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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 simtemp->temperatures.resize(n_lambda);
452 serializer->doRealArray(simtemp->temperatures.data(), 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);
766 if (serializer->reading())
768 pull->coord[g].coordIndex = g;
772 if (file_version >= tpxv_PullAverage)
776 v = pull->bXOutAverage;
777 serializer->doBool(&v);
778 pull->bXOutAverage = v;
779 v = pull->bFOutAverage;
780 serializer->doBool(&v);
781 pull->bFOutAverage = v;
786 static void do_rotgrp(gmx::ISerializer* serializer, t_rotgrp* rotg)
788 serializer->doEnumAsInt(&rotg->eType);
789 if (serializer->reading())
792 serializer->doInt(&temp);
793 rotg->bMassW = static_cast<bool>(temp);
797 int temp = static_cast<int>(rotg->bMassW);
798 serializer->doInt(&temp);
800 serializer->doInt(&rotg->nat);
801 if (serializer->reading())
803 snew(rotg->ind, rotg->nat);
805 serializer->doIntArray(rotg->ind, rotg->nat);
806 if (serializer->reading())
808 snew(rotg->x_ref, rotg->nat);
810 serializer->doRvecArray(rotg->x_ref, rotg->nat);
811 serializer->doRvec(&rotg->inputVec);
812 serializer->doRvec(&rotg->pivot);
813 serializer->doReal(&rotg->rate);
814 serializer->doReal(&rotg->k);
815 serializer->doReal(&rotg->slab_dist);
816 serializer->doReal(&rotg->min_gaussian);
817 serializer->doReal(&rotg->eps);
818 serializer->doEnumAsInt(&rotg->eFittype);
819 serializer->doInt(&rotg->PotAngle_nstep);
820 serializer->doReal(&rotg->PotAngle_step);
823 static void do_rot(gmx::ISerializer* serializer, t_rot* rot)
827 serializer->doInt(&rot->ngrp);
828 serializer->doInt(&rot->nstrout);
829 serializer->doInt(&rot->nstsout);
830 if (serializer->reading())
832 snew(rot->grp, rot->ngrp);
834 for (g = 0; g < rot->ngrp; g++)
836 do_rotgrp(serializer, &rot->grp[g]);
841 static void do_swapgroup(gmx::ISerializer* serializer, t_swapGroup* g)
844 /* Name of the group or molecule */
846 if (serializer->reading())
848 serializer->doString(&buf);
849 g->molname = gmx_strdup(buf.c_str());
854 serializer->doString(&buf);
857 /* Number of atoms in the group */
858 serializer->doInt(&g->nat);
860 /* The group's atom indices */
861 if (serializer->reading())
863 snew(g->ind, g->nat);
865 serializer->doIntArray(g->ind, g->nat);
867 /* Requested counts for compartments A and B */
868 serializer->doIntArray(g->nmolReq, eCompNR);
871 static void do_swapcoords_tpx(gmx::ISerializer* serializer, t_swapcoords* swap, int file_version)
873 /* Enums for better readability of the code */
886 if (file_version >= tpxv_CompElPolyatomicIonsAndMultipleIonTypes)
888 /* The total number of swap groups is the sum of the fixed groups
889 * (split0, split1, solvent), and the user-defined groups (2+ types of ions)
891 serializer->doInt(&swap->ngrp);
892 if (serializer->reading())
894 snew(swap->grp, swap->ngrp);
896 for (int ig = 0; ig < swap->ngrp; ig++)
898 do_swapgroup(serializer, &swap->grp[ig]);
900 serializer->doBool(&swap->massw_split[eChannel0]);
901 serializer->doBool(&swap->massw_split[eChannel1]);
902 serializer->doInt(&swap->nstswap);
903 serializer->doInt(&swap->nAverage);
904 serializer->doReal(&swap->threshold);
905 serializer->doReal(&swap->cyl0r);
906 serializer->doReal(&swap->cyl0u);
907 serializer->doReal(&swap->cyl0l);
908 serializer->doReal(&swap->cyl1r);
909 serializer->doReal(&swap->cyl1u);
910 serializer->doReal(&swap->cyl1l);
914 /*** Support reading older CompEl .tpr files ***/
916 /* In the original CompEl .tpr files, we always have 5 groups: */
918 snew(swap->grp, swap->ngrp);
920 swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname = gmx_strdup("split0"); // group 0: split0
921 swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname = gmx_strdup("split1"); // group 1: split1
922 swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname =
923 gmx_strdup("solvent"); // group 2: solvent
924 swap->grp[3].molname = gmx_strdup("anions"); // group 3: anions
925 swap->grp[4].molname = gmx_strdup("cations"); // group 4: cations
927 serializer->doInt(&swap->grp[3].nat);
928 serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].nat);
929 serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].nat);
930 serializer->doBool(&swap->massw_split[eChannel0]);
931 serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].nat);
932 serializer->doBool(&swap->massw_split[eChannel1]);
933 serializer->doInt(&swap->nstswap);
934 serializer->doInt(&swap->nAverage);
935 serializer->doReal(&swap->threshold);
936 serializer->doReal(&swap->cyl0r);
937 serializer->doReal(&swap->cyl0u);
938 serializer->doReal(&swap->cyl0l);
939 serializer->doReal(&swap->cyl1r);
940 serializer->doReal(&swap->cyl1u);
941 serializer->doReal(&swap->cyl1l);
943 // The order[] array keeps compatibility with older .tpr files
944 // by reading in the groups in the classic order
946 const int order[4] = { 3,
947 static_cast<int>(SwapGroupSplittingType::Solvent),
948 static_cast<int>(SwapGroupSplittingType::Split0),
949 static_cast<int>(SwapGroupSplittingType::Split1) };
951 for (int ig = 0; ig < 4; ig++)
954 snew(swap->grp[g].ind, swap->grp[g].nat);
955 serializer->doIntArray(swap->grp[g].ind, swap->grp[g].nat);
959 for (int j = eCompA; j <= eCompB; j++)
961 serializer->doInt(&swap->grp[3].nmolReq[j]); // group 3 = anions
962 serializer->doInt(&swap->grp[4].nmolReq[j]); // group 4 = cations
964 } /* End support reading older CompEl .tpr files */
966 if (file_version >= tpxv_CompElWithSwapLayerOffset)
968 serializer->doReal(&swap->bulkOffset[eCompA]);
969 serializer->doReal(&swap->bulkOffset[eCompB]);
973 static void do_legacy_efield(gmx::ISerializer* serializer, gmx::KeyValueTreeObjectBuilder* root)
975 const char* const dimName[] = { "x", "y", "z" };
977 auto appliedForcesObj = root->addObject("applied-forces");
978 auto efieldObj = appliedForcesObj.addObject("electric-field");
979 // The content of the tpr file for this feature has
980 // been the same since gromacs 4.0 that was used for
982 for (int j = 0; j < DIM; ++j)
985 serializer->doInt(&n);
986 serializer->doInt(&nt);
987 std::vector<real> aa(n + 1), phi(nt + 1), at(nt + 1), phit(nt + 1);
988 serializer->doRealArray(aa.data(), n);
989 serializer->doRealArray(phi.data(), n);
990 serializer->doRealArray(at.data(), nt);
991 serializer->doRealArray(phit.data(), nt);
997 "Can not handle tpr files with more than one electric field term per "
1000 auto dimObj = efieldObj.addObject(dimName[j]);
1001 dimObj.addValue<real>("E0", aa[0]);
1002 dimObj.addValue<real>("omega", at[0]);
1003 dimObj.addValue<real>("t0", phi[0]);
1004 dimObj.addValue<real>("sigma", phit[0]);
1010 static void do_inputrec(gmx::ISerializer* serializer, t_inputrec* ir, int file_version)
1012 int i, j, k, idum = 0;
1014 gmx_bool bdum = false;
1016 if (file_version != tpx_version)
1018 /* Give a warning about features that are not accessible */
1019 fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n", file_version, tpx_version);
1022 if (file_version == 0)
1027 gmx::KeyValueTreeBuilder paramsBuilder;
1028 gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
1030 /* Basic inputrec stuff */
1031 serializer->doEnumAsInt(&ir->eI);
1032 if (file_version >= 62)
1034 serializer->doInt64(&ir->nsteps);
1038 serializer->doInt(&idum);
1042 if (file_version >= 62)
1044 serializer->doInt64(&ir->init_step);
1048 serializer->doInt(&idum);
1049 ir->init_step = idum;
1052 serializer->doInt(&ir->simulation_part);
1054 if (file_version >= tpxv_MTS)
1056 serializer->doBool(&ir->useMts);
1057 int numLevels = ir->mtsLevels.size();
1060 serializer->doInt(&numLevels);
1062 ir->mtsLevels.resize(numLevels);
1063 for (auto& mtsLevel : ir->mtsLevels)
1065 int forceGroups = mtsLevel.forceGroups.to_ulong();
1066 serializer->doInt(&forceGroups);
1067 mtsLevel.forceGroups = std::bitset<static_cast<int>(gmx::MtsForceGroups::Count)>(forceGroups);
1068 serializer->doInt(&mtsLevel.stepFactor);
1074 ir->mtsLevels.clear();
1077 if (file_version >= 67)
1079 serializer->doInt(&ir->nstcalcenergy);
1083 ir->nstcalcenergy = 1;
1085 if (file_version >= 81)
1087 serializer->doEnumAsInt(&ir->cutoff_scheme);
1088 if (file_version < 94)
1090 // Need to invert the scheme order
1091 switch (ir->cutoff_scheme)
1093 case (CutoffScheme::Group): ir->cutoff_scheme = CutoffScheme::Verlet; break;
1094 case (CutoffScheme::Verlet): ir->cutoff_scheme = CutoffScheme::Group; break;
1095 default: GMX_RELEASE_ASSERT(false, "Unhandled cutoff scheme type");
1101 ir->cutoff_scheme = CutoffScheme::Group;
1103 serializer->doInt(&idum); /* used to be ns_type; not used anymore */
1104 serializer->doInt(&ir->nstlist);
1105 serializer->doInt(&idum); /* used to be ndelta; not used anymore */
1107 serializer->doReal(&ir->rtpi);
1109 serializer->doInt(&ir->nstcomm);
1110 serializer->doEnumAsInt(&ir->comm_mode);
1112 /* ignore nstcheckpoint */
1113 if (file_version < tpxv_RemoveObsoleteParameters1)
1115 serializer->doInt(&idum);
1118 serializer->doInt(&ir->nstcgsteep);
1120 serializer->doInt(&ir->nbfgscorr);
1122 serializer->doInt(&ir->nstlog);
1123 serializer->doInt(&ir->nstxout);
1124 serializer->doInt(&ir->nstvout);
1125 serializer->doInt(&ir->nstfout);
1126 serializer->doInt(&ir->nstenergy);
1127 serializer->doInt(&ir->nstxout_compressed);
1128 if (file_version >= 59)
1130 serializer->doDouble(&ir->init_t);
1131 serializer->doDouble(&ir->delta_t);
1135 serializer->doReal(&rdum);
1137 serializer->doReal(&rdum);
1140 serializer->doReal(&ir->x_compression_precision);
1141 if (file_version >= 81)
1143 serializer->doReal(&ir->verletbuf_tol);
1147 ir->verletbuf_tol = 0;
1149 serializer->doReal(&ir->rlist);
1150 if (file_version >= 67 && file_version < tpxv_RemoveTwinRange)
1152 if (serializer->reading())
1154 // Reading such a file version could invoke the twin-range
1155 // scheme, about which mdrun should give a fatal error.
1156 real dummy_rlistlong = -1;
1157 serializer->doReal(&dummy_rlistlong);
1159 ir->useTwinRange = (ir->rlist > 0 && (dummy_rlistlong == 0 || dummy_rlistlong > ir->rlist));
1160 // When true, this forces mdrun to issue an error (regardless of
1161 // ir->cutoff_scheme).
1163 // Otherwise, grompp used to set rlistlong actively. Users
1164 // were probably also confused and set rlistlong == rlist.
1165 // However, in all remaining cases, it is safe to let
1166 // mdrun proceed normally.
1171 // No need to read or write anything
1172 ir->useTwinRange = false;
1174 if (file_version >= 82 && file_version != 90)
1176 // Multiple time-stepping is no longer enabled, but the old
1177 // support required the twin-range scheme, for which mdrun
1178 // already emits a fatal error.
1179 int dummy_nstcalclr = -1;
1180 serializer->doInt(&dummy_nstcalclr);
1182 serializer->doEnumAsInt(&ir->coulombtype);
1183 if (file_version >= 81)
1185 serializer->doEnumAsInt(&ir->coulomb_modifier);
1189 ir->coulomb_modifier = (ir->cutoff_scheme == CutoffScheme::Verlet ? InteractionModifiers::PotShift
1190 : InteractionModifiers::None);
1192 serializer->doReal(&ir->rcoulomb_switch);
1193 serializer->doReal(&ir->rcoulomb);
1194 serializer->doEnumAsInt(&ir->vdwtype);
1195 if (file_version >= 81)
1197 serializer->doEnumAsInt(&ir->vdw_modifier);
1201 ir->vdw_modifier = (ir->cutoff_scheme == CutoffScheme::Verlet ? InteractionModifiers::PotShift
1202 : InteractionModifiers::None);
1204 serializer->doReal(&ir->rvdw_switch);
1205 serializer->doReal(&ir->rvdw);
1206 serializer->doEnumAsInt(&ir->eDispCorr);
1207 serializer->doReal(&ir->epsilon_r);
1208 serializer->doReal(&ir->epsilon_rf);
1209 serializer->doReal(&ir->tabext);
1211 // This permits reading a .tpr file that used implicit solvent,
1212 // and later permitting mdrun to refuse to run it.
1213 if (serializer->reading())
1215 if (file_version < tpxv_RemoveImplicitSolvation)
1217 serializer->doInt(&idum);
1218 serializer->doInt(&idum);
1219 serializer->doReal(&rdum);
1220 serializer->doReal(&rdum);
1221 serializer->doInt(&idum);
1222 ir->implicit_solvent = (idum > 0);
1226 ir->implicit_solvent = false;
1228 if (file_version < tpxv_RemoveImplicitSolvation)
1230 serializer->doReal(&rdum);
1231 serializer->doReal(&rdum);
1232 serializer->doReal(&rdum);
1233 serializer->doReal(&rdum);
1234 if (file_version >= 60)
1236 serializer->doReal(&rdum);
1237 serializer->doInt(&idum);
1239 serializer->doReal(&rdum);
1243 if (file_version >= 81)
1245 serializer->doReal(&ir->fourier_spacing);
1249 ir->fourier_spacing = 0.0;
1251 serializer->doInt(&ir->nkx);
1252 serializer->doInt(&ir->nky);
1253 serializer->doInt(&ir->nkz);
1254 serializer->doInt(&ir->pme_order);
1255 serializer->doReal(&ir->ewald_rtol);
1257 if (file_version >= 93)
1259 serializer->doReal(&ir->ewald_rtol_lj);
1263 ir->ewald_rtol_lj = ir->ewald_rtol;
1265 serializer->doEnumAsInt(&ir->ewald_geometry);
1266 serializer->doReal(&ir->epsilon_surface);
1268 /* ignore bOptFFT */
1269 if (file_version < tpxv_RemoveObsoleteParameters1)
1271 serializer->doBool(&bdum);
1274 if (file_version >= 93)
1276 serializer->doEnumAsInt(&ir->ljpme_combination_rule);
1278 serializer->doBool(&ir->bContinuation);
1279 serializer->doEnumAsInt(&ir->etc);
1280 /* before version 18, ir->etc was a gmx_bool (ir->btc),
1281 * but the values 0 and 1 still mean no and
1282 * berendsen temperature coupling, respectively.
1284 if (file_version >= 79)
1286 serializer->doBool(&ir->bPrintNHChains);
1288 if (file_version >= 71)
1290 serializer->doInt(&ir->nsttcouple);
1294 ir->nsttcouple = ir->nstcalcenergy;
1296 serializer->doEnumAsInt(&ir->epc);
1297 serializer->doEnumAsInt(&ir->epct);
1298 if (file_version >= 71)
1300 serializer->doInt(&ir->nstpcouple);
1304 ir->nstpcouple = ir->nstcalcenergy;
1306 serializer->doReal(&ir->tau_p);
1307 serializer->doRvec(&ir->ref_p[XX]);
1308 serializer->doRvec(&ir->ref_p[YY]);
1309 serializer->doRvec(&ir->ref_p[ZZ]);
1310 serializer->doRvec(&ir->compress[XX]);
1311 serializer->doRvec(&ir->compress[YY]);
1312 serializer->doRvec(&ir->compress[ZZ]);
1313 serializer->doEnumAsInt(&ir->refcoord_scaling);
1314 serializer->doRvec(&ir->posres_com);
1315 serializer->doRvec(&ir->posres_comB);
1317 if (file_version < 79)
1319 serializer->doInt(&ir->andersen_seed);
1323 ir->andersen_seed = 0;
1326 serializer->doReal(&ir->shake_tol);
1328 serializer->doEnumAsInt(&ir->efep);
1329 if (serializer->reading())
1331 ir->fepvals = std::make_unique<t_lambda>();
1333 do_fepvals(serializer, ir->fepvals.get(), file_version);
1335 if (file_version >= 79)
1337 serializer->doBool(&ir->bSimTemp);
1340 ir->bSimTemp = TRUE;
1345 ir->bSimTemp = FALSE;
1349 if (serializer->reading())
1351 ir->simtempvals = std::make_unique<t_simtemp>();
1353 do_simtempvals(serializer, ir->simtempvals.get(), ir->fepvals->n_lambda, file_version);
1356 if (file_version >= 79)
1358 serializer->doBool(&ir->bExpanded);
1362 if (serializer->reading())
1364 ir->expandedvals = std::make_unique<t_expanded>();
1366 do_expandedvals(serializer, ir->expandedvals.get(), ir->fepvals.get(), file_version);
1369 serializer->doEnumAsInt(&ir->eDisre);
1370 serializer->doEnumAsInt(&ir->eDisreWeighting);
1371 serializer->doBool(&ir->bDisreMixed);
1372 serializer->doReal(&ir->dr_fc);
1373 serializer->doReal(&ir->dr_tau);
1374 serializer->doInt(&ir->nstdisreout);
1375 serializer->doReal(&ir->orires_fc);
1376 serializer->doReal(&ir->orires_tau);
1377 serializer->doInt(&ir->nstorireout);
1379 /* ignore dihre_fc */
1380 if (file_version < 79)
1382 serializer->doReal(&rdum);
1385 serializer->doReal(&ir->em_stepsize);
1386 serializer->doReal(&ir->em_tol);
1387 serializer->doBool(&ir->bShakeSOR);
1388 serializer->doInt(&ir->niter);
1389 serializer->doReal(&ir->fc_stepsize);
1390 serializer->doEnumAsInt(&ir->eConstrAlg);
1391 serializer->doInt(&ir->nProjOrder);
1392 serializer->doReal(&ir->LincsWarnAngle);
1393 serializer->doInt(&ir->nLincsIter);
1394 serializer->doReal(&ir->bd_fric);
1395 if (file_version >= tpxv_Use64BitRandomSeed)
1397 serializer->doInt64(&ir->ld_seed);
1401 serializer->doInt(&idum);
1405 for (i = 0; i < DIM; i++)
1407 serializer->doRvec(&ir->deform[i]);
1409 serializer->doReal(&ir->cos_accel);
1411 serializer->doInt(&ir->userint1);
1412 serializer->doInt(&ir->userint2);
1413 serializer->doInt(&ir->userint3);
1414 serializer->doInt(&ir->userint4);
1415 serializer->doReal(&ir->userreal1);
1416 serializer->doReal(&ir->userreal2);
1417 serializer->doReal(&ir->userreal3);
1418 serializer->doReal(&ir->userreal4);
1420 /* AdResS is removed, but we need to be able to read old files,
1421 and let mdrun refuse to run them */
1422 if (file_version >= 77 && file_version < tpxv_RemoveAdress)
1424 serializer->doBool(&ir->bAdress);
1427 int idum, numThermoForceGroups, numEnergyGroups;
1430 serializer->doInt(&idum);
1431 serializer->doReal(&rdum);
1432 serializer->doReal(&rdum);
1433 serializer->doReal(&rdum);
1434 serializer->doInt(&idum);
1435 serializer->doInt(&idum);
1436 serializer->doRvec(&rvecdum);
1437 serializer->doInt(&numThermoForceGroups);
1438 serializer->doReal(&rdum);
1439 serializer->doInt(&numEnergyGroups);
1440 serializer->doInt(&idum);
1442 if (numThermoForceGroups > 0)
1444 std::vector<int> idumn(numThermoForceGroups);
1445 serializer->doIntArray(idumn.data(), idumn.size());
1447 if (numEnergyGroups > 0)
1449 std::vector<int> idumn(numEnergyGroups);
1450 serializer->doIntArray(idumn.data(), idumn.size());
1456 ir->bAdress = FALSE;
1461 PullingAlgorithm ePullOld = PullingAlgorithm::Umbrella;
1463 if (file_version >= tpxv_PullCoordTypeGeom)
1465 serializer->doBool(&ir->bPull);
1469 serializer->doEnumAsInt(&ePullOld);
1470 ir->bPull = (ePullOld != PullingAlgorithm::Umbrella);
1471 /* We removed the first ePull=ePullNo for the enum */
1474 case (PullingAlgorithm::Umbrella): break; // this is equal to not using pulling
1475 case (PullingAlgorithm::Constraint): ePullOld = PullingAlgorithm::Umbrella; break;
1476 case (PullingAlgorithm::ConstantForce):
1477 ePullOld = PullingAlgorithm::Constraint;
1479 case (PullingAlgorithm::FlatBottom):
1480 ePullOld = PullingAlgorithm::ConstantForce;
1482 case (PullingAlgorithm::FlatBottomHigh):
1483 ePullOld = PullingAlgorithm::FlatBottom;
1485 case (PullingAlgorithm::External):
1486 ePullOld = PullingAlgorithm::FlatBottomHigh;
1488 case (PullingAlgorithm::Count): ePullOld = PullingAlgorithm::External; break;
1489 default: GMX_RELEASE_ASSERT(false, "Unhandled old pull algorithm");
1494 if (serializer->reading())
1496 ir->pull = std::make_unique<pull_params_t>();
1498 do_pull(serializer, ir->pull.get(), file_version, ePullOld);
1502 if (file_version >= tpxv_AcceleratedWeightHistogram)
1504 serializer->doBool(&ir->bDoAwh);
1508 if (serializer->reading())
1510 ir->awhParams = std::make_unique<gmx::AwhParams>(serializer);
1514 ir->awhParams->serialize(serializer);
1523 /* Enforced rotation */
1524 if (file_version >= 74)
1526 serializer->doBool(&ir->bRot);
1529 if (serializer->reading())
1533 do_rot(serializer, ir->rot);
1541 /* Interactive molecular dynamics */
1542 if (file_version >= tpxv_InteractiveMolecularDynamics)
1544 serializer->doBool(&ir->bIMD);
1547 if (serializer->reading())
1551 do_imd(serializer, ir->imd);
1556 /* We don't support IMD sessions for old .tpr files */
1561 serializer->doInt(&ir->opts.ngtc);
1562 if (file_version >= 69)
1564 serializer->doInt(&ir->opts.nhchainlength);
1568 ir->opts.nhchainlength = 1;
1570 int removedOptsNgacc = 0;
1571 if (serializer->reading() && file_version < tpxv_RemovedConstantAcceleration)
1573 serializer->doInt(&removedOptsNgacc);
1575 serializer->doInt(&ir->opts.ngfrz);
1576 serializer->doInt(&ir->opts.ngener);
1578 if (serializer->reading())
1580 snew(ir->opts.nrdf, ir->opts.ngtc);
1581 snew(ir->opts.ref_t, ir->opts.ngtc);
1582 snew(ir->opts.annealing, ir->opts.ngtc);
1583 snew(ir->opts.anneal_npoints, ir->opts.ngtc);
1584 snew(ir->opts.anneal_time, ir->opts.ngtc);
1585 snew(ir->opts.anneal_temp, ir->opts.ngtc);
1586 snew(ir->opts.tau_t, ir->opts.ngtc);
1587 snew(ir->opts.nFreeze, ir->opts.ngfrz);
1588 snew(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
1590 if (ir->opts.ngtc > 0)
1592 serializer->doRealArray(ir->opts.nrdf, ir->opts.ngtc);
1593 serializer->doRealArray(ir->opts.ref_t, ir->opts.ngtc);
1594 serializer->doRealArray(ir->opts.tau_t, ir->opts.ngtc);
1596 if (ir->opts.ngfrz > 0)
1598 serializer->doIvecArray(ir->opts.nFreeze, ir->opts.ngfrz);
1600 if (serializer->reading() && file_version < tpxv_RemovedConstantAcceleration && removedOptsNgacc > 0)
1602 std::vector<gmx::RVec> dummy;
1603 dummy.resize(removedOptsNgacc);
1604 serializer->doRvecArray(reinterpret_cast<rvec*>(dummy.data()), removedOptsNgacc);
1605 ir->useConstantAcceleration = std::any_of(dummy.begin(), dummy.end(), [](const gmx::RVec& vec) {
1606 return vec[XX] != 0.0 || vec[YY] != 0.0 || vec[ZZ] != 0.0;
1611 ir->useConstantAcceleration = false;
1613 serializer->doIntArray(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
1615 /* First read the lists with annealing and npoints for each group */
1616 serializer->doEnumArrayAsInt(ir->opts.annealing, ir->opts.ngtc);
1617 serializer->doIntArray(ir->opts.anneal_npoints, ir->opts.ngtc);
1618 for (j = 0; j < (ir->opts.ngtc); j++)
1620 k = ir->opts.anneal_npoints[j];
1621 if (serializer->reading())
1623 snew(ir->opts.anneal_time[j], k);
1624 snew(ir->opts.anneal_temp[j], k);
1626 serializer->doRealArray(ir->opts.anneal_time[j], k);
1627 serializer->doRealArray(ir->opts.anneal_temp[j], k);
1631 serializer->doInt(&ir->nwall);
1632 serializer->doEnumAsInt(&ir->wall_type);
1633 serializer->doReal(&ir->wall_r_linpot);
1634 serializer->doInt(&ir->wall_atomtype[0]);
1635 serializer->doInt(&ir->wall_atomtype[1]);
1636 serializer->doReal(&ir->wall_density[0]);
1637 serializer->doReal(&ir->wall_density[1]);
1638 serializer->doReal(&ir->wall_ewald_zfac);
1641 /* Cosine stuff for electric fields */
1642 if (file_version < tpxv_GenericParamsForElectricField)
1644 do_legacy_efield(serializer, ¶msObj);
1648 if (file_version >= tpxv_ComputationalElectrophysiology)
1650 serializer->doEnumAsInt(&ir->eSwapCoords);
1651 if (ir->eSwapCoords != SwapType::No)
1653 if (serializer->reading())
1657 do_swapcoords_tpx(serializer, ir->swap, file_version);
1661 /* QMMM reading - despite defunct we require reading for backwards
1662 * compability and correct serialization
1665 serializer->doBool(&ir->bQMMM);
1667 serializer->doInt(&qmmmScheme);
1668 real unusedScalefactor;
1669 serializer->doReal(&unusedScalefactor);
1671 // this is still used in Mimic
1672 serializer->doInt(&ir->opts.ngQM);
1673 if (ir->opts.ngQM > 0 && ir->bQMMM)
1675 /* We leave in dummy i/o for removed parameters to avoid
1676 * changing the tpr format.
1678 std::vector<int> dummyIntVec(4 * ir->opts.ngQM, 0);
1679 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1680 dummyIntVec.clear();
1682 // std::vector<bool> has no data()
1683 std::vector<char> dummyBoolVec(ir->opts.ngQM * sizeof(bool) / sizeof(char));
1684 serializer->doBoolArray(reinterpret_cast<bool*>(dummyBoolVec.data()), dummyBoolVec.size());
1685 dummyBoolVec.clear();
1687 dummyIntVec.resize(2 * ir->opts.ngQM, 0);
1688 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1689 dummyIntVec.clear();
1691 std::vector<real> dummyRealVec(2 * ir->opts.ngQM, 0);
1692 serializer->doRealArray(dummyRealVec.data(), dummyRealVec.size());
1693 dummyRealVec.clear();
1695 dummyIntVec.resize(3 * ir->opts.ngQM, 0);
1696 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1697 dummyIntVec.clear();
1699 /* end of QMMM stuff */
1702 if (file_version >= tpxv_GenericParamsForElectricField)
1704 if (serializer->reading())
1706 paramsObj.mergeObject(gmx::deserializeKeyValueTree(serializer));
1710 GMX_RELEASE_ASSERT(ir->params != nullptr,
1711 "Parameters should be present when writing inputrec");
1712 gmx::serializeKeyValueTree(*ir->params, serializer);
1715 if (serializer->reading())
1717 ir->params = new gmx::KeyValueTreeObject(paramsBuilder.build());
1718 // Initialize internal parameters to an empty kvt for all tpr versions
1719 ir->internalParameters = std::make_unique<gmx::KeyValueTreeObject>();
1722 if (file_version >= tpxv_GenericInternalParameters)
1724 if (serializer->reading())
1726 ir->internalParameters =
1727 std::make_unique<gmx::KeyValueTreeObject>(gmx::deserializeKeyValueTree(serializer));
1731 GMX_RELEASE_ASSERT(ir->internalParameters != nullptr,
1732 "Parameters should be present when writing inputrec");
1733 gmx::serializeKeyValueTree(*ir->internalParameters, serializer);
1739 static void do_harm(gmx::ISerializer* serializer, t_iparams* iparams)
1741 serializer->doReal(&iparams->harmonic.rA);
1742 serializer->doReal(&iparams->harmonic.krA);
1743 serializer->doReal(&iparams->harmonic.rB);
1744 serializer->doReal(&iparams->harmonic.krB);
1747 static void do_iparams(gmx::ISerializer* serializer, t_functype ftype, t_iparams* iparams, int file_version)
1760 do_harm(serializer, iparams);
1761 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && serializer->reading())
1763 /* Correct incorrect storage of parameters */
1764 iparams->pdihs.phiB = iparams->pdihs.phiA;
1765 iparams->pdihs.cpB = iparams->pdihs.cpA;
1769 serializer->doReal(&iparams->harmonic.rA);
1770 serializer->doReal(&iparams->harmonic.krA);
1772 case F_LINEAR_ANGLES:
1773 serializer->doReal(&iparams->linangle.klinA);
1774 serializer->doReal(&iparams->linangle.aA);
1775 serializer->doReal(&iparams->linangle.klinB);
1776 serializer->doReal(&iparams->linangle.aB);
1779 serializer->doReal(&iparams->fene.bm);
1780 serializer->doReal(&iparams->fene.kb);
1784 serializer->doReal(&iparams->restraint.lowA);
1785 serializer->doReal(&iparams->restraint.up1A);
1786 serializer->doReal(&iparams->restraint.up2A);
1787 serializer->doReal(&iparams->restraint.kA);
1788 serializer->doReal(&iparams->restraint.lowB);
1789 serializer->doReal(&iparams->restraint.up1B);
1790 serializer->doReal(&iparams->restraint.up2B);
1791 serializer->doReal(&iparams->restraint.kB);
1797 serializer->doReal(&iparams->tab.kA);
1798 serializer->doInt(&iparams->tab.table);
1799 serializer->doReal(&iparams->tab.kB);
1801 case F_CROSS_BOND_BONDS:
1802 serializer->doReal(&iparams->cross_bb.r1e);
1803 serializer->doReal(&iparams->cross_bb.r2e);
1804 serializer->doReal(&iparams->cross_bb.krr);
1806 case F_CROSS_BOND_ANGLES:
1807 serializer->doReal(&iparams->cross_ba.r1e);
1808 serializer->doReal(&iparams->cross_ba.r2e);
1809 serializer->doReal(&iparams->cross_ba.r3e);
1810 serializer->doReal(&iparams->cross_ba.krt);
1812 case F_UREY_BRADLEY:
1813 serializer->doReal(&iparams->u_b.thetaA);
1814 serializer->doReal(&iparams->u_b.kthetaA);
1815 serializer->doReal(&iparams->u_b.r13A);
1816 serializer->doReal(&iparams->u_b.kUBA);
1817 if (file_version >= 79)
1819 serializer->doReal(&iparams->u_b.thetaB);
1820 serializer->doReal(&iparams->u_b.kthetaB);
1821 serializer->doReal(&iparams->u_b.r13B);
1822 serializer->doReal(&iparams->u_b.kUBB);
1826 iparams->u_b.thetaB = iparams->u_b.thetaA;
1827 iparams->u_b.kthetaB = iparams->u_b.kthetaA;
1828 iparams->u_b.r13B = iparams->u_b.r13A;
1829 iparams->u_b.kUBB = iparams->u_b.kUBA;
1832 case F_QUARTIC_ANGLES:
1833 serializer->doReal(&iparams->qangle.theta);
1834 serializer->doRealArray(iparams->qangle.c, 5);
1837 serializer->doReal(&iparams->bham.a);
1838 serializer->doReal(&iparams->bham.b);
1839 serializer->doReal(&iparams->bham.c);
1842 serializer->doReal(&iparams->morse.b0A);
1843 serializer->doReal(&iparams->morse.cbA);
1844 serializer->doReal(&iparams->morse.betaA);
1845 if (file_version >= 79)
1847 serializer->doReal(&iparams->morse.b0B);
1848 serializer->doReal(&iparams->morse.cbB);
1849 serializer->doReal(&iparams->morse.betaB);
1853 iparams->morse.b0B = iparams->morse.b0A;
1854 iparams->morse.cbB = iparams->morse.cbA;
1855 iparams->morse.betaB = iparams->morse.betaA;
1859 serializer->doReal(&iparams->cubic.b0);
1860 serializer->doReal(&iparams->cubic.kb);
1861 serializer->doReal(&iparams->cubic.kcub);
1863 case F_CONNBONDS: break;
1864 case F_POLARIZATION: serializer->doReal(&iparams->polarize.alpha); break;
1866 serializer->doReal(&iparams->anharm_polarize.alpha);
1867 serializer->doReal(&iparams->anharm_polarize.drcut);
1868 serializer->doReal(&iparams->anharm_polarize.khyp);
1871 serializer->doReal(&iparams->wpol.al_x);
1872 serializer->doReal(&iparams->wpol.al_y);
1873 serializer->doReal(&iparams->wpol.al_z);
1874 serializer->doReal(&iparams->wpol.rOH);
1875 serializer->doReal(&iparams->wpol.rHH);
1876 serializer->doReal(&iparams->wpol.rOD);
1879 serializer->doReal(&iparams->thole.a);
1880 serializer->doReal(&iparams->thole.alpha1);
1881 serializer->doReal(&iparams->thole.alpha2);
1882 serializer->doReal(&iparams->thole.rfac);
1885 serializer->doReal(&iparams->lj.c6);
1886 serializer->doReal(&iparams->lj.c12);
1889 serializer->doReal(&iparams->lj14.c6A);
1890 serializer->doReal(&iparams->lj14.c12A);
1891 serializer->doReal(&iparams->lj14.c6B);
1892 serializer->doReal(&iparams->lj14.c12B);
1895 serializer->doReal(&iparams->ljc14.fqq);
1896 serializer->doReal(&iparams->ljc14.qi);
1897 serializer->doReal(&iparams->ljc14.qj);
1898 serializer->doReal(&iparams->ljc14.c6);
1899 serializer->doReal(&iparams->ljc14.c12);
1901 case F_LJC_PAIRS_NB:
1902 serializer->doReal(&iparams->ljcnb.qi);
1903 serializer->doReal(&iparams->ljcnb.qj);
1904 serializer->doReal(&iparams->ljcnb.c6);
1905 serializer->doReal(&iparams->ljcnb.c12);
1911 serializer->doReal(&iparams->pdihs.phiA);
1912 serializer->doReal(&iparams->pdihs.cpA);
1913 serializer->doReal(&iparams->pdihs.phiB);
1914 serializer->doReal(&iparams->pdihs.cpB);
1915 serializer->doInt(&iparams->pdihs.mult);
1918 serializer->doReal(&iparams->pdihs.phiA);
1919 serializer->doReal(&iparams->pdihs.cpA);
1922 serializer->doInt(&iparams->disres.label);
1923 serializer->doInt(&iparams->disres.type);
1924 serializer->doReal(&iparams->disres.low);
1925 serializer->doReal(&iparams->disres.up1);
1926 serializer->doReal(&iparams->disres.up2);
1927 serializer->doReal(&iparams->disres.kfac);
1930 serializer->doInt(&iparams->orires.ex);
1931 serializer->doInt(&iparams->orires.label);
1932 serializer->doInt(&iparams->orires.power);
1933 serializer->doReal(&iparams->orires.c);
1934 serializer->doReal(&iparams->orires.obs);
1935 serializer->doReal(&iparams->orires.kfac);
1938 if (file_version < 82)
1940 serializer->doInt(&idum);
1941 serializer->doInt(&idum);
1943 serializer->doReal(&iparams->dihres.phiA);
1944 serializer->doReal(&iparams->dihres.dphiA);
1945 serializer->doReal(&iparams->dihres.kfacA);
1946 if (file_version >= 82)
1948 serializer->doReal(&iparams->dihres.phiB);
1949 serializer->doReal(&iparams->dihres.dphiB);
1950 serializer->doReal(&iparams->dihres.kfacB);
1954 iparams->dihres.phiB = iparams->dihres.phiA;
1955 iparams->dihres.dphiB = iparams->dihres.dphiA;
1956 iparams->dihres.kfacB = iparams->dihres.kfacA;
1960 serializer->doRvec(&iparams->posres.pos0A);
1961 serializer->doRvec(&iparams->posres.fcA);
1962 serializer->doRvec(&iparams->posres.pos0B);
1963 serializer->doRvec(&iparams->posres.fcB);
1966 serializer->doInt(&iparams->fbposres.geom);
1967 serializer->doRvec(&iparams->fbposres.pos0);
1968 serializer->doReal(&iparams->fbposres.r);
1969 serializer->doReal(&iparams->fbposres.k);
1971 case F_CBTDIHS: serializer->doRealArray(iparams->cbtdihs.cbtcA, NR_CBTDIHS); break;
1973 // Fall-through intended
1975 /* Fourier dihedrals are internally represented
1976 * as Ryckaert-Bellemans since those are faster to compute.
1978 serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
1979 serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
1983 serializer->doReal(&iparams->constr.dA);
1984 serializer->doReal(&iparams->constr.dB);
1987 serializer->doReal(&iparams->settle.doh);
1988 serializer->doReal(&iparams->settle.dhh);
1990 case F_VSITE1: break; // VSite1 has 0 parameters
1992 case F_VSITE2FD: serializer->doReal(&iparams->vsite.a); break;
1996 serializer->doReal(&iparams->vsite.a);
1997 serializer->doReal(&iparams->vsite.b);
2002 serializer->doReal(&iparams->vsite.a);
2003 serializer->doReal(&iparams->vsite.b);
2004 serializer->doReal(&iparams->vsite.c);
2007 serializer->doInt(&iparams->vsiten.n);
2008 serializer->doReal(&iparams->vsiten.a);
2010 case F_GB12_NOLONGERUSED:
2011 case F_GB13_NOLONGERUSED:
2012 case F_GB14_NOLONGERUSED:
2013 // Implicit solvent parameters can still be read, but never used
2014 if (serializer->reading())
2016 if (file_version < 68)
2018 serializer->doReal(&rdum);
2019 serializer->doReal(&rdum);
2020 serializer->doReal(&rdum);
2021 serializer->doReal(&rdum);
2023 if (file_version < tpxv_RemoveImplicitSolvation)
2025 serializer->doReal(&rdum);
2026 serializer->doReal(&rdum);
2027 serializer->doReal(&rdum);
2028 serializer->doReal(&rdum);
2029 serializer->doReal(&rdum);
2034 serializer->doInt(&iparams->cmap.cmapA);
2035 serializer->doInt(&iparams->cmap.cmapB);
2039 "unknown function type %d (%s) in %s line %d",
2041 interaction_function[ftype].name,
2047 static void do_ilist(gmx::ISerializer* serializer, InteractionList* ilist)
2049 int nr = ilist->size();
2050 serializer->doInt(&nr);
2051 if (serializer->reading())
2053 ilist->iatoms.resize(nr);
2055 serializer->doIntArray(ilist->iatoms.data(), ilist->size());
2058 static void do_ffparams(gmx::ISerializer* serializer, gmx_ffparams_t* ffparams, int file_version)
2060 serializer->doInt(&ffparams->atnr);
2061 int numTypes = ffparams->numTypes();
2062 serializer->doInt(&numTypes);
2063 if (serializer->reading())
2065 ffparams->functype.resize(numTypes);
2066 ffparams->iparams.resize(numTypes);
2068 /* Read/write all the function types */
2069 serializer->doIntArray(ffparams->functype.data(), ffparams->functype.size());
2071 if (file_version >= 66)
2073 serializer->doDouble(&ffparams->reppow);
2077 ffparams->reppow = 12.0;
2080 serializer->doReal(&ffparams->fudgeQQ);
2082 /* Check whether all these function types are supported by the code.
2083 * In practice the code is backwards compatible, which means that the
2084 * numbering may have to be altered from old numbering to new numbering
2086 for (int i = 0; i < ffparams->numTypes(); i++)
2088 if (serializer->reading())
2090 /* Loop over file versions */
2091 for (int k = 0; k < NFTUPD; k++)
2093 /* Compare the read file_version to the update table */
2094 if ((file_version < ftupd[k].fvnr) && (ffparams->functype[i] >= ftupd[k].ftype))
2096 ffparams->functype[i] += 1;
2101 do_iparams(serializer, ffparams->functype[i], &ffparams->iparams[i], file_version);
2105 static void add_settle_atoms(InteractionList* ilist)
2109 /* Settle used to only store the first atom: add the other two */
2110 ilist->iatoms.resize(2 * ilist->size());
2111 for (i = ilist->size() / 4 - 1; i >= 0; i--)
2113 ilist->iatoms[4 * i + 0] = ilist->iatoms[2 * i + 0];
2114 ilist->iatoms[4 * i + 1] = ilist->iatoms[2 * i + 1];
2115 ilist->iatoms[4 * i + 2] = ilist->iatoms[2 * i + 1] + 1;
2116 ilist->iatoms[4 * i + 3] = ilist->iatoms[2 * i + 1] + 2;
2120 static void do_ilists(gmx::ISerializer* serializer, InteractionLists* ilists, int file_version)
2122 GMX_RELEASE_ASSERT(ilists, "Need a valid ilists object");
2123 GMX_RELEASE_ASSERT(ilists->size() == F_NRE,
2124 "The code needs to be in sync with InteractionLists");
2126 for (int j = 0; j < F_NRE; j++)
2128 InteractionList& ilist = (*ilists)[j];
2129 gmx_bool bClear = FALSE;
2130 if (serializer->reading())
2132 for (int k = 0; k < NFTUPD; k++)
2134 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
2142 ilist.iatoms.clear();
2146 do_ilist(serializer, &ilist);
2147 if (file_version < 78 && j == F_SETTLE && !ilist.empty())
2149 add_settle_atoms(&ilist);
2155 static void do_block(gmx::ISerializer* serializer, t_block* block)
2157 serializer->doInt(&block->nr);
2158 if (serializer->reading())
2160 if ((block->nalloc_index > 0) && (nullptr != block->index))
2162 sfree(block->index);
2164 block->nalloc_index = block->nr + 1;
2165 snew(block->index, block->nalloc_index);
2167 serializer->doIntArray(block->index, block->nr + 1);
2170 static void doListOfLists(gmx::ISerializer* serializer, gmx::ListOfLists<int>* listOfLists)
2172 int numLists = listOfLists->ssize();
2173 serializer->doInt(&numLists);
2174 int numElements = listOfLists->elementsView().ssize();
2175 serializer->doInt(&numElements);
2176 if (serializer->reading())
2178 std::vector<int> listRanges(numLists + 1);
2179 serializer->doIntArray(listRanges.data(), numLists + 1);
2180 std::vector<int> elements(numElements);
2181 serializer->doIntArray(elements.data(), numElements);
2182 *listOfLists = gmx::ListOfLists<int>(std::move(listRanges), std::move(elements));
2186 serializer->doIntArray(const_cast<int*>(listOfLists->listRangesView().data()), numLists + 1);
2187 serializer->doIntArray(const_cast<int*>(listOfLists->elementsView().data()), numElements);
2191 /* This is a primitive routine to make it possible to translate atomic numbers
2192 * to element names when reading TPR files, without making the Gromacs library
2193 * directory a dependency on mdrun (which is the case if we need elements.dat).
2195 static const char* atomicnumber_to_element(int atomicnumber)
2199 /* This does not have to be complete, so we only include elements likely
2200 * to occur in PDB files.
2202 switch (atomicnumber)
2204 case 1: p = "H"; break;
2205 case 5: p = "B"; break;
2206 case 6: p = "C"; break;
2207 case 7: p = "N"; break;
2208 case 8: p = "O"; break;
2209 case 9: p = "F"; break;
2210 case 11: p = "Na"; break;
2211 case 12: p = "Mg"; break;
2212 case 15: p = "P"; break;
2213 case 16: p = "S"; break;
2214 case 17: p = "Cl"; break;
2215 case 18: p = "Ar"; break;
2216 case 19: p = "K"; break;
2217 case 20: p = "Ca"; break;
2218 case 25: p = "Mn"; break;
2219 case 26: p = "Fe"; break;
2220 case 28: p = "Ni"; break;
2221 case 29: p = "Cu"; break;
2222 case 30: p = "Zn"; break;
2223 case 35: p = "Br"; break;
2224 case 47: p = "Ag"; break;
2225 default: p = ""; break;
2231 static void do_atom(gmx::ISerializer* serializer, t_atom* atom)
2233 serializer->doReal(&atom->m);
2234 serializer->doReal(&atom->q);
2235 serializer->doReal(&atom->mB);
2236 serializer->doReal(&atom->qB);
2237 serializer->doUShort(&atom->type);
2238 serializer->doUShort(&atom->typeB);
2239 serializer->doEnumAsInt(&atom->ptype);
2240 serializer->doInt(&atom->resind);
2241 serializer->doInt(&atom->atomnumber);
2242 if (serializer->reading())
2244 /* Set element string from atomic number if present.
2245 * This routine returns an empty string if the name is not found.
2247 std::strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
2248 /* avoid warnings about potentially unterminated string */
2249 atom->elem[3] = '\0';
2253 static void do_grps(gmx::ISerializer* serializer, gmx::ArrayRef<AtomGroupIndices> grps)
2255 for (auto& group : grps)
2257 int size = group.size();
2258 serializer->doInt(&size);
2259 if (serializer->reading())
2263 serializer->doIntArray(group.data(), size);
2267 static void do_symstr(gmx::ISerializer* serializer, char*** nm, t_symtab* symtab)
2271 if (serializer->reading())
2273 serializer->doInt(&ls);
2274 *nm = get_symtab_handle(symtab, ls);
2278 ls = lookup_symtab(symtab, *nm);
2279 serializer->doInt(&ls);
2283 static void do_strstr(gmx::ISerializer* serializer, int nstr, char*** nm, t_symtab* symtab)
2287 for (j = 0; (j < nstr); j++)
2289 do_symstr(serializer, &(nm[j]), symtab);
2293 static void do_resinfo(gmx::ISerializer* serializer, int n, t_resinfo* ri, t_symtab* symtab, int file_version)
2297 for (j = 0; (j < n); j++)
2299 do_symstr(serializer, &(ri[j].name), symtab);
2300 if (file_version >= 63)
2302 serializer->doInt(&ri[j].nr);
2303 serializer->doUChar(&ri[j].ic);
2313 static void do_atoms(gmx::ISerializer* serializer, t_atoms* atoms, t_symtab* symtab, int file_version)
2317 serializer->doInt(&atoms->nr);
2318 serializer->doInt(&atoms->nres);
2319 if (serializer->reading())
2321 /* Since we have always written all t_atom properties in the tpr file
2322 * (at least for all backward compatible versions), we don't store
2323 * but simple set the booleans here.
2325 atoms->haveMass = TRUE;
2326 atoms->haveCharge = TRUE;
2327 atoms->haveType = TRUE;
2328 atoms->haveBState = TRUE;
2329 atoms->havePdbInfo = FALSE;
2331 snew(atoms->atom, atoms->nr);
2332 snew(atoms->atomname, atoms->nr);
2333 snew(atoms->atomtype, atoms->nr);
2334 snew(atoms->atomtypeB, atoms->nr);
2335 snew(atoms->resinfo, atoms->nres);
2336 atoms->pdbinfo = nullptr;
2340 GMX_RELEASE_ASSERT(atoms->haveMass && atoms->haveCharge && atoms->haveType && atoms->haveBState,
2341 "Mass, charge, atomtype and B-state parameters should be present in "
2342 "t_atoms when writing a tpr file");
2344 for (i = 0; (i < atoms->nr); i++)
2346 do_atom(serializer, &atoms->atom[i]);
2348 do_strstr(serializer, atoms->nr, atoms->atomname, symtab);
2349 do_strstr(serializer, atoms->nr, atoms->atomtype, symtab);
2350 do_strstr(serializer, atoms->nr, atoms->atomtypeB, symtab);
2352 do_resinfo(serializer, atoms->nres, atoms->resinfo, symtab, file_version);
2355 static void do_groups(gmx::ISerializer* serializer, SimulationGroups* groups, t_symtab* symtab)
2357 do_grps(serializer, groups->groups);
2358 int numberOfGroupNames = groups->groupNames.size();
2359 serializer->doInt(&numberOfGroupNames);
2360 if (serializer->reading())
2362 groups->groupNames.resize(numberOfGroupNames);
2364 do_strstr(serializer, numberOfGroupNames, groups->groupNames.data(), symtab);
2365 for (auto group : gmx::keysOf(groups->groupNumbers))
2367 int numberOfGroupNumbers = groups->numberOfGroupNumbers(group);
2368 serializer->doInt(&numberOfGroupNumbers);
2369 if (numberOfGroupNumbers != 0)
2371 if (serializer->reading())
2373 groups->groupNumbers[group].resize(numberOfGroupNumbers);
2375 serializer->doUCharArray(groups->groupNumbers[group].data(), numberOfGroupNumbers);
2380 static void do_atomtypes(gmx::ISerializer* serializer, t_atomtypes* atomtypes, int file_version)
2384 serializer->doInt(&atomtypes->nr);
2386 if (serializer->reading())
2388 snew(atomtypes->atomnumber, j);
2390 if (serializer->reading() && file_version < tpxv_RemoveImplicitSolvation)
2392 std::vector<real> dummy(atomtypes->nr, 0);
2393 serializer->doRealArray(dummy.data(), dummy.size());
2394 serializer->doRealArray(dummy.data(), dummy.size());
2395 serializer->doRealArray(dummy.data(), dummy.size());
2397 serializer->doIntArray(atomtypes->atomnumber, j);
2399 if (serializer->reading() && file_version >= 60 && file_version < tpxv_RemoveImplicitSolvation)
2401 std::vector<real> dummy(atomtypes->nr, 0);
2402 serializer->doRealArray(dummy.data(), dummy.size());
2403 serializer->doRealArray(dummy.data(), dummy.size());
2407 static void do_symtab(gmx::ISerializer* serializer, t_symtab* symtab)
2412 serializer->doInt(&symtab->nr);
2414 if (serializer->reading())
2416 snew(symtab->symbuf, 1);
2417 symbuf = symtab->symbuf;
2418 symbuf->bufsize = nr;
2419 snew(symbuf->buf, nr);
2420 for (i = 0; (i < nr); i++)
2423 serializer->doString(&buf);
2424 symbuf->buf[i] = gmx_strdup(buf.c_str());
2429 symbuf = symtab->symbuf;
2430 while (symbuf != nullptr)
2432 for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
2434 std::string buf = symbuf->buf[i];
2435 serializer->doString(&buf);
2438 symbuf = symbuf->next;
2442 gmx_fatal(FARGS, "nr of symtab strings left: %d", nr);
2447 static void do_cmap(gmx::ISerializer* serializer, gmx_cmap_t* cmap_grid)
2450 int ngrid = cmap_grid->cmapdata.size();
2451 serializer->doInt(&ngrid);
2452 serializer->doInt(&cmap_grid->grid_spacing);
2454 int gs = cmap_grid->grid_spacing;
2455 int nelem = gs * gs;
2457 if (serializer->reading())
2459 cmap_grid->cmapdata.resize(ngrid);
2461 for (int i = 0; i < ngrid; i++)
2463 cmap_grid->cmapdata[i].cmap.resize(4 * nelem);
2467 for (int i = 0; i < ngrid; i++)
2469 for (int j = 0; j < nelem; j++)
2471 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4]);
2472 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 1]);
2473 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 2]);
2474 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 3]);
2480 static void do_moltype(gmx::ISerializer* serializer, gmx_moltype_t* molt, t_symtab* symtab, int file_version)
2482 do_symstr(serializer, &(molt->name), symtab);
2484 do_atoms(serializer, &molt->atoms, symtab, file_version);
2486 do_ilists(serializer, &molt->ilist, file_version);
2488 /* TODO: Remove the obsolete charge group index from the file */
2490 cgs.nr = molt->atoms.nr;
2491 cgs.nalloc_index = cgs.nr + 1;
2492 snew(cgs.index, cgs.nalloc_index);
2493 for (int i = 0; i < cgs.nr + 1; i++)
2497 do_block(serializer, &cgs);
2500 /* This used to be in the atoms struct */
2501 doListOfLists(serializer, &molt->excls);
2504 static void do_molblock(gmx::ISerializer* serializer, gmx_molblock_t* molb, int numAtomsPerMolecule)
2506 serializer->doInt(&molb->type);
2507 serializer->doInt(&molb->nmol);
2508 /* To maintain forward topology reading compatibility, we store #atoms.
2509 * TODO: Change this to conditional reading of a dummy int when we
2510 * increase tpx_generation.
2512 serializer->doInt(&numAtomsPerMolecule);
2513 /* Position restraint coordinates */
2514 int numPosres_xA = molb->posres_xA.size();
2515 serializer->doInt(&numPosres_xA);
2516 if (numPosres_xA > 0)
2518 if (serializer->reading())
2520 molb->posres_xA.resize(numPosres_xA);
2522 serializer->doRvecArray(as_rvec_array(molb->posres_xA.data()), numPosres_xA);
2524 int numPosres_xB = molb->posres_xB.size();
2525 serializer->doInt(&numPosres_xB);
2526 if (numPosres_xB > 0)
2528 if (serializer->reading())
2530 molb->posres_xB.resize(numPosres_xB);
2532 serializer->doRvecArray(as_rvec_array(molb->posres_xB.data()), numPosres_xB);
2536 static void set_disres_npair(gmx_mtop_t* mtop)
2538 gmx_mtop_ilistloop_t iloop;
2541 gmx::ArrayRef<t_iparams> ip = mtop->ffparams.iparams;
2543 iloop = gmx_mtop_ilistloop_init(*mtop);
2544 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
2546 const InteractionList& il = (*ilist)[F_DISRES];
2550 gmx::ArrayRef<const int> a = il.iatoms;
2552 for (int i = 0; i < il.size(); i += 3)
2555 if (i + 3 == il.size() || ip[a[i]].disres.label != ip[a[i + 3]].disres.label)
2557 ip[a[i]].disres.npair = npair;
2565 static void do_mtop(gmx::ISerializer* serializer, gmx_mtop_t* mtop, int file_version)
2567 do_symtab(serializer, &(mtop->symtab));
2569 do_symstr(serializer, &(mtop->name), &(mtop->symtab));
2571 do_ffparams(serializer, &mtop->ffparams, file_version);
2573 int nmoltype = mtop->moltype.size();
2574 serializer->doInt(&nmoltype);
2575 if (serializer->reading())
2577 mtop->moltype.resize(nmoltype);
2579 for (gmx_moltype_t& moltype : mtop->moltype)
2581 do_moltype(serializer, &moltype, &mtop->symtab, file_version);
2584 int nmolblock = mtop->molblock.size();
2585 serializer->doInt(&nmolblock);
2586 if (serializer->reading())
2588 mtop->molblock.resize(nmolblock);
2590 for (gmx_molblock_t& molblock : mtop->molblock)
2592 int numAtomsPerMolecule = (serializer->reading() ? 0 : mtop->moltype[molblock.type].atoms.nr);
2593 do_molblock(serializer, &molblock, numAtomsPerMolecule);
2595 serializer->doInt(&mtop->natoms);
2597 if (file_version >= tpxv_IntermolecularBondeds)
2599 serializer->doBool(&mtop->bIntermolecularInteractions);
2600 if (mtop->bIntermolecularInteractions)
2602 if (serializer->reading())
2604 mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
2606 do_ilists(serializer, mtop->intermolecular_ilist.get(), file_version);
2611 mtop->bIntermolecularInteractions = FALSE;
2614 do_atomtypes(serializer, &(mtop->atomtypes), file_version);
2616 if (file_version >= 65)
2618 do_cmap(serializer, &mtop->ffparams.cmap_grid);
2622 mtop->ffparams.cmap_grid.grid_spacing = 0;
2623 mtop->ffparams.cmap_grid.cmapdata.clear();
2626 do_groups(serializer, &mtop->groups, &(mtop->symtab));
2627 if (file_version < tpxv_RemovedConstantAcceleration)
2629 mtop->groups.groups[SimulationAtomGroupType::AccelerationUnused].clear();
2630 mtop->groups.groupNumbers[SimulationAtomGroupType::AccelerationUnused].clear();
2633 mtop->haveMoleculeIndices = true;
2635 if (file_version >= tpxv_StoreNonBondedInteractionExclusionGroup)
2637 std::int64_t intermolecularExclusionGroupSize = gmx::ssize(mtop->intermolecularExclusionGroup);
2638 serializer->doInt64(&intermolecularExclusionGroupSize);
2639 GMX_RELEASE_ASSERT(intermolecularExclusionGroupSize >= 0,
2640 "Number of atoms with excluded intermolecular non-bonded interactions "
2642 mtop->intermolecularExclusionGroup.resize(intermolecularExclusionGroupSize); // no effect when writing
2643 serializer->doIntArray(mtop->intermolecularExclusionGroup.data(),
2644 mtop->intermolecularExclusionGroup.size());
2647 if (serializer->reading())
2649 close_symtab(&(mtop->symtab));
2654 * Read the first part of the TPR file to find general system information.
2656 * If \p TopOnlyOK is true then we can read even future versions
2657 * of tpx files, provided the \p fileGeneration hasn't changed.
2658 * If it is false, we need the \p ir too, and bail out
2659 * if the file is newer than the program.
2661 * The version and generation of the topology (see top of this file)
2662 * are returned in the two last arguments, if those arguments are non-nullptr.
2664 * If possible, we will read the \p ir even when \p TopOnlyOK is true.
2666 * \param[in,out] serializer The serializer used to handle header processing.
2667 * \param[in,out] tpx File header datastructure.
2668 * \param[in] filename The name of the file being read/written
2669 * \param[in,out] fio File handle.
2670 * \param[in] TopOnlyOK If not reading \p ir is fine or not.
2672 static void do_tpxheader(gmx::FileIOXdrSerializer* serializer,
2674 const char* filename,
2682 /* XDR binary topology file */
2683 precision = sizeof(real);
2685 std::string fileTag;
2686 if (serializer->reading())
2688 serializer->doString(&buf);
2689 if (std::strncmp(buf.c_str(), "VERSION", 7) != 0)
2693 "Can not read file %s,\n"
2694 " this file is from a GROMACS version which is older than 2.0\n"
2695 " Make a new one with grompp or use a gro or pdb file, if possible",
2698 // We need to know the precision used to write the TPR file, to match it
2699 // to the precision of the currently running binary. If the precisions match
2700 // there is no problem, but mismatching precision needs to be accounted for
2701 // by reading into temporary variables of the correct precision instead
2702 // of the desired target datastructures.
2703 serializer->doInt(&precision);
2704 tpx->isDouble = (precision == sizeof(double));
2705 if ((precision != sizeof(float)) && !tpx->isDouble)
2708 "Unknown precision in file %s: real is %d bytes "
2709 "instead of %zu or %zu",
2715 gmx_fio_setprecision(fio, tpx->isDouble);
2717 "Reading file %s, %s (%s precision)\n",
2720 tpx->isDouble ? "double" : "single");
2724 buf = gmx::formatString("VERSION %s", gmx_version());
2725 serializer->doString(&buf);
2726 gmx_fio_setprecision(fio, tpx->isDouble);
2727 serializer->doInt(&precision);
2728 fileTag = gmx::formatString("%s", tpx_tag);
2731 /* Check versions! */
2732 serializer->doInt(&tpx->fileVersion);
2734 /* This is for backward compatibility with development versions 77-79
2735 * where the tag was, mistakenly, placed before the generation,
2736 * which would cause a segv instead of a proper error message
2737 * when reading the topology only from tpx with <77 code.
2739 if (tpx->fileVersion >= 77 && tpx->fileVersion <= 79)
2741 serializer->doString(&fileTag);
2744 serializer->doInt(&tpx->fileGeneration);
2746 if (tpx->fileVersion >= 81)
2748 serializer->doString(&fileTag);
2750 if (serializer->reading())
2752 if (tpx->fileVersion < 77)
2754 /* Versions before 77 don't have the tag, set it to release */
2755 fileTag = gmx::formatString("%s", TPX_TAG_RELEASE);
2758 if (fileTag != tpx_tag)
2760 fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n", fileTag.c_str(), tpx_tag);
2762 /* We only support reading tpx files with the same tag as the code
2763 * or tpx files with the release tag and with lower version number.
2765 if (fileTag != TPX_TAG_RELEASE && tpx->fileVersion < tpx_version)
2768 "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' "
2769 "with program for tpx version %d, tag '%s'",
2779 if ((tpx->fileVersion <= tpx_incompatible_version)
2780 || ((tpx->fileVersion > tpx_version) && !TopOnlyOK) || (tpx->fileGeneration > tpx_generation)
2781 || tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
2784 "reading tpx file (%s) version %d with version %d program",
2790 serializer->doInt(&tpx->natoms);
2791 serializer->doInt(&tpx->ngtc);
2793 if (tpx->fileVersion < 62)
2795 serializer->doInt(&idum);
2796 serializer->doReal(&rdum);
2798 if (tpx->fileVersion >= 79)
2800 serializer->doInt(&tpx->fep_state);
2802 serializer->doReal(&tpx->lambda);
2803 serializer->doBool(&tpx->bIr);
2804 serializer->doBool(&tpx->bTop);
2805 serializer->doBool(&tpx->bX);
2806 serializer->doBool(&tpx->bV);
2807 serializer->doBool(&tpx->bF);
2808 serializer->doBool(&tpx->bBox);
2810 if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
2812 if (!serializer->reading())
2814 GMX_RELEASE_ASSERT(tpx->sizeOfTprBody != 0,
2815 "Not possible to write new file with zero TPR body size");
2817 serializer->doInt64(&tpx->sizeOfTprBody);
2820 if ((tpx->fileGeneration > tpx_generation))
2822 /* This can only happen if TopOnlyOK=TRUE */
2827 #define do_test(serializer, b, p) \
2828 if ((serializer)->reading() && ((p) != nullptr) && !(b)) \
2829 gmx_fatal(FARGS, "No %s in input file", #p)
2832 * Process the first part of the TPR into the state datastructure.
2834 * Due to the structure of the legacy code, it is necessary
2835 * to split up the state reading into two parts, with the
2836 * box and legacy temperature coupling processed before the
2837 * topology datastructures.
2839 * See the documentation for do_tpx_body for the correct order of
2840 * the operations for reading a tpr file.
2842 * \param[in] serializer Abstract serializer used to read/write data.
2843 * \param[in] tpx The file header data.
2844 * \param[in, out] state Global state data.
2846 static void do_tpx_state_first(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state)
2848 if (serializer->reading())
2851 init_gtc_state(state, tpx->ngtc, 0, 0);
2853 do_test(serializer, tpx->bBox, state->box);
2856 serializer->doRvecArray(state->box, DIM);
2857 if (tpx->fileVersion >= 51)
2859 serializer->doRvecArray(state->box_rel, DIM);
2863 /* We initialize box_rel after reading the inputrec */
2864 clear_mat(state->box_rel);
2866 serializer->doRvecArray(state->boxv, DIM);
2867 if (tpx->fileVersion < 56)
2870 serializer->doRvecArray(mdum, DIM);
2874 if (state->ngtc > 0)
2877 snew(dumv, state->ngtc);
2878 if (tpx->fileVersion < 69)
2880 serializer->doRealArray(dumv, state->ngtc);
2882 /* These used to be the Berendsen tcoupl_lambda's */
2883 serializer->doRealArray(dumv, state->ngtc);
2889 * Process global topology data.
2891 * See the documentation for do_tpx_body for the correct order of
2892 * the operations for reading a tpr file.
2894 * \param[in] serializer Abstract serializer used to read/write data.
2895 * \param[in] tpx The file header data.
2896 * \param[in,out] mtop Global topology.
2898 static void do_tpx_mtop(gmx::ISerializer* serializer, TpxFileHeader* tpx, gmx_mtop_t* mtop)
2900 do_test(serializer, tpx->bTop, mtop);
2905 do_mtop(serializer, mtop, tpx->fileVersion);
2906 set_disres_npair(mtop);
2912 do_mtop(serializer, &dum_top, tpx->fileVersion);
2917 * Process coordinate vectors for state data.
2919 * Main part of state gets processed here.
2921 * See the documentation for do_tpx_body for the correct order of
2922 * the operations for reading a tpr file.
2924 * \param[in] serializer Abstract serializer used to read/write data.
2925 * \param[in] tpx The file header data.
2926 * \param[in,out] state Global state data.
2927 * \param[in,out] x Individual coordinates for processing, deprecated.
2928 * \param[in,out] v Individual velocities for processing, deprecated.
2930 static void do_tpx_state_second(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state, rvec* x, rvec* v)
2932 if (!serializer->reading())
2935 x == nullptr && v == nullptr,
2936 "Passing separate x and v pointers to do_tpx() is not supported when writing");
2940 GMX_RELEASE_ASSERT(!(x == nullptr && v != nullptr),
2941 "Passing x==NULL and v!=NULL is not supported");
2944 if (serializer->reading())
2948 // v is also nullptr by the above assertion, so we may
2949 // need to make memory in state for storing the contents
2953 state->flags |= enumValueToBitMask(StateEntry::X);
2957 state->flags |= enumValueToBitMask(StateEntry::V);
2959 state_change_natoms(state, tpx->natoms);
2965 x = state->x.rvec_array();
2966 v = state->v.rvec_array();
2968 do_test(serializer, tpx->bX, x);
2971 if (serializer->reading())
2973 state->flags |= enumValueToBitMask(StateEntry::X);
2975 serializer->doRvecArray(x, tpx->natoms);
2978 do_test(serializer, tpx->bV, v);
2981 if (serializer->reading())
2983 state->flags |= enumValueToBitMask(StateEntry::V);
2987 std::vector<gmx::RVec> dummyVelocities(tpx->natoms);
2988 serializer->doRvecArray(as_rvec_array(dummyVelocities.data()), tpx->natoms);
2992 serializer->doRvecArray(v, tpx->natoms);
2996 // No need to run do_test when the last argument is NULL
2999 std::vector<gmx::RVec> dummyForces(state->natoms);
3000 serializer->doRvecArray(as_rvec_array(dummyForces.data()), tpx->natoms);
3004 * Process simulation parameters.
3006 * See the documentation for do_tpx_body for the correct order of
3007 * the operations for reading a tpr file.
3009 * \param[in] serializer Abstract serializer used to read/write data.
3010 * \param[in] tpx The file header data.
3011 * \param[in,out] ir Datastructure with simulation parameters.
3013 static PbcType do_tpx_ir(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir)
3016 gmx_bool bPeriodicMols;
3018 /* Starting with tpx version 26, we have the inputrec
3019 * at the end of the file, so we can ignore it
3020 * if the file is never than the software (but still the
3021 * same generation - see comments at the top of this file.
3025 pbcType = PbcType::Unset;
3026 bPeriodicMols = FALSE;
3028 do_test(serializer, tpx->bIr, ir);
3031 if (tpx->fileVersion >= 53)
3033 /* Removed the pbc info from do_inputrec, since we always want it */
3034 if (!serializer->reading())
3036 pbcType = ir->pbcType;
3037 bPeriodicMols = ir->bPeriodicMols;
3039 serializer->doInt(reinterpret_cast<int*>(&pbcType));
3040 serializer->doBool(&bPeriodicMols);
3042 if (tpx->fileGeneration <= tpx_generation && ir)
3044 do_inputrec(serializer, ir, tpx->fileVersion);
3045 if (tpx->fileVersion < 53)
3047 pbcType = ir->pbcType;
3048 bPeriodicMols = ir->bPeriodicMols;
3051 if (serializer->reading() && ir && tpx->fileVersion >= 53)
3053 /* We need to do this after do_inputrec, since that initializes ir */
3054 ir->pbcType = pbcType;
3055 ir->bPeriodicMols = bPeriodicMols;
3062 * Correct and finalize read information.
3064 * If \p state is nullptr, skip the parts dependent on it.
3066 * See the documentation for do_tpx_body for the correct order of
3067 * the operations for reading a tpr file.
3069 * \param[in] tpx The file header used to check version numbers.
3070 * \param[out] ir Input rec that needs correction.
3071 * \param[out] state State needing correction.
3072 * \param[out] mtop Topology to finalize.
3074 static void do_tpx_finalize(TpxFileHeader* tpx, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
3076 if (tpx->fileVersion < 51 && state)
3078 set_box_rel(ir, state);
3082 if (state && state->ngtc == 0)
3084 /* Reading old version without tcoupl state data: set it */
3085 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
3087 if (tpx->bTop && mtop)
3089 if (tpx->fileVersion < 57)
3091 ir->eDisre = !mtop->moltype[0].ilist[F_DISRES].empty()
3092 ? DistanceRestraintRefinement::Simple
3093 : DistanceRestraintRefinement::None;
3100 * Process TPR data for file reading/writing.
3102 * The TPR file gets processed in in four stages due to the organization
3103 * of the data within it.
3105 * First, state data for the box is processed in do_tpx_state_first.
3106 * This is followed by processing the topology in do_tpx_mtop.
3107 * Coordinate and velocity vectors are handled next in do_tpx_state_second.
3108 * The last file information processed is the collection of simulation parameters in do_tpx_ir.
3109 * When reading, a final processing step is undertaken at the end.
3111 * \param[in] serializer Abstract serializer used to read/write data.
3112 * \param[in] tpx The file header data.
3113 * \param[in,out] ir Datastructures with simulation parameters.
3114 * \param[in,out] state Global state data.
3115 * \param[in,out] x Individual coordinates for processing, deprecated.
3116 * \param[in,out] v Individual velocities for processing, deprecated.
3117 * \param[in,out] mtop Global topology.
3119 static PbcType do_tpx_body(gmx::ISerializer* serializer,
3129 do_tpx_state_first(serializer, tpx, state);
3131 do_tpx_mtop(serializer, tpx, mtop);
3134 do_tpx_state_second(serializer, tpx, state, x, v);
3136 PbcType pbcType = do_tpx_ir(serializer, tpx, ir);
3137 if (serializer->reading())
3139 do_tpx_finalize(tpx, ir, state, mtop);
3145 * Overload for do_tpx_body that defaults to state vectors being nullptr.
3147 * \param[in] serializer Abstract serializer used to read/write data.
3148 * \param[in] tpx The file header data.
3149 * \param[in,out] ir Datastructures with simulation parameters.
3150 * \param[in,out] mtop Global topology.
3152 static PbcType do_tpx_body(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir, gmx_mtop_t* mtop)
3154 return do_tpx_body(serializer, tpx, ir, nullptr, nullptr, nullptr, mtop);
3157 static t_fileio* open_tpx(const char* fn, const char* mode)
3159 return gmx_fio_open(fn, mode);
3162 static void close_tpx(t_fileio* fio)
3168 * Fill information into the header only from state before writing.
3170 * Populating the header needs to be independent from writing the information
3171 * to file to allow things like writing the raw byte stream.
3173 * \param[in] state The current simulation state. Can't write without it.
3174 * \param[in] ir Parameter and system information.
3175 * \param[in] mtop Global topology.
3176 * \returns Fully populated header.
3178 static TpxFileHeader populateTpxHeader(const t_state& state, const t_inputrec* ir, const gmx_mtop_t* mtop)
3180 TpxFileHeader header;
3181 header.natoms = state.natoms;
3182 header.ngtc = state.ngtc;
3183 header.fep_state = state.fep_state;
3184 header.lambda = state.lambda[FreeEnergyPerturbationCouplingType::Fep];
3185 header.bIr = ir != nullptr;
3186 header.bTop = mtop != nullptr;
3187 header.bX = (state.flags & enumValueToBitMask(StateEntry::X)) != 0;
3188 header.bV = (state.flags & enumValueToBitMask(StateEntry::V)) != 0;
3191 header.fileVersion = tpx_version;
3192 header.fileGeneration = tpx_generation;
3193 header.isDouble = (sizeof(real) == sizeof(double));
3199 * Process the body of a TPR file as an opaque data buffer.
3201 * Reads/writes the information in \p buffer from/to the \p serializer
3202 * provided to the function. Does not interact with the actual
3203 * TPR datastructures but with an in memory representation of the
3204 * data, so that this data can be efficiently read or written from/to
3205 * an original source.
3207 * \param[in] serializer The abstract serializer used for reading or writing
3208 * the information in \p buffer.
3209 * \param[in,out] buffer Information from TPR file as char buffer.
3211 static void doTpxBodyBuffer(gmx::ISerializer* serializer, gmx::ArrayRef<char> buffer)
3213 serializer->doOpaque(buffer.data(), buffer.size());
3217 * Populates simulation datastructures.
3219 * Here the information from the serialization interface \p serializer
3220 * is used to first populate the datastructures containing the simulation
3221 * information. Depending on the version found in the header \p tpx,
3222 * this is done using the new reading of the data as one block from disk,
3223 * followed by complete deserialization of the information read from there.
3224 * Otherwise, the datastructures are populated as before one by one from disk.
3225 * The second version is the default for the legacy tools that read the
3226 * coordinates and velocities separate from the state.
3228 * After reading in the data, a separate buffer is populated from them
3229 * containing only \p ir and \p mtop that can be communicated directly
3230 * to nodes needing the information to set up a simulation.
3232 * \param[in] tpx The file header.
3233 * \param[in] serializer The Serialization interface used to read the TPR.
3234 * \param[out] ir Input rec to populate.
3235 * \param[out] state State vectors to populate.
3236 * \param[out] x Coordinates to populate if needed.
3237 * \param[out] v Velocities to populate if needed.
3238 * \param[out] mtop Global topology to populate.
3240 * \returns Partial de-serialized TPR used for communication to nodes.
3242 static PartialDeserializedTprFile readTpxBody(TpxFileHeader* tpx,
3243 gmx::ISerializer* serializer,
3250 PartialDeserializedTprFile partialDeserializedTpr;
3251 if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
3253 partialDeserializedTpr.body.resize(tpx->sizeOfTprBody);
3254 partialDeserializedTpr.header = *tpx;
3255 doTpxBodyBuffer(serializer, partialDeserializedTpr.body);
3257 partialDeserializedTpr.pbcType =
3258 completeTprDeserialization(&partialDeserializedTpr, ir, state, x, v, mtop);
3262 partialDeserializedTpr.pbcType = do_tpx_body(serializer, tpx, ir, state, x, v, mtop);
3264 // Update header to system info for communication to nodes.
3265 // As we only need to communicate the inputrec and mtop to other nodes,
3266 // we prepare a new char buffer with the information we have already read
3268 partialDeserializedTpr.header = populateTpxHeader(*state, ir, mtop);
3269 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3270 // but since we just used the default XDR format (which is big endian) for the TPR
3271 // header it would cause third-party libraries reading our raw data to tear their hair
3272 // if we swap the endian in the middle of the file, so we stick to big endian in the
3273 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3274 gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3275 do_tpx_body(&tprBodySerializer, &partialDeserializedTpr.header, ir, mtop);
3276 partialDeserializedTpr.body = tprBodySerializer.finishAndGetBuffer();
3278 return partialDeserializedTpr;
3281 /************************************************************
3283 * The following routines are the exported ones
3285 ************************************************************/
3287 TpxFileHeader readTpxHeader(const char* fileName, bool canReadTopologyOnly)
3291 fio = open_tpx(fileName, "r");
3292 gmx::FileIOXdrSerializer serializer(fio);
3295 do_tpxheader(&serializer, &tpx, fileName, fio, canReadTopologyOnly);
3300 void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t& mtop)
3302 /* To write a state, we first need to write the state information to a buffer before
3303 * we append the raw bytes to the file. For this, the header information needs to be
3304 * populated before we write the main body because it has some information that is
3305 * otherwise not available.
3310 TpxFileHeader tpx = populateTpxHeader(*state, ir, &mtop);
3311 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3312 // but since we just used the default XDR format (which is big endian) for the TPR
3313 // header it would cause third-party libraries reading our raw data to tear their hair
3314 // if we swap the endian in the middle of the file, so we stick to big endian in the
3315 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3316 gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3318 do_tpx_body(&tprBodySerializer,
3320 const_cast<t_inputrec*>(ir),
3321 const_cast<t_state*>(state),
3324 const_cast<gmx_mtop_t*>(&mtop));
3326 std::vector<char> tprBody = tprBodySerializer.finishAndGetBuffer();
3327 tpx.sizeOfTprBody = tprBody.size();
3329 fio = open_tpx(fn, "w");
3330 gmx::FileIOXdrSerializer serializer(fio);
3331 do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
3332 doTpxBodyBuffer(&serializer, tprBody);
3337 PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
3344 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3345 // but since we just used the default XDR format (which is big endian) for the TPR
3346 // header it would cause third-party libraries reading our raw data to tear their hair
3347 // if we swap the endian in the middle of the file, so we stick to big endian in the
3348 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3349 gmx::InMemoryDeserializer tprBodyDeserializer(partialDeserializedTpr->body,
3350 partialDeserializedTpr->header.isDouble,
3351 gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3352 return do_tpx_body(&tprBodyDeserializer, &partialDeserializedTpr->header, ir, state, x, v, mtop);
3355 PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
3359 return completeTprDeserialization(partialDeserializedTpr, ir, nullptr, nullptr, nullptr, mtop);
3362 PartialDeserializedTprFile read_tpx_state(const char* fn, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
3365 fio = open_tpx(fn, "r");
3366 gmx::FileIOXdrSerializer serializer(fio);
3367 PartialDeserializedTprFile partialDeserializedTpr;
3368 do_tpxheader(&serializer, &partialDeserializedTpr.header, fn, fio, ir == nullptr);
3369 partialDeserializedTpr =
3370 readTpxBody(&partialDeserializedTpr.header, &serializer, ir, state, nullptr, nullptr, mtop);
3372 return partialDeserializedTpr;
3375 PbcType read_tpx(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, gmx_mtop_t* mtop)
3381 fio = open_tpx(fn, "r");
3382 gmx::FileIOXdrSerializer serializer(fio);
3383 do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
3384 PartialDeserializedTprFile partialDeserializedTpr =
3385 readTpxBody(&tpx, &serializer, ir, &state, x, v, mtop);
3387 if (mtop != nullptr && natoms != nullptr)
3389 *natoms = mtop->natoms;
3393 copy_mat(state.box, box);
3395 return partialDeserializedTpr.pbcType;
3398 PbcType read_tpx_top(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, t_topology* top)
3403 pbcType = read_tpx(fn, ir, box, natoms, x, v, &mtop);
3405 *top = gmx_mtop_t_to_t_topology(&mtop, true);
3410 gmx_bool fn2bTPX(const char* file)
3412 return (efTPR == fn2ftp(file));
3415 void pr_tpxheader(FILE* fp, int indent, const char* title, const TpxFileHeader* sh)
3417 if (available(fp, sh, indent, title))
3419 indent = pr_title(fp, indent, title);
3420 pr_indent(fp, indent);
3421 fprintf(fp, "bIr = %spresent\n", sh->bIr ? "" : "not ");
3422 pr_indent(fp, indent);
3423 fprintf(fp, "bBox = %spresent\n", sh->bBox ? "" : "not ");
3424 pr_indent(fp, indent);
3425 fprintf(fp, "bTop = %spresent\n", sh->bTop ? "" : "not ");
3426 pr_indent(fp, indent);
3427 fprintf(fp, "bX = %spresent\n", sh->bX ? "" : "not ");
3428 pr_indent(fp, indent);
3429 fprintf(fp, "bV = %spresent\n", sh->bV ? "" : "not ");
3430 pr_indent(fp, indent);
3431 fprintf(fp, "bF = %spresent\n", sh->bF ? "" : "not ");
3433 pr_indent(fp, indent);
3434 fprintf(fp, "natoms = %d\n", sh->natoms);
3435 pr_indent(fp, indent);
3436 fprintf(fp, "lambda = %e\n", sh->lambda);
3437 pr_indent(fp, indent);
3438 fprintf(fp, "buffer size = %" PRId64 "\n", sh->sizeOfTprBody);