_modifier);
1166 }
1167 else
1168 {
1169 ir->vdw_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1170 }
1171 gmx_fio_do_real(fio, ir->rvdw_switch);
1172 gmx_fio_do_real(fio, ir->rvdw);
1173 gmx_fio_do_int(fio, ir->eDispCorr);
1174 gmx_fio_do_real(fio, ir->epsilon_r);
1175 if (file_version >= 37)
1176 {
1177 gmx_fio_do_real(fio, ir->epsilon_rf);
1178 }
1179 else
1180 {
1181 if (EEL_RF(ir->coulombtype))
1182 {
1183 ir->epsilon_rf = ir->epsilon_r;
1184 ir->epsilon_r = 1.0;
1185 }
1186 else
1187 {
1188 ir->epsilon_rf = 1.0;
1189 }
1190 }
1191 if (file_version >= 29)
1192 {
1193 gmx_fio_do_real(fio, ir->tabext);
1194 }
1195 else
1196 {
1197 ir->tabext = 1.0;
1198 }
1199
1200 if (file_version > 25)
1201 {
1202 gmx_fio_do_int(fio, ir->gb_algorithm);
1203 gmx_fio_do_int(fio, ir->nstgbradii);
1204 gmx_fio_do_real(fio, ir->rgbradii);
1205 gmx_fio_do_real(fio, ir->gb_saltconc);
1206 gmx_fio_do_int(fio, ir->implicit_solvent);
1207 }
1208 else
1209 {
1210 ir->gb_algorithm = egbSTILL;
1211 ir->nstgbradii = 1;
1212 ir->rgbradii = 1.0;
1213 ir->gb_saltconc = 0;
1214 ir->implicit_solvent = eisNO;
1215 }
1216 if (file_version >= 55)
1217 {
1218 gmx_fio_do_real(fio, ir->gb_epsilon_solvent);
1219 gmx_fio_do_real(fio, ir->gb_obc_alpha);
1220 gmx_fio_do_real(fio, ir->gb_obc_beta);
1221 gmx_fio_do_real(fio, ir->gb_obc_gamma);
1222 if (file_version >= 60)
1223 {
1224 gmx_fio_do_real(fio, ir->gb_dielectric_offset);
1225 gmx_fio_do_int(fio, ir->sa_algorithm);
1226 }
1227 else
1228 {
1229 ir->gb_dielectric_offset = 0.009;
1230 ir->sa_algorithm = esaAPPROX;
1231 }
1232 gmx_fio_do_real(fio, ir->sa_surface_tension);
1233
1234 /* Override sa_surface_tension if it is not changed in the mpd-file */
1235 if (ir->sa_surface_tension < 0)
1236 {
1237 if (ir->gb_algorithm == egbSTILL)
1238 {
1239 ir->sa_surface_tension = 0.0049 * 100 * CAL2JOULE;
1240 }
1241 else if (ir->gb_algorithm == egbHCT || ir->gb_algorithm == egbOBC)
1242 {
1243 ir->sa_surface_tension = 0.0054 * 100 * CAL2JOULE;
1244 }
1245 }
1246
1247 }
1248 else
1249 {
1250 /* Better use sensible values than insane (0.0) ones... */
1251 ir->gb_epsilon_solvent = 80;
1252 ir->gb_obc_alpha = 1.0;
1253 ir->gb_obc_beta = 0.8;
1254 ir->gb_obc_gamma = 4.85;
1255 ir->sa_surface_tension = 2.092;
1256 }
1257
1258
1259 if (file_version >= 81)
1260 {
1261 gmx_fio_do_real(fio, ir->fourier_spacing);
1262 }
1263 else
1264 {
1265 ir->fourier_spacing = 0.0;
1266 }
1267 gmx_fio_do_int(fio, ir->nkx);
1268 gmx_fio_do_int(fio, ir->nky);
1269 gmx_fio_do_int(fio, ir->nkz);
1270 gmx_fio_do_int(fio, ir->pme_order);
1271 gmx_fio_do_real(fio, ir->ewald_rtol);
1272
1273 if (file_version >= 93)
1274 {
1275 gmx_fio_do_real(fio, ir->ewald_rtol_lj);
1276 }
1277 else
1278 {
1279 ir->ewald_rtol_lj = ir->ewald_rtol;
1280 }
1281
1282 if (file_version >= 24)
1283 {
1284 gmx_fio_do_int(fio, ir->ewald_geometry);
1285 }
1286 else
1287 {
1288 ir->ewald_geometry = eewg3D;
1289 }
1290
1291 if (file_version <= 17)
1292 {
1293 ir->epsilon_surface = 0;
1294 if (file_version == 17)
1295 {
1296 gmx_fio_do_int(fio, idum);
1297 }
1298 }
1299 else
1300 {
1301 gmx_fio_do_real(fio, ir->epsilon_surface);
1302 }
1303
1304 /* ignore bOptFFT */
1305 if (file_version < tpxv_RemoveObsoleteParameters1)
1306 {
1307 gmx_fio_do_gmx_bool(fio, bdum);
1308 }
1309
1310 if (file_version >= 93)
1311 {
1312 gmx_fio_do_int(fio, ir->ljpme_combination_rule);
1313 }
1314 gmx_fio_do_gmx_bool(fio, ir->bContinuation);
1315 gmx_fio_do_int(fio, ir->etc);
1316 /* before version 18, ir->etc was a gmx_bool (ir->btc),
1317 * but the values 0 and 1 still mean no and
1318 * berendsen temperature coupling, respectively.
1319 */
1320 if (file_version >= 79)
1321 {
1322 gmx_fio_do_gmx_bool(fio, ir->bPrintNHChains);
1323 }
1324 if (file_version >= 71)
1325 {
1326 gmx_fio_do_int(fio, ir->nsttcouple);
1327 }
1328 else
1329 {
1330 ir->nsttcouple = ir->nstcalcenergy;
1331 }
1332 if (file_version <= 15)
1333 {
1334 gmx_fio_do_int(fio, idum);
1335 }
1336 if (file_version <= 17)
1337 {
1338 gmx_fio_do_int(fio, ir->epct);
1339 if (file_version <= 15)
1340 {
1341 if (ir->epct == 5)
1342 {
1343 ir->epct = epctSURFACETENSION;
1344 }
1345 gmx_fio_do_int(fio, idum);
1346 }
1347 ir->epct -= 1;
1348 /* we have removed the NO alternative at the beginning */
1349 if (ir->epct == -1)
1350 {
1351 ir->epc = epcNO;
1352 ir->epct = epctISOTROPIC;
1353 }
1354 else
1355 {
1356 ir->epc = epcBERENDSEN;
1357 }
1358 }
1359 else
1360 {
1361 gmx_fio_do_int(fio, ir->epc);
1362 gmx_fio_do_int(fio, ir->epct);
1363 }
1364 if (file_version >= 71)
1365 {
1366 gmx_fio_do_int(fio, ir->nstpcouple);
1367 }
1368 else
1369 {
1370 ir->nstpcouple = ir->nstcalcenergy;
1371 }
1372 gmx_fio_do_real(fio, ir->tau_p);
1373 if (file_version <= 15)
1374 {
1375 gmx_fio_do_rvec(fio, vdum);
1376 clear_mat(ir->ref_p);
1377 for (i = 0; i < DIM; i++)
1378 {
1379 ir->ref_p[i][i] = vdum[i];
1380 }
1381 }
1382 else
1383 {
1384 gmx_fio_do_rvec(fio, ir->ref_p[XX]);
1385 gmx_fio_do_rvec(fio, ir->ref_p[YY]);
1386 gmx_fio_do_rvec(fio, ir->ref_p[ZZ]);
1387 }
1388 if (file_version <= 15)
1389 {
1390 gmx_fio_do_rvec(fio, vdum);
1391 clear_mat(ir->compress);
1392 for (i = 0; i < DIM; i++)
1393 {
1394 ir->compress[i][i] = vdum[i];
1395 }
1396 }
1397 else
1398 {
1399 gmx_fio_do_rvec(fio, ir->compress[XX]);
1400 gmx_fio_do_rvec(fio, ir->compress[YY]);
1401 gmx_fio_do_rvec(fio, ir->compress[ZZ]);
1402 }
1403 if (file_version >= 47)
1404 {
1405 gmx_fio_do_int(fio, ir->refcoord_scaling);
1406 gmx_fio_do_rvec(fio, ir->posres_com);
1407 gmx_fio_do_rvec(fio, ir->posres_comB);
1408 }
1409 else
1410 {
1411 ir->refcoord_scaling = erscNO;
1412 clear_rvec(ir->posres_com);
1413 clear_rvec(ir->posres_comB);
1414 }
1415 if ((file_version > 25) && (file_version < 79))
1416 {
1417 gmx_fio_do_int(fio, ir->andersen_seed);
1418 }
1419 else
1420 {
1421 ir->andersen_seed = 0;
1422 }
1423 if (file_version < 26)
1424 {
1425 gmx_fio_do_gmx_bool(fio, bSimAnn);
1426 gmx_fio_do_real(fio, zerotemptime);
1427 }
1428
1429 if (file_version < 37)
1430 {
1431 gmx_fio_do_real(fio, rdum);
1432 }
1433
1434 gmx_fio_do_real(fio, ir->shake_tol);
1435 if (file_version < 54)
1436 {
1437 gmx_fio_do_real(fio, *fudgeQQ);
1438 }
1439
1440 gmx_fio_do_int(fio, ir->efep);
1441 if (file_version <= 14 && ir->efep != efepNO)
1442 {
1443 ir->efep = efepYES;
1444 }
1445 do_fepvals(fio, ir->fepvals, bRead, file_version);
1446
1447 if (file_version >= 79)
1448 {
1449 gmx_fio_do_gmx_bool(fio, ir->bSimTemp);
1450 if (ir->bSimTemp)
1451 {
1452 ir->bSimTemp = TRUE;
1453 }
1454 }
1455 else
1456 {
1457 ir->bSimTemp = FALSE;
1458 }
1459 if (ir->bSimTemp)
1460 {
1461 do_simtempvals(fio, ir->simtempvals, ir->fepvals->n_lambda, bRead, file_version);
1462 }
1463
1464 if (file_version >= 79)
1465 {
1466 gmx_fio_do_gmx_bool(fio, ir->bExpanded);
1467 if (ir->bExpanded)
1468 {
1469 ir->bExpanded = TRUE;
1470 }
1471 else
1472 {
1473 ir->bExpanded = FALSE;
1474 }
1475 }
1476 if (ir->bExpanded)
1477 {
1478 do_expandedvals(fio, ir->expandedvals, ir->fepvals, bRead, file_version);
1479 }
1480 if (file_version >= 57)
1481 {
1482 gmx_fio_do_int(fio, ir->eDisre);
1483 }
1484 gmx_fio_do_int(fio, ir->eDisreWeighting);
1485 if (file_version < 22)
1486 {
1487 if (ir->eDisreWeighting == 0)
1488 {
1489 ir->eDisreWeighting = edrwEqual;
1490 }
1491 else
1492 {
1493 ir->eDisreWeighting = edrwConservative;
1494 }
1495 }
1496 gmx_fio_do_gmx_bool(fio, ir->bDisreMixed);
1497 gmx_fio_do_real(fio, ir->dr_fc);
1498 gmx_fio_do_real(fio, ir->dr_tau);
1499 gmx_fio_do_int(fio, ir->nstdisreout);
1500 if (file_version >= 22)
1501 {
1502 gmx_fio_do_real(fio, ir->orires_fc);
1503 gmx_fio_do_real(fio, ir->orires_tau);
1504 gmx_fio_do_int(fio, ir->nstorireout);
1505 }
1506 else
1507 {
1508 ir->orires_fc = 0;
1509 ir->orires_tau = 0;
1510 ir->nstorireout = 0;
1511 }
1512
1513 /* ignore dihre_fc */
1514 if (file_version >= 26 && file_version < 79)
1515 {
1516 gmx_fio_do_real(fio, rdum);
1517 if (file_version < 56)
1518 {
1519 gmx_fio_do_real(fio, rdum);
1520 gmx_fio_do_int(fio, idum);
1521 }
1522 }
1523
1524 gmx_fio_do_real(fio, ir->em_stepsize);
1525 gmx_fio_do_real(fio, ir->em_tol);
1526 if (file_version >= 22)
1527 {
1528 gmx_fio_do_gmx_bool(fio, ir->bShakeSOR);
1529 }
1530 else if (bRead)
1531 {
1532 ir->bShakeSOR = TRUE;
1533 }
1534 if (file_version >= 11)
1535 {
1536 gmx_fio_do_int(fio, ir->niter);
1537 }
1538 else if (bRead)
1539 {
1540 ir->niter = 25;
1541 fprintf(stderr, "Note: niter not in run input file, setting it to %d\n",
1542 ir->niter);
1543 }
1544 if (file_version >= 21)
1545 {
1546 gmx_fio_do_real(fio, ir->fc_stepsize);
1547 }
1548 else
1549 {
1550 ir->fc_stepsize = 0;
1551 }
1552 gmx_fio_do_int(fio, ir->eConstrAlg);
1553 gmx_fio_do_int(fio, ir->nProjOrder);
1554 gmx_fio_do_real(fio, ir->LincsWarnAngle);
1555 if (file_version <= 14)
1556 {
1557 gmx_fio_do_int(fio, idum);
1558 }
1559 if (file_version >= 26)
1560 {
1561 gmx_fio_do_int(fio, ir->nLincsIter);
1562 }
1563 else if (bRead)
1564 {
1565 ir->nLincsIter = 1;
1566 fprintf(stderr, "Note: nLincsIter not in run input file, setting it to %d\n",
1567 ir->nLincsIter);
1568 }
1569 if (file_version < 33)
1570 {
1571 gmx_fio_do_real(fio, bd_temp);
1572 }
1573 gmx_fio_do_real(fio, ir->bd_fric);
1574 if (file_version >= tpxv_Use64BitRandomSeed)
1575 {
1576 gmx_fio_do_int64(fio, ir->ld_seed);
1577 }
1578 else
1579 {
1580 gmx_fio_do_int(fio, idum);
1581 ir->ld_seed = idum;
1582 }
1583 if (file_version >= 33)
1584 {
1585 for (i = 0; i < DIM; i++)
1586 {
1587 gmx_fio_do_rvec(fio, ir->deform[i]);
1588 }
1589 }
1590 else
1591 {
1592 for (i = 0; i < DIM; i++)
1593 {
1594 clear_rvec(ir->deform[i]);
1595 }
1596 }
1597 if (file_version >= 14)
1598 {
1599 gmx_fio_do_real(fio, ir->cos_accel);
1600 }
1601 else if (bRead)
1602 {
1603 ir->cos_accel = 0;
1604 }
1605 gmx_fio_do_int(fio, ir->userint1);
1606 gmx_fio_do_int(fio, ir->userint2);
1607 gmx_fio_do_int(fio, ir->userint3);
1608 gmx_fio_do_int(fio, ir->userint4);
1609 gmx_fio_do_real(fio, ir->userreal1);
1610 gmx_fio_do_real(fio, ir->userreal2);
1611 gmx_fio_do_real(fio, ir->userreal3);
1612 gmx_fio_do_real(fio, ir->userreal4);
1613
1614 /* AdResS is removed, but we need to be able to read old files,
1615 and let mdrun refuse to run them */
1616 if (file_version >= 77 && file_version < tpxv_RemoveAdress)
1617 {
1618 gmx_fio_do_gmx_bool(fio, ir->bAdress);
1619 if (ir->bAdress)
1620 {
1621 int idum, numThermoForceGroups, numEnergyGroups;
1622 real rdum;
1623 rvec rvecdum;
1624 gmx_fio_do_int(fio, idum);
1625 gmx_fio_do_real(fio, rdum);
1626 gmx_fio_do_real(fio, rdum);
1627 gmx_fio_do_real(fio, rdum);
1628 gmx_fio_do_int(fio, idum);
1629 gmx_fio_do_int(fio, idum);
1630 gmx_fio_do_rvec(fio, rvecdum);
1631 gmx_fio_do_int(fio, numThermoForceGroups);
1632 gmx_fio_do_real(fio, rdum);
1633 gmx_fio_do_int(fio, numEnergyGroups);
1634 gmx_fio_do_int(fio, idum);
1635
1636 if (numThermoForceGroups > 0)
1637 {
1638 std::vector<int> idumn(numThermoForceGroups);
1639 gmx_fio_ndo_int(fio, idumn.data(), idumn.size());
1640 }
1641 if (numEnergyGroups > 0)
1642 {
1643 std::vector<int> idumn(numEnergyGroups);
1644 gmx_fio_ndo_int(fio, idumn.data(), idumn.size());
1645 }
1646 }
1647 }
1648 else
1649 {
1650 ir->bAdress = FALSE;
1651 }
1652
1653 /* pull stuff */
1654 if (file_version >= 48)
1655 {
1656 int ePullOld = 0;
1657
1658 if (file_version >= tpxv_PullCoordTypeGeom)
1659 {
1660 gmx_fio_do_gmx_bool(fio, ir->bPull);
1661 }
1662 else
1663 {
1664 gmx_fio_do_int(fio, ePullOld);
1665 ir->bPull = (ePullOld > 0);
1666 /* We removed the first ePull=ePullNo for the enum */
1667 ePullOld -= 1;
1668 }
1669 if (ir->bPull)
1670 {
1671 if (bRead)
1672 {
1673 snew(ir->pull, 1);
1674 }
1675 do_pull(fio, ir->pull, bRead, file_version, ePullOld);
1676 }
1677 }
1678 else
1679 {
1680 ir->bPull = FALSE;
1681 }
1682
1683 /* Enforced rotation */
1684 if (file_version >= 74)
1685 {
1686 gmx_fio_do_int(fio, ir->bRot);
1687 if (ir->bRot == TRUE)
1688 {
1689 if (bRead)
1690 {
1691 snew(ir->rot, 1);
1692 }
1693 do_rot(fio, ir->rot, bRead);
1694 }
1695 }
1696 else
1697 {
1698 ir->bRot = FALSE;
1699 }
1700
1701 /* Interactive molecular dynamics */
1702 if (file_version >= tpxv_InteractiveMolecularDynamics)
1703 {
1704 gmx_fio_do_int(fio, ir->bIMD);
1705 if (TRUE == ir->bIMD)
1706 {
1707 if (bRead)
1708 {
1709 snew(ir->imd, 1);
1710 }
1711 do_imd(fio, ir->imd, bRead);
1712 }
1713 }
1714 else
1715 {
1716 /* We don't support IMD sessions for old .tpr files */
1717 ir->bIMD = FALSE;
1718 }
1719
1720 /* grpopts stuff */
1721 gmx_fio_do_int(fio, ir->opts.ngtc);
1722 if (file_version >= 69)
1723 {
1724 gmx_fio_do_int(fio, ir->opts.nhchainlength);
1725 }
1726 else
1727 {
1728 ir->opts.nhchainlength = 1;
1729 }
1730 gmx_fio_do_int(fio, ir->opts.ngacc);
1731 gmx_fio_do_int(fio, ir->opts.ngfrz);
1732 gmx_fio_do_int(fio, ir->opts.ngener);
1733
1734 if (bRead)
1735 {
1736 snew(ir->opts.nrdf, ir->opts.ngtc);
1737 snew(ir->opts.ref_t, ir->opts.ngtc);
1738 snew(ir->opts.annealing, ir->opts.ngtc);
1739 snew(ir->opts.anneal_npoints, ir->opts.ngtc);
1740 snew(ir->opts.anneal_time, ir->opts.ngtc);
1741 snew(ir->opts.anneal_temp, ir->opts.ngtc);
1742 snew(ir->opts.tau_t, ir->opts.ngtc);
1743 snew(ir->opts.nFreeze, ir->opts.ngfrz);
1744 snew(ir->opts.acc, ir->opts.ngacc);
1745 snew(ir->opts.egp_flags, ir->opts.ngener*ir->opts.ngener);
1746 }
1747 if (ir->opts.ngtc > 0)
1748 {
1749 if (bRead && file_version < 13)
1750 {
1751 snew(tmp, ir->opts.ngtc);
1752 gmx_fio_ndo_int(fio, tmp, ir->opts.ngtc);
1753 for (i = 0; i < ir->opts.ngtc; i++)
1754 {
1755 ir->opts.nrdf[i] = tmp[i];
1756 }
1757 sfree(tmp);
1758 }
1759 else
1760 {
1761 gmx_fio_ndo_real(fio, ir->opts.nrdf, ir->opts.ngtc);
1762 }
1763 gmx_fio_ndo_real(fio, ir->opts.ref_t, ir->opts.ngtc);
1764 gmx_fio_ndo_real(fio, ir->opts.tau_t, ir->opts.ngtc);
1765 if (file_version < 33 && ir->eI == eiBD)
1766 {
1767 for (i = 0; i < ir->opts.ngtc; i++)
1768 {
1769 ir->opts.tau_t[i] = bd_temp;
1770 }
1771 }
1772 }
1773 if (ir->opts.ngfrz > 0)
1774 {
1775 gmx_fio_ndo_ivec(fio, ir->opts.nFreeze, ir->opts.ngfrz);
1776 }
1777 if (ir->opts.ngacc > 0)
1778 {
1779 gmx_fio_ndo_rvec(fio, ir->opts.acc, ir->opts.ngacc);
1780 }
1781 if (file_version >= 12)
1782 {
1783 gmx_fio_ndo_int(fio, ir->opts.egp_flags,
1784 ir->opts.ngener*ir->opts.ngener);
1785 }
1786
1787 if (bRead && file_version < 26)
1788 {
1789 for (i = 0; i < ir->opts.ngtc; i++)
1790 {
1791 if (bSimAnn)
1792 {
1793 ir->opts.annealing[i] = eannSINGLE;
1794 ir->opts.anneal_npoints[i] = 2;
1795 snew(ir->opts.anneal_time[i], 2);
1796 snew(ir->opts.anneal_temp[i], 2);
1797 /* calculate the starting/ending temperatures from reft, zerotemptime, and nsteps */
1798 finish_t = ir->init_t + ir->nsteps * ir->delta_t;
1799 init_temp = ir->opts.ref_t[i]*(1-ir->init_t/zerotemptime);
1800 finish_temp = ir->opts.ref_t[i]*(1-finish_t/zerotemptime);
1801 ir->opts.anneal_time[i][0] = ir->init_t;
1802 ir->opts.anneal_time[i][1] = finish_t;
1803 ir->opts.anneal_temp[i][0] = init_temp;
1804 ir->opts.anneal_temp[i][1] = finish_temp;
1805 }
1806 else
1807 {
1808 ir->opts.annealing[i] = eannNO;
1809 ir->opts.anneal_npoints[i] = 0;
1810 }
1811 }
1812 }
1813 else
1814 {
1815 /* file version 26 or later */
1816 /* First read the lists with annealing and npoints for each group */
1817 gmx_fio_ndo_int(fio, ir->opts.annealing, ir->opts.ngtc);
1818 gmx_fio_ndo_int(fio, ir->opts.anneal_npoints, ir->opts.ngtc);
1819 for (j = 0; j < (ir->opts.ngtc); j++)
1820 {
1821 k = ir->opts.anneal_npoints[j];
1822 if (bRead)
1823 {
1824 snew(ir->opts.anneal_time[j], k);
1825 snew(ir->opts.anneal_temp[j], k);
1826 }
1827 gmx_fio_ndo_real(fio, ir->opts.anneal_time[j], k);
1828 gmx_fio_ndo_real(fio, ir->opts.anneal_temp[j], k);
1829 }
1830 }
1831 /* Walls */
1832 if (file_version >= 45)
1833 {
1834 gmx_fio_do_int(fio, ir->nwall);
1835 gmx_fio_do_int(fio, ir->wall_type);
1836 if (file_version >= 50)
1837 {
1838 gmx_fio_do_real(fio, ir->wall_r_linpot);
1839 }
1840 else
1841 {
1842 ir->wall_r_linpot = -1;
1843 }
1844 gmx_fio_do_int(fio, ir->wall_atomtype[0]);
1845 gmx_fio_do_int(fio, ir->wall_atomtype[1]);
1846 gmx_fio_do_real(fio, ir->wall_density[0]);
1847 gmx_fio_do_real(fio, ir->wall_density[1]);
1848 gmx_fio_do_real(fio, ir->wall_ewald_zfac);
1849 }
1850 else
1851 {
1852 ir->nwall = 0;
1853 ir->wall_type = 0;
1854 ir->wall_atomtype[0] = -1;
1855 ir->wall_atomtype[1] = -1;
1856 ir->wall_density[0] = 0;
1857 ir->wall_density[1] = 0;
1858 ir->wall_ewald_zfac = 3;
1859 }
1860 /* Cosine stuff for electric fields */
1861 for (j = 0; (j < DIM); j++)
1862 {
1863 gmx_fio_do_int(fio, ir->ex[j].n);
1864 gmx_fio_do_int(fio, ir->et[j].n);
1865 if (bRead)
1866 {
1867 snew(ir->ex[j].a, ir->ex[j].n);
1868 snew(ir->ex[j].phi, ir->ex[j].n);
1869 snew(ir->et[j].a, ir->et[j].n);
1870 snew(ir->et[j].phi, ir->et[j].n);
1871 }
1872 gmx_fio_ndo_real(fio, ir->ex[j].a, ir->ex[j].n);
1873 gmx_fio_ndo_real(fio, ir->ex[j].phi, ir->ex[j].n);
1874 gmx_fio_ndo_real(fio, ir->et[j].a, ir->et[j].n);
1875 gmx_fio_ndo_real(fio, ir->et[j].phi, ir->et[j].n);
1876 }
1877
1878 /* Swap ions */
1879 if (file_version >= tpxv_ComputationalElectrophysiology)
1880 {
1881 gmx_fio_do_int(fio, ir->eSwapCoords);
1882 if (ir->eSwapCoords != eswapNO)
1883 {
1884 if (bRead)
1885 {
1886 snew(ir->swap, 1);
1887 }
1888 do_swapcoords_tpx(fio, ir->swap, bRead, file_version);
1889 }
1890 }
1891
1892 /* QMMM stuff */
1893 if (file_version >= 39)
1894 {
1895 gmx_fio_do_gmx_bool(fio, ir->bQMMM);
1896 gmx_fio_do_int(fio, ir->QMMMscheme);
1897 gmx_fio_do_real(fio, ir->scalefactor);
1898 gmx_fio_do_int(fio, ir->opts.ngQM);
1899 if (bRead)
1900 {
1901 snew(ir->opts.QMmethod, ir->opts.ngQM);
1902 snew(ir->opts.QMbasis, ir->opts.ngQM);
1903 snew(ir->opts.QMcharge, ir->opts.ngQM);
1904 snew(ir->opts.QMmult, ir->opts.ngQM);
1905 snew(ir->opts.bSH, ir->opts.ngQM);
1906 snew(ir->opts.CASorbitals, ir->opts.ngQM);
1907 snew(ir->opts.CASelectrons, ir->opts.ngQM);
1908 snew(ir->opts.SAon, ir->opts.ngQM);
1909 snew(ir->opts.SAoff, ir->opts.ngQM);
1910 snew(ir->opts.SAsteps, ir->opts.ngQM);
1911 snew(ir->opts.bOPT, ir->opts.ngQM);
1912 snew(ir->opts.bTS, ir->opts.ngQM);
1913 }
1914 if (ir->opts.ngQM > 0)
1915 {
1916 gmx_fio_ndo_int(fio, ir->opts.QMmethod, ir->opts.ngQM);
1917 gmx_fio_ndo_int(fio, ir->opts.QMbasis, ir->opts.ngQM);
1918 gmx_fio_ndo_int(fio, ir->opts.QMcharge, ir->opts.ngQM);
1919 gmx_fio_ndo_int(fio, ir->opts.QMmult, ir->opts.ngQM);
1920 gmx_fio_ndo_gmx_bool(fio, ir->opts.bSH, ir->opts.ngQM);
1921 gmx_fio_ndo_int(fio, ir->opts.CASorbitals, ir->opts.ngQM);
1922 gmx_fio_ndo_int(fio, ir->opts.CASelectrons, ir->opts.ngQM);
1923 gmx_fio_ndo_real(fio, ir->opts.SAon, ir->opts.ngQM);
1924 gmx_fio_ndo_real(fio, ir->opts.SAoff, ir->opts.ngQM);
1925 gmx_fio_ndo_int(fio, ir->opts.SAsteps, ir->opts.ngQM);
1926 gmx_fio_ndo_gmx_bool(fio, ir->opts.bOPT, ir->opts.ngQM);
1927 gmx_fio_ndo_gmx_bool(fio, ir->opts.bTS, ir->opts.ngQM);
1928 }
1929 /* end of QMMM stuff */
1930 }
1931 }
1932
1933
1934 static void do_harm(t_fileio *fio, t_iparams *iparams)
1935 {
1936 gmx_fio_do_real(fio, iparams->harmonic.rA);
1937 gmx_fio_do_real(fio, iparams->harmonic.krA);
1938 gmx_fio_do_real(fio, iparams->harmonic.rB);
1939 gmx_fio_do_real(fio, iparams->harmonic.krB);
1940 }
1941
1942 void do_iparams(t_fileio *fio, t_functype ftype, t_iparams *iparams,
1943 gmx_bool bRead, int file_version)
1944 {
1945 int idum;
1946 real rdum;
1947
1948 switch (ftype)
1949 {
1950 case F_ANGLES:
1951 case F_G96ANGLES:
1952 case F_BONDS:
1953 case F_G96BONDS:
1954 case F_HARMONIC:
1955 case F_IDIHS:
1956 do_harm(fio, iparams);
1957 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && bRead)
1958 {
1959 /* Correct incorrect storage of parameters */
1960 iparams->pdihs.phiB = iparams->pdihs.phiA;
1961 iparams->pdihs.cpB = iparams->pdihs.cpA;
1962 }
1963 break;
1964 case F_RESTRANGLES:
1965 gmx_fio_do_real(fio, iparams->harmonic.rA);
1966 gmx_fio_do_real(fio, iparams->harmonic.krA);
1967 break;
1968 case F_LINEAR_ANGLES:
1969 gmx_fio_do_real(fio, iparams->linangle.klinA);
1970 gmx_fio_do_real(fio, iparams->linangle.aA);
1971 gmx_fio_do_real(fio, iparams->linangle.klinB);
1972 gmx_fio_do_real(fio, iparams->linangle.aB);
1973 break;
1974 case F_FENEBONDS:
1975 gmx_fio_do_real(fio, iparams->fene.bm);
1976 gmx_fio_do_real(fio, iparams->fene.kb);
1977 break;
1978
1979 case F_RESTRBONDS:
1980 gmx_fio_do_real(fio, iparams->restraint.lowA);
1981 gmx_fio_do_real(fio, iparams->restraint.up1A);
1982 gmx_fio_do_real(fio, iparams->restraint.up2A);
1983 gmx_fio_do_real(fio, iparams->restraint.kA);
1984 gmx_fio_do_real(fio, iparams->restraint.lowB);
1985 gmx_fio_do_real(fio, iparams->restraint.up1B);
1986 gmx_fio_do_real(fio, iparams->restraint.up2B);
1987 gmx_fio_do_real(fio, iparams->restraint.kB);
1988 break;
1989 case F_TABBONDS:
1990 case F_TABBONDSNC:
1991 case F_TABANGLES:
1992 case F_TABDIHS:
1993 gmx_fio_do_real(fio, iparams->tab.kA);
1994 gmx_fio_do_int(fio, iparams->tab.table);
1995 gmx_fio_do_real(fio, iparams->tab.kB);
1996 break;
1997 case F_CROSS_BOND_BONDS:
1998 gmx_fio_do_real(fio, iparams->cross_bb.r1e);
1999 gmx_fio_do_real(fio, iparams->cross_bb.r2e);
2000 gmx_fio_do_real(fio, iparams->cross_bb.krr);
2001 break;
2002 case F_CROSS_BOND_ANGLES:
2003 gmx_fio_do_real(fio, iparams->cross_ba.r1e);
2004 gmx_fio_do_real(fio, iparams->cross_ba.r2e);
2005 gmx_fio_do_real(fio, iparams->cross_ba.r3e);
2006 gmx_fio_do_real(fio, iparams->cross_ba.krt);
2007 break;
2008 case F_UREY_BRADLEY:
2009 gmx_fio_do_real(fio, iparams->u_b.thetaA);
2010 gmx_fio_do_real(fio, iparams->u_b.kthetaA);
2011 gmx_fio_do_real(fio, iparams->u_b.r13A);
2012 gmx_fio_do_real(fio, iparams->u_b.kUBA);
2013 if (file_version >= 79)
2014 {
2015 gmx_fio_do_real(fio, iparams->u_b.thetaB);
2016 gmx_fio_do_real(fio, iparams->u_b.kthetaB);
2017 gmx_fio_do_real(fio, iparams->u_b.r13B);
2018 gmx_fio_do_real(fio, iparams->u_b.kUBB);
2019 }
2020 else
2021 {
2022 iparams->u_b.thetaB = iparams->u_b.thetaA;
2023 iparams->u_b.kthetaB = iparams->u_b.kthetaA;
2024 iparams->u_b.r13B = iparams->u_b.r13A;
2025 iparams->u_b.kUBB = iparams->u_b.kUBA;
2026 }
2027 break;
2028 case F_QUARTIC_ANGLES:
2029 gmx_fio_do_real(fio, iparams->qangle.theta);
2030 gmx_fio_ndo_real(fio, iparams->qangle.c, 5);
2031 break;
2032 case F_BHAM:
2033 gmx_fio_do_real(fio, iparams->bham.a);
2034 gmx_fio_do_real(fio, iparams->bham.b);
2035 gmx_fio_do_real(fio, iparams->bham.c);
2036 break;
2037 case F_MORSE:
2038 gmx_fio_do_real(fio, iparams->morse.b0A);
2039 gmx_fio_do_real(fio, iparams->morse.cbA);
2040 gmx_fio_do_real(fio, iparams->morse.betaA);
2041 if (file_version >= 79)
2042 {
2043 gmx_fio_do_real(fio, iparams->morse.b0B);
2044 gmx_fio_do_real(fio, iparams->morse.cbB);
2045 gmx_fio_do_real(fio, iparams->morse.betaB);
2046 }
2047 else
2048 {
2049 iparams->morse.b0B = iparams->morse.b0A;
2050 iparams->morse.cbB = iparams->morse.cbA;
2051 iparams->morse.betaB = iparams->morse.betaA;
2052 }
2053 break;
2054 case F_CUBICBONDS:
2055 gmx_fio_do_real(fio, iparams->cubic.b0);
2056 gmx_fio_do_real(fio, iparams->cubic.kb);
2057 gmx_fio_do_real(fio, iparams->cubic.kcub);
2058 break;
2059 case F_CONNBONDS:
2060 break;
2061 case F_POLARIZATION:
2062 gmx_fio_do_real(fio, iparams->polarize.alpha);
2063 break;
2064 case F_ANHARM_POL:
2065 gmx_fio_do_real(fio, iparams->anharm_polarize.alpha);
2066 gmx_fio_do_real(fio, iparams->anharm_polarize.drcut);
2067 gmx_fio_do_real(fio, iparams->anharm_polarize.khyp);
2068 break;
2069 case F_WATER_POL:
2070 if (file_version < 31)
2071 {
2072 gmx_fatal(FARGS, "Old tpr files with water_polarization not supported. Make a new.");
2073 }
2074 gmx_fio_do_real(fio, iparams->wpol.al_x);
2075 gmx_fio_do_real(fio, iparams->wpol.al_y);
2076 gmx_fio_do_real(fio, iparams->wpol.al_z);
2077 gmx_fio_do_real(fio, iparams->wpol.rOH);
2078 gmx_fio_do_real(fio, iparams->wpol.rHH);
2079 gmx_fio_do_real(fio, iparams->wpol.rOD);
2080 break;
2081 case F_THOLE_POL:
2082 gmx_fio_do_real(fio, iparams->thole.a);
2083 gmx_fio_do_real(fio, iparams->thole.alpha1);
2084 gmx_fio_do_real(fio, iparams->thole.alpha2);
2085 gmx_fio_do_real(fio, iparams->thole.rfac);
2086 break;
2087 case F_LJ:
2088 gmx_fio_do_real(fio, iparams->lj.c6);
2089 gmx_fio_do_real(fio, iparams->lj.c12);
2090 break;
2091 case F_LJ14:
2092 gmx_fio_do_real(fio, iparams->lj14.c6A);
2093 gmx_fio_do_real(fio, iparams->lj14.c12A);
2094 gmx_fio_do_real(fio, iparams->lj14.c6B);
2095 gmx_fio_do_real(fio, iparams->lj14.c12B);
2096 break;
2097 case F_LJC14_Q:
2098 gmx_fio_do_real(fio, iparams->ljc14.fqq);
2099 gmx_fio_do_real(fio, iparams->ljc14.qi);
2100 gmx_fio_do_real(fio, iparams->ljc14.qj);
2101 gmx_fio_do_real(fio, iparams->ljc14.c6);
2102 gmx_fio_do_real(fio, iparams->ljc14.c12);
2103 break;
2104 case F_LJC_PAIRS_NB:
2105 gmx_fio_do_real(fio, iparams->ljcnb.qi);
2106 gmx_fio_do_real(fio, iparams->ljcnb.qj);
2107 gmx_fio_do_real(fio, iparams->ljcnb.c6);
2108 gmx_fio_do_real(fio, iparams->ljcnb.c12);
2109 break;
2110 case F_PDIHS:
2111 case F_PIDIHS:
2112 case F_ANGRES:
2113 case F_ANGRESZ:
2114 gmx_fio_do_real(fio, iparams->pdihs.phiA);
2115 gmx_fio_do_real(fio, iparams->pdihs.cpA);
2116 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && file_version < 42)
2117 {
2118 /* Read the incorrectly stored multiplicity */
2119 gmx_fio_do_real(fio, iparams->harmonic.rB);
2120 gmx_fio_do_real(fio, iparams->harmonic.krB);
2121 iparams->pdihs.phiB = iparams->pdihs.phiA;
2122 iparams->pdihs.cpB = iparams->pdihs.cpA;
2123 }
2124 else
2125 {
2126 gmx_fio_do_real(fio, iparams->pdihs.phiB);
2127 gmx_fio_do_real(fio, iparams->pdihs.cpB);
2128 gmx_fio_do_int(fio, iparams->pdihs.mult);
2129 }
2130 break;
2131 case F_RESTRDIHS:
2132 gmx_fio_do_real(fio, iparams->pdihs.phiA);
2133 gmx_fio_do_real(fio, iparams->pdihs.cpA);
2134 break;
2135 case F_DISRES:
2136 gmx_fio_do_int(fio, iparams->disres.label);
2137 gmx_fio_do_int(fio, iparams->disres.type);
2138 gmx_fio_do_real(fio, iparams->disres.low);
2139 gmx_fio_do_real(fio, iparams->disres.up1);
2140 gmx_fio_do_real(fio, iparams->disres.up2);
2141 gmx_fio_do_real(fio, iparams->disres.kfac);
2142 break;
2143 case F_ORIRES:
2144 gmx_fio_do_int(fio, iparams->orires.ex);
2145 gmx_fio_do_int(fio, iparams->orires.label);
2146 gmx_fio_do_int(fio, iparams->orires.power);
2147 gmx_fio_do_real(fio, iparams->orires.c);
2148 gmx_fio_do_real(fio, iparams->orires.obs);
2149 gmx_fio_do_real(fio, iparams->orires.kfac);
2150 break;
2151 case F_DIHRES:
2152 if (file_version < 82)
2153 {
2154 gmx_fio_do_int(fio, idum);
2155 gmx_fio_do_int(fio, idum);
2156 }
2157 gmx_fio_do_real(fio, iparams->dihres.phiA);
2158 gmx_fio_do_real(fio, iparams->dihres.dphiA);
2159 gmx_fio_do_real(fio, iparams->dihres.kfacA);
2160 if (file_version >= 82)
2161 {
2162 gmx_fio_do_real(fio, iparams->dihres.phiB);
2163 gmx_fio_do_real(fio, iparams->dihres.dphiB);
2164 gmx_fio_do_real(fio, iparams->dihres.kfacB);
2165 }
2166 else
2167 {
2168 iparams->dihres.phiB = iparams->dihres.phiA;
2169 iparams->dihres.dphiB = iparams->dihres.dphiA;
2170 iparams->dihres.kfacB = iparams->dihres.kfacA;
2171 }
2172 break;
2173 case F_POSRES:
2174 gmx_fio_do_rvec(fio, iparams->posres.pos0A);
2175 gmx_fio_do_rvec(fio, iparams->posres.fcA);
2176 if (bRead && file_version < 27)
2177 {
2178 copy_rvec(iparams->posres.pos0A, iparams->posres.pos0B);
2179 copy_rvec(iparams->posres.fcA, iparams->posres.fcB);
2180 }
2181 else
2182 {
2183 gmx_fio_do_rvec(fio, iparams->posres.pos0B);
2184 gmx_fio_do_rvec(fio, iparams->posres.fcB);
2185 }
2186 break;
2187 case F_FBPOSRES:
2188 gmx_fio_do_int(fio, iparams->fbposres.geom);
2189 gmx_fio_do_rvec(fio, iparams->fbposres.pos0);
2190 gmx_fio_do_real(fio, iparams->fbposres.r);
2191 gmx_fio_do_real(fio, iparams->fbposres.k);
2192 break;
2193 case F_CBTDIHS:
2194 gmx_fio_ndo_real(fio, iparams->cbtdihs.cbtcA, NR_CBTDIHS);
2195 break;
2196 case F_RBDIHS:
2197 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
2198 if (file_version >= 25)
2199 {
2200 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
2201 }
2202 break;
2203 case F_FOURDIHS:
2204 /* Fourier dihedrals are internally represented
2205 * as Ryckaert-Bellemans since those are faster to compute.
2206 */
2207 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
2208 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
2209 break;
2210 case F_CONSTR:
2211 case F_CONSTRNC:
2212 gmx_fio_do_real(fio, iparams->constr.dA);
2213 gmx_fio_do_real(fio, iparams->constr.dB);
2214 break;
2215 case F_SETTLE:
2216 gmx_fio_do_real(fio, iparams->settle.doh);
2217 gmx_fio_do_real(fio, iparams->settle.dhh);
2218 break;
2219 case F_VSITE2:
2220 gmx_fio_do_real(fio, iparams->vsite.a);
2221 break;
2222 case F_VSITE3:
2223 case F_VSITE3FD:
2224 case F_VSITE3FAD:
2225 gmx_fio_do_real(fio, iparams->vsite.a);
2226 gmx_fio_do_real(fio, iparams->vsite.b);
2227 break;
2228 case F_VSITE3OUT:
2229 case F_VSITE4FD:
2230 case F_VSITE4FDN:
2231 gmx_fio_do_real(fio, iparams->vsite.a);
2232 gmx_fio_do_real(fio, iparams->vsite.b);
2233 gmx_fio_do_real(fio, iparams->vsite.c);
2234 break;
2235 case F_VSITEN:
2236 gmx_fio_do_int(fio, iparams->vsiten.n);
2237 gmx_fio_do_real(fio, iparams->vsiten.a);
2238 break;
2239 case F_GB12:
2240 case F_GB13:
2241 case F_GB14:
2242 /* We got rid of some parameters in version 68 */
2243 if (bRead && file_version < 68)
2244 {
2245 gmx_fio_do_real(fio, rdum);
2246 gmx_fio_do_real(fio, rdum);
2247 gmx_fio_do_real(fio, rdum);
2248 gmx_fio_do_real(fio, rdum);
2249 }
2250 gmx_fio_do_real(fio, iparams->gb.sar);
2251 gmx_fio_do_real(fio, iparams->gb.st);
2252 gmx_fio_do_real(fio, iparams->gb.pi);
2253 gmx_fio_do_real(fio, iparams->gb.gbr);
2254 gmx_fio_do_real(fio, iparams->gb.bmlt);
2255 break;
2256 case F_CMAP:
2257 gmx_fio_do_int(fio, iparams->cmap.cmapA);
2258 gmx_fio_do_int(fio, iparams->cmap.cmapB);
2259 break;
2260 default:
2261 gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
2262 ftype, interaction_function[ftype].name, __FILE__, __LINE__);
2263 }
2264 }
2265
2266 static void do_ilist(t_fileio *fio, t_ilist *ilist, gmx_bool bRead, int file_version)
2267 {
2268 int i, idum;
2269
2270 if (file_version < 44)
2271 {
2272 for (i = 0; i < MAXNODES; i++)
2273 {
2274 gmx_fio_do_int(fio, idum);
2275 }
2276 }
2277 gmx_fio_do_int(fio, ilist->nr);
2278 if (bRead)
2279 {
2280 snew(ilist->iatoms, ilist->nr);
2281 }
2282 gmx_fio_ndo_int(fio, ilist->iatoms, ilist->nr);
2283 }
2284
2285 static void do_ffparams(t_fileio *fio, gmx_ffparams_t *ffparams,
2286 gmx_bool bRead, int file_version)
2287 {
2288 int idum, i;
2289 unsigned int k;
2290
2291 gmx_fio_do_int(fio, ffparams->atnr);
2292 if (file_version < 57)
2293 {
2294 gmx_fio_do_int(fio, idum);
2295 }
2296 gmx_fio_do_int(fio, ffparams->ntypes);
2297 if (bRead)
2298 {
2299 snew(ffparams->functype, ffparams->ntypes);
2300 snew(ffparams->iparams, ffparams->ntypes);
2301 }
2302 /* Read/write all the function types */
2303 gmx_fio_ndo_int(fio, ffparams->functype, ffparams->ntypes);
2304
2305 if (file_version >= 66)
2306 {
2307 gmx_fio_do_double(fio, ffparams->reppow);
2308 }
2309 else
2310 {
2311 ffparams->reppow = 12.0;
2312 }
2313
2314 if (file_version >= 57)
2315 {
2316 gmx_fio_do_real(fio, ffparams->fudgeQQ);
2317 }
2318
2319 /* Check whether all these function types are supported by the code.
2320 * In practice the code is backwards compatible, which means that the
2321 * numbering may have to be altered from old numbering to new numbering
2322 */
2323 for (i = 0; (i < ffparams->ntypes); i++)
2324 {
2325 if (bRead)
2326 {
2327 /* Loop over file versions */
2328 for (k = 0; (k < NFTUPD); k++)
2329 {
2330 /* Compare the read file_version to the update table */
2331 if ((file_version < ftupd[k].fvnr) &&
2332 (ffparams->functype[i] >= ftupd[k].ftype))
2333 {
2334 ffparams->functype[i] += 1;
2335 }
2336 }
2337 }
2338
2339 do_iparams(fio, ffparams->functype[i], &ffparams->iparams[i], bRead,
2340 file_version);
2341 }
2342 }
2343
2344 static void add_settle_atoms(t_ilist *ilist)
2345 {
2346 int i;
2347
2348 /* Settle used to only store the first atom: add the other two */
2349 srenew(ilist->iatoms, 2*ilist->nr);
2350 for (i = ilist->nr/2-1; i >= 0; i--)
2351 {
2352 ilist->iatoms[4*i+0] = ilist->iatoms[2*i+0];
2353 ilist->iatoms[4*i+1] = ilist->iatoms[2*i+1];
2354 ilist->iatoms[4*i+2] = ilist->iatoms[2*i+1] + 1;
2355 ilist->iatoms[4*i+3] = ilist->iatoms[2*i+1] + 2;
2356 }
2357 ilist->nr = 2*ilist->nr;
2358 }
2359
2360 static void do_ilists(t_fileio *fio, t_ilist *ilist, gmx_bool bRead,
2361 int file_version)
2362 {
2363 int j;
2364 gmx_bool bClear;
2365 unsigned int k;
2366
2367 for (j = 0; (j < F_NRE); j++)
2368 {
2369 bClear = FALSE;
2370 if (bRead)
2371 {
2372 for (k = 0; k < NFTUPD; k++)
2373 {
2374 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
2375 {
2376 bClear = TRUE;
2377 }
2378 }
2379 }
2380 if (bClear)
2381 {
2382 ilist[j].nr = 0;
2383 ilist[j].iatoms = NULL;
2384 }
2385 else
2386 {
2387 do_ilist(fio, &ilist[j], bRead, file_version);
2388 if (file_version < 78 && j == F_SETTLE && ilist[j].nr > 0)
2389 {
2390 add_settle_atoms(&ilist[j]);
2391 }
2392 }
2393 }
2394 }
2395
2396 static void do_idef(t_fileio *fio, gmx_ffparams_t *ffparams, gmx_moltype_t *molt,
2397 gmx_bool bRead, int file_version)
2398 {
2399 do_ffparams(fio, ffparams, bRead, file_version);
2400
2401 if (file_version >= 54)
2402 {
2403 gmx_fio_do_real(fio, ffparams->fudgeQQ);
2404 }
2405
2406 do_ilists(fio, molt->ilist, bRead, file_version);
2407 }
2408
2409 static void do_block(t_fileio *fio, t_block *block, gmx_bool bRead, int file_version)
2410 {
2411 int i, idum, dum_nra, *dum_a;
2412
2413 if (file_version < 44)
2414 {
2415 for (i = 0; i < MAXNODES; i++)
2416 {
2417 gmx_fio_do_int(fio, idum);
2418 }
2419 }
2420 gmx_fio_do_int(fio, block->nr);
2421 if (file_version < 51)
2422 {
2423 gmx_fio_do_int(fio, dum_nra);
2424 }
2425 if (bRead)
2426 {
2427 if ((block->nalloc_index > 0) && (NULL != block->index))
2428 {
2429 sfree(block->index);
2430 }
2431 block->nalloc_index = block->nr+1;
2432 snew(block->index, block->nalloc_index);
2433 }
2434 gmx_fio_ndo_int(fio, block->index, block->nr+1);
2435
2436 if (file_version < 51 && dum_nra > 0)
2437 {
2438 snew(dum_a, dum_nra);
2439 gmx_fio_ndo_int(fio, dum_a, dum_nra);
2440 sfree(dum_a);
2441 }
2442 }
2443
2444 static void do_blocka(t_fileio *fio, t_blocka *block, gmx_bool bRead,
2445 int file_version)
2446 {
2447 int i, idum;
2448
2449 if (file_version < 44)
2450 {
2451 for (i = 0; i < MAXNODES; i++)
2452 {
2453 gmx_fio_do_int(fio, idum);
2454 }
2455 }
2456 gmx_fio_do_int(fio, block->nr);
2457 gmx_fio_do_int(fio, block->nra);
2458 if (bRead)
2459 {
2460 block->nalloc_index = block->nr+1;
2461 snew(block->index, block->nalloc_index);
2462 block->nalloc_a = block->nra;
2463 snew(block->a, block->nalloc_a);
2464 }
2465 gmx_fio_ndo_int(fio, block->index, block->nr+1);
2466 gmx_fio_ndo_int(fio, block->a, block->nra);
2467 }
2468
2469 /* This is a primitive routine to make it possible to translate atomic numbers
2470 * to element names when reading TPR files, without making the Gromacs library
2471 * directory a dependency on mdrun (which is the case if we need elements.dat).
2472 */
2473 static const char *
2474 atomicnumber_to_element(int atomicnumber)
2475 {
2476 const char * p;
2477
2478 /* This does not have to be complete, so we only include elements likely
2479 * to occur in PDB files.
2480 */
2481 switch (atomicnumber)
2482 {
2483 case 1: p = "H"; break;
2484 case 5: p = "B"; break;
2485 case 6: p = "C"; break;
2486 case 7: p = "N"; break;
2487 case 8: p = "O"; break;
2488 case 9: p = "F"; break;
2489 case 11: p = "Na"; break;
2490 case 12: p = "Mg"; break;
2491 case 15: p = "P"; break;
2492 case 16: p = "S"; break;
2493 case 17: p = "Cl"; break;
2494 case 18: p = "Ar"; break;
2495 case 19: p = "K"; break;
2496 case 20: p = "Ca"; break;
2497 case 25: p = "Mn"; break;
2498 case 26: p = "Fe"; break;
2499 case 28: p = "Ni"; break;
2500 case 29: p = "Cu"; break;
2501 case 30: p = "Zn"; break;
2502 case 35: p = "Br"; break;
2503 case 47: p = "Ag"; break;
2504 default: p = ""; break;
2505 }
2506 return p;
2507 }
2508
2509
2510 static void do_atom(t_fileio *fio, t_atom *atom, int ngrp, gmx_bool bRead,
2511 int file_version, gmx_groups_t *groups, int atnr)
2512 {
2513 int i, myngrp;
2514
2515 gmx_fio_do_real(fio, atom->m);
2516 gmx_fio_do_real(fio, atom->q);
2517 gmx_fio_do_real(fio, atom->mB);
2518 gmx_fio_do_real(fio, atom->qB);
2519 gmx_fio_do_ushort(fio, atom->type);
2520 gmx_fio_do_ushort(fio, atom->typeB);
2521 gmx_fio_do_int(fio, atom->ptype);
2522 gmx_fio_do_int(fio, atom->resind);
2523 if (file_version >= 52)
2524 {
2525 gmx_fio_do_int(fio, atom->atomnumber);
2526 if (bRead)
2527 {
2528 /* Set element string from atomic number if present.
2529 * This routine returns an empty string if the name is not found.
2530 */
2531 std::strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
2532 /* avoid warnings about potentially unterminated string */
2533 atom->elem[3] = '\0';
2534 }
2535 }
2536 else if (bRead)
2537 {
2538 atom->atomnumber = 0;
2539 }
2540 if (file_version < 23)
2541 {
2542 myngrp = 8;
2543 }
2544 else if (file_version < 39)
2545 {
2546 myngrp = 9;
2547 }
2548 else
2549 {
2550 myngrp = ngrp;
2551 }
2552
2553 if (file_version < 57)
2554 {
2555 unsigned char uchar[egcNR];
2556 gmx_fio_ndo_uchar(fio, uchar, myngrp);
2557 for (i = myngrp; (i < ngrp); i++)
2558 {
2559 uchar[i] = 0;
2560 }
2561 /* Copy the old data format to the groups struct */
2562 for (i = 0; i < ngrp; i++)
2563 {
2564 groups->grpnr[i][atnr] = uchar[i];
2565 }
2566 }
2567 }
2568
2569 static void do_grps(t_fileio *fio, int ngrp, t_grps grps[], gmx_bool bRead,
2570 int file_version)
2571 {
2572 int j, myngrp;
2573
2574 if (file_version < 23)
2575 {
2576 myngrp = 8;
2577 }
2578 else if (file_version < 39)
2579 {
2580 myngrp = 9;
2581 }
2582 else
2583 {
2584 myngrp = ngrp;
2585 }
2586
2587 for (j = 0; (j < ngrp); j++)
2588 {
2589 if (j < myngrp)
2590 {
2591 gmx_fio_do_int(fio, grps[j].nr);
2592 if (bRead)
2593 {
2594 snew(grps[j].nm_ind, grps[j].nr);
2595 }
2596 gmx_fio_ndo_int(fio, grps[j].nm_ind, grps[j].nr);
2597 }
2598 else
2599 {
2600 grps[j].nr = 1;
2601 snew(grps[j].nm_ind, grps[j].nr);
2602 }
2603 }
2604 }
2605
2606 static void do_symstr(t_fileio *fio, char ***nm, gmx_bool bRead, t_symtab *symtab)
2607 {
2608 int ls;
2609
2610 if (bRead)
2611 {
2612 gmx_fio_do_int(fio, ls);
2613 *nm = get_symtab_handle(symtab, ls);
2614 }
2615 else
2616 {
2617 ls = lookup_symtab(symtab, *nm);
2618 gmx_fio_do_int(fio, ls);
2619 }
2620 }
2621
2622 static void do_strstr(t_fileio *fio, int nstr, char ***nm, gmx_bool bRead,
2623 t_symtab *symtab)
2624 {
2625 int j;
2626
2627 for (j = 0; (j < nstr); j++)
2628 {
2629 do_symstr(fio, &(nm[j]), bRead, symtab);
2630 }
2631 }
2632
2633 static void do_resinfo(t_fileio *fio, int n, t_resinfo *ri, gmx_bool bRead,
2634 t_symtab *symtab, int file_version)
2635 {
2636 int j;
2637
2638 for (j = 0; (j < n); j++)
2639 {
2640 do_symstr(fio, &(ri[j].name), bRead, symtab);
2641 if (file_version >= 63)
2642 {
2643 gmx_fio_do_int(fio, ri[j].nr);
2644 gmx_fio_do_uchar(fio, ri[j].ic);
2645 }
2646 else
2647 {
2648 ri[j].nr = j + 1;
2649 ri[j].ic = ' ';
2650 }
2651 }
2652 }
2653
2654 static void do_atoms(t_fileio *fio, t_atoms *atoms, gmx_bool bRead, t_symtab *symtab,
2655 int file_version,
2656 gmx_groups_t *groups)
2657 {
2658 int i;
2659
2660 gmx_fio_do_int(fio, atoms->nr);
2661 gmx_fio_do_int(fio, atoms->nres);
2662 if (file_version < 57)
2663 {
2664 gmx_fio_do_int(fio, groups->ngrpname);
2665 for (i = 0; i < egcNR; i++)
2666 {
2667 groups->ngrpnr[i] = atoms->nr;
2668 snew(groups->grpnr[i], groups->ngrpnr[i]);
2669 }
2670 }
2671 if (bRead)
2672 {
2673 snew(atoms->atom, atoms->nr);
2674 snew(atoms->atomname, atoms->nr);
2675 snew(atoms->atomtype, atoms->nr);
2676 snew(atoms->atomtypeB, atoms->nr);
2677 snew(atoms->resinfo, atoms->nres);
2678 if (file_version < 57)
2679 {
2680 snew(groups->grpname, groups->ngrpname);
2681 }
2682 atoms->pdbinfo = NULL;
2683 }
2684 for (i = 0; (i < atoms->nr); i++)
2685 {
2686 do_atom(fio, &atoms->atom[i], egcNR, bRead, file_version, groups, i);
2687 }
2688 do_strstr(fio, atoms->nr, atoms->atomname, bRead, symtab);
2689 if (bRead && (file_version <= 20))
2690 {
2691 for (i = 0; i < atoms->nr; i++)
2692 {
2693 atoms->atomtype[i] = put_symtab(symtab, "?");
2694 atoms->atomtypeB[i] = put_symtab(symtab, "?");
2695 }
2696 }
2697 else
2698 {
2699 do_strstr(fio, atoms->nr, atoms->atomtype, bRead, symtab);
2700 do_strstr(fio, atoms->nr, atoms->atomtypeB, bRead, symtab);
2701 }
2702 do_resinfo(fio, atoms->nres, atoms->resinfo, bRead, symtab, file_version);
2703
2704 if (file_version < 57)
2705 {
2706 do_strstr(fio, groups->ngrpname, groups->grpname, bRead, symtab);
2707
2708 do_grps(fio, egcNR, groups->grps, bRead, file_version);
2709 }
2710 }
2711
2712 static void do_groups(t_fileio *fio, gmx_groups_t *groups,
2713 gmx_bool bRead, t_symtab *symtab,
2714 int file_version)
2715 {
2716 int g;
2717
2718 do_grps(fio, egcNR, groups->grps, bRead, file_version);
2719 gmx_fio_do_int(fio, groups->ngrpname);
2720 if (bRead)
2721 {
2722 snew(groups->grpname, groups->ngrpname);
2723 }
2724 do_strstr(fio, groups->ngrpname, groups->grpname, bRead, symtab);
2725 for (g = 0; g < egcNR; g++)
2726 {
2727 gmx_fio_do_int(fio, groups->ngrpnr[g]);
2728 if (groups->ngrpnr[g] == 0)
2729 {
2730 if (bRead)
2731 {
2732 groups->grpnr[g] = NULL;
2733 }
2734 }
2735 else
2736 {
2737 if (bRead)
2738 {
2739 snew(groups->grpnr[g], groups->ngrpnr[g]);
2740 }
2741 gmx_fio_ndo_uchar(fio, groups->grpnr[g], groups->ngrpnr[g]);
2742 }
2743 }
2744 }
2745
2746 static void do_atomtypes(t_fileio *fio, t_atomtypes *atomtypes, gmx_bool bRead,
2747 int file_version)
2748 {
2749 int j;
2750
2751 if (file_version > 25)
2752 {
2753 gmx_fio_do_int(fio, atomtypes->nr);
2754 j = atomtypes->nr;
2755 if (bRead)
2756 {
2757 snew(atomtypes->radius, j);
2758 snew(atomtypes->vol, j);
2759 snew(atomtypes->surftens, j);
2760 snew(atomtypes->atomnumber, j);
2761 snew(atomtypes->gb_radius, j);
2762 snew(atomtypes->S_hct, j);
2763 }
2764 gmx_fio_ndo_real(fio, atomtypes->radius, j);
2765 gmx_fio_ndo_real(fio, atomtypes->vol, j);
2766 gmx_fio_ndo_real(fio, atomtypes->surftens, j);
2767 if (file_version >= 40)
2768 {
2769 gmx_fio_ndo_int(fio, atomtypes->atomnumber, j);
2770 }
2771 if (file_version >= 60)
2772 {
2773 gmx_fio_ndo_real(fio, atomtypes->gb_radius, j);
2774 gmx_fio_ndo_real(fio, atomtypes->S_hct, j);
2775 }
2776 }
2777 else
2778 {
2779 /* File versions prior to 26 cannot do GBSA,
2780 * so they dont use this structure
2781 */
2782 atomtypes->nr = 0;
2783 atomtypes->radius = NULL;
2784 atomtypes->vol = NULL;
2785 atomtypes->surftens = NULL;
2786 atomtypes->atomnumber = NULL;
2787 atomtypes->gb_radius = NULL;
2788 atomtypes->S_hct = NULL;
2789 }
2790 }
2791
2792 static void do_symtab(t_fileio *fio, t_symtab *symtab, gmx_bool bRead)
2793 {
2794 int i, nr;
2795 t_symbuf *symbuf;
2796 char buf[STRLEN];
2797
2798 gmx_fio_do_int(fio, symtab->nr);
2799 nr = symtab->nr;
2800 if (bRead)
2801 {
2802 snew(symtab->symbuf, 1);
2803 symbuf = symtab->symbuf;
2804 symbuf->bufsize = nr;
2805 snew(symbuf->buf, nr);
2806 for (i = 0; (i < nr); i++)
2807 {
2808 gmx_fio_do_string(fio, buf);
2809 symbuf->buf[i] = gmx_strdup(buf);
2810 }
2811 }
2812 else
2813 {
2814 symbuf = symtab->symbuf;
2815 while (symbuf != NULL)
2816 {
2817 for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
2818 {
2819 gmx_fio_do_string(fio, symbuf->buf[i]);
2820 }
2821 nr -= i;
2822 symbuf = symbuf->next;
2823 }
2824 if (nr != 0)
2825 {
2826 gmx_fatal(FARGS, "nr of symtab strings left: %d", nr);
2827 }
2828 }
2829 }
2830
2831 static void do_cmap(t_fileio *fio, gmx_cmap_t *cmap_grid, gmx_bool bRead)
2832 {
2833 int i, j, ngrid, gs, nelem;
2834
2835 gmx_fio_do_int(fio, cmap_grid->ngrid);
2836 gmx_fio_do_int(fio, cmap_grid->grid_spacing);
2837
2838 ngrid = cmap_grid->ngrid;
2839 gs = cmap_grid->grid_spacing;
2840 nelem = gs * gs;
2841
2842 if (bRead)
2843 {
2844 snew(cmap_grid->cmapdata, ngrid);
2845
2846 for (i = 0; i < cmap_grid->ngrid; i++)
2847 {
2848 snew(cmap_grid->cmapdata[i].cmap, 4*nelem);
2849 }
2850 }
2851
2852 for (i = 0; i < cmap_grid->ngrid; i++)
2853 {
2854 for (j = 0; j < nelem; j++)
2855 {
2856 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4]);
2857 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+1]);
2858 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+2]);
2859 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+3]);
2860 }
2861 }
2862 }
2863
2864
2865 static void do_moltype(t_fileio *fio, gmx_moltype_t *molt, gmx_bool bRead,
2866 t_symtab *symtab, int file_version,
2867 gmx_groups_t *groups)
2868 {
2869 if (file_version >= 57)
2870 {
2871 do_symstr(fio, &(molt->name), bRead, symtab);
2872 }
2873
2874 do_atoms(fio, &molt->atoms, bRead, symtab, file_version, groups);
2875
2876 if (file_version >= 57)
2877 {
2878 do_ilists(fio, molt->ilist, bRead, file_version);
2879
2880 do_block(fio, &molt->cgs, bRead, file_version);
2881 }
2882
2883 /* This used to be in the atoms struct */
2884 do_blocka(fio, &molt->excls, bRead, file_version);
2885 }
2886
2887 static void do_molblock(t_fileio *fio, gmx_molblock_t *molb, gmx_bool bRead)
2888 {
2889 gmx_fio_do_int(fio, molb->type);
2890 gmx_fio_do_int(fio, molb->nmol);
2891 gmx_fio_do_int(fio, molb->natoms_mol);
2892 /* Position restraint coordinates */
2893 gmx_fio_do_int(fio, molb->nposres_xA);
2894 if (molb->nposres_xA > 0)
2895 {
2896 if (bRead)
2897 {
2898 snew(molb->posres_xA, molb->nposres_xA);
2899 }
2900 gmx_fio_ndo_rvec(fio, molb->posres_xA, molb->nposres_xA);
2901 }
2902 gmx_fio_do_int(fio, molb->nposres_xB);
2903 if (molb->nposres_xB > 0)
2904 {
2905 if (bRead)
2906 {
2907 snew(molb->posres_xB, molb->nposres_xB);
2908 }
2909 gmx_fio_ndo_rvec(fio, molb->posres_xB, molb->nposres_xB);
2910 }
2911
2912 }
2913
2914 static t_block mtop_mols(gmx_mtop_t *mtop)
2915 {
2916 int mb, m, a, mol;
2917 t_block mols;
2918
2919 mols.nr = 0;
2920 for (mb = 0; mb < mtop->nmolblock; mb++)
2921 {
2922 mols.nr += mtop->molblock[mb].nmol;
2923 }
2924 mols.nalloc_index = mols.nr + 1;
2925 snew(mols.index, mols.nalloc_index);
2926
2927 a = 0;
2928 m = 0;
2929 mols.index[m] = a;
2930 for (mb = 0; mb < mtop->nmolblock; mb++)
2931 {
2932 for (mol = 0; mol < mtop->molblock[mb].nmol; mol++)
2933 {
2934 a += mtop->molblock[mb].natoms_mol;
2935 m++;
2936 mols.index[m] = a;
2937 }
2938 }
2939
2940 return mols;
2941 }
2942
2943 static void add_posres_molblock(gmx_mtop_t *mtop)
2944 {
2945 t_ilist *il, *ilfb;
2946 int am, i, mol, a;
2947 gmx_bool bFE;
2948 gmx_molblock_t *molb;
2949 t_iparams *ip;
2950
2951 /* posres reference positions are stored in ip->posres (if present) and
2952 in ip->fbposres (if present). If normal and flat-bottomed posres are present,
2953 posres.pos0A are identical to fbposres.pos0. */
2954 il = &mtop->moltype[0].ilist[F_POSRES];
2955 ilfb = &mtop->moltype[0].ilist[F_FBPOSRES];
2956 if (il->nr == 0 && ilfb->nr == 0)
2957 {
2958 return;
2959 }
2960 am = 0;
2961 bFE = FALSE;
2962 for (i = 0; i < il->nr; i += 2)
2963 {
2964 ip = &mtop->ffparams.iparams[il->iatoms[i]];
2965 am = std::max(am, il->iatoms[i+1]);
2966 if (ip->posres.pos0B[XX] != ip->posres.pos0A[XX] ||
2967 ip->posres.pos0B[YY] != ip->posres.pos0A[YY] ||
2968 ip->posres.pos0B[ZZ] != ip->posres.pos0A[ZZ])
2969 {
2970 bFE = TRUE;
2971 }
2972 }
2973 /* This loop is required if we have only flat-bottomed posres:
2974 - set am
2975 - bFE == FALSE (no B-state for flat-bottomed posres) */
2976 if (il->nr == 0)
2977 {
2978 for (i = 0; i < ilfb->nr; i += 2)
2979 {
2980 am = std::max(am, ilfb->iatoms[i+1]);
2981 }
2982 }
2983 /* Make the posres coordinate block end at a molecule end */
2984 mol = 0;
2985 while (am >= mtop->mols.index[mol+1])
2986 {
2987 mol++;
2988 }
2989 molb = &mtop->molblock[0];
2990 molb->nposres_xA = mtop->mols.index[mol+1];
2991 snew(molb->posres_xA, molb->nposres_xA);
2992 if (bFE)
2993 {
2994 molb->nposres_xB = molb->nposres_xA;
2995 snew(molb->posres_xB, molb->nposres_xB);
2996 }
2997 else
2998 {
2999 molb->nposres_xB = 0;
3000 }
3001 for (i = 0; i < il->nr; i += 2)
3002 {
3003 ip = &mtop->ffparams.iparams[il->iatoms[i]];
3004 a = il->iatoms[i+1];
3005 molb->posres_xA[a][XX] = ip->posres.pos0A[XX];
3006 molb->posres_xA[a][YY] = ip->posres.pos0A[YY];
3007 molb->posres_xA[a][ZZ] = ip->posres.pos0A[ZZ];
3008 if (bFE)
3009 {
3010 molb->posres_xB[a][XX] = ip->posres.pos0B[XX];
3011 molb->posres_xB[a][YY] = ip->posres.pos0B[YY];
3012 molb->posres_xB[a][ZZ] = ip->posres.pos0B[ZZ];
3013 }
3014 }
3015 if (il->nr == 0)
3016 {
3017 /* If only flat-bottomed posres are present, take reference pos from them.
3018 Here: bFE == FALSE */
3019 for (i = 0; i < ilfb->nr; i += 2)
3020 {
3021 ip = &mtop->ffparams.iparams[ilfb->iatoms[i]];
3022 a = ilfb->iatoms[i+1];
3023 molb->posres_xA[a][XX] = ip->fbposres.pos0[XX];
3024 molb->posres_xA[a][YY] = ip->fbposres.pos0[YY];
3025 molb->posres_xA[a][ZZ] = ip->fbposres.pos0[ZZ];
3026 }
3027 }
3028 }
3029
3030 static void set_disres_npair(gmx_mtop_t *mtop)
3031 {
3032 t_iparams *ip;
3033 gmx_mtop_ilistloop_t iloop;
3034 t_ilist *ilist, *il;
3035 int nmol, i, npair;
3036 t_iatom *a;
3037
3038 ip = mtop->ffparams.iparams;
3039
3040 iloop = gmx_mtop_ilistloop_init(mtop);
3041 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3042 {
3043 il = &ilist[F_DISRES];
3044
3045 if (il->nr > 0)
3046 {
3047 a = il->iatoms;
3048 npair = 0;
3049 for (i = 0; i < il->nr; i += 3)
3050 {
3051 npair++;
3052 if (i+3 == il->nr || ip[a[i]].disres.label != ip[a[i+3]].disres.label)
3053 {
3054 ip[a[i]].disres.npair = npair;
3055 npair = 0;
3056 }
3057 }
3058 }
3059 }
3060 }
3061
3062 static void do_mtop(t_fileio *fio, gmx_mtop_t *mtop, gmx_bool bRead,
3063 int file_version)
3064 {
3065 int mt, mb;
3066 t_blocka dumb;
3067
3068 if (bRead)
3069 {
3070 init_mtop(mtop);
3071 }
3072 do_symtab(fio, &(mtop->symtab), bRead);
3073
3074 do_symstr(fio, &(mtop->name), bRead, &(mtop->symtab));
3075
3076 if (file_version >= 57)
3077 {
3078 do_ffparams(fio, &mtop->ffparams, bRead, file_version);
3079
3080 gmx_fio_do_int(fio, mtop->nmoltype);
3081 }
3082 else
3083 {
3084 mtop->nmoltype = 1;
3085 }
3086 if (bRead)
3087 {
3088 snew(mtop->moltype, mtop->nmoltype);
3089 if (file_version < 57)
3090 {
3091 mtop->moltype[0].name = mtop->name;
3092 }
3093 }
3094 for (mt = 0; mt < mtop->nmoltype; mt++)
3095 {
3096 do_moltype(fio, &mtop->moltype[mt], bRead, &mtop->symtab, file_version,
3097 &mtop->groups);
3098 }
3099
3100 if (file_version >= 57)
3101 {
3102 gmx_fio_do_int(fio, mtop->nmolblock);
3103 }
3104 else
3105 {
3106 mtop->nmolblock = 1;
3107 }
3108 if (bRead)
3109 {
3110 snew(mtop->molblock, mtop->nmolblock);
3111 }
3112 if (file_version >= 57)
3113 {
3114 for (mb = 0; mb < mtop->nmolblock; mb++)
3115 {
3116 do_molblock(fio, &mtop->molblock[mb], bRead);
3117 }
3118 gmx_fio_do_int(fio, mtop->natoms);
3119 }
3120 else
3121 {
3122 mtop->molblock[0].type = 0;
3123 mtop->molblock[0].nmol = 1;
3124 mtop->molblock[0].natoms_mol = mtop->moltype[0].atoms.nr;
3125 mtop->molblock[0].nposres_xA = 0;
3126 mtop->molblock[0].nposres_xB = 0;
3127 }
3128
3129 if (file_version >= tpxv_IntermolecularBondeds)
3130 {
3131 gmx_fio_do_gmx_bool(fio, mtop->bIntermolecularInteractions);
3132 if (mtop->bIntermolecularInteractions)
3133 {
3134 if (bRead)
3135 {
3136 snew(mtop->intermolecular_ilist, F_NRE);
3137 }
3138 do_ilists(fio, mtop->intermolecular_ilist, bRead, file_version);
3139 }
3140 }
3141 else
3142 {
3143 mtop->bIntermolecularInteractions = FALSE;
3144 }
3145
3146 do_atomtypes (fio, &(mtop->atomtypes), bRead, file_version);
3147
3148 if (file_version < 57)
3149 {
3150 do_idef (fio, &mtop->ffparams, &mtop->moltype[0], bRead, file_version);
3151 mtop->natoms = mtop->moltype[0].atoms.nr;
3152 }
3153
3154 if (file_version >= 65)
3155 {
3156 do_cmap(fio, &mtop->ffparams.cmap_grid, bRead);
3157 }
3158 else
3159 {
3160 mtop->ffparams.cmap_grid.ngrid = 0;
3161 mtop->ffparams.cmap_grid.grid_spacing = 0;
3162 mtop->ffparams.cmap_grid.cmapdata = NULL;
3163 }
3164
3165 if (file_version >= 57)
3166 {
3167 do_groups(fio, &mtop->groups, bRead, &(mtop->symtab), file_version);
3168 }
3169
3170 if (file_version < 57)
3171 {
3172 do_block(fio, &mtop->moltype[0].cgs, bRead, file_version);
3173 do_block(fio, &mtop->mols, bRead, file_version);
3174 /* Add the posres coordinates to the molblock */
3175 add_posres_molblock(mtop);
3176 }
3177 if (bRead)
3178 {
3179 if (file_version >= 57)
3180 {
3181 done_block(&mtop->mols);
3182 mtop->mols = mtop_mols(mtop);
3183 }
3184 }
3185
3186 if (file_version < 51)
3187 {
3188 /* Here used to be the shake blocks */
3189 do_blocka(fio, &dumb, bRead, file_version);
3190 if (dumb.nr > 0)
3191 {
3192 sfree(dumb.index);
3193 }
3194 if (dumb.nra > 0)
3195 {
3196 sfree(dumb.a);
3197 }
3198 }
3199
3200 if (bRead)
3201 {
3202 close_symtab(&(mtop->symtab));
3203 }
3204 }
3205
3206 /* If TopOnlyOK is TRUE then we can read even future versions
3207 * of tpx files, provided the file_generation hasn't changed.
3208 * If it is FALSE, we need the inputrecord too, and bail out
3209 * if the file is newer than the program.
3210 *
3211 * The version and generation if the topology (see top of this file)
3212 * are returned in the two last arguments.
3213 *
3214 * If possible, we will read the inputrec even when TopOnlyOK is TRUE.
3215 */
3216 static void do_tpxheader(t_fileio *fio, gmx_bool bRead, t_tpxheader *tpx,
3217 gmx_bool TopOnlyOK, int *file_version,
3218 int *file_generation)
3219 {
3220 char buf[STRLEN];
3221 char file_tag[STRLEN];
3222 gmx_bool bDouble;
3223 int precision;
3224 int fver, fgen;
3225 int idum = 0;
3226 real rdum = 0;
3227
3228 /* XDR binary topology file */
3229 precision = sizeof(real);
3230 if (bRead)
3231 {
3232 gmx_fio_do_string(fio, buf);
3233 if (std::strncmp(buf, "VERSION", 7))
3234 {
3235 gmx_fatal(FARGS, "Can not read file %s,\n"
3236 " this file is from a GROMACS version which is older than 2.0\n"
3237 " Make a new one with grompp or use a gro or pdb file, if possible",
3238 gmx_fio_getname(fio));
3239 }
3240 gmx_fio_do_int(fio, precision);
3241 bDouble = (precision == sizeof(double));
3242 if ((precision != sizeof(float)) && !bDouble)
3243 {
3244 gmx_fatal(FARGS, "Unknown precision in file %s: real is %d bytes "
3245 "instead of %d or %d",
3246 gmx_fio_getname(fio), precision, sizeof(float), sizeof(double));
3247 }
3248 gmx_fio_setprecision(fio, bDouble);
3249 fprintf(stderr, "Reading file %s, %s (%s precision)\n",
3250 gmx_fio_getname(fio), buf, bDouble ? "double" : "single");
3251 }
3252 else
3253 {
3254 gmx_fio_write_string(fio, gmx_version());
3255 bDouble = (precision == sizeof(double));
3256 gmx_fio_setprecision(fio, bDouble);
3257 gmx_fio_do_int(fio, precision);
3258 fver = tpx_version;
3259 sprintf(file_tag, "%s", tpx_tag);
3260 fgen = tpx_generation;
3261 }
3262
3263 /* Check versions! */
3264 gmx_fio_do_int(fio, fver);
3265
3266 /* This is for backward compatibility with development versions 77-79
3267 * where the tag was, mistakenly, placed before the generation,
3268 * which would cause a segv instead of a proper error message
3269 * when reading the topology only from tpx with <77 code.
3270 */
3271 if (fver >= 77 && fver <= 79)
3272 {
3273 gmx_fio_do_string(fio, file_tag);
3274 }
3275
3276 if (fver >= 26)
3277 {
3278 gmx_fio_do_int(fio, fgen);
3279 }
3280 else
3281 {
3282 fgen = 0;
3283 }
3284
3285 if (fver >= 81)
3286 {
3287 gmx_fio_do_string(fio, file_tag);
3288 }
3289 if (bRead)
3290 {
3291 if (fver < 77)
3292 {
3293 /* Versions before 77 don't have the tag, set it to release */
3294 sprintf(file_tag, "%s", TPX_TAG_RELEASE);
3295 }
3296
3297 if (std::strcmp(file_tag, tpx_tag) != 0)
3298 {
3299 fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n",
3300 file_tag, tpx_tag);
3301
3302 /* We only support reading tpx files with the same tag as the code
3303 * or tpx files with the release tag and with lower version number.
3304 */
3305 if (std::strcmp(file_tag, TPX_TAG_RELEASE) != 0 && fver < tpx_version)
3306 {
3307 gmx_fatal(FARGS, "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
3308 gmx_fio_getname(fio), fver, file_tag,
3309 tpx_version, tpx_tag);
3310 }
3311 }
3312 }
3313
3314 if (file_version != NULL)
3315 {
3316 *file_version = fver;
3317 }
3318 if (file_generation != NULL)
3319 {
3320 *file_generation = fgen;
3321 }
3322
3323
3324 if ((fver <= tpx_incompatible_version) ||
3325 ((fver > tpx_version) && !TopOnlyOK) ||
3326 (fgen > tpx_generation) ||
3327 tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
3328 {
3329 gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program",
3330 gmx_fio_getname(fio), fver, tpx_version);
3331 }
3332
3333 gmx_fio_do_int(fio, tpx->natoms);
3334 if (fver >= 28)
3335 {
3336 gmx_fio_do_int(fio, tpx->ngtc);
3337 }
3338 else
3339 {
3340 tpx->ngtc = 0;
3341 }
3342 if (fver < 62)
3343 {
3344 gmx_fio_do_int(fio, idum);
3345 gmx_fio_do_real(fio, rdum);
3346 }
3347 if (fver >= 79)
3348 {
3349 gmx_fio_do_int(fio, tpx->fep_state);
3350 }
3351 gmx_fio_do_real(fio, tpx->lambda);
3352 gmx_fio_do_int(fio, tpx->bIr);
3353 gmx_fio_do_int(fio, tpx->bTop);
3354 gmx_fio_do_int(fio, tpx->bX);
3355 gmx_fio_do_int(fio, tpx->bV);
3356 gmx_fio_do_int(fio, tpx->bF);
3357 gmx_fio_do_int(fio, tpx->bBox);
3358
3359 if ((fgen > tpx_generation))
3360 {
3361 /* This can only happen if TopOnlyOK=TRUE */
3362 tpx->bIr = FALSE;
3363 }
3364 }
3365
3366 static int do_tpx(t_fileio *fio, gmx_bool bRead,
3367 t_inputrec *ir, t_state *state, gmx_mtop_t *mtop,
3368 gmx_bool bXVallocated)
3369 {
3370 t_tpxheader tpx;
3371 t_inputrec dum_ir;
3372 gmx_mtop_t dum_top;
3373 gmx_bool TopOnlyOK;
3374 int file_version, file_generation;
3375 rvec *xptr, *vptr;
3376 int ePBC;
3377 gmx_bool bPeriodicMols;
3378
3379 if (!bRead)
3380 {
3381 tpx.natoms = state->natoms;
3382 tpx.ngtc = state->ngtc;
3383 tpx.fep_state = state->fep_state;
3384 tpx.lambda = state->lambda[efptFEP];
3385 tpx.bIr = (ir != NULL);
3386 tpx.bTop = (mtop != NULL);
3387 tpx.bX = (state->x != NULL);
3388 tpx.bV = (state->v != NULL);
3389 tpx.bF = FALSE;
3390 tpx.bBox = TRUE;
3391 }
3392
3393 TopOnlyOK = (ir == NULL);
3394
3395 do_tpxheader(fio, bRead, &tpx, TopOnlyOK, &file_version, &file_generation);
3396
3397 if (bRead)
3398 {
3399 state->flags = 0;
3400 if (bXVallocated)
3401 {
3402 xptr = state->x;
3403 vptr = state->v;
3404 init_state(state, 0, tpx.ngtc, 0, 0, 0);
3405 state->natoms = tpx.natoms;
3406 state->nalloc = tpx.natoms;
3407 state->x = xptr;
3408 state->v = vptr;
3409 }
3410 else
3411 {
3412 init_state(state, tpx.natoms, tpx.ngtc, 0, 0, 0);
3413 }
3414 }
3415
3416 #define do_test(fio, b, p) if (bRead && (p != NULL) && !b) gmx_fatal(FARGS, "No %s in %s",#p, gmx_fio_getname(fio))
3417
3418 do_test(fio, tpx.bBox, state->box);
3419 if (tpx.bBox)
3420 {
3421 gmx_fio_ndo_rvec(fio, state->box, DIM);
3422 if (file_version >= 51)
3423 {
3424 gmx_fio_ndo_rvec(fio, state->box_rel, DIM);
3425 }
3426 else
3427 {
3428 /* We initialize box_rel after reading the inputrec */
3429 clear_mat(state->box_rel);
3430 }
3431 if (file_version >= 28)
3432 {
3433 gmx_fio_ndo_rvec(fio, state->boxv, DIM);
3434 if (file_version < 56)
3435 {
3436 matrix mdum;
3437 gmx_fio_ndo_rvec(fio, mdum, DIM);
3438 }
3439 }
3440 }
3441
3442 if (state->ngtc > 0 && file_version >= 28)
3443 {
3444 real *dumv;
3445 snew(dumv, state->ngtc);
3446 if (file_version < 69)
3447 {
3448 gmx_fio_ndo_real(fio, dumv, state->ngtc);
3449 }
3450 /* These used to be the Berendsen tcoupl_lambda's */
3451 gmx_fio_ndo_real(fio, dumv, state->ngtc);
3452 sfree(dumv);
3453 }
3454
3455 /* Prior to tpx version 26, the inputrec was here.
3456 * I moved it to enable partial forward-compatibility
3457 * for analysis/viewer programs.
3458 */
3459 if (file_version < 26)
3460 {
3461 do_test(fio, tpx.bIr, ir);
3462 if (tpx.bIr)
3463 {
3464 if (ir)
3465 {
3466 do_inputrec(fio, ir, bRead, file_version,
3467 mtop ? &mtop->ffparams.fudgeQQ : NULL);
3468 }
3469 else
3470 {
3471 do_inputrec(fio, &dum_ir, bRead, file_version,
3472 mtop ? &mtop->ffparams.fudgeQQ : NULL);
3473 done_inputrec(&dum_ir);
3474 }
3475
3476 }
3477 }
3478
3479 do_test(fio, tpx.bTop, mtop);
3480 if (tpx.bTop)
3481 {
3482 if (mtop)
3483 {
3484 do_mtop(fio, mtop, bRead, file_version);
3485 }
3486 else
3487 {
3488 do_mtop(fio, &dum_top, bRead, file_version);
3489 done_mtop(&dum_top, TRUE);
3490 }
3491 }
3492 do_test(fio, tpx.bX, state->x);
3493 if (tpx.bX)
3494 {
3495 if (bRead)
3496 {
3497 state->flags |= (1<<estX);
3498 }
3499 gmx_fio_ndo_rvec(fio, state->x, state->natoms);
3500 }
3501
3502 do_test(fio, tpx.bV, state->v);
3503 if (tpx.bV)
3504 {
3505 if (bRead)
3506 {
3507 state->flags |= (1<<estV);
3508 }
3509 gmx_fio_ndo_rvec(fio, state->v, state->natoms);
3510 }
3511
3512 // No need to run do_test when the last argument is NULL
3513 if (tpx.bF)
3514 {
3515 rvec *dummyForces;
3516 snew(dummyForces, state->natoms);
3517 gmx_fio_ndo_rvec(fio, dummyForces, state->natoms);
3518 sfree(dummyForces);
3519 }
3520
3521 /* Starting with tpx version 26, we have the inputrec
3522 * at the end of the file, so we can ignore it
3523 * if the file is never than the software (but still the
3524 * same generation - see comments at the top of this file.
3525 *
3526 *
3527 */
3528 ePBC = -1;
3529 bPeriodicMols = FALSE;
3530 if (file_version >= 26)
3531 {
3532 do_test(fio, tpx.bIr, ir);
3533 if (tpx.bIr)
3534 {
3535 if (file_version >= 53)
3536 {
3537 /* Removed the pbc info from do_inputrec, since we always want it */
3538 if (!bRead)
3539 {
3540 ePBC = ir->ePBC;
3541 bPeriodicMols = ir->bPeriodicMols;
3542 }
3543 gmx_fio_do_int(fio, ePBC);
3544 gmx_fio_do_gmx_bool(fio, bPeriodicMols);
3545 }
3546 if (file_generation <= tpx_generation && ir)
3547 {
3548 do_inputrec(fio, ir, bRead, file_version, mtop ? &mtop->ffparams.fudgeQQ : NULL);
3549 if (file_version < 51)
3550 {
3551 set_box_rel(ir, state);
3552 }
3553 if (file_version < 53)
3554 {
3555 ePBC = ir->ePBC;
3556 bPeriodicMols = ir->bPeriodicMols;
3557 }
3558 }
3559 if (bRead && ir && file_version >= 53)
3560 {
3561 /* We need to do this after do_inputrec, since that initializes ir */
3562 ir->ePBC = ePBC;
3563 ir->bPeriodicMols = bPeriodicMols;
3564 }
3565 }
3566 }
3567
3568 if (bRead)
3569 {
3570 if (tpx.bIr && ir)
3571 {
3572 if (state->ngtc == 0)
3573 {
3574 /* Reading old version without tcoupl state data: set it */
3575 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
3576 }
3577 if (tpx.bTop && mtop)
3578 {
3579 if (file_version < 57)
3580 {
3581 if (mtop->moltype[0].ilist[F_DISRES].nr > 0)
3582 {
3583 ir->eDisre = edrSimple;
3584 }
3585 else
3586 {
3587 ir->eDisre = edrNone;
3588 }
3589 }
3590 set_disres_npair(mtop);
3591 }
3592 }
3593
3594 if (tpx.bTop && mtop)
3595 {
3596 gmx_mtop_finalize(mtop);
3597 }
3598 }
3599
3600 return ePBC;
3601 }
3602
3603 static t_fileio *open_tpx(const char *fn, const char *mode)
3604 {
3605 return gmx_fio_open(fn, mode);
3606 }
3607
3608 static void close_tpx(t_fileio *fio)
3609 {
3610 gmx_fio_close(fio);
3611 }
3612
3613 /************************************************************
3614 *
3615 * The following routines are the exported ones
3616 *
3617 ************************************************************/
3618
3619 void read_tpxheader(const char *fn, t_tpxheader *tpx, gmx_bool TopOnlyOK,
3620 int *file_version, int *file_generation)
3621 {
3622 t_fileio *fio;
3623
3624 fio = open_tpx(fn, "r");
3625 do_tpxheader(fio, TRUE, tpx, TopOnlyOK, file_version, file_generation);
3626 close_tpx(fio);
3627 }
3628
3629 void write_tpx_state(const char *fn,
3630 t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
3631 {
3632 t_fileio *fio;
3633
3634 fio = open_tpx(fn, "w");
3635 do_tpx(fio, FALSE, ir, state, mtop, FALSE);
3636 close_tpx(fio);
3637 }
3638
3639 void read_tpx_state(const char *fn,
3640 t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
3641 {
3642 t_fileio *fio;
3643
3644 fio = open_tpx(fn, "r");
3645 do_tpx(fio, TRUE, ir, state, mtop, FALSE);
3646 close_tpx(fio);
3647 }
3648
3649 int read_tpx(const char *fn,
3650 t_inputrec *ir, matrix box, int *natoms,
3651 rvec *x, rvec *v, gmx_mtop_t *mtop)
3652 {
3653 t_fileio *fio;
3654 t_state state;
3655 int ePBC;
3656
3657 state.x = x;
3658 state.v = v;
3659 fio = open_tpx(fn, "r");
3660 ePBC = do_tpx(fio, TRUE, ir, &state, mtop, TRUE);
3661 close_tpx(fio);
3662 *natoms = state.natoms;
3663 if (box)
3664 {
3665 copy_mat(state.box, box);
3666 }
3667 state.x = NULL;
3668 state.v = NULL;
3669 done_state(&state);
3670
3671 return ePBC;
3672 }
3673
3674 int read_tpx_top(const char *fn,
3675 t_inputrec *ir, matrix box, int *natoms,
3676 rvec *x, rvec *v, t_topology *top)
3677 {
3678 gmx_mtop_t mtop;
3679 int ePBC;
3680
3681 ePBC = read_tpx(fn, ir, box, natoms, x, v, &mtop);
3682
3683 *top = gmx_mtop_t_to_t_topology(&mtop);
3684
3685 return ePBC;
3686 }
3687
3688 gmx_bool fn2bTPX(const char *file)
3689 {
3690 return (efTPR == fn2ftp(file));
3691 }
3692
3693 void pr_tpxheader(FILE *fp, int indent, const char *title, const t_tpxheader *sh)
3694 {
3695 if (available(fp, sh, indent, title))
3696 {
3697 indent = pr_title(fp, indent, title);
3698 pr_indent(fp, indent);
3699 fprintf(fp, "bIr = %spresent\n", sh->bIr ? "" : "not ");
3700 pr_indent(fp, indent);
3701 fprintf(fp, "bBox = %spresent\n", sh->bBox ? "" : "not ");
3702 pr_indent(fp, indent);
3703 fprintf(fp, "bTop = %spresent\n", sh->bTop ? "" : "not ");
3704 pr_indent(fp, indent);
3705 fprintf(fp, "bX = %spresent\n", sh->bX ? "" : "not ");
3706 pr_indent(fp, indent);
3707 fprintf(fp, "bV = %spresent\n", sh->bV ? "" : "not ");
3708 pr_indent(fp, indent);
3709 fprintf(fp, "bF = %spresent\n", sh->bF ? "" : "not ");
3710
3711 pr_indent(fp, indent);
3712 fprintf(fp, "natoms = %d\n", sh->natoms);
3713 pr_indent(fp, indent);
3714 fprintf(fp, "lambda = %e\n", sh->lambda);
3715 }
3716 }
The ultimate molecular dynamics simulation package