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40 /* This file is completely threadsafe - keep it that way! */
52 #include "gromacs/fileio/filetypes.h"
53 #include "gromacs/fileio/gmxfio.h"
54 #include "gromacs/fileio/gmxfio_xdr.h"
55 #include "gromacs/math/units.h"
56 #include "gromacs/math/vec.h"
57 #include "gromacs/mdtypes/awh_history.h"
58 #include "gromacs/mdtypes/awh_params.h"
59 #include "gromacs/mdtypes/inputrec.h"
60 #include "gromacs/mdtypes/md_enums.h"
61 #include "gromacs/mdtypes/pull_params.h"
62 #include "gromacs/mdtypes/state.h"
63 #include "gromacs/pbcutil/boxutilities.h"
64 #include "gromacs/pbcutil/pbc.h"
65 #include "gromacs/topology/block.h"
66 #include "gromacs/topology/ifunc.h"
67 #include "gromacs/topology/mtop_util.h"
68 #include "gromacs/topology/symtab.h"
69 #include "gromacs/topology/topology.h"
70 #include "gromacs/utility/arraysize.h"
71 #include "gromacs/utility/baseversion.h"
72 #include "gromacs/utility/cstringutil.h"
73 #include "gromacs/utility/fatalerror.h"
74 #include "gromacs/utility/futil.h"
75 #include "gromacs/utility/gmxassert.h"
76 #include "gromacs/utility/inmemoryserializer.h"
77 #include "gromacs/utility/keyvaluetreebuilder.h"
78 #include "gromacs/utility/keyvaluetreeserializer.h"
79 #include "gromacs/utility/smalloc.h"
80 #include "gromacs/utility/snprintf.h"
81 #include "gromacs/utility/txtdump.h"
83 #define TPX_TAG_RELEASE "release"
85 /*! \brief Tag string for the file format written to run input files
86 * written by this version of the code.
88 * Change this if you want to change the run input format in a feature
89 * branch. This ensures that there will not be different run input
90 * formats around which cannot be distinguished, while not causing
91 * problems rebasing the feature branch onto upstream changes. When
92 * merging with mainstream GROMACS, set this tag string back to
93 * TPX_TAG_RELEASE, and instead add an element to tpxv.
95 static const char* tpx_tag = TPX_TAG_RELEASE;
97 /*! \brief Enum of values that describe the contents of a tpr file
98 * whose format matches a version number
100 * The enum helps the code be more self-documenting and ensure merges
101 * do not silently resolve when two patches make the same bump. When
102 * adding new functionality, add a new element just above tpxv_Count
103 * in this enumeration, and write code below that does the right thing
104 * according to the value of file_version.
108 tpxv_ComputationalElectrophysiology =
109 96, /**< support for ion/water position swaps (computational electrophysiology) */
110 tpxv_Use64BitRandomSeed, /**< change ld_seed from int to int64_t */
111 tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, /**< potentials for supporting coarse-grained force fields */
112 tpxv_InteractiveMolecularDynamics, /**< interactive molecular dynamics (IMD) */
113 tpxv_RemoveObsoleteParameters1, /**< remove optimize_fft, dihre_fc, nstcheckpoint */
114 tpxv_PullCoordTypeGeom, /**< add pull type and geometry per group and flat-bottom */
115 tpxv_PullGeomDirRel, /**< add pull geometry direction-relative */
116 tpxv_IntermolecularBondeds, /**< permit inter-molecular bonded interactions in the topology */
117 tpxv_CompElWithSwapLayerOffset, /**< added parameters for improved CompEl setups */
118 tpxv_CompElPolyatomicIonsAndMultipleIonTypes, /**< CompEl now can handle polyatomic ions and more than two types of ions */
119 tpxv_RemoveAdress, /**< removed support for AdResS */
120 tpxv_PullCoordNGroup, /**< add ngroup to pull coord */
121 tpxv_RemoveTwinRange, /**< removed support for twin-range interactions */
122 tpxv_ReplacePullPrintCOM12, /**< Replaced print-com-1, 2 with pull-print-com */
123 tpxv_PullExternalPotential, /**< Added pull type external potential */
124 tpxv_GenericParamsForElectricField, /**< Introduced KeyValueTree and moved electric field parameters */
125 tpxv_AcceleratedWeightHistogram, /**< sampling with accelerated weight histogram method (AWH) */
126 tpxv_RemoveImplicitSolvation, /**< removed support for implicit solvation */
127 tpxv_PullPrevStepCOMAsReference, /**< Enabled using the COM of the pull group of the last frame as reference for PBC */
128 tpxv_MimicQMMM, /**< Introduced support for MiMiC QM/MM interface */
129 tpxv_PullAverage, /**< Added possibility to output average pull force and position */
130 tpxv_GenericInternalParameters, /**< Added internal parameters for mdrun modules*/
131 tpxv_VSite2FD, /**< Added 2FD type virtual site */
132 tpxv_AddSizeField, /**< Added field with information about the size of the serialized tpr file in bytes, excluding the header */
133 tpxv_StoreNonBondedInteractionExclusionGroup, /**< Store the non bonded interaction exclusion group in the topology */
134 tpxv_VSite1, /**< Added 1 type virtual site */
135 tpxv_Count /**< the total number of tpxv versions */
138 /*! \brief Version number of the file format written to run input
139 * files by this version of the code.
141 * The tpx_version increases whenever the file format in the main
142 * development branch changes, due to an extension of the tpxv enum above.
143 * Backward compatibility for reading old run input files is maintained
144 * by checking this version number against that of the file and then using
145 * the correct code path.
147 * When developing a feature branch that needs to change the run input
148 * file format, change tpx_tag instead. */
149 static const int tpx_version = tpxv_Count - 1;
152 /* This number should only be increased when you edit the TOPOLOGY section
153 * or the HEADER of the tpx format.
154 * This way we can maintain forward compatibility too for all analysis tools
155 * and/or external programs that only need to know the atom/residue names,
156 * charges, and bond connectivity.
158 * It first appeared in tpx version 26, when I also moved the inputrecord
159 * to the end of the tpx file, so we can just skip it if we only
162 * In particular, it must be increased when adding new elements to
163 * ftupd, so that old code can read new .tpr files.
165 * Updated for added field that contains the number of bytes of the tpr body, excluding the header.
167 static const int tpx_generation = 27;
169 /* This number should be the most recent backwards incompatible version
170 * I.e., if this number is 9, we cannot read tpx version 9 with this code.
172 static const int tpx_incompatible_version = 57; // GMX4.0 has version 58
175 /* Struct used to maintain tpx compatibility when function types are added */
178 int fvnr; /* file version number in which the function type first appeared */
179 int ftype; /* function type */
183 * TODO The following three lines make little sense, please clarify if
184 * you've had to work out how ftupd works.
186 * The entries should be ordered in:
187 * 1. ascending function type number
188 * 2. ascending file version number
190 * Because we support reading of old .tpr file versions (even when
191 * mdrun can no longer run the simulation), we need to be able to read
192 * obsolete t_interaction_function types. Any data read from such
193 * fields is discarded. Their names have _NOLONGERUSED appended to
194 * them to make things clear.
196 static const t_ftupd ftupd[] = {
197 { 70, F_RESTRBONDS },
198 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
199 { 76, F_LINEAR_ANGLES },
200 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
201 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
203 { 60, F_GB12_NOLONGERUSED },
204 { 61, F_GB13_NOLONGERUSED },
205 { 61, F_GB14_NOLONGERUSED },
206 { 72, F_GBPOL_NOLONGERUSED },
207 { 72, F_NPSOLVATION_NOLONGERUSED },
209 { 76, F_ANHARM_POL },
211 { tpxv_VSite1, F_VSITE1 },
212 { tpxv_VSite2FD, F_VSITE2FD },
213 { tpxv_GenericInternalParameters, F_DENSITYFITTING },
214 { 69, F_VTEMP_NOLONGERUSED },
225 { 79, F_DVDL_RESTRAINT },
226 { 79, F_DVDL_TEMPERATURE },
228 #define NFTUPD asize(ftupd)
230 /* Needed for backward compatibility */
233 /**************************************************************
235 * Now the higer level routines that do io of the structures and arrays
237 **************************************************************/
238 static void do_pullgrp_tpx_pre95(gmx::ISerializer* serializer, t_pull_group* pgrp, t_pull_coord* pcrd)
242 serializer->doInt(&pgrp->nat);
243 if (serializer->reading())
245 snew(pgrp->ind, pgrp->nat);
247 serializer->doIntArray(pgrp->ind, pgrp->nat);
248 serializer->doInt(&pgrp->nweight);
249 if (serializer->reading())
251 snew(pgrp->weight, pgrp->nweight);
253 serializer->doRealArray(pgrp->weight, pgrp->nweight);
254 serializer->doInt(&pgrp->pbcatom);
255 serializer->doRvec(&pcrd->vec);
256 clear_rvec(pcrd->origin);
257 serializer->doRvec(&tmp);
259 serializer->doReal(&pcrd->rate);
260 serializer->doReal(&pcrd->k);
261 serializer->doReal(&pcrd->kB);
264 static void do_pull_group(gmx::ISerializer* serializer, t_pull_group* pgrp)
266 serializer->doInt(&pgrp->nat);
267 if (serializer->reading())
269 snew(pgrp->ind, pgrp->nat);
271 serializer->doIntArray(pgrp->ind, pgrp->nat);
272 serializer->doInt(&pgrp->nweight);
273 if (serializer->reading())
275 snew(pgrp->weight, pgrp->nweight);
277 serializer->doRealArray(pgrp->weight, pgrp->nweight);
278 serializer->doInt(&pgrp->pbcatom);
281 static void do_pull_coord(gmx::ISerializer* serializer,
288 if (file_version >= tpxv_PullCoordNGroup)
290 serializer->doInt(&pcrd->eType);
291 if (file_version >= tpxv_PullExternalPotential)
293 if (pcrd->eType == epullEXTERNAL)
296 if (serializer->reading())
298 serializer->doString(&buf);
299 pcrd->externalPotentialProvider = gmx_strdup(buf.c_str());
303 buf = pcrd->externalPotentialProvider;
304 serializer->doString(&buf);
309 pcrd->externalPotentialProvider = nullptr;
314 if (serializer->reading())
316 pcrd->externalPotentialProvider = nullptr;
319 /* Note that we try to support adding new geometries without
320 * changing the tpx version. This requires checks when printing the
321 * geometry string and a check and fatal_error in init_pull.
323 serializer->doInt(&pcrd->eGeom);
324 serializer->doInt(&pcrd->ngroup);
325 if (pcrd->ngroup <= c_pullCoordNgroupMax)
327 serializer->doIntArray(pcrd->group, pcrd->ngroup);
331 /* More groups in file than supported, this must be a new geometry
332 * that is not supported by our current code. Since we will not
333 * use the groups for this coord (checks in the pull and WHAM code
334 * ensure this), we can ignore the groups and set ngroup=0.
337 snew(dum, pcrd->ngroup);
338 serializer->doIntArray(dum, pcrd->ngroup);
343 serializer->doIvec(&pcrd->dim);
348 serializer->doInt(&pcrd->group[0]);
349 serializer->doInt(&pcrd->group[1]);
350 if (file_version >= tpxv_PullCoordTypeGeom)
352 pcrd->ngroup = (pcrd->eGeom == epullgDIRRELATIVE ? 4 : 2);
353 serializer->doInt(&pcrd->eType);
354 serializer->doInt(&pcrd->eGeom);
355 if (pcrd->ngroup == 4)
357 serializer->doInt(&pcrd->group[2]);
358 serializer->doInt(&pcrd->group[3]);
360 serializer->doIvec(&pcrd->dim);
364 pcrd->eType = ePullOld;
365 pcrd->eGeom = eGeomOld;
366 copy_ivec(dimOld, pcrd->dim);
369 serializer->doRvec(&pcrd->origin);
370 serializer->doRvec(&pcrd->vec);
371 if (file_version >= tpxv_PullCoordTypeGeom)
373 serializer->doBool(&pcrd->bStart);
377 /* This parameter is only printed, but not actually used by mdrun */
378 pcrd->bStart = FALSE;
380 serializer->doReal(&pcrd->init);
381 serializer->doReal(&pcrd->rate);
382 serializer->doReal(&pcrd->k);
383 serializer->doReal(&pcrd->kB);
386 static void do_expandedvals(gmx::ISerializer* serializer, t_expanded* expand, t_lambda* fepvals, int file_version)
388 int n_lambda = fepvals->n_lambda;
390 /* reset the lambda calculation window */
391 fepvals->lambda_start_n = 0;
392 fepvals->lambda_stop_n = n_lambda;
393 if (file_version >= 79)
397 if (serializer->reading())
399 snew(expand->init_lambda_weights, n_lambda);
401 serializer->doRealArray(expand->init_lambda_weights, n_lambda);
402 serializer->doBool(&expand->bInit_weights);
405 serializer->doInt(&expand->nstexpanded);
406 serializer->doInt(&expand->elmcmove);
407 serializer->doInt(&expand->elamstats);
408 serializer->doInt(&expand->lmc_repeats);
409 serializer->doInt(&expand->gibbsdeltalam);
410 serializer->doInt(&expand->lmc_forced_nstart);
411 serializer->doInt(&expand->lmc_seed);
412 serializer->doReal(&expand->mc_temp);
413 serializer->doBool(&expand->bSymmetrizedTMatrix);
414 serializer->doInt(&expand->nstTij);
415 serializer->doInt(&expand->minvarmin);
416 serializer->doInt(&expand->c_range);
417 serializer->doReal(&expand->wl_scale);
418 serializer->doReal(&expand->wl_ratio);
419 serializer->doReal(&expand->init_wl_delta);
420 serializer->doBool(&expand->bWLoneovert);
421 serializer->doInt(&expand->elmceq);
422 serializer->doInt(&expand->equil_steps);
423 serializer->doInt(&expand->equil_samples);
424 serializer->doInt(&expand->equil_n_at_lam);
425 serializer->doReal(&expand->equil_wl_delta);
426 serializer->doReal(&expand->equil_ratio);
430 static void do_simtempvals(gmx::ISerializer* serializer, t_simtemp* simtemp, int n_lambda, int file_version)
432 if (file_version >= 79)
434 serializer->doInt(&simtemp->eSimTempScale);
435 serializer->doReal(&simtemp->simtemp_high);
436 serializer->doReal(&simtemp->simtemp_low);
439 if (serializer->reading())
441 snew(simtemp->temperatures, n_lambda);
443 serializer->doRealArray(simtemp->temperatures, n_lambda);
448 static void do_imd(gmx::ISerializer* serializer, t_IMD* imd)
450 serializer->doInt(&imd->nat);
451 if (serializer->reading())
453 snew(imd->ind, imd->nat);
455 serializer->doIntArray(imd->ind, imd->nat);
458 static void do_fepvals(gmx::ISerializer* serializer, t_lambda* fepvals, int file_version)
460 /* i is defined in the ndo_double macro; use g to iterate. */
464 /* free energy values */
466 if (file_version >= 79)
468 serializer->doInt(&fepvals->init_fep_state);
469 serializer->doDouble(&fepvals->init_lambda);
470 serializer->doDouble(&fepvals->delta_lambda);
472 else if (file_version >= 59)
474 serializer->doDouble(&fepvals->init_lambda);
475 serializer->doDouble(&fepvals->delta_lambda);
479 serializer->doReal(&rdum);
480 fepvals->init_lambda = rdum;
481 serializer->doReal(&rdum);
482 fepvals->delta_lambda = rdum;
484 if (file_version >= 79)
486 serializer->doInt(&fepvals->n_lambda);
487 if (serializer->reading())
489 snew(fepvals->all_lambda, efptNR);
491 for (g = 0; g < efptNR; g++)
493 if (fepvals->n_lambda > 0)
495 if (serializer->reading())
497 snew(fepvals->all_lambda[g], fepvals->n_lambda);
499 serializer->doDoubleArray(fepvals->all_lambda[g], fepvals->n_lambda);
500 serializer->doBoolArray(fepvals->separate_dvdl, efptNR);
502 else if (fepvals->init_lambda >= 0)
504 fepvals->separate_dvdl[efptFEP] = TRUE;
508 else if (file_version >= 64)
510 serializer->doInt(&fepvals->n_lambda);
511 if (serializer->reading())
515 snew(fepvals->all_lambda, efptNR);
516 /* still allocate the all_lambda array's contents. */
517 for (g = 0; g < efptNR; g++)
519 if (fepvals->n_lambda > 0)
521 snew(fepvals->all_lambda[g], fepvals->n_lambda);
525 serializer->doDoubleArray(fepvals->all_lambda[efptFEP], fepvals->n_lambda);
526 if (fepvals->init_lambda >= 0)
530 fepvals->separate_dvdl[efptFEP] = TRUE;
532 if (serializer->reading())
534 /* copy the contents of the efptFEP lambda component to all
535 the other components */
536 for (g = 0; g < efptNR; g++)
538 for (h = 0; h < fepvals->n_lambda; h++)
542 fepvals->all_lambda[g][h] = fepvals->all_lambda[efptFEP][h];
551 fepvals->n_lambda = 0;
552 fepvals->all_lambda = nullptr;
553 if (fepvals->init_lambda >= 0)
555 fepvals->separate_dvdl[efptFEP] = TRUE;
558 serializer->doReal(&fepvals->sc_alpha);
559 serializer->doInt(&fepvals->sc_power);
560 if (file_version >= 79)
562 serializer->doReal(&fepvals->sc_r_power);
566 fepvals->sc_r_power = 6.0;
568 if (fepvals->sc_r_power != 6.0)
570 gmx_fatal(FARGS, "sc-r-power=48 is no longer supported");
572 serializer->doReal(&fepvals->sc_sigma);
573 if (serializer->reading())
575 if (file_version >= 71)
577 fepvals->sc_sigma_min = fepvals->sc_sigma;
581 fepvals->sc_sigma_min = 0;
584 if (file_version >= 79)
586 serializer->doBool(&fepvals->bScCoul);
590 fepvals->bScCoul = TRUE;
592 if (file_version >= 64)
594 serializer->doInt(&fepvals->nstdhdl);
598 fepvals->nstdhdl = 1;
601 if (file_version >= 73)
603 serializer->doInt(&fepvals->separate_dhdl_file);
604 serializer->doInt(&fepvals->dhdl_derivatives);
608 fepvals->separate_dhdl_file = esepdhdlfileYES;
609 fepvals->dhdl_derivatives = edhdlderivativesYES;
611 if (file_version >= 71)
613 serializer->doInt(&fepvals->dh_hist_size);
614 serializer->doDouble(&fepvals->dh_hist_spacing);
618 fepvals->dh_hist_size = 0;
619 fepvals->dh_hist_spacing = 0.1;
621 if (file_version >= 79)
623 serializer->doInt(&fepvals->edHdLPrintEnergy);
627 fepvals->edHdLPrintEnergy = edHdLPrintEnergyNO;
630 /* handle lambda_neighbors */
631 if ((file_version >= 83 && file_version < 90) || file_version >= 92)
633 serializer->doInt(&fepvals->lambda_neighbors);
634 if ((fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0)
635 && (fepvals->init_lambda < 0))
637 fepvals->lambda_start_n = (fepvals->init_fep_state - fepvals->lambda_neighbors);
638 fepvals->lambda_stop_n = (fepvals->init_fep_state + fepvals->lambda_neighbors + 1);
639 if (fepvals->lambda_start_n < 0)
641 fepvals->lambda_start_n = 0;
643 if (fepvals->lambda_stop_n >= fepvals->n_lambda)
645 fepvals->lambda_stop_n = fepvals->n_lambda;
650 fepvals->lambda_start_n = 0;
651 fepvals->lambda_stop_n = fepvals->n_lambda;
656 fepvals->lambda_start_n = 0;
657 fepvals->lambda_stop_n = fepvals->n_lambda;
661 static void do_awhBias(gmx::ISerializer* serializer, gmx::AwhBiasParams* awhBiasParams, int gmx_unused file_version)
663 serializer->doInt(&awhBiasParams->eTarget);
664 serializer->doDouble(&awhBiasParams->targetBetaScaling);
665 serializer->doDouble(&awhBiasParams->targetCutoff);
666 serializer->doInt(&awhBiasParams->eGrowth);
667 serializer->doInt(&awhBiasParams->bUserData);
668 serializer->doDouble(&awhBiasParams->errorInitial);
669 serializer->doInt(&awhBiasParams->ndim);
670 serializer->doInt(&awhBiasParams->shareGroup);
671 serializer->doBool(&awhBiasParams->equilibrateHistogram);
673 if (serializer->reading())
675 snew(awhBiasParams->dimParams, awhBiasParams->ndim);
678 for (int d = 0; d < awhBiasParams->ndim; d++)
680 gmx::AwhDimParams* dimParams = &awhBiasParams->dimParams[d];
682 serializer->doInt(&dimParams->eCoordProvider);
683 serializer->doInt(&dimParams->coordIndex);
684 serializer->doDouble(&dimParams->origin);
685 serializer->doDouble(&dimParams->end);
686 serializer->doDouble(&dimParams->period);
687 serializer->doDouble(&dimParams->forceConstant);
688 serializer->doDouble(&dimParams->diffusion);
689 serializer->doDouble(&dimParams->coordValueInit);
690 serializer->doDouble(&dimParams->coverDiameter);
694 static void do_awh(gmx::ISerializer* serializer, gmx::AwhParams* awhParams, int gmx_unused file_version)
696 serializer->doInt(&awhParams->numBias);
697 serializer->doInt(&awhParams->nstOut);
698 serializer->doInt64(&awhParams->seed);
699 serializer->doInt(&awhParams->nstSampleCoord);
700 serializer->doInt(&awhParams->numSamplesUpdateFreeEnergy);
701 serializer->doInt(&awhParams->ePotential);
702 serializer->doBool(&awhParams->shareBiasMultisim);
704 if (awhParams->numBias > 0)
706 if (serializer->reading())
708 snew(awhParams->awhBiasParams, awhParams->numBias);
711 for (int k = 0; k < awhParams->numBias; k++)
713 do_awhBias(serializer, &awhParams->awhBiasParams[k], file_version);
718 static void do_pull(gmx::ISerializer* serializer, pull_params_t* pull, int file_version, int ePullOld)
724 if (file_version >= 95)
726 serializer->doInt(&pull->ngroup);
728 serializer->doInt(&pull->ncoord);
729 if (file_version < 95)
731 pull->ngroup = pull->ncoord + 1;
733 if (file_version < tpxv_PullCoordTypeGeom)
737 serializer->doInt(&eGeomOld);
738 serializer->doIvec(&dimOld);
739 /* The inner cylinder radius, now removed */
740 serializer->doReal(&dum);
742 serializer->doReal(&pull->cylinder_r);
743 serializer->doReal(&pull->constr_tol);
744 if (file_version >= 95)
746 serializer->doBool(&pull->bPrintCOM);
747 /* With file_version < 95 this value is set below */
749 if (file_version >= tpxv_ReplacePullPrintCOM12)
751 serializer->doBool(&pull->bPrintRefValue);
752 serializer->doBool(&pull->bPrintComp);
754 else if (file_version >= tpxv_PullCoordTypeGeom)
757 serializer->doInt(&idum); /* used to be bPrintCOM2 */
758 serializer->doBool(&pull->bPrintRefValue);
759 serializer->doBool(&pull->bPrintComp);
763 pull->bPrintRefValue = FALSE;
764 pull->bPrintComp = TRUE;
766 serializer->doInt(&pull->nstxout);
767 serializer->doInt(&pull->nstfout);
768 if (file_version >= tpxv_PullPrevStepCOMAsReference)
770 serializer->doBool(&pull->bSetPbcRefToPrevStepCOM);
774 pull->bSetPbcRefToPrevStepCOM = FALSE;
776 if (serializer->reading())
778 snew(pull->group, pull->ngroup);
779 snew(pull->coord, pull->ncoord);
781 if (file_version < 95)
783 /* epullgPOS for position pulling, before epullgDIRPBC was removed */
784 if (eGeomOld == epullgDIRPBC)
786 gmx_fatal(FARGS, "pull-geometry=position is no longer supported");
788 if (eGeomOld > epullgDIRPBC)
793 for (g = 0; g < pull->ngroup; g++)
795 /* We read and ignore a pull coordinate for group 0 */
796 do_pullgrp_tpx_pre95(serializer, &pull->group[g], &pull->coord[std::max(g - 1, 0)]);
799 pull->coord[g - 1].group[0] = 0;
800 pull->coord[g - 1].group[1] = g;
804 pull->bPrintCOM = (pull->group[0].nat > 0);
808 for (g = 0; g < pull->ngroup; g++)
810 do_pull_group(serializer, &pull->group[g]);
812 for (g = 0; g < pull->ncoord; g++)
814 do_pull_coord(serializer, &pull->coord[g], file_version, ePullOld, eGeomOld, dimOld);
817 if (file_version >= tpxv_PullAverage)
821 v = pull->bXOutAverage;
822 serializer->doBool(&v);
823 pull->bXOutAverage = v;
824 v = pull->bFOutAverage;
825 serializer->doBool(&v);
826 pull->bFOutAverage = v;
831 static void do_rotgrp(gmx::ISerializer* serializer, t_rotgrp* rotg)
833 serializer->doInt(&rotg->eType);
834 serializer->doInt(&rotg->bMassW);
835 serializer->doInt(&rotg->nat);
836 if (serializer->reading())
838 snew(rotg->ind, rotg->nat);
840 serializer->doIntArray(rotg->ind, rotg->nat);
841 if (serializer->reading())
843 snew(rotg->x_ref, rotg->nat);
845 serializer->doRvecArray(rotg->x_ref, rotg->nat);
846 serializer->doRvec(&rotg->inputVec);
847 serializer->doRvec(&rotg->pivot);
848 serializer->doReal(&rotg->rate);
849 serializer->doReal(&rotg->k);
850 serializer->doReal(&rotg->slab_dist);
851 serializer->doReal(&rotg->min_gaussian);
852 serializer->doReal(&rotg->eps);
853 serializer->doInt(&rotg->eFittype);
854 serializer->doInt(&rotg->PotAngle_nstep);
855 serializer->doReal(&rotg->PotAngle_step);
858 static void do_rot(gmx::ISerializer* serializer, t_rot* rot)
862 serializer->doInt(&rot->ngrp);
863 serializer->doInt(&rot->nstrout);
864 serializer->doInt(&rot->nstsout);
865 if (serializer->reading())
867 snew(rot->grp, rot->ngrp);
869 for (g = 0; g < rot->ngrp; g++)
871 do_rotgrp(serializer, &rot->grp[g]);
876 static void do_swapgroup(gmx::ISerializer* serializer, t_swapGroup* g)
879 /* Name of the group or molecule */
881 if (serializer->reading())
883 serializer->doString(&buf);
884 g->molname = gmx_strdup(buf.c_str());
889 serializer->doString(&buf);
892 /* Number of atoms in the group */
893 serializer->doInt(&g->nat);
895 /* The group's atom indices */
896 if (serializer->reading())
898 snew(g->ind, g->nat);
900 serializer->doIntArray(g->ind, g->nat);
902 /* Requested counts for compartments A and B */
903 serializer->doIntArray(g->nmolReq, eCompNR);
906 static void do_swapcoords_tpx(gmx::ISerializer* serializer, t_swapcoords* swap, int file_version)
908 /* Enums for better readability of the code */
921 if (file_version >= tpxv_CompElPolyatomicIonsAndMultipleIonTypes)
923 /* The total number of swap groups is the sum of the fixed groups
924 * (split0, split1, solvent), and the user-defined groups (2+ types of ions)
926 serializer->doInt(&swap->ngrp);
927 if (serializer->reading())
929 snew(swap->grp, swap->ngrp);
931 for (int ig = 0; ig < swap->ngrp; ig++)
933 do_swapgroup(serializer, &swap->grp[ig]);
935 serializer->doBool(&swap->massw_split[eChannel0]);
936 serializer->doBool(&swap->massw_split[eChannel1]);
937 serializer->doInt(&swap->nstswap);
938 serializer->doInt(&swap->nAverage);
939 serializer->doReal(&swap->threshold);
940 serializer->doReal(&swap->cyl0r);
941 serializer->doReal(&swap->cyl0u);
942 serializer->doReal(&swap->cyl0l);
943 serializer->doReal(&swap->cyl1r);
944 serializer->doReal(&swap->cyl1u);
945 serializer->doReal(&swap->cyl1l);
949 /*** Support reading older CompEl .tpr files ***/
951 /* In the original CompEl .tpr files, we always have 5 groups: */
953 snew(swap->grp, swap->ngrp);
955 swap->grp[eGrpSplit0].molname = gmx_strdup("split0"); // group 0: split0
956 swap->grp[eGrpSplit1].molname = gmx_strdup("split1"); // group 1: split1
957 swap->grp[eGrpSolvent].molname = gmx_strdup("solvent"); // group 2: solvent
958 swap->grp[3].molname = gmx_strdup("anions"); // group 3: anions
959 swap->grp[4].molname = gmx_strdup("cations"); // group 4: cations
961 serializer->doInt(&swap->grp[3].nat);
962 serializer->doInt(&swap->grp[eGrpSolvent].nat);
963 serializer->doInt(&swap->grp[eGrpSplit0].nat);
964 serializer->doBool(&swap->massw_split[eChannel0]);
965 serializer->doInt(&swap->grp[eGrpSplit1].nat);
966 serializer->doBool(&swap->massw_split[eChannel1]);
967 serializer->doInt(&swap->nstswap);
968 serializer->doInt(&swap->nAverage);
969 serializer->doReal(&swap->threshold);
970 serializer->doReal(&swap->cyl0r);
971 serializer->doReal(&swap->cyl0u);
972 serializer->doReal(&swap->cyl0l);
973 serializer->doReal(&swap->cyl1r);
974 serializer->doReal(&swap->cyl1u);
975 serializer->doReal(&swap->cyl1l);
977 // The order[] array keeps compatibility with older .tpr files
978 // by reading in the groups in the classic order
980 const int order[4] = { 3, eGrpSolvent, eGrpSplit0, eGrpSplit1 };
982 for (int ig = 0; ig < 4; ig++)
985 snew(swap->grp[g].ind, swap->grp[g].nat);
986 serializer->doIntArray(swap->grp[g].ind, swap->grp[g].nat);
990 for (int j = eCompA; j <= eCompB; j++)
992 serializer->doInt(&swap->grp[3].nmolReq[j]); // group 3 = anions
993 serializer->doInt(&swap->grp[4].nmolReq[j]); // group 4 = cations
995 } /* End support reading older CompEl .tpr files */
997 if (file_version >= tpxv_CompElWithSwapLayerOffset)
999 serializer->doReal(&swap->bulkOffset[eCompA]);
1000 serializer->doReal(&swap->bulkOffset[eCompB]);
1004 static void do_legacy_efield(gmx::ISerializer* serializer, gmx::KeyValueTreeObjectBuilder* root)
1006 const char* const dimName[] = { "x", "y", "z" };
1008 auto appliedForcesObj = root->addObject("applied-forces");
1009 auto efieldObj = appliedForcesObj.addObject("electric-field");
1010 // The content of the tpr file for this feature has
1011 // been the same since gromacs 4.0 that was used for
1013 for (int j = 0; j < DIM; ++j)
1016 serializer->doInt(&n);
1017 serializer->doInt(&nt);
1018 std::vector<real> aa(n + 1), phi(nt + 1), at(nt + 1), phit(nt + 1);
1019 serializer->doRealArray(aa.data(), n);
1020 serializer->doRealArray(phi.data(), n);
1021 serializer->doRealArray(at.data(), nt);
1022 serializer->doRealArray(phit.data(), nt);
1025 if (n > 1 || nt > 1)
1028 "Can not handle tpr files with more than one electric field term per "
1031 auto dimObj = efieldObj.addObject(dimName[j]);
1032 dimObj.addValue<real>("E0", aa[0]);
1033 dimObj.addValue<real>("omega", at[0]);
1034 dimObj.addValue<real>("t0", phi[0]);
1035 dimObj.addValue<real>("sigma", phit[0]);
1041 static void do_inputrec(gmx::ISerializer* serializer, t_inputrec* ir, int file_version)
1043 int i, j, k, idum = 0;
1045 gmx_bool bdum = false;
1047 if (file_version != tpx_version)
1049 /* Give a warning about features that are not accessible */
1050 fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n", file_version, tpx_version);
1053 if (file_version == 0)
1058 gmx::KeyValueTreeBuilder paramsBuilder;
1059 gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
1061 /* Basic inputrec stuff */
1062 serializer->doInt(&ir->eI);
1063 if (file_version >= 62)
1065 serializer->doInt64(&ir->nsteps);
1069 serializer->doInt(&idum);
1073 if (file_version >= 62)
1075 serializer->doInt64(&ir->init_step);
1079 serializer->doInt(&idum);
1080 ir->init_step = idum;
1083 serializer->doInt(&ir->simulation_part);
1085 if (file_version >= 67)
1087 serializer->doInt(&ir->nstcalcenergy);
1091 ir->nstcalcenergy = 1;
1093 if (file_version >= 81)
1095 serializer->doInt(&ir->cutoff_scheme);
1096 if (file_version < 94)
1098 ir->cutoff_scheme = 1 - ir->cutoff_scheme;
1103 ir->cutoff_scheme = ecutsGROUP;
1105 serializer->doInt(&idum); /* used to be ns_type; not used anymore */
1106 serializer->doInt(&ir->nstlist);
1107 serializer->doInt(&idum); /* used to be ndelta; not used anymore */
1109 serializer->doReal(&ir->rtpi);
1111 serializer->doInt(&ir->nstcomm);
1112 serializer->doInt(&ir->comm_mode);
1114 /* ignore nstcheckpoint */
1115 if (file_version < tpxv_RemoveObsoleteParameters1)
1117 serializer->doInt(&idum);
1120 serializer->doInt(&ir->nstcgsteep);
1122 serializer->doInt(&ir->nbfgscorr);
1124 serializer->doInt(&ir->nstlog);
1125 serializer->doInt(&ir->nstxout);
1126 serializer->doInt(&ir->nstvout);
1127 serializer->doInt(&ir->nstfout);
1128 serializer->doInt(&ir->nstenergy);
1129 serializer->doInt(&ir->nstxout_compressed);
1130 if (file_version >= 59)
1132 serializer->doDouble(&ir->init_t);
1133 serializer->doDouble(&ir->delta_t);
1137 serializer->doReal(&rdum);
1139 serializer->doReal(&rdum);
1142 serializer->doReal(&ir->x_compression_precision);
1143 if (file_version >= 81)
1145 serializer->doReal(&ir->verletbuf_tol);
1149 ir->verletbuf_tol = 0;
1151 serializer->doReal(&ir->rlist);
1152 if (file_version >= 67 && file_version < tpxv_RemoveTwinRange)
1154 if (serializer->reading())
1156 // Reading such a file version could invoke the twin-range
1157 // scheme, about which mdrun should give a fatal error.
1158 real dummy_rlistlong = -1;
1159 serializer->doReal(&dummy_rlistlong);
1161 ir->useTwinRange = (ir->rlist > 0 && (dummy_rlistlong == 0 || dummy_rlistlong > ir->rlist));
1162 // When true, this forces mdrun to issue an error (regardless of
1163 // ir->cutoff_scheme).
1165 // Otherwise, grompp used to set rlistlong actively. Users
1166 // were probably also confused and set rlistlong == rlist.
1167 // However, in all remaining cases, it is safe to let
1168 // mdrun proceed normally.
1173 // No need to read or write anything
1174 ir->useTwinRange = false;
1176 if (file_version >= 82 && file_version != 90)
1178 // Multiple time-stepping is no longer enabled, but the old
1179 // support required the twin-range scheme, for which mdrun
1180 // already emits a fatal error.
1181 int dummy_nstcalclr = -1;
1182 serializer->doInt(&dummy_nstcalclr);
1184 serializer->doInt(&ir->coulombtype);
1185 if (file_version >= 81)
1187 serializer->doInt(&ir->coulomb_modifier);
1191 ir->coulomb_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1193 serializer->doReal(&ir->rcoulomb_switch);
1194 serializer->doReal(&ir->rcoulomb);
1195 serializer->doInt(&ir->vdwtype);
1196 if (file_version >= 81)
1198 serializer->doInt(&ir->vdw_modifier);
1202 ir->vdw_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1204 serializer->doReal(&ir->rvdw_switch);
1205 serializer->doReal(&ir->rvdw);
1206 serializer->doInt(&ir->eDispCorr);
1207 serializer->doReal(&ir->epsilon_r);
1208 serializer->doReal(&ir->epsilon_rf);
1209 serializer->doReal(&ir->tabext);
1211 // This permits reading a .tpr file that used implicit solvent,
1212 // and later permitting mdrun to refuse to run it.
1213 if (serializer->reading())
1215 if (file_version < tpxv_RemoveImplicitSolvation)
1217 serializer->doInt(&idum);
1218 serializer->doInt(&idum);
1219 serializer->doReal(&rdum);
1220 serializer->doReal(&rdum);
1221 serializer->doInt(&idum);
1222 ir->implicit_solvent = (idum > 0);
1226 ir->implicit_solvent = false;
1228 if (file_version < tpxv_RemoveImplicitSolvation)
1230 serializer->doReal(&rdum);
1231 serializer->doReal(&rdum);
1232 serializer->doReal(&rdum);
1233 serializer->doReal(&rdum);
1234 if (file_version >= 60)
1236 serializer->doReal(&rdum);
1237 serializer->doInt(&idum);
1239 serializer->doReal(&rdum);
1243 if (file_version >= 81)
1245 serializer->doReal(&ir->fourier_spacing);
1249 ir->fourier_spacing = 0.0;
1251 serializer->doInt(&ir->nkx);
1252 serializer->doInt(&ir->nky);
1253 serializer->doInt(&ir->nkz);
1254 serializer->doInt(&ir->pme_order);
1255 serializer->doReal(&ir->ewald_rtol);
1257 if (file_version >= 93)
1259 serializer->doReal(&ir->ewald_rtol_lj);
1263 ir->ewald_rtol_lj = ir->ewald_rtol;
1265 serializer->doInt(&ir->ewald_geometry);
1266 serializer->doReal(&ir->epsilon_surface);
1268 /* ignore bOptFFT */
1269 if (file_version < tpxv_RemoveObsoleteParameters1)
1271 serializer->doBool(&bdum);
1274 if (file_version >= 93)
1276 serializer->doInt(&ir->ljpme_combination_rule);
1278 serializer->doBool(&ir->bContinuation);
1279 serializer->doInt(&ir->etc);
1280 /* before version 18, ir->etc was a gmx_bool (ir->btc),
1281 * but the values 0 and 1 still mean no and
1282 * berendsen temperature coupling, respectively.
1284 if (file_version >= 79)
1286 serializer->doBool(&ir->bPrintNHChains);
1288 if (file_version >= 71)
1290 serializer->doInt(&ir->nsttcouple);
1294 ir->nsttcouple = ir->nstcalcenergy;
1296 serializer->doInt(&ir->epc);
1297 serializer->doInt(&ir->epct);
1298 if (file_version >= 71)
1300 serializer->doInt(&ir->nstpcouple);
1304 ir->nstpcouple = ir->nstcalcenergy;
1306 serializer->doReal(&ir->tau_p);
1307 serializer->doRvec(&ir->ref_p[XX]);
1308 serializer->doRvec(&ir->ref_p[YY]);
1309 serializer->doRvec(&ir->ref_p[ZZ]);
1310 serializer->doRvec(&ir->compress[XX]);
1311 serializer->doRvec(&ir->compress[YY]);
1312 serializer->doRvec(&ir->compress[ZZ]);
1313 serializer->doInt(&ir->refcoord_scaling);
1314 serializer->doRvec(&ir->posres_com);
1315 serializer->doRvec(&ir->posres_comB);
1317 if (file_version < 79)
1319 serializer->doInt(&ir->andersen_seed);
1323 ir->andersen_seed = 0;
1326 serializer->doReal(&ir->shake_tol);
1328 serializer->doInt(&ir->efep);
1329 do_fepvals(serializer, ir->fepvals, file_version);
1331 if (file_version >= 79)
1333 serializer->doBool(&ir->bSimTemp);
1336 ir->bSimTemp = TRUE;
1341 ir->bSimTemp = FALSE;
1345 do_simtempvals(serializer, ir->simtempvals, ir->fepvals->n_lambda, file_version);
1348 if (file_version >= 79)
1350 serializer->doBool(&ir->bExpanded);
1354 do_expandedvals(serializer, ir->expandedvals, ir->fepvals, file_version);
1357 serializer->doInt(&ir->eDisre);
1358 serializer->doInt(&ir->eDisreWeighting);
1359 serializer->doBool(&ir->bDisreMixed);
1360 serializer->doReal(&ir->dr_fc);
1361 serializer->doReal(&ir->dr_tau);
1362 serializer->doInt(&ir->nstdisreout);
1363 serializer->doReal(&ir->orires_fc);
1364 serializer->doReal(&ir->orires_tau);
1365 serializer->doInt(&ir->nstorireout);
1367 /* ignore dihre_fc */
1368 if (file_version < 79)
1370 serializer->doReal(&rdum);
1373 serializer->doReal(&ir->em_stepsize);
1374 serializer->doReal(&ir->em_tol);
1375 serializer->doBool(&ir->bShakeSOR);
1376 serializer->doInt(&ir->niter);
1377 serializer->doReal(&ir->fc_stepsize);
1378 serializer->doInt(&ir->eConstrAlg);
1379 serializer->doInt(&ir->nProjOrder);
1380 serializer->doReal(&ir->LincsWarnAngle);
1381 serializer->doInt(&ir->nLincsIter);
1382 serializer->doReal(&ir->bd_fric);
1383 if (file_version >= tpxv_Use64BitRandomSeed)
1385 serializer->doInt64(&ir->ld_seed);
1389 serializer->doInt(&idum);
1393 for (i = 0; i < DIM; i++)
1395 serializer->doRvec(&ir->deform[i]);
1397 serializer->doReal(&ir->cos_accel);
1399 serializer->doInt(&ir->userint1);
1400 serializer->doInt(&ir->userint2);
1401 serializer->doInt(&ir->userint3);
1402 serializer->doInt(&ir->userint4);
1403 serializer->doReal(&ir->userreal1);
1404 serializer->doReal(&ir->userreal2);
1405 serializer->doReal(&ir->userreal3);
1406 serializer->doReal(&ir->userreal4);
1408 /* AdResS is removed, but we need to be able to read old files,
1409 and let mdrun refuse to run them */
1410 if (file_version >= 77 && file_version < tpxv_RemoveAdress)
1412 serializer->doBool(&ir->bAdress);
1415 int idum, numThermoForceGroups, numEnergyGroups;
1418 serializer->doInt(&idum);
1419 serializer->doReal(&rdum);
1420 serializer->doReal(&rdum);
1421 serializer->doReal(&rdum);
1422 serializer->doInt(&idum);
1423 serializer->doInt(&idum);
1424 serializer->doRvec(&rvecdum);
1425 serializer->doInt(&numThermoForceGroups);
1426 serializer->doReal(&rdum);
1427 serializer->doInt(&numEnergyGroups);
1428 serializer->doInt(&idum);
1430 if (numThermoForceGroups > 0)
1432 std::vector<int> idumn(numThermoForceGroups);
1433 serializer->doIntArray(idumn.data(), idumn.size());
1435 if (numEnergyGroups > 0)
1437 std::vector<int> idumn(numEnergyGroups);
1438 serializer->doIntArray(idumn.data(), idumn.size());
1444 ir->bAdress = FALSE;
1451 if (file_version >= tpxv_PullCoordTypeGeom)
1453 serializer->doBool(&ir->bPull);
1457 serializer->doInt(&ePullOld);
1458 ir->bPull = (ePullOld > 0);
1459 /* We removed the first ePull=ePullNo for the enum */
1464 if (serializer->reading())
1468 do_pull(serializer, ir->pull, file_version, ePullOld);
1472 if (file_version >= tpxv_AcceleratedWeightHistogram)
1474 serializer->doBool(&ir->bDoAwh);
1478 if (serializer->reading())
1480 snew(ir->awhParams, 1);
1482 do_awh(serializer, ir->awhParams, file_version);
1490 /* Enforced rotation */
1491 if (file_version >= 74)
1493 serializer->doBool(&ir->bRot);
1496 if (serializer->reading())
1500 do_rot(serializer, ir->rot);
1508 /* Interactive molecular dynamics */
1509 if (file_version >= tpxv_InteractiveMolecularDynamics)
1511 serializer->doBool(&ir->bIMD);
1514 if (serializer->reading())
1518 do_imd(serializer, ir->imd);
1523 /* We don't support IMD sessions for old .tpr files */
1528 serializer->doInt(&ir->opts.ngtc);
1529 if (file_version >= 69)
1531 serializer->doInt(&ir->opts.nhchainlength);
1535 ir->opts.nhchainlength = 1;
1537 serializer->doInt(&ir->opts.ngacc);
1538 serializer->doInt(&ir->opts.ngfrz);
1539 serializer->doInt(&ir->opts.ngener);
1541 if (serializer->reading())
1543 snew(ir->opts.nrdf, ir->opts.ngtc);
1544 snew(ir->opts.ref_t, ir->opts.ngtc);
1545 snew(ir->opts.annealing, ir->opts.ngtc);
1546 snew(ir->opts.anneal_npoints, ir->opts.ngtc);
1547 snew(ir->opts.anneal_time, ir->opts.ngtc);
1548 snew(ir->opts.anneal_temp, ir->opts.ngtc);
1549 snew(ir->opts.tau_t, ir->opts.ngtc);
1550 snew(ir->opts.nFreeze, ir->opts.ngfrz);
1551 snew(ir->opts.acc, ir->opts.ngacc);
1552 snew(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
1554 if (ir->opts.ngtc > 0)
1556 serializer->doRealArray(ir->opts.nrdf, ir->opts.ngtc);
1557 serializer->doRealArray(ir->opts.ref_t, ir->opts.ngtc);
1558 serializer->doRealArray(ir->opts.tau_t, ir->opts.ngtc);
1560 if (ir->opts.ngfrz > 0)
1562 serializer->doIvecArray(ir->opts.nFreeze, ir->opts.ngfrz);
1564 if (ir->opts.ngacc > 0)
1566 serializer->doRvecArray(ir->opts.acc, ir->opts.ngacc);
1568 serializer->doIntArray(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
1570 /* First read the lists with annealing and npoints for each group */
1571 serializer->doIntArray(ir->opts.annealing, ir->opts.ngtc);
1572 serializer->doIntArray(ir->opts.anneal_npoints, ir->opts.ngtc);
1573 for (j = 0; j < (ir->opts.ngtc); j++)
1575 k = ir->opts.anneal_npoints[j];
1576 if (serializer->reading())
1578 snew(ir->opts.anneal_time[j], k);
1579 snew(ir->opts.anneal_temp[j], k);
1581 serializer->doRealArray(ir->opts.anneal_time[j], k);
1582 serializer->doRealArray(ir->opts.anneal_temp[j], k);
1586 serializer->doInt(&ir->nwall);
1587 serializer->doInt(&ir->wall_type);
1588 serializer->doReal(&ir->wall_r_linpot);
1589 serializer->doInt(&ir->wall_atomtype[0]);
1590 serializer->doInt(&ir->wall_atomtype[1]);
1591 serializer->doReal(&ir->wall_density[0]);
1592 serializer->doReal(&ir->wall_density[1]);
1593 serializer->doReal(&ir->wall_ewald_zfac);
1596 /* Cosine stuff for electric fields */
1597 if (file_version < tpxv_GenericParamsForElectricField)
1599 do_legacy_efield(serializer, ¶msObj);
1603 if (file_version >= tpxv_ComputationalElectrophysiology)
1605 serializer->doInt(&ir->eSwapCoords);
1606 if (ir->eSwapCoords != eswapNO)
1608 if (serializer->reading())
1612 do_swapcoords_tpx(serializer, ir->swap, file_version);
1616 /* QMMM reading - despite defunct we require reading for backwards
1617 * compability and correct serialization
1620 serializer->doBool(&ir->bQMMM);
1622 serializer->doInt(&qmmmScheme);
1623 real unusedScalefactor;
1624 serializer->doReal(&unusedScalefactor);
1626 // this is still used in Mimic
1627 serializer->doInt(&ir->opts.ngQM);
1628 if (ir->opts.ngQM > 0 && ir->bQMMM)
1630 /* We leave in dummy i/o for removed parameters to avoid
1631 * changing the tpr format.
1633 std::vector<int> dummyIntVec(4 * ir->opts.ngQM, 0);
1634 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1635 dummyIntVec.clear();
1637 // std::vector<bool> has no data()
1638 std::vector<char> dummyBoolVec(ir->opts.ngQM * sizeof(bool) / sizeof(char));
1639 serializer->doBoolArray(reinterpret_cast<bool*>(dummyBoolVec.data()), dummyBoolVec.size());
1640 dummyBoolVec.clear();
1642 dummyIntVec.resize(2 * ir->opts.ngQM, 0);
1643 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1644 dummyIntVec.clear();
1646 std::vector<real> dummyRealVec(2 * ir->opts.ngQM, 0);
1647 serializer->doRealArray(dummyRealVec.data(), dummyRealVec.size());
1648 dummyRealVec.clear();
1650 dummyIntVec.resize(3 * ir->opts.ngQM, 0);
1651 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1652 dummyIntVec.clear();
1654 /* end of QMMM stuff */
1657 if (file_version >= tpxv_GenericParamsForElectricField)
1659 if (serializer->reading())
1661 paramsObj.mergeObject(gmx::deserializeKeyValueTree(serializer));
1665 GMX_RELEASE_ASSERT(ir->params != nullptr,
1666 "Parameters should be present when writing inputrec");
1667 gmx::serializeKeyValueTree(*ir->params, serializer);
1670 if (serializer->reading())
1672 ir->params = new gmx::KeyValueTreeObject(paramsBuilder.build());
1673 // Initialize internal parameters to an empty kvt for all tpr versions
1674 ir->internalParameters = std::make_unique<gmx::KeyValueTreeObject>();
1677 if (file_version >= tpxv_GenericInternalParameters)
1679 if (serializer->reading())
1681 ir->internalParameters =
1682 std::make_unique<gmx::KeyValueTreeObject>(gmx::deserializeKeyValueTree(serializer));
1686 GMX_RELEASE_ASSERT(ir->internalParameters != nullptr,
1687 "Parameters should be present when writing inputrec");
1688 gmx::serializeKeyValueTree(*ir->internalParameters, serializer);
1694 static void do_harm(gmx::ISerializer* serializer, t_iparams* iparams)
1696 serializer->doReal(&iparams->harmonic.rA);
1697 serializer->doReal(&iparams->harmonic.krA);
1698 serializer->doReal(&iparams->harmonic.rB);
1699 serializer->doReal(&iparams->harmonic.krB);
1702 static void do_iparams(gmx::ISerializer* serializer, t_functype ftype, t_iparams* iparams, int file_version)
1715 do_harm(serializer, iparams);
1716 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && serializer->reading())
1718 /* Correct incorrect storage of parameters */
1719 iparams->pdihs.phiB = iparams->pdihs.phiA;
1720 iparams->pdihs.cpB = iparams->pdihs.cpA;
1724 serializer->doReal(&iparams->harmonic.rA);
1725 serializer->doReal(&iparams->harmonic.krA);
1727 case F_LINEAR_ANGLES:
1728 serializer->doReal(&iparams->linangle.klinA);
1729 serializer->doReal(&iparams->linangle.aA);
1730 serializer->doReal(&iparams->linangle.klinB);
1731 serializer->doReal(&iparams->linangle.aB);
1734 serializer->doReal(&iparams->fene.bm);
1735 serializer->doReal(&iparams->fene.kb);
1739 serializer->doReal(&iparams->restraint.lowA);
1740 serializer->doReal(&iparams->restraint.up1A);
1741 serializer->doReal(&iparams->restraint.up2A);
1742 serializer->doReal(&iparams->restraint.kA);
1743 serializer->doReal(&iparams->restraint.lowB);
1744 serializer->doReal(&iparams->restraint.up1B);
1745 serializer->doReal(&iparams->restraint.up2B);
1746 serializer->doReal(&iparams->restraint.kB);
1752 serializer->doReal(&iparams->tab.kA);
1753 serializer->doInt(&iparams->tab.table);
1754 serializer->doReal(&iparams->tab.kB);
1756 case F_CROSS_BOND_BONDS:
1757 serializer->doReal(&iparams->cross_bb.r1e);
1758 serializer->doReal(&iparams->cross_bb.r2e);
1759 serializer->doReal(&iparams->cross_bb.krr);
1761 case F_CROSS_BOND_ANGLES:
1762 serializer->doReal(&iparams->cross_ba.r1e);
1763 serializer->doReal(&iparams->cross_ba.r2e);
1764 serializer->doReal(&iparams->cross_ba.r3e);
1765 serializer->doReal(&iparams->cross_ba.krt);
1767 case F_UREY_BRADLEY:
1768 serializer->doReal(&iparams->u_b.thetaA);
1769 serializer->doReal(&iparams->u_b.kthetaA);
1770 serializer->doReal(&iparams->u_b.r13A);
1771 serializer->doReal(&iparams->u_b.kUBA);
1772 if (file_version >= 79)
1774 serializer->doReal(&iparams->u_b.thetaB);
1775 serializer->doReal(&iparams->u_b.kthetaB);
1776 serializer->doReal(&iparams->u_b.r13B);
1777 serializer->doReal(&iparams->u_b.kUBB);
1781 iparams->u_b.thetaB = iparams->u_b.thetaA;
1782 iparams->u_b.kthetaB = iparams->u_b.kthetaA;
1783 iparams->u_b.r13B = iparams->u_b.r13A;
1784 iparams->u_b.kUBB = iparams->u_b.kUBA;
1787 case F_QUARTIC_ANGLES:
1788 serializer->doReal(&iparams->qangle.theta);
1789 serializer->doRealArray(iparams->qangle.c, 5);
1792 serializer->doReal(&iparams->bham.a);
1793 serializer->doReal(&iparams->bham.b);
1794 serializer->doReal(&iparams->bham.c);
1797 serializer->doReal(&iparams->morse.b0A);
1798 serializer->doReal(&iparams->morse.cbA);
1799 serializer->doReal(&iparams->morse.betaA);
1800 if (file_version >= 79)
1802 serializer->doReal(&iparams->morse.b0B);
1803 serializer->doReal(&iparams->morse.cbB);
1804 serializer->doReal(&iparams->morse.betaB);
1808 iparams->morse.b0B = iparams->morse.b0A;
1809 iparams->morse.cbB = iparams->morse.cbA;
1810 iparams->morse.betaB = iparams->morse.betaA;
1814 serializer->doReal(&iparams->cubic.b0);
1815 serializer->doReal(&iparams->cubic.kb);
1816 serializer->doReal(&iparams->cubic.kcub);
1818 case F_CONNBONDS: break;
1819 case F_POLARIZATION: serializer->doReal(&iparams->polarize.alpha); break;
1821 serializer->doReal(&iparams->anharm_polarize.alpha);
1822 serializer->doReal(&iparams->anharm_polarize.drcut);
1823 serializer->doReal(&iparams->anharm_polarize.khyp);
1826 serializer->doReal(&iparams->wpol.al_x);
1827 serializer->doReal(&iparams->wpol.al_y);
1828 serializer->doReal(&iparams->wpol.al_z);
1829 serializer->doReal(&iparams->wpol.rOH);
1830 serializer->doReal(&iparams->wpol.rHH);
1831 serializer->doReal(&iparams->wpol.rOD);
1834 serializer->doReal(&iparams->thole.a);
1835 serializer->doReal(&iparams->thole.alpha1);
1836 serializer->doReal(&iparams->thole.alpha2);
1837 serializer->doReal(&iparams->thole.rfac);
1840 serializer->doReal(&iparams->lj.c6);
1841 serializer->doReal(&iparams->lj.c12);
1844 serializer->doReal(&iparams->lj14.c6A);
1845 serializer->doReal(&iparams->lj14.c12A);
1846 serializer->doReal(&iparams->lj14.c6B);
1847 serializer->doReal(&iparams->lj14.c12B);
1850 serializer->doReal(&iparams->ljc14.fqq);
1851 serializer->doReal(&iparams->ljc14.qi);
1852 serializer->doReal(&iparams->ljc14.qj);
1853 serializer->doReal(&iparams->ljc14.c6);
1854 serializer->doReal(&iparams->ljc14.c12);
1856 case F_LJC_PAIRS_NB:
1857 serializer->doReal(&iparams->ljcnb.qi);
1858 serializer->doReal(&iparams->ljcnb.qj);
1859 serializer->doReal(&iparams->ljcnb.c6);
1860 serializer->doReal(&iparams->ljcnb.c12);
1866 serializer->doReal(&iparams->pdihs.phiA);
1867 serializer->doReal(&iparams->pdihs.cpA);
1868 serializer->doReal(&iparams->pdihs.phiB);
1869 serializer->doReal(&iparams->pdihs.cpB);
1870 serializer->doInt(&iparams->pdihs.mult);
1873 serializer->doReal(&iparams->pdihs.phiA);
1874 serializer->doReal(&iparams->pdihs.cpA);
1877 serializer->doInt(&iparams->disres.label);
1878 serializer->doInt(&iparams->disres.type);
1879 serializer->doReal(&iparams->disres.low);
1880 serializer->doReal(&iparams->disres.up1);
1881 serializer->doReal(&iparams->disres.up2);
1882 serializer->doReal(&iparams->disres.kfac);
1885 serializer->doInt(&iparams->orires.ex);
1886 serializer->doInt(&iparams->orires.label);
1887 serializer->doInt(&iparams->orires.power);
1888 serializer->doReal(&iparams->orires.c);
1889 serializer->doReal(&iparams->orires.obs);
1890 serializer->doReal(&iparams->orires.kfac);
1893 if (file_version < 82)
1895 serializer->doInt(&idum);
1896 serializer->doInt(&idum);
1898 serializer->doReal(&iparams->dihres.phiA);
1899 serializer->doReal(&iparams->dihres.dphiA);
1900 serializer->doReal(&iparams->dihres.kfacA);
1901 if (file_version >= 82)
1903 serializer->doReal(&iparams->dihres.phiB);
1904 serializer->doReal(&iparams->dihres.dphiB);
1905 serializer->doReal(&iparams->dihres.kfacB);
1909 iparams->dihres.phiB = iparams->dihres.phiA;
1910 iparams->dihres.dphiB = iparams->dihres.dphiA;
1911 iparams->dihres.kfacB = iparams->dihres.kfacA;
1915 serializer->doRvec(&iparams->posres.pos0A);
1916 serializer->doRvec(&iparams->posres.fcA);
1917 serializer->doRvec(&iparams->posres.pos0B);
1918 serializer->doRvec(&iparams->posres.fcB);
1921 serializer->doInt(&iparams->fbposres.geom);
1922 serializer->doRvec(&iparams->fbposres.pos0);
1923 serializer->doReal(&iparams->fbposres.r);
1924 serializer->doReal(&iparams->fbposres.k);
1926 case F_CBTDIHS: serializer->doRealArray(iparams->cbtdihs.cbtcA, NR_CBTDIHS); break;
1928 // Fall-through intended
1930 /* Fourier dihedrals are internally represented
1931 * as Ryckaert-Bellemans since those are faster to compute.
1933 serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
1934 serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
1938 serializer->doReal(&iparams->constr.dA);
1939 serializer->doReal(&iparams->constr.dB);
1942 serializer->doReal(&iparams->settle.doh);
1943 serializer->doReal(&iparams->settle.dhh);
1945 case F_VSITE1: break; // VSite1 has 0 parameters
1947 case F_VSITE2FD: serializer->doReal(&iparams->vsite.a); break;
1951 serializer->doReal(&iparams->vsite.a);
1952 serializer->doReal(&iparams->vsite.b);
1957 serializer->doReal(&iparams->vsite.a);
1958 serializer->doReal(&iparams->vsite.b);
1959 serializer->doReal(&iparams->vsite.c);
1962 serializer->doInt(&iparams->vsiten.n);
1963 serializer->doReal(&iparams->vsiten.a);
1965 case F_GB12_NOLONGERUSED:
1966 case F_GB13_NOLONGERUSED:
1967 case F_GB14_NOLONGERUSED:
1968 // Implicit solvent parameters can still be read, but never used
1969 if (serializer->reading())
1971 if (file_version < 68)
1973 serializer->doReal(&rdum);
1974 serializer->doReal(&rdum);
1975 serializer->doReal(&rdum);
1976 serializer->doReal(&rdum);
1978 if (file_version < tpxv_RemoveImplicitSolvation)
1980 serializer->doReal(&rdum);
1981 serializer->doReal(&rdum);
1982 serializer->doReal(&rdum);
1983 serializer->doReal(&rdum);
1984 serializer->doReal(&rdum);
1989 serializer->doInt(&iparams->cmap.cmapA);
1990 serializer->doInt(&iparams->cmap.cmapB);
1993 gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d", ftype,
1994 interaction_function[ftype].name, __FILE__, __LINE__);
1998 static void do_ilist(gmx::ISerializer* serializer, InteractionList* ilist)
2000 int nr = ilist->size();
2001 serializer->doInt(&nr);
2002 if (serializer->reading())
2004 ilist->iatoms.resize(nr);
2006 serializer->doIntArray(ilist->iatoms.data(), ilist->size());
2009 static void do_ffparams(gmx::ISerializer* serializer, gmx_ffparams_t* ffparams, int file_version)
2011 serializer->doInt(&ffparams->atnr);
2012 int numTypes = ffparams->numTypes();
2013 serializer->doInt(&numTypes);
2014 if (serializer->reading())
2016 ffparams->functype.resize(numTypes);
2017 ffparams->iparams.resize(numTypes);
2019 /* Read/write all the function types */
2020 serializer->doIntArray(ffparams->functype.data(), ffparams->functype.size());
2022 if (file_version >= 66)
2024 serializer->doDouble(&ffparams->reppow);
2028 ffparams->reppow = 12.0;
2031 serializer->doReal(&ffparams->fudgeQQ);
2033 /* Check whether all these function types are supported by the code.
2034 * In practice the code is backwards compatible, which means that the
2035 * numbering may have to be altered from old numbering to new numbering
2037 for (int i = 0; i < ffparams->numTypes(); i++)
2039 if (serializer->reading())
2041 /* Loop over file versions */
2042 for (int k = 0; k < NFTUPD; k++)
2044 /* Compare the read file_version to the update table */
2045 if ((file_version < ftupd[k].fvnr) && (ffparams->functype[i] >= ftupd[k].ftype))
2047 ffparams->functype[i] += 1;
2052 do_iparams(serializer, ffparams->functype[i], &ffparams->iparams[i], file_version);
2056 static void add_settle_atoms(InteractionList* ilist)
2060 /* Settle used to only store the first atom: add the other two */
2061 ilist->iatoms.resize(2 * ilist->size());
2062 for (i = ilist->size() / 4 - 1; i >= 0; i--)
2064 ilist->iatoms[4 * i + 0] = ilist->iatoms[2 * i + 0];
2065 ilist->iatoms[4 * i + 1] = ilist->iatoms[2 * i + 1];
2066 ilist->iatoms[4 * i + 2] = ilist->iatoms[2 * i + 1] + 1;
2067 ilist->iatoms[4 * i + 3] = ilist->iatoms[2 * i + 1] + 2;
2071 static void do_ilists(gmx::ISerializer* serializer, InteractionLists* ilists, int file_version)
2073 GMX_RELEASE_ASSERT(ilists, "Need a valid ilists object");
2074 GMX_RELEASE_ASSERT(ilists->size() == F_NRE,
2075 "The code needs to be in sync with InteractionLists");
2077 for (int j = 0; j < F_NRE; j++)
2079 InteractionList& ilist = (*ilists)[j];
2080 gmx_bool bClear = FALSE;
2081 if (serializer->reading())
2083 for (int k = 0; k < NFTUPD; k++)
2085 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
2093 ilist.iatoms.clear();
2097 do_ilist(serializer, &ilist);
2098 if (file_version < 78 && j == F_SETTLE && !ilist.empty())
2100 add_settle_atoms(&ilist);
2106 static void do_block(gmx::ISerializer* serializer, t_block* block)
2108 serializer->doInt(&block->nr);
2109 if (serializer->reading())
2111 if ((block->nalloc_index > 0) && (nullptr != block->index))
2113 sfree(block->index);
2115 block->nalloc_index = block->nr + 1;
2116 snew(block->index, block->nalloc_index);
2118 serializer->doIntArray(block->index, block->nr + 1);
2121 static void doListOfLists(gmx::ISerializer* serializer, gmx::ListOfLists<int>* listOfLists)
2123 int numLists = listOfLists->ssize();
2124 serializer->doInt(&numLists);
2125 int numElements = listOfLists->elementsView().ssize();
2126 serializer->doInt(&numElements);
2127 if (serializer->reading())
2129 std::vector<int> listRanges(numLists + 1);
2130 serializer->doIntArray(listRanges.data(), numLists + 1);
2131 std::vector<int> elements(numElements);
2132 serializer->doIntArray(elements.data(), numElements);
2133 *listOfLists = gmx::ListOfLists<int>(std::move(listRanges), std::move(elements));
2137 serializer->doIntArray(const_cast<int*>(listOfLists->listRangesView().data()), numLists + 1);
2138 serializer->doIntArray(const_cast<int*>(listOfLists->elementsView().data()), numElements);
2142 /* This is a primitive routine to make it possible to translate atomic numbers
2143 * to element names when reading TPR files, without making the Gromacs library
2144 * directory a dependency on mdrun (which is the case if we need elements.dat).
2146 static const char* atomicnumber_to_element(int atomicnumber)
2150 /* This does not have to be complete, so we only include elements likely
2151 * to occur in PDB files.
2153 switch (atomicnumber)
2155 case 1: p = "H"; break;
2156 case 5: p = "B"; break;
2157 case 6: p = "C"; break;
2158 case 7: p = "N"; break;
2159 case 8: p = "O"; break;
2160 case 9: p = "F"; break;
2161 case 11: p = "Na"; break;
2162 case 12: p = "Mg"; break;
2163 case 15: p = "P"; break;
2164 case 16: p = "S"; break;
2165 case 17: p = "Cl"; break;
2166 case 18: p = "Ar"; break;
2167 case 19: p = "K"; break;
2168 case 20: p = "Ca"; break;
2169 case 25: p = "Mn"; break;
2170 case 26: p = "Fe"; break;
2171 case 28: p = "Ni"; break;
2172 case 29: p = "Cu"; break;
2173 case 30: p = "Zn"; break;
2174 case 35: p = "Br"; break;
2175 case 47: p = "Ag"; break;
2176 default: p = ""; break;
2182 static void do_atom(gmx::ISerializer* serializer, t_atom* atom)
2184 serializer->doReal(&atom->m);
2185 serializer->doReal(&atom->q);
2186 serializer->doReal(&atom->mB);
2187 serializer->doReal(&atom->qB);
2188 serializer->doUShort(&atom->type);
2189 serializer->doUShort(&atom->typeB);
2190 serializer->doInt(&atom->ptype);
2191 serializer->doInt(&atom->resind);
2192 serializer->doInt(&atom->atomnumber);
2193 if (serializer->reading())
2195 /* Set element string from atomic number if present.
2196 * This routine returns an empty string if the name is not found.
2198 std::strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
2199 /* avoid warnings about potentially unterminated string */
2200 atom->elem[3] = '\0';
2204 static void do_grps(gmx::ISerializer* serializer, gmx::ArrayRef<AtomGroupIndices> grps)
2206 for (auto& group : grps)
2208 int size = group.size();
2209 serializer->doInt(&size);
2210 if (serializer->reading())
2214 serializer->doIntArray(group.data(), size);
2218 static void do_symstr(gmx::ISerializer* serializer, char*** nm, t_symtab* symtab)
2222 if (serializer->reading())
2224 serializer->doInt(&ls);
2225 *nm = get_symtab_handle(symtab, ls);
2229 ls = lookup_symtab(symtab, *nm);
2230 serializer->doInt(&ls);
2234 static void do_strstr(gmx::ISerializer* serializer, int nstr, char*** nm, t_symtab* symtab)
2238 for (j = 0; (j < nstr); j++)
2240 do_symstr(serializer, &(nm[j]), symtab);
2244 static void do_resinfo(gmx::ISerializer* serializer, int n, t_resinfo* ri, t_symtab* symtab, int file_version)
2248 for (j = 0; (j < n); j++)
2250 do_symstr(serializer, &(ri[j].name), symtab);
2251 if (file_version >= 63)
2253 serializer->doInt(&ri[j].nr);
2254 serializer->doUChar(&ri[j].ic);
2264 static void do_atoms(gmx::ISerializer* serializer, t_atoms* atoms, t_symtab* symtab, int file_version)
2268 serializer->doInt(&atoms->nr);
2269 serializer->doInt(&atoms->nres);
2270 if (serializer->reading())
2272 /* Since we have always written all t_atom properties in the tpr file
2273 * (at least for all backward compatible versions), we don't store
2274 * but simple set the booleans here.
2276 atoms->haveMass = TRUE;
2277 atoms->haveCharge = TRUE;
2278 atoms->haveType = TRUE;
2279 atoms->haveBState = TRUE;
2280 atoms->havePdbInfo = FALSE;
2282 snew(atoms->atom, atoms->nr);
2283 snew(atoms->atomname, atoms->nr);
2284 snew(atoms->atomtype, atoms->nr);
2285 snew(atoms->atomtypeB, atoms->nr);
2286 snew(atoms->resinfo, atoms->nres);
2287 atoms->pdbinfo = nullptr;
2291 GMX_RELEASE_ASSERT(atoms->haveMass && atoms->haveCharge && atoms->haveType && atoms->haveBState,
2292 "Mass, charge, atomtype and B-state parameters should be present in "
2293 "t_atoms when writing a tpr file");
2295 for (i = 0; (i < atoms->nr); i++)
2297 do_atom(serializer, &atoms->atom[i]);
2299 do_strstr(serializer, atoms->nr, atoms->atomname, symtab);
2300 do_strstr(serializer, atoms->nr, atoms->atomtype, symtab);
2301 do_strstr(serializer, atoms->nr, atoms->atomtypeB, symtab);
2303 do_resinfo(serializer, atoms->nres, atoms->resinfo, symtab, file_version);
2306 static void do_groups(gmx::ISerializer* serializer, SimulationGroups* groups, t_symtab* symtab)
2308 do_grps(serializer, groups->groups);
2309 int numberOfGroupNames = groups->groupNames.size();
2310 serializer->doInt(&numberOfGroupNames);
2311 if (serializer->reading())
2313 groups->groupNames.resize(numberOfGroupNames);
2315 do_strstr(serializer, numberOfGroupNames, groups->groupNames.data(), symtab);
2316 for (auto group : gmx::keysOf(groups->groupNumbers))
2318 int numberOfGroupNumbers = groups->numberOfGroupNumbers(group);
2319 serializer->doInt(&numberOfGroupNumbers);
2320 if (numberOfGroupNumbers != 0)
2322 if (serializer->reading())
2324 groups->groupNumbers[group].resize(numberOfGroupNumbers);
2326 serializer->doUCharArray(groups->groupNumbers[group].data(), numberOfGroupNumbers);
2331 static void do_atomtypes(gmx::ISerializer* serializer, t_atomtypes* atomtypes, int file_version)
2335 serializer->doInt(&atomtypes->nr);
2337 if (serializer->reading())
2339 snew(atomtypes->atomnumber, j);
2341 if (serializer->reading() && file_version < tpxv_RemoveImplicitSolvation)
2343 std::vector<real> dummy(atomtypes->nr, 0);
2344 serializer->doRealArray(dummy.data(), dummy.size());
2345 serializer->doRealArray(dummy.data(), dummy.size());
2346 serializer->doRealArray(dummy.data(), dummy.size());
2348 serializer->doIntArray(atomtypes->atomnumber, j);
2350 if (serializer->reading() && file_version >= 60 && file_version < tpxv_RemoveImplicitSolvation)
2352 std::vector<real> dummy(atomtypes->nr, 0);
2353 serializer->doRealArray(dummy.data(), dummy.size());
2354 serializer->doRealArray(dummy.data(), dummy.size());
2358 static void do_symtab(gmx::ISerializer* serializer, t_symtab* symtab)
2363 serializer->doInt(&symtab->nr);
2365 if (serializer->reading())
2367 snew(symtab->symbuf, 1);
2368 symbuf = symtab->symbuf;
2369 symbuf->bufsize = nr;
2370 snew(symbuf->buf, nr);
2371 for (i = 0; (i < nr); i++)
2374 serializer->doString(&buf);
2375 symbuf->buf[i] = gmx_strdup(buf.c_str());
2380 symbuf = symtab->symbuf;
2381 while (symbuf != nullptr)
2383 for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
2385 std::string buf = symbuf->buf[i];
2386 serializer->doString(&buf);
2389 symbuf = symbuf->next;
2393 gmx_fatal(FARGS, "nr of symtab strings left: %d", nr);
2398 static void do_cmap(gmx::ISerializer* serializer, gmx_cmap_t* cmap_grid)
2401 int ngrid = cmap_grid->cmapdata.size();
2402 serializer->doInt(&ngrid);
2403 serializer->doInt(&cmap_grid->grid_spacing);
2405 int gs = cmap_grid->grid_spacing;
2406 int nelem = gs * gs;
2408 if (serializer->reading())
2410 cmap_grid->cmapdata.resize(ngrid);
2412 for (int i = 0; i < ngrid; i++)
2414 cmap_grid->cmapdata[i].cmap.resize(4 * nelem);
2418 for (int i = 0; i < ngrid; i++)
2420 for (int j = 0; j < nelem; j++)
2422 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4]);
2423 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 1]);
2424 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 2]);
2425 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 3]);
2431 static void do_moltype(gmx::ISerializer* serializer, gmx_moltype_t* molt, t_symtab* symtab, int file_version)
2433 do_symstr(serializer, &(molt->name), symtab);
2435 do_atoms(serializer, &molt->atoms, symtab, file_version);
2437 do_ilists(serializer, &molt->ilist, file_version);
2439 /* TODO: Remove the obsolete charge group index from the file */
2441 cgs.nr = molt->atoms.nr;
2442 cgs.nalloc_index = cgs.nr + 1;
2443 snew(cgs.index, cgs.nalloc_index);
2444 for (int i = 0; i < cgs.nr + 1; i++)
2448 do_block(serializer, &cgs);
2451 /* This used to be in the atoms struct */
2452 doListOfLists(serializer, &molt->excls);
2455 static void do_molblock(gmx::ISerializer* serializer, gmx_molblock_t* molb, int numAtomsPerMolecule)
2457 serializer->doInt(&molb->type);
2458 serializer->doInt(&molb->nmol);
2459 /* To maintain forward topology reading compatibility, we store #atoms.
2460 * TODO: Change this to conditional reading of a dummy int when we
2461 * increase tpx_generation.
2463 serializer->doInt(&numAtomsPerMolecule);
2464 /* Position restraint coordinates */
2465 int numPosres_xA = molb->posres_xA.size();
2466 serializer->doInt(&numPosres_xA);
2467 if (numPosres_xA > 0)
2469 if (serializer->reading())
2471 molb->posres_xA.resize(numPosres_xA);
2473 serializer->doRvecArray(as_rvec_array(molb->posres_xA.data()), numPosres_xA);
2475 int numPosres_xB = molb->posres_xB.size();
2476 serializer->doInt(&numPosres_xB);
2477 if (numPosres_xB > 0)
2479 if (serializer->reading())
2481 molb->posres_xB.resize(numPosres_xB);
2483 serializer->doRvecArray(as_rvec_array(molb->posres_xB.data()), numPosres_xB);
2487 static void set_disres_npair(gmx_mtop_t* mtop)
2489 gmx_mtop_ilistloop_t iloop;
2492 gmx::ArrayRef<t_iparams> ip = mtop->ffparams.iparams;
2494 iloop = gmx_mtop_ilistloop_init(mtop);
2495 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
2497 const InteractionList& il = (*ilist)[F_DISRES];
2501 gmx::ArrayRef<const int> a = il.iatoms;
2503 for (int i = 0; i < il.size(); i += 3)
2506 if (i + 3 == il.size() || ip[a[i]].disres.label != ip[a[i + 3]].disres.label)
2508 ip[a[i]].disres.npair = npair;
2516 static void do_mtop(gmx::ISerializer* serializer, gmx_mtop_t* mtop, int file_version)
2518 do_symtab(serializer, &(mtop->symtab));
2520 do_symstr(serializer, &(mtop->name), &(mtop->symtab));
2522 do_ffparams(serializer, &mtop->ffparams, file_version);
2524 int nmoltype = mtop->moltype.size();
2525 serializer->doInt(&nmoltype);
2526 if (serializer->reading())
2528 mtop->moltype.resize(nmoltype);
2530 for (gmx_moltype_t& moltype : mtop->moltype)
2532 do_moltype(serializer, &moltype, &mtop->symtab, file_version);
2535 int nmolblock = mtop->molblock.size();
2536 serializer->doInt(&nmolblock);
2537 if (serializer->reading())
2539 mtop->molblock.resize(nmolblock);
2541 for (gmx_molblock_t& molblock : mtop->molblock)
2543 int numAtomsPerMolecule = (serializer->reading() ? 0 : mtop->moltype[molblock.type].atoms.nr);
2544 do_molblock(serializer, &molblock, numAtomsPerMolecule);
2546 serializer->doInt(&mtop->natoms);
2548 if (file_version >= tpxv_IntermolecularBondeds)
2550 serializer->doBool(&mtop->bIntermolecularInteractions);
2551 if (mtop->bIntermolecularInteractions)
2553 if (serializer->reading())
2555 mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
2557 do_ilists(serializer, mtop->intermolecular_ilist.get(), file_version);
2562 mtop->bIntermolecularInteractions = FALSE;
2565 do_atomtypes(serializer, &(mtop->atomtypes), file_version);
2567 if (file_version >= 65)
2569 do_cmap(serializer, &mtop->ffparams.cmap_grid);
2573 mtop->ffparams.cmap_grid.grid_spacing = 0;
2574 mtop->ffparams.cmap_grid.cmapdata.clear();
2577 do_groups(serializer, &mtop->groups, &(mtop->symtab));
2579 mtop->haveMoleculeIndices = true;
2581 if (file_version >= tpxv_StoreNonBondedInteractionExclusionGroup)
2583 std::int64_t intermolecularExclusionGroupSize = gmx::ssize(mtop->intermolecularExclusionGroup);
2584 serializer->doInt64(&intermolecularExclusionGroupSize);
2585 GMX_RELEASE_ASSERT(intermolecularExclusionGroupSize >= 0,
2586 "Number of atoms with excluded intermolecular non-bonded interactions "
2588 mtop->intermolecularExclusionGroup.resize(intermolecularExclusionGroupSize); // no effect when writing
2589 serializer->doIntArray(mtop->intermolecularExclusionGroup.data(),
2590 mtop->intermolecularExclusionGroup.size());
2593 if (serializer->reading())
2595 close_symtab(&(mtop->symtab));
2600 * Read the first part of the TPR file to find general system information.
2602 * If \p TopOnlyOK is true then we can read even future versions
2603 * of tpx files, provided the \p fileGeneration hasn't changed.
2604 * If it is false, we need the \p ir too, and bail out
2605 * if the file is newer than the program.
2607 * The version and generation of the topology (see top of this file)
2608 * are returned in the two last arguments, if those arguments are non-nullptr.
2610 * If possible, we will read the \p ir even when \p TopOnlyOK is true.
2612 * \param[in,out] serializer The serializer used to handle header processing.
2613 * \param[in,out] tpx File header datastructure.
2614 * \param[in] filename The name of the file being read/written
2615 * \param[in,out] fio File handle.
2616 * \param[in] TopOnlyOK If not reading \p ir is fine or not.
2618 static void do_tpxheader(gmx::FileIOXdrSerializer* serializer,
2620 const char* filename,
2628 /* XDR binary topology file */
2629 precision = sizeof(real);
2631 std::string fileTag;
2632 if (serializer->reading())
2634 serializer->doString(&buf);
2635 if (std::strncmp(buf.c_str(), "VERSION", 7) != 0)
2639 "Can not read file %s,\n"
2640 " this file is from a GROMACS version which is older than 2.0\n"
2641 " Make a new one with grompp or use a gro or pdb file, if possible",
2644 // We need to know the precision used to write the TPR file, to match it
2645 // to the precision of the currently running binary. If the precisions match
2646 // there is no problem, but mismatching precision needs to be accounted for
2647 // by reading into temporary variables of the correct precision instead
2648 // of the desired target datastructures.
2649 serializer->doInt(&precision);
2650 tpx->isDouble = (precision == sizeof(double));
2651 if ((precision != sizeof(float)) && !tpx->isDouble)
2654 "Unknown precision in file %s: real is %d bytes "
2655 "instead of %zu or %zu",
2656 filename, precision, sizeof(float), sizeof(double));
2658 gmx_fio_setprecision(fio, tpx->isDouble);
2659 fprintf(stderr, "Reading file %s, %s (%s precision)\n", filename, buf.c_str(),
2660 tpx->isDouble ? "double" : "single");
2664 buf = gmx::formatString("VERSION %s", gmx_version());
2665 serializer->doString(&buf);
2666 gmx_fio_setprecision(fio, tpx->isDouble);
2667 serializer->doInt(&precision);
2668 fileTag = gmx::formatString("%s", tpx_tag);
2671 /* Check versions! */
2672 serializer->doInt(&tpx->fileVersion);
2674 /* This is for backward compatibility with development versions 77-79
2675 * where the tag was, mistakenly, placed before the generation,
2676 * which would cause a segv instead of a proper error message
2677 * when reading the topology only from tpx with <77 code.
2679 if (tpx->fileVersion >= 77 && tpx->fileVersion <= 79)
2681 serializer->doString(&fileTag);
2684 serializer->doInt(&tpx->fileGeneration);
2686 if (tpx->fileVersion >= 81)
2688 serializer->doString(&fileTag);
2690 if (serializer->reading())
2692 if (tpx->fileVersion < 77)
2694 /* Versions before 77 don't have the tag, set it to release */
2695 fileTag = gmx::formatString("%s", TPX_TAG_RELEASE);
2698 if (fileTag != tpx_tag)
2700 fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n", fileTag.c_str(), tpx_tag);
2702 /* We only support reading tpx files with the same tag as the code
2703 * or tpx files with the release tag and with lower version number.
2705 if (fileTag != TPX_TAG_RELEASE && tpx->fileVersion < tpx_version)
2708 "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' "
2709 "with program for tpx version %d, tag '%s'",
2710 filename, tpx->fileVersion, fileTag.c_str(), tpx_version, tpx_tag);
2715 if ((tpx->fileVersion <= tpx_incompatible_version)
2716 || ((tpx->fileVersion > tpx_version) && !TopOnlyOK) || (tpx->fileGeneration > tpx_generation)
2717 || tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
2719 gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program", filename,
2720 tpx->fileVersion, tpx_version);
2723 serializer->doInt(&tpx->natoms);
2724 serializer->doInt(&tpx->ngtc);
2726 if (tpx->fileVersion < 62)
2728 serializer->doInt(&idum);
2729 serializer->doReal(&rdum);
2731 if (tpx->fileVersion >= 79)
2733 serializer->doInt(&tpx->fep_state);
2735 serializer->doReal(&tpx->lambda);
2736 serializer->doBool(&tpx->bIr);
2737 serializer->doBool(&tpx->bTop);
2738 serializer->doBool(&tpx->bX);
2739 serializer->doBool(&tpx->bV);
2740 serializer->doBool(&tpx->bF);
2741 serializer->doBool(&tpx->bBox);
2743 if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
2745 if (!serializer->reading())
2747 GMX_RELEASE_ASSERT(tpx->sizeOfTprBody != 0,
2748 "Not possible to write new file with zero TPR body size");
2750 serializer->doInt64(&tpx->sizeOfTprBody);
2753 if ((tpx->fileGeneration > tpx_generation))
2755 /* This can only happen if TopOnlyOK=TRUE */
2760 #define do_test(serializer, b, p) \
2761 if ((serializer)->reading() && ((p) != nullptr) && !(b)) \
2762 gmx_fatal(FARGS, "No %s in input file", #p)
2765 * Process the first part of the TPR into the state datastructure.
2767 * Due to the structure of the legacy code, it is necessary
2768 * to split up the state reading into two parts, with the
2769 * box and legacy temperature coupling processed before the
2770 * topology datastructures.
2772 * See the documentation for do_tpx_body for the correct order of
2773 * the operations for reading a tpr file.
2775 * \param[in] serializer Abstract serializer used to read/write data.
2776 * \param[in] tpx The file header data.
2777 * \param[in, out] state Global state data.
2779 static void do_tpx_state_first(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state)
2781 if (serializer->reading())
2784 init_gtc_state(state, tpx->ngtc, 0, 0);
2786 do_test(serializer, tpx->bBox, state->box);
2789 serializer->doRvecArray(state->box, DIM);
2790 if (tpx->fileVersion >= 51)
2792 serializer->doRvecArray(state->box_rel, DIM);
2796 /* We initialize box_rel after reading the inputrec */
2797 clear_mat(state->box_rel);
2799 serializer->doRvecArray(state->boxv, DIM);
2800 if (tpx->fileVersion < 56)
2803 serializer->doRvecArray(mdum, DIM);
2807 if (state->ngtc > 0)
2810 snew(dumv, state->ngtc);
2811 if (tpx->fileVersion < 69)
2813 serializer->doRealArray(dumv, state->ngtc);
2815 /* These used to be the Berendsen tcoupl_lambda's */
2816 serializer->doRealArray(dumv, state->ngtc);
2822 * Process global topology data.
2824 * See the documentation for do_tpx_body for the correct order of
2825 * the operations for reading a tpr file.
2827 * \param[in] serializer Abstract serializer used to read/write data.
2828 * \param[in] tpx The file header data.
2829 * \param[in,out] mtop Global topology.
2831 static void do_tpx_mtop(gmx::ISerializer* serializer, TpxFileHeader* tpx, gmx_mtop_t* mtop)
2833 do_test(serializer, tpx->bTop, mtop);
2838 do_mtop(serializer, mtop, tpx->fileVersion);
2839 set_disres_npair(mtop);
2845 do_mtop(serializer, &dum_top, tpx->fileVersion);
2850 * Process coordinate vectors for state data.
2852 * Main part of state gets processed here.
2854 * See the documentation for do_tpx_body for the correct order of
2855 * the operations for reading a tpr file.
2857 * \param[in] serializer Abstract serializer used to read/write data.
2858 * \param[in] tpx The file header data.
2859 * \param[in,out] state Global state data.
2860 * \param[in,out] x Individual coordinates for processing, deprecated.
2861 * \param[in,out] v Individual velocities for processing, deprecated.
2863 static void do_tpx_state_second(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state, rvec* x, rvec* v)
2865 if (!serializer->reading())
2868 x == nullptr && v == nullptr,
2869 "Passing separate x and v pointers to do_tpx() is not supported when writing");
2873 GMX_RELEASE_ASSERT(!(x == nullptr && v != nullptr),
2874 "Passing x==NULL and v!=NULL is not supported");
2877 if (serializer->reading())
2881 // v is also nullptr by the above assertion, so we may
2882 // need to make memory in state for storing the contents
2886 state->flags |= (1 << estX);
2890 state->flags |= (1 << estV);
2892 state_change_natoms(state, tpx->natoms);
2898 x = state->x.rvec_array();
2899 v = state->v.rvec_array();
2901 do_test(serializer, tpx->bX, x);
2904 if (serializer->reading())
2906 state->flags |= (1 << estX);
2908 serializer->doRvecArray(x, tpx->natoms);
2911 do_test(serializer, tpx->bV, v);
2914 if (serializer->reading())
2916 state->flags |= (1 << estV);
2920 std::vector<gmx::RVec> dummyVelocities(tpx->natoms);
2921 serializer->doRvecArray(as_rvec_array(dummyVelocities.data()), tpx->natoms);
2925 serializer->doRvecArray(v, tpx->natoms);
2929 // No need to run do_test when the last argument is NULL
2932 std::vector<gmx::RVec> dummyForces(state->natoms);
2933 serializer->doRvecArray(as_rvec_array(dummyForces.data()), tpx->natoms);
2937 * Process simulation parameters.
2939 * See the documentation for do_tpx_body for the correct order of
2940 * the operations for reading a tpr file.
2942 * \param[in] serializer Abstract serializer used to read/write data.
2943 * \param[in] tpx The file header data.
2944 * \param[in,out] ir Datastructure with simulation parameters.
2946 static PbcType do_tpx_ir(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir)
2949 gmx_bool bPeriodicMols;
2951 /* Starting with tpx version 26, we have the inputrec
2952 * at the end of the file, so we can ignore it
2953 * if the file is never than the software (but still the
2954 * same generation - see comments at the top of this file.
2958 pbcType = PbcType::Unset;
2959 bPeriodicMols = FALSE;
2961 do_test(serializer, tpx->bIr, ir);
2964 if (tpx->fileVersion >= 53)
2966 /* Removed the pbc info from do_inputrec, since we always want it */
2967 if (!serializer->reading())
2969 pbcType = ir->pbcType;
2970 bPeriodicMols = ir->bPeriodicMols;
2972 serializer->doInt(reinterpret_cast<int*>(&pbcType));
2973 serializer->doBool(&bPeriodicMols);
2975 if (tpx->fileGeneration <= tpx_generation && ir)
2977 do_inputrec(serializer, ir, tpx->fileVersion);
2978 if (tpx->fileVersion < 53)
2980 pbcType = ir->pbcType;
2981 bPeriodicMols = ir->bPeriodicMols;
2984 if (serializer->reading() && ir && tpx->fileVersion >= 53)
2986 /* We need to do this after do_inputrec, since that initializes ir */
2987 ir->pbcType = pbcType;
2988 ir->bPeriodicMols = bPeriodicMols;
2995 * Correct and finalize read information.
2997 * If \p state is nullptr, skip the parts dependent on it.
2999 * See the documentation for do_tpx_body for the correct order of
3000 * the operations for reading a tpr file.
3002 * \param[in] tpx The file header used to check version numbers.
3003 * \param[out] ir Input rec that needs correction.
3004 * \param[out] state State needing correction.
3005 * \param[out] mtop Topology to finalize.
3007 static void do_tpx_finalize(TpxFileHeader* tpx, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
3009 if (tpx->fileVersion < 51 && state)
3011 set_box_rel(ir, state);
3015 if (state && state->ngtc == 0)
3017 /* Reading old version without tcoupl state data: set it */
3018 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
3020 if (tpx->bTop && mtop)
3022 if (tpx->fileVersion < 57)
3024 if (!mtop->moltype[0].ilist[F_DISRES].empty())
3026 ir->eDisre = edrSimple;
3030 ir->eDisre = edrNone;
3038 * Process TPR data for file reading/writing.
3040 * The TPR file gets processed in in four stages due to the organization
3041 * of the data within it.
3043 * First, state data for the box is processed in do_tpx_state_first.
3044 * This is followed by processing the topology in do_tpx_mtop.
3045 * Coordinate and velocity vectors are handled next in do_tpx_state_second.
3046 * The last file information processed is the collection of simulation parameters in do_tpx_ir.
3047 * When reading, a final processing step is undertaken at the end.
3049 * \param[in] serializer Abstract serializer used to read/write data.
3050 * \param[in] tpx The file header data.
3051 * \param[in,out] ir Datastructures with simulation parameters.
3052 * \param[in,out] state Global state data.
3053 * \param[in,out] x Individual coordinates for processing, deprecated.
3054 * \param[in,out] v Individual velocities for processing, deprecated.
3055 * \param[in,out] mtop Global topology.
3057 static PbcType do_tpx_body(gmx::ISerializer* serializer,
3067 do_tpx_state_first(serializer, tpx, state);
3069 do_tpx_mtop(serializer, tpx, mtop);
3072 do_tpx_state_second(serializer, tpx, state, x, v);
3074 PbcType pbcType = do_tpx_ir(serializer, tpx, ir);
3075 if (serializer->reading())
3077 do_tpx_finalize(tpx, ir, state, mtop);
3083 * Overload for do_tpx_body that defaults to state vectors being nullptr.
3085 * \param[in] serializer Abstract serializer used to read/write data.
3086 * \param[in] tpx The file header data.
3087 * \param[in,out] ir Datastructures with simulation parameters.
3088 * \param[in,out] mtop Global topology.
3090 static PbcType do_tpx_body(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir, gmx_mtop_t* mtop)
3092 return do_tpx_body(serializer, tpx, ir, nullptr, nullptr, nullptr, mtop);
3095 static t_fileio* open_tpx(const char* fn, const char* mode)
3097 return gmx_fio_open(fn, mode);
3100 static void close_tpx(t_fileio* fio)
3106 * Fill information into the header only from state before writing.
3108 * Populating the header needs to be independent from writing the information
3109 * to file to allow things like writing the raw byte stream.
3111 * \param[in] state The current simulation state. Can't write without it.
3112 * \param[in] ir Parameter and system information.
3113 * \param[in] mtop Global topology.
3114 * \returns Fully populated header.
3116 static TpxFileHeader populateTpxHeader(const t_state& state, const t_inputrec* ir, const gmx_mtop_t* mtop)
3118 TpxFileHeader header;
3119 header.natoms = state.natoms;
3120 header.ngtc = state.ngtc;
3121 header.fep_state = state.fep_state;
3122 header.lambda = state.lambda[efptFEP];
3123 header.bIr = ir != nullptr;
3124 header.bTop = mtop != nullptr;
3125 header.bX = (state.flags & (1 << estX)) != 0;
3126 header.bV = (state.flags & (1 << estV)) != 0;
3129 header.fileVersion = tpx_version;
3130 header.fileGeneration = tpx_generation;
3131 header.isDouble = (sizeof(real) == sizeof(double));
3137 * Process the body of a TPR file as an opaque data buffer.
3139 * Reads/writes the information in \p buffer from/to the \p serializer
3140 * provided to the function. Does not interact with the actual
3141 * TPR datastructures but with an in memory representation of the
3142 * data, so that this data can be efficiently read or written from/to
3143 * an original source.
3145 * \param[in] serializer The abstract serializer used for reading or writing
3146 * the information in \p buffer.
3147 * \param[in,out] buffer Information from TPR file as char buffer.
3149 static void doTpxBodyBuffer(gmx::ISerializer* serializer, gmx::ArrayRef<char> buffer)
3151 serializer->doOpaque(buffer.data(), buffer.size());
3155 * Populates simulation datastructures.
3157 * Here the information from the serialization interface \p serializer
3158 * is used to first populate the datastructures containing the simulation
3159 * information. Depending on the version found in the header \p tpx,
3160 * this is done using the new reading of the data as one block from disk,
3161 * followed by complete deserialization of the information read from there.
3162 * Otherwise, the datastructures are populated as before one by one from disk.
3163 * The second version is the default for the legacy tools that read the
3164 * coordinates and velocities separate from the state.
3166 * After reading in the data, a separate buffer is populated from them
3167 * containing only \p ir and \p mtop that can be communicated directly
3168 * to nodes needing the information to set up a simulation.
3170 * \param[in] tpx The file header.
3171 * \param[in] serializer The Serialization interface used to read the TPR.
3172 * \param[out] ir Input rec to populate.
3173 * \param[out] state State vectors to populate.
3174 * \param[out] x Coordinates to populate if needed.
3175 * \param[out] v Velocities to populate if needed.
3176 * \param[out] mtop Global topology to populate.
3178 * \returns Partial de-serialized TPR used for communication to nodes.
3180 static PartialDeserializedTprFile readTpxBody(TpxFileHeader* tpx,
3181 gmx::ISerializer* serializer,
3188 PartialDeserializedTprFile partialDeserializedTpr;
3189 if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
3191 partialDeserializedTpr.body.resize(tpx->sizeOfTprBody);
3192 partialDeserializedTpr.header = *tpx;
3193 doTpxBodyBuffer(serializer, partialDeserializedTpr.body);
3195 partialDeserializedTpr.pbcType =
3196 completeTprDeserialization(&partialDeserializedTpr, ir, state, x, v, mtop);
3200 partialDeserializedTpr.pbcType = do_tpx_body(serializer, tpx, ir, state, x, v, mtop);
3202 // Update header to system info for communication to nodes.
3203 // As we only need to communicate the inputrec and mtop to other nodes,
3204 // we prepare a new char buffer with the information we have already read
3206 partialDeserializedTpr.header = populateTpxHeader(*state, ir, mtop);
3207 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3208 // but since we just used the default XDR format (which is big endian) for the TPR
3209 // header it would cause third-party libraries reading our raw data to tear their hair
3210 // if we swap the endian in the middle of the file, so we stick to big endian in the
3211 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3212 gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3213 do_tpx_body(&tprBodySerializer, &partialDeserializedTpr.header, ir, mtop);
3214 partialDeserializedTpr.body = tprBodySerializer.finishAndGetBuffer();
3216 return partialDeserializedTpr;
3219 /************************************************************
3221 * The following routines are the exported ones
3223 ************************************************************/
3225 TpxFileHeader readTpxHeader(const char* fileName, bool canReadTopologyOnly)
3229 fio = open_tpx(fileName, "r");
3230 gmx::FileIOXdrSerializer serializer(fio);
3233 do_tpxheader(&serializer, &tpx, fileName, fio, canReadTopologyOnly);
3238 void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t* mtop)
3240 /* To write a state, we first need to write the state information to a buffer before
3241 * we append the raw bytes to the file. For this, the header information needs to be
3242 * populated before we write the main body because it has some information that is
3243 * otherwise not available.
3248 TpxFileHeader tpx = populateTpxHeader(*state, ir, mtop);
3249 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3250 // but since we just used the default XDR format (which is big endian) for the TPR
3251 // header it would cause third-party libraries reading our raw data to tear their hair
3252 // if we swap the endian in the middle of the file, so we stick to big endian in the
3253 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3254 gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3256 do_tpx_body(&tprBodySerializer, &tpx, const_cast<t_inputrec*>(ir), const_cast<t_state*>(state),
3257 nullptr, nullptr, const_cast<gmx_mtop_t*>(mtop));
3259 std::vector<char> tprBody = tprBodySerializer.finishAndGetBuffer();
3260 tpx.sizeOfTprBody = tprBody.size();
3262 fio = open_tpx(fn, "w");
3263 gmx::FileIOXdrSerializer serializer(fio);
3264 do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
3265 doTpxBodyBuffer(&serializer, tprBody);
3270 PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
3277 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3278 // but since we just used the default XDR format (which is big endian) for the TPR
3279 // header it would cause third-party libraries reading our raw data to tear their hair
3280 // if we swap the endian in the middle of the file, so we stick to big endian in the
3281 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3282 gmx::InMemoryDeserializer tprBodyDeserializer(partialDeserializedTpr->body,
3283 partialDeserializedTpr->header.isDouble,
3284 gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3285 return do_tpx_body(&tprBodyDeserializer, &partialDeserializedTpr->header, ir, state, x, v, mtop);
3288 PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
3292 return completeTprDeserialization(partialDeserializedTpr, ir, nullptr, nullptr, nullptr, mtop);
3295 PartialDeserializedTprFile read_tpx_state(const char* fn, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
3298 fio = open_tpx(fn, "r");
3299 gmx::FileIOXdrSerializer serializer(fio);
3300 PartialDeserializedTprFile partialDeserializedTpr;
3301 do_tpxheader(&serializer, &partialDeserializedTpr.header, fn, fio, ir == nullptr);
3302 partialDeserializedTpr =
3303 readTpxBody(&partialDeserializedTpr.header, &serializer, ir, state, nullptr, nullptr, mtop);
3305 return partialDeserializedTpr;
3308 PbcType read_tpx(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, gmx_mtop_t* mtop)
3314 fio = open_tpx(fn, "r");
3315 gmx::FileIOXdrSerializer serializer(fio);
3316 do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
3317 PartialDeserializedTprFile partialDeserializedTpr =
3318 readTpxBody(&tpx, &serializer, ir, &state, x, v, mtop);
3320 if (mtop != nullptr && natoms != nullptr)
3322 *natoms = mtop->natoms;
3326 copy_mat(state.box, box);
3328 return partialDeserializedTpr.pbcType;
3331 PbcType read_tpx_top(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, t_topology* top)
3336 pbcType = read_tpx(fn, ir, box, natoms, x, v, &mtop);
3338 *top = gmx_mtop_t_to_t_topology(&mtop, true);
3343 gmx_bool fn2bTPX(const char* file)
3345 return (efTPR == fn2ftp(file));
3348 void pr_tpxheader(FILE* fp, int indent, const char* title, const TpxFileHeader* sh)
3350 if (available(fp, sh, indent, title))
3352 indent = pr_title(fp, indent, title);
3353 pr_indent(fp, indent);
3354 fprintf(fp, "bIr = %spresent\n", sh->bIr ? "" : "not ");
3355 pr_indent(fp, indent);
3356 fprintf(fp, "bBox = %spresent\n", sh->bBox ? "" : "not ");
3357 pr_indent(fp, indent);
3358 fprintf(fp, "bTop = %spresent\n", sh->bTop ? "" : "not ");
3359 pr_indent(fp, indent);
3360 fprintf(fp, "bX = %spresent\n", sh->bX ? "" : "not ");
3361 pr_indent(fp, indent);
3362 fprintf(fp, "bV = %spresent\n", sh->bV ? "" : "not ");
3363 pr_indent(fp, indent);
3364 fprintf(fp, "bF = %spresent\n", sh->bF ? "" : "not ");
3366 pr_indent(fp, indent);
3367 fprintf(fp, "natoms = %d\n", sh->natoms);
3368 pr_indent(fp, indent);
3369 fprintf(fp, "lambda = %e\n", sh->lambda);
3370 pr_indent(fp, indent);
3371 fprintf(fp, "buffer size = %" PRId64 "\n", sh->sizeOfTprBody);