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Refactor gmx_group_t to SimulationAtomGroups
[gromacs.git] / src / gromacs / fileio / tpxio.cpp
blob5e7c77c73bc81322f8180cc79e1878ca9eec7e9e
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) 2013,2014,2015,2016,2017,2018,2019, 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.
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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 <memory>
49 #include <vector>
50
51 #include "gromacs/fileio/filetypes.h"
52 #include "gromacs/fileio/gmxfio.h"
53 #include "gromacs/fileio/gmxfio_xdr.h"
54 #include "gromacs/math/units.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/mdtypes/awh_history.h"
57 #include "gromacs/mdtypes/awh_params.h"
58 #include "gromacs/mdtypes/inputrec.h"
59 #include "gromacs/mdtypes/md_enums.h"
60 #include "gromacs/mdtypes/pull_params.h"
61 #include "gromacs/mdtypes/state.h"
62 #include "gromacs/pbcutil/boxutilities.h"
63 #include "gromacs/pbcutil/pbc.h"
64 #include "gromacs/topology/block.h"
65 #include "gromacs/topology/ifunc.h"
66 #include "gromacs/topology/mtop_util.h"
67 #include "gromacs/topology/symtab.h"
68 #include "gromacs/topology/topology.h"
69 #include "gromacs/utility/arraysize.h"
70 #include "gromacs/utility/baseversion.h"
71 #include "gromacs/utility/cstringutil.h"
72 #include "gromacs/utility/fatalerror.h"
73 #include "gromacs/utility/futil.h"
74 #include "gromacs/utility/gmxassert.h"
75 #include "gromacs/utility/keyvaluetreebuilder.h"
76 #include "gromacs/utility/keyvaluetreeserializer.h"
77 #include "gromacs/utility/smalloc.h"
78 #include "gromacs/utility/snprintf.h"
79 #include "gromacs/utility/txtdump.h"
80
81 #define TPX_TAG_RELEASE "release"
82
83 /*! \brief Tag string for the file format written to run input files
84 * written by this version of the code.
85 *
86 * Change this if you want to change the run input format in a feature
87 * branch. This ensures that there will not be different run input
88 * formats around which cannot be distinguished, while not causing
89 * problems rebasing the feature branch onto upstream changes. When
90 * merging with mainstream GROMACS, set this tag string back to
91 * TPX_TAG_RELEASE, and instead add an element to tpxv.
92 */
93 static const char *tpx_tag = TPX_TAG_RELEASE;
94
95 /*! \brief Enum of values that describe the contents of a tpr file
96 * whose format matches a version number
97 *
98 * The enum helps the code be more self-documenting and ensure merges
99 * do not silently resolve when two patches make the same bump. When
100 * adding new functionality, add a new element just above tpxv_Count
101 * in this enumeration, and write code below that does the right thing
102 * according to the value of file_version.
103 */
104 enum tpxv {
105 tpxv_ComputationalElectrophysiology = 96, /**< support for ion/water position swaps (computational electrophysiology) */
106 tpxv_Use64BitRandomSeed, /**< change ld_seed from int to int64_t */
107 tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, /**< potentials for supporting coarse-grained force fields */
108 tpxv_InteractiveMolecularDynamics, /**< interactive molecular dynamics (IMD) */
109 tpxv_RemoveObsoleteParameters1, /**< remove optimize_fft, dihre_fc, nstcheckpoint */
110 tpxv_PullCoordTypeGeom, /**< add pull type and geometry per group and flat-bottom */
111 tpxv_PullGeomDirRel, /**< add pull geometry direction-relative */
112 tpxv_IntermolecularBondeds, /**< permit inter-molecular bonded interactions in the topology */
113 tpxv_CompElWithSwapLayerOffset, /**< added parameters for improved CompEl setups */
114 tpxv_CompElPolyatomicIonsAndMultipleIonTypes, /**< CompEl now can handle polyatomic ions and more than two types of ions */
115 tpxv_RemoveAdress, /**< removed support for AdResS */
116 tpxv_PullCoordNGroup, /**< add ngroup to pull coord */
117 tpxv_RemoveTwinRange, /**< removed support for twin-range interactions */
118 tpxv_ReplacePullPrintCOM12, /**< Replaced print-com-1, 2 with pull-print-com */
119 tpxv_PullExternalPotential, /**< Added pull type external potential */
120 tpxv_GenericParamsForElectricField, /**< Introduced KeyValueTree and moved electric field parameters */
121 tpxv_AcceleratedWeightHistogram, /**< sampling with accelerated weight histogram method (AWH) */
122 tpxv_RemoveImplicitSolvation, /**< removed support for implicit solvation */
123 tpxv_PullPrevStepCOMAsReference, /**< Enabled using the COM of the pull group of the last frame as reference for PBC */
124 tpxv_MimicQMMM, /**< Inroduced support for MiMiC QM/MM interface */
125 tpxv_PullAverage, /**< Added possibility to output average pull force and position */
126 tpxv_Count /**< the total number of tpxv versions */
127 };
128
129 /*! \brief Version number of the file format written to run input
130 * files by this version of the code.
131 *
132 * The tpx_version increases whenever the file format in the main
133 * development branch changes, due to an extension of the tpxv enum above.
134 * Backward compatibility for reading old run input files is maintained
135 * by checking this version number against that of the file and then using
136 * the correct code path.
137 *
138 * When developing a feature branch that needs to change the run input
139 * file format, change tpx_tag instead. */
140 static const int tpx_version = tpxv_Count - 1;
141
142
143 /* This number should only be increased when you edit the TOPOLOGY section
144 * or the HEADER of the tpx format.
145 * This way we can maintain forward compatibility too for all analysis tools
146 * and/or external programs that only need to know the atom/residue names,
147 * charges, and bond connectivity.
148 *
149 * It first appeared in tpx version 26, when I also moved the inputrecord
150 * to the end of the tpx file, so we can just skip it if we only
151 * want the topology.
152 *
153 * In particular, it must be increased when adding new elements to
154 * ftupd, so that old code can read new .tpr files.
155 */
156 static const int tpx_generation = 26;
157
158 /* This number should be the most recent backwards incompatible version
159 * I.e., if this number is 9, we cannot read tpx version 9 with this code.
160 */
161 static const int tpx_incompatible_version = 57; // GMX4.0 has version 58
162
163
164
165 /* Struct used to maintain tpx compatibility when function types are added */
166 typedef struct {
167 int fvnr; /* file version number in which the function type first appeared */
168 int ftype; /* function type */
169 } t_ftupd;
170
171 /*
172 * TODO The following three lines make little sense, please clarify if
173 * you've had to work out how ftupd works.
174 *
175 * The entries should be ordered in:
176 * 1. ascending function type number
177 * 2. ascending file version number
178 *
179 * Because we support reading of old .tpr file versions (even when
180 * mdrun can no longer run the simulation), we need to be able to read
181 * obsolete t_interaction_function types. Any data read from such
182 * fields is discarded. Their names have _NOLONGERUSED appended to
183 * them to make things clear.
184 */
185 static const t_ftupd ftupd[] = {
186 { 70, F_RESTRBONDS },
187 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
188 { 76, F_LINEAR_ANGLES },
189 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
190 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
191 { 65, F_CMAP },
192 { 60, F_GB12_NOLONGERUSED },
193 { 61, F_GB13_NOLONGERUSED },
194 { 61, F_GB14_NOLONGERUSED },
195 { 72, F_GBPOL_NOLONGERUSED },
196 { 72, F_NPSOLVATION_NOLONGERUSED },
197 { 93, F_LJ_RECIP },
198 { 90, F_FBPOSRES },
199 { 69, F_VTEMP_NOLONGERUSED},
200 { 66, F_PDISPCORR },
201 { 76, F_ANHARM_POL },
202 { 79, F_DVDL_COUL },
203 { 79, F_DVDL_VDW, },
204 { 79, F_DVDL_BONDED, },
205 { 79, F_DVDL_RESTRAINT },
206 { 79, F_DVDL_TEMPERATURE },
207 };
208 #define NFTUPD asize(ftupd)
209
210 /* Needed for backward compatibility */
211 #define MAXNODES 256
212
213 /**************************************************************
214 *
215 * Now the higer level routines that do io of the structures and arrays
216 *
217 **************************************************************/
218 static void do_pullgrp_tpx_pre95(t_fileio *fio,
219 t_pull_group *pgrp,
220 t_pull_coord *pcrd,
221 gmx_bool bRead)
222 {
223 rvec tmp;
224
225 gmx_fio_do_int(fio, pgrp->nat);
226 if (bRead)
227 {
228 snew(pgrp->ind, pgrp->nat);
229 }
230 gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
231 gmx_fio_do_int(fio, pgrp->nweight);
232 if (bRead)
233 {
234 snew(pgrp->weight, pgrp->nweight);
235 }
236 gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight);
237 gmx_fio_do_int(fio, pgrp->pbcatom);
238 gmx_fio_do_rvec(fio, pcrd->vec);
239 clear_rvec(pcrd->origin);
240 gmx_fio_do_rvec(fio, tmp);
241 pcrd->init = tmp[0];
242 gmx_fio_do_real(fio, pcrd->rate);
243 gmx_fio_do_real(fio, pcrd->k);
244 gmx_fio_do_real(fio, pcrd->kB);
245 }
246
247 static void do_pull_group(t_fileio *fio, t_pull_group *pgrp, gmx_bool bRead)
248 {
249 gmx_fio_do_int(fio, pgrp->nat);
250 if (bRead)
251 {
252 snew(pgrp->ind, pgrp->nat);
253 }
254 gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
255 gmx_fio_do_int(fio, pgrp->nweight);
256 if (bRead)
257 {
258 snew(pgrp->weight, pgrp->nweight);
259 }
260 gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight);
261 gmx_fio_do_int(fio, pgrp->pbcatom);
262 }
263
264 static void do_pull_coord(t_fileio *fio, t_pull_coord *pcrd,
265 gmx_bool bRead, int file_version,
266 int ePullOld, int eGeomOld, ivec dimOld)
267 {
268 if (file_version >= tpxv_PullCoordNGroup)
269 {
270 gmx_fio_do_int(fio, pcrd->eType);
271 if (file_version >= tpxv_PullExternalPotential)
272 {
273 if (pcrd->eType == epullEXTERNAL)
274 {
275 if (bRead)
276 {
277 char buf[STRLEN];
278
279 gmx_fio_do_string(fio, buf);
280 pcrd->externalPotentialProvider = gmx_strdup(buf);
281 }
282 else
283 {
284 gmx_fio_do_string(fio, pcrd->externalPotentialProvider);
285 }
286 }
287 else
288 {
289 pcrd->externalPotentialProvider = nullptr;
290 }
291 }
292 else
293 {
294 if (bRead)
295 {
296 pcrd->externalPotentialProvider = nullptr;
297 }
298 }
299 /* Note that we try to support adding new geometries without
300 * changing the tpx version. This requires checks when printing the
301 * geometry string and a check and fatal_error in init_pull.
302 */
303 gmx_fio_do_int(fio, pcrd->eGeom);
304 gmx_fio_do_int(fio, pcrd->ngroup);
305 if (pcrd->ngroup <= c_pullCoordNgroupMax)
306 {
307 gmx_fio_ndo_int(fio, pcrd->group, pcrd->ngroup);
308 }
309 else
310 {
311 /* More groups in file than supported, this must be a new geometry
312 * that is not supported by our current code. Since we will not
313 * use the groups for this coord (checks in the pull and WHAM code
314 * ensure this), we can ignore the groups and set ngroup=0.
315 */
316 int *dum;
317 snew(dum, pcrd->ngroup);
318 gmx_fio_ndo_int(fio, dum, pcrd->ngroup);
319 sfree(dum);
320
321 pcrd->ngroup = 0;
322 }
323 gmx_fio_do_ivec(fio, pcrd->dim);
324 }
325 else
326 {
327 pcrd->ngroup = 2;
328 gmx_fio_do_int(fio, pcrd->group[0]);
329 gmx_fio_do_int(fio, pcrd->group[1]);
330 if (file_version >= tpxv_PullCoordTypeGeom)
331 {
332 pcrd->ngroup = (pcrd->eGeom == epullgDIRRELATIVE ? 4 : 2);
333 gmx_fio_do_int(fio, pcrd->eType);
334 gmx_fio_do_int(fio, pcrd->eGeom);
335 if (pcrd->ngroup == 4)
336 {
337 gmx_fio_do_int(fio, pcrd->group[2]);
338 gmx_fio_do_int(fio, pcrd->group[3]);
339 }
340 gmx_fio_do_ivec(fio, pcrd->dim);
341 }
342 else
343 {
344 pcrd->eType = ePullOld;
345 pcrd->eGeom = eGeomOld;
346 copy_ivec(dimOld, pcrd->dim);
347 }
348 }
349 gmx_fio_do_rvec(fio, pcrd->origin);
350 gmx_fio_do_rvec(fio, pcrd->vec);
351 if (file_version >= tpxv_PullCoordTypeGeom)
352 {
353 gmx_fio_do_gmx_bool(fio, pcrd->bStart);
354 }
355 else
356 {
357 /* This parameter is only printed, but not actually used by mdrun */
358 pcrd->bStart = FALSE;
359 }
360 gmx_fio_do_real(fio, pcrd->init);
361 gmx_fio_do_real(fio, pcrd->rate);
362 gmx_fio_do_real(fio, pcrd->k);
363 gmx_fio_do_real(fio, pcrd->kB);
364 }
365
366 static void do_expandedvals(t_fileio *fio, t_expanded *expand, t_lambda *fepvals, gmx_bool bRead, int file_version)
367 {
368 int n_lambda = fepvals->n_lambda;
369
370 /* reset the lambda calculation window */
371 fepvals->lambda_start_n = 0;
372 fepvals->lambda_stop_n = n_lambda;
373 if (file_version >= 79)
374 {
375 if (n_lambda > 0)
376 {
377 if (bRead)
378 {
379 snew(expand->init_lambda_weights, n_lambda);
380 }
381 gmx_fio_ndo_real(fio, expand->init_lambda_weights, n_lambda);
382 gmx_fio_do_gmx_bool(fio, expand->bInit_weights);
383 }
384
385 gmx_fio_do_int(fio, expand->nstexpanded);
386 gmx_fio_do_int(fio, expand->elmcmove);
387 gmx_fio_do_int(fio, expand->elamstats);
388 gmx_fio_do_int(fio, expand->lmc_repeats);
389 gmx_fio_do_int(fio, expand->gibbsdeltalam);
390 gmx_fio_do_int(fio, expand->lmc_forced_nstart);
391 gmx_fio_do_int(fio, expand->lmc_seed);
392 gmx_fio_do_real(fio, expand->mc_temp);
393 gmx_fio_do_gmx_bool(fio, expand->bSymmetrizedTMatrix);
394 gmx_fio_do_int(fio, expand->nstTij);
395 gmx_fio_do_int(fio, expand->minvarmin);
396 gmx_fio_do_int(fio, expand->c_range);
397 gmx_fio_do_real(fio, expand->wl_scale);
398 gmx_fio_do_real(fio, expand->wl_ratio);
399 gmx_fio_do_real(fio, expand->init_wl_delta);
400 gmx_fio_do_gmx_bool(fio, expand->bWLoneovert);
401 gmx_fio_do_int(fio, expand->elmceq);
402 gmx_fio_do_int(fio, expand->equil_steps);
403 gmx_fio_do_int(fio, expand->equil_samples);
404 gmx_fio_do_int(fio, expand->equil_n_at_lam);
405 gmx_fio_do_real(fio, expand->equil_wl_delta);
406 gmx_fio_do_real(fio, expand->equil_ratio);
407 }
408 }
409
410 static void do_simtempvals(t_fileio *fio, t_simtemp *simtemp, int n_lambda, gmx_bool bRead,
411 int file_version)
412 {
413 if (file_version >= 79)
414 {
415 gmx_fio_do_int(fio, simtemp->eSimTempScale);
416 gmx_fio_do_real(fio, simtemp->simtemp_high);
417 gmx_fio_do_real(fio, simtemp->simtemp_low);
418 if (n_lambda > 0)
419 {
420 if (bRead)
421 {
422 snew(simtemp->temperatures, n_lambda);
423 }
424 gmx_fio_ndo_real(fio, simtemp->temperatures, n_lambda);
425 }
426 }
427 }
428
429 static void do_imd(t_fileio *fio, t_IMD *imd, gmx_bool bRead)
430 {
431 gmx_fio_do_int(fio, imd->nat);
432 if (bRead)
433 {
434 snew(imd->ind, imd->nat);
435 }
436 gmx_fio_ndo_int(fio, imd->ind, imd->nat);
437 }
438
439 static void do_fepvals(t_fileio *fio, t_lambda *fepvals, gmx_bool bRead, int file_version)
440 {
441 /* i is defined in the ndo_double macro; use g to iterate. */
442 int g;
443 real rdum;
444
445 /* free energy values */
446
447 if (file_version >= 79)
448 {
449 gmx_fio_do_int(fio, fepvals->init_fep_state);
450 gmx_fio_do_double(fio, fepvals->init_lambda);
451 gmx_fio_do_double(fio, fepvals->delta_lambda);
452 }
453 else if (file_version >= 59)
454 {
455 gmx_fio_do_double(fio, fepvals->init_lambda);
456 gmx_fio_do_double(fio, fepvals->delta_lambda);
457 }
458 else
459 {
460 gmx_fio_do_real(fio, rdum);
461 fepvals->init_lambda = rdum;
462 gmx_fio_do_real(fio, rdum);
463 fepvals->delta_lambda = rdum;
464 }
465 if (file_version >= 79)
466 {
467 gmx_fio_do_int(fio, fepvals->n_lambda);
468 if (bRead)
469 {
470 snew(fepvals->all_lambda, efptNR);
471 }
472 for (g = 0; g < efptNR; g++)
473 {
474 if (fepvals->n_lambda > 0)
475 {
476 if (bRead)
477 {
478 snew(fepvals->all_lambda[g], fepvals->n_lambda);
479 }
480 gmx_fio_ndo_double(fio, fepvals->all_lambda[g], fepvals->n_lambda);
481 gmx_fio_ndo_gmx_bool(fio, fepvals->separate_dvdl, efptNR);
482 }
483 else if (fepvals->init_lambda >= 0)
484 {
485 fepvals->separate_dvdl[efptFEP] = TRUE;
486 }
487 }
488 }
489 else if (file_version >= 64)
490 {
491 gmx_fio_do_int(fio, fepvals->n_lambda);
492 if (bRead)
493 {
494 int g;
495
496 snew(fepvals->all_lambda, efptNR);
497 /* still allocate the all_lambda array's contents. */
498 for (g = 0; g < efptNR; g++)
499 {
500 if (fepvals->n_lambda > 0)
501 {
502 snew(fepvals->all_lambda[g], fepvals->n_lambda);
503 }
504 }
505 }
506 gmx_fio_ndo_double(fio, fepvals->all_lambda[efptFEP],
507 fepvals->n_lambda);
508 if (fepvals->init_lambda >= 0)
509 {
510 int g, h;
511
512 fepvals->separate_dvdl[efptFEP] = TRUE;
513
514 if (bRead)
515 {
516 /* copy the contents of the efptFEP lambda component to all
517 the other components */
518 for (g = 0; g < efptNR; g++)
519 {
520 for (h = 0; h < fepvals->n_lambda; h++)
521 {
522 if (g != efptFEP)
523 {
524 fepvals->all_lambda[g][h] =
525 fepvals->all_lambda[efptFEP][h];
526 }
527 }
528 }
529 }
530 }
531 }
532 else
533 {
534 fepvals->n_lambda = 0;
535 fepvals->all_lambda = nullptr;
536 if (fepvals->init_lambda >= 0)
537 {
538 fepvals->separate_dvdl[efptFEP] = TRUE;
539 }
540 }
541 gmx_fio_do_real(fio, fepvals->sc_alpha);
542 gmx_fio_do_int(fio, fepvals->sc_power);
543 if (file_version >= 79)
544 {
545 gmx_fio_do_real(fio, fepvals->sc_r_power);
546 }
547 else
548 {
549 fepvals->sc_r_power = 6.0;
550 }
551 gmx_fio_do_real(fio, fepvals->sc_sigma);
552 if (bRead)
553 {
554 if (file_version >= 71)
555 {
556 fepvals->sc_sigma_min = fepvals->sc_sigma;
557 }
558 else
559 {
560 fepvals->sc_sigma_min = 0;
561 }
562 }
563 if (file_version >= 79)
564 {
565 gmx_fio_do_gmx_bool(fio, fepvals->bScCoul);
566 }
567 else
568 {
569 fepvals->bScCoul = TRUE;
570 }
571 if (file_version >= 64)
572 {
573 gmx_fio_do_int(fio, fepvals->nstdhdl);
574 }
575 else
576 {
577 fepvals->nstdhdl = 1;
578 }
579
580 if (file_version >= 73)
581 {
582 gmx_fio_do_int(fio, fepvals->separate_dhdl_file);
583 gmx_fio_do_int(fio, fepvals->dhdl_derivatives);
584 }
585 else
586 {
587 fepvals->separate_dhdl_file = esepdhdlfileYES;
588 fepvals->dhdl_derivatives = edhdlderivativesYES;
589 }
590 if (file_version >= 71)
591 {
592 gmx_fio_do_int(fio, fepvals->dh_hist_size);
593 gmx_fio_do_double(fio, fepvals->dh_hist_spacing);
594 }
595 else
596 {
597 fepvals->dh_hist_size = 0;
598 fepvals->dh_hist_spacing = 0.1;
599 }
600 if (file_version >= 79)
601 {
602 gmx_fio_do_int(fio, fepvals->edHdLPrintEnergy);
603 }
604 else
605 {
606 fepvals->edHdLPrintEnergy = edHdLPrintEnergyNO;
607 }
608
609 /* handle lambda_neighbors */
610 if ((file_version >= 83 && file_version < 90) || file_version >= 92)
611 {
612 gmx_fio_do_int(fio, fepvals->lambda_neighbors);
613 if ( (fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0) &&
614 (fepvals->init_lambda < 0) )
615 {
616 fepvals->lambda_start_n = (fepvals->init_fep_state -
617 fepvals->lambda_neighbors);
618 fepvals->lambda_stop_n = (fepvals->init_fep_state +
619 fepvals->lambda_neighbors + 1);
620 if (fepvals->lambda_start_n < 0)
621 {
622 fepvals->lambda_start_n = 0;;
623 }
624 if (fepvals->lambda_stop_n >= fepvals->n_lambda)
625 {
626 fepvals->lambda_stop_n = fepvals->n_lambda;
627 }
628 }
629 else
630 {
631 fepvals->lambda_start_n = 0;
632 fepvals->lambda_stop_n = fepvals->n_lambda;
633 }
634 }
635 else
636 {
637 fepvals->lambda_start_n = 0;
638 fepvals->lambda_stop_n = fepvals->n_lambda;
639 }
640 }
641
642 static void do_awhBias(t_fileio *fio, gmx::AwhBiasParams *awhBiasParams, gmx_bool bRead,
643 int gmx_unused file_version)
644 {
645 gmx_fio_do_int(fio, awhBiasParams->eTarget);
646 gmx_fio_do_double(fio, awhBiasParams->targetBetaScaling);
647 gmx_fio_do_double(fio, awhBiasParams->targetCutoff);
648 gmx_fio_do_int(fio, awhBiasParams->eGrowth);
649 gmx_fio_do_int(fio, awhBiasParams->bUserData);
650 gmx_fio_do_double(fio, awhBiasParams->errorInitial);
651 gmx_fio_do_int(fio, awhBiasParams->ndim);
652 gmx_fio_do_int(fio, awhBiasParams->shareGroup);
653 gmx_fio_do_gmx_bool(fio, awhBiasParams->equilibrateHistogram);
654
655 if (bRead)
656 {
657 snew(awhBiasParams->dimParams, awhBiasParams->ndim);
658 }
659
660 for (int d = 0; d < awhBiasParams->ndim; d++)
661 {
662 gmx::AwhDimParams *dimParams = &awhBiasParams->dimParams[d];
663
664 gmx_fio_do_int(fio, dimParams->eCoordProvider);
665 gmx_fio_do_int(fio, dimParams->coordIndex);
666 gmx_fio_do_double(fio, dimParams->origin);
667 gmx_fio_do_double(fio, dimParams->end);
668 gmx_fio_do_double(fio, dimParams->period);
669 gmx_fio_do_double(fio, dimParams->forceConstant);
670 gmx_fio_do_double(fio, dimParams->diffusion);
671 gmx_fio_do_double(fio, dimParams->coordValueInit);
672 gmx_fio_do_double(fio, dimParams->coverDiameter);
673 }
674 }
675
676 static void do_awh(t_fileio *fio, gmx::AwhParams *awhParams, gmx_bool bRead,
677 int gmx_unused file_version)
678 {
679 gmx_fio_do_int(fio, awhParams->numBias);
680 gmx_fio_do_int(fio, awhParams->nstOut);
681 gmx_fio_do_int64(fio, awhParams->seed);
682 gmx_fio_do_int(fio, awhParams->nstSampleCoord);
683 gmx_fio_do_int(fio, awhParams->numSamplesUpdateFreeEnergy);
684 gmx_fio_do_int(fio, awhParams->ePotential);
685 gmx_fio_do_gmx_bool(fio, awhParams->shareBiasMultisim);
686
687 if (awhParams->numBias > 0)
688 {
689 if (bRead)
690 {
691 snew(awhParams->awhBiasParams, awhParams->numBias);
692 }
693
694 for (int k = 0; k < awhParams->numBias; k++)
695 {
696 do_awhBias(fio, &awhParams->awhBiasParams[k], bRead, file_version);
697 }
698 }
699 }
700
701 static void do_pull(t_fileio *fio, pull_params_t *pull, gmx_bool bRead,
702 int file_version, int ePullOld)
703 {
704 int eGeomOld = -1;
705 ivec dimOld;
706 int g;
707
708 if (file_version >= 95)
709 {
710 gmx_fio_do_int(fio, pull->ngroup);
711 }
712 gmx_fio_do_int(fio, pull->ncoord);
713 if (file_version < 95)
714 {
715 pull->ngroup = pull->ncoord + 1;
716 }
717 if (file_version < tpxv_PullCoordTypeGeom)
718 {
719 real dum;
720
721 gmx_fio_do_int(fio, eGeomOld);
722 gmx_fio_do_ivec(fio, dimOld);
723 /* The inner cylinder radius, now removed */
724 gmx_fio_do_real(fio, dum);
725 }
726 gmx_fio_do_real(fio, pull->cylinder_r);
727 gmx_fio_do_real(fio, pull->constr_tol);
728 if (file_version >= 95)
729 {
730 gmx_fio_do_gmx_bool(fio, pull->bPrintCOM);
731 /* With file_version < 95 this value is set below */
732 }
733 if (file_version >= tpxv_ReplacePullPrintCOM12)
734 {
735 gmx_fio_do_gmx_bool(fio, pull->bPrintRefValue);
736 gmx_fio_do_gmx_bool(fio, pull->bPrintComp);
737 }
738 else if (file_version >= tpxv_PullCoordTypeGeom)
739 {
740 int idum;
741 gmx_fio_do_int(fio, idum); /* used to be bPrintCOM2 */
742 gmx_fio_do_gmx_bool(fio, pull->bPrintRefValue);
743 gmx_fio_do_gmx_bool(fio, pull->bPrintComp);
744 }
745 else
746 {
747 pull->bPrintRefValue = FALSE;
748 pull->bPrintComp = TRUE;
749 }
750 gmx_fio_do_int(fio, pull->nstxout);
751 gmx_fio_do_int(fio, pull->nstfout);
752 if (file_version >= tpxv_PullPrevStepCOMAsReference)
753 {
754 gmx_fio_do_gmx_bool(fio, pull->bSetPbcRefToPrevStepCOM);
755 }
756 else
757 {
758 pull->bSetPbcRefToPrevStepCOM = FALSE;
759 }
760 if (bRead)
761 {
762 snew(pull->group, pull->ngroup);
763 snew(pull->coord, pull->ncoord);
764 }
765 if (file_version < 95)
766 {
767 /* epullgPOS for position pulling, before epullgDIRPBC was removed */
768 if (eGeomOld == epullgDIRPBC)
769 {
770 gmx_fatal(FARGS, "pull-geometry=position is no longer supported");
771 }
772 if (eGeomOld > epullgDIRPBC)
773 {
774 eGeomOld -= 1;
775 }
776
777 for (g = 0; g < pull->ngroup; g++)
778 {
779 /* We read and ignore a pull coordinate for group 0 */
780 do_pullgrp_tpx_pre95(fio, &pull->group[g], &pull->coord[std::max(g-1, 0)],
781 bRead);
782 if (g > 0)
783 {
784 pull->coord[g-1].group[0] = 0;
785 pull->coord[g-1].group[1] = g;
786 }
787 }
788
789 pull->bPrintCOM = (pull->group[0].nat > 0);
790 }
791 else
792 {
793 for (g = 0; g < pull->ngroup; g++)
794 {
795 do_pull_group(fio, &pull->group[g], bRead);
796 }
797 for (g = 0; g < pull->ncoord; g++)
798 {
799 do_pull_coord(fio, &pull->coord[g],
800 bRead, file_version, ePullOld, eGeomOld, dimOld);
801 }
802 }
803 if (file_version >= tpxv_PullAverage)
804 {
805 gmx_bool v;
806
807 v = pull->bXOutAverage;
808 gmx_fio_do_gmx_bool(fio, v);
809 pull->bXOutAverage = v;
810 v = pull->bFOutAverage;
811 gmx_fio_do_gmx_bool(fio, v);
812 pull->bFOutAverage = v;
813 }
814 }
815
816
817 static void do_rotgrp(t_fileio *fio, t_rotgrp *rotg, gmx_bool bRead)
818 {
819 gmx_fio_do_int(fio, rotg->eType);
820 gmx_fio_do_int(fio, rotg->bMassW);
821 gmx_fio_do_int(fio, rotg->nat);
822 if (bRead)
823 {
824 snew(rotg->ind, rotg->nat);
825 }
826 gmx_fio_ndo_int(fio, rotg->ind, rotg->nat);
827 if (bRead)
828 {
829 snew(rotg->x_ref, rotg->nat);
830 }
831 gmx_fio_ndo_rvec(fio, rotg->x_ref, rotg->nat);
832 gmx_fio_do_rvec(fio, rotg->inputVec);
833 gmx_fio_do_rvec(fio, rotg->pivot);
834 gmx_fio_do_real(fio, rotg->rate);
835 gmx_fio_do_real(fio, rotg->k);
836 gmx_fio_do_real(fio, rotg->slab_dist);
837 gmx_fio_do_real(fio, rotg->min_gaussian);
838 gmx_fio_do_real(fio, rotg->eps);
839 gmx_fio_do_int(fio, rotg->eFittype);
840 gmx_fio_do_int(fio, rotg->PotAngle_nstep);
841 gmx_fio_do_real(fio, rotg->PotAngle_step);
842 }
843
844 static void do_rot(t_fileio *fio, t_rot *rot, gmx_bool bRead)
845 {
846 int g;
847
848 gmx_fio_do_int(fio, rot->ngrp);
849 gmx_fio_do_int(fio, rot->nstrout);
850 gmx_fio_do_int(fio, rot->nstsout);
851 if (bRead)
852 {
853 snew(rot->grp, rot->ngrp);
854 }
855 for (g = 0; g < rot->ngrp; g++)
856 {
857 do_rotgrp(fio, &rot->grp[g], bRead);
858 }
859 }
860
861
862 static void do_swapgroup(t_fileio *fio, t_swapGroup *g, gmx_bool bRead)
863 {
864
865 /* Name of the group or molecule */
866 if (bRead)
867 {
868 char buf[STRLEN];
869
870 gmx_fio_do_string(fio, buf);
871 g->molname = gmx_strdup(buf);
872 }
873 else
874 {
875 gmx_fio_do_string(fio, g->molname);
876 }
877
878 /* Number of atoms in the group */
879 gmx_fio_do_int(fio, g->nat);
880
881 /* The group's atom indices */
882 if (bRead)
883 {
884 snew(g->ind, g->nat);
885 }
886 gmx_fio_ndo_int(fio, g->ind, g->nat);
887
888 /* Requested counts for compartments A and B */
889 gmx_fio_ndo_int(fio, g->nmolReq, eCompNR);
890 }
891
892 static void do_swapcoords_tpx(t_fileio *fio, t_swapcoords *swap, gmx_bool bRead, int file_version)
893 {
894 /* Enums for better readability of the code */
895 enum {
896 eCompA = 0, eCompB
897 };
898 enum {
899 eChannel0 = 0, eChannel1
900 };
901
902
903 if (file_version >= tpxv_CompElPolyatomicIonsAndMultipleIonTypes)
904 {
905 /* The total number of swap groups is the sum of the fixed groups
906 * (split0, split1, solvent), and the user-defined groups (2+ types of ions)
907 */
908 gmx_fio_do_int(fio, swap->ngrp);
909 if (bRead)
910 {
911 snew(swap->grp, swap->ngrp);
912 }
913 for (int ig = 0; ig < swap->ngrp; ig++)
914 {
915 do_swapgroup(fio, &swap->grp[ig], bRead);
916 }
917 gmx_fio_do_gmx_bool(fio, swap->massw_split[eChannel0]);
918 gmx_fio_do_gmx_bool(fio, swap->massw_split[eChannel1]);
919 gmx_fio_do_int(fio, swap->nstswap);
920 gmx_fio_do_int(fio, swap->nAverage);
921 gmx_fio_do_real(fio, swap->threshold);
922 gmx_fio_do_real(fio, swap->cyl0r);
923 gmx_fio_do_real(fio, swap->cyl0u);
924 gmx_fio_do_real(fio, swap->cyl0l);
925 gmx_fio_do_real(fio, swap->cyl1r);
926 gmx_fio_do_real(fio, swap->cyl1u);
927 gmx_fio_do_real(fio, swap->cyl1l);
928 }
929 else
930 {
931 /*** Support reading older CompEl .tpr files ***/
932
933 /* In the original CompEl .tpr files, we always have 5 groups: */
934 swap->ngrp = 5;
935 snew(swap->grp, swap->ngrp);
936
937 swap->grp[eGrpSplit0 ].molname = gmx_strdup("split0" ); // group 0: split0
938 swap->grp[eGrpSplit1 ].molname = gmx_strdup("split1" ); // group 1: split1
939 swap->grp[eGrpSolvent].molname = gmx_strdup("solvent"); // group 2: solvent
940 swap->grp[3 ].molname = gmx_strdup("anions" ); // group 3: anions
941 swap->grp[4 ].molname = gmx_strdup("cations"); // group 4: cations
942
943 gmx_fio_do_int(fio, swap->grp[3].nat);
944 gmx_fio_do_int(fio, swap->grp[eGrpSolvent].nat);
945 gmx_fio_do_int(fio, swap->grp[eGrpSplit0].nat);
946 gmx_fio_do_gmx_bool(fio, swap->massw_split[eChannel0]);
947 gmx_fio_do_int(fio, swap->grp[eGrpSplit1].nat);
948 gmx_fio_do_gmx_bool(fio, swap->massw_split[eChannel1]);
949 gmx_fio_do_int(fio, swap->nstswap);
950 gmx_fio_do_int(fio, swap->nAverage);
951 gmx_fio_do_real(fio, swap->threshold);
952 gmx_fio_do_real(fio, swap->cyl0r);
953 gmx_fio_do_real(fio, swap->cyl0u);
954 gmx_fio_do_real(fio, swap->cyl0l);
955 gmx_fio_do_real(fio, swap->cyl1r);
956 gmx_fio_do_real(fio, swap->cyl1u);
957 gmx_fio_do_real(fio, swap->cyl1l);
958
959 // The order[] array keeps compatibility with older .tpr files
960 // by reading in the groups in the classic order
961 {
962 const int order[4] = {3, eGrpSolvent, eGrpSplit0, eGrpSplit1 };
963
964 for (int ig = 0; ig < 4; ig++)
965 {
966 int g = order[ig];
967 snew(swap->grp[g].ind, swap->grp[g].nat);
968 gmx_fio_ndo_int(fio, swap->grp[g].ind, swap->grp[g].nat);
969 }
970 }
971
972 for (int j = eCompA; j <= eCompB; j++)
973 {
974 gmx_fio_do_int(fio, swap->grp[3].nmolReq[j]); // group 3 = anions
975 gmx_fio_do_int(fio, swap->grp[4].nmolReq[j]); // group 4 = cations
976 }
977 } /* End support reading older CompEl .tpr files */
978
979 if (file_version >= tpxv_CompElWithSwapLayerOffset)
980 {
981 gmx_fio_do_real(fio, swap->bulkOffset[eCompA]);
982 gmx_fio_do_real(fio, swap->bulkOffset[eCompB]);
983 }
984
985 }
986
987 static void do_legacy_efield(t_fileio *fio, gmx::KeyValueTreeObjectBuilder *root)
988 {
989 const char *const dimName[] = { "x", "y", "z" };
990
991 auto appliedForcesObj = root->addObject("applied-forces");
992 auto efieldObj = appliedForcesObj.addObject("electric-field");
993 // The content of the tpr file for this feature has
994 // been the same since gromacs 4.0 that was used for
995 // developing.
996 for (int j = 0; j < DIM; ++j)
997 {
998 int n, nt;
999 gmx_fio_do_int(fio, n);
1000 gmx_fio_do_int(fio, nt);
1001 std::vector<real> aa(n+1), phi(nt+1), at(nt+1), phit(nt+1);
1002 gmx_fio_ndo_real(fio, aa.data(), n);
1003 gmx_fio_ndo_real(fio, phi.data(), n);
1004 gmx_fio_ndo_real(fio, at.data(), nt);
1005 gmx_fio_ndo_real(fio, phit.data(), nt);
1006 if (n > 0)
1007 {
1008 if (n > 1 || nt > 1)
1009 {
1010 gmx_fatal(FARGS, "Can not handle tpr files with more than one electric field term per direction.");
1011 }
1012 auto dimObj = efieldObj.addObject(dimName[j]);
1013 dimObj.addValue<real>("E0", aa[0]);
1014 dimObj.addValue<real>("omega", at[0]);
1015 dimObj.addValue<real>("t0", phi[0]);
1016 dimObj.addValue<real>("sigma", phit[0]);
1017 }
1018 }
1019 }
1020
1021
1022 static void do_inputrec(t_fileio *fio, t_inputrec *ir, gmx_bool bRead,
1023 int file_version)
1024 {
1025 int i, j, k, idum = 0;
1026 real rdum;
1027 gmx_bool bdum = false;
1028
1029 if (file_version != tpx_version)
1030 {
1031 /* Give a warning about features that are not accessible */
1032 fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n",
1033 file_version, tpx_version);
1034 }
1035
1036 if (file_version == 0)
1037 {
1038 return;
1039 }
1040
1041 gmx::KeyValueTreeBuilder paramsBuilder;
1042 gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
1043
1044 /* Basic inputrec stuff */
1045 gmx_fio_do_int(fio, ir->eI);
1046 if (file_version >= 62)
1047 {
1048 gmx_fio_do_int64(fio, ir->nsteps);
1049 }
1050 else
1051 {
1052 gmx_fio_do_int(fio, idum);
1053 ir->nsteps = idum;
1054 }
1055
1056 if (file_version >= 62)
1057 {
1058 gmx_fio_do_int64(fio, ir->init_step);
1059 }
1060 else
1061 {
1062 gmx_fio_do_int(fio, idum);
1063 ir->init_step = idum;
1064 }
1065
1066 gmx_fio_do_int(fio, ir->simulation_part);
1067
1068 if (file_version >= 67)
1069 {
1070 gmx_fio_do_int(fio, ir->nstcalcenergy);
1071 }
1072 else
1073 {
1074 ir->nstcalcenergy = 1;
1075 }
1076 if (file_version >= 81)
1077 {
1078 gmx_fio_do_int(fio, ir->cutoff_scheme);
1079 if (file_version < 94)
1080 {
1081 ir->cutoff_scheme = 1 - ir->cutoff_scheme;
1082 }
1083 }
1084 else
1085 {
1086 ir->cutoff_scheme = ecutsGROUP;
1087 }
1088 gmx_fio_do_int(fio, ir->ns_type);
1089 gmx_fio_do_int(fio, ir->nstlist);
1090 gmx_fio_do_int(fio, idum); /* used to be ndelta; not used anymore */
1091
1092 gmx_fio_do_real(fio, ir->rtpi);
1093
1094 gmx_fio_do_int(fio, ir->nstcomm);
1095 gmx_fio_do_int(fio, ir->comm_mode);
1096
1097 /* ignore nstcheckpoint */
1098 if (file_version < tpxv_RemoveObsoleteParameters1)
1099 {
1100 gmx_fio_do_int(fio, idum);
1101 }
1102
1103 gmx_fio_do_int(fio, ir->nstcgsteep);
1104
1105 gmx_fio_do_int(fio, ir->nbfgscorr);
1106
1107 gmx_fio_do_int(fio, ir->nstlog);
1108 gmx_fio_do_int(fio, ir->nstxout);
1109 gmx_fio_do_int(fio, ir->nstvout);
1110 gmx_fio_do_int(fio, ir->nstfout);
1111 gmx_fio_do_int(fio, ir->nstenergy);
1112 gmx_fio_do_int(fio, ir->nstxout_compressed);
1113 if (file_version >= 59)
1114 {
1115 gmx_fio_do_double(fio, ir->init_t);
1116 gmx_fio_do_double(fio, ir->delta_t);
1117 }
1118 else
1119 {
1120 gmx_fio_do_real(fio, rdum);
1121 ir->init_t = rdum;
1122 gmx_fio_do_real(fio, rdum);
1123 ir->delta_t = rdum;
1124 }
1125 gmx_fio_do_real(fio, ir->x_compression_precision);
1126 if (file_version >= 81)
1127 {
1128 gmx_fio_do_real(fio, ir->verletbuf_tol);
1129 }
1130 else
1131 {
1132 ir->verletbuf_tol = 0;
1133 }
1134 gmx_fio_do_real(fio, ir->rlist);
1135 if (file_version >= 67 && file_version < tpxv_RemoveTwinRange)
1136 {
1137 if (bRead)
1138 {
1139 // Reading such a file version could invoke the twin-range
1140 // scheme, about which mdrun should give a fatal error.
1141 real dummy_rlistlong = -1;
1142 gmx_fio_do_real(fio, dummy_rlistlong);
1143
1144 if (ir->rlist > 0 && (dummy_rlistlong == 0 || dummy_rlistlong > ir->rlist))
1145 {
1146 // Get mdrun to issue an error (regardless of
1147 // ir->cutoff_scheme).
1148 ir->useTwinRange = true;
1149 }
1150 else
1151 {
1152 // grompp used to set rlistlong actively. Users were
1153 // probably also confused and set rlistlong == rlist.
1154 // However, in all remaining cases, it is safe to let
1155 // mdrun proceed normally.
1156 ir->useTwinRange = false;
1157 }
1158 }
1159 }
1160 else
1161 {
1162 // No need to read or write anything
1163 ir->useTwinRange = false;
1164 }
1165 if (file_version >= 82 && file_version != 90)
1166 {
1167 // Multiple time-stepping is no longer enabled, but the old
1168 // support required the twin-range scheme, for which mdrun
1169 // already emits a fatal error.
1170 int dummy_nstcalclr = -1;
1171 gmx_fio_do_int(fio, dummy_nstcalclr);
1172 }
1173 gmx_fio_do_int(fio, ir->coulombtype);
1174 if (file_version >= 81)
1175 {
1176 gmx_fio_do_int(fio, ir->coulomb_modifier);
1177 }
1178 else
1179 {
1180 ir->coulomb_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1181 }
1182 gmx_fio_do_real(fio, ir->rcoulomb_switch);
1183 gmx_fio_do_real(fio, ir->rcoulomb);
1184 gmx_fio_do_int(fio, ir->vdwtype);
1185 if (file_version >= 81)
1186 {
1187 gmx_fio_do_int(fio, ir->vdw_modifier);
1188 }
1189 else
1190 {
1191 ir->vdw_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1192 }
1193 gmx_fio_do_real(fio, ir->rvdw_switch);
1194 gmx_fio_do_real(fio, ir->rvdw);
1195 gmx_fio_do_int(fio, ir->eDispCorr);
1196 gmx_fio_do_real(fio, ir->epsilon_r);
1197 gmx_fio_do_real(fio, ir->epsilon_rf);
1198 gmx_fio_do_real(fio, ir->tabext);
1199
1200 // This permits reading a .tpr file that used implicit solvent,
1201 // and later permitting mdrun to refuse to run it.
1202 if (bRead)
1203 {
1204 if (file_version < tpxv_RemoveImplicitSolvation)
1205 {
1206 gmx_fio_do_int(fio, idum);
1207 gmx_fio_do_int(fio, idum);
1208 gmx_fio_do_real(fio, rdum);
1209 gmx_fio_do_real(fio, rdum);
1210 gmx_fio_do_int(fio, idum);
1211 ir->implicit_solvent = (idum > 0);
1212 }
1213 else
1214 {
1215 ir->implicit_solvent = false;
1216 }
1217 if (file_version < tpxv_RemoveImplicitSolvation)
1218 {
1219 gmx_fio_do_real(fio, rdum);
1220 gmx_fio_do_real(fio, rdum);
1221 gmx_fio_do_real(fio, rdum);
1222 gmx_fio_do_real(fio, rdum);
1223 if (file_version >= 60)
1224 {
1225 gmx_fio_do_real(fio, rdum);
1226 gmx_fio_do_int(fio, idum);
1227 }
1228 gmx_fio_do_real(fio, rdum);
1229 }
1230 }
1231
1232 if (file_version >= 81)
1233 {
1234 gmx_fio_do_real(fio, ir->fourier_spacing);
1235 }
1236 else
1237 {
1238 ir->fourier_spacing = 0.0;
1239 }
1240 gmx_fio_do_int(fio, ir->nkx);
1241 gmx_fio_do_int(fio, ir->nky);
1242 gmx_fio_do_int(fio, ir->nkz);
1243 gmx_fio_do_int(fio, ir->pme_order);
1244 gmx_fio_do_real(fio, ir->ewald_rtol);
1245
1246 if (file_version >= 93)
1247 {
1248 gmx_fio_do_real(fio, ir->ewald_rtol_lj);
1249 }
1250 else
1251 {
1252 ir->ewald_rtol_lj = ir->ewald_rtol;
1253 }
1254 gmx_fio_do_int(fio, ir->ewald_geometry);
1255 gmx_fio_do_real(fio, ir->epsilon_surface);
1256
1257 /* ignore bOptFFT */
1258 if (file_version < tpxv_RemoveObsoleteParameters1)
1259 {
1260 gmx_fio_do_gmx_bool(fio, bdum);
1261 }
1262
1263 if (file_version >= 93)
1264 {
1265 gmx_fio_do_int(fio, ir->ljpme_combination_rule);
1266 }
1267 gmx_fio_do_gmx_bool(fio, ir->bContinuation);
1268 gmx_fio_do_int(fio, ir->etc);
1269 /* before version 18, ir->etc was a gmx_bool (ir->btc),
1270 * but the values 0 and 1 still mean no and
1271 * berendsen temperature coupling, respectively.
1272 */
1273 if (file_version >= 79)
1274 {
1275 gmx_fio_do_gmx_bool(fio, ir->bPrintNHChains);
1276 }
1277 if (file_version >= 71)
1278 {
1279 gmx_fio_do_int(fio, ir->nsttcouple);
1280 }
1281 else
1282 {
1283 ir->nsttcouple = ir->nstcalcenergy;
1284 }
1285 gmx_fio_do_int(fio, ir->epc);
1286 gmx_fio_do_int(fio, ir->epct);
1287 if (file_version >= 71)
1288 {
1289 gmx_fio_do_int(fio, ir->nstpcouple);
1290 }
1291 else
1292 {
1293 ir->nstpcouple = ir->nstcalcenergy;
1294 }
1295 gmx_fio_do_real(fio, ir->tau_p);
1296 gmx_fio_do_rvec(fio, ir->ref_p[XX]);
1297 gmx_fio_do_rvec(fio, ir->ref_p[YY]);
1298 gmx_fio_do_rvec(fio, ir->ref_p[ZZ]);
1299 gmx_fio_do_rvec(fio, ir->compress[XX]);
1300 gmx_fio_do_rvec(fio, ir->compress[YY]);
1301 gmx_fio_do_rvec(fio, ir->compress[ZZ]);
1302 gmx_fio_do_int(fio, ir->refcoord_scaling);
1303 gmx_fio_do_rvec(fio, ir->posres_com);
1304 gmx_fio_do_rvec(fio, ir->posres_comB);
1305
1306 if (file_version < 79)
1307 {
1308 gmx_fio_do_int(fio, ir->andersen_seed);
1309 }
1310 else
1311 {
1312 ir->andersen_seed = 0;
1313 }
1314
1315 gmx_fio_do_real(fio, ir->shake_tol);
1316
1317 gmx_fio_do_int(fio, ir->efep);
1318 do_fepvals(fio, ir->fepvals, bRead, file_version);
1319
1320 if (file_version >= 79)
1321 {
1322 gmx_fio_do_gmx_bool(fio, ir->bSimTemp);
1323 if (ir->bSimTemp)
1324 {
1325 ir->bSimTemp = TRUE;
1326 }
1327 }
1328 else
1329 {
1330 ir->bSimTemp = FALSE;
1331 }
1332 if (ir->bSimTemp)
1333 {
1334 do_simtempvals(fio, ir->simtempvals, ir->fepvals->n_lambda, bRead, file_version);
1335 }
1336
1337 if (file_version >= 79)
1338 {
1339 gmx_fio_do_gmx_bool(fio, ir->bExpanded);
1340 if (ir->bExpanded)
1341 {
1342 ir->bExpanded = TRUE;
1343 }
1344 else
1345 {
1346 ir->bExpanded = FALSE;
1347 }
1348 }
1349 if (ir->bExpanded)
1350 {
1351 do_expandedvals(fio, ir->expandedvals, ir->fepvals, bRead, file_version);
1352 }
1353
1354 gmx_fio_do_int(fio, ir->eDisre);
1355 gmx_fio_do_int(fio, ir->eDisreWeighting);
1356 gmx_fio_do_gmx_bool(fio, ir->bDisreMixed);
1357 gmx_fio_do_real(fio, ir->dr_fc);
1358 gmx_fio_do_real(fio, ir->dr_tau);
1359 gmx_fio_do_int(fio, ir->nstdisreout);
1360 gmx_fio_do_real(fio, ir->orires_fc);
1361 gmx_fio_do_real(fio, ir->orires_tau);
1362 gmx_fio_do_int(fio, ir->nstorireout);
1363
1364 /* ignore dihre_fc */
1365 if (file_version < 79)
1366 {
1367 gmx_fio_do_real(fio, rdum);
1368 }
1369
1370 gmx_fio_do_real(fio, ir->em_stepsize);
1371 gmx_fio_do_real(fio, ir->em_tol);
1372 gmx_fio_do_gmx_bool(fio, ir->bShakeSOR);
1373 gmx_fio_do_int(fio, ir->niter);
1374 gmx_fio_do_real(fio, ir->fc_stepsize);
1375 gmx_fio_do_int(fio, ir->eConstrAlg);
1376 gmx_fio_do_int(fio, ir->nProjOrder);
1377 gmx_fio_do_real(fio, ir->LincsWarnAngle);
1378 gmx_fio_do_int(fio, ir->nLincsIter);
1379 gmx_fio_do_real(fio, ir->bd_fric);
1380 if (file_version >= tpxv_Use64BitRandomSeed)
1381 {
1382 gmx_fio_do_int64(fio, ir->ld_seed);
1383 }
1384 else
1385 {
1386 gmx_fio_do_int(fio, idum);
1387 ir->ld_seed = idum;
1388 }
1389
1390 for (i = 0; i < DIM; i++)
1391 {
1392 gmx_fio_do_rvec(fio, ir->deform[i]);
1393 }
1394 gmx_fio_do_real(fio, ir->cos_accel);
1395
1396 gmx_fio_do_int(fio, ir->userint1);
1397 gmx_fio_do_int(fio, ir->userint2);
1398 gmx_fio_do_int(fio, ir->userint3);
1399 gmx_fio_do_int(fio, ir->userint4);
1400 gmx_fio_do_real(fio, ir->userreal1);
1401 gmx_fio_do_real(fio, ir->userreal2);
1402 gmx_fio_do_real(fio, ir->userreal3);
1403 gmx_fio_do_real(fio, ir->userreal4);
1404
1405 /* AdResS is removed, but we need to be able to read old files,
1406 and let mdrun refuse to run them */
1407 if (file_version >= 77 && file_version < tpxv_RemoveAdress)
1408 {
1409 gmx_fio_do_gmx_bool(fio, ir->bAdress);
1410 if (ir->bAdress)
1411 {
1412 int idum, numThermoForceGroups, numEnergyGroups;
1413 real rdum;
1414 rvec rvecdum;
1415 gmx_fio_do_int(fio, idum);
1416 gmx_fio_do_real(fio, rdum);
1417 gmx_fio_do_real(fio, rdum);
1418 gmx_fio_do_real(fio, rdum);
1419 gmx_fio_do_int(fio, idum);
1420 gmx_fio_do_int(fio, idum);
1421 gmx_fio_do_rvec(fio, rvecdum);
1422 gmx_fio_do_int(fio, numThermoForceGroups);
1423 gmx_fio_do_real(fio, rdum);
1424 gmx_fio_do_int(fio, numEnergyGroups);
1425 gmx_fio_do_int(fio, idum);
1426
1427 if (numThermoForceGroups > 0)
1428 {
1429 std::vector<int> idumn(numThermoForceGroups);
1430 gmx_fio_ndo_int(fio, idumn.data(), idumn.size());
1431 }
1432 if (numEnergyGroups > 0)
1433 {
1434 std::vector<int> idumn(numEnergyGroups);
1435 gmx_fio_ndo_int(fio, idumn.data(), idumn.size());
1436 }
1437 }
1438 }
1439 else
1440 {
1441 ir->bAdress = FALSE;
1442 }
1443
1444 /* pull stuff */
1445 {
1446 int ePullOld = 0;
1447
1448 if (file_version >= tpxv_PullCoordTypeGeom)
1449 {
1450 gmx_fio_do_gmx_bool(fio, ir->bPull);
1451 }
1452 else
1453 {
1454 gmx_fio_do_int(fio, ePullOld);
1455 ir->bPull = (ePullOld > 0);
1456 /* We removed the first ePull=ePullNo for the enum */
1457 ePullOld -= 1;
1458 }
1459 if (ir->bPull)
1460 {
1461 if (bRead)
1462 {
1463 snew(ir->pull, 1);
1464 }
1465 do_pull(fio, ir->pull, bRead, file_version, ePullOld);
1466 }
1467 }
1468
1469 if (file_version >= tpxv_AcceleratedWeightHistogram)
1470 {
1471 gmx_fio_do_gmx_bool(fio, ir->bDoAwh);
1472
1473 if (ir->bDoAwh)
1474 {
1475 if (bRead)
1476 {
1477 snew(ir->awhParams, 1);
1478 }
1479 do_awh(fio, ir->awhParams, bRead, file_version);
1480 }
1481 }
1482 else
1483 {
1484 ir->bDoAwh = FALSE;
1485 }
1486
1487 /* Enforced rotation */
1488 if (file_version >= 74)
1489 {
1490 gmx_fio_do_gmx_bool(fio, ir->bRot);
1491 if (ir->bRot)
1492 {
1493 if (bRead)
1494 {
1495 snew(ir->rot, 1);
1496 }
1497 do_rot(fio, ir->rot, bRead);
1498 }
1499 }
1500 else
1501 {
1502 ir->bRot = FALSE;
1503 }
1504
1505 /* Interactive molecular dynamics */
1506 if (file_version >= tpxv_InteractiveMolecularDynamics)
1507 {
1508 gmx_fio_do_gmx_bool(fio, ir->bIMD);
1509 if (ir->bIMD)
1510 {
1511 if (bRead)
1512 {
1513 snew(ir->imd, 1);
1514 }
1515 do_imd(fio, ir->imd, bRead);
1516 }
1517 }
1518 else
1519 {
1520 /* We don't support IMD sessions for old .tpr files */
1521 ir->bIMD = FALSE;
1522 }
1523
1524 /* grpopts stuff */
1525 gmx_fio_do_int(fio, ir->opts.ngtc);
1526 if (file_version >= 69)
1527 {
1528 gmx_fio_do_int(fio, ir->opts.nhchainlength);
1529 }
1530 else
1531 {
1532 ir->opts.nhchainlength = 1;
1533 }
1534 gmx_fio_do_int(fio, ir->opts.ngacc);
1535 gmx_fio_do_int(fio, ir->opts.ngfrz);
1536 gmx_fio_do_int(fio, ir->opts.ngener);
1537
1538 if (bRead)
1539 {
1540 snew(ir->opts.nrdf, ir->opts.ngtc);
1541 snew(ir->opts.ref_t, ir->opts.ngtc);
1542 snew(ir->opts.annealing, ir->opts.ngtc);
1543 snew(ir->opts.anneal_npoints, ir->opts.ngtc);
1544 snew(ir->opts.anneal_time, ir->opts.ngtc);
1545 snew(ir->opts.anneal_temp, ir->opts.ngtc);
1546 snew(ir->opts.tau_t, ir->opts.ngtc);
1547 snew(ir->opts.nFreeze, ir->opts.ngfrz);
1548 snew(ir->opts.acc, ir->opts.ngacc);
1549 snew(ir->opts.egp_flags, ir->opts.ngener*ir->opts.ngener);
1550 }
1551 if (ir->opts.ngtc > 0)
1552 {
1553 gmx_fio_ndo_real(fio, ir->opts.nrdf, ir->opts.ngtc);
1554 gmx_fio_ndo_real(fio, ir->opts.ref_t, ir->opts.ngtc);
1555 gmx_fio_ndo_real(fio, ir->opts.tau_t, ir->opts.ngtc);
1556 }
1557 if (ir->opts.ngfrz > 0)
1558 {
1559 gmx_fio_ndo_ivec(fio, ir->opts.nFreeze, ir->opts.ngfrz);
1560 }
1561 if (ir->opts.ngacc > 0)
1562 {
1563 gmx_fio_ndo_rvec(fio, ir->opts.acc, ir->opts.ngacc);
1564 }
1565 gmx_fio_ndo_int(fio, ir->opts.egp_flags,
1566 ir->opts.ngener*ir->opts.ngener);
1567
1568 /* First read the lists with annealing and npoints for each group */
1569 gmx_fio_ndo_int(fio, ir->opts.annealing, ir->opts.ngtc);
1570 gmx_fio_ndo_int(fio, ir->opts.anneal_npoints, ir->opts.ngtc);
1571 for (j = 0; j < (ir->opts.ngtc); j++)
1572 {
1573 k = ir->opts.anneal_npoints[j];
1574 if (bRead)
1575 {
1576 snew(ir->opts.anneal_time[j], k);
1577 snew(ir->opts.anneal_temp[j], k);
1578 }
1579 gmx_fio_ndo_real(fio, ir->opts.anneal_time[j], k);
1580 gmx_fio_ndo_real(fio, ir->opts.anneal_temp[j], k);
1581 }
1582 /* Walls */
1583 {
1584 gmx_fio_do_int(fio, ir->nwall);
1585 gmx_fio_do_int(fio, ir->wall_type);
1586 gmx_fio_do_real(fio, ir->wall_r_linpot);
1587 gmx_fio_do_int(fio, ir->wall_atomtype[0]);
1588 gmx_fio_do_int(fio, ir->wall_atomtype[1]);
1589 gmx_fio_do_real(fio, ir->wall_density[0]);
1590 gmx_fio_do_real(fio, ir->wall_density[1]);
1591 gmx_fio_do_real(fio, ir->wall_ewald_zfac);
1592 }
1593
1594 /* Cosine stuff for electric fields */
1595 if (file_version < tpxv_GenericParamsForElectricField)
1596 {
1597 do_legacy_efield(fio, &paramsObj);
1598 }
1599
1600 /* Swap ions */
1601 if (file_version >= tpxv_ComputationalElectrophysiology)
1602 {
1603 gmx_fio_do_int(fio, ir->eSwapCoords);
1604 if (ir->eSwapCoords != eswapNO)
1605 {
1606 if (bRead)
1607 {
1608 snew(ir->swap, 1);
1609 }
1610 do_swapcoords_tpx(fio, ir->swap, bRead, file_version);
1611 }
1612 }
1613
1614 /* QMMM stuff */
1615 {
1616 gmx_fio_do_gmx_bool(fio, ir->bQMMM);
1617 gmx_fio_do_int(fio, ir->QMMMscheme);
1618 gmx_fio_do_real(fio, ir->scalefactor);
1619 gmx_fio_do_int(fio, ir->opts.ngQM);
1620 if (bRead)
1621 {
1622 snew(ir->opts.QMmethod, ir->opts.ngQM);
1623 snew(ir->opts.QMbasis, ir->opts.ngQM);
1624 snew(ir->opts.QMcharge, ir->opts.ngQM);
1625 snew(ir->opts.QMmult, ir->opts.ngQM);
1626 snew(ir->opts.bSH, ir->opts.ngQM);
1627 snew(ir->opts.CASorbitals, ir->opts.ngQM);
1628 snew(ir->opts.CASelectrons, ir->opts.ngQM);
1629 snew(ir->opts.SAon, ir->opts.ngQM);
1630 snew(ir->opts.SAoff, ir->opts.ngQM);
1631 snew(ir->opts.SAsteps, ir->opts.ngQM);
1632 }
1633 if (ir->opts.ngQM > 0 && ir->bQMMM)
1634 {
1635 gmx_fio_ndo_int(fio, ir->opts.QMmethod, ir->opts.ngQM);
1636 gmx_fio_ndo_int(fio, ir->opts.QMbasis, ir->opts.ngQM);
1637 gmx_fio_ndo_int(fio, ir->opts.QMcharge, ir->opts.ngQM);
1638 gmx_fio_ndo_int(fio, ir->opts.QMmult, ir->opts.ngQM);
1639 gmx_fio_ndo_gmx_bool(fio, ir->opts.bSH, ir->opts.ngQM);
1640 gmx_fio_ndo_int(fio, ir->opts.CASorbitals, ir->opts.ngQM);
1641 gmx_fio_ndo_int(fio, ir->opts.CASelectrons, ir->opts.ngQM);
1642 gmx_fio_ndo_real(fio, ir->opts.SAon, ir->opts.ngQM);
1643 gmx_fio_ndo_real(fio, ir->opts.SAoff, ir->opts.ngQM);
1644 gmx_fio_ndo_int(fio, ir->opts.SAsteps, ir->opts.ngQM);
1645 /* We leave in dummy i/o for removed parameters to avoid
1646 * changing the tpr format for every QMMM change.
1647 */
1648 std::vector<int> dummy(ir->opts.ngQM, 0);
1649 gmx_fio_ndo_int(fio, dummy.data(), ir->opts.ngQM);
1650 gmx_fio_ndo_int(fio, dummy.data(), ir->opts.ngQM);
1651 }
1652 /* end of QMMM stuff */
1653 }
1654
1655 if (file_version >= tpxv_GenericParamsForElectricField)
1656 {
1657 gmx::FileIOXdrSerializer serializer(fio);
1658 if (bRead)
1659 {
1660 paramsObj.mergeObject(
1661 gmx::deserializeKeyValueTree(&serializer));
1662 }
1663 else
1664 {
1665 GMX_RELEASE_ASSERT(ir->params != nullptr,
1666 "Parameters should be present when writing inputrec");
1667 gmx::serializeKeyValueTree(*ir->params, &serializer);
1668 }
1669 }
1670 if (bRead)
1671 {
1672 ir->params = new gmx::KeyValueTreeObject(paramsBuilder.build());
1673 }
1674 }
1675
1676
1677 static void do_harm(t_fileio *fio, t_iparams *iparams)
1678 {
1679 gmx_fio_do_real(fio, iparams->harmonic.rA);
1680 gmx_fio_do_real(fio, iparams->harmonic.krA);
1681 gmx_fio_do_real(fio, iparams->harmonic.rB);
1682 gmx_fio_do_real(fio, iparams->harmonic.krB);
1683 }
1684
1685 static void do_iparams(t_fileio *fio, t_functype ftype, t_iparams *iparams,
1686 gmx_bool bRead, int file_version)
1687 {
1688 int idum;
1689 real rdum;
1690
1691 switch (ftype)
1692 {
1693 case F_ANGLES:
1694 case F_G96ANGLES:
1695 case F_BONDS:
1696 case F_G96BONDS:
1697 case F_HARMONIC:
1698 case F_IDIHS:
1699 do_harm(fio, iparams);
1700 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && bRead)
1701 {
1702 /* Correct incorrect storage of parameters */
1703 iparams->pdihs.phiB = iparams->pdihs.phiA;
1704 iparams->pdihs.cpB = iparams->pdihs.cpA;
1705 }
1706 break;
1707 case F_RESTRANGLES:
1708 gmx_fio_do_real(fio, iparams->harmonic.rA);
1709 gmx_fio_do_real(fio, iparams->harmonic.krA);
1710 break;
1711 case F_LINEAR_ANGLES:
1712 gmx_fio_do_real(fio, iparams->linangle.klinA);
1713 gmx_fio_do_real(fio, iparams->linangle.aA);
1714 gmx_fio_do_real(fio, iparams->linangle.klinB);
1715 gmx_fio_do_real(fio, iparams->linangle.aB);
1716 break;
1717 case F_FENEBONDS:
1718 gmx_fio_do_real(fio, iparams->fene.bm);
1719 gmx_fio_do_real(fio, iparams->fene.kb);
1720 break;
1721
1722 case F_RESTRBONDS:
1723 gmx_fio_do_real(fio, iparams->restraint.lowA);
1724 gmx_fio_do_real(fio, iparams->restraint.up1A);
1725 gmx_fio_do_real(fio, iparams->restraint.up2A);
1726 gmx_fio_do_real(fio, iparams->restraint.kA);
1727 gmx_fio_do_real(fio, iparams->restraint.lowB);
1728 gmx_fio_do_real(fio, iparams->restraint.up1B);
1729 gmx_fio_do_real(fio, iparams->restraint.up2B);
1730 gmx_fio_do_real(fio, iparams->restraint.kB);
1731 break;
1732 case F_TABBONDS:
1733 case F_TABBONDSNC:
1734 case F_TABANGLES:
1735 case F_TABDIHS:
1736 gmx_fio_do_real(fio, iparams->tab.kA);
1737 gmx_fio_do_int(fio, iparams->tab.table);
1738 gmx_fio_do_real(fio, iparams->tab.kB);
1739 break;
1740 case F_CROSS_BOND_BONDS:
1741 gmx_fio_do_real(fio, iparams->cross_bb.r1e);
1742 gmx_fio_do_real(fio, iparams->cross_bb.r2e);
1743 gmx_fio_do_real(fio, iparams->cross_bb.krr);
1744 break;
1745 case F_CROSS_BOND_ANGLES:
1746 gmx_fio_do_real(fio, iparams->cross_ba.r1e);
1747 gmx_fio_do_real(fio, iparams->cross_ba.r2e);
1748 gmx_fio_do_real(fio, iparams->cross_ba.r3e);
1749 gmx_fio_do_real(fio, iparams->cross_ba.krt);
1750 break;
1751 case F_UREY_BRADLEY:
1752 gmx_fio_do_real(fio, iparams->u_b.thetaA);
1753 gmx_fio_do_real(fio, iparams->u_b.kthetaA);
1754 gmx_fio_do_real(fio, iparams->u_b.r13A);
1755 gmx_fio_do_real(fio, iparams->u_b.kUBA);
1756 if (file_version >= 79)
1757 {
1758 gmx_fio_do_real(fio, iparams->u_b.thetaB);
1759 gmx_fio_do_real(fio, iparams->u_b.kthetaB);
1760 gmx_fio_do_real(fio, iparams->u_b.r13B);
1761 gmx_fio_do_real(fio, iparams->u_b.kUBB);
1762 }
1763 else
1764 {
1765 iparams->u_b.thetaB = iparams->u_b.thetaA;
1766 iparams->u_b.kthetaB = iparams->u_b.kthetaA;
1767 iparams->u_b.r13B = iparams->u_b.r13A;
1768 iparams->u_b.kUBB = iparams->u_b.kUBA;
1769 }
1770 break;
1771 case F_QUARTIC_ANGLES:
1772 gmx_fio_do_real(fio, iparams->qangle.theta);
1773 gmx_fio_ndo_real(fio, iparams->qangle.c, 5);
1774 break;
1775 case F_BHAM:
1776 gmx_fio_do_real(fio, iparams->bham.a);
1777 gmx_fio_do_real(fio, iparams->bham.b);
1778 gmx_fio_do_real(fio, iparams->bham.c);
1779 break;
1780 case F_MORSE:
1781 gmx_fio_do_real(fio, iparams->morse.b0A);
1782 gmx_fio_do_real(fio, iparams->morse.cbA);
1783 gmx_fio_do_real(fio, iparams->morse.betaA);
1784 if (file_version >= 79)
1785 {
1786 gmx_fio_do_real(fio, iparams->morse.b0B);
1787 gmx_fio_do_real(fio, iparams->morse.cbB);
1788 gmx_fio_do_real(fio, iparams->morse.betaB);
1789 }
1790 else
1791 {
1792 iparams->morse.b0B = iparams->morse.b0A;
1793 iparams->morse.cbB = iparams->morse.cbA;
1794 iparams->morse.betaB = iparams->morse.betaA;
1795 }
1796 break;
1797 case F_CUBICBONDS:
1798 gmx_fio_do_real(fio, iparams->cubic.b0);
1799 gmx_fio_do_real(fio, iparams->cubic.kb);
1800 gmx_fio_do_real(fio, iparams->cubic.kcub);
1801 break;
1802 case F_CONNBONDS:
1803 break;
1804 case F_POLARIZATION:
1805 gmx_fio_do_real(fio, iparams->polarize.alpha);
1806 break;
1807 case F_ANHARM_POL:
1808 gmx_fio_do_real(fio, iparams->anharm_polarize.alpha);
1809 gmx_fio_do_real(fio, iparams->anharm_polarize.drcut);
1810 gmx_fio_do_real(fio, iparams->anharm_polarize.khyp);
1811 break;
1812 case F_WATER_POL:
1813 gmx_fio_do_real(fio, iparams->wpol.al_x);
1814 gmx_fio_do_real(fio, iparams->wpol.al_y);
1815 gmx_fio_do_real(fio, iparams->wpol.al_z);
1816 gmx_fio_do_real(fio, iparams->wpol.rOH);
1817 gmx_fio_do_real(fio, iparams->wpol.rHH);
1818 gmx_fio_do_real(fio, iparams->wpol.rOD);
1819 break;
1820 case F_THOLE_POL:
1821 gmx_fio_do_real(fio, iparams->thole.a);
1822 gmx_fio_do_real(fio, iparams->thole.alpha1);
1823 gmx_fio_do_real(fio, iparams->thole.alpha2);
1824 gmx_fio_do_real(fio, iparams->thole.rfac);
1825 break;
1826 case F_LJ:
1827 gmx_fio_do_real(fio, iparams->lj.c6);
1828 gmx_fio_do_real(fio, iparams->lj.c12);
1829 break;
1830 case F_LJ14:
1831 gmx_fio_do_real(fio, iparams->lj14.c6A);
1832 gmx_fio_do_real(fio, iparams->lj14.c12A);
1833 gmx_fio_do_real(fio, iparams->lj14.c6B);
1834 gmx_fio_do_real(fio, iparams->lj14.c12B);
1835 break;
1836 case F_LJC14_Q:
1837 gmx_fio_do_real(fio, iparams->ljc14.fqq);
1838 gmx_fio_do_real(fio, iparams->ljc14.qi);
1839 gmx_fio_do_real(fio, iparams->ljc14.qj);
1840 gmx_fio_do_real(fio, iparams->ljc14.c6);
1841 gmx_fio_do_real(fio, iparams->ljc14.c12);
1842 break;
1843 case F_LJC_PAIRS_NB:
1844 gmx_fio_do_real(fio, iparams->ljcnb.qi);
1845 gmx_fio_do_real(fio, iparams->ljcnb.qj);
1846 gmx_fio_do_real(fio, iparams->ljcnb.c6);
1847 gmx_fio_do_real(fio, iparams->ljcnb.c12);
1848 break;
1849 case F_PDIHS:
1850 case F_PIDIHS:
1851 case F_ANGRES:
1852 case F_ANGRESZ:
1853 gmx_fio_do_real(fio, iparams->pdihs.phiA);
1854 gmx_fio_do_real(fio, iparams->pdihs.cpA);
1855 gmx_fio_do_real(fio, iparams->pdihs.phiB);
1856 gmx_fio_do_real(fio, iparams->pdihs.cpB);
1857 gmx_fio_do_int(fio, iparams->pdihs.mult);
1858 break;
1859 case F_RESTRDIHS:
1860 gmx_fio_do_real(fio, iparams->pdihs.phiA);
1861 gmx_fio_do_real(fio, iparams->pdihs.cpA);
1862 break;
1863 case F_DISRES:
1864 gmx_fio_do_int(fio, iparams->disres.label);
1865 gmx_fio_do_int(fio, iparams->disres.type);
1866 gmx_fio_do_real(fio, iparams->disres.low);
1867 gmx_fio_do_real(fio, iparams->disres.up1);
1868 gmx_fio_do_real(fio, iparams->disres.up2);
1869 gmx_fio_do_real(fio, iparams->disres.kfac);
1870 break;
1871 case F_ORIRES:
1872 gmx_fio_do_int(fio, iparams->orires.ex);
1873 gmx_fio_do_int(fio, iparams->orires.label);
1874 gmx_fio_do_int(fio, iparams->orires.power);
1875 gmx_fio_do_real(fio, iparams->orires.c);
1876 gmx_fio_do_real(fio, iparams->orires.obs);
1877 gmx_fio_do_real(fio, iparams->orires.kfac);
1878 break;
1879 case F_DIHRES:
1880 if (file_version < 82)
1881 {
1882 gmx_fio_do_int(fio, idum);
1883 gmx_fio_do_int(fio, idum);
1884 }
1885 gmx_fio_do_real(fio, iparams->dihres.phiA);
1886 gmx_fio_do_real(fio, iparams->dihres.dphiA);
1887 gmx_fio_do_real(fio, iparams->dihres.kfacA);
1888 if (file_version >= 82)
1889 {
1890 gmx_fio_do_real(fio, iparams->dihres.phiB);
1891 gmx_fio_do_real(fio, iparams->dihres.dphiB);
1892 gmx_fio_do_real(fio, iparams->dihres.kfacB);
1893 }
1894 else
1895 {
1896 iparams->dihres.phiB = iparams->dihres.phiA;
1897 iparams->dihres.dphiB = iparams->dihres.dphiA;
1898 iparams->dihres.kfacB = iparams->dihres.kfacA;
1899 }
1900 break;
1901 case F_POSRES:
1902 gmx_fio_do_rvec(fio, iparams->posres.pos0A);
1903 gmx_fio_do_rvec(fio, iparams->posres.fcA);
1904 gmx_fio_do_rvec(fio, iparams->posres.pos0B);
1905 gmx_fio_do_rvec(fio, iparams->posres.fcB);
1906 break;
1907 case F_FBPOSRES:
1908 gmx_fio_do_int(fio, iparams->fbposres.geom);
1909 gmx_fio_do_rvec(fio, iparams->fbposres.pos0);
1910 gmx_fio_do_real(fio, iparams->fbposres.r);
1911 gmx_fio_do_real(fio, iparams->fbposres.k);
1912 break;
1913 case F_CBTDIHS:
1914 gmx_fio_ndo_real(fio, iparams->cbtdihs.cbtcA, NR_CBTDIHS);
1915 break;
1916 case F_RBDIHS:
1917 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
1918 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
1919 break;
1920 case F_FOURDIHS:
1921 /* Fourier dihedrals are internally represented
1922 * as Ryckaert-Bellemans since those are faster to compute.
1923 */
1924 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
1925 gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
1926 break;
1927 case F_CONSTR:
1928 case F_CONSTRNC:
1929 gmx_fio_do_real(fio, iparams->constr.dA);
1930 gmx_fio_do_real(fio, iparams->constr.dB);
1931 break;
1932 case F_SETTLE:
1933 gmx_fio_do_real(fio, iparams->settle.doh);
1934 gmx_fio_do_real(fio, iparams->settle.dhh);
1935 break;
1936 case F_VSITE2:
1937 gmx_fio_do_real(fio, iparams->vsite.a);
1938 break;
1939 case F_VSITE3:
1940 case F_VSITE3FD:
1941 case F_VSITE3FAD:
1942 gmx_fio_do_real(fio, iparams->vsite.a);
1943 gmx_fio_do_real(fio, iparams->vsite.b);
1944 break;
1945 case F_VSITE3OUT:
1946 case F_VSITE4FD:
1947 case F_VSITE4FDN:
1948 gmx_fio_do_real(fio, iparams->vsite.a);
1949 gmx_fio_do_real(fio, iparams->vsite.b);
1950 gmx_fio_do_real(fio, iparams->vsite.c);
1951 break;
1952 case F_VSITEN:
1953 gmx_fio_do_int(fio, iparams->vsiten.n);
1954 gmx_fio_do_real(fio, iparams->vsiten.a);
1955 break;
1956 case F_GB12_NOLONGERUSED:
1957 case F_GB13_NOLONGERUSED:
1958 case F_GB14_NOLONGERUSED:
1959 // Implicit solvent parameters can still be read, but never used
1960 if (bRead)
1961 {
1962 if (file_version < 68)
1963 {
1964 gmx_fio_do_real(fio, rdum);
1965 gmx_fio_do_real(fio, rdum);
1966 gmx_fio_do_real(fio, rdum);
1967 gmx_fio_do_real(fio, rdum);
1968 }
1969 if (file_version < tpxv_RemoveImplicitSolvation)
1970 {
1971 gmx_fio_do_real(fio, rdum);
1972 gmx_fio_do_real(fio, rdum);
1973 gmx_fio_do_real(fio, rdum);
1974 gmx_fio_do_real(fio, rdum);
1975 gmx_fio_do_real(fio, rdum);
1976 }
1977 }
1978 break;
1979 case F_CMAP:
1980 gmx_fio_do_int(fio, iparams->cmap.cmapA);
1981 gmx_fio_do_int(fio, iparams->cmap.cmapB);
1982 break;
1983 default:
1984 gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
1985 ftype, interaction_function[ftype].name, __FILE__, __LINE__);
1986 }
1987 }
1988
1989 static void do_ilist(t_fileio *fio, InteractionList *ilist, gmx_bool bRead)
1990 {
1991 int nr = ilist->size();
1992 gmx_fio_do_int(fio, nr);
1993 if (bRead)
1994 {
1995 ilist->iatoms.resize(nr);
1996 }
1997 gmx_fio_ndo_int(fio, ilist->iatoms.data(), ilist->size());
1998 }
1999
2000 static void do_ffparams(t_fileio *fio, gmx_ffparams_t *ffparams,
2001 gmx_bool bRead, int file_version)
2002 {
2003 gmx_fio_do_int(fio, ffparams->atnr);
2004 int numTypes = ffparams->numTypes();
2005 gmx_fio_do_int(fio, numTypes);
2006 if (bRead)
2007 {
2008 ffparams->functype.resize(numTypes);
2009 ffparams->iparams.resize(numTypes);
2010 }
2011 /* Read/write all the function types */
2012 gmx_fio_ndo_int(fio, ffparams->functype.data(), ffparams->functype.size());
2013
2014 if (file_version >= 66)
2015 {
2016 gmx_fio_do_double(fio, ffparams->reppow);
2017 }
2018 else
2019 {
2020 ffparams->reppow = 12.0;
2021 }
2022
2023 gmx_fio_do_real(fio, ffparams->fudgeQQ);
2024
2025 /* Check whether all these function types are supported by the code.
2026 * In practice the code is backwards compatible, which means that the
2027 * numbering may have to be altered from old numbering to new numbering
2028 */
2029 for (int i = 0; i < ffparams->numTypes(); i++)
2030 {
2031 if (bRead)
2032 {
2033 /* Loop over file versions */
2034 for (int k = 0; k < NFTUPD; k++)
2035 {
2036 /* Compare the read file_version to the update table */
2037 if ((file_version < ftupd[k].fvnr) &&
2038 (ffparams->functype[i] >= ftupd[k].ftype))
2039 {
2040 ffparams->functype[i] += 1;
2041 }
2042 }
2043 }
2044
2045 do_iparams(fio, ffparams->functype[i], &ffparams->iparams[i], bRead,
2046 file_version);
2047 }
2048 }
2049
2050 static void add_settle_atoms(InteractionList *ilist)
2051 {
2052 int i;
2053
2054 /* Settle used to only store the first atom: add the other two */
2055 ilist->iatoms.resize(2*ilist->size());
2056 for (i = ilist->size()/4 - 1; i >= 0; i--)
2057 {
2058 ilist->iatoms[4*i+0] = ilist->iatoms[2*i+0];
2059 ilist->iatoms[4*i+1] = ilist->iatoms[2*i+1];
2060 ilist->iatoms[4*i+2] = ilist->iatoms[2*i+1] + 1;
2061 ilist->iatoms[4*i+3] = ilist->iatoms[2*i+1] + 2;
2062 }
2063 }
2064
2065 static void do_ilists(t_fileio *fio, InteractionLists *ilists, gmx_bool bRead,
2066 int file_version)
2067 {
2068 GMX_RELEASE_ASSERT(ilists, "Need a valid ilists object");
2069 GMX_RELEASE_ASSERT(ilists->size() == F_NRE, "The code needs to be in sync with InteractionLists");
2070
2071 for (int j = 0; j < F_NRE; j++)
2072 {
2073 InteractionList &ilist = (*ilists)[j];
2074 gmx_bool bClear = FALSE;
2075 if (bRead)
2076 {
2077 for (int k = 0; k < NFTUPD; k++)
2078 {
2079 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
2080 {
2081 bClear = TRUE;
2082 }
2083 }
2084 }
2085 if (bClear)
2086 {
2087 ilist.iatoms.clear();
2088 }
2089 else
2090 {
2091 do_ilist(fio, &ilist, bRead);
2092 if (file_version < 78 && j == F_SETTLE && ilist.size() > 0)
2093 {
2094 add_settle_atoms(&ilist);
2095 }
2096 }
2097 }
2098 }
2099
2100 static void do_block(t_fileio *fio, t_block *block, gmx_bool bRead)
2101 {
2102 gmx_fio_do_int(fio, block->nr);
2103 if (bRead)
2104 {
2105 if ((block->nalloc_index > 0) && (nullptr != block->index))
2106 {
2107 sfree(block->index);
2108 }
2109 block->nalloc_index = block->nr+1;
2110 snew(block->index, block->nalloc_index);
2111 }
2112 gmx_fio_ndo_int(fio, block->index, block->nr+1);
2113 }
2114
2115 static void do_blocka(t_fileio *fio, t_blocka *block, gmx_bool bRead)
2116 {
2117 gmx_fio_do_int(fio, block->nr);
2118 gmx_fio_do_int(fio, block->nra);
2119 if (bRead)
2120 {
2121 block->nalloc_index = block->nr+1;
2122 snew(block->index, block->nalloc_index);
2123 block->nalloc_a = block->nra;
2124 snew(block->a, block->nalloc_a);
2125 }
2126 gmx_fio_ndo_int(fio, block->index, block->nr+1);
2127 gmx_fio_ndo_int(fio, block->a, block->nra);
2128 }
2129
2130 /* This is a primitive routine to make it possible to translate atomic numbers
2131 * to element names when reading TPR files, without making the Gromacs library
2132 * directory a dependency on mdrun (which is the case if we need elements.dat).
2133 */
2134 static const char *
2135 atomicnumber_to_element(int atomicnumber)
2136 {
2137 const char * p;
2138
2139 /* This does not have to be complete, so we only include elements likely
2140 * to occur in PDB files.
2141 */
2142 switch (atomicnumber)
2143 {
2144 case 1: p = "H"; break;
2145 case 5: p = "B"; break;
2146 case 6: p = "C"; break;
2147 case 7: p = "N"; break;
2148 case 8: p = "O"; break;
2149 case 9: p = "F"; break;
2150 case 11: p = "Na"; break;
2151 case 12: p = "Mg"; break;
2152 case 15: p = "P"; break;
2153 case 16: p = "S"; break;
2154 case 17: p = "Cl"; break;
2155 case 18: p = "Ar"; break;
2156 case 19: p = "K"; break;
2157 case 20: p = "Ca"; break;
2158 case 25: p = "Mn"; break;
2159 case 26: p = "Fe"; break;
2160 case 28: p = "Ni"; break;
2161 case 29: p = "Cu"; break;
2162 case 30: p = "Zn"; break;
2163 case 35: p = "Br"; break;
2164 case 47: p = "Ag"; break;
2165 default: p = ""; break;
2166 }
2167 return p;
2168 }
2169
2170
2171 static void do_atom(t_fileio *fio, t_atom *atom, gmx_bool bRead)
2172 {
2173 gmx_fio_do_real(fio, atom->m);
2174 gmx_fio_do_real(fio, atom->q);
2175 gmx_fio_do_real(fio, atom->mB);
2176 gmx_fio_do_real(fio, atom->qB);
2177 gmx_fio_do_ushort(fio, atom->type);
2178 gmx_fio_do_ushort(fio, atom->typeB);
2179 gmx_fio_do_int(fio, atom->ptype);
2180 gmx_fio_do_int(fio, atom->resind);
2181 gmx_fio_do_int(fio, atom->atomnumber);
2182 if (bRead)
2183 {
2184 /* Set element string from atomic number if present.
2185 * This routine returns an empty string if the name is not found.
2186 */
2187 std::strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
2188 /* avoid warnings about potentially unterminated string */
2189 atom->elem[3] = '\0';
2190 }
2191 }
2192
2193 static void do_grps(t_fileio *fio,
2194 gmx::ArrayRef<t_grps> grps,
2195 gmx_bool bRead)
2196 {
2197 for (auto &group : grps)
2198 {
2199 gmx_fio_do_int(fio, group.nr);
2200 if (bRead)
2201 {
2202 snew(group.nm_ind, group.nr);
2203 }
2204 gmx_fio_ndo_int(fio, group.nm_ind, group.nr);
2205 }
2206 }
2207
2208 static void do_symstr(t_fileio *fio, char ***nm, gmx_bool bRead, t_symtab *symtab)
2209 {
2210 int ls;
2211
2212 if (bRead)
2213 {
2214 gmx_fio_do_int(fio, ls);
2215 *nm = get_symtab_handle(symtab, ls);
2216 }
2217 else
2218 {
2219 ls = lookup_symtab(symtab, *nm);
2220 gmx_fio_do_int(fio, ls);
2221 }
2222 }
2223
2224 static void do_strstr(t_fileio *fio, int nstr, char ***nm, gmx_bool bRead,
2225 t_symtab *symtab)
2226 {
2227 int j;
2228
2229 for (j = 0; (j < nstr); j++)
2230 {
2231 do_symstr(fio, &(nm[j]), bRead, symtab);
2232 }
2233 }
2234
2235 static void do_resinfo(t_fileio *fio, int n, t_resinfo *ri, gmx_bool bRead,
2236 t_symtab *symtab, int file_version)
2237 {
2238 int j;
2239
2240 for (j = 0; (j < n); j++)
2241 {
2242 do_symstr(fio, &(ri[j].name), bRead, symtab);
2243 if (file_version >= 63)
2244 {
2245 gmx_fio_do_int(fio, ri[j].nr);
2246 gmx_fio_do_uchar(fio, ri[j].ic);
2247 }
2248 else
2249 {
2250 ri[j].nr = j + 1;
2251 ri[j].ic = ' ';
2252 }
2253 }
2254 }
2255
2256 static void do_atoms(t_fileio *fio, t_atoms *atoms, gmx_bool bRead, t_symtab *symtab,
2257 int file_version)
2258 {
2259 int i;
2260
2261 gmx_fio_do_int(fio, atoms->nr);
2262 gmx_fio_do_int(fio, atoms->nres);
2263 if (bRead)
2264 {
2265 /* Since we have always written all t_atom properties in the tpr file
2266 * (at least for all backward compatible versions), we don't store
2267 * but simple set the booleans here.
2268 */
2269 atoms->haveMass = TRUE;
2270 atoms->haveCharge = TRUE;
2271 atoms->haveType = TRUE;
2272 atoms->haveBState = TRUE;
2273 atoms->havePdbInfo = FALSE;
2274
2275 snew(atoms->atom, atoms->nr);
2276 snew(atoms->atomname, atoms->nr);
2277 snew(atoms->atomtype, atoms->nr);
2278 snew(atoms->atomtypeB, atoms->nr);
2279 snew(atoms->resinfo, atoms->nres);
2280 atoms->pdbinfo = nullptr;
2281 }
2282 else
2283 {
2284 GMX_RELEASE_ASSERT(atoms->haveMass && atoms->haveCharge && atoms->haveType && atoms->haveBState, "Mass, charge, atomtype and B-state parameters should be present in t_atoms when writing a tpr file");
2285 }
2286 for (i = 0; (i < atoms->nr); i++)
2287 {
2288 do_atom(fio, &atoms->atom[i], bRead);
2289 }
2290 do_strstr(fio, atoms->nr, atoms->atomname, bRead, symtab);
2291 do_strstr(fio, atoms->nr, atoms->atomtype, bRead, symtab);
2292 do_strstr(fio, atoms->nr, atoms->atomtypeB, bRead, symtab);
2293
2294 do_resinfo(fio, atoms->nres, atoms->resinfo, bRead, symtab, file_version);
2295 }
2296
2297 static void do_groups(t_fileio *fio, SimulationGroups *groups,
2298 gmx_bool bRead, t_symtab *symtab)
2299 {
2300 do_grps(fio, groups->groups, bRead);
2301 int numberOfGroupNames = groups->groupNames.size();
2302 gmx_fio_do_int(fio, numberOfGroupNames);
2303 if (bRead)
2304 {
2305 groups->groupNames.resize(numberOfGroupNames);
2306 }
2307 do_strstr(fio, numberOfGroupNames, groups->groupNames.data(), bRead, symtab);
2308 for (auto group : gmx::keysOf(groups->groupNumbers))
2309 {
2310 int numberOfGroupNumbers = groups->numberOfGroupNumbers(group);
2311 gmx_fio_do_int(fio, numberOfGroupNumbers);
2312 if (numberOfGroupNumbers != 0)
2313 {
2314 if (bRead)
2315 {
2316 groups->groupNumbers[group].resize(numberOfGroupNumbers);
2317 }
2318 gmx_fio_ndo_uchar(fio, groups->groupNumbers[group].data(), numberOfGroupNumbers);
2319 }
2320 }
2321 }
2322
2323 static void do_atomtypes(t_fileio *fio, t_atomtypes *atomtypes, gmx_bool bRead,
2324 int file_version)
2325 {
2326 int j;
2327
2328 gmx_fio_do_int(fio, atomtypes->nr);
2329 j = atomtypes->nr;
2330 if (bRead)
2331 {
2332 snew(atomtypes->atomnumber, j);
2333 }
2334 if (bRead && file_version < tpxv_RemoveImplicitSolvation)
2335 {
2336 std::vector<real> dummy(atomtypes->nr, 0);
2337 gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
2338 gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
2339 gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
2340 }
2341 gmx_fio_ndo_int(fio, atomtypes->atomnumber, j);
2342
2343 if (bRead && file_version >= 60 && file_version < tpxv_RemoveImplicitSolvation)
2344 {
2345 std::vector<real> dummy(atomtypes->nr, 0);
2346 gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
2347 gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
2348 }
2349 }
2350
2351 static void do_symtab(t_fileio *fio, t_symtab *symtab, gmx_bool bRead)
2352 {
2353 int i, nr;
2354 t_symbuf *symbuf;
2355 char buf[STRLEN];
2356
2357 gmx_fio_do_int(fio, symtab->nr);
2358 nr = symtab->nr;
2359 if (bRead)
2360 {
2361 snew(symtab->symbuf, 1);
2362 symbuf = symtab->symbuf;
2363 symbuf->bufsize = nr;
2364 snew(symbuf->buf, nr);
2365 for (i = 0; (i < nr); i++)
2366 {
2367 gmx_fio_do_string(fio, buf);
2368 symbuf->buf[i] = gmx_strdup(buf);
2369 }
2370 }
2371 else
2372 {
2373 symbuf = symtab->symbuf;
2374 while (symbuf != nullptr)
2375 {
2376 for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
2377 {
2378 gmx_fio_do_string(fio, symbuf->buf[i]);
2379 }
2380 nr -= i;
2381 symbuf = symbuf->next;
2382 }
2383 if (nr != 0)
2384 {
2385 gmx_fatal(FARGS, "nr of symtab strings left: %d", nr);
2386 }
2387 }
2388 }
2389
2390 static void do_cmap(t_fileio *fio, gmx_cmap_t *cmap_grid, gmx_bool bRead)
2391 {
2392
2393 int ngrid = cmap_grid->cmapdata.size();
2394 gmx_fio_do_int(fio, ngrid);
2395 gmx_fio_do_int(fio, cmap_grid->grid_spacing);
2396
2397 int gs = cmap_grid->grid_spacing;
2398 int nelem = gs * gs;
2399
2400 if (bRead)
2401 {
2402 cmap_grid->cmapdata.resize(ngrid);
2403
2404 for (int i = 0; i < ngrid; i++)
2405 {
2406 cmap_grid->cmapdata[i].cmap.resize(4*nelem);
2407 }
2408 }
2409
2410 for (int i = 0; i < ngrid; i++)
2411 {
2412 for (int j = 0; j < nelem; j++)
2413 {
2414 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4]);
2415 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+1]);
2416 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+2]);
2417 gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+3]);
2418 }
2419 }
2420 }
2421
2422
2423 static void do_moltype(t_fileio *fio, gmx_moltype_t *molt, gmx_bool bRead,
2424 t_symtab *symtab, int file_version)
2425 {
2426 do_symstr(fio, &(molt->name), bRead, symtab);
2427
2428 do_atoms(fio, &molt->atoms, bRead, symtab, file_version);
2429
2430 do_ilists(fio, &molt->ilist, bRead, file_version);
2431
2432 do_block(fio, &molt->cgs, bRead);
2433
2434 /* This used to be in the atoms struct */
2435 do_blocka(fio, &molt->excls, bRead);
2436 }
2437
2438 static void do_molblock(t_fileio *fio, gmx_molblock_t *molb,
2439 int numAtomsPerMolecule,
2440 gmx_bool bRead)
2441 {
2442 gmx_fio_do_int(fio, molb->type);
2443 gmx_fio_do_int(fio, molb->nmol);
2444 /* To maintain forward topology reading compatibility, we store #atoms.
2445 * TODO: Change this to conditional reading of a dummy int when we
2446 * increase tpx_generation.
2447 */
2448 gmx_fio_do_int(fio, numAtomsPerMolecule);
2449 /* Position restraint coordinates */
2450 int numPosres_xA = molb->posres_xA.size();
2451 gmx_fio_do_int(fio, numPosres_xA);
2452 if (numPosres_xA > 0)
2453 {
2454 if (bRead)
2455 {
2456 molb->posres_xA.resize(numPosres_xA);
2457 }
2458 gmx_fio_ndo_rvec(fio, as_rvec_array(molb->posres_xA.data()), numPosres_xA);
2459 }
2460 int numPosres_xB = molb->posres_xB.size();
2461 gmx_fio_do_int(fio, numPosres_xB);
2462 if (numPosres_xB > 0)
2463 {
2464 if (bRead)
2465 {
2466 molb->posres_xB.resize(numPosres_xB);
2467 }
2468 gmx_fio_ndo_rvec(fio, as_rvec_array(molb->posres_xB.data()), numPosres_xB);
2469 }
2470
2471 }
2472
2473 static void set_disres_npair(gmx_mtop_t *mtop)
2474 {
2475 gmx_mtop_ilistloop_t iloop;
2476 int nmol;
2477
2478 gmx::ArrayRef<t_iparams> ip = mtop->ffparams.iparams;
2479
2480 iloop = gmx_mtop_ilistloop_init(mtop);
2481 while (const InteractionLists *ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
2482 {
2483 const InteractionList &il = (*ilist)[F_DISRES];
2484
2485 if (il.size() > 0)
2486 {
2487 gmx::ArrayRef<const int> a = il.iatoms;
2488 int npair = 0;
2489 for (int i = 0; i < il.size(); i += 3)
2490 {
2491 npair++;
2492 if (i+3 == il.size() || ip[a[i]].disres.label != ip[a[i+3]].disres.label)
2493 {
2494 ip[a[i]].disres.npair = npair;
2495 npair = 0;
2496 }
2497 }
2498 }
2499 }
2500 }
2501
2502 static void do_mtop(t_fileio *fio, gmx_mtop_t *mtop, gmx_bool bRead,
2503 int file_version)
2504 {
2505 do_symtab(fio, &(mtop->symtab), bRead);
2506
2507 do_symstr(fio, &(mtop->name), bRead, &(mtop->symtab));
2508
2509 do_ffparams(fio, &mtop->ffparams, bRead, file_version);
2510
2511 int nmoltype = mtop->moltype.size();
2512 gmx_fio_do_int(fio, nmoltype);
2513 if (bRead)
2514 {
2515 mtop->moltype.resize(nmoltype);
2516 }
2517 for (gmx_moltype_t &moltype : mtop->moltype)
2518 {
2519 do_moltype(fio, &moltype, bRead, &mtop->symtab, file_version);
2520 }
2521
2522 int nmolblock = mtop->molblock.size();
2523 gmx_fio_do_int(fio, nmolblock);
2524 if (bRead)
2525 {
2526 mtop->molblock.resize(nmolblock);
2527 }
2528 for (gmx_molblock_t &molblock : mtop->molblock)
2529 {
2530 int numAtomsPerMolecule = (bRead ? 0 : mtop->moltype[molblock.type].atoms.nr);
2531 do_molblock(fio, &molblock, numAtomsPerMolecule, bRead);
2532 }
2533 gmx_fio_do_int(fio, mtop->natoms);
2534
2535 if (file_version >= tpxv_IntermolecularBondeds)
2536 {
2537 gmx_fio_do_gmx_bool(fio, mtop->bIntermolecularInteractions);
2538 if (mtop->bIntermolecularInteractions)
2539 {
2540 if (bRead)
2541 {
2542 mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
2543 }
2544 do_ilists(fio, mtop->intermolecular_ilist.get(), bRead, file_version);
2545 }
2546 }
2547 else
2548 {
2549 mtop->bIntermolecularInteractions = FALSE;
2550 }
2551
2552 do_atomtypes (fio, &(mtop->atomtypes), bRead, file_version);
2553
2554 if (file_version >= 65)
2555 {
2556 do_cmap(fio, &mtop->ffparams.cmap_grid, bRead);
2557 }
2558 else
2559 {
2560 mtop->ffparams.cmap_grid.grid_spacing = 0;
2561 mtop->ffparams.cmap_grid.cmapdata.clear();
2562 }
2563
2564 do_groups(fio, &mtop->groups, bRead, &(mtop->symtab));
2565
2566 mtop->haveMoleculeIndices = true;
2567
2568 if (bRead)
2569 {
2570 close_symtab(&(mtop->symtab));
2571 }
2572 }
2573
2574 /* If TopOnlyOK is TRUE then we can read even future versions
2575 * of tpx files, provided the fileGeneration hasn't changed.
2576 * If it is FALSE, we need the inputrecord too, and bail out
2577 * if the file is newer than the program.
2578 *
2579 * The version and generation of the topology (see top of this file)
2580 * are returned in the two last arguments, if those arguments are non-NULL.
2581 *
2582 * If possible, we will read the inputrec even when TopOnlyOK is TRUE.
2583 */
2584 static void do_tpxheader(t_fileio *fio, gmx_bool bRead, t_tpxheader *tpx,
2585 gmx_bool TopOnlyOK, int *fileVersionPointer, int *fileGenerationPointer)
2586 {
2587 char buf[STRLEN];
2588 char file_tag[STRLEN];
2589 gmx_bool bDouble;
2590 int precision;
2591 int idum = 0;
2592 real rdum = 0;
2593 int fileVersion; /* Version number of the code that wrote the file */
2594 int fileGeneration; /* Generation version number of the code that wrote the file */
2595
2596 /* XDR binary topology file */
2597 precision = sizeof(real);
2598 if (bRead)
2599 {
2600 gmx_fio_do_string(fio, buf);
2601 if (std::strncmp(buf, "VERSION", 7) != 0)
2602 {
2603 gmx_fatal(FARGS, "Can not read file %s,\n"
2604 " this file is from a GROMACS version which is older than 2.0\n"
2605 " Make a new one with grompp or use a gro or pdb file, if possible",
2606 gmx_fio_getname(fio));
2607 }
2608 gmx_fio_do_int(fio, precision);
2609 bDouble = (precision == sizeof(double));
2610 if ((precision != sizeof(float)) && !bDouble)
2611 {
2612 gmx_fatal(FARGS, "Unknown precision in file %s: real is %d bytes "
2613 "instead of %zu or %zu",
2614 gmx_fio_getname(fio), precision, sizeof(float), sizeof(double));
2615 }
2616 gmx_fio_setprecision(fio, bDouble);
2617 fprintf(stderr, "Reading file %s, %s (%s precision)\n",
2618 gmx_fio_getname(fio), buf, bDouble ? "double" : "single");
2619 }
2620 else
2621 {
2622 snprintf(buf, STRLEN, "VERSION %s", gmx_version());
2623 gmx_fio_write_string(fio, buf);
2624 bDouble = (precision == sizeof(double));
2625 gmx_fio_setprecision(fio, bDouble);
2626 gmx_fio_do_int(fio, precision);
2627 fileVersion = tpx_version;
2628 sprintf(file_tag, "%s", tpx_tag);
2629 fileGeneration = tpx_generation;
2630 }
2631
2632 /* Check versions! */
2633 gmx_fio_do_int(fio, fileVersion);
2634
2635 /* This is for backward compatibility with development versions 77-79
2636 * where the tag was, mistakenly, placed before the generation,
2637 * which would cause a segv instead of a proper error message
2638 * when reading the topology only from tpx with <77 code.
2639 */
2640 if (fileVersion >= 77 && fileVersion <= 79)
2641 {
2642 gmx_fio_do_string(fio, file_tag);
2643 }
2644
2645 gmx_fio_do_int(fio, fileGeneration);
2646
2647 if (fileVersion >= 81)
2648 {
2649 gmx_fio_do_string(fio, file_tag);
2650 }
2651 if (bRead)
2652 {
2653 if (fileVersion < 77)
2654 {
2655 /* Versions before 77 don't have the tag, set it to release */
2656 sprintf(file_tag, "%s", TPX_TAG_RELEASE);
2657 }
2658
2659 if (std::strcmp(file_tag, tpx_tag) != 0)
2660 {
2661 fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n",
2662 file_tag, tpx_tag);
2663
2664 /* We only support reading tpx files with the same tag as the code
2665 * or tpx files with the release tag and with lower version number.
2666 */
2667 if (std::strcmp(file_tag, TPX_TAG_RELEASE) != 0 && fileVersion < tpx_version)
2668 {
2669 gmx_fatal(FARGS, "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
2670 gmx_fio_getname(fio), fileVersion, file_tag,
2671 tpx_version, tpx_tag);
2672 }
2673 }
2674 }
2675
2676 if (fileVersionPointer)
2677 {
2678 *fileVersionPointer = fileVersion;
2679 }
2680 if (fileGenerationPointer)
2681 {
2682 *fileGenerationPointer = fileGeneration;
2683 }
2684
2685 if ((fileVersion <= tpx_incompatible_version) ||
2686 ((fileVersion > tpx_version) && !TopOnlyOK) ||
2687 (fileGeneration > tpx_generation) ||
2688 tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
2689 {
2690 gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program",
2691 gmx_fio_getname(fio), fileVersion, tpx_version);
2692 }
2693
2694 gmx_fio_do_int(fio, tpx->natoms);
2695 gmx_fio_do_int(fio, tpx->ngtc);
2696
2697 if (fileVersion < 62)
2698 {
2699 gmx_fio_do_int(fio, idum);
2700 gmx_fio_do_real(fio, rdum);
2701 }
2702 if (fileVersion >= 79)
2703 {
2704 gmx_fio_do_int(fio, tpx->fep_state);
2705 }
2706 gmx_fio_do_real(fio, tpx->lambda);
2707 gmx_fio_do_gmx_bool(fio, tpx->bIr);
2708 gmx_fio_do_gmx_bool(fio, tpx->bTop);
2709 gmx_fio_do_gmx_bool(fio, tpx->bX);
2710 gmx_fio_do_gmx_bool(fio, tpx->bV);
2711 gmx_fio_do_gmx_bool(fio, tpx->bF);
2712 gmx_fio_do_gmx_bool(fio, tpx->bBox);
2713
2714 if ((fileGeneration > tpx_generation))
2715 {
2716 /* This can only happen if TopOnlyOK=TRUE */
2717 tpx->bIr = FALSE;
2718 }
2719 }
2720
2721 static int do_tpx(t_fileio *fio, gmx_bool bRead,
2722 t_inputrec *ir, t_state *state, rvec *x, rvec *v,
2723 gmx_mtop_t *mtop)
2724 {
2725 t_tpxheader tpx;
2726 gmx_bool TopOnlyOK;
2727 int ePBC;
2728 gmx_bool bPeriodicMols;
2729
2730 if (!bRead)
2731 {
2732 GMX_RELEASE_ASSERT(state != nullptr, "Cannot write a null state");
2733 GMX_RELEASE_ASSERT(x == nullptr && v == nullptr, "Passing separate x and v pointers to do_tpx() is not supported when writing");
2734
2735 tpx.natoms = state->natoms;
2736 tpx.ngtc = state->ngtc;
2737 tpx.fep_state = state->fep_state;
2738 tpx.lambda = state->lambda[efptFEP];
2739 tpx.bIr = ir != nullptr;
2740 tpx.bTop = mtop != nullptr;
2741 tpx.bX = (state->flags & (1 << estX)) != 0;
2742 tpx.bV = (state->flags & (1 << estV)) != 0;
2743 tpx.bF = FALSE;
2744 tpx.bBox = TRUE;
2745 }
2746 else
2747 {
2748 GMX_RELEASE_ASSERT(!(x == nullptr && v != nullptr), "Passing x==NULL and v!=NULL is not supported");
2749 }
2750
2751 TopOnlyOK = (ir == nullptr);
2752
2753 int fileVersion; /* Version number of the code that wrote the file */
2754 int fileGeneration; /* Generation version number of the code that wrote the file */
2755 do_tpxheader(fio, bRead, &tpx, TopOnlyOK, &fileVersion, &fileGeneration);
2756
2757 if (bRead)
2758 {
2759 state->flags = 0;
2760 init_gtc_state(state, tpx.ngtc, 0, 0);
2761 if (x == nullptr)
2762 {
2763 // v is also nullptr by the above assertion, so we may
2764 // need to make memory in state for storing the contents
2765 // of the tpx file.
2766 if (tpx.bX)
2767 {
2768 state->flags |= (1 << estX);
2769 }
2770 if (tpx.bV)
2771 {
2772 state->flags |= (1 << estV);
2773 }
2774 state_change_natoms(state, tpx.natoms);
2775 }
2776 }
2777
2778 if (x == nullptr)
2779 {
2780 x = state->x.rvec_array();
2781 v = state->v.rvec_array();
2782 }
2783
2784 #define do_test(fio, b, p) if (bRead && ((p) != NULL) && !(b)) gmx_fatal(FARGS, "No %s in %s",#p, gmx_fio_getname(fio))
2785
2786 do_test(fio, tpx.bBox, state->box);
2787 if (tpx.bBox)
2788 {
2789 gmx_fio_ndo_rvec(fio, state->box, DIM);
2790 if (fileVersion >= 51)
2791 {
2792 gmx_fio_ndo_rvec(fio, state->box_rel, DIM);
2793 }
2794 else
2795 {
2796 /* We initialize box_rel after reading the inputrec */
2797 clear_mat(state->box_rel);
2798 }
2799 gmx_fio_ndo_rvec(fio, state->boxv, DIM);
2800 if (fileVersion < 56)
2801 {
2802 matrix mdum;
2803 gmx_fio_ndo_rvec(fio, mdum, DIM);
2804 }
2805 }
2806
2807 if (state->ngtc > 0)
2808 {
2809 real *dumv;
2810 snew(dumv, state->ngtc);
2811 if (fileVersion < 69)
2812 {
2813 gmx_fio_ndo_real(fio, dumv, state->ngtc);
2814 }
2815 /* These used to be the Berendsen tcoupl_lambda's */
2816 gmx_fio_ndo_real(fio, dumv, state->ngtc);
2817 sfree(dumv);
2818 }
2819
2820 do_test(fio, tpx.bTop, mtop);
2821 if (tpx.bTop)
2822 {
2823 if (mtop)
2824 {
2825 do_mtop(fio, mtop, bRead, fileVersion);
2826 }
2827 else
2828 {
2829 gmx_mtop_t dum_top;
2830 do_mtop(fio, &dum_top, bRead, fileVersion);
2831 }
2832 }
2833 do_test(fio, tpx.bX, x);
2834 if (tpx.bX)
2835 {
2836 if (bRead)
2837 {
2838 state->flags |= (1<<estX);
2839 }
2840 gmx_fio_ndo_rvec(fio, x, tpx.natoms);
2841 }
2842
2843 do_test(fio, tpx.bV, v);
2844 if (tpx.bV)
2845 {
2846 if (bRead)
2847 {
2848 state->flags |= (1<<estV);
2849 }
2850 gmx_fio_ndo_rvec(fio, v, tpx.natoms);
2851 }
2852
2853 // No need to run do_test when the last argument is NULL
2854 if (tpx.bF)
2855 {
2856 rvec *dummyForces;
2857 snew(dummyForces, state->natoms);
2858 gmx_fio_ndo_rvec(fio, dummyForces, tpx.natoms);
2859 sfree(dummyForces);
2860 }
2861
2862 /* Starting with tpx version 26, we have the inputrec
2863 * at the end of the file, so we can ignore it
2864 * if the file is never than the software (but still the
2865 * same generation - see comments at the top of this file.
2866 *
2867 *
2868 */
2869 ePBC = -1;
2870 bPeriodicMols = FALSE;
2871
2872 do_test(fio, tpx.bIr, ir);
2873 if (tpx.bIr)
2874 {
2875 if (fileVersion >= 53)
2876 {
2877 /* Removed the pbc info from do_inputrec, since we always want it */
2878 if (!bRead)
2879 {
2880 ePBC = ir->ePBC;
2881 bPeriodicMols = ir->bPeriodicMols;
2882 }
2883 gmx_fio_do_int(fio, ePBC);
2884 gmx_fio_do_gmx_bool(fio, bPeriodicMols);
2885 }
2886 if (fileGeneration <= tpx_generation && ir)
2887 {
2888 do_inputrec(fio, ir, bRead, fileVersion);
2889 if (fileVersion < 51)
2890 {
2891 set_box_rel(ir, state);
2892 }
2893 if (fileVersion < 53)
2894 {
2895 ePBC = ir->ePBC;
2896 bPeriodicMols = ir->bPeriodicMols;
2897 }
2898 }
2899 if (bRead && ir && fileVersion >= 53)
2900 {
2901 /* We need to do this after do_inputrec, since that initializes ir */
2902 ir->ePBC = ePBC;
2903 ir->bPeriodicMols = bPeriodicMols;
2904 }
2905 }
2906
2907 if (bRead)
2908 {
2909 if (tpx.bIr && ir)
2910 {
2911 if (state->ngtc == 0)
2912 {
2913 /* Reading old version without tcoupl state data: set it */
2914 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
2915 }
2916 if (tpx.bTop && mtop)
2917 {
2918 if (fileVersion < 57)
2919 {
2920 if (mtop->moltype[0].ilist[F_DISRES].size() > 0)
2921 {
2922 ir->eDisre = edrSimple;
2923 }
2924 else
2925 {
2926 ir->eDisre = edrNone;
2927 }
2928 }
2929 set_disres_npair(mtop);
2930 }
2931 }
2932
2933 if (tpx.bTop && mtop)
2934 {
2935 gmx_mtop_finalize(mtop);
2936 }
2937 }
2938
2939 return ePBC;
2940 }
2941
2942 static t_fileio *open_tpx(const char *fn, const char *mode)
2943 {
2944 return gmx_fio_open(fn, mode);
2945 }
2946
2947 static void close_tpx(t_fileio *fio)
2948 {
2949 gmx_fio_close(fio);
2950 }
2951
2952 /************************************************************
2953 *
2954 * The following routines are the exported ones
2955 *
2956 ************************************************************/
2957
2958 void read_tpxheader(const char *fn, t_tpxheader *tpx, gmx_bool TopOnlyOK)
2959 {
2960 t_fileio *fio;
2961
2962 fio = open_tpx(fn, "r");
2963 do_tpxheader(fio, TRUE, tpx, TopOnlyOK, nullptr, nullptr);
2964 close_tpx(fio);
2965 }
2966
2967 void write_tpx_state(const char *fn,
2968 const t_inputrec *ir, const t_state *state, const gmx_mtop_t *mtop)
2969 {
2970 t_fileio *fio;
2971
2972 fio = open_tpx(fn, "w");
2973 do_tpx(fio, FALSE,
2974 const_cast<t_inputrec *>(ir),
2975 const_cast<t_state *>(state), nullptr, nullptr,
2976 const_cast<gmx_mtop_t *>(mtop));
2977 close_tpx(fio);
2978 }
2979
2980 void read_tpx_state(const char *fn,
2981 t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
2982 {
2983 t_fileio *fio;
2984
2985 fio = open_tpx(fn, "r");
2986 do_tpx(fio, TRUE, ir, state, nullptr, nullptr, mtop);
2987 close_tpx(fio);
2988 }
2989
2990 int read_tpx(const char *fn,
2991 t_inputrec *ir, matrix box, int *natoms,
2992 rvec *x, rvec *v, gmx_mtop_t *mtop)
2993 {
2994 t_fileio *fio;
2995 t_state state;
2996 int ePBC;
2997
2998 fio = open_tpx(fn, "r");
2999 ePBC = do_tpx(fio, TRUE, ir, &state, x, v, mtop);
3000 close_tpx(fio);
3001 if (mtop != nullptr && natoms != nullptr)
3002 {
3003 *natoms = mtop->natoms;
3004 }
3005 if (box)
3006 {
3007 copy_mat(state.box, box);
3008 }
3009
3010 return ePBC;
3011 }
3012
3013 int read_tpx_top(const char *fn,
3014 t_inputrec *ir, matrix box, int *natoms,
3015 rvec *x, rvec *v, t_topology *top)
3016 {
3017 gmx_mtop_t mtop;
3018 int ePBC;
3019
3020 ePBC = read_tpx(fn, ir, box, natoms, x, v, &mtop);
3021
3022 *top = gmx_mtop_t_to_t_topology(&mtop, true);
3023
3024 return ePBC;
3025 }
3026
3027 gmx_bool fn2bTPX(const char *file)
3028 {
3029 return (efTPR == fn2ftp(file));
3030 }
3031
3032 void pr_tpxheader(FILE *fp, int indent, const char *title, const t_tpxheader *sh)
3033 {
3034 if (available(fp, sh, indent, title))
3035 {
3036 indent = pr_title(fp, indent, title);
3037 pr_indent(fp, indent);
3038 fprintf(fp, "bIr = %spresent\n", sh->bIr ? "" : "not ");
3039 pr_indent(fp, indent);
3040 fprintf(fp, "bBox = %spresent\n", sh->bBox ? "" : "not ");
3041 pr_indent(fp, indent);
3042 fprintf(fp, "bTop = %spresent\n", sh->bTop ? "" : "not ");
3043 pr_indent(fp, indent);
3044 fprintf(fp, "bX = %spresent\n", sh->bX ? "" : "not ");
3045 pr_indent(fp, indent);
3046 fprintf(fp, "bV = %spresent\n", sh->bV ? "" : "not ");
3047 pr_indent(fp, indent);
3048 fprintf(fp, "bF = %spresent\n", sh->bF ? "" : "not ");
3049
3050 pr_indent(fp, indent);
3051 fprintf(fp, "natoms = %d\n", sh->natoms);
3052 pr_indent(fp, indent);
3053 fprintf(fp, "lambda = %e\n", sh->lambda);
3054 }
3055 }
The ultimate molecular dynamics simulation package