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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 char* 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_Count /**< the total number of tpxv versions */
143 /*! \brief Version number of the file format written to run input
144 * files by this version of the code.
146 * The tpx_version increases whenever the file format in the main
147 * development branch changes, due to an extension of the tpxv enum above.
148 * Backward compatibility for reading old run input files is maintained
149 * by checking this version number against that of the file and then using
150 * the correct code path.
152 * When developing a feature branch that needs to change the run input
153 * file format, change tpx_tag instead. */
154 static const int tpx_version = tpxv_Count - 1;
158 * Enum keeping track of incompatible changes for older TPR versions.
160 * The enum should be updated with a new field when editing the TOPOLOGY
161 * or HEADER of the tpx format. In particular, updating ftupd or
162 * changing the fields of TprHeaderVersion often trigger such needs.
164 * This way we can maintain forward compatibility too for all analysis tools
165 * and/or external programs that only need to know the atom/residue names,
166 * charges, and bond connectivity.
168 * It first appeared in tpx version 26, when I also moved the inputrecord
169 * to the end of the tpx file, so we can just skip it if we only
172 * In particular, it must be increased when adding new elements to
173 * ftupd, so that old code can read new .tpr files.
175 enum class TpxGeneration : int
177 Initial = 26, //! First version is 26
178 AddSizeField, //! TPR header modified for writing as a block.
179 AddVSite1, //! ftupd changed to include VSite1 type.
180 Count //! Number of entries.
183 //! Value of Current TPR generation.
184 static const int tpx_generation = static_cast<int>(TpxGeneration::Count) - 1;
186 /* This number should be the most recent backwards incompatible version
187 * I.e., if this number is 9, we cannot read tpx version 9 with this code.
189 static const int tpx_incompatible_version = 57; // GMX4.0 has version 58
192 /* Struct used to maintain tpx compatibility when function types are added */
195 int fvnr; /* file version number in which the function type first appeared */
196 int ftype; /* function type */
200 * TODO The following three lines make little sense, please clarify if
201 * you've had to work out how ftupd works.
203 * The entries should be ordered in:
204 * 1. ascending function type number
205 * 2. ascending file version number
207 * Because we support reading of old .tpr file versions (even when
208 * mdrun can no longer run the simulation), we need to be able to read
209 * obsolete t_interaction_function types. Any data read from such
210 * fields is discarded. Their names have _NOLONGERUSED appended to
211 * them to make things clear.
213 * When adding to or making breaking changes to reading this struct,
214 * update TpxGeneration.
216 static const t_ftupd ftupd[] = {
217 { 70, F_RESTRBONDS },
218 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
219 { 76, F_LINEAR_ANGLES },
220 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
221 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
223 { 60, F_GB12_NOLONGERUSED },
224 { 61, F_GB13_NOLONGERUSED },
225 { 61, F_GB14_NOLONGERUSED },
226 { 72, F_GBPOL_NOLONGERUSED },
227 { 72, F_NPSOLVATION_NOLONGERUSED },
229 { 76, F_ANHARM_POL },
231 { tpxv_VSite1, F_VSITE1 },
232 { tpxv_VSite2FD, F_VSITE2FD },
233 { tpxv_GenericInternalParameters, F_DENSITYFITTING },
234 { 69, F_VTEMP_NOLONGERUSED },
245 { 79, F_DVDL_RESTRAINT },
246 { 79, F_DVDL_TEMPERATURE },
248 #define NFTUPD asize(ftupd)
250 /* Needed for backward compatibility */
253 /**************************************************************
255 * Now the higer level routines that do io of the structures and arrays
257 **************************************************************/
258 static void do_pullgrp_tpx_pre95(gmx::ISerializer* serializer, t_pull_group* pgrp, t_pull_coord* pcrd)
262 int numAtoms = pgrp->ind.size();
263 serializer->doInt(&numAtoms);
264 pgrp->ind.resize(numAtoms);
265 serializer->doIntArray(pgrp->ind.data(), numAtoms);
266 int numWeights = pgrp->weight.size();
267 serializer->doInt(&numWeights);
268 pgrp->weight.resize(numWeights);
269 serializer->doRealArray(pgrp->weight.data(), numWeights);
270 serializer->doInt(&pgrp->pbcatom);
271 serializer->doRvec(&pcrd->vec.as_vec());
272 clear_rvec(pcrd->origin);
273 serializer->doRvec(&tmp);
275 serializer->doReal(&pcrd->rate);
276 serializer->doReal(&pcrd->k);
277 serializer->doReal(&pcrd->kB);
280 static void do_pull_group(gmx::ISerializer* serializer, t_pull_group* pgrp)
282 int numAtoms = pgrp->ind.size();
283 serializer->doInt(&numAtoms);
284 pgrp->ind.resize(numAtoms);
285 serializer->doIntArray(pgrp->ind.data(), numAtoms);
286 int numWeights = pgrp->weight.size();
287 serializer->doInt(&numWeights);
288 pgrp->weight.resize(numWeights);
289 serializer->doRealArray(pgrp->weight.data(), numWeights);
290 serializer->doInt(&pgrp->pbcatom);
293 static void do_pull_coord(gmx::ISerializer* serializer,
296 PullingAlgorithm ePullOld,
297 PullGroupGeometry eGeomOld,
300 if (file_version >= tpxv_PullCoordNGroup)
302 serializer->doEnumAsInt(&pcrd->eType);
303 if (file_version >= tpxv_PullExternalPotential)
305 if (pcrd->eType == PullingAlgorithm::External)
308 if (serializer->reading())
310 serializer->doString(&buf);
311 pcrd->externalPotentialProvider = gmx_strdup(buf.c_str());
315 buf = pcrd->externalPotentialProvider;
316 serializer->doString(&buf);
321 pcrd->externalPotentialProvider.clear();
326 if (serializer->reading())
328 pcrd->externalPotentialProvider.clear();
331 /* Note that we try to support adding new geometries without
332 * changing the tpx version. This requires checks when printing the
333 * geometry string and a check and fatal_error in init_pull.
335 serializer->doEnumAsInt(&pcrd->eGeom);
336 serializer->doInt(&pcrd->ngroup);
337 if (pcrd->ngroup <= c_pullCoordNgroupMax)
339 serializer->doIntArray(pcrd->group.data(), pcrd->ngroup);
343 /* More groups in file than supported, this must be a new geometry
344 * that is not supported by our current code. Since we will not
345 * use the groups for this coord (checks in the pull and WHAM code
346 * ensure this), we can ignore the groups and set ngroup=0.
349 snew(dum, pcrd->ngroup);
350 serializer->doIntArray(dum, pcrd->ngroup);
355 serializer->doIvec(&pcrd->dim.as_vec());
360 serializer->doInt(&pcrd->group[0]);
361 serializer->doInt(&pcrd->group[1]);
362 if (file_version >= tpxv_PullCoordTypeGeom)
364 pcrd->ngroup = (pcrd->eGeom == PullGroupGeometry::DirectionRelative ? 4 : 2);
365 serializer->doEnumAsInt(&pcrd->eType);
366 serializer->doEnumAsInt(&pcrd->eGeom);
367 if (pcrd->ngroup == 4)
369 serializer->doInt(&pcrd->group[2]);
370 serializer->doInt(&pcrd->group[3]);
372 serializer->doIvec(&pcrd->dim.as_vec());
376 pcrd->eType = ePullOld;
377 pcrd->eGeom = eGeomOld;
378 copy_ivec(dimOld, pcrd->dim);
381 serializer->doRvec(&pcrd->origin.as_vec());
382 serializer->doRvec(&pcrd->vec.as_vec());
383 if (file_version >= tpxv_PullCoordTypeGeom)
385 serializer->doBool(&pcrd->bStart);
389 /* This parameter is only printed, but not actually used by mdrun */
390 pcrd->bStart = FALSE;
392 serializer->doReal(&pcrd->init);
393 serializer->doReal(&pcrd->rate);
394 serializer->doReal(&pcrd->k);
395 serializer->doReal(&pcrd->kB);
398 static void do_expandedvals(gmx::ISerializer* serializer, t_expanded* expand, t_lambda* fepvals, int file_version)
400 int n_lambda = fepvals->n_lambda;
402 /* reset the lambda calculation window */
403 fepvals->lambda_start_n = 0;
404 fepvals->lambda_stop_n = n_lambda;
405 if (file_version >= 79)
409 expand->init_lambda_weights.resize(n_lambda);
410 serializer->doRealArray(expand->init_lambda_weights.data(), n_lambda);
411 serializer->doBool(&expand->bInit_weights);
414 serializer->doInt(&expand->nstexpanded);
415 serializer->doEnumAsInt(&expand->elmcmove);
416 serializer->doEnumAsInt(&expand->elamstats);
417 serializer->doInt(&expand->lmc_repeats);
418 serializer->doInt(&expand->gibbsdeltalam);
419 serializer->doInt(&expand->lmc_forced_nstart);
420 serializer->doInt(&expand->lmc_seed);
421 serializer->doReal(&expand->mc_temp);
422 serializer->doBool(&expand->bSymmetrizedTMatrix);
423 serializer->doInt(&expand->nstTij);
424 serializer->doInt(&expand->minvarmin);
425 serializer->doInt(&expand->c_range);
426 serializer->doReal(&expand->wl_scale);
427 serializer->doReal(&expand->wl_ratio);
428 serializer->doReal(&expand->init_wl_delta);
429 serializer->doBool(&expand->bWLoneovert);
430 serializer->doEnumAsInt(&expand->elmceq);
431 serializer->doInt(&expand->equil_steps);
432 serializer->doInt(&expand->equil_samples);
433 serializer->doInt(&expand->equil_n_at_lam);
434 serializer->doReal(&expand->equil_wl_delta);
435 serializer->doReal(&expand->equil_ratio);
439 static void do_simtempvals(gmx::ISerializer* serializer, t_simtemp* simtemp, int n_lambda, int file_version)
441 if (file_version >= 79)
443 serializer->doEnumAsInt(&simtemp->eSimTempScale);
444 serializer->doReal(&simtemp->simtemp_high);
445 serializer->doReal(&simtemp->simtemp_low);
448 if (serializer->reading())
450 snew(simtemp->temperatures, n_lambda);
452 serializer->doRealArray(simtemp->temperatures, n_lambda);
457 static void do_imd(gmx::ISerializer* serializer, t_IMD* imd)
459 serializer->doInt(&imd->nat);
460 if (serializer->reading())
462 snew(imd->ind, imd->nat);
464 serializer->doIntArray(imd->ind, imd->nat);
467 static void do_fepvals(gmx::ISerializer* serializer, t_lambda* fepvals, int file_version)
469 /* i is defined in the ndo_double macro; use g to iterate. */
472 /* free energy values */
474 if (file_version >= 79)
476 serializer->doInt(&fepvals->init_fep_state);
477 serializer->doDouble(&fepvals->init_lambda);
478 serializer->doDouble(&fepvals->delta_lambda);
480 else if (file_version >= 59)
482 serializer->doDouble(&fepvals->init_lambda);
483 serializer->doDouble(&fepvals->delta_lambda);
487 serializer->doReal(&rdum);
488 fepvals->init_lambda = rdum;
489 serializer->doReal(&rdum);
490 fepvals->delta_lambda = rdum;
492 if (file_version >= 79)
494 serializer->doInt(&fepvals->n_lambda);
495 for (auto g : keysOf(fepvals->all_lambda))
497 if (fepvals->n_lambda > 0)
499 fepvals->all_lambda[g].resize(fepvals->n_lambda);
500 serializer->doDoubleArray(fepvals->all_lambda[g].data(), fepvals->n_lambda);
501 serializer->doBoolArray(
502 fepvals->separate_dvdl.begin(),
503 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real>::size());
505 else if (fepvals->init_lambda >= 0)
507 fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
511 else if (file_version >= 64)
513 serializer->doInt(&fepvals->n_lambda);
514 if (serializer->reading())
516 /* still allocate the all_lambda array's contents. */
517 for (auto g : keysOf(fepvals->all_lambda))
519 if (fepvals->n_lambda > 0)
521 fepvals->all_lambda[g].resize(fepvals->n_lambda);
525 serializer->doDoubleArray(fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Fep].data(),
527 if (fepvals->init_lambda >= 0)
529 fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
531 if (serializer->reading())
533 /* copy the contents of the efptFEP lambda component to all
534 the other components */
535 for (auto g : keysOf(fepvals->all_lambda))
537 for (int h = 0; h < fepvals->n_lambda; h++)
539 if (g != FreeEnergyPerturbationCouplingType::Fep)
541 fepvals->all_lambda[g][h] =
542 fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Fep][h];
551 fepvals->n_lambda = 0;
552 if (fepvals->init_lambda >= 0)
554 fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
557 serializer->doReal(&fepvals->sc_alpha);
558 serializer->doInt(&fepvals->sc_power);
559 if (file_version >= 79)
561 serializer->doReal(&fepvals->sc_r_power);
565 fepvals->sc_r_power = 6.0;
567 if (fepvals->sc_r_power != 6.0)
569 gmx_fatal(FARGS, "sc-r-power=48 is no longer supported");
571 serializer->doReal(&fepvals->sc_sigma);
572 if (serializer->reading())
574 if (file_version >= 71)
576 fepvals->sc_sigma_min = fepvals->sc_sigma;
580 fepvals->sc_sigma_min = 0;
583 if (file_version >= 79)
585 serializer->doBool(&fepvals->bScCoul);
589 fepvals->bScCoul = TRUE;
591 if (file_version >= 64)
593 serializer->doInt(&fepvals->nstdhdl);
597 fepvals->nstdhdl = 1;
600 if (file_version >= 73)
602 serializer->doEnumAsInt(&fepvals->separate_dhdl_file);
603 serializer->doEnumAsInt(&fepvals->dhdl_derivatives);
607 fepvals->separate_dhdl_file = SeparateDhdlFile::Yes;
608 fepvals->dhdl_derivatives = DhDlDerivativeCalculation::Yes;
610 if (file_version >= 71)
612 serializer->doInt(&fepvals->dh_hist_size);
613 serializer->doDouble(&fepvals->dh_hist_spacing);
617 fepvals->dh_hist_size = 0;
618 fepvals->dh_hist_spacing = 0.1;
620 if (file_version >= 79)
622 serializer->doEnumAsInt(&fepvals->edHdLPrintEnergy);
626 fepvals->edHdLPrintEnergy = FreeEnergyPrintEnergy::No;
629 /* handle lambda_neighbors */
630 if ((file_version >= 83 && file_version < 90) || file_version >= 92)
632 serializer->doInt(&fepvals->lambda_neighbors);
633 if ((fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0)
634 && (fepvals->init_lambda < 0))
636 fepvals->lambda_start_n = (fepvals->init_fep_state - fepvals->lambda_neighbors);
637 fepvals->lambda_stop_n = (fepvals->init_fep_state + fepvals->lambda_neighbors + 1);
638 if (fepvals->lambda_start_n < 0)
640 fepvals->lambda_start_n = 0;
642 if (fepvals->lambda_stop_n >= fepvals->n_lambda)
644 fepvals->lambda_stop_n = fepvals->n_lambda;
649 fepvals->lambda_start_n = 0;
650 fepvals->lambda_stop_n = fepvals->n_lambda;
655 fepvals->lambda_start_n = 0;
656 fepvals->lambda_stop_n = fepvals->n_lambda;
660 static void do_pull(gmx::ISerializer* serializer, pull_params_t* pull, int file_version, PullingAlgorithm ePullOld)
662 PullGroupGeometry eGeomOld = PullGroupGeometry::Count;
666 if (file_version >= 95)
668 serializer->doInt(&pull->ngroup);
670 serializer->doInt(&pull->ncoord);
671 if (file_version < 95)
673 pull->ngroup = pull->ncoord + 1;
675 if (file_version < tpxv_PullCoordTypeGeom)
679 serializer->doEnumAsInt(&eGeomOld);
680 serializer->doIvec(&dimOld);
681 /* The inner cylinder radius, now removed */
682 serializer->doReal(&dum);
684 serializer->doReal(&pull->cylinder_r);
685 serializer->doReal(&pull->constr_tol);
686 if (file_version >= 95)
688 serializer->doBool(&pull->bPrintCOM);
689 /* With file_version < 95 this value is set below */
691 if (file_version >= tpxv_ReplacePullPrintCOM12)
693 serializer->doBool(&pull->bPrintRefValue);
694 serializer->doBool(&pull->bPrintComp);
696 else if (file_version >= tpxv_PullCoordTypeGeom)
699 serializer->doInt(&idum); /* used to be bPrintCOM2 */
700 serializer->doBool(&pull->bPrintRefValue);
701 serializer->doBool(&pull->bPrintComp);
705 pull->bPrintRefValue = FALSE;
706 pull->bPrintComp = TRUE;
708 serializer->doInt(&pull->nstxout);
709 serializer->doInt(&pull->nstfout);
710 if (file_version >= tpxv_PullPrevStepCOMAsReference)
712 serializer->doBool(&pull->bSetPbcRefToPrevStepCOM);
716 pull->bSetPbcRefToPrevStepCOM = FALSE;
718 pull->group.resize(pull->ngroup);
719 pull->coord.resize(pull->ncoord);
720 if (file_version < 95)
722 /* epullgPOS for position pulling, before epullgDIRPBC was removed */
723 if (eGeomOld == PullGroupGeometry::DirectionPBC)
725 gmx_fatal(FARGS, "pull-geometry=position is no longer supported");
727 if (eGeomOld > PullGroupGeometry::DirectionPBC)
731 case (PullGroupGeometry::DirectionRelative):
732 eGeomOld = PullGroupGeometry::DirectionPBC;
734 case (PullGroupGeometry::Angle):
735 eGeomOld = PullGroupGeometry::DirectionRelative;
737 case (PullGroupGeometry::Dihedral): eGeomOld = PullGroupGeometry::Angle; break;
738 case (PullGroupGeometry::AngleAxis): eGeomOld = PullGroupGeometry::Dihedral; break;
739 case (PullGroupGeometry::Count): eGeomOld = PullGroupGeometry::AngleAxis; break;
740 default: GMX_RELEASE_ASSERT(false, "Unhandled old pull type");
744 for (g = 0; g < pull->ngroup; g++)
746 /* We read and ignore a pull coordinate for group 0 */
747 do_pullgrp_tpx_pre95(serializer, &pull->group[g], &pull->coord[std::max(g - 1, 0)]);
750 pull->coord[g - 1].group[0] = 0;
751 pull->coord[g - 1].group[1] = g;
755 pull->bPrintCOM = (!pull->group[0].ind.empty());
759 for (g = 0; g < pull->ngroup; g++)
761 do_pull_group(serializer, &pull->group[g]);
763 for (g = 0; g < pull->ncoord; g++)
765 do_pull_coord(serializer, &pull->coord[g], file_version, ePullOld, eGeomOld, dimOld);
768 if (file_version >= tpxv_PullAverage)
772 v = pull->bXOutAverage;
773 serializer->doBool(&v);
774 pull->bXOutAverage = v;
775 v = pull->bFOutAverage;
776 serializer->doBool(&v);
777 pull->bFOutAverage = v;
782 static void do_rotgrp(gmx::ISerializer* serializer, t_rotgrp* rotg)
784 serializer->doEnumAsInt(&rotg->eType);
785 if (serializer->reading())
788 serializer->doInt(&temp);
789 rotg->bMassW = static_cast<bool>(temp);
793 int temp = static_cast<int>(rotg->bMassW);
794 serializer->doInt(&temp);
796 serializer->doInt(&rotg->nat);
797 if (serializer->reading())
799 snew(rotg->ind, rotg->nat);
801 serializer->doIntArray(rotg->ind, rotg->nat);
802 if (serializer->reading())
804 snew(rotg->x_ref, rotg->nat);
806 serializer->doRvecArray(rotg->x_ref, rotg->nat);
807 serializer->doRvec(&rotg->inputVec);
808 serializer->doRvec(&rotg->pivot);
809 serializer->doReal(&rotg->rate);
810 serializer->doReal(&rotg->k);
811 serializer->doReal(&rotg->slab_dist);
812 serializer->doReal(&rotg->min_gaussian);
813 serializer->doReal(&rotg->eps);
814 serializer->doEnumAsInt(&rotg->eFittype);
815 serializer->doInt(&rotg->PotAngle_nstep);
816 serializer->doReal(&rotg->PotAngle_step);
819 static void do_rot(gmx::ISerializer* serializer, t_rot* rot)
823 serializer->doInt(&rot->ngrp);
824 serializer->doInt(&rot->nstrout);
825 serializer->doInt(&rot->nstsout);
826 if (serializer->reading())
828 snew(rot->grp, rot->ngrp);
830 for (g = 0; g < rot->ngrp; g++)
832 do_rotgrp(serializer, &rot->grp[g]);
837 static void do_swapgroup(gmx::ISerializer* serializer, t_swapGroup* g)
840 /* Name of the group or molecule */
842 if (serializer->reading())
844 serializer->doString(&buf);
845 g->molname = gmx_strdup(buf.c_str());
850 serializer->doString(&buf);
853 /* Number of atoms in the group */
854 serializer->doInt(&g->nat);
856 /* The group's atom indices */
857 if (serializer->reading())
859 snew(g->ind, g->nat);
861 serializer->doIntArray(g->ind, g->nat);
863 /* Requested counts for compartments A and B */
864 serializer->doIntArray(g->nmolReq, eCompNR);
867 static void do_swapcoords_tpx(gmx::ISerializer* serializer, t_swapcoords* swap, int file_version)
869 /* Enums for better readability of the code */
882 if (file_version >= tpxv_CompElPolyatomicIonsAndMultipleIonTypes)
884 /* The total number of swap groups is the sum of the fixed groups
885 * (split0, split1, solvent), and the user-defined groups (2+ types of ions)
887 serializer->doInt(&swap->ngrp);
888 if (serializer->reading())
890 snew(swap->grp, swap->ngrp);
892 for (int ig = 0; ig < swap->ngrp; ig++)
894 do_swapgroup(serializer, &swap->grp[ig]);
896 serializer->doBool(&swap->massw_split[eChannel0]);
897 serializer->doBool(&swap->massw_split[eChannel1]);
898 serializer->doInt(&swap->nstswap);
899 serializer->doInt(&swap->nAverage);
900 serializer->doReal(&swap->threshold);
901 serializer->doReal(&swap->cyl0r);
902 serializer->doReal(&swap->cyl0u);
903 serializer->doReal(&swap->cyl0l);
904 serializer->doReal(&swap->cyl1r);
905 serializer->doReal(&swap->cyl1u);
906 serializer->doReal(&swap->cyl1l);
910 /*** Support reading older CompEl .tpr files ***/
912 /* In the original CompEl .tpr files, we always have 5 groups: */
914 snew(swap->grp, swap->ngrp);
916 swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname = gmx_strdup("split0"); // group 0: split0
917 swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname = gmx_strdup("split1"); // group 1: split1
918 swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname =
919 gmx_strdup("solvent"); // group 2: solvent
920 swap->grp[3].molname = gmx_strdup("anions"); // group 3: anions
921 swap->grp[4].molname = gmx_strdup("cations"); // group 4: cations
923 serializer->doInt(&swap->grp[3].nat);
924 serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].nat);
925 serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].nat);
926 serializer->doBool(&swap->massw_split[eChannel0]);
927 serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].nat);
928 serializer->doBool(&swap->massw_split[eChannel1]);
929 serializer->doInt(&swap->nstswap);
930 serializer->doInt(&swap->nAverage);
931 serializer->doReal(&swap->threshold);
932 serializer->doReal(&swap->cyl0r);
933 serializer->doReal(&swap->cyl0u);
934 serializer->doReal(&swap->cyl0l);
935 serializer->doReal(&swap->cyl1r);
936 serializer->doReal(&swap->cyl1u);
937 serializer->doReal(&swap->cyl1l);
939 // The order[] array keeps compatibility with older .tpr files
940 // by reading in the groups in the classic order
942 const int order[4] = { 3,
943 static_cast<int>(SwapGroupSplittingType::Solvent),
944 static_cast<int>(SwapGroupSplittingType::Split0),
945 static_cast<int>(SwapGroupSplittingType::Split1) };
947 for (int ig = 0; ig < 4; ig++)
950 snew(swap->grp[g].ind, swap->grp[g].nat);
951 serializer->doIntArray(swap->grp[g].ind, swap->grp[g].nat);
955 for (int j = eCompA; j <= eCompB; j++)
957 serializer->doInt(&swap->grp[3].nmolReq[j]); // group 3 = anions
958 serializer->doInt(&swap->grp[4].nmolReq[j]); // group 4 = cations
960 } /* End support reading older CompEl .tpr files */
962 if (file_version >= tpxv_CompElWithSwapLayerOffset)
964 serializer->doReal(&swap->bulkOffset[eCompA]);
965 serializer->doReal(&swap->bulkOffset[eCompB]);
969 static void do_legacy_efield(gmx::ISerializer* serializer, gmx::KeyValueTreeObjectBuilder* root)
971 const char* const dimName[] = { "x", "y", "z" };
973 auto appliedForcesObj = root->addObject("applied-forces");
974 auto efieldObj = appliedForcesObj.addObject("electric-field");
975 // The content of the tpr file for this feature has
976 // been the same since gromacs 4.0 that was used for
978 for (int j = 0; j < DIM; ++j)
981 serializer->doInt(&n);
982 serializer->doInt(&nt);
983 std::vector<real> aa(n + 1), phi(nt + 1), at(nt + 1), phit(nt + 1);
984 serializer->doRealArray(aa.data(), n);
985 serializer->doRealArray(phi.data(), n);
986 serializer->doRealArray(at.data(), nt);
987 serializer->doRealArray(phit.data(), nt);
993 "Can not handle tpr files with more than one electric field term per "
996 auto dimObj = efieldObj.addObject(dimName[j]);
997 dimObj.addValue<real>("E0", aa[0]);
998 dimObj.addValue<real>("omega", at[0]);
999 dimObj.addValue<real>("t0", phi[0]);
1000 dimObj.addValue<real>("sigma", phit[0]);
1006 static void do_inputrec(gmx::ISerializer* serializer, t_inputrec* ir, int file_version)
1008 int i, j, k, idum = 0;
1010 gmx_bool bdum = false;
1012 if (file_version != tpx_version)
1014 /* Give a warning about features that are not accessible */
1015 fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n", file_version, tpx_version);
1018 if (file_version == 0)
1023 gmx::KeyValueTreeBuilder paramsBuilder;
1024 gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
1026 /* Basic inputrec stuff */
1027 serializer->doEnumAsInt(&ir->eI);
1028 if (file_version >= 62)
1030 serializer->doInt64(&ir->nsteps);
1034 serializer->doInt(&idum);
1038 if (file_version >= 62)
1040 serializer->doInt64(&ir->init_step);
1044 serializer->doInt(&idum);
1045 ir->init_step = idum;
1048 serializer->doInt(&ir->simulation_part);
1050 if (file_version >= tpxv_MTS)
1052 serializer->doBool(&ir->useMts);
1053 int numLevels = ir->mtsLevels.size();
1056 serializer->doInt(&numLevels);
1058 ir->mtsLevels.resize(numLevels);
1059 for (auto& mtsLevel : ir->mtsLevels)
1061 int forceGroups = mtsLevel.forceGroups.to_ulong();
1062 serializer->doInt(&forceGroups);
1063 mtsLevel.forceGroups = std::bitset<static_cast<int>(gmx::MtsForceGroups::Count)>(forceGroups);
1064 serializer->doInt(&mtsLevel.stepFactor);
1070 ir->mtsLevels.clear();
1073 if (file_version >= 67)
1075 serializer->doInt(&ir->nstcalcenergy);
1079 ir->nstcalcenergy = 1;
1081 if (file_version >= 81)
1083 serializer->doEnumAsInt(&ir->cutoff_scheme);
1084 if (file_version < 94)
1086 // Need to invert the scheme order
1087 switch (ir->cutoff_scheme)
1089 case (CutoffScheme::Group): ir->cutoff_scheme = CutoffScheme::Verlet; break;
1090 case (CutoffScheme::Verlet): ir->cutoff_scheme = CutoffScheme::Group; break;
1091 default: GMX_RELEASE_ASSERT(false, "Unhandled cutoff scheme type");
1097 ir->cutoff_scheme = CutoffScheme::Group;
1099 serializer->doInt(&idum); /* used to be ns_type; not used anymore */
1100 serializer->doInt(&ir->nstlist);
1101 serializer->doInt(&idum); /* used to be ndelta; not used anymore */
1103 serializer->doReal(&ir->rtpi);
1105 serializer->doInt(&ir->nstcomm);
1106 serializer->doEnumAsInt(&ir->comm_mode);
1108 /* ignore nstcheckpoint */
1109 if (file_version < tpxv_RemoveObsoleteParameters1)
1111 serializer->doInt(&idum);
1114 serializer->doInt(&ir->nstcgsteep);
1116 serializer->doInt(&ir->nbfgscorr);
1118 serializer->doInt(&ir->nstlog);
1119 serializer->doInt(&ir->nstxout);
1120 serializer->doInt(&ir->nstvout);
1121 serializer->doInt(&ir->nstfout);
1122 serializer->doInt(&ir->nstenergy);
1123 serializer->doInt(&ir->nstxout_compressed);
1124 if (file_version >= 59)
1126 serializer->doDouble(&ir->init_t);
1127 serializer->doDouble(&ir->delta_t);
1131 serializer->doReal(&rdum);
1133 serializer->doReal(&rdum);
1136 serializer->doReal(&ir->x_compression_precision);
1137 if (file_version >= 81)
1139 serializer->doReal(&ir->verletbuf_tol);
1143 ir->verletbuf_tol = 0;
1145 serializer->doReal(&ir->rlist);
1146 if (file_version >= 67 && file_version < tpxv_RemoveTwinRange)
1148 if (serializer->reading())
1150 // Reading such a file version could invoke the twin-range
1151 // scheme, about which mdrun should give a fatal error.
1152 real dummy_rlistlong = -1;
1153 serializer->doReal(&dummy_rlistlong);
1155 ir->useTwinRange = (ir->rlist > 0 && (dummy_rlistlong == 0 || dummy_rlistlong > ir->rlist));
1156 // When true, this forces mdrun to issue an error (regardless of
1157 // ir->cutoff_scheme).
1159 // Otherwise, grompp used to set rlistlong actively. Users
1160 // were probably also confused and set rlistlong == rlist.
1161 // However, in all remaining cases, it is safe to let
1162 // mdrun proceed normally.
1167 // No need to read or write anything
1168 ir->useTwinRange = false;
1170 if (file_version >= 82 && file_version != 90)
1172 // Multiple time-stepping is no longer enabled, but the old
1173 // support required the twin-range scheme, for which mdrun
1174 // already emits a fatal error.
1175 int dummy_nstcalclr = -1;
1176 serializer->doInt(&dummy_nstcalclr);
1178 serializer->doEnumAsInt(&ir->coulombtype);
1179 if (file_version >= 81)
1181 serializer->doEnumAsInt(&ir->coulomb_modifier);
1185 ir->coulomb_modifier = (ir->cutoff_scheme == CutoffScheme::Verlet ? InteractionModifiers::PotShift
1186 : InteractionModifiers::None);
1188 serializer->doReal(&ir->rcoulomb_switch);
1189 serializer->doReal(&ir->rcoulomb);
1190 serializer->doEnumAsInt(&ir->vdwtype);
1191 if (file_version >= 81)
1193 serializer->doEnumAsInt(&ir->vdw_modifier);
1197 ir->vdw_modifier = (ir->cutoff_scheme == CutoffScheme::Verlet ? InteractionModifiers::PotShift
1198 : InteractionModifiers::None);
1200 serializer->doReal(&ir->rvdw_switch);
1201 serializer->doReal(&ir->rvdw);
1202 serializer->doEnumAsInt(&ir->eDispCorr);
1203 serializer->doReal(&ir->epsilon_r);
1204 serializer->doReal(&ir->epsilon_rf);
1205 serializer->doReal(&ir->tabext);
1207 // This permits reading a .tpr file that used implicit solvent,
1208 // and later permitting mdrun to refuse to run it.
1209 if (serializer->reading())
1211 if (file_version < tpxv_RemoveImplicitSolvation)
1213 serializer->doInt(&idum);
1214 serializer->doInt(&idum);
1215 serializer->doReal(&rdum);
1216 serializer->doReal(&rdum);
1217 serializer->doInt(&idum);
1218 ir->implicit_solvent = (idum > 0);
1222 ir->implicit_solvent = false;
1224 if (file_version < tpxv_RemoveImplicitSolvation)
1226 serializer->doReal(&rdum);
1227 serializer->doReal(&rdum);
1228 serializer->doReal(&rdum);
1229 serializer->doReal(&rdum);
1230 if (file_version >= 60)
1232 serializer->doReal(&rdum);
1233 serializer->doInt(&idum);
1235 serializer->doReal(&rdum);
1239 if (file_version >= 81)
1241 serializer->doReal(&ir->fourier_spacing);
1245 ir->fourier_spacing = 0.0;
1247 serializer->doInt(&ir->nkx);
1248 serializer->doInt(&ir->nky);
1249 serializer->doInt(&ir->nkz);
1250 serializer->doInt(&ir->pme_order);
1251 serializer->doReal(&ir->ewald_rtol);
1253 if (file_version >= 93)
1255 serializer->doReal(&ir->ewald_rtol_lj);
1259 ir->ewald_rtol_lj = ir->ewald_rtol;
1261 serializer->doEnumAsInt(&ir->ewald_geometry);
1262 serializer->doReal(&ir->epsilon_surface);
1264 /* ignore bOptFFT */
1265 if (file_version < tpxv_RemoveObsoleteParameters1)
1267 serializer->doBool(&bdum);
1270 if (file_version >= 93)
1272 serializer->doEnumAsInt(&ir->ljpme_combination_rule);
1274 serializer->doBool(&ir->bContinuation);
1275 serializer->doEnumAsInt(&ir->etc);
1276 /* before version 18, ir->etc was a gmx_bool (ir->btc),
1277 * but the values 0 and 1 still mean no and
1278 * berendsen temperature coupling, respectively.
1280 if (file_version >= 79)
1282 serializer->doBool(&ir->bPrintNHChains);
1284 if (file_version >= 71)
1286 serializer->doInt(&ir->nsttcouple);
1290 ir->nsttcouple = ir->nstcalcenergy;
1292 serializer->doEnumAsInt(&ir->epc);
1293 serializer->doEnumAsInt(&ir->epct);
1294 if (file_version >= 71)
1296 serializer->doInt(&ir->nstpcouple);
1300 ir->nstpcouple = ir->nstcalcenergy;
1302 serializer->doReal(&ir->tau_p);
1303 serializer->doRvec(&ir->ref_p[XX]);
1304 serializer->doRvec(&ir->ref_p[YY]);
1305 serializer->doRvec(&ir->ref_p[ZZ]);
1306 serializer->doRvec(&ir->compress[XX]);
1307 serializer->doRvec(&ir->compress[YY]);
1308 serializer->doRvec(&ir->compress[ZZ]);
1309 serializer->doEnumAsInt(&ir->refcoord_scaling);
1310 serializer->doRvec(&ir->posres_com);
1311 serializer->doRvec(&ir->posres_comB);
1313 if (file_version < 79)
1315 serializer->doInt(&ir->andersen_seed);
1319 ir->andersen_seed = 0;
1322 serializer->doReal(&ir->shake_tol);
1324 serializer->doEnumAsInt(&ir->efep);
1325 if (serializer->reading())
1327 ir->fepvals = std::make_unique<t_lambda>();
1329 do_fepvals(serializer, ir->fepvals.get(), file_version);
1331 if (file_version >= 79)
1333 serializer->doBool(&ir->bSimTemp);
1336 ir->bSimTemp = TRUE;
1341 ir->bSimTemp = FALSE;
1345 if (serializer->reading())
1347 ir->simtempvals = std::make_unique<t_simtemp>();
1349 do_simtempvals(serializer, ir->simtempvals.get(), ir->fepvals->n_lambda, file_version);
1352 if (file_version >= 79)
1354 serializer->doBool(&ir->bExpanded);
1358 if (serializer->reading())
1360 ir->expandedvals = std::make_unique<t_expanded>();
1362 do_expandedvals(serializer, ir->expandedvals.get(), ir->fepvals.get(), file_version);
1365 serializer->doEnumAsInt(&ir->eDisre);
1366 serializer->doEnumAsInt(&ir->eDisreWeighting);
1367 serializer->doBool(&ir->bDisreMixed);
1368 serializer->doReal(&ir->dr_fc);
1369 serializer->doReal(&ir->dr_tau);
1370 serializer->doInt(&ir->nstdisreout);
1371 serializer->doReal(&ir->orires_fc);
1372 serializer->doReal(&ir->orires_tau);
1373 serializer->doInt(&ir->nstorireout);
1375 /* ignore dihre_fc */
1376 if (file_version < 79)
1378 serializer->doReal(&rdum);
1381 serializer->doReal(&ir->em_stepsize);
1382 serializer->doReal(&ir->em_tol);
1383 serializer->doBool(&ir->bShakeSOR);
1384 serializer->doInt(&ir->niter);
1385 serializer->doReal(&ir->fc_stepsize);
1386 serializer->doEnumAsInt(&ir->eConstrAlg);
1387 serializer->doInt(&ir->nProjOrder);
1388 serializer->doReal(&ir->LincsWarnAngle);
1389 serializer->doInt(&ir->nLincsIter);
1390 serializer->doReal(&ir->bd_fric);
1391 if (file_version >= tpxv_Use64BitRandomSeed)
1393 serializer->doInt64(&ir->ld_seed);
1397 serializer->doInt(&idum);
1401 for (i = 0; i < DIM; i++)
1403 serializer->doRvec(&ir->deform[i]);
1405 serializer->doReal(&ir->cos_accel);
1407 serializer->doInt(&ir->userint1);
1408 serializer->doInt(&ir->userint2);
1409 serializer->doInt(&ir->userint3);
1410 serializer->doInt(&ir->userint4);
1411 serializer->doReal(&ir->userreal1);
1412 serializer->doReal(&ir->userreal2);
1413 serializer->doReal(&ir->userreal3);
1414 serializer->doReal(&ir->userreal4);
1416 /* AdResS is removed, but we need to be able to read old files,
1417 and let mdrun refuse to run them */
1418 if (file_version >= 77 && file_version < tpxv_RemoveAdress)
1420 serializer->doBool(&ir->bAdress);
1423 int idum, numThermoForceGroups, numEnergyGroups;
1426 serializer->doInt(&idum);
1427 serializer->doReal(&rdum);
1428 serializer->doReal(&rdum);
1429 serializer->doReal(&rdum);
1430 serializer->doInt(&idum);
1431 serializer->doInt(&idum);
1432 serializer->doRvec(&rvecdum);
1433 serializer->doInt(&numThermoForceGroups);
1434 serializer->doReal(&rdum);
1435 serializer->doInt(&numEnergyGroups);
1436 serializer->doInt(&idum);
1438 if (numThermoForceGroups > 0)
1440 std::vector<int> idumn(numThermoForceGroups);
1441 serializer->doIntArray(idumn.data(), idumn.size());
1443 if (numEnergyGroups > 0)
1445 std::vector<int> idumn(numEnergyGroups);
1446 serializer->doIntArray(idumn.data(), idumn.size());
1452 ir->bAdress = FALSE;
1457 PullingAlgorithm ePullOld = PullingAlgorithm::Umbrella;
1459 if (file_version >= tpxv_PullCoordTypeGeom)
1461 serializer->doBool(&ir->bPull);
1465 serializer->doEnumAsInt(&ePullOld);
1466 ir->bPull = (ePullOld != PullingAlgorithm::Umbrella);
1467 /* We removed the first ePull=ePullNo for the enum */
1470 case (PullingAlgorithm::Umbrella): break; // this is equal to not using pulling
1471 case (PullingAlgorithm::Constraint): ePullOld = PullingAlgorithm::Umbrella; break;
1472 case (PullingAlgorithm::ConstantForce):
1473 ePullOld = PullingAlgorithm::Constraint;
1475 case (PullingAlgorithm::FlatBottom):
1476 ePullOld = PullingAlgorithm::ConstantForce;
1478 case (PullingAlgorithm::FlatBottomHigh):
1479 ePullOld = PullingAlgorithm::FlatBottom;
1481 case (PullingAlgorithm::External):
1482 ePullOld = PullingAlgorithm::FlatBottomHigh;
1484 case (PullingAlgorithm::Count): ePullOld = PullingAlgorithm::External; break;
1485 default: GMX_RELEASE_ASSERT(false, "Unhandled old pull algorithm");
1490 if (serializer->reading())
1492 ir->pull = std::make_unique<pull_params_t>();
1494 do_pull(serializer, ir->pull.get(), file_version, ePullOld);
1498 if (file_version >= tpxv_AcceleratedWeightHistogram)
1500 serializer->doBool(&ir->bDoAwh);
1504 if (serializer->reading())
1506 ir->awhParams = std::make_unique<gmx::AwhParams>(serializer);
1510 ir->awhParams->serialize(serializer);
1519 /* Enforced rotation */
1520 if (file_version >= 74)
1522 serializer->doBool(&ir->bRot);
1525 if (serializer->reading())
1529 do_rot(serializer, ir->rot);
1537 /* Interactive molecular dynamics */
1538 if (file_version >= tpxv_InteractiveMolecularDynamics)
1540 serializer->doBool(&ir->bIMD);
1543 if (serializer->reading())
1547 do_imd(serializer, ir->imd);
1552 /* We don't support IMD sessions for old .tpr files */
1557 serializer->doInt(&ir->opts.ngtc);
1558 if (file_version >= 69)
1560 serializer->doInt(&ir->opts.nhchainlength);
1564 ir->opts.nhchainlength = 1;
1566 int removedOptsNgacc = 0;
1567 if (serializer->reading() && file_version < tpxv_RemovedConstantAcceleration)
1569 serializer->doInt(&removedOptsNgacc);
1571 serializer->doInt(&ir->opts.ngfrz);
1572 serializer->doInt(&ir->opts.ngener);
1574 if (serializer->reading())
1576 snew(ir->opts.nrdf, ir->opts.ngtc);
1577 snew(ir->opts.ref_t, ir->opts.ngtc);
1578 snew(ir->opts.annealing, ir->opts.ngtc);
1579 snew(ir->opts.anneal_npoints, ir->opts.ngtc);
1580 snew(ir->opts.anneal_time, ir->opts.ngtc);
1581 snew(ir->opts.anneal_temp, ir->opts.ngtc);
1582 snew(ir->opts.tau_t, ir->opts.ngtc);
1583 snew(ir->opts.nFreeze, ir->opts.ngfrz);
1584 snew(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
1586 if (ir->opts.ngtc > 0)
1588 serializer->doRealArray(ir->opts.nrdf, ir->opts.ngtc);
1589 serializer->doRealArray(ir->opts.ref_t, ir->opts.ngtc);
1590 serializer->doRealArray(ir->opts.tau_t, ir->opts.ngtc);
1592 if (ir->opts.ngfrz > 0)
1594 serializer->doIvecArray(ir->opts.nFreeze, ir->opts.ngfrz);
1596 if (serializer->reading() && file_version < tpxv_RemovedConstantAcceleration && removedOptsNgacc > 0)
1598 std::vector<gmx::RVec> dummy;
1599 dummy.resize(removedOptsNgacc);
1600 serializer->doRvecArray(reinterpret_cast<rvec*>(dummy.data()), removedOptsNgacc);
1601 ir->useConstantAcceleration = std::any_of(dummy.begin(), dummy.end(), [](const gmx::RVec& vec) {
1602 return vec[XX] != 0.0 || vec[YY] != 0.0 || vec[ZZ] != 0.0;
1607 ir->useConstantAcceleration = false;
1609 serializer->doIntArray(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
1611 /* First read the lists with annealing and npoints for each group */
1612 serializer->doEnumArrayAsInt(ir->opts.annealing, ir->opts.ngtc);
1613 serializer->doIntArray(ir->opts.anneal_npoints, ir->opts.ngtc);
1614 for (j = 0; j < (ir->opts.ngtc); j++)
1616 k = ir->opts.anneal_npoints[j];
1617 if (serializer->reading())
1619 snew(ir->opts.anneal_time[j], k);
1620 snew(ir->opts.anneal_temp[j], k);
1622 serializer->doRealArray(ir->opts.anneal_time[j], k);
1623 serializer->doRealArray(ir->opts.anneal_temp[j], k);
1627 serializer->doInt(&ir->nwall);
1628 serializer->doEnumAsInt(&ir->wall_type);
1629 serializer->doReal(&ir->wall_r_linpot);
1630 serializer->doInt(&ir->wall_atomtype[0]);
1631 serializer->doInt(&ir->wall_atomtype[1]);
1632 serializer->doReal(&ir->wall_density[0]);
1633 serializer->doReal(&ir->wall_density[1]);
1634 serializer->doReal(&ir->wall_ewald_zfac);
1637 /* Cosine stuff for electric fields */
1638 if (file_version < tpxv_GenericParamsForElectricField)
1640 do_legacy_efield(serializer, ¶msObj);
1644 if (file_version >= tpxv_ComputationalElectrophysiology)
1646 serializer->doEnumAsInt(&ir->eSwapCoords);
1647 if (ir->eSwapCoords != SwapType::No)
1649 if (serializer->reading())
1653 do_swapcoords_tpx(serializer, ir->swap, file_version);
1657 /* QMMM reading - despite defunct we require reading for backwards
1658 * compability and correct serialization
1661 serializer->doBool(&ir->bQMMM);
1663 serializer->doInt(&qmmmScheme);
1664 real unusedScalefactor;
1665 serializer->doReal(&unusedScalefactor);
1667 // this is still used in Mimic
1668 serializer->doInt(&ir->opts.ngQM);
1669 if (ir->opts.ngQM > 0 && ir->bQMMM)
1671 /* We leave in dummy i/o for removed parameters to avoid
1672 * changing the tpr format.
1674 std::vector<int> dummyIntVec(4 * ir->opts.ngQM, 0);
1675 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1676 dummyIntVec.clear();
1678 // std::vector<bool> has no data()
1679 std::vector<char> dummyBoolVec(ir->opts.ngQM * sizeof(bool) / sizeof(char));
1680 serializer->doBoolArray(reinterpret_cast<bool*>(dummyBoolVec.data()), dummyBoolVec.size());
1681 dummyBoolVec.clear();
1683 dummyIntVec.resize(2 * ir->opts.ngQM, 0);
1684 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1685 dummyIntVec.clear();
1687 std::vector<real> dummyRealVec(2 * ir->opts.ngQM, 0);
1688 serializer->doRealArray(dummyRealVec.data(), dummyRealVec.size());
1689 dummyRealVec.clear();
1691 dummyIntVec.resize(3 * ir->opts.ngQM, 0);
1692 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1693 dummyIntVec.clear();
1695 /* end of QMMM stuff */
1698 if (file_version >= tpxv_GenericParamsForElectricField)
1700 if (serializer->reading())
1702 paramsObj.mergeObject(gmx::deserializeKeyValueTree(serializer));
1706 GMX_RELEASE_ASSERT(ir->params != nullptr,
1707 "Parameters should be present when writing inputrec");
1708 gmx::serializeKeyValueTree(*ir->params, serializer);
1711 if (serializer->reading())
1713 ir->params = new gmx::KeyValueTreeObject(paramsBuilder.build());
1714 // Initialize internal parameters to an empty kvt for all tpr versions
1715 ir->internalParameters = std::make_unique<gmx::KeyValueTreeObject>();
1718 if (file_version >= tpxv_GenericInternalParameters)
1720 if (serializer->reading())
1722 ir->internalParameters =
1723 std::make_unique<gmx::KeyValueTreeObject>(gmx::deserializeKeyValueTree(serializer));
1727 GMX_RELEASE_ASSERT(ir->internalParameters != nullptr,
1728 "Parameters should be present when writing inputrec");
1729 gmx::serializeKeyValueTree(*ir->internalParameters, serializer);
1735 static void do_harm(gmx::ISerializer* serializer, t_iparams* iparams)
1737 serializer->doReal(&iparams->harmonic.rA);
1738 serializer->doReal(&iparams->harmonic.krA);
1739 serializer->doReal(&iparams->harmonic.rB);
1740 serializer->doReal(&iparams->harmonic.krB);
1743 static void do_iparams(gmx::ISerializer* serializer, t_functype ftype, t_iparams* iparams, int file_version)
1756 do_harm(serializer, iparams);
1757 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && serializer->reading())
1759 /* Correct incorrect storage of parameters */
1760 iparams->pdihs.phiB = iparams->pdihs.phiA;
1761 iparams->pdihs.cpB = iparams->pdihs.cpA;
1765 serializer->doReal(&iparams->harmonic.rA);
1766 serializer->doReal(&iparams->harmonic.krA);
1768 case F_LINEAR_ANGLES:
1769 serializer->doReal(&iparams->linangle.klinA);
1770 serializer->doReal(&iparams->linangle.aA);
1771 serializer->doReal(&iparams->linangle.klinB);
1772 serializer->doReal(&iparams->linangle.aB);
1775 serializer->doReal(&iparams->fene.bm);
1776 serializer->doReal(&iparams->fene.kb);
1780 serializer->doReal(&iparams->restraint.lowA);
1781 serializer->doReal(&iparams->restraint.up1A);
1782 serializer->doReal(&iparams->restraint.up2A);
1783 serializer->doReal(&iparams->restraint.kA);
1784 serializer->doReal(&iparams->restraint.lowB);
1785 serializer->doReal(&iparams->restraint.up1B);
1786 serializer->doReal(&iparams->restraint.up2B);
1787 serializer->doReal(&iparams->restraint.kB);
1793 serializer->doReal(&iparams->tab.kA);
1794 serializer->doInt(&iparams->tab.table);
1795 serializer->doReal(&iparams->tab.kB);
1797 case F_CROSS_BOND_BONDS:
1798 serializer->doReal(&iparams->cross_bb.r1e);
1799 serializer->doReal(&iparams->cross_bb.r2e);
1800 serializer->doReal(&iparams->cross_bb.krr);
1802 case F_CROSS_BOND_ANGLES:
1803 serializer->doReal(&iparams->cross_ba.r1e);
1804 serializer->doReal(&iparams->cross_ba.r2e);
1805 serializer->doReal(&iparams->cross_ba.r3e);
1806 serializer->doReal(&iparams->cross_ba.krt);
1808 case F_UREY_BRADLEY:
1809 serializer->doReal(&iparams->u_b.thetaA);
1810 serializer->doReal(&iparams->u_b.kthetaA);
1811 serializer->doReal(&iparams->u_b.r13A);
1812 serializer->doReal(&iparams->u_b.kUBA);
1813 if (file_version >= 79)
1815 serializer->doReal(&iparams->u_b.thetaB);
1816 serializer->doReal(&iparams->u_b.kthetaB);
1817 serializer->doReal(&iparams->u_b.r13B);
1818 serializer->doReal(&iparams->u_b.kUBB);
1822 iparams->u_b.thetaB = iparams->u_b.thetaA;
1823 iparams->u_b.kthetaB = iparams->u_b.kthetaA;
1824 iparams->u_b.r13B = iparams->u_b.r13A;
1825 iparams->u_b.kUBB = iparams->u_b.kUBA;
1828 case F_QUARTIC_ANGLES:
1829 serializer->doReal(&iparams->qangle.theta);
1830 serializer->doRealArray(iparams->qangle.c, 5);
1833 serializer->doReal(&iparams->bham.a);
1834 serializer->doReal(&iparams->bham.b);
1835 serializer->doReal(&iparams->bham.c);
1838 serializer->doReal(&iparams->morse.b0A);
1839 serializer->doReal(&iparams->morse.cbA);
1840 serializer->doReal(&iparams->morse.betaA);
1841 if (file_version >= 79)
1843 serializer->doReal(&iparams->morse.b0B);
1844 serializer->doReal(&iparams->morse.cbB);
1845 serializer->doReal(&iparams->morse.betaB);
1849 iparams->morse.b0B = iparams->morse.b0A;
1850 iparams->morse.cbB = iparams->morse.cbA;
1851 iparams->morse.betaB = iparams->morse.betaA;
1855 serializer->doReal(&iparams->cubic.b0);
1856 serializer->doReal(&iparams->cubic.kb);
1857 serializer->doReal(&iparams->cubic.kcub);
1859 case F_CONNBONDS: break;
1860 case F_POLARIZATION: serializer->doReal(&iparams->polarize.alpha); break;
1862 serializer->doReal(&iparams->anharm_polarize.alpha);
1863 serializer->doReal(&iparams->anharm_polarize.drcut);
1864 serializer->doReal(&iparams->anharm_polarize.khyp);
1867 serializer->doReal(&iparams->wpol.al_x);
1868 serializer->doReal(&iparams->wpol.al_y);
1869 serializer->doReal(&iparams->wpol.al_z);
1870 serializer->doReal(&iparams->wpol.rOH);
1871 serializer->doReal(&iparams->wpol.rHH);
1872 serializer->doReal(&iparams->wpol.rOD);
1875 serializer->doReal(&iparams->thole.a);
1876 serializer->doReal(&iparams->thole.alpha1);
1877 serializer->doReal(&iparams->thole.alpha2);
1878 serializer->doReal(&iparams->thole.rfac);
1881 serializer->doReal(&iparams->lj.c6);
1882 serializer->doReal(&iparams->lj.c12);
1885 serializer->doReal(&iparams->lj14.c6A);
1886 serializer->doReal(&iparams->lj14.c12A);
1887 serializer->doReal(&iparams->lj14.c6B);
1888 serializer->doReal(&iparams->lj14.c12B);
1891 serializer->doReal(&iparams->ljc14.fqq);
1892 serializer->doReal(&iparams->ljc14.qi);
1893 serializer->doReal(&iparams->ljc14.qj);
1894 serializer->doReal(&iparams->ljc14.c6);
1895 serializer->doReal(&iparams->ljc14.c12);
1897 case F_LJC_PAIRS_NB:
1898 serializer->doReal(&iparams->ljcnb.qi);
1899 serializer->doReal(&iparams->ljcnb.qj);
1900 serializer->doReal(&iparams->ljcnb.c6);
1901 serializer->doReal(&iparams->ljcnb.c12);
1907 serializer->doReal(&iparams->pdihs.phiA);
1908 serializer->doReal(&iparams->pdihs.cpA);
1909 serializer->doReal(&iparams->pdihs.phiB);
1910 serializer->doReal(&iparams->pdihs.cpB);
1911 serializer->doInt(&iparams->pdihs.mult);
1914 serializer->doReal(&iparams->pdihs.phiA);
1915 serializer->doReal(&iparams->pdihs.cpA);
1918 serializer->doInt(&iparams->disres.label);
1919 serializer->doInt(&iparams->disres.type);
1920 serializer->doReal(&iparams->disres.low);
1921 serializer->doReal(&iparams->disres.up1);
1922 serializer->doReal(&iparams->disres.up2);
1923 serializer->doReal(&iparams->disres.kfac);
1926 serializer->doInt(&iparams->orires.ex);
1927 serializer->doInt(&iparams->orires.label);
1928 serializer->doInt(&iparams->orires.power);
1929 serializer->doReal(&iparams->orires.c);
1930 serializer->doReal(&iparams->orires.obs);
1931 serializer->doReal(&iparams->orires.kfac);
1934 if (file_version < 82)
1936 serializer->doInt(&idum);
1937 serializer->doInt(&idum);
1939 serializer->doReal(&iparams->dihres.phiA);
1940 serializer->doReal(&iparams->dihres.dphiA);
1941 serializer->doReal(&iparams->dihres.kfacA);
1942 if (file_version >= 82)
1944 serializer->doReal(&iparams->dihres.phiB);
1945 serializer->doReal(&iparams->dihres.dphiB);
1946 serializer->doReal(&iparams->dihres.kfacB);
1950 iparams->dihres.phiB = iparams->dihres.phiA;
1951 iparams->dihres.dphiB = iparams->dihres.dphiA;
1952 iparams->dihres.kfacB = iparams->dihres.kfacA;
1956 serializer->doRvec(&iparams->posres.pos0A);
1957 serializer->doRvec(&iparams->posres.fcA);
1958 serializer->doRvec(&iparams->posres.pos0B);
1959 serializer->doRvec(&iparams->posres.fcB);
1962 serializer->doInt(&iparams->fbposres.geom);
1963 serializer->doRvec(&iparams->fbposres.pos0);
1964 serializer->doReal(&iparams->fbposres.r);
1965 serializer->doReal(&iparams->fbposres.k);
1967 case F_CBTDIHS: serializer->doRealArray(iparams->cbtdihs.cbtcA, NR_CBTDIHS); break;
1969 // Fall-through intended
1971 /* Fourier dihedrals are internally represented
1972 * as Ryckaert-Bellemans since those are faster to compute.
1974 serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
1975 serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
1979 serializer->doReal(&iparams->constr.dA);
1980 serializer->doReal(&iparams->constr.dB);
1983 serializer->doReal(&iparams->settle.doh);
1984 serializer->doReal(&iparams->settle.dhh);
1986 case F_VSITE1: break; // VSite1 has 0 parameters
1988 case F_VSITE2FD: serializer->doReal(&iparams->vsite.a); break;
1992 serializer->doReal(&iparams->vsite.a);
1993 serializer->doReal(&iparams->vsite.b);
1998 serializer->doReal(&iparams->vsite.a);
1999 serializer->doReal(&iparams->vsite.b);
2000 serializer->doReal(&iparams->vsite.c);
2003 serializer->doInt(&iparams->vsiten.n);
2004 serializer->doReal(&iparams->vsiten.a);
2006 case F_GB12_NOLONGERUSED:
2007 case F_GB13_NOLONGERUSED:
2008 case F_GB14_NOLONGERUSED:
2009 // Implicit solvent parameters can still be read, but never used
2010 if (serializer->reading())
2012 if (file_version < 68)
2014 serializer->doReal(&rdum);
2015 serializer->doReal(&rdum);
2016 serializer->doReal(&rdum);
2017 serializer->doReal(&rdum);
2019 if (file_version < tpxv_RemoveImplicitSolvation)
2021 serializer->doReal(&rdum);
2022 serializer->doReal(&rdum);
2023 serializer->doReal(&rdum);
2024 serializer->doReal(&rdum);
2025 serializer->doReal(&rdum);
2030 serializer->doInt(&iparams->cmap.cmapA);
2031 serializer->doInt(&iparams->cmap.cmapB);
2035 "unknown function type %d (%s) in %s line %d",
2037 interaction_function[ftype].name,
2043 static void do_ilist(gmx::ISerializer* serializer, InteractionList* ilist)
2045 int nr = ilist->size();
2046 serializer->doInt(&nr);
2047 if (serializer->reading())
2049 ilist->iatoms.resize(nr);
2051 serializer->doIntArray(ilist->iatoms.data(), ilist->size());
2054 static void do_ffparams(gmx::ISerializer* serializer, gmx_ffparams_t* ffparams, int file_version)
2056 serializer->doInt(&ffparams->atnr);
2057 int numTypes = ffparams->numTypes();
2058 serializer->doInt(&numTypes);
2059 if (serializer->reading())
2061 ffparams->functype.resize(numTypes);
2062 ffparams->iparams.resize(numTypes);
2064 /* Read/write all the function types */
2065 serializer->doIntArray(ffparams->functype.data(), ffparams->functype.size());
2067 if (file_version >= 66)
2069 serializer->doDouble(&ffparams->reppow);
2073 ffparams->reppow = 12.0;
2076 serializer->doReal(&ffparams->fudgeQQ);
2078 /* Check whether all these function types are supported by the code.
2079 * In practice the code is backwards compatible, which means that the
2080 * numbering may have to be altered from old numbering to new numbering
2082 for (int i = 0; i < ffparams->numTypes(); i++)
2084 if (serializer->reading())
2086 /* Loop over file versions */
2087 for (int k = 0; k < NFTUPD; k++)
2089 /* Compare the read file_version to the update table */
2090 if ((file_version < ftupd[k].fvnr) && (ffparams->functype[i] >= ftupd[k].ftype))
2092 ffparams->functype[i] += 1;
2097 do_iparams(serializer, ffparams->functype[i], &ffparams->iparams[i], file_version);
2101 static void add_settle_atoms(InteractionList* ilist)
2105 /* Settle used to only store the first atom: add the other two */
2106 ilist->iatoms.resize(2 * ilist->size());
2107 for (i = ilist->size() / 4 - 1; i >= 0; i--)
2109 ilist->iatoms[4 * i + 0] = ilist->iatoms[2 * i + 0];
2110 ilist->iatoms[4 * i + 1] = ilist->iatoms[2 * i + 1];
2111 ilist->iatoms[4 * i + 2] = ilist->iatoms[2 * i + 1] + 1;
2112 ilist->iatoms[4 * i + 3] = ilist->iatoms[2 * i + 1] + 2;
2116 static void do_ilists(gmx::ISerializer* serializer, InteractionLists* ilists, int file_version)
2118 GMX_RELEASE_ASSERT(ilists, "Need a valid ilists object");
2119 GMX_RELEASE_ASSERT(ilists->size() == F_NRE,
2120 "The code needs to be in sync with InteractionLists");
2122 for (int j = 0; j < F_NRE; j++)
2124 InteractionList& ilist = (*ilists)[j];
2125 gmx_bool bClear = FALSE;
2126 if (serializer->reading())
2128 for (int k = 0; k < NFTUPD; k++)
2130 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
2138 ilist.iatoms.clear();
2142 do_ilist(serializer, &ilist);
2143 if (file_version < 78 && j == F_SETTLE && !ilist.empty())
2145 add_settle_atoms(&ilist);
2151 static void do_block(gmx::ISerializer* serializer, t_block* block)
2153 serializer->doInt(&block->nr);
2154 if (serializer->reading())
2156 if ((block->nalloc_index > 0) && (nullptr != block->index))
2158 sfree(block->index);
2160 block->nalloc_index = block->nr + 1;
2161 snew(block->index, block->nalloc_index);
2163 serializer->doIntArray(block->index, block->nr + 1);
2166 static void doListOfLists(gmx::ISerializer* serializer, gmx::ListOfLists<int>* listOfLists)
2168 int numLists = listOfLists->ssize();
2169 serializer->doInt(&numLists);
2170 int numElements = listOfLists->elementsView().ssize();
2171 serializer->doInt(&numElements);
2172 if (serializer->reading())
2174 std::vector<int> listRanges(numLists + 1);
2175 serializer->doIntArray(listRanges.data(), numLists + 1);
2176 std::vector<int> elements(numElements);
2177 serializer->doIntArray(elements.data(), numElements);
2178 *listOfLists = gmx::ListOfLists<int>(std::move(listRanges), std::move(elements));
2182 serializer->doIntArray(const_cast<int*>(listOfLists->listRangesView().data()), numLists + 1);
2183 serializer->doIntArray(const_cast<int*>(listOfLists->elementsView().data()), numElements);
2187 /* This is a primitive routine to make it possible to translate atomic numbers
2188 * to element names when reading TPR files, without making the Gromacs library
2189 * directory a dependency on mdrun (which is the case if we need elements.dat).
2191 static const char* atomicnumber_to_element(int atomicnumber)
2195 /* This does not have to be complete, so we only include elements likely
2196 * to occur in PDB files.
2198 switch (atomicnumber)
2200 case 1: p = "H"; break;
2201 case 5: p = "B"; break;
2202 case 6: p = "C"; break;
2203 case 7: p = "N"; break;
2204 case 8: p = "O"; break;
2205 case 9: p = "F"; break;
2206 case 11: p = "Na"; break;
2207 case 12: p = "Mg"; break;
2208 case 15: p = "P"; break;
2209 case 16: p = "S"; break;
2210 case 17: p = "Cl"; break;
2211 case 18: p = "Ar"; break;
2212 case 19: p = "K"; break;
2213 case 20: p = "Ca"; break;
2214 case 25: p = "Mn"; break;
2215 case 26: p = "Fe"; break;
2216 case 28: p = "Ni"; break;
2217 case 29: p = "Cu"; break;
2218 case 30: p = "Zn"; break;
2219 case 35: p = "Br"; break;
2220 case 47: p = "Ag"; break;
2221 default: p = ""; break;
2227 static void do_atom(gmx::ISerializer* serializer, t_atom* atom)
2229 serializer->doReal(&atom->m);
2230 serializer->doReal(&atom->q);
2231 serializer->doReal(&atom->mB);
2232 serializer->doReal(&atom->qB);
2233 serializer->doUShort(&atom->type);
2234 serializer->doUShort(&atom->typeB);
2235 serializer->doEnumAsInt(&atom->ptype);
2236 serializer->doInt(&atom->resind);
2237 serializer->doInt(&atom->atomnumber);
2238 if (serializer->reading())
2240 /* Set element string from atomic number if present.
2241 * This routine returns an empty string if the name is not found.
2243 std::strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
2244 /* avoid warnings about potentially unterminated string */
2245 atom->elem[3] = '\0';
2249 static void do_grps(gmx::ISerializer* serializer, gmx::ArrayRef<AtomGroupIndices> grps)
2251 for (auto& group : grps)
2253 int size = group.size();
2254 serializer->doInt(&size);
2255 if (serializer->reading())
2259 serializer->doIntArray(group.data(), size);
2263 static void do_symstr(gmx::ISerializer* serializer, char*** nm, t_symtab* symtab)
2267 if (serializer->reading())
2269 serializer->doInt(&ls);
2270 *nm = get_symtab_handle(symtab, ls);
2274 ls = lookup_symtab(symtab, *nm);
2275 serializer->doInt(&ls);
2279 static void do_strstr(gmx::ISerializer* serializer, int nstr, char*** nm, t_symtab* symtab)
2283 for (j = 0; (j < nstr); j++)
2285 do_symstr(serializer, &(nm[j]), symtab);
2289 static void do_resinfo(gmx::ISerializer* serializer, int n, t_resinfo* ri, t_symtab* symtab, int file_version)
2293 for (j = 0; (j < n); j++)
2295 do_symstr(serializer, &(ri[j].name), symtab);
2296 if (file_version >= 63)
2298 serializer->doInt(&ri[j].nr);
2299 serializer->doUChar(&ri[j].ic);
2309 static void do_atoms(gmx::ISerializer* serializer, t_atoms* atoms, t_symtab* symtab, int file_version)
2313 serializer->doInt(&atoms->nr);
2314 serializer->doInt(&atoms->nres);
2315 if (serializer->reading())
2317 /* Since we have always written all t_atom properties in the tpr file
2318 * (at least for all backward compatible versions), we don't store
2319 * but simple set the booleans here.
2321 atoms->haveMass = TRUE;
2322 atoms->haveCharge = TRUE;
2323 atoms->haveType = TRUE;
2324 atoms->haveBState = TRUE;
2325 atoms->havePdbInfo = FALSE;
2327 snew(atoms->atom, atoms->nr);
2328 snew(atoms->atomname, atoms->nr);
2329 snew(atoms->atomtype, atoms->nr);
2330 snew(atoms->atomtypeB, atoms->nr);
2331 snew(atoms->resinfo, atoms->nres);
2332 atoms->pdbinfo = nullptr;
2336 GMX_RELEASE_ASSERT(atoms->haveMass && atoms->haveCharge && atoms->haveType && atoms->haveBState,
2337 "Mass, charge, atomtype and B-state parameters should be present in "
2338 "t_atoms when writing a tpr file");
2340 for (i = 0; (i < atoms->nr); i++)
2342 do_atom(serializer, &atoms->atom[i]);
2344 do_strstr(serializer, atoms->nr, atoms->atomname, symtab);
2345 do_strstr(serializer, atoms->nr, atoms->atomtype, symtab);
2346 do_strstr(serializer, atoms->nr, atoms->atomtypeB, symtab);
2348 do_resinfo(serializer, atoms->nres, atoms->resinfo, symtab, file_version);
2351 static void do_groups(gmx::ISerializer* serializer, SimulationGroups* groups, t_symtab* symtab)
2353 do_grps(serializer, groups->groups);
2354 int numberOfGroupNames = groups->groupNames.size();
2355 serializer->doInt(&numberOfGroupNames);
2356 if (serializer->reading())
2358 groups->groupNames.resize(numberOfGroupNames);
2360 do_strstr(serializer, numberOfGroupNames, groups->groupNames.data(), symtab);
2361 for (auto group : gmx::keysOf(groups->groupNumbers))
2363 int numberOfGroupNumbers = groups->numberOfGroupNumbers(group);
2364 serializer->doInt(&numberOfGroupNumbers);
2365 if (numberOfGroupNumbers != 0)
2367 if (serializer->reading())
2369 groups->groupNumbers[group].resize(numberOfGroupNumbers);
2371 serializer->doUCharArray(groups->groupNumbers[group].data(), numberOfGroupNumbers);
2376 static void do_atomtypes(gmx::ISerializer* serializer, t_atomtypes* atomtypes, int file_version)
2380 serializer->doInt(&atomtypes->nr);
2382 if (serializer->reading())
2384 snew(atomtypes->atomnumber, j);
2386 if (serializer->reading() && file_version < tpxv_RemoveImplicitSolvation)
2388 std::vector<real> dummy(atomtypes->nr, 0);
2389 serializer->doRealArray(dummy.data(), dummy.size());
2390 serializer->doRealArray(dummy.data(), dummy.size());
2391 serializer->doRealArray(dummy.data(), dummy.size());
2393 serializer->doIntArray(atomtypes->atomnumber, j);
2395 if (serializer->reading() && file_version >= 60 && file_version < tpxv_RemoveImplicitSolvation)
2397 std::vector<real> dummy(atomtypes->nr, 0);
2398 serializer->doRealArray(dummy.data(), dummy.size());
2399 serializer->doRealArray(dummy.data(), dummy.size());
2403 static void do_symtab(gmx::ISerializer* serializer, t_symtab* symtab)
2408 serializer->doInt(&symtab->nr);
2410 if (serializer->reading())
2412 snew(symtab->symbuf, 1);
2413 symbuf = symtab->symbuf;
2414 symbuf->bufsize = nr;
2415 snew(symbuf->buf, nr);
2416 for (i = 0; (i < nr); i++)
2419 serializer->doString(&buf);
2420 symbuf->buf[i] = gmx_strdup(buf.c_str());
2425 symbuf = symtab->symbuf;
2426 while (symbuf != nullptr)
2428 for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
2430 std::string buf = symbuf->buf[i];
2431 serializer->doString(&buf);
2434 symbuf = symbuf->next;
2438 gmx_fatal(FARGS, "nr of symtab strings left: %d", nr);
2443 static void do_cmap(gmx::ISerializer* serializer, gmx_cmap_t* cmap_grid)
2446 int ngrid = cmap_grid->cmapdata.size();
2447 serializer->doInt(&ngrid);
2448 serializer->doInt(&cmap_grid->grid_spacing);
2450 int gs = cmap_grid->grid_spacing;
2451 int nelem = gs * gs;
2453 if (serializer->reading())
2455 cmap_grid->cmapdata.resize(ngrid);
2457 for (int i = 0; i < ngrid; i++)
2459 cmap_grid->cmapdata[i].cmap.resize(4 * nelem);
2463 for (int i = 0; i < ngrid; i++)
2465 for (int j = 0; j < nelem; j++)
2467 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4]);
2468 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 1]);
2469 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 2]);
2470 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 3]);
2476 static void do_moltype(gmx::ISerializer* serializer, gmx_moltype_t* molt, t_symtab* symtab, int file_version)
2478 do_symstr(serializer, &(molt->name), symtab);
2480 do_atoms(serializer, &molt->atoms, symtab, file_version);
2482 do_ilists(serializer, &molt->ilist, file_version);
2484 /* TODO: Remove the obsolete charge group index from the file */
2486 cgs.nr = molt->atoms.nr;
2487 cgs.nalloc_index = cgs.nr + 1;
2488 snew(cgs.index, cgs.nalloc_index);
2489 for (int i = 0; i < cgs.nr + 1; i++)
2493 do_block(serializer, &cgs);
2496 /* This used to be in the atoms struct */
2497 doListOfLists(serializer, &molt->excls);
2500 static void do_molblock(gmx::ISerializer* serializer, gmx_molblock_t* molb, int numAtomsPerMolecule)
2502 serializer->doInt(&molb->type);
2503 serializer->doInt(&molb->nmol);
2504 /* To maintain forward topology reading compatibility, we store #atoms.
2505 * TODO: Change this to conditional reading of a dummy int when we
2506 * increase tpx_generation.
2508 serializer->doInt(&numAtomsPerMolecule);
2509 /* Position restraint coordinates */
2510 int numPosres_xA = molb->posres_xA.size();
2511 serializer->doInt(&numPosres_xA);
2512 if (numPosres_xA > 0)
2514 if (serializer->reading())
2516 molb->posres_xA.resize(numPosres_xA);
2518 serializer->doRvecArray(as_rvec_array(molb->posres_xA.data()), numPosres_xA);
2520 int numPosres_xB = molb->posres_xB.size();
2521 serializer->doInt(&numPosres_xB);
2522 if (numPosres_xB > 0)
2524 if (serializer->reading())
2526 molb->posres_xB.resize(numPosres_xB);
2528 serializer->doRvecArray(as_rvec_array(molb->posres_xB.data()), numPosres_xB);
2532 static void set_disres_npair(gmx_mtop_t* mtop)
2534 gmx_mtop_ilistloop_t iloop;
2537 gmx::ArrayRef<t_iparams> ip = mtop->ffparams.iparams;
2539 iloop = gmx_mtop_ilistloop_init(*mtop);
2540 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
2542 const InteractionList& il = (*ilist)[F_DISRES];
2546 gmx::ArrayRef<const int> a = il.iatoms;
2548 for (int i = 0; i < il.size(); i += 3)
2551 if (i + 3 == il.size() || ip[a[i]].disres.label != ip[a[i + 3]].disres.label)
2553 ip[a[i]].disres.npair = npair;
2561 static void do_mtop(gmx::ISerializer* serializer, gmx_mtop_t* mtop, int file_version)
2563 do_symtab(serializer, &(mtop->symtab));
2565 do_symstr(serializer, &(mtop->name), &(mtop->symtab));
2567 do_ffparams(serializer, &mtop->ffparams, file_version);
2569 int nmoltype = mtop->moltype.size();
2570 serializer->doInt(&nmoltype);
2571 if (serializer->reading())
2573 mtop->moltype.resize(nmoltype);
2575 for (gmx_moltype_t& moltype : mtop->moltype)
2577 do_moltype(serializer, &moltype, &mtop->symtab, file_version);
2580 int nmolblock = mtop->molblock.size();
2581 serializer->doInt(&nmolblock);
2582 if (serializer->reading())
2584 mtop->molblock.resize(nmolblock);
2586 for (gmx_molblock_t& molblock : mtop->molblock)
2588 int numAtomsPerMolecule = (serializer->reading() ? 0 : mtop->moltype[molblock.type].atoms.nr);
2589 do_molblock(serializer, &molblock, numAtomsPerMolecule);
2591 serializer->doInt(&mtop->natoms);
2593 if (file_version >= tpxv_IntermolecularBondeds)
2595 serializer->doBool(&mtop->bIntermolecularInteractions);
2596 if (mtop->bIntermolecularInteractions)
2598 if (serializer->reading())
2600 mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
2602 do_ilists(serializer, mtop->intermolecular_ilist.get(), file_version);
2607 mtop->bIntermolecularInteractions = FALSE;
2610 do_atomtypes(serializer, &(mtop->atomtypes), file_version);
2612 if (file_version >= 65)
2614 do_cmap(serializer, &mtop->ffparams.cmap_grid);
2618 mtop->ffparams.cmap_grid.grid_spacing = 0;
2619 mtop->ffparams.cmap_grid.cmapdata.clear();
2622 do_groups(serializer, &mtop->groups, &(mtop->symtab));
2623 if (file_version < tpxv_RemovedConstantAcceleration)
2625 mtop->groups.groups[SimulationAtomGroupType::AccelerationUnused].clear();
2626 mtop->groups.groupNumbers[SimulationAtomGroupType::AccelerationUnused].clear();
2629 mtop->haveMoleculeIndices = true;
2631 if (file_version >= tpxv_StoreNonBondedInteractionExclusionGroup)
2633 std::int64_t intermolecularExclusionGroupSize = gmx::ssize(mtop->intermolecularExclusionGroup);
2634 serializer->doInt64(&intermolecularExclusionGroupSize);
2635 GMX_RELEASE_ASSERT(intermolecularExclusionGroupSize >= 0,
2636 "Number of atoms with excluded intermolecular non-bonded interactions "
2638 mtop->intermolecularExclusionGroup.resize(intermolecularExclusionGroupSize); // no effect when writing
2639 serializer->doIntArray(mtop->intermolecularExclusionGroup.data(),
2640 mtop->intermolecularExclusionGroup.size());
2643 if (serializer->reading())
2645 close_symtab(&(mtop->symtab));
2650 * Read the first part of the TPR file to find general system information.
2652 * If \p TopOnlyOK is true then we can read even future versions
2653 * of tpx files, provided the \p fileGeneration hasn't changed.
2654 * If it is false, we need the \p ir too, and bail out
2655 * if the file is newer than the program.
2657 * The version and generation of the topology (see top of this file)
2658 * are returned in the two last arguments, if those arguments are non-nullptr.
2660 * If possible, we will read the \p ir even when \p TopOnlyOK is true.
2662 * \param[in,out] serializer The serializer used to handle header processing.
2663 * \param[in,out] tpx File header datastructure.
2664 * \param[in] filename The name of the file being read/written
2665 * \param[in,out] fio File handle.
2666 * \param[in] TopOnlyOK If not reading \p ir is fine or not.
2668 static void do_tpxheader(gmx::FileIOXdrSerializer* serializer,
2670 const char* filename,
2678 /* XDR binary topology file */
2679 precision = sizeof(real);
2681 std::string fileTag;
2682 if (serializer->reading())
2684 serializer->doString(&buf);
2685 if (std::strncmp(buf.c_str(), "VERSION", 7) != 0)
2689 "Can not read file %s,\n"
2690 " this file is from a GROMACS version which is older than 2.0\n"
2691 " Make a new one with grompp or use a gro or pdb file, if possible",
2694 // We need to know the precision used to write the TPR file, to match it
2695 // to the precision of the currently running binary. If the precisions match
2696 // there is no problem, but mismatching precision needs to be accounted for
2697 // by reading into temporary variables of the correct precision instead
2698 // of the desired target datastructures.
2699 serializer->doInt(&precision);
2700 tpx->isDouble = (precision == sizeof(double));
2701 if ((precision != sizeof(float)) && !tpx->isDouble)
2704 "Unknown precision in file %s: real is %d bytes "
2705 "instead of %zu or %zu",
2711 gmx_fio_setprecision(fio, tpx->isDouble);
2713 "Reading file %s, %s (%s precision)\n",
2716 tpx->isDouble ? "double" : "single");
2720 buf = gmx::formatString("VERSION %s", gmx_version());
2721 serializer->doString(&buf);
2722 gmx_fio_setprecision(fio, tpx->isDouble);
2723 serializer->doInt(&precision);
2724 fileTag = gmx::formatString("%s", tpx_tag);
2727 /* Check versions! */
2728 serializer->doInt(&tpx->fileVersion);
2730 /* This is for backward compatibility with development versions 77-79
2731 * where the tag was, mistakenly, placed before the generation,
2732 * which would cause a segv instead of a proper error message
2733 * when reading the topology only from tpx with <77 code.
2735 if (tpx->fileVersion >= 77 && tpx->fileVersion <= 79)
2737 serializer->doString(&fileTag);
2740 serializer->doInt(&tpx->fileGeneration);
2742 if (tpx->fileVersion >= 81)
2744 serializer->doString(&fileTag);
2746 if (serializer->reading())
2748 if (tpx->fileVersion < 77)
2750 /* Versions before 77 don't have the tag, set it to release */
2751 fileTag = gmx::formatString("%s", TPX_TAG_RELEASE);
2754 if (fileTag != tpx_tag)
2756 fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n", fileTag.c_str(), tpx_tag);
2758 /* We only support reading tpx files with the same tag as the code
2759 * or tpx files with the release tag and with lower version number.
2761 if (fileTag != TPX_TAG_RELEASE && tpx->fileVersion < tpx_version)
2764 "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' "
2765 "with program for tpx version %d, tag '%s'",
2775 if ((tpx->fileVersion <= tpx_incompatible_version)
2776 || ((tpx->fileVersion > tpx_version) && !TopOnlyOK) || (tpx->fileGeneration > tpx_generation)
2777 || tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
2780 "reading tpx file (%s) version %d with version %d program",
2786 serializer->doInt(&tpx->natoms);
2787 serializer->doInt(&tpx->ngtc);
2789 if (tpx->fileVersion < 62)
2791 serializer->doInt(&idum);
2792 serializer->doReal(&rdum);
2794 if (tpx->fileVersion >= 79)
2796 serializer->doInt(&tpx->fep_state);
2798 serializer->doReal(&tpx->lambda);
2799 serializer->doBool(&tpx->bIr);
2800 serializer->doBool(&tpx->bTop);
2801 serializer->doBool(&tpx->bX);
2802 serializer->doBool(&tpx->bV);
2803 serializer->doBool(&tpx->bF);
2804 serializer->doBool(&tpx->bBox);
2806 if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
2808 if (!serializer->reading())
2810 GMX_RELEASE_ASSERT(tpx->sizeOfTprBody != 0,
2811 "Not possible to write new file with zero TPR body size");
2813 serializer->doInt64(&tpx->sizeOfTprBody);
2816 if ((tpx->fileGeneration > tpx_generation))
2818 /* This can only happen if TopOnlyOK=TRUE */
2823 #define do_test(serializer, b, p) \
2824 if ((serializer)->reading() && ((p) != nullptr) && !(b)) \
2825 gmx_fatal(FARGS, "No %s in input file", #p)
2828 * Process the first part of the TPR into the state datastructure.
2830 * Due to the structure of the legacy code, it is necessary
2831 * to split up the state reading into two parts, with the
2832 * box and legacy temperature coupling processed before the
2833 * topology datastructures.
2835 * See the documentation for do_tpx_body for the correct order of
2836 * the operations for reading a tpr file.
2838 * \param[in] serializer Abstract serializer used to read/write data.
2839 * \param[in] tpx The file header data.
2840 * \param[in, out] state Global state data.
2842 static void do_tpx_state_first(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state)
2844 if (serializer->reading())
2847 init_gtc_state(state, tpx->ngtc, 0, 0);
2849 do_test(serializer, tpx->bBox, state->box);
2852 serializer->doRvecArray(state->box, DIM);
2853 if (tpx->fileVersion >= 51)
2855 serializer->doRvecArray(state->box_rel, DIM);
2859 /* We initialize box_rel after reading the inputrec */
2860 clear_mat(state->box_rel);
2862 serializer->doRvecArray(state->boxv, DIM);
2863 if (tpx->fileVersion < 56)
2866 serializer->doRvecArray(mdum, DIM);
2870 if (state->ngtc > 0)
2873 snew(dumv, state->ngtc);
2874 if (tpx->fileVersion < 69)
2876 serializer->doRealArray(dumv, state->ngtc);
2878 /* These used to be the Berendsen tcoupl_lambda's */
2879 serializer->doRealArray(dumv, state->ngtc);
2885 * Process global topology data.
2887 * See the documentation for do_tpx_body for the correct order of
2888 * the operations for reading a tpr file.
2890 * \param[in] serializer Abstract serializer used to read/write data.
2891 * \param[in] tpx The file header data.
2892 * \param[in,out] mtop Global topology.
2894 static void do_tpx_mtop(gmx::ISerializer* serializer, TpxFileHeader* tpx, gmx_mtop_t* mtop)
2896 do_test(serializer, tpx->bTop, mtop);
2901 do_mtop(serializer, mtop, tpx->fileVersion);
2902 set_disres_npair(mtop);
2908 do_mtop(serializer, &dum_top, tpx->fileVersion);
2913 * Process coordinate vectors for state data.
2915 * Main part of state gets processed here.
2917 * See the documentation for do_tpx_body for the correct order of
2918 * the operations for reading a tpr file.
2920 * \param[in] serializer Abstract serializer used to read/write data.
2921 * \param[in] tpx The file header data.
2922 * \param[in,out] state Global state data.
2923 * \param[in,out] x Individual coordinates for processing, deprecated.
2924 * \param[in,out] v Individual velocities for processing, deprecated.
2926 static void do_tpx_state_second(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state, rvec* x, rvec* v)
2928 if (!serializer->reading())
2931 x == nullptr && v == nullptr,
2932 "Passing separate x and v pointers to do_tpx() is not supported when writing");
2936 GMX_RELEASE_ASSERT(!(x == nullptr && v != nullptr),
2937 "Passing x==NULL and v!=NULL is not supported");
2940 if (serializer->reading())
2944 // v is also nullptr by the above assertion, so we may
2945 // need to make memory in state for storing the contents
2949 state->flags |= enumValueToBitMask(StateEntry::X);
2953 state->flags |= enumValueToBitMask(StateEntry::V);
2955 state_change_natoms(state, tpx->natoms);
2961 x = state->x.rvec_array();
2962 v = state->v.rvec_array();
2964 do_test(serializer, tpx->bX, x);
2967 if (serializer->reading())
2969 state->flags |= enumValueToBitMask(StateEntry::X);
2971 serializer->doRvecArray(x, tpx->natoms);
2974 do_test(serializer, tpx->bV, v);
2977 if (serializer->reading())
2979 state->flags |= enumValueToBitMask(StateEntry::V);
2983 std::vector<gmx::RVec> dummyVelocities(tpx->natoms);
2984 serializer->doRvecArray(as_rvec_array(dummyVelocities.data()), tpx->natoms);
2988 serializer->doRvecArray(v, tpx->natoms);
2992 // No need to run do_test when the last argument is NULL
2995 std::vector<gmx::RVec> dummyForces(state->natoms);
2996 serializer->doRvecArray(as_rvec_array(dummyForces.data()), tpx->natoms);
3000 * Process simulation parameters.
3002 * See the documentation for do_tpx_body for the correct order of
3003 * the operations for reading a tpr file.
3005 * \param[in] serializer Abstract serializer used to read/write data.
3006 * \param[in] tpx The file header data.
3007 * \param[in,out] ir Datastructure with simulation parameters.
3009 static PbcType do_tpx_ir(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir)
3012 gmx_bool bPeriodicMols;
3014 /* Starting with tpx version 26, we have the inputrec
3015 * at the end of the file, so we can ignore it
3016 * if the file is never than the software (but still the
3017 * same generation - see comments at the top of this file.
3021 pbcType = PbcType::Unset;
3022 bPeriodicMols = FALSE;
3024 do_test(serializer, tpx->bIr, ir);
3027 if (tpx->fileVersion >= 53)
3029 /* Removed the pbc info from do_inputrec, since we always want it */
3030 if (!serializer->reading())
3032 pbcType = ir->pbcType;
3033 bPeriodicMols = ir->bPeriodicMols;
3035 serializer->doInt(reinterpret_cast<int*>(&pbcType));
3036 serializer->doBool(&bPeriodicMols);
3038 if (tpx->fileGeneration <= tpx_generation && ir)
3040 do_inputrec(serializer, ir, tpx->fileVersion);
3041 if (tpx->fileVersion < 53)
3043 pbcType = ir->pbcType;
3044 bPeriodicMols = ir->bPeriodicMols;
3047 if (serializer->reading() && ir && tpx->fileVersion >= 53)
3049 /* We need to do this after do_inputrec, since that initializes ir */
3050 ir->pbcType = pbcType;
3051 ir->bPeriodicMols = bPeriodicMols;
3058 * Correct and finalize read information.
3060 * If \p state is nullptr, skip the parts dependent on it.
3062 * See the documentation for do_tpx_body for the correct order of
3063 * the operations for reading a tpr file.
3065 * \param[in] tpx The file header used to check version numbers.
3066 * \param[out] ir Input rec that needs correction.
3067 * \param[out] state State needing correction.
3068 * \param[out] mtop Topology to finalize.
3070 static void do_tpx_finalize(TpxFileHeader* tpx, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
3072 if (tpx->fileVersion < 51 && state)
3074 set_box_rel(ir, state);
3078 if (state && state->ngtc == 0)
3080 /* Reading old version without tcoupl state data: set it */
3081 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
3083 if (tpx->bTop && mtop)
3085 if (tpx->fileVersion < 57)
3087 ir->eDisre = !mtop->moltype[0].ilist[F_DISRES].empty()
3088 ? DistanceRestraintRefinement::Simple
3089 : DistanceRestraintRefinement::None;
3096 * Process TPR data for file reading/writing.
3098 * The TPR file gets processed in in four stages due to the organization
3099 * of the data within it.
3101 * First, state data for the box is processed in do_tpx_state_first.
3102 * This is followed by processing the topology in do_tpx_mtop.
3103 * Coordinate and velocity vectors are handled next in do_tpx_state_second.
3104 * The last file information processed is the collection of simulation parameters in do_tpx_ir.
3105 * When reading, a final processing step is undertaken at the end.
3107 * \param[in] serializer Abstract serializer used to read/write data.
3108 * \param[in] tpx The file header data.
3109 * \param[in,out] ir Datastructures with simulation parameters.
3110 * \param[in,out] state Global state data.
3111 * \param[in,out] x Individual coordinates for processing, deprecated.
3112 * \param[in,out] v Individual velocities for processing, deprecated.
3113 * \param[in,out] mtop Global topology.
3115 static PbcType do_tpx_body(gmx::ISerializer* serializer,
3125 do_tpx_state_first(serializer, tpx, state);
3127 do_tpx_mtop(serializer, tpx, mtop);
3130 do_tpx_state_second(serializer, tpx, state, x, v);
3132 PbcType pbcType = do_tpx_ir(serializer, tpx, ir);
3133 if (serializer->reading())
3135 do_tpx_finalize(tpx, ir, state, mtop);
3141 * Overload for do_tpx_body that defaults to state vectors being nullptr.
3143 * \param[in] serializer Abstract serializer used to read/write data.
3144 * \param[in] tpx The file header data.
3145 * \param[in,out] ir Datastructures with simulation parameters.
3146 * \param[in,out] mtop Global topology.
3148 static PbcType do_tpx_body(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir, gmx_mtop_t* mtop)
3150 return do_tpx_body(serializer, tpx, ir, nullptr, nullptr, nullptr, mtop);
3153 static t_fileio* open_tpx(const char* fn, const char* mode)
3155 return gmx_fio_open(fn, mode);
3158 static void close_tpx(t_fileio* fio)
3164 * Fill information into the header only from state before writing.
3166 * Populating the header needs to be independent from writing the information
3167 * to file to allow things like writing the raw byte stream.
3169 * \param[in] state The current simulation state. Can't write without it.
3170 * \param[in] ir Parameter and system information.
3171 * \param[in] mtop Global topology.
3172 * \returns Fully populated header.
3174 static TpxFileHeader populateTpxHeader(const t_state& state, const t_inputrec* ir, const gmx_mtop_t* mtop)
3176 TpxFileHeader header;
3177 header.natoms = state.natoms;
3178 header.ngtc = state.ngtc;
3179 header.fep_state = state.fep_state;
3180 header.lambda = state.lambda[FreeEnergyPerturbationCouplingType::Fep];
3181 header.bIr = ir != nullptr;
3182 header.bTop = mtop != nullptr;
3183 header.bX = (state.flags & enumValueToBitMask(StateEntry::X)) != 0;
3184 header.bV = (state.flags & enumValueToBitMask(StateEntry::V)) != 0;
3187 header.fileVersion = tpx_version;
3188 header.fileGeneration = tpx_generation;
3189 header.isDouble = (sizeof(real) == sizeof(double));
3195 * Process the body of a TPR file as an opaque data buffer.
3197 * Reads/writes the information in \p buffer from/to the \p serializer
3198 * provided to the function. Does not interact with the actual
3199 * TPR datastructures but with an in memory representation of the
3200 * data, so that this data can be efficiently read or written from/to
3201 * an original source.
3203 * \param[in] serializer The abstract serializer used for reading or writing
3204 * the information in \p buffer.
3205 * \param[in,out] buffer Information from TPR file as char buffer.
3207 static void doTpxBodyBuffer(gmx::ISerializer* serializer, gmx::ArrayRef<char> buffer)
3209 serializer->doOpaque(buffer.data(), buffer.size());
3213 * Populates simulation datastructures.
3215 * Here the information from the serialization interface \p serializer
3216 * is used to first populate the datastructures containing the simulation
3217 * information. Depending on the version found in the header \p tpx,
3218 * this is done using the new reading of the data as one block from disk,
3219 * followed by complete deserialization of the information read from there.
3220 * Otherwise, the datastructures are populated as before one by one from disk.
3221 * The second version is the default for the legacy tools that read the
3222 * coordinates and velocities separate from the state.
3224 * After reading in the data, a separate buffer is populated from them
3225 * containing only \p ir and \p mtop that can be communicated directly
3226 * to nodes needing the information to set up a simulation.
3228 * \param[in] tpx The file header.
3229 * \param[in] serializer The Serialization interface used to read the TPR.
3230 * \param[out] ir Input rec to populate.
3231 * \param[out] state State vectors to populate.
3232 * \param[out] x Coordinates to populate if needed.
3233 * \param[out] v Velocities to populate if needed.
3234 * \param[out] mtop Global topology to populate.
3236 * \returns Partial de-serialized TPR used for communication to nodes.
3238 static PartialDeserializedTprFile readTpxBody(TpxFileHeader* tpx,
3239 gmx::ISerializer* serializer,
3246 PartialDeserializedTprFile partialDeserializedTpr;
3247 if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
3249 partialDeserializedTpr.body.resize(tpx->sizeOfTprBody);
3250 partialDeserializedTpr.header = *tpx;
3251 doTpxBodyBuffer(serializer, partialDeserializedTpr.body);
3253 partialDeserializedTpr.pbcType =
3254 completeTprDeserialization(&partialDeserializedTpr, ir, state, x, v, mtop);
3258 partialDeserializedTpr.pbcType = do_tpx_body(serializer, tpx, ir, state, x, v, mtop);
3260 // Update header to system info for communication to nodes.
3261 // As we only need to communicate the inputrec and mtop to other nodes,
3262 // we prepare a new char buffer with the information we have already read
3264 partialDeserializedTpr.header = populateTpxHeader(*state, ir, mtop);
3265 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3266 // but since we just used the default XDR format (which is big endian) for the TPR
3267 // header it would cause third-party libraries reading our raw data to tear their hair
3268 // if we swap the endian in the middle of the file, so we stick to big endian in the
3269 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3270 gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3271 do_tpx_body(&tprBodySerializer, &partialDeserializedTpr.header, ir, mtop);
3272 partialDeserializedTpr.body = tprBodySerializer.finishAndGetBuffer();
3274 return partialDeserializedTpr;
3277 /************************************************************
3279 * The following routines are the exported ones
3281 ************************************************************/
3283 TpxFileHeader readTpxHeader(const char* fileName, bool canReadTopologyOnly)
3287 fio = open_tpx(fileName, "r");
3288 gmx::FileIOXdrSerializer serializer(fio);
3291 do_tpxheader(&serializer, &tpx, fileName, fio, canReadTopologyOnly);
3296 void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t& mtop)
3298 /* To write a state, we first need to write the state information to a buffer before
3299 * we append the raw bytes to the file. For this, the header information needs to be
3300 * populated before we write the main body because it has some information that is
3301 * otherwise not available.
3306 TpxFileHeader tpx = populateTpxHeader(*state, ir, &mtop);
3307 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3308 // but since we just used the default XDR format (which is big endian) for the TPR
3309 // header it would cause third-party libraries reading our raw data to tear their hair
3310 // if we swap the endian in the middle of the file, so we stick to big endian in the
3311 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3312 gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3314 do_tpx_body(&tprBodySerializer,
3316 const_cast<t_inputrec*>(ir),
3317 const_cast<t_state*>(state),
3320 const_cast<gmx_mtop_t*>(&mtop));
3322 std::vector<char> tprBody = tprBodySerializer.finishAndGetBuffer();
3323 tpx.sizeOfTprBody = tprBody.size();
3325 fio = open_tpx(fn, "w");
3326 gmx::FileIOXdrSerializer serializer(fio);
3327 do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
3328 doTpxBodyBuffer(&serializer, tprBody);
3333 PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
3340 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3341 // but since we just used the default XDR format (which is big endian) for the TPR
3342 // header it would cause third-party libraries reading our raw data to tear their hair
3343 // if we swap the endian in the middle of the file, so we stick to big endian in the
3344 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3345 gmx::InMemoryDeserializer tprBodyDeserializer(partialDeserializedTpr->body,
3346 partialDeserializedTpr->header.isDouble,
3347 gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3348 return do_tpx_body(&tprBodyDeserializer, &partialDeserializedTpr->header, ir, state, x, v, mtop);
3351 PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
3355 return completeTprDeserialization(partialDeserializedTpr, ir, nullptr, nullptr, nullptr, mtop);
3358 PartialDeserializedTprFile read_tpx_state(const char* fn, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
3361 fio = open_tpx(fn, "r");
3362 gmx::FileIOXdrSerializer serializer(fio);
3363 PartialDeserializedTprFile partialDeserializedTpr;
3364 do_tpxheader(&serializer, &partialDeserializedTpr.header, fn, fio, ir == nullptr);
3365 partialDeserializedTpr =
3366 readTpxBody(&partialDeserializedTpr.header, &serializer, ir, state, nullptr, nullptr, mtop);
3368 return partialDeserializedTpr;
3371 PbcType read_tpx(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, gmx_mtop_t* mtop)
3377 fio = open_tpx(fn, "r");
3378 gmx::FileIOXdrSerializer serializer(fio);
3379 do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
3380 PartialDeserializedTprFile partialDeserializedTpr =
3381 readTpxBody(&tpx, &serializer, ir, &state, x, v, mtop);
3383 if (mtop != nullptr && natoms != nullptr)
3385 *natoms = mtop->natoms;
3389 copy_mat(state.box, box);
3391 return partialDeserializedTpr.pbcType;
3394 PbcType read_tpx_top(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, t_topology* top)
3399 pbcType = read_tpx(fn, ir, box, natoms, x, v, &mtop);
3401 *top = gmx_mtop_t_to_t_topology(&mtop, true);
3406 gmx_bool fn2bTPX(const char* file)
3408 return (efTPR == fn2ftp(file));
3411 void pr_tpxheader(FILE* fp, int indent, const char* title, const TpxFileHeader* sh)
3413 if (available(fp, sh, indent, title))
3415 indent = pr_title(fp, indent, title);
3416 pr_indent(fp, indent);
3417 fprintf(fp, "bIr = %spresent\n", sh->bIr ? "" : "not ");
3418 pr_indent(fp, indent);
3419 fprintf(fp, "bBox = %spresent\n", sh->bBox ? "" : "not ");
3420 pr_indent(fp, indent);
3421 fprintf(fp, "bTop = %spresent\n", sh->bTop ? "" : "not ");
3422 pr_indent(fp, indent);
3423 fprintf(fp, "bX = %spresent\n", sh->bX ? "" : "not ");
3424 pr_indent(fp, indent);
3425 fprintf(fp, "bV = %spresent\n", sh->bV ? "" : "not ");
3426 pr_indent(fp, indent);
3427 fprintf(fp, "bF = %spresent\n", sh->bF ? "" : "not ");
3429 pr_indent(fp, indent);
3430 fprintf(fp, "natoms = %d\n", sh->natoms);
3431 pr_indent(fp, indent);
3432 fprintf(fp, "lambda = %e\n", sh->lambda);
3433 pr_indent(fp, indent);
3434 fprintf(fp, "buffer size = %" PRId64 "\n", sh->sizeOfTprBody);