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40 /* This file is completely threadsafe - keep it that way! */
42 #include "gromacs/fileio/tpxio.h"
52 #include "gromacs/applied_forces/awh/read_params.h"
53 #include "gromacs/fileio/filetypes.h"
54 #include "gromacs/fileio/gmxfio.h"
55 #include "gromacs/fileio/gmxfio_xdr.h"
56 #include "gromacs/math/units.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/mdtypes/awh_history.h"
59 #include "gromacs/mdtypes/awh_params.h"
60 #include "gromacs/mdtypes/inputrec.h"
61 #include "gromacs/mdtypes/md_enums.h"
62 #include "gromacs/mdtypes/multipletimestepping.h"
63 #include "gromacs/mdtypes/pull_params.h"
64 #include "gromacs/mdtypes/state.h"
65 #include "gromacs/pbcutil/boxutilities.h"
66 #include "gromacs/pbcutil/pbc.h"
67 #include "gromacs/topology/block.h"
68 #include "gromacs/topology/ifunc.h"
69 #include "gromacs/topology/mtop_util.h"
70 #include "gromacs/topology/symtab.h"
71 #include "gromacs/topology/topology.h"
72 #include "gromacs/utility/arraysize.h"
73 #include "gromacs/utility/baseversion.h"
74 #include "gromacs/utility/cstringutil.h"
75 #include "gromacs/utility/fatalerror.h"
76 #include "gromacs/utility/futil.h"
77 #include "gromacs/utility/gmxassert.h"
78 #include "gromacs/utility/inmemoryserializer.h"
79 #include "gromacs/utility/iserializer.h"
80 #include "gromacs/utility/keyvaluetreebuilder.h"
81 #include "gromacs/utility/keyvaluetreeserializer.h"
82 #include "gromacs/utility/smalloc.h"
83 #include "gromacs/utility/snprintf.h"
84 #include "gromacs/utility/txtdump.h"
86 #define TPX_TAG_RELEASE "release"
88 /*! \brief Tag string for the file format written to run input files
89 * written by this version of the code.
91 * Change this if you want to change the run input format in a feature
92 * branch. This ensures that there will not be different run input
93 * formats around which cannot be distinguished, while not causing
94 * problems rebasing the feature branch onto upstream changes. When
95 * merging with mainstream GROMACS, set this tag string back to
96 * TPX_TAG_RELEASE, and instead add an element to tpxv.
98 static const std::string tpx_tag = TPX_TAG_RELEASE;
100 /*! \brief Enum of values that describe the contents of a tpr file
101 * whose format matches a version number
103 * The enum helps the code be more self-documenting and ensure merges
104 * do not silently resolve when two patches make the same bump. When
105 * adding new functionality, add a new element just above tpxv_Count
106 * in this enumeration, and write code below that does the right thing
107 * according to the value of file_version.
111 tpxv_ComputationalElectrophysiology =
112 96, /**< support for ion/water position swaps (computational electrophysiology) */
113 tpxv_Use64BitRandomSeed, /**< change ld_seed from int to int64_t */
114 tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, /**< potentials for supporting coarse-grained force fields */
115 tpxv_InteractiveMolecularDynamics, /**< interactive molecular dynamics (IMD) */
116 tpxv_RemoveObsoleteParameters1, /**< remove optimize_fft, dihre_fc, nstcheckpoint */
117 tpxv_PullCoordTypeGeom, /**< add pull type and geometry per group and flat-bottom */
118 tpxv_PullGeomDirRel, /**< add pull geometry direction-relative */
119 tpxv_IntermolecularBondeds, /**< permit inter-molecular bonded interactions in the topology */
120 tpxv_CompElWithSwapLayerOffset, /**< added parameters for improved CompEl setups */
121 tpxv_CompElPolyatomicIonsAndMultipleIonTypes, /**< CompEl now can handle polyatomic ions and more than two types of ions */
122 tpxv_RemoveAdress, /**< removed support for AdResS */
123 tpxv_PullCoordNGroup, /**< add ngroup to pull coord */
124 tpxv_RemoveTwinRange, /**< removed support for twin-range interactions */
125 tpxv_ReplacePullPrintCOM12, /**< Replaced print-com-1, 2 with pull-print-com */
126 tpxv_PullExternalPotential, /**< Added pull type external potential */
127 tpxv_GenericParamsForElectricField, /**< Introduced KeyValueTree and moved electric field parameters */
128 tpxv_AcceleratedWeightHistogram, /**< sampling with accelerated weight histogram method (AWH) */
129 tpxv_RemoveImplicitSolvation, /**< removed support for implicit solvation */
130 tpxv_PullPrevStepCOMAsReference, /**< Enabled using the COM of the pull group of the last frame as reference for PBC */
131 tpxv_MimicQMMM, /**< Introduced support for MiMiC QM/MM interface */
132 tpxv_PullAverage, /**< Added possibility to output average pull force and position */
133 tpxv_GenericInternalParameters, /**< Added internal parameters for mdrun modules*/
134 tpxv_VSite2FD, /**< Added 2FD type virtual site */
135 tpxv_AddSizeField, /**< Added field with information about the size of the serialized tpr file in bytes, excluding the header */
136 tpxv_StoreNonBondedInteractionExclusionGroup, /**< Store the non bonded interaction exclusion group in the topology */
137 tpxv_VSite1, /**< Added 1 type virtual site */
138 tpxv_MTS, /**< Added multiple time stepping */
139 tpxv_RemovedConstantAcceleration, /**< Removed support for constant acceleration NEMD. */
140 tpxv_TransformationPullCoord, /**< Support for transformation pull coordinates */
141 tpxv_Count /**< the total number of tpxv versions */
144 /*! \brief Version number of the file format written to run input
145 * files by this version of the code.
147 * The tpx_version increases whenever the file format in the main
148 * development branch changes, due to an extension of the tpxv enum above.
149 * Backward compatibility for reading old run input files is maintained
150 * by checking this version number against that of the file and then using
151 * the correct code path.
153 * When developing a feature branch that needs to change the run input
154 * file format, change tpx_tag instead. */
155 static const int tpx_version = tpxv_Count - 1;
159 * Enum keeping track of incompatible changes for older TPR versions.
161 * The enum should be updated with a new field when editing the TOPOLOGY
162 * or HEADER of the tpx format. In particular, updating ftupd or
163 * changing the fields of TprHeaderVersion often trigger such needs.
165 * This way we can maintain forward compatibility too for all analysis tools
166 * and/or external programs that only need to know the atom/residue names,
167 * charges, and bond connectivity.
169 * It first appeared in tpx version 26, when I also moved the inputrecord
170 * to the end of the tpx file, so we can just skip it if we only
173 * In particular, it must be increased when adding new elements to
174 * ftupd, so that old code can read new .tpr files.
176 enum class TpxGeneration : int
178 Initial = 26, //! First version is 26
179 AddSizeField, //! TPR header modified for writing as a block.
180 AddVSite1, //! ftupd changed to include VSite1 type.
181 Count //! Number of entries.
184 //! Value of Current TPR generation.
185 static const int tpx_generation = static_cast<int>(TpxGeneration::Count) - 1;
187 /* This number should be the most recent backwards incompatible version
188 * I.e., if this number is 9, we cannot read tpx version 9 with this code.
190 static const int tpx_incompatible_version = 57; // GMX4.0 has version 58
193 /* Struct used to maintain tpx compatibility when function types are added */
196 int fvnr; /* file version number in which the function type first appeared */
197 int ftype; /* function type */
201 * TODO The following three lines make little sense, please clarify if
202 * you've had to work out how ftupd works.
204 * The entries should be ordered in:
205 * 1. ascending function type number
206 * 2. ascending file version number
208 * Because we support reading of old .tpr file versions (even when
209 * mdrun can no longer run the simulation), we need to be able to read
210 * obsolete t_interaction_function types. Any data read from such
211 * fields is discarded. Their names have _NOLONGERUSED appended to
212 * them to make things clear.
214 * When adding to or making breaking changes to reading this struct,
215 * update TpxGeneration.
217 static const t_ftupd ftupd[] = {
218 { 70, F_RESTRBONDS },
219 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
220 { 76, F_LINEAR_ANGLES },
221 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
222 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
224 { 60, F_GB12_NOLONGERUSED },
225 { 61, F_GB13_NOLONGERUSED },
226 { 61, F_GB14_NOLONGERUSED },
227 { 72, F_GBPOL_NOLONGERUSED },
228 { 72, F_NPSOLVATION_NOLONGERUSED },
230 { 76, F_ANHARM_POL },
232 { tpxv_VSite1, F_VSITE1 },
233 { tpxv_VSite2FD, F_VSITE2FD },
234 { tpxv_GenericInternalParameters, F_DENSITYFITTING },
235 { 69, F_VTEMP_NOLONGERUSED },
246 { 79, F_DVDL_RESTRAINT },
247 { 79, F_DVDL_TEMPERATURE },
249 #define NFTUPD asize(ftupd)
251 /**************************************************************
253 * Now the higer level routines that do io of the structures and arrays
255 **************************************************************/
256 static void do_pullgrp_tpx_pre95(gmx::ISerializer* serializer, t_pull_group* pgrp, t_pull_coord* pcrd)
260 int numAtoms = pgrp->ind.size();
261 serializer->doInt(&numAtoms);
262 pgrp->ind.resize(numAtoms);
263 serializer->doIntArray(pgrp->ind.data(), numAtoms);
264 int numWeights = pgrp->weight.size();
265 serializer->doInt(&numWeights);
266 pgrp->weight.resize(numWeights);
267 serializer->doRealArray(pgrp->weight.data(), numWeights);
268 serializer->doInt(&pgrp->pbcatom);
269 serializer->doRvec(&pcrd->vec.as_vec());
270 clear_rvec(pcrd->origin);
271 serializer->doRvec(&tmp);
273 serializer->doReal(&pcrd->rate);
274 serializer->doReal(&pcrd->k);
275 serializer->doReal(&pcrd->kB);
278 static void do_pull_group(gmx::ISerializer* serializer, t_pull_group* pgrp)
280 int numAtoms = pgrp->ind.size();
281 serializer->doInt(&numAtoms);
282 pgrp->ind.resize(numAtoms);
283 serializer->doIntArray(pgrp->ind.data(), numAtoms);
284 int numWeights = pgrp->weight.size();
285 serializer->doInt(&numWeights);
286 pgrp->weight.resize(numWeights);
287 serializer->doRealArray(pgrp->weight.data(), numWeights);
288 serializer->doInt(&pgrp->pbcatom);
291 static void do_pull_coord(gmx::ISerializer* serializer,
294 PullingAlgorithm ePullOld,
295 PullGroupGeometry eGeomOld,
298 if (file_version >= tpxv_PullCoordNGroup)
300 serializer->doEnumAsInt(&pcrd->eType);
301 if (file_version >= tpxv_PullExternalPotential)
303 if (pcrd->eType == PullingAlgorithm::External)
305 serializer->doString(&pcrd->externalPotentialProvider);
309 pcrd->externalPotentialProvider.clear();
314 if (serializer->reading())
316 pcrd->externalPotentialProvider.clear();
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->doEnumAsInt(&pcrd->eGeom);
324 serializer->doInt(&pcrd->ngroup);
325 if (pcrd->ngroup <= c_pullCoordNgroupMax)
327 serializer->doIntArray(pcrd->group.data(), 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.as_vec());
344 if (file_version >= tpxv_TransformationPullCoord)
346 serializer->doString(&pcrd->expression);
350 if (serializer->reading())
352 pcrd->expression.clear();
359 serializer->doInt(&pcrd->group[0]);
360 serializer->doInt(&pcrd->group[1]);
361 if (file_version >= tpxv_PullCoordTypeGeom)
363 pcrd->ngroup = (pcrd->eGeom == PullGroupGeometry::DirectionRelative ? 4 : 2);
364 serializer->doEnumAsInt(&pcrd->eType);
365 serializer->doEnumAsInt(&pcrd->eGeom);
366 if (pcrd->ngroup == 4)
368 serializer->doInt(&pcrd->group[2]);
369 serializer->doInt(&pcrd->group[3]);
371 serializer->doIvec(&pcrd->dim.as_vec());
375 pcrd->eType = ePullOld;
376 pcrd->eGeom = eGeomOld;
377 copy_ivec(dimOld, pcrd->dim);
380 serializer->doRvec(&pcrd->origin.as_vec());
381 serializer->doRvec(&pcrd->vec.as_vec());
382 if (file_version >= tpxv_PullCoordTypeGeom)
384 serializer->doBool(&pcrd->bStart);
388 /* This parameter is only printed, but not actually used by mdrun */
389 pcrd->bStart = FALSE;
391 serializer->doReal(&pcrd->init);
392 serializer->doReal(&pcrd->rate);
393 serializer->doReal(&pcrd->k);
394 serializer->doReal(&pcrd->kB);
397 static void do_expandedvals(gmx::ISerializer* serializer, t_expanded* expand, t_lambda* fepvals, int file_version)
399 int n_lambda = fepvals->n_lambda;
401 /* reset the lambda calculation window */
402 fepvals->lambda_start_n = 0;
403 fepvals->lambda_stop_n = n_lambda;
404 if (file_version >= 79)
408 expand->init_lambda_weights.resize(n_lambda);
409 serializer->doRealArray(expand->init_lambda_weights.data(), n_lambda);
410 serializer->doBool(&expand->bInit_weights);
413 serializer->doInt(&expand->nstexpanded);
414 serializer->doEnumAsInt(&expand->elmcmove);
415 serializer->doEnumAsInt(&expand->elamstats);
416 serializer->doInt(&expand->lmc_repeats);
417 serializer->doInt(&expand->gibbsdeltalam);
418 serializer->doInt(&expand->lmc_forced_nstart);
419 serializer->doInt(&expand->lmc_seed);
420 serializer->doReal(&expand->mc_temp);
421 serializer->doBool(&expand->bSymmetrizedTMatrix);
422 serializer->doInt(&expand->nstTij);
423 serializer->doInt(&expand->minvarmin);
424 serializer->doInt(&expand->c_range);
425 serializer->doReal(&expand->wl_scale);
426 serializer->doReal(&expand->wl_ratio);
427 serializer->doReal(&expand->init_wl_delta);
428 serializer->doBool(&expand->bWLoneovert);
429 serializer->doEnumAsInt(&expand->elmceq);
430 serializer->doInt(&expand->equil_steps);
431 serializer->doInt(&expand->equil_samples);
432 serializer->doInt(&expand->equil_n_at_lam);
433 serializer->doReal(&expand->equil_wl_delta);
434 serializer->doReal(&expand->equil_ratio);
438 static void do_simtempvals(gmx::ISerializer* serializer, t_simtemp* simtemp, int n_lambda, int file_version)
440 if (file_version >= 79)
442 serializer->doEnumAsInt(&simtemp->eSimTempScale);
443 serializer->doReal(&simtemp->simtemp_high);
444 serializer->doReal(&simtemp->simtemp_low);
447 if (serializer->reading())
449 simtemp->temperatures.resize(n_lambda);
451 serializer->doRealArray(simtemp->temperatures.data(), n_lambda);
456 static void do_imd(gmx::ISerializer* serializer, t_IMD* imd)
458 serializer->doInt(&imd->nat);
459 if (serializer->reading())
461 snew(imd->ind, imd->nat);
463 serializer->doIntArray(imd->ind, imd->nat);
466 static void do_fepvals(gmx::ISerializer* serializer, t_lambda* fepvals, int file_version)
468 /* i is defined in the ndo_double macro; use g to iterate. */
471 /* free energy values */
473 if (file_version >= 79)
475 serializer->doInt(&fepvals->init_fep_state);
476 serializer->doDouble(&fepvals->init_lambda);
477 serializer->doDouble(&fepvals->delta_lambda);
479 else if (file_version >= 59)
481 serializer->doDouble(&fepvals->init_lambda);
482 serializer->doDouble(&fepvals->delta_lambda);
486 serializer->doReal(&rdum);
487 fepvals->init_lambda = rdum;
488 serializer->doReal(&rdum);
489 fepvals->delta_lambda = rdum;
491 if (file_version >= 79)
493 serializer->doInt(&fepvals->n_lambda);
494 for (auto g : keysOf(fepvals->all_lambda))
496 if (fepvals->n_lambda > 0)
498 fepvals->all_lambda[g].resize(fepvals->n_lambda);
499 serializer->doDoubleArray(fepvals->all_lambda[g].data(), fepvals->n_lambda);
500 serializer->doBoolArray(fepvals->separate_dvdl.begin(), fepvals->separate_dvdl.size());
502 else if (fepvals->init_lambda >= 0)
504 fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
508 else if (file_version >= 64)
510 serializer->doInt(&fepvals->n_lambda);
511 if (serializer->reading())
513 /* still allocate the all_lambda array's contents. */
514 for (auto g : keysOf(fepvals->all_lambda))
516 if (fepvals->n_lambda > 0)
518 fepvals->all_lambda[g].resize(fepvals->n_lambda);
522 serializer->doDoubleArray(fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Fep].data(),
524 if (fepvals->init_lambda >= 0)
526 fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
528 if (serializer->reading())
530 /* copy the contents of the efptFEP lambda component to all
531 the other components */
532 for (auto g : keysOf(fepvals->all_lambda))
534 for (int h = 0; h < fepvals->n_lambda; h++)
536 if (g != FreeEnergyPerturbationCouplingType::Fep)
538 fepvals->all_lambda[g][h] =
539 fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Fep][h];
548 fepvals->n_lambda = 0;
549 if (fepvals->init_lambda >= 0)
551 fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
554 serializer->doReal(&fepvals->sc_alpha);
555 serializer->doInt(&fepvals->sc_power);
556 if (file_version >= 79)
558 serializer->doReal(&fepvals->sc_r_power);
562 fepvals->sc_r_power = 6.0;
564 if (fepvals->sc_r_power != 6.0)
566 gmx_fatal(FARGS, "sc-r-power=48 is no longer supported");
568 serializer->doReal(&fepvals->sc_sigma);
569 if (serializer->reading())
571 if (file_version >= 71)
573 fepvals->sc_sigma_min = fepvals->sc_sigma;
577 fepvals->sc_sigma_min = 0;
580 if (file_version >= 79)
582 serializer->doBool(&fepvals->bScCoul);
586 fepvals->bScCoul = TRUE;
588 if (file_version >= 64)
590 serializer->doInt(&fepvals->nstdhdl);
594 fepvals->nstdhdl = 1;
597 if (file_version >= 73)
599 serializer->doEnumAsInt(&fepvals->separate_dhdl_file);
600 serializer->doEnumAsInt(&fepvals->dhdl_derivatives);
604 fepvals->separate_dhdl_file = SeparateDhdlFile::Yes;
605 fepvals->dhdl_derivatives = DhDlDerivativeCalculation::Yes;
607 if (file_version >= 71)
609 serializer->doInt(&fepvals->dh_hist_size);
610 serializer->doDouble(&fepvals->dh_hist_spacing);
614 fepvals->dh_hist_size = 0;
615 fepvals->dh_hist_spacing = 0.1;
617 if (file_version >= 79)
619 serializer->doEnumAsInt(&fepvals->edHdLPrintEnergy);
623 fepvals->edHdLPrintEnergy = FreeEnergyPrintEnergy::No;
626 /* handle lambda_neighbors */
627 if ((file_version >= 83 && file_version < 90) || file_version >= 92)
629 serializer->doInt(&fepvals->lambda_neighbors);
630 if ((fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0)
631 && (fepvals->init_lambda < 0))
633 fepvals->lambda_start_n = (fepvals->init_fep_state - fepvals->lambda_neighbors);
634 fepvals->lambda_stop_n = (fepvals->init_fep_state + fepvals->lambda_neighbors + 1);
635 if (fepvals->lambda_start_n < 0)
637 fepvals->lambda_start_n = 0;
639 if (fepvals->lambda_stop_n >= fepvals->n_lambda)
641 fepvals->lambda_stop_n = fepvals->n_lambda;
646 fepvals->lambda_start_n = 0;
647 fepvals->lambda_stop_n = fepvals->n_lambda;
652 fepvals->lambda_start_n = 0;
653 fepvals->lambda_stop_n = fepvals->n_lambda;
657 static void do_pull(gmx::ISerializer* serializer, pull_params_t* pull, int file_version, PullingAlgorithm ePullOld)
659 PullGroupGeometry eGeomOld = PullGroupGeometry::Count;
663 if (file_version >= 95)
665 serializer->doInt(&pull->ngroup);
667 serializer->doInt(&pull->ncoord);
668 if (file_version < 95)
670 pull->ngroup = pull->ncoord + 1;
672 if (file_version < tpxv_PullCoordTypeGeom)
676 serializer->doEnumAsInt(&eGeomOld);
677 serializer->doIvec(&dimOld);
678 /* The inner cylinder radius, now removed */
679 serializer->doReal(&dum);
681 serializer->doReal(&pull->cylinder_r);
682 serializer->doReal(&pull->constr_tol);
683 if (file_version >= 95)
685 serializer->doBool(&pull->bPrintCOM);
686 /* With file_version < 95 this value is set below */
688 if (file_version >= tpxv_ReplacePullPrintCOM12)
690 serializer->doBool(&pull->bPrintRefValue);
691 serializer->doBool(&pull->bPrintComp);
693 else if (file_version >= tpxv_PullCoordTypeGeom)
696 serializer->doInt(&idum); /* used to be bPrintCOM2 */
697 serializer->doBool(&pull->bPrintRefValue);
698 serializer->doBool(&pull->bPrintComp);
702 pull->bPrintRefValue = FALSE;
703 pull->bPrintComp = TRUE;
705 serializer->doInt(&pull->nstxout);
706 serializer->doInt(&pull->nstfout);
707 if (file_version >= tpxv_PullPrevStepCOMAsReference)
709 serializer->doBool(&pull->bSetPbcRefToPrevStepCOM);
713 pull->bSetPbcRefToPrevStepCOM = FALSE;
715 pull->group.resize(pull->ngroup);
716 pull->coord.resize(pull->ncoord);
717 if (file_version < 95)
719 /* epullgPOS for position pulling, before epullgDIRPBC was removed */
720 if (eGeomOld == PullGroupGeometry::DirectionPBC)
722 gmx_fatal(FARGS, "pull-geometry=position is no longer supported");
724 if (eGeomOld > PullGroupGeometry::DirectionPBC)
728 case (PullGroupGeometry::DirectionRelative):
729 eGeomOld = PullGroupGeometry::DirectionPBC;
731 case (PullGroupGeometry::Angle):
732 eGeomOld = PullGroupGeometry::DirectionRelative;
734 case (PullGroupGeometry::Dihedral): eGeomOld = PullGroupGeometry::Angle; break;
735 case (PullGroupGeometry::AngleAxis): eGeomOld = PullGroupGeometry::Dihedral; break;
736 case (PullGroupGeometry::Count): eGeomOld = PullGroupGeometry::AngleAxis; break;
737 default: GMX_RELEASE_ASSERT(false, "Unhandled old pull type");
741 for (g = 0; g < pull->ngroup; g++)
743 /* We read and ignore a pull coordinate for group 0 */
744 do_pullgrp_tpx_pre95(serializer, &pull->group[g], &pull->coord[std::max(g - 1, 0)]);
747 pull->coord[g - 1].group[0] = 0;
748 pull->coord[g - 1].group[1] = g;
752 pull->bPrintCOM = (!pull->group[0].ind.empty());
756 for (g = 0; g < pull->ngroup; g++)
758 do_pull_group(serializer, &pull->group[g]);
760 for (g = 0; g < pull->ncoord; g++)
762 do_pull_coord(serializer, &pull->coord[g], file_version, ePullOld, eGeomOld, dimOld);
763 if (serializer->reading())
765 pull->coord[g].coordIndex = g;
769 if (file_version >= tpxv_PullAverage)
773 v = pull->bXOutAverage;
774 serializer->doBool(&v);
775 pull->bXOutAverage = v;
776 v = pull->bFOutAverage;
777 serializer->doBool(&v);
778 pull->bFOutAverage = v;
783 static void do_rotgrp(gmx::ISerializer* serializer, t_rotgrp* rotg)
785 serializer->doEnumAsInt(&rotg->eType);
786 if (serializer->reading())
789 serializer->doInt(&temp);
790 rotg->bMassW = static_cast<bool>(temp);
794 int temp = static_cast<int>(rotg->bMassW);
795 serializer->doInt(&temp);
797 serializer->doInt(&rotg->nat);
798 if (serializer->reading())
800 snew(rotg->ind, rotg->nat);
802 serializer->doIntArray(rotg->ind, rotg->nat);
803 if (serializer->reading())
805 snew(rotg->x_ref, rotg->nat);
807 serializer->doRvecArray(rotg->x_ref, rotg->nat);
808 serializer->doRvec(&rotg->inputVec);
809 serializer->doRvec(&rotg->pivot);
810 serializer->doReal(&rotg->rate);
811 serializer->doReal(&rotg->k);
812 serializer->doReal(&rotg->slab_dist);
813 serializer->doReal(&rotg->min_gaussian);
814 serializer->doReal(&rotg->eps);
815 serializer->doEnumAsInt(&rotg->eFittype);
816 serializer->doInt(&rotg->PotAngle_nstep);
817 serializer->doReal(&rotg->PotAngle_step);
820 static void do_rot(gmx::ISerializer* serializer, t_rot* rot)
824 serializer->doInt(&rot->ngrp);
825 serializer->doInt(&rot->nstrout);
826 serializer->doInt(&rot->nstsout);
827 if (serializer->reading())
829 snew(rot->grp, rot->ngrp);
831 for (g = 0; g < rot->ngrp; g++)
833 do_rotgrp(serializer, &rot->grp[g]);
838 static void do_swapgroup(gmx::ISerializer* serializer, t_swapGroup* g)
841 /* Name of the group or molecule */
843 if (serializer->reading())
845 serializer->doString(&buf);
846 g->molname = gmx_strdup(buf.c_str());
851 serializer->doString(&buf);
854 /* Number of atoms in the group */
855 serializer->doInt(&g->nat);
857 /* The group's atom indices */
858 if (serializer->reading())
860 snew(g->ind, g->nat);
862 serializer->doIntArray(g->ind, g->nat);
864 /* Requested counts for compartments A and B */
865 serializer->doIntArray(g->nmolReq.data(), static_cast<int>(Compartment::Count));
868 static void do_swapcoords_tpx(gmx::ISerializer* serializer, t_swapcoords* swap, int file_version)
870 /* Enums for better readability of the code */
883 if (file_version >= tpxv_CompElPolyatomicIonsAndMultipleIonTypes)
885 /* The total number of swap groups is the sum of the fixed groups
886 * (split0, split1, solvent), and the user-defined groups (2+ types of ions)
888 serializer->doInt(&swap->ngrp);
889 if (serializer->reading())
891 snew(swap->grp, swap->ngrp);
893 for (int ig = 0; ig < swap->ngrp; ig++)
895 do_swapgroup(serializer, &swap->grp[ig]);
897 serializer->doBool(&swap->massw_split[eChannel0]);
898 serializer->doBool(&swap->massw_split[eChannel1]);
899 serializer->doInt(&swap->nstswap);
900 serializer->doInt(&swap->nAverage);
901 serializer->doReal(&swap->threshold);
902 serializer->doReal(&swap->cyl0r);
903 serializer->doReal(&swap->cyl0u);
904 serializer->doReal(&swap->cyl0l);
905 serializer->doReal(&swap->cyl1r);
906 serializer->doReal(&swap->cyl1u);
907 serializer->doReal(&swap->cyl1l);
911 /*** Support reading older CompEl .tpr files ***/
913 /* In the original CompEl .tpr files, we always have 5 groups: */
915 snew(swap->grp, swap->ngrp);
917 swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname = gmx_strdup("split0"); // group 0: split0
918 swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname = gmx_strdup("split1"); // group 1: split1
919 swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname =
920 gmx_strdup("solvent"); // group 2: solvent
921 swap->grp[3].molname = gmx_strdup("anions"); // group 3: anions
922 swap->grp[4].molname = gmx_strdup("cations"); // group 4: cations
924 serializer->doInt(&swap->grp[3].nat);
925 serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].nat);
926 serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].nat);
927 serializer->doBool(&swap->massw_split[eChannel0]);
928 serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].nat);
929 serializer->doBool(&swap->massw_split[eChannel1]);
930 serializer->doInt(&swap->nstswap);
931 serializer->doInt(&swap->nAverage);
932 serializer->doReal(&swap->threshold);
933 serializer->doReal(&swap->cyl0r);
934 serializer->doReal(&swap->cyl0u);
935 serializer->doReal(&swap->cyl0l);
936 serializer->doReal(&swap->cyl1r);
937 serializer->doReal(&swap->cyl1u);
938 serializer->doReal(&swap->cyl1l);
940 // The order[] array keeps compatibility with older .tpr files
941 // by reading in the groups in the classic order
943 const int order[4] = { 3,
944 static_cast<int>(SwapGroupSplittingType::Solvent),
945 static_cast<int>(SwapGroupSplittingType::Split0),
946 static_cast<int>(SwapGroupSplittingType::Split1) };
948 for (int ig = 0; ig < 4; ig++)
951 snew(swap->grp[g].ind, swap->grp[g].nat);
952 serializer->doIntArray(swap->grp[g].ind, swap->grp[g].nat);
956 for (int j = eCompA; j <= eCompB; j++)
958 serializer->doInt(&swap->grp[3].nmolReq[j]); // group 3 = anions
959 serializer->doInt(&swap->grp[4].nmolReq[j]); // group 4 = cations
961 } /* End support reading older CompEl .tpr files */
963 if (file_version >= tpxv_CompElWithSwapLayerOffset)
965 serializer->doReal(&swap->bulkOffset[eCompA]);
966 serializer->doReal(&swap->bulkOffset[eCompB]);
970 static void do_legacy_efield(gmx::ISerializer* serializer, gmx::KeyValueTreeObjectBuilder* root)
972 const char* const dimName[] = { "x", "y", "z" };
974 auto appliedForcesObj = root->addObject("applied-forces");
975 auto efieldObj = appliedForcesObj.addObject("electric-field");
976 // The content of the tpr file for this feature has
977 // been the same since gromacs 4.0 that was used for
979 for (int j = 0; j < DIM; ++j)
982 serializer->doInt(&n);
983 serializer->doInt(&nt);
984 std::vector<real> aa(n + 1), phi(nt + 1), at(nt + 1), phit(nt + 1);
985 serializer->doRealArray(aa.data(), n);
986 serializer->doRealArray(phi.data(), n);
987 serializer->doRealArray(at.data(), nt);
988 serializer->doRealArray(phit.data(), nt);
994 "Can not handle tpr files with more than one electric field term per "
997 auto dimObj = efieldObj.addObject(dimName[j]);
998 dimObj.addValue<real>("E0", aa[0]);
999 dimObj.addValue<real>("omega", at[0]);
1000 dimObj.addValue<real>("t0", phi[0]);
1001 dimObj.addValue<real>("sigma", phit[0]);
1007 static void do_inputrec(gmx::ISerializer* serializer, t_inputrec* ir, int file_version)
1009 int i, j, k, idum = 0;
1011 gmx_bool bdum = false;
1013 if (file_version != tpx_version)
1015 /* Give a warning about features that are not accessible */
1016 fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n", file_version, tpx_version);
1019 if (file_version == 0)
1024 gmx::KeyValueTreeBuilder paramsBuilder;
1025 gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
1027 /* Basic inputrec stuff */
1028 serializer->doEnumAsInt(&ir->eI);
1029 if (file_version >= 62)
1031 serializer->doInt64(&ir->nsteps);
1035 serializer->doInt(&idum);
1039 if (file_version >= 62)
1041 serializer->doInt64(&ir->init_step);
1045 serializer->doInt(&idum);
1046 ir->init_step = idum;
1049 serializer->doInt(&ir->simulation_part);
1051 if (file_version >= tpxv_MTS)
1053 serializer->doBool(&ir->useMts);
1054 int numLevels = ir->mtsLevels.size();
1057 serializer->doInt(&numLevels);
1059 ir->mtsLevels.resize(numLevels);
1060 for (auto& mtsLevel : ir->mtsLevels)
1062 int forceGroups = mtsLevel.forceGroups.to_ulong();
1063 serializer->doInt(&forceGroups);
1064 mtsLevel.forceGroups = std::bitset<static_cast<int>(gmx::MtsForceGroups::Count)>(forceGroups);
1065 serializer->doInt(&mtsLevel.stepFactor);
1071 ir->mtsLevels.clear();
1074 if (file_version >= 67)
1076 serializer->doInt(&ir->nstcalcenergy);
1080 ir->nstcalcenergy = 1;
1082 if (file_version >= 81)
1084 serializer->doEnumAsInt(&ir->cutoff_scheme);
1085 if (file_version < 94)
1087 // Need to invert the scheme order
1088 switch (ir->cutoff_scheme)
1090 case (CutoffScheme::Group): ir->cutoff_scheme = CutoffScheme::Verlet; break;
1091 case (CutoffScheme::Verlet): ir->cutoff_scheme = CutoffScheme::Group; break;
1092 default: GMX_RELEASE_ASSERT(false, "Unhandled cutoff scheme type");
1098 ir->cutoff_scheme = CutoffScheme::Group;
1100 serializer->doInt(&idum); /* used to be ns_type; not used anymore */
1101 serializer->doInt(&ir->nstlist);
1102 serializer->doInt(&idum); /* used to be ndelta; not used anymore */
1104 serializer->doReal(&ir->rtpi);
1106 serializer->doInt(&ir->nstcomm);
1107 serializer->doEnumAsInt(&ir->comm_mode);
1109 /* ignore nstcheckpoint */
1110 if (file_version < tpxv_RemoveObsoleteParameters1)
1112 serializer->doInt(&idum);
1115 serializer->doInt(&ir->nstcgsteep);
1117 serializer->doInt(&ir->nbfgscorr);
1119 serializer->doInt(&ir->nstlog);
1120 serializer->doInt(&ir->nstxout);
1121 serializer->doInt(&ir->nstvout);
1122 serializer->doInt(&ir->nstfout);
1123 serializer->doInt(&ir->nstenergy);
1124 serializer->doInt(&ir->nstxout_compressed);
1125 if (file_version >= 59)
1127 serializer->doDouble(&ir->init_t);
1128 serializer->doDouble(&ir->delta_t);
1132 serializer->doReal(&rdum);
1134 serializer->doReal(&rdum);
1137 serializer->doReal(&ir->x_compression_precision);
1138 if (file_version >= 81)
1140 serializer->doReal(&ir->verletbuf_tol);
1144 ir->verletbuf_tol = 0;
1146 serializer->doReal(&ir->rlist);
1147 if (file_version >= 67 && file_version < tpxv_RemoveTwinRange)
1149 if (serializer->reading())
1151 // Reading such a file version could invoke the twin-range
1152 // scheme, about which mdrun should give a fatal error.
1153 real dummy_rlistlong = -1;
1154 serializer->doReal(&dummy_rlistlong);
1156 ir->useTwinRange = (ir->rlist > 0 && (dummy_rlistlong == 0 || dummy_rlistlong > ir->rlist));
1157 // When true, this forces mdrun to issue an error (regardless of
1158 // ir->cutoff_scheme).
1160 // Otherwise, grompp used to set rlistlong actively. Users
1161 // were probably also confused and set rlistlong == rlist.
1162 // However, in all remaining cases, it is safe to let
1163 // mdrun proceed normally.
1168 // No need to read or write anything
1169 ir->useTwinRange = false;
1171 if (file_version >= 82 && file_version != 90)
1173 // Multiple time-stepping is no longer enabled, but the old
1174 // support required the twin-range scheme, for which mdrun
1175 // already emits a fatal error.
1176 int dummy_nstcalclr = -1;
1177 serializer->doInt(&dummy_nstcalclr);
1179 serializer->doEnumAsInt(&ir->coulombtype);
1180 if (file_version >= 81)
1182 serializer->doEnumAsInt(&ir->coulomb_modifier);
1186 ir->coulomb_modifier = (ir->cutoff_scheme == CutoffScheme::Verlet ? InteractionModifiers::PotShift
1187 : InteractionModifiers::None);
1189 serializer->doReal(&ir->rcoulomb_switch);
1190 serializer->doReal(&ir->rcoulomb);
1191 serializer->doEnumAsInt(&ir->vdwtype);
1192 if (file_version >= 81)
1194 serializer->doEnumAsInt(&ir->vdw_modifier);
1198 ir->vdw_modifier = (ir->cutoff_scheme == CutoffScheme::Verlet ? InteractionModifiers::PotShift
1199 : InteractionModifiers::None);
1201 serializer->doReal(&ir->rvdw_switch);
1202 serializer->doReal(&ir->rvdw);
1203 serializer->doEnumAsInt(&ir->eDispCorr);
1204 serializer->doReal(&ir->epsilon_r);
1205 serializer->doReal(&ir->epsilon_rf);
1206 serializer->doReal(&ir->tabext);
1208 // This permits reading a .tpr file that used implicit solvent,
1209 // and later permitting mdrun to refuse to run it.
1210 if (serializer->reading())
1212 if (file_version < tpxv_RemoveImplicitSolvation)
1214 serializer->doInt(&idum);
1215 serializer->doInt(&idum);
1216 serializer->doReal(&rdum);
1217 serializer->doReal(&rdum);
1218 serializer->doInt(&idum);
1219 ir->implicit_solvent = (idum > 0);
1223 ir->implicit_solvent = false;
1225 if (file_version < tpxv_RemoveImplicitSolvation)
1227 serializer->doReal(&rdum);
1228 serializer->doReal(&rdum);
1229 serializer->doReal(&rdum);
1230 serializer->doReal(&rdum);
1231 if (file_version >= 60)
1233 serializer->doReal(&rdum);
1234 serializer->doInt(&idum);
1236 serializer->doReal(&rdum);
1240 if (file_version >= 81)
1242 serializer->doReal(&ir->fourier_spacing);
1246 ir->fourier_spacing = 0.0;
1248 serializer->doInt(&ir->nkx);
1249 serializer->doInt(&ir->nky);
1250 serializer->doInt(&ir->nkz);
1251 serializer->doInt(&ir->pme_order);
1252 serializer->doReal(&ir->ewald_rtol);
1254 if (file_version >= 93)
1256 serializer->doReal(&ir->ewald_rtol_lj);
1260 ir->ewald_rtol_lj = ir->ewald_rtol;
1262 serializer->doEnumAsInt(&ir->ewald_geometry);
1263 serializer->doReal(&ir->epsilon_surface);
1265 /* ignore bOptFFT */
1266 if (file_version < tpxv_RemoveObsoleteParameters1)
1268 serializer->doBool(&bdum);
1271 if (file_version >= 93)
1273 serializer->doEnumAsInt(&ir->ljpme_combination_rule);
1275 serializer->doBool(&ir->bContinuation);
1276 serializer->doEnumAsInt(&ir->etc);
1277 /* before version 18, ir->etc was a gmx_bool (ir->btc),
1278 * but the values 0 and 1 still mean no and
1279 * berendsen temperature coupling, respectively.
1281 if (file_version >= 79)
1283 serializer->doBool(&ir->bPrintNHChains);
1285 if (file_version >= 71)
1287 serializer->doInt(&ir->nsttcouple);
1291 ir->nsttcouple = ir->nstcalcenergy;
1293 serializer->doEnumAsInt(&ir->epc);
1294 serializer->doEnumAsInt(&ir->epct);
1295 if (file_version >= 71)
1297 serializer->doInt(&ir->nstpcouple);
1301 ir->nstpcouple = ir->nstcalcenergy;
1303 serializer->doReal(&ir->tau_p);
1304 serializer->doRvec(&ir->ref_p[XX]);
1305 serializer->doRvec(&ir->ref_p[YY]);
1306 serializer->doRvec(&ir->ref_p[ZZ]);
1307 serializer->doRvec(&ir->compress[XX]);
1308 serializer->doRvec(&ir->compress[YY]);
1309 serializer->doRvec(&ir->compress[ZZ]);
1310 serializer->doEnumAsInt(&ir->refcoord_scaling);
1311 serializer->doRvec(&ir->posres_com);
1312 serializer->doRvec(&ir->posres_comB);
1314 if (file_version < 79)
1316 serializer->doInt(&ir->andersen_seed);
1320 ir->andersen_seed = 0;
1323 serializer->doReal(&ir->shake_tol);
1325 serializer->doEnumAsInt(&ir->efep);
1326 if (serializer->reading())
1328 ir->fepvals = std::make_unique<t_lambda>();
1330 do_fepvals(serializer, ir->fepvals.get(), file_version);
1332 if (file_version >= 79)
1334 serializer->doBool(&ir->bSimTemp);
1337 ir->bSimTemp = TRUE;
1342 ir->bSimTemp = FALSE;
1346 if (serializer->reading())
1348 ir->simtempvals = std::make_unique<t_simtemp>();
1350 do_simtempvals(serializer, ir->simtempvals.get(), ir->fepvals->n_lambda, file_version);
1353 if (file_version >= 79)
1355 serializer->doBool(&ir->bExpanded);
1359 if (serializer->reading())
1361 ir->expandedvals = std::make_unique<t_expanded>();
1363 do_expandedvals(serializer, ir->expandedvals.get(), ir->fepvals.get(), file_version);
1366 serializer->doEnumAsInt(&ir->eDisre);
1367 serializer->doEnumAsInt(&ir->eDisreWeighting);
1368 serializer->doBool(&ir->bDisreMixed);
1369 serializer->doReal(&ir->dr_fc);
1370 serializer->doReal(&ir->dr_tau);
1371 serializer->doInt(&ir->nstdisreout);
1372 serializer->doReal(&ir->orires_fc);
1373 serializer->doReal(&ir->orires_tau);
1374 serializer->doInt(&ir->nstorireout);
1376 /* ignore dihre_fc */
1377 if (file_version < 79)
1379 serializer->doReal(&rdum);
1382 serializer->doReal(&ir->em_stepsize);
1383 serializer->doReal(&ir->em_tol);
1384 serializer->doBool(&ir->bShakeSOR);
1385 serializer->doInt(&ir->niter);
1386 serializer->doReal(&ir->fc_stepsize);
1387 serializer->doEnumAsInt(&ir->eConstrAlg);
1388 serializer->doInt(&ir->nProjOrder);
1389 serializer->doReal(&ir->LincsWarnAngle);
1390 serializer->doInt(&ir->nLincsIter);
1391 serializer->doReal(&ir->bd_fric);
1392 if (file_version >= tpxv_Use64BitRandomSeed)
1394 serializer->doInt64(&ir->ld_seed);
1398 serializer->doInt(&idum);
1402 for (i = 0; i < DIM; i++)
1404 serializer->doRvec(&ir->deform[i]);
1406 serializer->doReal(&ir->cos_accel);
1408 serializer->doInt(&ir->userint1);
1409 serializer->doInt(&ir->userint2);
1410 serializer->doInt(&ir->userint3);
1411 serializer->doInt(&ir->userint4);
1412 serializer->doReal(&ir->userreal1);
1413 serializer->doReal(&ir->userreal2);
1414 serializer->doReal(&ir->userreal3);
1415 serializer->doReal(&ir->userreal4);
1417 /* AdResS is removed, but we need to be able to read old files,
1418 and let mdrun refuse to run them */
1419 if (file_version >= 77 && file_version < tpxv_RemoveAdress)
1421 serializer->doBool(&ir->bAdress);
1424 int idum, numThermoForceGroups, numEnergyGroups;
1427 serializer->doInt(&idum);
1428 serializer->doReal(&rdum);
1429 serializer->doReal(&rdum);
1430 serializer->doReal(&rdum);
1431 serializer->doInt(&idum);
1432 serializer->doInt(&idum);
1433 serializer->doRvec(&rvecdum);
1434 serializer->doInt(&numThermoForceGroups);
1435 serializer->doReal(&rdum);
1436 serializer->doInt(&numEnergyGroups);
1437 serializer->doInt(&idum);
1439 if (numThermoForceGroups > 0)
1441 std::vector<int> idumn(numThermoForceGroups);
1442 serializer->doIntArray(idumn.data(), idumn.size());
1444 if (numEnergyGroups > 0)
1446 std::vector<int> idumn(numEnergyGroups);
1447 serializer->doIntArray(idumn.data(), idumn.size());
1453 ir->bAdress = FALSE;
1458 PullingAlgorithm ePullOld = PullingAlgorithm::Umbrella;
1460 if (file_version >= tpxv_PullCoordTypeGeom)
1462 serializer->doBool(&ir->bPull);
1466 serializer->doEnumAsInt(&ePullOld);
1467 ir->bPull = (ePullOld != PullingAlgorithm::Umbrella);
1468 /* We removed the first ePull=ePullNo for the enum */
1471 case (PullingAlgorithm::Umbrella): break; // this is equal to not using pulling
1472 case (PullingAlgorithm::Constraint): ePullOld = PullingAlgorithm::Umbrella; break;
1473 case (PullingAlgorithm::ConstantForce):
1474 ePullOld = PullingAlgorithm::Constraint;
1476 case (PullingAlgorithm::FlatBottom):
1477 ePullOld = PullingAlgorithm::ConstantForce;
1479 case (PullingAlgorithm::FlatBottomHigh):
1480 ePullOld = PullingAlgorithm::FlatBottom;
1482 case (PullingAlgorithm::External):
1483 ePullOld = PullingAlgorithm::FlatBottomHigh;
1485 case (PullingAlgorithm::Count): ePullOld = PullingAlgorithm::External; break;
1486 default: GMX_RELEASE_ASSERT(false, "Unhandled old pull algorithm");
1491 if (serializer->reading())
1493 ir->pull = std::make_unique<pull_params_t>();
1495 do_pull(serializer, ir->pull.get(), file_version, ePullOld);
1499 if (file_version >= tpxv_AcceleratedWeightHistogram)
1501 serializer->doBool(&ir->bDoAwh);
1505 if (serializer->reading())
1507 ir->awhParams = std::make_unique<gmx::AwhParams>(serializer);
1511 ir->awhParams->serialize(serializer);
1520 /* Enforced rotation */
1521 if (file_version >= 74)
1523 serializer->doBool(&ir->bRot);
1526 if (serializer->reading())
1530 do_rot(serializer, ir->rot);
1538 /* Interactive molecular dynamics */
1539 if (file_version >= tpxv_InteractiveMolecularDynamics)
1541 serializer->doBool(&ir->bIMD);
1544 if (serializer->reading())
1548 do_imd(serializer, ir->imd);
1553 /* We don't support IMD sessions for old .tpr files */
1558 serializer->doInt(&ir->opts.ngtc);
1559 if (file_version >= 69)
1561 serializer->doInt(&ir->opts.nhchainlength);
1565 ir->opts.nhchainlength = 1;
1567 int removedOptsNgacc = 0;
1568 if (serializer->reading() && file_version < tpxv_RemovedConstantAcceleration)
1570 serializer->doInt(&removedOptsNgacc);
1572 serializer->doInt(&ir->opts.ngfrz);
1573 serializer->doInt(&ir->opts.ngener);
1575 if (serializer->reading())
1577 snew(ir->opts.nrdf, ir->opts.ngtc);
1578 snew(ir->opts.ref_t, ir->opts.ngtc);
1579 snew(ir->opts.annealing, ir->opts.ngtc);
1580 snew(ir->opts.anneal_npoints, ir->opts.ngtc);
1581 snew(ir->opts.anneal_time, ir->opts.ngtc);
1582 snew(ir->opts.anneal_temp, ir->opts.ngtc);
1583 snew(ir->opts.tau_t, ir->opts.ngtc);
1584 snew(ir->opts.nFreeze, ir->opts.ngfrz);
1585 snew(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
1587 if (ir->opts.ngtc > 0)
1589 serializer->doRealArray(ir->opts.nrdf, ir->opts.ngtc);
1590 serializer->doRealArray(ir->opts.ref_t, ir->opts.ngtc);
1591 serializer->doRealArray(ir->opts.tau_t, ir->opts.ngtc);
1593 if (ir->opts.ngfrz > 0)
1595 serializer->doIvecArray(ir->opts.nFreeze, ir->opts.ngfrz);
1597 if (serializer->reading() && file_version < tpxv_RemovedConstantAcceleration && removedOptsNgacc > 0)
1599 std::vector<gmx::RVec> dummy;
1600 dummy.resize(removedOptsNgacc);
1601 serializer->doRvecArray(reinterpret_cast<rvec*>(dummy.data()), removedOptsNgacc);
1602 ir->useConstantAcceleration = std::any_of(dummy.begin(), dummy.end(), [](const gmx::RVec& vec) {
1603 return vec[XX] != 0.0 || vec[YY] != 0.0 || vec[ZZ] != 0.0;
1608 ir->useConstantAcceleration = false;
1610 serializer->doIntArray(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
1612 /* First read the lists with annealing and npoints for each group */
1613 serializer->doEnumArrayAsInt(ir->opts.annealing, ir->opts.ngtc);
1614 serializer->doIntArray(ir->opts.anneal_npoints, ir->opts.ngtc);
1615 for (j = 0; j < (ir->opts.ngtc); j++)
1617 k = ir->opts.anneal_npoints[j];
1618 if (serializer->reading())
1620 snew(ir->opts.anneal_time[j], k);
1621 snew(ir->opts.anneal_temp[j], k);
1623 serializer->doRealArray(ir->opts.anneal_time[j], k);
1624 serializer->doRealArray(ir->opts.anneal_temp[j], k);
1628 serializer->doInt(&ir->nwall);
1629 serializer->doEnumAsInt(&ir->wall_type);
1630 serializer->doReal(&ir->wall_r_linpot);
1631 serializer->doInt(&ir->wall_atomtype[0]);
1632 serializer->doInt(&ir->wall_atomtype[1]);
1633 serializer->doReal(&ir->wall_density[0]);
1634 serializer->doReal(&ir->wall_density[1]);
1635 serializer->doReal(&ir->wall_ewald_zfac);
1638 /* Cosine stuff for electric fields */
1639 if (file_version < tpxv_GenericParamsForElectricField)
1641 do_legacy_efield(serializer, ¶msObj);
1645 if (file_version >= tpxv_ComputationalElectrophysiology)
1647 serializer->doEnumAsInt(&ir->eSwapCoords);
1648 if (ir->eSwapCoords != SwapType::No)
1650 if (serializer->reading())
1654 do_swapcoords_tpx(serializer, ir->swap, file_version);
1658 /* QMMM reading - despite defunct we require reading for backwards
1659 * compability and correct serialization
1662 serializer->doBool(&ir->bQMMM);
1664 serializer->doInt(&qmmmScheme);
1665 real unusedScalefactor;
1666 serializer->doReal(&unusedScalefactor);
1668 // this is still used in Mimic
1669 serializer->doInt(&ir->opts.ngQM);
1670 if (ir->opts.ngQM > 0 && ir->bQMMM)
1672 /* We leave in dummy i/o for removed parameters to avoid
1673 * changing the tpr format.
1675 std::vector<int> dummyIntVec(4 * ir->opts.ngQM, 0);
1676 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1677 dummyIntVec.clear();
1679 // std::vector<bool> has no data()
1680 std::vector<char> dummyBoolVec(ir->opts.ngQM * sizeof(bool) / sizeof(char));
1681 serializer->doBoolArray(reinterpret_cast<bool*>(dummyBoolVec.data()), dummyBoolVec.size());
1682 dummyBoolVec.clear();
1684 dummyIntVec.resize(2 * ir->opts.ngQM, 0);
1685 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1686 dummyIntVec.clear();
1688 std::vector<real> dummyRealVec(2 * ir->opts.ngQM, 0);
1689 serializer->doRealArray(dummyRealVec.data(), dummyRealVec.size());
1690 dummyRealVec.clear();
1692 dummyIntVec.resize(3 * ir->opts.ngQM, 0);
1693 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1694 dummyIntVec.clear();
1696 /* end of QMMM stuff */
1699 if (file_version >= tpxv_GenericParamsForElectricField)
1701 if (serializer->reading())
1703 paramsObj.mergeObject(gmx::deserializeKeyValueTree(serializer));
1707 GMX_RELEASE_ASSERT(ir->params != nullptr,
1708 "Parameters should be present when writing inputrec");
1709 gmx::serializeKeyValueTree(*ir->params, serializer);
1712 if (serializer->reading())
1714 ir->params = new gmx::KeyValueTreeObject(paramsBuilder.build());
1715 // Initialize internal parameters to an empty kvt for all tpr versions
1716 ir->internalParameters = std::make_unique<gmx::KeyValueTreeObject>();
1719 if (file_version >= tpxv_GenericInternalParameters)
1721 if (serializer->reading())
1723 ir->internalParameters =
1724 std::make_unique<gmx::KeyValueTreeObject>(gmx::deserializeKeyValueTree(serializer));
1728 GMX_RELEASE_ASSERT(ir->internalParameters != nullptr,
1729 "Parameters should be present when writing inputrec");
1730 gmx::serializeKeyValueTree(*ir->internalParameters, serializer);
1736 static void do_harm(gmx::ISerializer* serializer, t_iparams* iparams)
1738 serializer->doReal(&iparams->harmonic.rA);
1739 serializer->doReal(&iparams->harmonic.krA);
1740 serializer->doReal(&iparams->harmonic.rB);
1741 serializer->doReal(&iparams->harmonic.krB);
1744 static void do_iparams(gmx::ISerializer* serializer, t_functype ftype, t_iparams* iparams, int file_version)
1757 do_harm(serializer, iparams);
1758 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && serializer->reading())
1760 /* Correct incorrect storage of parameters */
1761 iparams->pdihs.phiB = iparams->pdihs.phiA;
1762 iparams->pdihs.cpB = iparams->pdihs.cpA;
1766 serializer->doReal(&iparams->harmonic.rA);
1767 serializer->doReal(&iparams->harmonic.krA);
1769 case F_LINEAR_ANGLES:
1770 serializer->doReal(&iparams->linangle.klinA);
1771 serializer->doReal(&iparams->linangle.aA);
1772 serializer->doReal(&iparams->linangle.klinB);
1773 serializer->doReal(&iparams->linangle.aB);
1776 serializer->doReal(&iparams->fene.bm);
1777 serializer->doReal(&iparams->fene.kb);
1781 serializer->doReal(&iparams->restraint.lowA);
1782 serializer->doReal(&iparams->restraint.up1A);
1783 serializer->doReal(&iparams->restraint.up2A);
1784 serializer->doReal(&iparams->restraint.kA);
1785 serializer->doReal(&iparams->restraint.lowB);
1786 serializer->doReal(&iparams->restraint.up1B);
1787 serializer->doReal(&iparams->restraint.up2B);
1788 serializer->doReal(&iparams->restraint.kB);
1794 serializer->doReal(&iparams->tab.kA);
1795 serializer->doInt(&iparams->tab.table);
1796 serializer->doReal(&iparams->tab.kB);
1798 case F_CROSS_BOND_BONDS:
1799 serializer->doReal(&iparams->cross_bb.r1e);
1800 serializer->doReal(&iparams->cross_bb.r2e);
1801 serializer->doReal(&iparams->cross_bb.krr);
1803 case F_CROSS_BOND_ANGLES:
1804 serializer->doReal(&iparams->cross_ba.r1e);
1805 serializer->doReal(&iparams->cross_ba.r2e);
1806 serializer->doReal(&iparams->cross_ba.r3e);
1807 serializer->doReal(&iparams->cross_ba.krt);
1809 case F_UREY_BRADLEY:
1810 serializer->doReal(&iparams->u_b.thetaA);
1811 serializer->doReal(&iparams->u_b.kthetaA);
1812 serializer->doReal(&iparams->u_b.r13A);
1813 serializer->doReal(&iparams->u_b.kUBA);
1814 if (file_version >= 79)
1816 serializer->doReal(&iparams->u_b.thetaB);
1817 serializer->doReal(&iparams->u_b.kthetaB);
1818 serializer->doReal(&iparams->u_b.r13B);
1819 serializer->doReal(&iparams->u_b.kUBB);
1823 iparams->u_b.thetaB = iparams->u_b.thetaA;
1824 iparams->u_b.kthetaB = iparams->u_b.kthetaA;
1825 iparams->u_b.r13B = iparams->u_b.r13A;
1826 iparams->u_b.kUBB = iparams->u_b.kUBA;
1829 case F_QUARTIC_ANGLES:
1830 serializer->doReal(&iparams->qangle.theta);
1831 serializer->doRealArray(iparams->qangle.c, 5);
1834 serializer->doReal(&iparams->bham.a);
1835 serializer->doReal(&iparams->bham.b);
1836 serializer->doReal(&iparams->bham.c);
1839 serializer->doReal(&iparams->morse.b0A);
1840 serializer->doReal(&iparams->morse.cbA);
1841 serializer->doReal(&iparams->morse.betaA);
1842 if (file_version >= 79)
1844 serializer->doReal(&iparams->morse.b0B);
1845 serializer->doReal(&iparams->morse.cbB);
1846 serializer->doReal(&iparams->morse.betaB);
1850 iparams->morse.b0B = iparams->morse.b0A;
1851 iparams->morse.cbB = iparams->morse.cbA;
1852 iparams->morse.betaB = iparams->morse.betaA;
1856 serializer->doReal(&iparams->cubic.b0);
1857 serializer->doReal(&iparams->cubic.kb);
1858 serializer->doReal(&iparams->cubic.kcub);
1860 case F_CONNBONDS: break;
1861 case F_POLARIZATION: serializer->doReal(&iparams->polarize.alpha); break;
1863 serializer->doReal(&iparams->anharm_polarize.alpha);
1864 serializer->doReal(&iparams->anharm_polarize.drcut);
1865 serializer->doReal(&iparams->anharm_polarize.khyp);
1868 serializer->doReal(&iparams->wpol.al_x);
1869 serializer->doReal(&iparams->wpol.al_y);
1870 serializer->doReal(&iparams->wpol.al_z);
1871 serializer->doReal(&iparams->wpol.rOH);
1872 serializer->doReal(&iparams->wpol.rHH);
1873 serializer->doReal(&iparams->wpol.rOD);
1876 serializer->doReal(&iparams->thole.a);
1877 serializer->doReal(&iparams->thole.alpha1);
1878 serializer->doReal(&iparams->thole.alpha2);
1879 serializer->doReal(&iparams->thole.rfac);
1882 serializer->doReal(&iparams->lj.c6);
1883 serializer->doReal(&iparams->lj.c12);
1886 serializer->doReal(&iparams->lj14.c6A);
1887 serializer->doReal(&iparams->lj14.c12A);
1888 serializer->doReal(&iparams->lj14.c6B);
1889 serializer->doReal(&iparams->lj14.c12B);
1892 serializer->doReal(&iparams->ljc14.fqq);
1893 serializer->doReal(&iparams->ljc14.qi);
1894 serializer->doReal(&iparams->ljc14.qj);
1895 serializer->doReal(&iparams->ljc14.c6);
1896 serializer->doReal(&iparams->ljc14.c12);
1898 case F_LJC_PAIRS_NB:
1899 serializer->doReal(&iparams->ljcnb.qi);
1900 serializer->doReal(&iparams->ljcnb.qj);
1901 serializer->doReal(&iparams->ljcnb.c6);
1902 serializer->doReal(&iparams->ljcnb.c12);
1908 serializer->doReal(&iparams->pdihs.phiA);
1909 serializer->doReal(&iparams->pdihs.cpA);
1910 serializer->doReal(&iparams->pdihs.phiB);
1911 serializer->doReal(&iparams->pdihs.cpB);
1912 serializer->doInt(&iparams->pdihs.mult);
1915 serializer->doReal(&iparams->pdihs.phiA);
1916 serializer->doReal(&iparams->pdihs.cpA);
1919 serializer->doInt(&iparams->disres.label);
1920 serializer->doInt(&iparams->disres.type);
1921 serializer->doReal(&iparams->disres.low);
1922 serializer->doReal(&iparams->disres.up1);
1923 serializer->doReal(&iparams->disres.up2);
1924 serializer->doReal(&iparams->disres.kfac);
1927 serializer->doInt(&iparams->orires.ex);
1928 serializer->doInt(&iparams->orires.label);
1929 serializer->doInt(&iparams->orires.power);
1930 serializer->doReal(&iparams->orires.c);
1931 serializer->doReal(&iparams->orires.obs);
1932 serializer->doReal(&iparams->orires.kfac);
1935 if (file_version < 82)
1937 serializer->doInt(&idum);
1938 serializer->doInt(&idum);
1940 serializer->doReal(&iparams->dihres.phiA);
1941 serializer->doReal(&iparams->dihres.dphiA);
1942 serializer->doReal(&iparams->dihres.kfacA);
1943 if (file_version >= 82)
1945 serializer->doReal(&iparams->dihres.phiB);
1946 serializer->doReal(&iparams->dihres.dphiB);
1947 serializer->doReal(&iparams->dihres.kfacB);
1951 iparams->dihres.phiB = iparams->dihres.phiA;
1952 iparams->dihres.dphiB = iparams->dihres.dphiA;
1953 iparams->dihres.kfacB = iparams->dihres.kfacA;
1957 serializer->doRvec(&iparams->posres.pos0A);
1958 serializer->doRvec(&iparams->posres.fcA);
1959 serializer->doRvec(&iparams->posres.pos0B);
1960 serializer->doRvec(&iparams->posres.fcB);
1963 serializer->doInt(&iparams->fbposres.geom);
1964 serializer->doRvec(&iparams->fbposres.pos0);
1965 serializer->doReal(&iparams->fbposres.r);
1966 serializer->doReal(&iparams->fbposres.k);
1968 case F_CBTDIHS: serializer->doRealArray(iparams->cbtdihs.cbtcA, NR_CBTDIHS); break;
1970 // Fall-through intended
1972 /* Fourier dihedrals are internally represented
1973 * as Ryckaert-Bellemans since those are faster to compute.
1975 serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
1976 serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
1980 serializer->doReal(&iparams->constr.dA);
1981 serializer->doReal(&iparams->constr.dB);
1984 serializer->doReal(&iparams->settle.doh);
1985 serializer->doReal(&iparams->settle.dhh);
1987 case F_VSITE1: break; // VSite1 has 0 parameters
1989 case F_VSITE2FD: serializer->doReal(&iparams->vsite.a); break;
1993 serializer->doReal(&iparams->vsite.a);
1994 serializer->doReal(&iparams->vsite.b);
1999 serializer->doReal(&iparams->vsite.a);
2000 serializer->doReal(&iparams->vsite.b);
2001 serializer->doReal(&iparams->vsite.c);
2004 serializer->doInt(&iparams->vsiten.n);
2005 serializer->doReal(&iparams->vsiten.a);
2007 case F_GB12_NOLONGERUSED:
2008 case F_GB13_NOLONGERUSED:
2009 case F_GB14_NOLONGERUSED:
2010 // Implicit solvent parameters can still be read, but never used
2011 if (serializer->reading())
2013 if (file_version < 68)
2015 serializer->doReal(&rdum);
2016 serializer->doReal(&rdum);
2017 serializer->doReal(&rdum);
2018 serializer->doReal(&rdum);
2020 if (file_version < tpxv_RemoveImplicitSolvation)
2022 serializer->doReal(&rdum);
2023 serializer->doReal(&rdum);
2024 serializer->doReal(&rdum);
2025 serializer->doReal(&rdum);
2026 serializer->doReal(&rdum);
2031 serializer->doInt(&iparams->cmap.cmapA);
2032 serializer->doInt(&iparams->cmap.cmapB);
2036 "unknown function type %d (%s) in %s line %d",
2038 interaction_function[ftype].name,
2044 static void do_ilist(gmx::ISerializer* serializer, InteractionList* ilist)
2046 int nr = ilist->size();
2047 serializer->doInt(&nr);
2048 if (serializer->reading())
2050 ilist->iatoms.resize(nr);
2052 serializer->doIntArray(ilist->iatoms.data(), ilist->size());
2055 static void do_ffparams(gmx::ISerializer* serializer, gmx_ffparams_t* ffparams, int file_version)
2057 serializer->doInt(&ffparams->atnr);
2058 int numTypes = ffparams->numTypes();
2059 serializer->doInt(&numTypes);
2060 if (serializer->reading())
2062 ffparams->functype.resize(numTypes);
2063 ffparams->iparams.resize(numTypes);
2065 /* Read/write all the function types */
2066 serializer->doIntArray(ffparams->functype.data(), ffparams->functype.size());
2068 if (file_version >= 66)
2070 serializer->doDouble(&ffparams->reppow);
2074 ffparams->reppow = 12.0;
2077 serializer->doReal(&ffparams->fudgeQQ);
2079 /* Check whether all these function types are supported by the code.
2080 * In practice the code is backwards compatible, which means that the
2081 * numbering may have to be altered from old numbering to new numbering
2083 for (int i = 0; i < ffparams->numTypes(); i++)
2085 if (serializer->reading())
2087 /* Loop over file versions */
2088 for (int k = 0; k < NFTUPD; k++)
2090 /* Compare the read file_version to the update table */
2091 if ((file_version < ftupd[k].fvnr) && (ffparams->functype[i] >= ftupd[k].ftype))
2093 ffparams->functype[i] += 1;
2098 do_iparams(serializer, ffparams->functype[i], &ffparams->iparams[i], file_version);
2102 static void add_settle_atoms(InteractionList* ilist)
2106 /* Settle used to only store the first atom: add the other two */
2107 ilist->iatoms.resize(2 * ilist->size());
2108 for (i = ilist->size() / 4 - 1; i >= 0; i--)
2110 ilist->iatoms[4 * i + 0] = ilist->iatoms[2 * i + 0];
2111 ilist->iatoms[4 * i + 1] = ilist->iatoms[2 * i + 1];
2112 ilist->iatoms[4 * i + 2] = ilist->iatoms[2 * i + 1] + 1;
2113 ilist->iatoms[4 * i + 3] = ilist->iatoms[2 * i + 1] + 2;
2117 static void do_ilists(gmx::ISerializer* serializer, InteractionLists* ilists, int file_version)
2119 GMX_RELEASE_ASSERT(ilists, "Need a valid ilists object");
2120 GMX_RELEASE_ASSERT(ilists->size() == F_NRE,
2121 "The code needs to be in sync with InteractionLists");
2123 for (int j = 0; j < F_NRE; j++)
2125 InteractionList& ilist = (*ilists)[j];
2126 gmx_bool bClear = FALSE;
2127 if (serializer->reading())
2129 for (int k = 0; k < NFTUPD; k++)
2131 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
2139 ilist.iatoms.clear();
2143 do_ilist(serializer, &ilist);
2144 if (file_version < 78 && j == F_SETTLE && !ilist.empty())
2146 add_settle_atoms(&ilist);
2152 static void do_block(gmx::ISerializer* serializer, t_block* block)
2154 serializer->doInt(&block->nr);
2155 if (serializer->reading())
2157 if ((block->nalloc_index > 0) && (nullptr != block->index))
2159 sfree(block->index);
2161 block->nalloc_index = block->nr + 1;
2162 snew(block->index, block->nalloc_index);
2164 serializer->doIntArray(block->index, block->nr + 1);
2167 static void doListOfLists(gmx::ISerializer* serializer, gmx::ListOfLists<int>* listOfLists)
2169 int numLists = listOfLists->ssize();
2170 serializer->doInt(&numLists);
2171 int numElements = listOfLists->elementsView().ssize();
2172 serializer->doInt(&numElements);
2173 if (serializer->reading())
2175 std::vector<int> listRanges(numLists + 1);
2176 serializer->doIntArray(listRanges.data(), numLists + 1);
2177 std::vector<int> elements(numElements);
2178 serializer->doIntArray(elements.data(), numElements);
2179 *listOfLists = gmx::ListOfLists<int>(std::move(listRanges), std::move(elements));
2183 serializer->doIntArray(const_cast<int*>(listOfLists->listRangesView().data()), numLists + 1);
2184 serializer->doIntArray(const_cast<int*>(listOfLists->elementsView().data()), numElements);
2188 /* This is a primitive routine to make it possible to translate atomic numbers
2189 * to element names when reading TPR files, without making the Gromacs library
2190 * directory a dependency on mdrun (which is the case if we need elements.dat).
2192 static const char* atomicnumber_to_element(int atomicnumber)
2196 /* This does not have to be complete, so we only include elements likely
2197 * to occur in PDB files.
2199 switch (atomicnumber)
2201 case 1: p = "H"; break;
2202 case 5: p = "B"; break;
2203 case 6: p = "C"; break;
2204 case 7: p = "N"; break;
2205 case 8: p = "O"; break;
2206 case 9: p = "F"; break;
2207 case 11: p = "Na"; break;
2208 case 12: p = "Mg"; break;
2209 case 15: p = "P"; break;
2210 case 16: p = "S"; break;
2211 case 17: p = "Cl"; break;
2212 case 18: p = "Ar"; break;
2213 case 19: p = "K"; break;
2214 case 20: p = "Ca"; break;
2215 case 25: p = "Mn"; break;
2216 case 26: p = "Fe"; break;
2217 case 28: p = "Ni"; break;
2218 case 29: p = "Cu"; break;
2219 case 30: p = "Zn"; break;
2220 case 35: p = "Br"; break;
2221 case 47: p = "Ag"; break;
2222 default: p = ""; break;
2228 static void do_atom(gmx::ISerializer* serializer, t_atom* atom)
2230 serializer->doReal(&atom->m);
2231 serializer->doReal(&atom->q);
2232 serializer->doReal(&atom->mB);
2233 serializer->doReal(&atom->qB);
2234 serializer->doUShort(&atom->type);
2235 serializer->doUShort(&atom->typeB);
2236 serializer->doEnumAsInt(&atom->ptype);
2237 serializer->doInt(&atom->resind);
2238 serializer->doInt(&atom->atomnumber);
2239 if (serializer->reading())
2241 /* Set element string from atomic number if present.
2242 * This routine returns an empty string if the name is not found.
2244 std::strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
2245 /* avoid warnings about potentially unterminated string */
2246 atom->elem[3] = '\0';
2250 static void do_grps(gmx::ISerializer* serializer, gmx::ArrayRef<AtomGroupIndices> grps)
2252 for (auto& group : grps)
2254 int size = group.size();
2255 serializer->doInt(&size);
2256 if (serializer->reading())
2260 serializer->doIntArray(group.data(), size);
2264 static void do_symstr(gmx::ISerializer* serializer, char*** nm, t_symtab* symtab)
2268 if (serializer->reading())
2270 serializer->doInt(&ls);
2271 *nm = get_symtab_handle(symtab, ls);
2275 ls = lookup_symtab(symtab, *nm);
2276 serializer->doInt(&ls);
2280 static void do_strstr(gmx::ISerializer* serializer, int nstr, char*** nm, t_symtab* symtab)
2284 for (j = 0; (j < nstr); j++)
2286 do_symstr(serializer, &(nm[j]), symtab);
2290 static void do_resinfo(gmx::ISerializer* serializer, int n, t_resinfo* ri, t_symtab* symtab, int file_version)
2294 for (j = 0; (j < n); j++)
2296 do_symstr(serializer, &(ri[j].name), symtab);
2297 if (file_version >= 63)
2299 serializer->doInt(&ri[j].nr);
2300 serializer->doUChar(&ri[j].ic);
2310 static void do_atoms(gmx::ISerializer* serializer, t_atoms* atoms, t_symtab* symtab, int file_version)
2314 serializer->doInt(&atoms->nr);
2315 serializer->doInt(&atoms->nres);
2316 if (serializer->reading())
2318 /* Since we have always written all t_atom properties in the tpr file
2319 * (at least for all backward compatible versions), we don't store
2320 * but simple set the booleans here.
2322 atoms->haveMass = TRUE;
2323 atoms->haveCharge = TRUE;
2324 atoms->haveType = TRUE;
2325 atoms->haveBState = TRUE;
2326 atoms->havePdbInfo = FALSE;
2328 snew(atoms->atom, atoms->nr);
2329 snew(atoms->atomname, atoms->nr);
2330 snew(atoms->atomtype, atoms->nr);
2331 snew(atoms->atomtypeB, atoms->nr);
2332 snew(atoms->resinfo, atoms->nres);
2333 atoms->pdbinfo = nullptr;
2337 GMX_RELEASE_ASSERT(atoms->haveMass && atoms->haveCharge && atoms->haveType && atoms->haveBState,
2338 "Mass, charge, atomtype and B-state parameters should be present in "
2339 "t_atoms when writing a tpr file");
2341 for (i = 0; (i < atoms->nr); i++)
2343 do_atom(serializer, &atoms->atom[i]);
2345 do_strstr(serializer, atoms->nr, atoms->atomname, symtab);
2346 do_strstr(serializer, atoms->nr, atoms->atomtype, symtab);
2347 do_strstr(serializer, atoms->nr, atoms->atomtypeB, symtab);
2349 do_resinfo(serializer, atoms->nres, atoms->resinfo, symtab, file_version);
2352 static void do_groups(gmx::ISerializer* serializer, SimulationGroups* groups, t_symtab* symtab)
2354 do_grps(serializer, groups->groups);
2355 int numberOfGroupNames = groups->groupNames.size();
2356 serializer->doInt(&numberOfGroupNames);
2357 if (serializer->reading())
2359 groups->groupNames.resize(numberOfGroupNames);
2361 do_strstr(serializer, numberOfGroupNames, groups->groupNames.data(), symtab);
2362 for (auto group : gmx::keysOf(groups->groupNumbers))
2364 int numberOfGroupNumbers = groups->numberOfGroupNumbers(group);
2365 serializer->doInt(&numberOfGroupNumbers);
2366 if (numberOfGroupNumbers != 0)
2368 if (serializer->reading())
2370 groups->groupNumbers[group].resize(numberOfGroupNumbers);
2372 serializer->doUCharArray(groups->groupNumbers[group].data(), numberOfGroupNumbers);
2377 static void do_atomtypes(gmx::ISerializer* serializer, t_atomtypes* atomtypes, int file_version)
2381 serializer->doInt(&atomtypes->nr);
2383 if (serializer->reading())
2385 snew(atomtypes->atomnumber, j);
2387 if (serializer->reading() && file_version < tpxv_RemoveImplicitSolvation)
2389 std::vector<real> dummy(atomtypes->nr, 0);
2390 serializer->doRealArray(dummy.data(), dummy.size());
2391 serializer->doRealArray(dummy.data(), dummy.size());
2392 serializer->doRealArray(dummy.data(), dummy.size());
2394 serializer->doIntArray(atomtypes->atomnumber, j);
2396 if (serializer->reading() && file_version >= 60 && file_version < tpxv_RemoveImplicitSolvation)
2398 std::vector<real> dummy(atomtypes->nr, 0);
2399 serializer->doRealArray(dummy.data(), dummy.size());
2400 serializer->doRealArray(dummy.data(), dummy.size());
2404 static void do_symtab(gmx::ISerializer* serializer, t_symtab* symtab)
2409 serializer->doInt(&symtab->nr);
2411 if (serializer->reading())
2413 snew(symtab->symbuf, 1);
2414 symbuf = symtab->symbuf;
2415 symbuf->bufsize = nr;
2416 snew(symbuf->buf, nr);
2417 for (i = 0; (i < nr); i++)
2420 serializer->doString(&buf);
2421 symbuf->buf[i] = gmx_strdup(buf.c_str());
2426 symbuf = symtab->symbuf;
2427 while (symbuf != nullptr)
2429 for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
2431 std::string buf = symbuf->buf[i];
2432 serializer->doString(&buf);
2435 symbuf = symbuf->next;
2439 gmx_fatal(FARGS, "nr of symtab strings left: %d", nr);
2444 static void do_cmap(gmx::ISerializer* serializer, gmx_cmap_t* cmap_grid)
2447 int ngrid = cmap_grid->cmapdata.size();
2448 serializer->doInt(&ngrid);
2449 serializer->doInt(&cmap_grid->grid_spacing);
2451 int gs = cmap_grid->grid_spacing;
2452 int nelem = gs * gs;
2454 if (serializer->reading())
2456 cmap_grid->cmapdata.resize(ngrid);
2458 for (int i = 0; i < ngrid; i++)
2460 cmap_grid->cmapdata[i].cmap.resize(4 * nelem);
2464 for (int i = 0; i < ngrid; i++)
2466 for (int j = 0; j < nelem; j++)
2468 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4]);
2469 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 1]);
2470 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 2]);
2471 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 3]);
2477 static void do_moltype(gmx::ISerializer* serializer, gmx_moltype_t* molt, t_symtab* symtab, int file_version)
2479 do_symstr(serializer, &(molt->name), symtab);
2481 do_atoms(serializer, &molt->atoms, symtab, file_version);
2483 do_ilists(serializer, &molt->ilist, file_version);
2485 /* TODO: Remove the obsolete charge group index from the file */
2487 cgs.nr = molt->atoms.nr;
2488 cgs.nalloc_index = cgs.nr + 1;
2489 snew(cgs.index, cgs.nalloc_index);
2490 for (int i = 0; i < cgs.nr + 1; i++)
2494 do_block(serializer, &cgs);
2497 /* This used to be in the atoms struct */
2498 doListOfLists(serializer, &molt->excls);
2501 static void do_molblock(gmx::ISerializer* serializer, gmx_molblock_t* molb, int numAtomsPerMolecule)
2503 serializer->doInt(&molb->type);
2504 serializer->doInt(&molb->nmol);
2505 /* To maintain forward topology reading compatibility, we store #atoms.
2506 * TODO: Change this to conditional reading of a dummy int when we
2507 * increase tpx_generation.
2509 serializer->doInt(&numAtomsPerMolecule);
2510 /* Position restraint coordinates */
2511 int numPosres_xA = molb->posres_xA.size();
2512 serializer->doInt(&numPosres_xA);
2513 if (numPosres_xA > 0)
2515 if (serializer->reading())
2517 molb->posres_xA.resize(numPosres_xA);
2519 serializer->doRvecArray(as_rvec_array(molb->posres_xA.data()), numPosres_xA);
2521 int numPosres_xB = molb->posres_xB.size();
2522 serializer->doInt(&numPosres_xB);
2523 if (numPosres_xB > 0)
2525 if (serializer->reading())
2527 molb->posres_xB.resize(numPosres_xB);
2529 serializer->doRvecArray(as_rvec_array(molb->posres_xB.data()), numPosres_xB);
2533 static void set_disres_npair(gmx_mtop_t* mtop)
2535 gmx::ArrayRef<t_iparams> ip = mtop->ffparams.iparams;
2537 for (const auto ilist : IListRange(*mtop))
2539 const InteractionList& il = ilist.list()[F_DISRES];
2543 gmx::ArrayRef<const int> a = il.iatoms;
2545 for (int i = 0; i < il.size(); i += 3)
2548 if (i + 3 == il.size() || ip[a[i]].disres.label != ip[a[i + 3]].disres.label)
2550 ip[a[i]].disres.npair = npair;
2558 static void do_mtop(gmx::ISerializer* serializer, gmx_mtop_t* mtop, int file_version)
2560 do_symtab(serializer, &(mtop->symtab));
2562 do_symstr(serializer, &(mtop->name), &(mtop->symtab));
2564 do_ffparams(serializer, &mtop->ffparams, file_version);
2566 int nmoltype = mtop->moltype.size();
2567 serializer->doInt(&nmoltype);
2568 if (serializer->reading())
2570 mtop->moltype.resize(nmoltype);
2572 for (gmx_moltype_t& moltype : mtop->moltype)
2574 do_moltype(serializer, &moltype, &mtop->symtab, file_version);
2577 int nmolblock = mtop->molblock.size();
2578 serializer->doInt(&nmolblock);
2579 if (serializer->reading())
2581 mtop->molblock.resize(nmolblock);
2583 for (gmx_molblock_t& molblock : mtop->molblock)
2585 int numAtomsPerMolecule = (serializer->reading() ? 0 : mtop->moltype[molblock.type].atoms.nr);
2586 do_molblock(serializer, &molblock, numAtomsPerMolecule);
2588 serializer->doInt(&mtop->natoms);
2590 if (file_version >= tpxv_IntermolecularBondeds)
2592 serializer->doBool(&mtop->bIntermolecularInteractions);
2593 if (mtop->bIntermolecularInteractions)
2595 if (serializer->reading())
2597 mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
2599 do_ilists(serializer, mtop->intermolecular_ilist.get(), file_version);
2604 mtop->bIntermolecularInteractions = FALSE;
2607 do_atomtypes(serializer, &(mtop->atomtypes), file_version);
2609 if (file_version >= 65)
2611 do_cmap(serializer, &mtop->ffparams.cmap_grid);
2615 mtop->ffparams.cmap_grid.grid_spacing = 0;
2616 mtop->ffparams.cmap_grid.cmapdata.clear();
2619 do_groups(serializer, &mtop->groups, &(mtop->symtab));
2620 if (file_version < tpxv_RemovedConstantAcceleration)
2622 mtop->groups.groups[SimulationAtomGroupType::AccelerationUnused].clear();
2623 mtop->groups.groupNumbers[SimulationAtomGroupType::AccelerationUnused].clear();
2626 mtop->haveMoleculeIndices = true;
2628 if (file_version >= tpxv_StoreNonBondedInteractionExclusionGroup)
2630 std::int64_t intermolecularExclusionGroupSize = gmx::ssize(mtop->intermolecularExclusionGroup);
2631 serializer->doInt64(&intermolecularExclusionGroupSize);
2632 GMX_RELEASE_ASSERT(intermolecularExclusionGroupSize >= 0,
2633 "Number of atoms with excluded intermolecular non-bonded interactions "
2635 mtop->intermolecularExclusionGroup.resize(intermolecularExclusionGroupSize); // no effect when writing
2636 serializer->doIntArray(mtop->intermolecularExclusionGroup.data(),
2637 mtop->intermolecularExclusionGroup.size());
2640 if (serializer->reading())
2642 close_symtab(&(mtop->symtab));
2647 * Read the first part of the TPR file to find general system information.
2649 * If \p TopOnlyOK is true then we can read even future versions
2650 * of tpx files, provided the \p fileGeneration hasn't changed.
2651 * If it is false, we need the \p ir too, and bail out
2652 * if the file is newer than the program.
2654 * The version and generation of the topology (see top of this file)
2655 * are returned in the two last arguments, if those arguments are non-nullptr.
2657 * If possible, we will read the \p ir even when \p TopOnlyOK is true.
2659 * \param[in,out] serializer The serializer used to handle header processing.
2660 * \param[in,out] tpx File header datastructure.
2661 * \param[in] filename The name of the file being read/written
2662 * \param[in,out] fio File handle.
2663 * \param[in] TopOnlyOK If not reading \p ir is fine or not.
2665 static void do_tpxheader(gmx::FileIOXdrSerializer* serializer,
2667 const char* filename,
2675 /* XDR binary topology file */
2676 precision = sizeof(real);
2678 std::string fileTag;
2679 if (serializer->reading())
2681 serializer->doString(&buf);
2682 if (std::strncmp(buf.c_str(), "VERSION", 7) != 0)
2686 "Can not read file %s,\n"
2687 " this file is from a GROMACS version which is older than 2.0\n"
2688 " Make a new one with grompp or use a gro or pdb file, if possible",
2691 // We need to know the precision used to write the TPR file, to match it
2692 // to the precision of the currently running binary. If the precisions match
2693 // there is no problem, but mismatching precision needs to be accounted for
2694 // by reading into temporary variables of the correct precision instead
2695 // of the desired target datastructures.
2696 serializer->doInt(&precision);
2697 tpx->isDouble = (precision == sizeof(double));
2698 if ((precision != sizeof(float)) && !tpx->isDouble)
2701 "Unknown precision in file %s: real is %d bytes "
2702 "instead of %zu or %zu",
2708 gmx_fio_setprecision(fio, tpx->isDouble);
2710 "Reading file %s, %s (%s precision)\n",
2713 tpx->isDouble ? "double" : "single");
2717 buf = gmx::formatString("VERSION %s", gmx_version());
2718 serializer->doString(&buf);
2719 gmx_fio_setprecision(fio, tpx->isDouble);
2720 serializer->doInt(&precision);
2724 /* Check versions! */
2725 serializer->doInt(&tpx->fileVersion);
2727 /* This is for backward compatibility with development versions 77-79
2728 * where the tag was, mistakenly, placed before the generation,
2729 * which would cause a segv instead of a proper error message
2730 * when reading the topology only from tpx with <77 code.
2732 if (tpx->fileVersion >= 77 && tpx->fileVersion <= 79)
2734 serializer->doString(&fileTag);
2737 serializer->doInt(&tpx->fileGeneration);
2739 if (tpx->fileVersion >= 81)
2741 serializer->doString(&fileTag);
2743 if (serializer->reading())
2745 if (tpx->fileVersion < 77)
2747 /* Versions before 77 don't have the tag, set it to release */
2748 fileTag = gmx::formatString("%s", TPX_TAG_RELEASE);
2751 if (fileTag != tpx_tag)
2753 fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n", fileTag.c_str(), tpx_tag.c_str());
2755 /* We only support reading tpx files with the same tag as the code
2756 * or tpx files with the release tag and with lower version number.
2758 if (fileTag != TPX_TAG_RELEASE && tpx->fileVersion < tpx_version)
2761 "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' "
2762 "with program for tpx version %d, tag '%s'",
2772 if ((tpx->fileVersion <= tpx_incompatible_version)
2773 || ((tpx->fileVersion > tpx_version) && !TopOnlyOK) || (tpx->fileGeneration > tpx_generation)
2774 || tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
2777 "reading tpx file (%s) version %d with version %d program",
2783 serializer->doInt(&tpx->natoms);
2784 serializer->doInt(&tpx->ngtc);
2786 if (tpx->fileVersion < 62)
2788 serializer->doInt(&idum);
2789 serializer->doReal(&rdum);
2791 if (tpx->fileVersion >= 79)
2793 serializer->doInt(&tpx->fep_state);
2795 serializer->doReal(&tpx->lambda);
2796 serializer->doBool(&tpx->bIr);
2797 serializer->doBool(&tpx->bTop);
2798 serializer->doBool(&tpx->bX);
2799 serializer->doBool(&tpx->bV);
2800 serializer->doBool(&tpx->bF);
2801 serializer->doBool(&tpx->bBox);
2803 if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
2805 if (!serializer->reading())
2807 GMX_RELEASE_ASSERT(tpx->sizeOfTprBody != 0,
2808 "Not possible to write new file with zero TPR body size");
2810 serializer->doInt64(&tpx->sizeOfTprBody);
2813 if ((tpx->fileGeneration > tpx_generation))
2815 /* This can only happen if TopOnlyOK=TRUE */
2820 #define do_test(serializer, b, p) \
2821 if ((serializer)->reading() && ((p) != nullptr) && !(b)) \
2822 gmx_fatal(FARGS, "No %s in input file", #p)
2825 * Process the first part of the TPR into the state datastructure.
2827 * Due to the structure of the legacy code, it is necessary
2828 * to split up the state reading into two parts, with the
2829 * box and legacy temperature coupling processed before the
2830 * topology datastructures.
2832 * See the documentation for do_tpx_body for the correct order of
2833 * the operations for reading a tpr file.
2835 * \param[in] serializer Abstract serializer used to read/write data.
2836 * \param[in] tpx The file header data.
2837 * \param[in, out] state Global state data.
2839 static void do_tpx_state_first(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state)
2841 if (serializer->reading())
2844 init_gtc_state(state, tpx->ngtc, 0, 0);
2846 do_test(serializer, tpx->bBox, state->box);
2849 serializer->doRvecArray(state->box, DIM);
2850 if (tpx->fileVersion >= 51)
2852 serializer->doRvecArray(state->box_rel, DIM);
2856 /* We initialize box_rel after reading the inputrec */
2857 clear_mat(state->box_rel);
2859 serializer->doRvecArray(state->boxv, DIM);
2860 if (tpx->fileVersion < 56)
2863 serializer->doRvecArray(mdum, DIM);
2867 if (state->ngtc > 0)
2870 snew(dumv, state->ngtc);
2871 if (tpx->fileVersion < 69)
2873 serializer->doRealArray(dumv, state->ngtc);
2875 /* These used to be the Berendsen tcoupl_lambda's */
2876 serializer->doRealArray(dumv, state->ngtc);
2882 * Process global topology data.
2884 * See the documentation for do_tpx_body for the correct order of
2885 * the operations for reading a tpr file.
2887 * \param[in] serializer Abstract serializer used to read/write data.
2888 * \param[in] tpx The file header data.
2889 * \param[in,out] mtop Global topology.
2891 static void do_tpx_mtop(gmx::ISerializer* serializer, TpxFileHeader* tpx, gmx_mtop_t* mtop)
2893 do_test(serializer, tpx->bTop, mtop);
2898 do_mtop(serializer, mtop, tpx->fileVersion);
2899 set_disres_npair(mtop);
2905 do_mtop(serializer, &dum_top, tpx->fileVersion);
2910 * Process coordinate vectors for state data.
2912 * Main part of state gets processed here.
2914 * See the documentation for do_tpx_body for the correct order of
2915 * the operations for reading a tpr file.
2917 * \param[in] serializer Abstract serializer used to read/write data.
2918 * \param[in] tpx The file header data.
2919 * \param[in,out] state Global state data.
2920 * \param[in,out] x Individual coordinates for processing, deprecated.
2921 * \param[in,out] v Individual velocities for processing, deprecated.
2923 static void do_tpx_state_second(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state, rvec* x, rvec* v)
2925 if (!serializer->reading())
2928 x == nullptr && v == nullptr,
2929 "Passing separate x and v pointers to do_tpx() is not supported when writing");
2933 GMX_RELEASE_ASSERT(!(x == nullptr && v != nullptr),
2934 "Passing x==NULL and v!=NULL is not supported");
2937 if (serializer->reading())
2941 // v is also nullptr by the above assertion, so we may
2942 // need to make memory in state for storing the contents
2946 state->flags |= enumValueToBitMask(StateEntry::X);
2950 state->flags |= enumValueToBitMask(StateEntry::V);
2952 state_change_natoms(state, tpx->natoms);
2958 x = state->x.rvec_array();
2959 v = state->v.rvec_array();
2961 do_test(serializer, tpx->bX, x);
2964 if (serializer->reading())
2966 state->flags |= enumValueToBitMask(StateEntry::X);
2968 serializer->doRvecArray(x, tpx->natoms);
2971 do_test(serializer, tpx->bV, v);
2974 if (serializer->reading())
2976 state->flags |= enumValueToBitMask(StateEntry::V);
2980 std::vector<gmx::RVec> dummyVelocities(tpx->natoms);
2981 serializer->doRvecArray(as_rvec_array(dummyVelocities.data()), tpx->natoms);
2985 serializer->doRvecArray(v, tpx->natoms);
2989 // No need to run do_test when the last argument is NULL
2992 std::vector<gmx::RVec> dummyForces(state->natoms);
2993 serializer->doRvecArray(as_rvec_array(dummyForces.data()), tpx->natoms);
2997 * Process simulation parameters.
2999 * See the documentation for do_tpx_body for the correct order of
3000 * the operations for reading a tpr file.
3002 * \param[in] serializer Abstract serializer used to read/write data.
3003 * \param[in] tpx The file header data.
3004 * \param[in,out] ir Datastructure with simulation parameters.
3006 static PbcType do_tpx_ir(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir)
3009 gmx_bool bPeriodicMols;
3011 /* Starting with tpx version 26, we have the inputrec
3012 * at the end of the file, so we can ignore it
3013 * if the file is never than the software (but still the
3014 * same generation - see comments at the top of this file.
3018 pbcType = PbcType::Unset;
3019 bPeriodicMols = FALSE;
3021 do_test(serializer, tpx->bIr, ir);
3024 if (tpx->fileVersion >= 53)
3026 /* Removed the pbc info from do_inputrec, since we always want it */
3027 if (!serializer->reading())
3029 pbcType = ir->pbcType;
3030 bPeriodicMols = ir->bPeriodicMols;
3032 serializer->doInt(reinterpret_cast<int*>(&pbcType));
3033 serializer->doBool(&bPeriodicMols);
3035 if (tpx->fileGeneration <= tpx_generation && ir)
3037 do_inputrec(serializer, ir, tpx->fileVersion);
3038 if (tpx->fileVersion < 53)
3040 pbcType = ir->pbcType;
3041 bPeriodicMols = ir->bPeriodicMols;
3044 if (serializer->reading() && ir && tpx->fileVersion >= 53)
3046 /* We need to do this after do_inputrec, since that initializes ir */
3047 ir->pbcType = pbcType;
3048 ir->bPeriodicMols = bPeriodicMols;
3055 * Correct and finalize read information.
3057 * If \p state is nullptr, skip the parts dependent on it.
3059 * See the documentation for do_tpx_body for the correct order of
3060 * the operations for reading a tpr file.
3062 * \param[in] tpx The file header used to check version numbers.
3063 * \param[out] ir Input rec that needs correction.
3064 * \param[out] state State needing correction.
3065 * \param[out] mtop Topology to finalize.
3067 static void do_tpx_finalize(TpxFileHeader* tpx, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
3069 if (tpx->fileVersion < 51 && state)
3071 set_box_rel(ir, state);
3075 if (state && state->ngtc == 0)
3077 /* Reading old version without tcoupl state data: set it */
3078 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
3080 if (tpx->bTop && mtop)
3082 if (tpx->fileVersion < 57)
3084 ir->eDisre = !mtop->moltype[0].ilist[F_DISRES].empty()
3085 ? DistanceRestraintRefinement::Simple
3086 : DistanceRestraintRefinement::None;
3093 * Process TPR data for file reading/writing.
3095 * The TPR file gets processed in in four stages due to the organization
3096 * of the data within it.
3098 * First, state data for the box is processed in do_tpx_state_first.
3099 * This is followed by processing the topology in do_tpx_mtop.
3100 * Coordinate and velocity vectors are handled next in do_tpx_state_second.
3101 * The last file information processed is the collection of simulation parameters in do_tpx_ir.
3102 * When reading, a final processing step is undertaken at the end.
3104 * \param[in] serializer Abstract serializer used to read/write data.
3105 * \param[in] tpx The file header data.
3106 * \param[in,out] ir Datastructures with simulation parameters.
3107 * \param[in,out] state Global state data.
3108 * \param[in,out] x Individual coordinates for processing, deprecated.
3109 * \param[in,out] v Individual velocities for processing, deprecated.
3110 * \param[in,out] mtop Global topology.
3112 static PbcType do_tpx_body(gmx::ISerializer* serializer,
3122 do_tpx_state_first(serializer, tpx, state);
3124 do_tpx_mtop(serializer, tpx, mtop);
3127 do_tpx_state_second(serializer, tpx, state, x, v);
3129 PbcType pbcType = do_tpx_ir(serializer, tpx, ir);
3130 if (serializer->reading())
3132 do_tpx_finalize(tpx, ir, state, mtop);
3138 * Overload for do_tpx_body that defaults to state vectors being nullptr.
3140 * \param[in] serializer Abstract serializer used to read/write data.
3141 * \param[in] tpx The file header data.
3142 * \param[in,out] ir Datastructures with simulation parameters.
3143 * \param[in,out] mtop Global topology.
3145 static PbcType do_tpx_body(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir, gmx_mtop_t* mtop)
3147 return do_tpx_body(serializer, tpx, ir, nullptr, nullptr, nullptr, mtop);
3150 static t_fileio* open_tpx(const char* fn, const char* mode)
3152 return gmx_fio_open(fn, mode);
3155 static void close_tpx(t_fileio* fio)
3161 * Fill information into the header only from state before writing.
3163 * Populating the header needs to be independent from writing the information
3164 * to file to allow things like writing the raw byte stream.
3166 * \param[in] state The current simulation state. Can't write without it.
3167 * \param[in] ir Parameter and system information.
3168 * \param[in] mtop Global topology.
3169 * \returns Fully populated header.
3171 static TpxFileHeader populateTpxHeader(const t_state& state, const t_inputrec* ir, const gmx_mtop_t* mtop)
3173 TpxFileHeader header;
3174 header.natoms = state.natoms;
3175 header.ngtc = state.ngtc;
3176 header.fep_state = state.fep_state;
3177 header.lambda = state.lambda[FreeEnergyPerturbationCouplingType::Fep];
3178 header.bIr = ir != nullptr;
3179 header.bTop = mtop != nullptr;
3180 header.bX = (state.flags & enumValueToBitMask(StateEntry::X)) != 0;
3181 header.bV = (state.flags & enumValueToBitMask(StateEntry::V)) != 0;
3184 header.fileVersion = tpx_version;
3185 header.fileGeneration = tpx_generation;
3186 header.isDouble = (sizeof(real) == sizeof(double));
3192 * Process the body of a TPR file as an opaque data buffer.
3194 * Reads/writes the information in \p buffer from/to the \p serializer
3195 * provided to the function. Does not interact with the actual
3196 * TPR datastructures but with an in memory representation of the
3197 * data, so that this data can be efficiently read or written from/to
3198 * an original source.
3200 * \param[in] serializer The abstract serializer used for reading or writing
3201 * the information in \p buffer.
3202 * \param[in,out] buffer Information from TPR file as char buffer.
3204 static void doTpxBodyBuffer(gmx::ISerializer* serializer, gmx::ArrayRef<char> buffer)
3206 serializer->doOpaque(buffer.data(), buffer.size());
3210 * Populates simulation datastructures.
3212 * Here the information from the serialization interface \p serializer
3213 * is used to first populate the datastructures containing the simulation
3214 * information. Depending on the version found in the header \p tpx,
3215 * this is done using the new reading of the data as one block from disk,
3216 * followed by complete deserialization of the information read from there.
3217 * Otherwise, the datastructures are populated as before one by one from disk.
3218 * The second version is the default for the legacy tools that read the
3219 * coordinates and velocities separate from the state.
3221 * After reading in the data, a separate buffer is populated from them
3222 * containing only \p ir and \p mtop that can be communicated directly
3223 * to nodes needing the information to set up a simulation.
3225 * \param[in] tpx The file header.
3226 * \param[in] serializer The Serialization interface used to read the TPR.
3227 * \param[out] ir Input rec to populate.
3228 * \param[out] state State vectors to populate.
3229 * \param[out] x Coordinates to populate if needed.
3230 * \param[out] v Velocities to populate if needed.
3231 * \param[out] mtop Global topology to populate.
3233 * \returns Partial de-serialized TPR used for communication to nodes.
3235 static PartialDeserializedTprFile readTpxBody(TpxFileHeader* tpx,
3236 gmx::ISerializer* serializer,
3243 PartialDeserializedTprFile partialDeserializedTpr;
3244 if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
3246 partialDeserializedTpr.body.resize(tpx->sizeOfTprBody);
3247 partialDeserializedTpr.header = *tpx;
3248 doTpxBodyBuffer(serializer, partialDeserializedTpr.body);
3250 partialDeserializedTpr.pbcType =
3251 completeTprDeserialization(&partialDeserializedTpr, ir, state, x, v, mtop);
3255 partialDeserializedTpr.pbcType = do_tpx_body(serializer, tpx, ir, state, x, v, mtop);
3257 // Update header to system info for communication to nodes.
3258 // As we only need to communicate the inputrec and mtop to other nodes,
3259 // we prepare a new char buffer with the information we have already read
3261 partialDeserializedTpr.header = populateTpxHeader(*state, ir, mtop);
3262 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3263 // but since we just used the default XDR format (which is big endian) for the TPR
3264 // header it would cause third-party libraries reading our raw data to tear their hair
3265 // if we swap the endian in the middle of the file, so we stick to big endian in the
3266 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3267 gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3268 do_tpx_body(&tprBodySerializer, &partialDeserializedTpr.header, ir, mtop);
3269 partialDeserializedTpr.body = tprBodySerializer.finishAndGetBuffer();
3271 return partialDeserializedTpr;
3274 /************************************************************
3276 * The following routines are the exported ones
3278 ************************************************************/
3280 TpxFileHeader readTpxHeader(const char* fileName, bool canReadTopologyOnly)
3284 fio = open_tpx(fileName, "r");
3285 gmx::FileIOXdrSerializer serializer(fio);
3288 do_tpxheader(&serializer, &tpx, fileName, fio, canReadTopologyOnly);
3293 void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t& mtop)
3295 /* To write a state, we first need to write the state information to a buffer before
3296 * we append the raw bytes to the file. For this, the header information needs to be
3297 * populated before we write the main body because it has some information that is
3298 * otherwise not available.
3303 TpxFileHeader tpx = populateTpxHeader(*state, ir, &mtop);
3304 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3305 // but since we just used the default XDR format (which is big endian) for the TPR
3306 // header it would cause third-party libraries reading our raw data to tear their hair
3307 // if we swap the endian in the middle of the file, so we stick to big endian in the
3308 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3309 gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3311 do_tpx_body(&tprBodySerializer,
3313 const_cast<t_inputrec*>(ir),
3314 const_cast<t_state*>(state),
3317 const_cast<gmx_mtop_t*>(&mtop));
3319 std::vector<char> tprBody = tprBodySerializer.finishAndGetBuffer();
3320 tpx.sizeOfTprBody = tprBody.size();
3322 fio = open_tpx(fn, "w");
3323 gmx::FileIOXdrSerializer serializer(fio);
3324 do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
3325 doTpxBodyBuffer(&serializer, tprBody);
3330 PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
3337 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3338 // but since we just used the default XDR format (which is big endian) for the TPR
3339 // header it would cause third-party libraries reading our raw data to tear their hair
3340 // if we swap the endian in the middle of the file, so we stick to big endian in the
3341 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3342 gmx::InMemoryDeserializer tprBodyDeserializer(partialDeserializedTpr->body,
3343 partialDeserializedTpr->header.isDouble,
3344 gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3345 return do_tpx_body(&tprBodyDeserializer, &partialDeserializedTpr->header, ir, state, x, v, mtop);
3348 PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
3352 return completeTprDeserialization(partialDeserializedTpr, ir, nullptr, nullptr, nullptr, mtop);
3355 PartialDeserializedTprFile read_tpx_state(const char* fn, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
3358 fio = open_tpx(fn, "r");
3359 gmx::FileIOXdrSerializer serializer(fio);
3360 PartialDeserializedTprFile partialDeserializedTpr;
3361 do_tpxheader(&serializer, &partialDeserializedTpr.header, fn, fio, ir == nullptr);
3362 partialDeserializedTpr =
3363 readTpxBody(&partialDeserializedTpr.header, &serializer, ir, state, nullptr, nullptr, mtop);
3365 return partialDeserializedTpr;
3368 PbcType read_tpx(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, gmx_mtop_t* mtop)
3374 fio = open_tpx(fn, "r");
3375 gmx::FileIOXdrSerializer serializer(fio);
3376 do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
3377 PartialDeserializedTprFile partialDeserializedTpr =
3378 readTpxBody(&tpx, &serializer, ir, &state, x, v, mtop);
3380 if (mtop != nullptr && natoms != nullptr)
3382 *natoms = mtop->natoms;
3386 copy_mat(state.box, box);
3388 return partialDeserializedTpr.pbcType;
3391 PbcType read_tpx_top(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, t_topology* top)
3396 pbcType = read_tpx(fn, ir, box, natoms, x, v, &mtop);
3398 *top = gmx_mtop_t_to_t_topology(&mtop, true);
3403 gmx_bool fn2bTPX(const char* file)
3405 return (efTPR == fn2ftp(file));
3408 void pr_tpxheader(FILE* fp, int indent, const char* title, const TpxFileHeader* sh)
3410 if (available(fp, sh, indent, title))
3412 indent = pr_title(fp, indent, title);
3413 pr_indent(fp, indent);
3414 fprintf(fp, "bIr = %spresent\n", sh->bIr ? "" : "not ");
3415 pr_indent(fp, indent);
3416 fprintf(fp, "bBox = %spresent\n", sh->bBox ? "" : "not ");
3417 pr_indent(fp, indent);
3418 fprintf(fp, "bTop = %spresent\n", sh->bTop ? "" : "not ");
3419 pr_indent(fp, indent);
3420 fprintf(fp, "bX = %spresent\n", sh->bX ? "" : "not ");
3421 pr_indent(fp, indent);
3422 fprintf(fp, "bV = %spresent\n", sh->bV ? "" : "not ");
3423 pr_indent(fp, indent);
3424 fprintf(fp, "bF = %spresent\n", sh->bF ? "" : "not ");
3426 pr_indent(fp, indent);
3427 fprintf(fp, "natoms = %d\n", sh->natoms);
3428 pr_indent(fp, indent);
3429 fprintf(fp, "lambda = %e\n", sh->lambda);
3430 pr_indent(fp, indent);
3431 fprintf(fp, "buffer size = %" PRId64 "\n", sh->sizeOfTprBody);