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40 /* This file is completely threadsafe - keep it that way! */
42 #include "gromacs/fileio/tpxio.h"
52 #include "gromacs/applied_forces/awh/read_params.h"
53 #include "gromacs/fileio/filetypes.h"
54 #include "gromacs/fileio/gmxfio.h"
55 #include "gromacs/fileio/gmxfio_xdr.h"
56 #include "gromacs/math/units.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/mdtypes/awh_history.h"
59 #include "gromacs/mdtypes/awh_params.h"
60 #include "gromacs/mdtypes/inputrec.h"
61 #include "gromacs/mdtypes/md_enums.h"
62 #include "gromacs/mdtypes/multipletimestepping.h"
63 #include "gromacs/mdtypes/pull_params.h"
64 #include "gromacs/mdtypes/state.h"
65 #include "gromacs/pbcutil/boxutilities.h"
66 #include "gromacs/pbcutil/pbc.h"
67 #include "gromacs/topology/block.h"
68 #include "gromacs/topology/ifunc.h"
69 #include "gromacs/topology/mtop_util.h"
70 #include "gromacs/topology/symtab.h"
71 #include "gromacs/topology/topology.h"
72 #include "gromacs/utility/arraysize.h"
73 #include "gromacs/utility/baseversion.h"
74 #include "gromacs/utility/cstringutil.h"
75 #include "gromacs/utility/fatalerror.h"
76 #include "gromacs/utility/futil.h"
77 #include "gromacs/utility/gmxassert.h"
78 #include "gromacs/utility/inmemoryserializer.h"
79 #include "gromacs/utility/iserializer.h"
80 #include "gromacs/utility/keyvaluetreebuilder.h"
81 #include "gromacs/utility/keyvaluetreeserializer.h"
82 #include "gromacs/utility/smalloc.h"
83 #include "gromacs/utility/snprintf.h"
84 #include "gromacs/utility/txtdump.h"
86 #define TPX_TAG_RELEASE "release"
88 /*! \brief Tag string for the file format written to run input files
89 * written by this version of the code.
91 * Change this if you want to change the run input format in a feature
92 * branch. This ensures that there will not be different run input
93 * formats around which cannot be distinguished, while not causing
94 * problems rebasing the feature branch onto upstream changes. When
95 * merging with mainstream GROMACS, set this tag string back to
96 * TPX_TAG_RELEASE, and instead add an element to tpxv.
98 static const std::string tpx_tag = TPX_TAG_RELEASE;
100 /*! \brief Enum of values that describe the contents of a tpr file
101 * whose format matches a version number
103 * The enum helps the code be more self-documenting and ensure merges
104 * do not silently resolve when two patches make the same bump. When
105 * adding new functionality, add a new element just above tpxv_Count
106 * in this enumeration, and write code below that does the right thing
107 * according to the value of file_version.
111 tpxv_ComputationalElectrophysiology =
112 96, /**< support for ion/water position swaps (computational electrophysiology) */
113 tpxv_Use64BitRandomSeed, /**< change ld_seed from int to int64_t */
114 tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, /**< potentials for supporting coarse-grained force fields */
115 tpxv_InteractiveMolecularDynamics, /**< interactive molecular dynamics (IMD) */
116 tpxv_RemoveObsoleteParameters1, /**< remove optimize_fft, dihre_fc, nstcheckpoint */
117 tpxv_PullCoordTypeGeom, /**< add pull type and geometry per group and flat-bottom */
118 tpxv_PullGeomDirRel, /**< add pull geometry direction-relative */
119 tpxv_IntermolecularBondeds, /**< permit inter-molecular bonded interactions in the topology */
120 tpxv_CompElWithSwapLayerOffset, /**< added parameters for improved CompEl setups */
121 tpxv_CompElPolyatomicIonsAndMultipleIonTypes, /**< CompEl now can handle polyatomic ions and more than two types of ions */
122 tpxv_RemoveAdress, /**< removed support for AdResS */
123 tpxv_PullCoordNGroup, /**< add ngroup to pull coord */
124 tpxv_RemoveTwinRange, /**< removed support for twin-range interactions */
125 tpxv_ReplacePullPrintCOM12, /**< Replaced print-com-1, 2 with pull-print-com */
126 tpxv_PullExternalPotential, /**< Added pull type external potential */
127 tpxv_GenericParamsForElectricField, /**< Introduced KeyValueTree and moved electric field parameters */
128 tpxv_AcceleratedWeightHistogram, /**< sampling with accelerated weight histogram method (AWH) */
129 tpxv_RemoveImplicitSolvation, /**< removed support for implicit solvation */
130 tpxv_PullPrevStepCOMAsReference, /**< Enabled using the COM of the pull group of the last frame as reference for PBC */
131 tpxv_MimicQMMM, /**< Introduced support for MiMiC QM/MM interface */
132 tpxv_PullAverage, /**< Added possibility to output average pull force and position */
133 tpxv_GenericInternalParameters, /**< Added internal parameters for mdrun modules*/
134 tpxv_VSite2FD, /**< Added 2FD type virtual site */
135 tpxv_AddSizeField, /**< Added field with information about the size of the serialized tpr file in bytes, excluding the header */
136 tpxv_StoreNonBondedInteractionExclusionGroup, /**< Store the non bonded interaction exclusion group in the topology */
137 tpxv_VSite1, /**< Added 1 type virtual site */
138 tpxv_MTS, /**< Added multiple time stepping */
139 tpxv_RemovedConstantAcceleration, /**< Removed support for constant acceleration NEMD. */
140 tpxv_TransformationPullCoord, /**< Support for transformation pull coordinates */
141 tpxv_SoftcoreGapsys, /**< Added gapsys softcore function */
142 tpxv_ReaddedConstantAcceleration, /**< Re-added support for constant acceleration NEMD. */
143 tpxv_Count /**< the total number of tpxv versions */
146 /*! \brief Version number of the file format written to run input
147 * files by this version of the code.
149 * The tpx_version increases whenever the file format in the main
150 * development branch changes, due to an extension of the tpxv enum above.
151 * Backward compatibility for reading old run input files is maintained
152 * by checking this version number against that of the file and then using
153 * the correct code path.
155 * When developing a feature branch that needs to change the run input
156 * file format, change tpx_tag instead. */
157 static const int tpx_version = tpxv_Count - 1;
161 * Enum keeping track of incompatible changes for older TPR versions.
163 * The enum should be updated with a new field when editing the TOPOLOGY
164 * or HEADER of the tpx format. In particular, updating ftupd or
165 * changing the fields of TprHeaderVersion often trigger such needs.
167 * This way we can maintain forward compatibility too for all analysis tools
168 * and/or external programs that only need to know the atom/residue names,
169 * charges, and bond connectivity.
171 * It first appeared in tpx version 26, when I also moved the inputrecord
172 * to the end of the tpx file, so we can just skip it if we only
175 * In particular, it must be increased when adding new elements to
176 * ftupd, so that old code can read new .tpr files.
178 enum class TpxGeneration : int
180 Initial = 26, //! First version is 26
181 AddSizeField, //! TPR header modified for writing as a block.
182 AddVSite1, //! ftupd changed to include VSite1 type.
183 Count //! Number of entries.
186 //! Value of Current TPR generation.
187 static const int tpx_generation = static_cast<int>(TpxGeneration::Count) - 1;
189 /* This number should be the most recent backwards incompatible version
190 * I.e., if this number is 9, we cannot read tpx version 9 with this code.
192 static const int tpx_incompatible_version = 57; // GMX4.0 has version 58
195 /* Struct used to maintain tpx compatibility when function types are added */
198 int fvnr; /* file version number in which the function type first appeared */
199 int ftype; /* function type */
203 * TODO The following three lines make little sense, please clarify if
204 * you've had to work out how ftupd works.
206 * The entries should be ordered in:
207 * 1. ascending function type number
208 * 2. ascending file version number
210 * Because we support reading of old .tpr file versions (even when
211 * mdrun can no longer run the simulation), we need to be able to read
212 * obsolete t_interaction_function types. Any data read from such
213 * fields is discarded. Their names have _NOLONGERUSED appended to
214 * them to make things clear.
216 * When adding to or making breaking changes to reading this struct,
217 * update TpxGeneration.
219 static const t_ftupd ftupd[] = {
220 { 70, F_RESTRBONDS },
221 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
222 { 76, F_LINEAR_ANGLES },
223 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
224 { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
226 { 60, F_GB12_NOLONGERUSED },
227 { 61, F_GB13_NOLONGERUSED },
228 { 61, F_GB14_NOLONGERUSED },
229 { 72, F_GBPOL_NOLONGERUSED },
230 { 72, F_NPSOLVATION_NOLONGERUSED },
232 { 76, F_ANHARM_POL },
234 { tpxv_VSite1, F_VSITE1 },
235 { tpxv_VSite2FD, F_VSITE2FD },
236 { tpxv_GenericInternalParameters, F_DENSITYFITTING },
237 { 69, F_VTEMP_NOLONGERUSED },
248 { 79, F_DVDL_RESTRAINT },
249 { 79, F_DVDL_TEMPERATURE },
251 #define NFTUPD asize(ftupd)
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)
307 serializer->doString(&pcrd->externalPotentialProvider);
311 pcrd->externalPotentialProvider.clear();
316 if (serializer->reading())
318 pcrd->externalPotentialProvider.clear();
321 /* Note that we try to support adding new geometries without
322 * changing the tpx version. This requires checks when printing the
323 * geometry string and a check and fatal_error in init_pull.
325 serializer->doEnumAsInt(&pcrd->eGeom);
326 serializer->doInt(&pcrd->ngroup);
327 if (pcrd->ngroup <= c_pullCoordNgroupMax)
329 serializer->doIntArray(pcrd->group.data(), pcrd->ngroup);
333 /* More groups in file than supported, this must be a new geometry
334 * that is not supported by our current code. Since we will not
335 * use the groups for this coord (checks in the pull and WHAM code
336 * ensure this), we can ignore the groups and set ngroup=0.
339 snew(dum, pcrd->ngroup);
340 serializer->doIntArray(dum, pcrd->ngroup);
345 serializer->doIvec(&pcrd->dim.as_vec());
346 if (file_version >= tpxv_TransformationPullCoord)
348 serializer->doString(&pcrd->expression);
352 if (serializer->reading())
354 pcrd->expression.clear();
361 serializer->doInt(&pcrd->group[0]);
362 serializer->doInt(&pcrd->group[1]);
363 if (file_version >= tpxv_PullCoordTypeGeom)
365 pcrd->ngroup = (pcrd->eGeom == PullGroupGeometry::DirectionRelative ? 4 : 2);
366 serializer->doEnumAsInt(&pcrd->eType);
367 serializer->doEnumAsInt(&pcrd->eGeom);
368 if (pcrd->ngroup == 4)
370 serializer->doInt(&pcrd->group[2]);
371 serializer->doInt(&pcrd->group[3]);
373 serializer->doIvec(&pcrd->dim.as_vec());
377 pcrd->eType = ePullOld;
378 pcrd->eGeom = eGeomOld;
379 copy_ivec(dimOld, pcrd->dim);
382 serializer->doRvec(&pcrd->origin.as_vec());
383 serializer->doRvec(&pcrd->vec.as_vec());
384 if (file_version >= tpxv_PullCoordTypeGeom)
386 serializer->doBool(&pcrd->bStart);
390 /* This parameter is only printed, but not actually used by mdrun */
391 pcrd->bStart = FALSE;
393 serializer->doReal(&pcrd->init);
394 serializer->doReal(&pcrd->rate);
395 serializer->doReal(&pcrd->k);
396 serializer->doReal(&pcrd->kB);
399 static void do_expandedvals(gmx::ISerializer* serializer, t_expanded* expand, t_lambda* fepvals, int file_version)
401 int n_lambda = fepvals->n_lambda;
403 /* reset the lambda calculation window */
404 fepvals->lambda_start_n = 0;
405 fepvals->lambda_stop_n = n_lambda;
406 if (file_version >= 79)
410 expand->init_lambda_weights.resize(n_lambda);
411 serializer->doRealArray(expand->init_lambda_weights.data(), n_lambda);
412 serializer->doBool(&expand->bInit_weights);
415 serializer->doInt(&expand->nstexpanded);
416 serializer->doEnumAsInt(&expand->elmcmove);
417 serializer->doEnumAsInt(&expand->elamstats);
418 serializer->doInt(&expand->lmc_repeats);
419 serializer->doInt(&expand->gibbsdeltalam);
420 serializer->doInt(&expand->lmc_forced_nstart);
421 serializer->doInt(&expand->lmc_seed);
422 serializer->doReal(&expand->mc_temp);
423 serializer->doBool(&expand->bSymmetrizedTMatrix);
424 serializer->doInt(&expand->nstTij);
425 serializer->doInt(&expand->minvarmin);
426 serializer->doInt(&expand->c_range);
427 serializer->doReal(&expand->wl_scale);
428 serializer->doReal(&expand->wl_ratio);
429 serializer->doReal(&expand->init_wl_delta);
430 serializer->doBool(&expand->bWLoneovert);
431 serializer->doEnumAsInt(&expand->elmceq);
432 serializer->doInt(&expand->equil_steps);
433 serializer->doInt(&expand->equil_samples);
434 serializer->doInt(&expand->equil_n_at_lam);
435 serializer->doReal(&expand->equil_wl_delta);
436 serializer->doReal(&expand->equil_ratio);
440 static void do_simtempvals(gmx::ISerializer* serializer, t_simtemp* simtemp, int n_lambda, int file_version)
442 if (file_version >= 79)
444 serializer->doEnumAsInt(&simtemp->eSimTempScale);
445 serializer->doReal(&simtemp->simtemp_high);
446 serializer->doReal(&simtemp->simtemp_low);
449 if (serializer->reading())
451 simtemp->temperatures.resize(n_lambda);
453 serializer->doRealArray(simtemp->temperatures.data(), n_lambda);
458 static void do_imd(gmx::ISerializer* serializer, t_IMD* imd)
460 serializer->doInt(&imd->nat);
461 if (serializer->reading())
463 snew(imd->ind, imd->nat);
465 serializer->doIntArray(imd->ind, imd->nat);
468 static void do_fepvals(gmx::ISerializer* serializer, t_lambda* fepvals, int file_version)
470 /* i is defined in the ndo_double macro; use g to iterate. */
473 /* free energy values */
475 if (file_version >= 79)
477 serializer->doInt(&fepvals->init_fep_state);
478 serializer->doDouble(&fepvals->init_lambda);
479 serializer->doDouble(&fepvals->delta_lambda);
481 else if (file_version >= 59)
483 serializer->doDouble(&fepvals->init_lambda);
484 serializer->doDouble(&fepvals->delta_lambda);
488 serializer->doReal(&rdum);
489 fepvals->init_lambda = rdum;
490 serializer->doReal(&rdum);
491 fepvals->delta_lambda = rdum;
493 if (file_version >= 79)
495 serializer->doInt(&fepvals->n_lambda);
496 for (auto g : keysOf(fepvals->all_lambda))
498 if (fepvals->n_lambda > 0)
500 fepvals->all_lambda[g].resize(fepvals->n_lambda);
501 serializer->doDoubleArray(fepvals->all_lambda[g].data(), fepvals->n_lambda);
502 serializer->doBoolArray(fepvals->separate_dvdl.begin(), fepvals->separate_dvdl.size());
504 else if (fepvals->init_lambda >= 0)
506 fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
510 else if (file_version >= 64)
512 serializer->doInt(&fepvals->n_lambda);
513 if (serializer->reading())
515 /* still allocate the all_lambda array's contents. */
516 for (auto g : keysOf(fepvals->all_lambda))
518 if (fepvals->n_lambda > 0)
520 fepvals->all_lambda[g].resize(fepvals->n_lambda);
524 serializer->doDoubleArray(fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Fep].data(),
526 if (fepvals->init_lambda >= 0)
528 fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
530 if (serializer->reading())
532 /* copy the contents of the efptFEP lambda component to all
533 the other components */
534 for (auto g : keysOf(fepvals->all_lambda))
536 for (int h = 0; h < fepvals->n_lambda; h++)
538 if (g != FreeEnergyPerturbationCouplingType::Fep)
540 fepvals->all_lambda[g][h] =
541 fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Fep][h];
550 fepvals->n_lambda = 0;
551 if (fepvals->init_lambda >= 0)
553 fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
556 serializer->doReal(&fepvals->sc_alpha);
557 serializer->doInt(&fepvals->sc_power);
558 if (file_version >= 79)
560 serializer->doReal(&fepvals->sc_r_power);
564 fepvals->sc_r_power = 6.0;
566 if (fepvals->sc_r_power != 6.0)
568 gmx_fatal(FARGS, "sc-r-power=48 is no longer supported");
570 serializer->doReal(&fepvals->sc_sigma);
571 if (serializer->reading())
573 if (file_version >= 71)
575 fepvals->sc_sigma_min = fepvals->sc_sigma;
579 fepvals->sc_sigma_min = 0;
582 if (file_version >= 79)
584 serializer->doBool(&fepvals->bScCoul);
588 fepvals->bScCoul = TRUE;
590 if (file_version >= 64)
592 serializer->doInt(&fepvals->nstdhdl);
596 fepvals->nstdhdl = 1;
599 if (file_version >= 73)
601 serializer->doEnumAsInt(&fepvals->separate_dhdl_file);
602 serializer->doEnumAsInt(&fepvals->dhdl_derivatives);
606 fepvals->separate_dhdl_file = SeparateDhdlFile::Yes;
607 fepvals->dhdl_derivatives = DhDlDerivativeCalculation::Yes;
609 if (file_version >= 71)
611 serializer->doInt(&fepvals->dh_hist_size);
612 serializer->doDouble(&fepvals->dh_hist_spacing);
616 fepvals->dh_hist_size = 0;
617 fepvals->dh_hist_spacing = 0.1;
619 if (file_version >= 79)
621 serializer->doEnumAsInt(&fepvals->edHdLPrintEnergy);
625 fepvals->edHdLPrintEnergy = FreeEnergyPrintEnergy::No;
627 if (file_version >= tpxv_SoftcoreGapsys)
629 serializer->doInt(reinterpret_cast<int*>(&fepvals->softcoreFunction));
630 serializer->doReal(&fepvals->scGapsysScaleLinpointLJ);
631 serializer->doReal(&fepvals->scGapsysScaleLinpointQ);
632 serializer->doReal(&fepvals->scGapsysSigmaLJ);
636 fepvals->softcoreFunction = SoftcoreType::Beutler;
637 fepvals->scGapsysScaleLinpointLJ = 0.85;
638 fepvals->scGapsysScaleLinpointQ = 0.3;
639 fepvals->scGapsysSigmaLJ = 0.3;
642 /* handle lambda_neighbors */
643 if ((file_version >= 83 && file_version < 90) || file_version >= 92)
645 serializer->doInt(&fepvals->lambda_neighbors);
646 if ((fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0)
647 && (fepvals->init_lambda < 0))
649 fepvals->lambda_start_n = (fepvals->init_fep_state - fepvals->lambda_neighbors);
650 fepvals->lambda_stop_n = (fepvals->init_fep_state + fepvals->lambda_neighbors + 1);
651 if (fepvals->lambda_start_n < 0)
653 fepvals->lambda_start_n = 0;
655 if (fepvals->lambda_stop_n >= fepvals->n_lambda)
657 fepvals->lambda_stop_n = fepvals->n_lambda;
662 fepvals->lambda_start_n = 0;
663 fepvals->lambda_stop_n = fepvals->n_lambda;
668 fepvals->lambda_start_n = 0;
669 fepvals->lambda_stop_n = fepvals->n_lambda;
673 static void do_pull(gmx::ISerializer* serializer, pull_params_t* pull, int file_version, PullingAlgorithm ePullOld)
675 PullGroupGeometry eGeomOld = PullGroupGeometry::Count;
679 if (file_version >= 95)
681 serializer->doInt(&pull->ngroup);
683 serializer->doInt(&pull->ncoord);
684 if (file_version < 95)
686 pull->ngroup = pull->ncoord + 1;
688 if (file_version < tpxv_PullCoordTypeGeom)
692 serializer->doEnumAsInt(&eGeomOld);
693 serializer->doIvec(&dimOld);
694 /* The inner cylinder radius, now removed */
695 serializer->doReal(&dum);
697 serializer->doReal(&pull->cylinder_r);
698 serializer->doReal(&pull->constr_tol);
699 if (file_version >= 95)
701 serializer->doBool(&pull->bPrintCOM);
702 /* With file_version < 95 this value is set below */
704 if (file_version >= tpxv_ReplacePullPrintCOM12)
706 serializer->doBool(&pull->bPrintRefValue);
707 serializer->doBool(&pull->bPrintComp);
709 else if (file_version >= tpxv_PullCoordTypeGeom)
712 serializer->doInt(&idum); /* used to be bPrintCOM2 */
713 serializer->doBool(&pull->bPrintRefValue);
714 serializer->doBool(&pull->bPrintComp);
718 pull->bPrintRefValue = FALSE;
719 pull->bPrintComp = TRUE;
721 serializer->doInt(&pull->nstxout);
722 serializer->doInt(&pull->nstfout);
723 if (file_version >= tpxv_PullPrevStepCOMAsReference)
725 serializer->doBool(&pull->bSetPbcRefToPrevStepCOM);
729 pull->bSetPbcRefToPrevStepCOM = FALSE;
731 pull->group.resize(pull->ngroup);
732 pull->coord.resize(pull->ncoord);
733 if (file_version < 95)
735 /* epullgPOS for position pulling, before epullgDIRPBC was removed */
736 if (eGeomOld == PullGroupGeometry::DirectionPBC)
738 gmx_fatal(FARGS, "pull-geometry=position is no longer supported");
740 if (eGeomOld > PullGroupGeometry::DirectionPBC)
744 case (PullGroupGeometry::DirectionRelative):
745 eGeomOld = PullGroupGeometry::DirectionPBC;
747 case (PullGroupGeometry::Angle):
748 eGeomOld = PullGroupGeometry::DirectionRelative;
750 case (PullGroupGeometry::Dihedral): eGeomOld = PullGroupGeometry::Angle; break;
751 case (PullGroupGeometry::AngleAxis): eGeomOld = PullGroupGeometry::Dihedral; break;
752 case (PullGroupGeometry::Count): eGeomOld = PullGroupGeometry::AngleAxis; break;
753 default: GMX_RELEASE_ASSERT(false, "Unhandled old pull type");
757 for (g = 0; g < pull->ngroup; g++)
759 /* We read and ignore a pull coordinate for group 0 */
760 do_pullgrp_tpx_pre95(serializer, &pull->group[g], &pull->coord[std::max(g - 1, 0)]);
763 pull->coord[g - 1].group[0] = 0;
764 pull->coord[g - 1].group[1] = g;
768 pull->bPrintCOM = (!pull->group[0].ind.empty());
772 for (g = 0; g < pull->ngroup; g++)
774 do_pull_group(serializer, &pull->group[g]);
776 for (g = 0; g < pull->ncoord; g++)
778 do_pull_coord(serializer, &pull->coord[g], file_version, ePullOld, eGeomOld, dimOld);
779 if (serializer->reading())
781 pull->coord[g].coordIndex = g;
785 if (file_version >= tpxv_PullAverage)
789 v = pull->bXOutAverage;
790 serializer->doBool(&v);
791 pull->bXOutAverage = v;
792 v = pull->bFOutAverage;
793 serializer->doBool(&v);
794 pull->bFOutAverage = v;
799 static void do_rotgrp(gmx::ISerializer* serializer, t_rotgrp* rotg)
801 serializer->doEnumAsInt(&rotg->eType);
802 if (serializer->reading())
805 serializer->doInt(&temp);
806 rotg->bMassW = static_cast<bool>(temp);
810 int temp = static_cast<int>(rotg->bMassW);
811 serializer->doInt(&temp);
813 serializer->doInt(&rotg->nat);
814 if (serializer->reading())
816 snew(rotg->ind, rotg->nat);
818 serializer->doIntArray(rotg->ind, rotg->nat);
819 if (serializer->reading())
821 snew(rotg->x_ref, rotg->nat);
823 serializer->doRvecArray(rotg->x_ref, rotg->nat);
824 serializer->doRvec(&rotg->inputVec);
825 serializer->doRvec(&rotg->pivot);
826 serializer->doReal(&rotg->rate);
827 serializer->doReal(&rotg->k);
828 serializer->doReal(&rotg->slab_dist);
829 serializer->doReal(&rotg->min_gaussian);
830 serializer->doReal(&rotg->eps);
831 serializer->doEnumAsInt(&rotg->eFittype);
832 serializer->doInt(&rotg->PotAngle_nstep);
833 serializer->doReal(&rotg->PotAngle_step);
836 static void do_rot(gmx::ISerializer* serializer, t_rot* rot)
840 serializer->doInt(&rot->ngrp);
841 serializer->doInt(&rot->nstrout);
842 serializer->doInt(&rot->nstsout);
843 if (serializer->reading())
845 snew(rot->grp, rot->ngrp);
847 for (g = 0; g < rot->ngrp; g++)
849 do_rotgrp(serializer, &rot->grp[g]);
854 static void do_swapgroup(gmx::ISerializer* serializer, t_swapGroup* g)
857 /* Name of the group or molecule */
859 if (serializer->reading())
861 serializer->doString(&buf);
862 g->molname = gmx_strdup(buf.c_str());
867 serializer->doString(&buf);
870 /* Number of atoms in the group */
871 serializer->doInt(&g->nat);
873 /* The group's atom indices */
874 if (serializer->reading())
876 snew(g->ind, g->nat);
878 serializer->doIntArray(g->ind, g->nat);
880 /* Requested counts for compartments A and B */
881 serializer->doIntArray(g->nmolReq.data(), static_cast<int>(Compartment::Count));
884 static void do_swapcoords_tpx(gmx::ISerializer* serializer, t_swapcoords* swap, int file_version)
886 /* Enums for better readability of the code */
899 if (file_version >= tpxv_CompElPolyatomicIonsAndMultipleIonTypes)
901 /* The total number of swap groups is the sum of the fixed groups
902 * (split0, split1, solvent), and the user-defined groups (2+ types of ions)
904 serializer->doInt(&swap->ngrp);
905 if (serializer->reading())
907 snew(swap->grp, swap->ngrp);
909 for (int ig = 0; ig < swap->ngrp; ig++)
911 do_swapgroup(serializer, &swap->grp[ig]);
913 serializer->doBool(&swap->massw_split[eChannel0]);
914 serializer->doBool(&swap->massw_split[eChannel1]);
915 serializer->doInt(&swap->nstswap);
916 serializer->doInt(&swap->nAverage);
917 serializer->doReal(&swap->threshold);
918 serializer->doReal(&swap->cyl0r);
919 serializer->doReal(&swap->cyl0u);
920 serializer->doReal(&swap->cyl0l);
921 serializer->doReal(&swap->cyl1r);
922 serializer->doReal(&swap->cyl1u);
923 serializer->doReal(&swap->cyl1l);
927 /*** Support reading older CompEl .tpr files ***/
929 /* In the original CompEl .tpr files, we always have 5 groups: */
931 snew(swap->grp, swap->ngrp);
933 swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname = gmx_strdup("split0"); // group 0: split0
934 swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname = gmx_strdup("split1"); // group 1: split1
935 swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname =
936 gmx_strdup("solvent"); // group 2: solvent
937 swap->grp[3].molname = gmx_strdup("anions"); // group 3: anions
938 swap->grp[4].molname = gmx_strdup("cations"); // group 4: cations
940 serializer->doInt(&swap->grp[3].nat);
941 serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].nat);
942 serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].nat);
943 serializer->doBool(&swap->massw_split[eChannel0]);
944 serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].nat);
945 serializer->doBool(&swap->massw_split[eChannel1]);
946 serializer->doInt(&swap->nstswap);
947 serializer->doInt(&swap->nAverage);
948 serializer->doReal(&swap->threshold);
949 serializer->doReal(&swap->cyl0r);
950 serializer->doReal(&swap->cyl0u);
951 serializer->doReal(&swap->cyl0l);
952 serializer->doReal(&swap->cyl1r);
953 serializer->doReal(&swap->cyl1u);
954 serializer->doReal(&swap->cyl1l);
956 // The order[] array keeps compatibility with older .tpr files
957 // by reading in the groups in the classic order
959 const int order[4] = { 3,
960 static_cast<int>(SwapGroupSplittingType::Solvent),
961 static_cast<int>(SwapGroupSplittingType::Split0),
962 static_cast<int>(SwapGroupSplittingType::Split1) };
964 for (int ig = 0; ig < 4; ig++)
967 snew(swap->grp[g].ind, swap->grp[g].nat);
968 serializer->doIntArray(swap->grp[g].ind, swap->grp[g].nat);
972 for (int j = eCompA; j <= eCompB; j++)
974 serializer->doInt(&swap->grp[3].nmolReq[j]); // group 3 = anions
975 serializer->doInt(&swap->grp[4].nmolReq[j]); // group 4 = cations
977 } /* End support reading older CompEl .tpr files */
979 if (file_version >= tpxv_CompElWithSwapLayerOffset)
981 serializer->doReal(&swap->bulkOffset[eCompA]);
982 serializer->doReal(&swap->bulkOffset[eCompB]);
986 static void do_legacy_efield(gmx::ISerializer* serializer, gmx::KeyValueTreeObjectBuilder* root)
988 const char* const dimName[] = { "x", "y", "z" };
990 auto appliedForcesObj = root->addObject("applied-forces");
991 auto efieldObj = appliedForcesObj.addObject("electric-field");
992 // The content of the tpr file for this feature has
993 // been the same since gromacs 4.0 that was used for
995 for (int j = 0; j < DIM; ++j)
998 serializer->doInt(&n);
999 serializer->doInt(&nt);
1000 std::vector<real> aa(n + 1), phi(nt + 1), at(nt + 1), phit(nt + 1);
1001 serializer->doRealArray(aa.data(), n);
1002 serializer->doRealArray(phi.data(), n);
1003 serializer->doRealArray(at.data(), nt);
1004 serializer->doRealArray(phit.data(), nt);
1007 if (n > 1 || nt > 1)
1010 "Can not handle tpr files with more than one electric field term per "
1013 auto dimObj = efieldObj.addObject(dimName[j]);
1014 dimObj.addValue<real>("E0", aa[0]);
1015 dimObj.addValue<real>("omega", at[0]);
1016 dimObj.addValue<real>("t0", phi[0]);
1017 dimObj.addValue<real>("sigma", phit[0]);
1023 static void do_inputrec(gmx::ISerializer* serializer, t_inputrec* ir, int file_version)
1025 int i, j, k, idum = 0;
1027 gmx_bool bdum = false;
1029 if (file_version != tpx_version)
1031 /* Give a warning about features that are not accessible */
1032 fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n", file_version, tpx_version);
1035 if (file_version == 0)
1040 gmx::KeyValueTreeBuilder paramsBuilder;
1041 gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
1043 /* Basic inputrec stuff */
1044 serializer->doEnumAsInt(&ir->eI);
1045 if (file_version >= 62)
1047 serializer->doInt64(&ir->nsteps);
1051 serializer->doInt(&idum);
1055 if (file_version >= 62)
1057 serializer->doInt64(&ir->init_step);
1061 serializer->doInt(&idum);
1062 ir->init_step = idum;
1065 serializer->doInt(&ir->simulation_part);
1067 if (file_version >= tpxv_MTS)
1069 serializer->doBool(&ir->useMts);
1070 int numLevels = ir->mtsLevels.size();
1073 serializer->doInt(&numLevels);
1075 ir->mtsLevels.resize(numLevels);
1076 for (auto& mtsLevel : ir->mtsLevels)
1078 int forceGroups = mtsLevel.forceGroups.to_ulong();
1079 serializer->doInt(&forceGroups);
1080 mtsLevel.forceGroups = std::bitset<static_cast<int>(gmx::MtsForceGroups::Count)>(forceGroups);
1081 serializer->doInt(&mtsLevel.stepFactor);
1087 ir->mtsLevels.clear();
1090 if (file_version >= 67)
1092 serializer->doInt(&ir->nstcalcenergy);
1096 ir->nstcalcenergy = 1;
1098 if (file_version >= 81)
1100 serializer->doEnumAsInt(&ir->cutoff_scheme);
1101 if (file_version < 94)
1103 // Need to invert the scheme order
1104 switch (ir->cutoff_scheme)
1106 case (CutoffScheme::Group): ir->cutoff_scheme = CutoffScheme::Verlet; break;
1107 case (CutoffScheme::Verlet): ir->cutoff_scheme = CutoffScheme::Group; break;
1108 default: GMX_RELEASE_ASSERT(false, "Unhandled cutoff scheme type");
1114 ir->cutoff_scheme = CutoffScheme::Group;
1116 serializer->doInt(&idum); /* used to be ns_type; not used anymore */
1117 serializer->doInt(&ir->nstlist);
1118 serializer->doInt(&idum); /* used to be ndelta; not used anymore */
1120 serializer->doReal(&ir->rtpi);
1122 serializer->doInt(&ir->nstcomm);
1123 serializer->doEnumAsInt(&ir->comm_mode);
1125 /* ignore nstcheckpoint */
1126 if (file_version < tpxv_RemoveObsoleteParameters1)
1128 serializer->doInt(&idum);
1131 serializer->doInt(&ir->nstcgsteep);
1133 serializer->doInt(&ir->nbfgscorr);
1135 serializer->doInt(&ir->nstlog);
1136 serializer->doInt(&ir->nstxout);
1137 serializer->doInt(&ir->nstvout);
1138 serializer->doInt(&ir->nstfout);
1139 serializer->doInt(&ir->nstenergy);
1140 serializer->doInt(&ir->nstxout_compressed);
1141 if (file_version >= 59)
1143 serializer->doDouble(&ir->init_t);
1144 serializer->doDouble(&ir->delta_t);
1148 serializer->doReal(&rdum);
1150 serializer->doReal(&rdum);
1153 serializer->doReal(&ir->x_compression_precision);
1154 if (file_version >= 81)
1156 serializer->doReal(&ir->verletbuf_tol);
1160 ir->verletbuf_tol = 0;
1162 serializer->doReal(&ir->rlist);
1163 if (file_version >= 67 && file_version < tpxv_RemoveTwinRange)
1165 if (serializer->reading())
1167 // Reading such a file version could invoke the twin-range
1168 // scheme, about which mdrun should give a fatal error.
1169 real dummy_rlistlong = -1;
1170 serializer->doReal(&dummy_rlistlong);
1172 ir->useTwinRange = (ir->rlist > 0 && (dummy_rlistlong == 0 || dummy_rlistlong > ir->rlist));
1173 // When true, this forces mdrun to issue an error (regardless of
1174 // ir->cutoff_scheme).
1176 // Otherwise, grompp used to set rlistlong actively. Users
1177 // were probably also confused and set rlistlong == rlist.
1178 // However, in all remaining cases, it is safe to let
1179 // mdrun proceed normally.
1184 // No need to read or write anything
1185 ir->useTwinRange = false;
1187 if (file_version >= 82 && file_version != 90)
1189 // Multiple time-stepping is no longer enabled, but the old
1190 // support required the twin-range scheme, for which mdrun
1191 // already emits a fatal error.
1192 int dummy_nstcalclr = -1;
1193 serializer->doInt(&dummy_nstcalclr);
1195 serializer->doEnumAsInt(&ir->coulombtype);
1196 if (file_version >= 81)
1198 serializer->doEnumAsInt(&ir->coulomb_modifier);
1202 ir->coulomb_modifier = (ir->cutoff_scheme == CutoffScheme::Verlet ? InteractionModifiers::PotShift
1203 : InteractionModifiers::None);
1205 serializer->doReal(&ir->rcoulomb_switch);
1206 serializer->doReal(&ir->rcoulomb);
1207 serializer->doEnumAsInt(&ir->vdwtype);
1208 if (file_version >= 81)
1210 serializer->doEnumAsInt(&ir->vdw_modifier);
1214 ir->vdw_modifier = (ir->cutoff_scheme == CutoffScheme::Verlet ? InteractionModifiers::PotShift
1215 : InteractionModifiers::None);
1217 serializer->doReal(&ir->rvdw_switch);
1218 serializer->doReal(&ir->rvdw);
1219 serializer->doEnumAsInt(&ir->eDispCorr);
1220 serializer->doReal(&ir->epsilon_r);
1221 serializer->doReal(&ir->epsilon_rf);
1222 serializer->doReal(&ir->tabext);
1224 // This permits reading a .tpr file that used implicit solvent,
1225 // and later permitting mdrun to refuse to run it.
1226 if (serializer->reading())
1228 if (file_version < tpxv_RemoveImplicitSolvation)
1230 serializer->doInt(&idum);
1231 serializer->doInt(&idum);
1232 serializer->doReal(&rdum);
1233 serializer->doReal(&rdum);
1234 serializer->doInt(&idum);
1235 ir->implicit_solvent = (idum > 0);
1239 ir->implicit_solvent = false;
1241 if (file_version < tpxv_RemoveImplicitSolvation)
1243 serializer->doReal(&rdum);
1244 serializer->doReal(&rdum);
1245 serializer->doReal(&rdum);
1246 serializer->doReal(&rdum);
1247 if (file_version >= 60)
1249 serializer->doReal(&rdum);
1250 serializer->doInt(&idum);
1252 serializer->doReal(&rdum);
1256 if (file_version >= 81)
1258 serializer->doReal(&ir->fourier_spacing);
1262 ir->fourier_spacing = 0.0;
1264 serializer->doInt(&ir->nkx);
1265 serializer->doInt(&ir->nky);
1266 serializer->doInt(&ir->nkz);
1267 serializer->doInt(&ir->pme_order);
1268 serializer->doReal(&ir->ewald_rtol);
1270 if (file_version >= 93)
1272 serializer->doReal(&ir->ewald_rtol_lj);
1276 ir->ewald_rtol_lj = ir->ewald_rtol;
1278 serializer->doEnumAsInt(&ir->ewald_geometry);
1279 serializer->doReal(&ir->epsilon_surface);
1281 /* ignore bOptFFT */
1282 if (file_version < tpxv_RemoveObsoleteParameters1)
1284 serializer->doBool(&bdum);
1287 if (file_version >= 93)
1289 serializer->doEnumAsInt(&ir->ljpme_combination_rule);
1291 serializer->doBool(&ir->bContinuation);
1292 serializer->doEnumAsInt(&ir->etc);
1293 /* before version 18, ir->etc was a gmx_bool (ir->btc),
1294 * but the values 0 and 1 still mean no and
1295 * berendsen temperature coupling, respectively.
1297 if (file_version >= 79)
1299 serializer->doBool(&ir->bPrintNHChains);
1301 if (file_version >= 71)
1303 serializer->doInt(&ir->nsttcouple);
1307 ir->nsttcouple = ir->nstcalcenergy;
1309 serializer->doEnumAsInt(&ir->epc);
1310 serializer->doEnumAsInt(&ir->epct);
1311 if (file_version >= 71)
1313 serializer->doInt(&ir->nstpcouple);
1317 ir->nstpcouple = ir->nstcalcenergy;
1319 serializer->doReal(&ir->tau_p);
1320 serializer->doRvec(&ir->ref_p[XX]);
1321 serializer->doRvec(&ir->ref_p[YY]);
1322 serializer->doRvec(&ir->ref_p[ZZ]);
1323 serializer->doRvec(&ir->compress[XX]);
1324 serializer->doRvec(&ir->compress[YY]);
1325 serializer->doRvec(&ir->compress[ZZ]);
1326 serializer->doEnumAsInt(&ir->refcoord_scaling);
1327 serializer->doRvec(&ir->posres_com);
1328 serializer->doRvec(&ir->posres_comB);
1330 if (file_version < 79)
1332 serializer->doInt(&ir->andersen_seed);
1336 ir->andersen_seed = 0;
1339 serializer->doReal(&ir->shake_tol);
1341 serializer->doEnumAsInt(&ir->efep);
1342 if (serializer->reading())
1344 ir->fepvals = std::make_unique<t_lambda>();
1346 do_fepvals(serializer, ir->fepvals.get(), file_version);
1348 if (file_version >= 79)
1350 serializer->doBool(&ir->bSimTemp);
1353 ir->bSimTemp = TRUE;
1358 ir->bSimTemp = FALSE;
1362 if (serializer->reading())
1364 ir->simtempvals = std::make_unique<t_simtemp>();
1366 do_simtempvals(serializer, ir->simtempvals.get(), ir->fepvals->n_lambda, file_version);
1369 if (file_version >= 79)
1371 serializer->doBool(&ir->bExpanded);
1375 if (serializer->reading())
1377 ir->expandedvals = std::make_unique<t_expanded>();
1379 do_expandedvals(serializer, ir->expandedvals.get(), ir->fepvals.get(), file_version);
1382 serializer->doEnumAsInt(&ir->eDisre);
1383 serializer->doEnumAsInt(&ir->eDisreWeighting);
1384 serializer->doBool(&ir->bDisreMixed);
1385 serializer->doReal(&ir->dr_fc);
1386 serializer->doReal(&ir->dr_tau);
1387 serializer->doInt(&ir->nstdisreout);
1388 serializer->doReal(&ir->orires_fc);
1389 serializer->doReal(&ir->orires_tau);
1390 serializer->doInt(&ir->nstorireout);
1392 /* ignore dihre_fc */
1393 if (file_version < 79)
1395 serializer->doReal(&rdum);
1398 serializer->doReal(&ir->em_stepsize);
1399 serializer->doReal(&ir->em_tol);
1400 serializer->doBool(&ir->bShakeSOR);
1401 serializer->doInt(&ir->niter);
1402 serializer->doReal(&ir->fc_stepsize);
1403 serializer->doEnumAsInt(&ir->eConstrAlg);
1404 serializer->doInt(&ir->nProjOrder);
1405 serializer->doReal(&ir->LincsWarnAngle);
1406 serializer->doInt(&ir->nLincsIter);
1407 serializer->doReal(&ir->bd_fric);
1408 if (file_version >= tpxv_Use64BitRandomSeed)
1410 serializer->doInt64(&ir->ld_seed);
1414 serializer->doInt(&idum);
1418 for (i = 0; i < DIM; i++)
1420 serializer->doRvec(&ir->deform[i]);
1422 serializer->doReal(&ir->cos_accel);
1424 serializer->doInt(&ir->userint1);
1425 serializer->doInt(&ir->userint2);
1426 serializer->doInt(&ir->userint3);
1427 serializer->doInt(&ir->userint4);
1428 serializer->doReal(&ir->userreal1);
1429 serializer->doReal(&ir->userreal2);
1430 serializer->doReal(&ir->userreal3);
1431 serializer->doReal(&ir->userreal4);
1433 /* AdResS is removed, but we need to be able to read old files,
1434 and let mdrun refuse to run them */
1435 if (file_version >= 77 && file_version < tpxv_RemoveAdress)
1437 serializer->doBool(&ir->bAdress);
1440 int idum, numThermoForceGroups, numEnergyGroups;
1443 serializer->doInt(&idum);
1444 serializer->doReal(&rdum);
1445 serializer->doReal(&rdum);
1446 serializer->doReal(&rdum);
1447 serializer->doInt(&idum);
1448 serializer->doInt(&idum);
1449 serializer->doRvec(&rvecdum);
1450 serializer->doInt(&numThermoForceGroups);
1451 serializer->doReal(&rdum);
1452 serializer->doInt(&numEnergyGroups);
1453 serializer->doInt(&idum);
1455 if (numThermoForceGroups > 0)
1457 std::vector<int> idumn(numThermoForceGroups);
1458 serializer->doIntArray(idumn.data(), idumn.size());
1460 if (numEnergyGroups > 0)
1462 std::vector<int> idumn(numEnergyGroups);
1463 serializer->doIntArray(idumn.data(), idumn.size());
1469 ir->bAdress = FALSE;
1474 PullingAlgorithm ePullOld = PullingAlgorithm::Umbrella;
1476 if (file_version >= tpxv_PullCoordTypeGeom)
1478 serializer->doBool(&ir->bPull);
1482 serializer->doEnumAsInt(&ePullOld);
1483 ir->bPull = (ePullOld != PullingAlgorithm::Umbrella);
1484 /* We removed the first ePull=ePullNo for the enum */
1487 case (PullingAlgorithm::Umbrella): break; // this is equal to not using pulling
1488 case (PullingAlgorithm::Constraint): ePullOld = PullingAlgorithm::Umbrella; break;
1489 case (PullingAlgorithm::ConstantForce):
1490 ePullOld = PullingAlgorithm::Constraint;
1492 case (PullingAlgorithm::FlatBottom):
1493 ePullOld = PullingAlgorithm::ConstantForce;
1495 case (PullingAlgorithm::FlatBottomHigh):
1496 ePullOld = PullingAlgorithm::FlatBottom;
1498 case (PullingAlgorithm::External):
1499 ePullOld = PullingAlgorithm::FlatBottomHigh;
1501 case (PullingAlgorithm::Count): ePullOld = PullingAlgorithm::External; break;
1502 default: GMX_RELEASE_ASSERT(false, "Unhandled old pull algorithm");
1507 if (serializer->reading())
1509 ir->pull = std::make_unique<pull_params_t>();
1511 do_pull(serializer, ir->pull.get(), file_version, ePullOld);
1515 if (file_version >= tpxv_AcceleratedWeightHistogram)
1517 serializer->doBool(&ir->bDoAwh);
1521 if (serializer->reading())
1523 ir->awhParams = std::make_unique<gmx::AwhParams>(serializer);
1527 ir->awhParams->serialize(serializer);
1536 /* Enforced rotation */
1537 if (file_version >= 74)
1539 serializer->doBool(&ir->bRot);
1542 if (serializer->reading())
1546 do_rot(serializer, ir->rot);
1554 /* Interactive molecular dynamics */
1555 if (file_version >= tpxv_InteractiveMolecularDynamics)
1557 serializer->doBool(&ir->bIMD);
1560 if (serializer->reading())
1564 do_imd(serializer, ir->imd);
1569 /* We don't support IMD sessions for old .tpr files */
1574 serializer->doInt(&ir->opts.ngtc);
1575 if (file_version >= 69)
1577 serializer->doInt(&ir->opts.nhchainlength);
1581 ir->opts.nhchainlength = 1;
1583 if (serializer->reading() && file_version >= tpxv_RemovedConstantAcceleration
1584 && file_version < tpxv_ReaddedConstantAcceleration)
1590 serializer->doInt(&ir->opts.ngacc);
1592 serializer->doInt(&ir->opts.ngfrz);
1593 serializer->doInt(&ir->opts.ngener);
1595 if (serializer->reading())
1597 snew(ir->opts.nrdf, ir->opts.ngtc);
1598 snew(ir->opts.ref_t, ir->opts.ngtc);
1599 snew(ir->opts.annealing, ir->opts.ngtc);
1600 snew(ir->opts.anneal_npoints, ir->opts.ngtc);
1601 snew(ir->opts.anneal_time, ir->opts.ngtc);
1602 snew(ir->opts.anneal_temp, ir->opts.ngtc);
1603 snew(ir->opts.tau_t, ir->opts.ngtc);
1604 snew(ir->opts.nFreeze, ir->opts.ngfrz);
1605 snew(ir->opts.acceleration, ir->opts.ngacc);
1606 snew(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
1608 if (ir->opts.ngtc > 0)
1610 serializer->doRealArray(ir->opts.nrdf, ir->opts.ngtc);
1611 serializer->doRealArray(ir->opts.ref_t, ir->opts.ngtc);
1612 serializer->doRealArray(ir->opts.tau_t, ir->opts.ngtc);
1614 if (ir->opts.ngfrz > 0)
1616 serializer->doIvecArray(ir->opts.nFreeze, ir->opts.ngfrz);
1618 if (ir->opts.ngacc > 0)
1620 serializer->doRvecArray(ir->opts.acceleration, ir->opts.ngacc);
1622 if (serializer->reading())
1624 ir->useConstantAcceleration = false;
1625 for (int g = 0; g < ir->opts.ngacc; g++)
1627 if (norm2(ir->opts.acceleration[g]) != 0)
1629 ir->useConstantAcceleration = true;
1633 serializer->doIntArray(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
1635 /* First read the lists with annealing and npoints for each group */
1636 serializer->doEnumArrayAsInt(ir->opts.annealing, ir->opts.ngtc);
1637 serializer->doIntArray(ir->opts.anneal_npoints, ir->opts.ngtc);
1638 for (j = 0; j < (ir->opts.ngtc); j++)
1640 k = ir->opts.anneal_npoints[j];
1641 if (serializer->reading())
1643 snew(ir->opts.anneal_time[j], k);
1644 snew(ir->opts.anneal_temp[j], k);
1646 serializer->doRealArray(ir->opts.anneal_time[j], k);
1647 serializer->doRealArray(ir->opts.anneal_temp[j], k);
1651 serializer->doInt(&ir->nwall);
1652 serializer->doEnumAsInt(&ir->wall_type);
1653 serializer->doReal(&ir->wall_r_linpot);
1654 serializer->doInt(&ir->wall_atomtype[0]);
1655 serializer->doInt(&ir->wall_atomtype[1]);
1656 serializer->doReal(&ir->wall_density[0]);
1657 serializer->doReal(&ir->wall_density[1]);
1658 serializer->doReal(&ir->wall_ewald_zfac);
1661 /* Cosine stuff for electric fields */
1662 if (file_version < tpxv_GenericParamsForElectricField)
1664 do_legacy_efield(serializer, ¶msObj);
1668 if (file_version >= tpxv_ComputationalElectrophysiology)
1670 serializer->doEnumAsInt(&ir->eSwapCoords);
1671 if (ir->eSwapCoords != SwapType::No)
1673 if (serializer->reading())
1677 do_swapcoords_tpx(serializer, ir->swap, file_version);
1681 /* QMMM reading - despite defunct we require reading for backwards
1682 * compability and correct serialization
1685 serializer->doBool(&ir->bQMMM);
1687 serializer->doInt(&qmmmScheme);
1688 real unusedScalefactor;
1689 serializer->doReal(&unusedScalefactor);
1691 // this is still used in Mimic
1692 serializer->doInt(&ir->opts.ngQM);
1693 if (ir->opts.ngQM > 0 && ir->bQMMM)
1695 /* We leave in dummy i/o for removed parameters to avoid
1696 * changing the tpr format.
1698 std::vector<int> dummyIntVec(4 * ir->opts.ngQM, 0);
1699 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1700 dummyIntVec.clear();
1702 // std::vector<bool> has no data()
1703 std::vector<char> dummyBoolVec(ir->opts.ngQM * sizeof(bool) / sizeof(char));
1704 serializer->doBoolArray(reinterpret_cast<bool*>(dummyBoolVec.data()), dummyBoolVec.size());
1705 dummyBoolVec.clear();
1707 dummyIntVec.resize(2 * ir->opts.ngQM, 0);
1708 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1709 dummyIntVec.clear();
1711 std::vector<real> dummyRealVec(2 * ir->opts.ngQM, 0);
1712 serializer->doRealArray(dummyRealVec.data(), dummyRealVec.size());
1713 dummyRealVec.clear();
1715 dummyIntVec.resize(3 * ir->opts.ngQM, 0);
1716 serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
1717 dummyIntVec.clear();
1719 /* end of QMMM stuff */
1722 if (file_version >= tpxv_GenericParamsForElectricField)
1724 if (serializer->reading())
1726 paramsObj.mergeObject(gmx::deserializeKeyValueTree(serializer));
1730 GMX_RELEASE_ASSERT(ir->params != nullptr,
1731 "Parameters should be present when writing inputrec");
1732 gmx::serializeKeyValueTree(*ir->params, serializer);
1735 if (serializer->reading())
1737 ir->params = new gmx::KeyValueTreeObject(paramsBuilder.build());
1738 // Initialize internal parameters to an empty kvt for all tpr versions
1739 ir->internalParameters = std::make_unique<gmx::KeyValueTreeObject>();
1742 if (file_version >= tpxv_GenericInternalParameters)
1744 if (serializer->reading())
1746 ir->internalParameters =
1747 std::make_unique<gmx::KeyValueTreeObject>(gmx::deserializeKeyValueTree(serializer));
1751 GMX_RELEASE_ASSERT(ir->internalParameters != nullptr,
1752 "Parameters should be present when writing inputrec");
1753 gmx::serializeKeyValueTree(*ir->internalParameters, serializer);
1759 static void do_harm(gmx::ISerializer* serializer, t_iparams* iparams)
1761 serializer->doReal(&iparams->harmonic.rA);
1762 serializer->doReal(&iparams->harmonic.krA);
1763 serializer->doReal(&iparams->harmonic.rB);
1764 serializer->doReal(&iparams->harmonic.krB);
1767 static void do_iparams(gmx::ISerializer* serializer, t_functype ftype, t_iparams* iparams, int file_version)
1780 do_harm(serializer, iparams);
1781 if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && serializer->reading())
1783 /* Correct incorrect storage of parameters */
1784 iparams->pdihs.phiB = iparams->pdihs.phiA;
1785 iparams->pdihs.cpB = iparams->pdihs.cpA;
1789 serializer->doReal(&iparams->harmonic.rA);
1790 serializer->doReal(&iparams->harmonic.krA);
1792 case F_LINEAR_ANGLES:
1793 serializer->doReal(&iparams->linangle.klinA);
1794 serializer->doReal(&iparams->linangle.aA);
1795 serializer->doReal(&iparams->linangle.klinB);
1796 serializer->doReal(&iparams->linangle.aB);
1799 serializer->doReal(&iparams->fene.bm);
1800 serializer->doReal(&iparams->fene.kb);
1804 serializer->doReal(&iparams->restraint.lowA);
1805 serializer->doReal(&iparams->restraint.up1A);
1806 serializer->doReal(&iparams->restraint.up2A);
1807 serializer->doReal(&iparams->restraint.kA);
1808 serializer->doReal(&iparams->restraint.lowB);
1809 serializer->doReal(&iparams->restraint.up1B);
1810 serializer->doReal(&iparams->restraint.up2B);
1811 serializer->doReal(&iparams->restraint.kB);
1817 serializer->doReal(&iparams->tab.kA);
1818 serializer->doInt(&iparams->tab.table);
1819 serializer->doReal(&iparams->tab.kB);
1821 case F_CROSS_BOND_BONDS:
1822 serializer->doReal(&iparams->cross_bb.r1e);
1823 serializer->doReal(&iparams->cross_bb.r2e);
1824 serializer->doReal(&iparams->cross_bb.krr);
1826 case F_CROSS_BOND_ANGLES:
1827 serializer->doReal(&iparams->cross_ba.r1e);
1828 serializer->doReal(&iparams->cross_ba.r2e);
1829 serializer->doReal(&iparams->cross_ba.r3e);
1830 serializer->doReal(&iparams->cross_ba.krt);
1832 case F_UREY_BRADLEY:
1833 serializer->doReal(&iparams->u_b.thetaA);
1834 serializer->doReal(&iparams->u_b.kthetaA);
1835 serializer->doReal(&iparams->u_b.r13A);
1836 serializer->doReal(&iparams->u_b.kUBA);
1837 if (file_version >= 79)
1839 serializer->doReal(&iparams->u_b.thetaB);
1840 serializer->doReal(&iparams->u_b.kthetaB);
1841 serializer->doReal(&iparams->u_b.r13B);
1842 serializer->doReal(&iparams->u_b.kUBB);
1846 iparams->u_b.thetaB = iparams->u_b.thetaA;
1847 iparams->u_b.kthetaB = iparams->u_b.kthetaA;
1848 iparams->u_b.r13B = iparams->u_b.r13A;
1849 iparams->u_b.kUBB = iparams->u_b.kUBA;
1852 case F_QUARTIC_ANGLES:
1853 serializer->doReal(&iparams->qangle.theta);
1854 serializer->doRealArray(iparams->qangle.c, 5);
1857 serializer->doReal(&iparams->bham.a);
1858 serializer->doReal(&iparams->bham.b);
1859 serializer->doReal(&iparams->bham.c);
1862 serializer->doReal(&iparams->morse.b0A);
1863 serializer->doReal(&iparams->morse.cbA);
1864 serializer->doReal(&iparams->morse.betaA);
1865 if (file_version >= 79)
1867 serializer->doReal(&iparams->morse.b0B);
1868 serializer->doReal(&iparams->morse.cbB);
1869 serializer->doReal(&iparams->morse.betaB);
1873 iparams->morse.b0B = iparams->morse.b0A;
1874 iparams->morse.cbB = iparams->morse.cbA;
1875 iparams->morse.betaB = iparams->morse.betaA;
1879 serializer->doReal(&iparams->cubic.b0);
1880 serializer->doReal(&iparams->cubic.kb);
1881 serializer->doReal(&iparams->cubic.kcub);
1883 case F_CONNBONDS: break;
1884 case F_POLARIZATION: serializer->doReal(&iparams->polarize.alpha); break;
1886 serializer->doReal(&iparams->anharm_polarize.alpha);
1887 serializer->doReal(&iparams->anharm_polarize.drcut);
1888 serializer->doReal(&iparams->anharm_polarize.khyp);
1891 serializer->doReal(&iparams->wpol.al_x);
1892 serializer->doReal(&iparams->wpol.al_y);
1893 serializer->doReal(&iparams->wpol.al_z);
1894 serializer->doReal(&iparams->wpol.rOH);
1895 serializer->doReal(&iparams->wpol.rHH);
1896 serializer->doReal(&iparams->wpol.rOD);
1899 serializer->doReal(&iparams->thole.a);
1900 serializer->doReal(&iparams->thole.alpha1);
1901 serializer->doReal(&iparams->thole.alpha2);
1902 serializer->doReal(&iparams->thole.rfac);
1905 serializer->doReal(&iparams->lj.c6);
1906 serializer->doReal(&iparams->lj.c12);
1909 serializer->doReal(&iparams->lj14.c6A);
1910 serializer->doReal(&iparams->lj14.c12A);
1911 serializer->doReal(&iparams->lj14.c6B);
1912 serializer->doReal(&iparams->lj14.c12B);
1915 serializer->doReal(&iparams->ljc14.fqq);
1916 serializer->doReal(&iparams->ljc14.qi);
1917 serializer->doReal(&iparams->ljc14.qj);
1918 serializer->doReal(&iparams->ljc14.c6);
1919 serializer->doReal(&iparams->ljc14.c12);
1921 case F_LJC_PAIRS_NB:
1922 serializer->doReal(&iparams->ljcnb.qi);
1923 serializer->doReal(&iparams->ljcnb.qj);
1924 serializer->doReal(&iparams->ljcnb.c6);
1925 serializer->doReal(&iparams->ljcnb.c12);
1931 serializer->doReal(&iparams->pdihs.phiA);
1932 serializer->doReal(&iparams->pdihs.cpA);
1933 serializer->doReal(&iparams->pdihs.phiB);
1934 serializer->doReal(&iparams->pdihs.cpB);
1935 serializer->doInt(&iparams->pdihs.mult);
1938 serializer->doReal(&iparams->pdihs.phiA);
1939 serializer->doReal(&iparams->pdihs.cpA);
1942 serializer->doInt(&iparams->disres.label);
1943 serializer->doInt(&iparams->disres.type);
1944 serializer->doReal(&iparams->disres.low);
1945 serializer->doReal(&iparams->disres.up1);
1946 serializer->doReal(&iparams->disres.up2);
1947 serializer->doReal(&iparams->disres.kfac);
1950 serializer->doInt(&iparams->orires.ex);
1951 serializer->doInt(&iparams->orires.label);
1952 serializer->doInt(&iparams->orires.power);
1953 serializer->doReal(&iparams->orires.c);
1954 serializer->doReal(&iparams->orires.obs);
1955 serializer->doReal(&iparams->orires.kfac);
1958 if (file_version < 82)
1960 serializer->doInt(&idum);
1961 serializer->doInt(&idum);
1963 serializer->doReal(&iparams->dihres.phiA);
1964 serializer->doReal(&iparams->dihres.dphiA);
1965 serializer->doReal(&iparams->dihres.kfacA);
1966 if (file_version >= 82)
1968 serializer->doReal(&iparams->dihres.phiB);
1969 serializer->doReal(&iparams->dihres.dphiB);
1970 serializer->doReal(&iparams->dihres.kfacB);
1974 iparams->dihres.phiB = iparams->dihres.phiA;
1975 iparams->dihres.dphiB = iparams->dihres.dphiA;
1976 iparams->dihres.kfacB = iparams->dihres.kfacA;
1980 serializer->doRvec(&iparams->posres.pos0A);
1981 serializer->doRvec(&iparams->posres.fcA);
1982 serializer->doRvec(&iparams->posres.pos0B);
1983 serializer->doRvec(&iparams->posres.fcB);
1986 serializer->doInt(&iparams->fbposres.geom);
1987 serializer->doRvec(&iparams->fbposres.pos0);
1988 serializer->doReal(&iparams->fbposres.r);
1989 serializer->doReal(&iparams->fbposres.k);
1991 case F_CBTDIHS: serializer->doRealArray(iparams->cbtdihs.cbtcA, NR_CBTDIHS); break;
1993 // Fall-through intended
1995 /* Fourier dihedrals are internally represented
1996 * as Ryckaert-Bellemans since those are faster to compute.
1998 serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
1999 serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
2003 serializer->doReal(&iparams->constr.dA);
2004 serializer->doReal(&iparams->constr.dB);
2007 serializer->doReal(&iparams->settle.doh);
2008 serializer->doReal(&iparams->settle.dhh);
2010 case F_VSITE1: break; // VSite1 has 0 parameters
2012 case F_VSITE2FD: serializer->doReal(&iparams->vsite.a); break;
2016 serializer->doReal(&iparams->vsite.a);
2017 serializer->doReal(&iparams->vsite.b);
2022 serializer->doReal(&iparams->vsite.a);
2023 serializer->doReal(&iparams->vsite.b);
2024 serializer->doReal(&iparams->vsite.c);
2027 serializer->doInt(&iparams->vsiten.n);
2028 serializer->doReal(&iparams->vsiten.a);
2030 case F_GB12_NOLONGERUSED:
2031 case F_GB13_NOLONGERUSED:
2032 case F_GB14_NOLONGERUSED:
2033 // Implicit solvent parameters can still be read, but never used
2034 if (serializer->reading())
2036 if (file_version < 68)
2038 serializer->doReal(&rdum);
2039 serializer->doReal(&rdum);
2040 serializer->doReal(&rdum);
2041 serializer->doReal(&rdum);
2043 if (file_version < tpxv_RemoveImplicitSolvation)
2045 serializer->doReal(&rdum);
2046 serializer->doReal(&rdum);
2047 serializer->doReal(&rdum);
2048 serializer->doReal(&rdum);
2049 serializer->doReal(&rdum);
2054 serializer->doInt(&iparams->cmap.cmapA);
2055 serializer->doInt(&iparams->cmap.cmapB);
2059 "unknown function type %d (%s) in %s line %d",
2061 interaction_function[ftype].name,
2067 static void do_ilist(gmx::ISerializer* serializer, InteractionList* ilist)
2069 int nr = ilist->size();
2070 serializer->doInt(&nr);
2071 if (serializer->reading())
2073 ilist->iatoms.resize(nr);
2075 serializer->doIntArray(ilist->iatoms.data(), ilist->size());
2078 static void do_ffparams(gmx::ISerializer* serializer, gmx_ffparams_t* ffparams, int file_version)
2080 serializer->doInt(&ffparams->atnr);
2081 int numTypes = ffparams->numTypes();
2082 serializer->doInt(&numTypes);
2083 if (serializer->reading())
2085 ffparams->functype.resize(numTypes);
2086 ffparams->iparams.resize(numTypes);
2088 /* Read/write all the function types */
2089 serializer->doIntArray(ffparams->functype.data(), ffparams->functype.size());
2091 if (file_version >= 66)
2093 serializer->doDouble(&ffparams->reppow);
2097 ffparams->reppow = 12.0;
2100 serializer->doReal(&ffparams->fudgeQQ);
2102 /* Check whether all these function types are supported by the code.
2103 * In practice the code is backwards compatible, which means that the
2104 * numbering may have to be altered from old numbering to new numbering
2106 for (int i = 0; i < ffparams->numTypes(); i++)
2108 if (serializer->reading())
2110 /* Loop over file versions */
2111 for (int k = 0; k < NFTUPD; k++)
2113 /* Compare the read file_version to the update table */
2114 if ((file_version < ftupd[k].fvnr) && (ffparams->functype[i] >= ftupd[k].ftype))
2116 ffparams->functype[i] += 1;
2121 do_iparams(serializer, ffparams->functype[i], &ffparams->iparams[i], file_version);
2125 static void add_settle_atoms(InteractionList* ilist)
2129 /* Settle used to only store the first atom: add the other two */
2130 ilist->iatoms.resize(2 * ilist->size());
2131 for (i = ilist->size() / 4 - 1; i >= 0; i--)
2133 ilist->iatoms[4 * i + 0] = ilist->iatoms[2 * i + 0];
2134 ilist->iatoms[4 * i + 1] = ilist->iatoms[2 * i + 1];
2135 ilist->iatoms[4 * i + 2] = ilist->iatoms[2 * i + 1] + 1;
2136 ilist->iatoms[4 * i + 3] = ilist->iatoms[2 * i + 1] + 2;
2140 static void do_ilists(gmx::ISerializer* serializer, InteractionLists* ilists, int file_version)
2142 GMX_RELEASE_ASSERT(ilists, "Need a valid ilists object");
2143 GMX_RELEASE_ASSERT(ilists->size() == F_NRE,
2144 "The code needs to be in sync with InteractionLists");
2146 for (int j = 0; j < F_NRE; j++)
2148 InteractionList& ilist = (*ilists)[j];
2149 gmx_bool bClear = FALSE;
2150 if (serializer->reading())
2152 for (int k = 0; k < NFTUPD; k++)
2154 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
2162 ilist.iatoms.clear();
2166 do_ilist(serializer, &ilist);
2167 if (file_version < 78 && j == F_SETTLE && !ilist.empty())
2169 add_settle_atoms(&ilist);
2175 static void do_block(gmx::ISerializer* serializer, t_block* block)
2177 serializer->doInt(&block->nr);
2178 if (serializer->reading())
2180 if ((block->nalloc_index > 0) && (nullptr != block->index))
2182 sfree(block->index);
2184 block->nalloc_index = block->nr + 1;
2185 snew(block->index, block->nalloc_index);
2187 serializer->doIntArray(block->index, block->nr + 1);
2190 static void doListOfLists(gmx::ISerializer* serializer, gmx::ListOfLists<int>* listOfLists)
2192 int numLists = listOfLists->ssize();
2193 serializer->doInt(&numLists);
2194 int numElements = listOfLists->elementsView().ssize();
2195 serializer->doInt(&numElements);
2196 if (serializer->reading())
2198 std::vector<int> listRanges(numLists + 1);
2199 serializer->doIntArray(listRanges.data(), numLists + 1);
2200 std::vector<int> elements(numElements);
2201 serializer->doIntArray(elements.data(), numElements);
2202 *listOfLists = gmx::ListOfLists<int>(std::move(listRanges), std::move(elements));
2206 serializer->doIntArray(const_cast<int*>(listOfLists->listRangesView().data()), numLists + 1);
2207 serializer->doIntArray(const_cast<int*>(listOfLists->elementsView().data()), numElements);
2211 /* This is a primitive routine to make it possible to translate atomic numbers
2212 * to element names when reading TPR files, without making the Gromacs library
2213 * directory a dependency on mdrun (which is the case if we need elements.dat).
2215 static const char* atomicnumber_to_element(int atomicnumber)
2219 /* This does not have to be complete, so we only include elements likely
2220 * to occur in PDB files.
2222 switch (atomicnumber)
2224 case 1: p = "H"; break;
2225 case 5: p = "B"; break;
2226 case 6: p = "C"; break;
2227 case 7: p = "N"; break;
2228 case 8: p = "O"; break;
2229 case 9: p = "F"; break;
2230 case 11: p = "Na"; break;
2231 case 12: p = "Mg"; break;
2232 case 15: p = "P"; break;
2233 case 16: p = "S"; break;
2234 case 17: p = "Cl"; break;
2235 case 18: p = "Ar"; break;
2236 case 19: p = "K"; break;
2237 case 20: p = "Ca"; break;
2238 case 25: p = "Mn"; break;
2239 case 26: p = "Fe"; break;
2240 case 28: p = "Ni"; break;
2241 case 29: p = "Cu"; break;
2242 case 30: p = "Zn"; break;
2243 case 35: p = "Br"; break;
2244 case 47: p = "Ag"; break;
2245 default: p = ""; break;
2251 static void do_atom(gmx::ISerializer* serializer, t_atom* atom)
2253 serializer->doReal(&atom->m);
2254 serializer->doReal(&atom->q);
2255 serializer->doReal(&atom->mB);
2256 serializer->doReal(&atom->qB);
2257 serializer->doUShort(&atom->type);
2258 serializer->doUShort(&atom->typeB);
2259 serializer->doEnumAsInt(&atom->ptype);
2260 serializer->doInt(&atom->resind);
2261 serializer->doInt(&atom->atomnumber);
2262 if (serializer->reading())
2264 /* Set element string from atomic number if present.
2265 * This routine returns an empty string if the name is not found.
2267 std::strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
2268 /* avoid warnings about potentially unterminated string */
2269 atom->elem[3] = '\0';
2273 static void do_grps(gmx::ISerializer* serializer, gmx::ArrayRef<AtomGroupIndices> grps)
2275 for (auto& group : grps)
2277 int size = group.size();
2278 serializer->doInt(&size);
2279 if (serializer->reading())
2283 serializer->doIntArray(group.data(), size);
2287 static void do_symstr(gmx::ISerializer* serializer, char*** nm, t_symtab* symtab)
2291 if (serializer->reading())
2293 serializer->doInt(&ls);
2294 *nm = get_symtab_handle(symtab, ls);
2298 ls = lookup_symtab(symtab, *nm);
2299 serializer->doInt(&ls);
2303 static void do_strstr(gmx::ISerializer* serializer, int nstr, char*** nm, t_symtab* symtab)
2307 for (j = 0; (j < nstr); j++)
2309 do_symstr(serializer, &(nm[j]), symtab);
2313 static void do_resinfo(gmx::ISerializer* serializer, int n, t_resinfo* ri, t_symtab* symtab, int file_version)
2317 for (j = 0; (j < n); j++)
2319 do_symstr(serializer, &(ri[j].name), symtab);
2320 if (file_version >= 63)
2322 serializer->doInt(&ri[j].nr);
2323 serializer->doUChar(&ri[j].ic);
2333 static void do_atoms(gmx::ISerializer* serializer, t_atoms* atoms, t_symtab* symtab, int file_version)
2337 serializer->doInt(&atoms->nr);
2338 serializer->doInt(&atoms->nres);
2339 if (serializer->reading())
2341 /* Since we have always written all t_atom properties in the tpr file
2342 * (at least for all backward compatible versions), we don't store
2343 * but simple set the booleans here.
2345 atoms->haveMass = TRUE;
2346 atoms->haveCharge = TRUE;
2347 atoms->haveType = TRUE;
2348 atoms->haveBState = TRUE;
2349 atoms->havePdbInfo = FALSE;
2351 snew(atoms->atom, atoms->nr);
2352 snew(atoms->atomname, atoms->nr);
2353 snew(atoms->atomtype, atoms->nr);
2354 snew(atoms->atomtypeB, atoms->nr);
2355 snew(atoms->resinfo, atoms->nres);
2356 atoms->pdbinfo = nullptr;
2360 GMX_RELEASE_ASSERT(atoms->haveMass && atoms->haveCharge && atoms->haveType && atoms->haveBState,
2361 "Mass, charge, atomtype and B-state parameters should be present in "
2362 "t_atoms when writing a tpr file");
2364 for (i = 0; (i < atoms->nr); i++)
2366 do_atom(serializer, &atoms->atom[i]);
2368 do_strstr(serializer, atoms->nr, atoms->atomname, symtab);
2369 do_strstr(serializer, atoms->nr, atoms->atomtype, symtab);
2370 do_strstr(serializer, atoms->nr, atoms->atomtypeB, symtab);
2372 do_resinfo(serializer, atoms->nres, atoms->resinfo, symtab, file_version);
2375 static void do_groups(gmx::ISerializer* serializer, SimulationGroups* groups, t_symtab* symtab)
2377 do_grps(serializer, groups->groups);
2378 int numberOfGroupNames = groups->groupNames.size();
2379 serializer->doInt(&numberOfGroupNames);
2380 if (serializer->reading())
2382 groups->groupNames.resize(numberOfGroupNames);
2384 do_strstr(serializer, numberOfGroupNames, groups->groupNames.data(), symtab);
2385 for (auto group : gmx::keysOf(groups->groupNumbers))
2387 int numberOfGroupNumbers = groups->numberOfGroupNumbers(group);
2388 serializer->doInt(&numberOfGroupNumbers);
2389 if (numberOfGroupNumbers != 0)
2391 if (serializer->reading())
2393 groups->groupNumbers[group].resize(numberOfGroupNumbers);
2395 serializer->doUCharArray(groups->groupNumbers[group].data(), numberOfGroupNumbers);
2400 static void do_atomtypes(gmx::ISerializer* serializer, t_atomtypes* atomtypes, int file_version)
2404 serializer->doInt(&atomtypes->nr);
2406 if (serializer->reading())
2408 snew(atomtypes->atomnumber, j);
2410 if (serializer->reading() && file_version < tpxv_RemoveImplicitSolvation)
2412 std::vector<real> dummy(atomtypes->nr, 0);
2413 serializer->doRealArray(dummy.data(), dummy.size());
2414 serializer->doRealArray(dummy.data(), dummy.size());
2415 serializer->doRealArray(dummy.data(), dummy.size());
2417 serializer->doIntArray(atomtypes->atomnumber, j);
2419 if (serializer->reading() && file_version >= 60 && file_version < tpxv_RemoveImplicitSolvation)
2421 std::vector<real> dummy(atomtypes->nr, 0);
2422 serializer->doRealArray(dummy.data(), dummy.size());
2423 serializer->doRealArray(dummy.data(), dummy.size());
2427 static void do_symtab(gmx::ISerializer* serializer, t_symtab* symtab)
2432 serializer->doInt(&symtab->nr);
2434 if (serializer->reading())
2436 snew(symtab->symbuf, 1);
2437 symbuf = symtab->symbuf;
2438 symbuf->bufsize = nr;
2439 snew(symbuf->buf, nr);
2440 for (i = 0; (i < nr); i++)
2443 serializer->doString(&buf);
2444 symbuf->buf[i] = gmx_strdup(buf.c_str());
2449 symbuf = symtab->symbuf;
2450 while (symbuf != nullptr)
2452 for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
2454 std::string buf = symbuf->buf[i];
2455 serializer->doString(&buf);
2458 symbuf = symbuf->next;
2462 gmx_fatal(FARGS, "nr of symtab strings left: %d", nr);
2467 static void do_cmap(gmx::ISerializer* serializer, gmx_cmap_t* cmap_grid)
2470 int ngrid = cmap_grid->cmapdata.size();
2471 serializer->doInt(&ngrid);
2472 serializer->doInt(&cmap_grid->grid_spacing);
2474 int gs = cmap_grid->grid_spacing;
2475 int nelem = gs * gs;
2477 if (serializer->reading())
2479 cmap_grid->cmapdata.resize(ngrid);
2481 for (int i = 0; i < ngrid; i++)
2483 cmap_grid->cmapdata[i].cmap.resize(4 * nelem);
2487 for (int i = 0; i < ngrid; i++)
2489 for (int j = 0; j < nelem; j++)
2491 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4]);
2492 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 1]);
2493 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 2]);
2494 serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 3]);
2500 static void do_moltype(gmx::ISerializer* serializer, gmx_moltype_t* molt, t_symtab* symtab, int file_version)
2502 do_symstr(serializer, &(molt->name), symtab);
2504 do_atoms(serializer, &molt->atoms, symtab, file_version);
2506 do_ilists(serializer, &molt->ilist, file_version);
2508 /* TODO: Remove the obsolete charge group index from the file */
2510 cgs.nr = molt->atoms.nr;
2511 cgs.nalloc_index = cgs.nr + 1;
2512 snew(cgs.index, cgs.nalloc_index);
2513 for (int i = 0; i < cgs.nr + 1; i++)
2517 do_block(serializer, &cgs);
2520 /* This used to be in the atoms struct */
2521 doListOfLists(serializer, &molt->excls);
2524 static void do_molblock(gmx::ISerializer* serializer, gmx_molblock_t* molb, int numAtomsPerMolecule)
2526 serializer->doInt(&molb->type);
2527 serializer->doInt(&molb->nmol);
2528 /* To maintain forward topology reading compatibility, we store #atoms.
2529 * TODO: Change this to conditional reading of a dummy int when we
2530 * increase tpx_generation.
2532 serializer->doInt(&numAtomsPerMolecule);
2533 /* Position restraint coordinates */
2534 int numPosres_xA = molb->posres_xA.size();
2535 serializer->doInt(&numPosres_xA);
2536 if (numPosres_xA > 0)
2538 if (serializer->reading())
2540 molb->posres_xA.resize(numPosres_xA);
2542 serializer->doRvecArray(as_rvec_array(molb->posres_xA.data()), numPosres_xA);
2544 int numPosres_xB = molb->posres_xB.size();
2545 serializer->doInt(&numPosres_xB);
2546 if (numPosres_xB > 0)
2548 if (serializer->reading())
2550 molb->posres_xB.resize(numPosres_xB);
2552 serializer->doRvecArray(as_rvec_array(molb->posres_xB.data()), numPosres_xB);
2556 static void set_disres_npair(gmx_mtop_t* mtop)
2558 gmx::ArrayRef<t_iparams> ip = mtop->ffparams.iparams;
2560 for (const auto ilist : IListRange(*mtop))
2562 const InteractionList& il = ilist.list()[F_DISRES];
2566 gmx::ArrayRef<const int> a = il.iatoms;
2568 for (int i = 0; i < il.size(); i += 3)
2571 if (i + 3 == il.size() || ip[a[i]].disres.label != ip[a[i + 3]].disres.label)
2573 ip[a[i]].disres.npair = npair;
2581 static void do_mtop(gmx::ISerializer* serializer, gmx_mtop_t* mtop, int file_version)
2583 do_symtab(serializer, &(mtop->symtab));
2585 do_symstr(serializer, &(mtop->name), &(mtop->symtab));
2587 do_ffparams(serializer, &mtop->ffparams, file_version);
2589 int nmoltype = mtop->moltype.size();
2590 serializer->doInt(&nmoltype);
2591 if (serializer->reading())
2593 mtop->moltype.resize(nmoltype);
2595 for (gmx_moltype_t& moltype : mtop->moltype)
2597 do_moltype(serializer, &moltype, &mtop->symtab, file_version);
2600 int nmolblock = mtop->molblock.size();
2601 serializer->doInt(&nmolblock);
2602 if (serializer->reading())
2604 mtop->molblock.resize(nmolblock);
2606 for (gmx_molblock_t& molblock : mtop->molblock)
2608 int numAtomsPerMolecule = (serializer->reading() ? 0 : mtop->moltype[molblock.type].atoms.nr);
2609 do_molblock(serializer, &molblock, numAtomsPerMolecule);
2611 serializer->doInt(&mtop->natoms);
2613 if (file_version >= tpxv_IntermolecularBondeds)
2615 serializer->doBool(&mtop->bIntermolecularInteractions);
2616 if (mtop->bIntermolecularInteractions)
2618 if (serializer->reading())
2620 mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
2622 do_ilists(serializer, mtop->intermolecular_ilist.get(), file_version);
2627 mtop->bIntermolecularInteractions = FALSE;
2630 do_atomtypes(serializer, &(mtop->atomtypes), file_version);
2632 if (file_version >= 65)
2634 do_cmap(serializer, &mtop->ffparams.cmap_grid);
2638 mtop->ffparams.cmap_grid.grid_spacing = 0;
2639 mtop->ffparams.cmap_grid.cmapdata.clear();
2642 do_groups(serializer, &mtop->groups, &(mtop->symtab));
2644 mtop->haveMoleculeIndices = true;
2646 if (file_version >= tpxv_StoreNonBondedInteractionExclusionGroup)
2648 std::int64_t intermolecularExclusionGroupSize = gmx::ssize(mtop->intermolecularExclusionGroup);
2649 serializer->doInt64(&intermolecularExclusionGroupSize);
2650 GMX_RELEASE_ASSERT(intermolecularExclusionGroupSize >= 0,
2651 "Number of atoms with excluded intermolecular non-bonded interactions "
2653 mtop->intermolecularExclusionGroup.resize(intermolecularExclusionGroupSize); // no effect when writing
2654 serializer->doIntArray(mtop->intermolecularExclusionGroup.data(),
2655 mtop->intermolecularExclusionGroup.size());
2658 if (serializer->reading())
2660 close_symtab(&(mtop->symtab));
2665 * Read the first part of the TPR file to find general system information.
2667 * If \p TopOnlyOK is true then we can read even future versions
2668 * of tpx files, provided the \p fileGeneration hasn't changed.
2669 * If it is false, we need the \p ir too, and bail out
2670 * if the file is newer than the program.
2672 * The version and generation of the topology (see top of this file)
2673 * are returned in the two last arguments, if those arguments are non-nullptr.
2675 * If possible, we will read the \p ir even when \p TopOnlyOK is true.
2677 * \param[in,out] serializer The serializer used to handle header processing.
2678 * \param[in,out] tpx File header datastructure.
2679 * \param[in] filename The name of the file being read/written
2680 * \param[in,out] fio File handle.
2681 * \param[in] TopOnlyOK If not reading \p ir is fine or not.
2683 static void do_tpxheader(gmx::FileIOXdrSerializer* serializer,
2685 const char* filename,
2693 /* XDR binary topology file */
2694 precision = sizeof(real);
2696 std::string fileTag;
2697 if (serializer->reading())
2699 serializer->doString(&buf);
2700 if (std::strncmp(buf.c_str(), "VERSION", 7) != 0)
2704 "Can not read file %s,\n"
2705 " this file is from a GROMACS version which is older than 2.0\n"
2706 " Make a new one with grompp or use a gro or pdb file, if possible",
2709 // We need to know the precision used to write the TPR file, to match it
2710 // to the precision of the currently running binary. If the precisions match
2711 // there is no problem, but mismatching precision needs to be accounted for
2712 // by reading into temporary variables of the correct precision instead
2713 // of the desired target datastructures.
2714 serializer->doInt(&precision);
2715 tpx->isDouble = (precision == sizeof(double));
2716 if ((precision != sizeof(float)) && !tpx->isDouble)
2719 "Unknown precision in file %s: real is %d bytes "
2720 "instead of %zu or %zu",
2726 gmx_fio_setprecision(fio, tpx->isDouble);
2728 "Reading file %s, %s (%s precision)\n",
2731 tpx->isDouble ? "double" : "single");
2735 buf = gmx::formatString("VERSION %s", gmx_version());
2736 serializer->doString(&buf);
2737 gmx_fio_setprecision(fio, tpx->isDouble);
2738 serializer->doInt(&precision);
2742 /* Check versions! */
2743 serializer->doInt(&tpx->fileVersion);
2745 /* This is for backward compatibility with development versions 77-79
2746 * where the tag was, mistakenly, placed before the generation,
2747 * which would cause a segv instead of a proper error message
2748 * when reading the topology only from tpx with <77 code.
2750 if (tpx->fileVersion >= 77 && tpx->fileVersion <= 79)
2752 serializer->doString(&fileTag);
2755 serializer->doInt(&tpx->fileGeneration);
2757 if (tpx->fileVersion >= 81)
2759 serializer->doString(&fileTag);
2761 if (serializer->reading())
2763 if (tpx->fileVersion < 77)
2765 /* Versions before 77 don't have the tag, set it to release */
2766 fileTag = gmx::formatString("%s", TPX_TAG_RELEASE);
2769 if (fileTag != tpx_tag)
2771 fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n", fileTag.c_str(), tpx_tag.c_str());
2773 /* We only support reading tpx files with the same tag as the code
2774 * or tpx files with the release tag and with lower version number.
2776 if (fileTag != TPX_TAG_RELEASE && tpx->fileVersion < tpx_version)
2779 "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' "
2780 "with program for tpx version %d, tag '%s'",
2790 if ((tpx->fileVersion <= tpx_incompatible_version)
2791 || ((tpx->fileVersion > tpx_version) && !TopOnlyOK) || (tpx->fileGeneration > tpx_generation)
2792 || tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
2795 "reading tpx file (%s) version %d with version %d program",
2801 serializer->doInt(&tpx->natoms);
2802 serializer->doInt(&tpx->ngtc);
2804 if (tpx->fileVersion < 62)
2806 serializer->doInt(&idum);
2807 serializer->doReal(&rdum);
2809 if (tpx->fileVersion >= 79)
2811 serializer->doInt(&tpx->fep_state);
2813 serializer->doReal(&tpx->lambda);
2814 serializer->doBool(&tpx->bIr);
2815 serializer->doBool(&tpx->bTop);
2816 serializer->doBool(&tpx->bX);
2817 serializer->doBool(&tpx->bV);
2818 serializer->doBool(&tpx->bF);
2819 serializer->doBool(&tpx->bBox);
2821 if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
2823 if (!serializer->reading())
2825 GMX_RELEASE_ASSERT(tpx->sizeOfTprBody != 0,
2826 "Not possible to write new file with zero TPR body size");
2828 serializer->doInt64(&tpx->sizeOfTprBody);
2831 if ((tpx->fileGeneration > tpx_generation))
2833 /* This can only happen if TopOnlyOK=TRUE */
2838 #define do_test(serializer, b, p) \
2839 if ((serializer)->reading() && ((p) != nullptr) && !(b)) \
2840 gmx_fatal(FARGS, "No %s in input file", #p)
2843 * Process the first part of the TPR into the state datastructure.
2845 * Due to the structure of the legacy code, it is necessary
2846 * to split up the state reading into two parts, with the
2847 * box and legacy temperature coupling processed before the
2848 * topology datastructures.
2850 * See the documentation for do_tpx_body for the correct order of
2851 * the operations for reading a tpr file.
2853 * \param[in] serializer Abstract serializer used to read/write data.
2854 * \param[in] tpx The file header data.
2855 * \param[in, out] state Global state data.
2857 static void do_tpx_state_first(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state)
2859 if (serializer->reading())
2862 init_gtc_state(state, tpx->ngtc, 0, 0);
2864 do_test(serializer, tpx->bBox, state->box);
2867 serializer->doRvecArray(state->box, DIM);
2868 if (tpx->fileVersion >= 51)
2870 serializer->doRvecArray(state->box_rel, DIM);
2874 /* We initialize box_rel after reading the inputrec */
2875 clear_mat(state->box_rel);
2877 serializer->doRvecArray(state->boxv, DIM);
2878 if (tpx->fileVersion < 56)
2881 serializer->doRvecArray(mdum, DIM);
2885 if (state->ngtc > 0)
2888 snew(dumv, state->ngtc);
2889 if (tpx->fileVersion < 69)
2891 serializer->doRealArray(dumv, state->ngtc);
2893 /* These used to be the Berendsen tcoupl_lambda's */
2894 serializer->doRealArray(dumv, state->ngtc);
2900 * Process global topology data.
2902 * See the documentation for do_tpx_body for the correct order of
2903 * the operations for reading a tpr file.
2905 * \param[in] serializer Abstract serializer used to read/write data.
2906 * \param[in] tpx The file header data.
2907 * \param[in,out] mtop Global topology.
2909 static void do_tpx_mtop(gmx::ISerializer* serializer, TpxFileHeader* tpx, gmx_mtop_t* mtop)
2911 do_test(serializer, tpx->bTop, mtop);
2916 do_mtop(serializer, mtop, tpx->fileVersion);
2917 set_disres_npair(mtop);
2923 do_mtop(serializer, &dum_top, tpx->fileVersion);
2928 * Process coordinate vectors for state data.
2930 * Main part of state gets processed here.
2932 * See the documentation for do_tpx_body for the correct order of
2933 * the operations for reading a tpr file.
2935 * \param[in] serializer Abstract serializer used to read/write data.
2936 * \param[in] tpx The file header data.
2937 * \param[in,out] state Global state data.
2938 * \param[in,out] x Individual coordinates for processing, deprecated.
2939 * \param[in,out] v Individual velocities for processing, deprecated.
2941 static void do_tpx_state_second(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state, rvec* x, rvec* v)
2943 if (!serializer->reading())
2946 x == nullptr && v == nullptr,
2947 "Passing separate x and v pointers to do_tpx() is not supported when writing");
2951 GMX_RELEASE_ASSERT(!(x == nullptr && v != nullptr),
2952 "Passing x==NULL and v!=NULL is not supported");
2955 if (serializer->reading())
2959 // v is also nullptr by the above assertion, so we may
2960 // need to make memory in state for storing the contents
2964 state->flags |= enumValueToBitMask(StateEntry::X);
2968 state->flags |= enumValueToBitMask(StateEntry::V);
2970 state_change_natoms(state, tpx->natoms);
2976 x = state->x.rvec_array();
2977 v = state->v.rvec_array();
2979 do_test(serializer, tpx->bX, x);
2982 if (serializer->reading())
2984 state->flags |= enumValueToBitMask(StateEntry::X);
2986 serializer->doRvecArray(x, tpx->natoms);
2989 do_test(serializer, tpx->bV, v);
2992 if (serializer->reading())
2994 state->flags |= enumValueToBitMask(StateEntry::V);
2998 std::vector<gmx::RVec> dummyVelocities(tpx->natoms);
2999 serializer->doRvecArray(as_rvec_array(dummyVelocities.data()), tpx->natoms);
3003 serializer->doRvecArray(v, tpx->natoms);
3007 // No need to run do_test when the last argument is NULL
3010 std::vector<gmx::RVec> dummyForces(state->natoms);
3011 serializer->doRvecArray(as_rvec_array(dummyForces.data()), tpx->natoms);
3015 * Process simulation parameters.
3017 * See the documentation for do_tpx_body for the correct order of
3018 * the operations for reading a tpr file.
3020 * \param[in] serializer Abstract serializer used to read/write data.
3021 * \param[in] tpx The file header data.
3022 * \param[in,out] ir Datastructure with simulation parameters.
3024 static PbcType do_tpx_ir(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir)
3027 gmx_bool bPeriodicMols;
3029 /* Starting with tpx version 26, we have the inputrec
3030 * at the end of the file, so we can ignore it
3031 * if the file is never than the software (but still the
3032 * same generation - see comments at the top of this file.
3036 pbcType = PbcType::Unset;
3037 bPeriodicMols = FALSE;
3039 do_test(serializer, tpx->bIr, ir);
3042 if (tpx->fileVersion >= 53)
3044 /* Removed the pbc info from do_inputrec, since we always want it */
3045 if (!serializer->reading())
3047 pbcType = ir->pbcType;
3048 bPeriodicMols = ir->bPeriodicMols;
3050 serializer->doInt(reinterpret_cast<int*>(&pbcType));
3051 serializer->doBool(&bPeriodicMols);
3053 if (tpx->fileGeneration <= tpx_generation && ir)
3055 do_inputrec(serializer, ir, tpx->fileVersion);
3056 if (tpx->fileVersion < 53)
3058 pbcType = ir->pbcType;
3059 bPeriodicMols = ir->bPeriodicMols;
3062 if (serializer->reading() && ir && tpx->fileVersion >= 53)
3064 /* We need to do this after do_inputrec, since that initializes ir */
3065 ir->pbcType = pbcType;
3066 ir->bPeriodicMols = bPeriodicMols;
3073 * Correct and finalize read information.
3075 * If \p state is nullptr, skip the parts dependent on it.
3077 * See the documentation for do_tpx_body for the correct order of
3078 * the operations for reading a tpr file.
3080 * \param[in] tpx The file header used to check version numbers.
3081 * \param[out] ir Input rec that needs correction.
3082 * \param[out] state State needing correction.
3083 * \param[out] mtop Topology to finalize.
3085 static void do_tpx_finalize(TpxFileHeader* tpx, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
3087 if (tpx->fileVersion < 51 && state)
3089 set_box_rel(ir, state);
3093 if (state && state->ngtc == 0)
3095 /* Reading old version without tcoupl state data: set it */
3096 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
3098 if (tpx->bTop && mtop)
3100 if (tpx->fileVersion < 57)
3102 ir->eDisre = !mtop->moltype[0].ilist[F_DISRES].empty()
3103 ? DistanceRestraintRefinement::Simple
3104 : DistanceRestraintRefinement::None;
3111 * Process TPR data for file reading/writing.
3113 * The TPR file gets processed in in four stages due to the organization
3114 * of the data within it.
3116 * First, state data for the box is processed in do_tpx_state_first.
3117 * This is followed by processing the topology in do_tpx_mtop.
3118 * Coordinate and velocity vectors are handled next in do_tpx_state_second.
3119 * The last file information processed is the collection of simulation parameters in do_tpx_ir.
3120 * When reading, a final processing step is undertaken at the end.
3122 * \param[in] serializer Abstract serializer used to read/write data.
3123 * \param[in] tpx The file header data.
3124 * \param[in,out] ir Datastructures with simulation parameters.
3125 * \param[in,out] state Global state data.
3126 * \param[in,out] x Individual coordinates for processing, deprecated.
3127 * \param[in,out] v Individual velocities for processing, deprecated.
3128 * \param[in,out] mtop Global topology.
3130 static PbcType do_tpx_body(gmx::ISerializer* serializer,
3140 do_tpx_state_first(serializer, tpx, state);
3142 do_tpx_mtop(serializer, tpx, mtop);
3145 do_tpx_state_second(serializer, tpx, state, x, v);
3147 PbcType pbcType = do_tpx_ir(serializer, tpx, ir);
3148 if (serializer->reading())
3150 do_tpx_finalize(tpx, ir, state, mtop);
3156 * Overload for do_tpx_body that defaults to state vectors being nullptr.
3158 * \param[in] serializer Abstract serializer used to read/write data.
3159 * \param[in] tpx The file header data.
3160 * \param[in,out] ir Datastructures with simulation parameters.
3161 * \param[in,out] mtop Global topology.
3163 static PbcType do_tpx_body(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir, gmx_mtop_t* mtop)
3165 return do_tpx_body(serializer, tpx, ir, nullptr, nullptr, nullptr, mtop);
3168 static t_fileio* open_tpx(const char* fn, const char* mode)
3170 return gmx_fio_open(fn, mode);
3173 static void close_tpx(t_fileio* fio)
3179 * Fill information into the header only from state before writing.
3181 * Populating the header needs to be independent from writing the information
3182 * to file to allow things like writing the raw byte stream.
3184 * \param[in] state The current simulation state. Can't write without it.
3185 * \param[in] ir Parameter and system information.
3186 * \param[in] mtop Global topology.
3187 * \returns Fully populated header.
3189 static TpxFileHeader populateTpxHeader(const t_state& state, const t_inputrec* ir, const gmx_mtop_t* mtop)
3191 TpxFileHeader header;
3192 header.natoms = state.natoms;
3193 header.ngtc = state.ngtc;
3194 header.fep_state = state.fep_state;
3195 header.lambda = state.lambda[FreeEnergyPerturbationCouplingType::Fep];
3196 header.bIr = ir != nullptr;
3197 header.bTop = mtop != nullptr;
3198 header.bX = (state.flags & enumValueToBitMask(StateEntry::X)) != 0;
3199 header.bV = (state.flags & enumValueToBitMask(StateEntry::V)) != 0;
3202 header.fileVersion = tpx_version;
3203 header.fileGeneration = tpx_generation;
3204 header.isDouble = (sizeof(real) == sizeof(double));
3210 * Process the body of a TPR file as an opaque data buffer.
3212 * Reads/writes the information in \p buffer from/to the \p serializer
3213 * provided to the function. Does not interact with the actual
3214 * TPR datastructures but with an in memory representation of the
3215 * data, so that this data can be efficiently read or written from/to
3216 * an original source.
3218 * \param[in] serializer The abstract serializer used for reading or writing
3219 * the information in \p buffer.
3220 * \param[in,out] buffer Information from TPR file as char buffer.
3222 static void doTpxBodyBuffer(gmx::ISerializer* serializer, gmx::ArrayRef<char> buffer)
3224 serializer->doOpaque(buffer.data(), buffer.size());
3228 * Populates simulation datastructures.
3230 * Here the information from the serialization interface \p serializer
3231 * is used to first populate the datastructures containing the simulation
3232 * information. Depending on the version found in the header \p tpx,
3233 * this is done using the new reading of the data as one block from disk,
3234 * followed by complete deserialization of the information read from there.
3235 * Otherwise, the datastructures are populated as before one by one from disk.
3236 * The second version is the default for the legacy tools that read the
3237 * coordinates and velocities separate from the state.
3239 * After reading in the data, a separate buffer is populated from them
3240 * containing only \p ir and \p mtop that can be communicated directly
3241 * to nodes needing the information to set up a simulation.
3243 * \param[in] tpx The file header.
3244 * \param[in] serializer The Serialization interface used to read the TPR.
3245 * \param[out] ir Input rec to populate.
3246 * \param[out] state State vectors to populate.
3247 * \param[out] x Coordinates to populate if needed.
3248 * \param[out] v Velocities to populate if needed.
3249 * \param[out] mtop Global topology to populate.
3251 * \returns Partial de-serialized TPR used for communication to nodes.
3253 static PartialDeserializedTprFile readTpxBody(TpxFileHeader* tpx,
3254 gmx::ISerializer* serializer,
3261 PartialDeserializedTprFile partialDeserializedTpr;
3262 if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
3264 partialDeserializedTpr.body.resize(tpx->sizeOfTprBody);
3265 partialDeserializedTpr.header = *tpx;
3266 doTpxBodyBuffer(serializer, partialDeserializedTpr.body);
3268 partialDeserializedTpr.pbcType =
3269 completeTprDeserialization(&partialDeserializedTpr, ir, state, x, v, mtop);
3273 partialDeserializedTpr.pbcType = do_tpx_body(serializer, tpx, ir, state, x, v, mtop);
3275 // Update header to system info for communication to nodes.
3276 // As we only need to communicate the inputrec and mtop to other nodes,
3277 // we prepare a new char buffer with the information we have already read
3279 partialDeserializedTpr.header = populateTpxHeader(*state, ir, mtop);
3280 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3281 // but since we just used the default XDR format (which is big endian) for the TPR
3282 // header it would cause third-party libraries reading our raw data to tear their hair
3283 // if we swap the endian in the middle of the file, so we stick to big endian in the
3284 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3285 gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3286 do_tpx_body(&tprBodySerializer, &partialDeserializedTpr.header, ir, mtop);
3287 partialDeserializedTpr.body = tprBodySerializer.finishAndGetBuffer();
3289 return partialDeserializedTpr;
3292 /************************************************************
3294 * The following routines are the exported ones
3296 ************************************************************/
3298 TpxFileHeader readTpxHeader(const char* fileName, bool canReadTopologyOnly)
3302 fio = open_tpx(fileName, "r");
3303 gmx::FileIOXdrSerializer serializer(fio);
3306 do_tpxheader(&serializer, &tpx, fileName, fio, canReadTopologyOnly);
3311 void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t& mtop)
3313 /* To write a state, we first need to write the state information to a buffer before
3314 * we append the raw bytes to the file. For this, the header information needs to be
3315 * populated before we write the main body because it has some information that is
3316 * otherwise not available.
3321 TpxFileHeader tpx = populateTpxHeader(*state, ir, &mtop);
3322 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3323 // but since we just used the default XDR format (which is big endian) for the TPR
3324 // header it would cause third-party libraries reading our raw data to tear their hair
3325 // if we swap the endian in the middle of the file, so we stick to big endian in the
3326 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3327 gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3329 do_tpx_body(&tprBodySerializer,
3331 const_cast<t_inputrec*>(ir),
3332 const_cast<t_state*>(state),
3335 const_cast<gmx_mtop_t*>(&mtop));
3337 std::vector<char> tprBody = tprBodySerializer.finishAndGetBuffer();
3338 tpx.sizeOfTprBody = tprBody.size();
3340 fio = open_tpx(fn, "w");
3341 gmx::FileIOXdrSerializer serializer(fio);
3342 do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
3343 doTpxBodyBuffer(&serializer, tprBody);
3348 PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
3355 // Long-term we should move to use little endian in files to avoid extra byte swapping,
3356 // but since we just used the default XDR format (which is big endian) for the TPR
3357 // header it would cause third-party libraries reading our raw data to tear their hair
3358 // if we swap the endian in the middle of the file, so we stick to big endian in the
3359 // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
3360 gmx::InMemoryDeserializer tprBodyDeserializer(partialDeserializedTpr->body,
3361 partialDeserializedTpr->header.isDouble,
3362 gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
3363 return do_tpx_body(&tprBodyDeserializer, &partialDeserializedTpr->header, ir, state, x, v, mtop);
3366 PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
3370 return completeTprDeserialization(partialDeserializedTpr, ir, nullptr, nullptr, nullptr, mtop);
3373 PartialDeserializedTprFile read_tpx_state(const char* fn, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
3376 fio = open_tpx(fn, "r");
3377 gmx::FileIOXdrSerializer serializer(fio);
3378 PartialDeserializedTprFile partialDeserializedTpr;
3379 do_tpxheader(&serializer, &partialDeserializedTpr.header, fn, fio, ir == nullptr);
3380 partialDeserializedTpr =
3381 readTpxBody(&partialDeserializedTpr.header, &serializer, ir, state, nullptr, nullptr, mtop);
3383 return partialDeserializedTpr;
3386 PbcType read_tpx(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, gmx_mtop_t* mtop)
3392 fio = open_tpx(fn, "r");
3393 gmx::FileIOXdrSerializer serializer(fio);
3394 do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
3395 PartialDeserializedTprFile partialDeserializedTpr =
3396 readTpxBody(&tpx, &serializer, ir, &state, x, v, mtop);
3398 if (mtop != nullptr && natoms != nullptr)
3400 *natoms = mtop->natoms;
3404 copy_mat(state.box, box);
3406 return partialDeserializedTpr.pbcType;
3409 PbcType read_tpx_top(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, t_topology* top)
3414 pbcType = read_tpx(fn, ir, box, natoms, x, v, &mtop);
3416 *top = gmx_mtop_t_to_t_topology(&mtop, true);
3421 gmx_bool fn2bTPX(const char* file)
3423 return (efTPR == fn2ftp(file));
3426 void pr_tpxheader(FILE* fp, int indent, const char* title, const TpxFileHeader* sh)
3428 if (available(fp, sh, indent, title))
3430 indent = pr_title(fp, indent, title);
3431 pr_indent(fp, indent);
3432 fprintf(fp, "bIr = %spresent\n", sh->bIr ? "" : "not ");
3433 pr_indent(fp, indent);
3434 fprintf(fp, "bBox = %spresent\n", sh->bBox ? "" : "not ");
3435 pr_indent(fp, indent);
3436 fprintf(fp, "bTop = %spresent\n", sh->bTop ? "" : "not ");
3437 pr_indent(fp, indent);
3438 fprintf(fp, "bX = %spresent\n", sh->bX ? "" : "not ");
3439 pr_indent(fp, indent);
3440 fprintf(fp, "bV = %spresent\n", sh->bV ? "" : "not ");
3441 pr_indent(fp, indent);
3442 fprintf(fp, "bF = %spresent\n", sh->bF ? "" : "not ");
3444 pr_indent(fp, indent);
3445 fprintf(fp, "natoms = %d\n", sh->natoms);
3446 pr_indent(fp, indent);
3447 fprintf(fp, "lambda = %e\n", sh->lambda);
3448 pr_indent(fp, indent);
3449 fprintf(fp, "buffer size = %" PRId64 "\n", sh->sizeOfTprBody);