src/gromacs/fileio/tpxio.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
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  19  * Lesser General Public License for more details.
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  36  */
  37 #include "gmxpre.h"
  38
  39 /* This file is completely threadsafe - keep it that way! */
  40
  41 #include "tpxio.h"
  42
  43 #include <cstdio>
  44 #include <cstdlib>
  45 #include <cstring>
  46
  47 #include <algorithm>
  48 #include <memory>
  49 #include <vector>
  50
  51 #include "gromacs/fileio/filetypes.h"
  52 #include "gromacs/fileio/gmxfio.h"
  53 #include "gromacs/fileio/gmxfio_xdr.h"
  54 #include "gromacs/math/units.h"
  55 #include "gromacs/math/vec.h"
  56 #include "gromacs/mdtypes/awh_history.h"
  57 #include "gromacs/mdtypes/awh_params.h"
  58 #include "gromacs/mdtypes/inputrec.h"
  59 #include "gromacs/mdtypes/md_enums.h"
  60 #include "gromacs/mdtypes/pull_params.h"
  61 #include "gromacs/mdtypes/state.h"
  62 #include "gromacs/pbcutil/boxutilities.h"
  63 #include "gromacs/pbcutil/pbc.h"
  64 #include "gromacs/topology/block.h"
  65 #include "gromacs/topology/ifunc.h"
  66 #include "gromacs/topology/mtop_util.h"
  67 #include "gromacs/topology/symtab.h"
  68 #include "gromacs/topology/topology.h"
  69 #include "gromacs/utility/arraysize.h"
  70 #include "gromacs/utility/baseversion.h"
  71 #include "gromacs/utility/cstringutil.h"
  72 #include "gromacs/utility/fatalerror.h"
  73 #include "gromacs/utility/futil.h"
  74 #include "gromacs/utility/gmxassert.h"
  75 #include "gromacs/utility/keyvaluetreebuilder.h"
  76 #include "gromacs/utility/keyvaluetreeserializer.h"
  77 #include "gromacs/utility/smalloc.h"
  78 #include "gromacs/utility/snprintf.h"
  79 #include "gromacs/utility/txtdump.h"
  80
  81 #define TPX_TAG_RELEASE  "release"
  82
  83 /*! \brief Tag string for the file format written to run input files
  84  * written by this version of the code.
  85  *
  86  * Change this if you want to change the run input format in a feature
  87  * branch. This ensures that there will not be different run input
  88  * formats around which cannot be distinguished, while not causing
  89  * problems rebasing the feature branch onto upstream changes. When
  90  * merging with mainstream GROMACS, set this tag string back to
  91  * TPX_TAG_RELEASE, and instead add an element to tpxv.
  92  */
  93 static const char *tpx_tag = TPX_TAG_RELEASE;
  94
  95 /*! \brief Enum of values that describe the contents of a tpr file
  96  * whose format matches a version number
  97  *
  98  * The enum helps the code be more self-documenting and ensure merges
  99  * do not silently resolve when two patches make the same bump. When
 100  * adding new functionality, add a new element just above tpxv_Count
 101  * in this enumeration, and write code below that does the right thing
 102  * according to the value of file_version.
 103  */
 104 enum tpxv
 105 {
 106     tpxv_ComputationalElectrophysiology = 96,                /**< support for ion/water position swaps (computational electrophysiology) */
 107     tpxv_Use64BitRandomSeed,                                 /**< change ld_seed from int to int64_t */
 108     tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, /**< potentials for supporting coarse-grained force fields */
 109     tpxv_InteractiveMolecularDynamics,                       /**< interactive molecular dynamics (IMD) */
 110     tpxv_RemoveObsoleteParameters1,                          /**< remove optimize_fft, dihre_fc, nstcheckpoint */
 111     tpxv_PullCoordTypeGeom,                                  /**< add pull type and geometry per group and flat-bottom */
 112     tpxv_PullGeomDirRel,                                     /**< add pull geometry direction-relative */
 113     tpxv_IntermolecularBondeds,                              /**< permit inter-molecular bonded interactions in the topology */
 114     tpxv_CompElWithSwapLayerOffset,                          /**< added parameters for improved CompEl setups */
 115     tpxv_CompElPolyatomicIonsAndMultipleIonTypes,            /**< CompEl now can handle polyatomic ions and more than two types of ions */
 116     tpxv_RemoveAdress,                                       /**< removed support for AdResS */
 117     tpxv_PullCoordNGroup,                                    /**< add ngroup to pull coord */
 118     tpxv_RemoveTwinRange,                                    /**< removed support for twin-range interactions */
 119     tpxv_ReplacePullPrintCOM12,                              /**< Replaced print-com-1, 2 with pull-print-com */
 120     tpxv_PullExternalPotential,                              /**< Added pull type external potential */
 121     tpxv_GenericParamsForElectricField,                      /**< Introduced KeyValueTree and moved electric field parameters */
 122     tpxv_AcceleratedWeightHistogram,                         /**< sampling with accelerated weight histogram method (AWH) */
 123     tpxv_RemoveImplicitSolvation,                            /**< removed support for implicit solvation */
 124     tpxv_PullPrevStepCOMAsReference,                         /**< Enabled using the COM of the pull group of the last frame as reference for PBC */
 125     tpxv_MimicQMMM,                                          /**< Introduced support for MiMiC QM/MM interface */
 126     tpxv_PullAverage,                                        /**< Added possibility to output average pull force and position */
 127     tpxv_GenericInternalParameters,                          /**< Added internal parameters for mdrun modules*/
 128     tpxv_Count                                               /**< the total number of tpxv versions */
 129 };
 130
 131 /*! \brief Version number of the file format written to run input
 132  * files by this version of the code.
 133  *
 134  * The tpx_version increases whenever the file format in the main
 135  * development branch changes, due to an extension of the tpxv enum above.
 136  * Backward compatibility for reading old run input files is maintained
 137  * by checking this version number against that of the file and then using
 138  * the correct code path.
 139  *
 140  * When developing a feature branch that needs to change the run input
 141  * file format, change tpx_tag instead. */
 142 static const int tpx_version = tpxv_Count - 1;
 143
 144
 145 /* This number should only be increased when you edit the TOPOLOGY section
 146  * or the HEADER of the tpx format.
 147  * This way we can maintain forward compatibility too for all analysis tools
 148  * and/or external programs that only need to know the atom/residue names,
 149  * charges, and bond connectivity.
 150  *
 151  * It first appeared in tpx version 26, when I also moved the inputrecord
 152  * to the end of the tpx file, so we can just skip it if we only
 153  * want the topology.
 154  *
 155  * In particular, it must be increased when adding new elements to
 156  * ftupd, so that old code can read new .tpr files.
 157  */
 158 static const int tpx_generation = 26;
 159
 160 /* This number should be the most recent backwards incompatible version
 161  * I.e., if this number is 9, we cannot read tpx version 9 with this code.
 162  */
 163 static const int tpx_incompatible_version = 57; // GMX4.0 has version 58
 164
 165
 166
 167 /* Struct used to maintain tpx compatibility when function types are added */
 168 typedef struct {
 169     int fvnr;  /* file version number in which the function type first appeared */
 170     int ftype; /* function type */
 171 } t_ftupd;
 172
 173 /*
 174  * TODO The following three lines make little sense, please clarify if
 175  * you've had to work out how ftupd works.
 176  *
 177  * The entries should be ordered in:
 178  * 1. ascending function type number
 179  * 2. ascending file version number
 180  *
 181  * Because we support reading of old .tpr file versions (even when
 182  * mdrun can no longer run the simulation), we need to be able to read
 183  * obsolete t_interaction_function types. Any data read from such
 184  * fields is discarded. Their names have _NOLONGERUSED appended to
 185  * them to make things clear.
 186  */
 187 static const t_ftupd ftupd[] = {
 188     { 70, F_RESTRBONDS        },
 189     { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
 190     { 76, F_LINEAR_ANGLES     },
 191     { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
 192     { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
 193     { 65, F_CMAP              },
 194     { 60, F_GB12_NOLONGERUSED },
 195     { 61, F_GB13_NOLONGERUSED },
 196     { 61, F_GB14_NOLONGERUSED },
 197     { 72, F_GBPOL_NOLONGERUSED },
 198     { 72, F_NPSOLVATION_NOLONGERUSED },
 199     { 93, F_LJ_RECIP          },
 200     { 90, F_FBPOSRES          },
 201     { 69, F_VTEMP_NOLONGERUSED},
 202     { 66, F_PDISPCORR         },
 203     { 76, F_ANHARM_POL        },
 204     { 79, F_DVDL_COUL         },
 205     { 79, F_DVDL_VDW,         },
 206     { 79, F_DVDL_BONDED,      },
 207     { 79, F_DVDL_RESTRAINT    },
 208     { 79, F_DVDL_TEMPERATURE  },
 209     { tpxv_GenericInternalParameters, F_DENSITYFITTING },
 210 };
 211 #define NFTUPD asize(ftupd)
 212
 213 /* Needed for backward compatibility */
 214 #define MAXNODES 256
 215
 216 /**************************************************************
 217  *
 218  * Now the higer level routines that do io of the structures and arrays
 219  *
 220  **************************************************************/
 221 static void do_pullgrp_tpx_pre95(gmx::ISerializer         *serializer,
 222                                  t_pull_group             *pgrp,
 223                                  t_pull_coord             *pcrd)
 224 {
 225     rvec tmp;
 226
 227     serializer->doInt(&pgrp->nat);
 228     if (serializer->reading())
 229     {
 230         snew(pgrp->ind, pgrp->nat);
 231     }
 232     serializer->doIntArray(pgrp->ind, pgrp->nat);
 233     serializer->doInt(&pgrp->nweight);
 234     if (serializer->reading())
 235     {
 236         snew(pgrp->weight, pgrp->nweight);
 237     }
 238     serializer->doRealArray(pgrp->weight, pgrp->nweight);
 239     serializer->doInt(&pgrp->pbcatom);
 240     serializer->doRvec(&pcrd->vec);
 241     clear_rvec(pcrd->origin);
 242     serializer->doRvec(&tmp);
 243     pcrd->init = tmp[0];
 244     serializer->doReal(&pcrd->rate);
 245     serializer->doReal(&pcrd->k);
 246     serializer->doReal(&pcrd->kB);
 247 }
 248
 249 static void do_pull_group(gmx::ISerializer *serializer, t_pull_group *pgrp)
 250 {
 251     serializer->doInt(&pgrp->nat);
 252     if (serializer->reading())
 253     {
 254         snew(pgrp->ind, pgrp->nat);
 255     }
 256     serializer->doIntArray(pgrp->ind, pgrp->nat);
 257     serializer->doInt(&pgrp->nweight);
 258     if (serializer->reading())
 259     {
 260         snew(pgrp->weight, pgrp->nweight);
 261     }
 262     serializer->doRealArray(pgrp->weight, pgrp->nweight);
 263     serializer->doInt(&pgrp->pbcatom);
 264 }
 265
 266 static void do_pull_coord(gmx::ISerializer *serializer,
 267                           t_pull_coord *pcrd,
 268                           int file_version,
 269                           int ePullOld, int eGeomOld, ivec dimOld)
 270 {
 271     if (file_version >= tpxv_PullCoordNGroup)
 272     {
 273         serializer->doInt(&pcrd->eType);
 274         if (file_version >= tpxv_PullExternalPotential)
 275         {
 276             if (pcrd->eType == epullEXTERNAL)
 277             {
 278                 std::string buf;
 279                 if (serializer->reading())
 280                 {
 281                     serializer->doString(&buf);
 282                     pcrd->externalPotentialProvider = gmx_strdup(buf.c_str());
 283                 }
 284                 else
 285                 {
 286                     buf = pcrd->externalPotentialProvider;
 287                     serializer->doString(&buf);
 288                 }
 289             }
 290             else
 291             {
 292                 pcrd->externalPotentialProvider = nullptr;
 293             }
 294         }
 295         else
 296         {
 297             if (serializer->reading())
 298             {
 299                 pcrd->externalPotentialProvider = nullptr;
 300             }
 301         }
 302         /* Note that we try to support adding new geometries without
 303          * changing the tpx version. This requires checks when printing the
 304          * geometry string and a check and fatal_error in init_pull.
 305          */
 306         serializer->doInt(&pcrd->eGeom);
 307         serializer->doInt(&pcrd->ngroup);
 308         if (pcrd->ngroup <= c_pullCoordNgroupMax)
 309         {
 310             serializer->doIntArray(pcrd->group, pcrd->ngroup);
 311         }
 312         else
 313         {
 314             /* More groups in file than supported, this must be a new geometry
 315              * that is not supported by our current code. Since we will not
 316              * use the groups for this coord (checks in the pull and WHAM code
 317              * ensure this), we can ignore the groups and set ngroup=0.
 318              */
 319             int *dum;
 320             snew(dum, pcrd->ngroup);
 321             serializer->doIntArray(dum, pcrd->ngroup);
 322             sfree(dum);
 323
 324             pcrd->ngroup = 0;
 325         }
 326         serializer->doIvec(&pcrd->dim);
 327     }
 328     else
 329     {
 330         pcrd->ngroup = 2;
 331         serializer->doInt(&pcrd->group[0]);
 332         serializer->doInt(&pcrd->group[1]);
 333         if (file_version >= tpxv_PullCoordTypeGeom)
 334         {
 335             pcrd->ngroup = (pcrd->eGeom == epullgDIRRELATIVE ? 4 : 2);
 336             serializer->doInt(&pcrd->eType);
 337             serializer->doInt(&pcrd->eGeom);
 338             if (pcrd->ngroup == 4)
 339             {
 340                 serializer->doInt(&pcrd->group[2]);
 341                 serializer->doInt(&pcrd->group[3]);
 342             }
 343             serializer->doIvec(&pcrd->dim);
 344         }
 345         else
 346         {
 347             pcrd->eType = ePullOld;
 348             pcrd->eGeom = eGeomOld;
 349             copy_ivec(dimOld, pcrd->dim);
 350         }
 351     }
 352     serializer->doRvec(&pcrd->origin);
 353     serializer->doRvec(&pcrd->vec);
 354     if (file_version >= tpxv_PullCoordTypeGeom)
 355     {
 356         serializer->doBool(&pcrd->bStart);
 357     }
 358     else
 359     {
 360         /* This parameter is only printed, but not actually used by mdrun */
 361         pcrd->bStart = FALSE;
 362     }
 363     serializer->doReal(&pcrd->init);
 364     serializer->doReal(&pcrd->rate);
 365     serializer->doReal(&pcrd->k);
 366     serializer->doReal(&pcrd->kB);
 367 }
 368
 369 static void do_expandedvals(gmx::ISerializer         *serializer,
 370                             t_expanded               *expand,
 371                             t_lambda                 *fepvals,
 372                             int                       file_version)
 373 {
 374     int      n_lambda = fepvals->n_lambda;
 375
 376     /* reset the lambda calculation window */
 377     fepvals->lambda_start_n = 0;
 378     fepvals->lambda_stop_n  = n_lambda;
 379     if (file_version >= 79)
 380     {
 381         if (n_lambda > 0)
 382         {
 383             if (serializer->reading())
 384             {
 385                 snew(expand->init_lambda_weights, n_lambda);
 386             }
 387             serializer->doRealArray(expand->init_lambda_weights, n_lambda);
 388             serializer->doBool(&expand->bInit_weights);
 389         }
 390
 391         serializer->doInt(&expand->nstexpanded);
 392         serializer->doInt(&expand->elmcmove);
 393         serializer->doInt(&expand->elamstats);
 394         serializer->doInt(&expand->lmc_repeats);
 395         serializer->doInt(&expand->gibbsdeltalam);
 396         serializer->doInt(&expand->lmc_forced_nstart);
 397         serializer->doInt(&expand->lmc_seed);
 398         serializer->doReal(&expand->mc_temp);
 399         serializer->doBool(&expand->bSymmetrizedTMatrix);
 400         serializer->doInt(&expand->nstTij);
 401         serializer->doInt(&expand->minvarmin);
 402         serializer->doInt(&expand->c_range);
 403         serializer->doReal(&expand->wl_scale);
 404         serializer->doReal(&expand->wl_ratio);
 405         serializer->doReal(&expand->init_wl_delta);
 406         serializer->doBool(&expand->bWLoneovert);
 407         serializer->doInt(&expand->elmceq);
 408         serializer->doInt(&expand->equil_steps);
 409         serializer->doInt(&expand->equil_samples);
 410         serializer->doInt(&expand->equil_n_at_lam);
 411         serializer->doReal(&expand->equil_wl_delta);
 412         serializer->doReal(&expand->equil_ratio);
 413     }
 414 }
 415
 416 static void do_simtempvals(gmx::ISerializer         *serializer,
 417                            t_simtemp                *simtemp,
 418                            int                       n_lambda,
 419                            int                       file_version)
 420 {
 421     if (file_version >= 79)
 422     {
 423         serializer->doInt(&simtemp->eSimTempScale);
 424         serializer->doReal(&simtemp->simtemp_high);
 425         serializer->doReal(&simtemp->simtemp_low);
 426         if (n_lambda > 0)
 427         {
 428             if (serializer->reading())
 429             {
 430                 snew(simtemp->temperatures, n_lambda);
 431             }
 432             serializer->doRealArray(simtemp->temperatures, n_lambda);
 433         }
 434     }
 435 }
 436
 437 static void do_imd(gmx::ISerializer *serializer, t_IMD *imd)
 438 {
 439     serializer->doInt(&imd->nat);
 440     if (serializer->reading())
 441     {
 442         snew(imd->ind, imd->nat);
 443     }
 444     serializer->doIntArray(imd->ind, imd->nat);
 445 }
 446
 447 static void do_fepvals(gmx::ISerializer         *serializer,
 448                        t_lambda                 *fepvals,
 449                        int                       file_version)
 450 {
 451     /* i is defined in the ndo_double macro; use g to iterate. */
 452     int      g;
 453     real     rdum;
 454
 455     /* free energy values */
 456
 457     if (file_version >= 79)
 458     {
 459         serializer->doInt(&fepvals->init_fep_state);
 460         serializer->doDouble(&fepvals->init_lambda);
 461         serializer->doDouble(&fepvals->delta_lambda);
 462     }
 463     else if (file_version >= 59)
 464     {
 465         serializer->doDouble(&fepvals->init_lambda);
 466         serializer->doDouble(&fepvals->delta_lambda);
 467     }
 468     else
 469     {
 470         serializer->doReal(&rdum);
 471         fepvals->init_lambda = rdum;
 472         serializer->doReal(&rdum);
 473         fepvals->delta_lambda = rdum;
 474     }
 475     if (file_version >= 79)
 476     {
 477         serializer->doInt(&fepvals->n_lambda);
 478         if (serializer->reading())
 479         {
 480             snew(fepvals->all_lambda, efptNR);
 481         }
 482         for (g = 0; g < efptNR; g++)
 483         {
 484             if (fepvals->n_lambda > 0)
 485             {
 486                 if (serializer->reading())
 487                 {
 488                     snew(fepvals->all_lambda[g], fepvals->n_lambda);
 489                 }
 490                 serializer->doDoubleArray(fepvals->all_lambda[g], fepvals->n_lambda);
 491                 serializer->doBoolArray(fepvals->separate_dvdl, efptNR);
 492             }
 493             else if (fepvals->init_lambda >= 0)
 494             {
 495                 fepvals->separate_dvdl[efptFEP] = TRUE;
 496             }
 497         }
 498     }
 499     else if (file_version >= 64)
 500     {
 501         serializer->doInt(&fepvals->n_lambda);
 502         if (serializer->reading())
 503         {
 504             int g;
 505
 506             snew(fepvals->all_lambda, efptNR);
 507             /* still allocate the all_lambda array's contents. */
 508             for (g = 0; g < efptNR; g++)
 509             {
 510                 if (fepvals->n_lambda > 0)
 511                 {
 512                     snew(fepvals->all_lambda[g], fepvals->n_lambda);
 513                 }
 514             }
 515         }
 516         serializer->doDoubleArray(fepvals->all_lambda[efptFEP], fepvals->n_lambda);
 517         if (fepvals->init_lambda >= 0)
 518         {
 519             int g, h;
 520
 521             fepvals->separate_dvdl[efptFEP] = TRUE;
 522
 523             if (serializer->reading())
 524             {
 525                 /* copy the contents of the efptFEP lambda component to all
 526                    the other components */
 527                 for (g = 0; g < efptNR; g++)
 528                 {
 529                     for (h = 0; h < fepvals->n_lambda; h++)
 530                     {
 531                         if (g != efptFEP)
 532                         {
 533                             fepvals->all_lambda[g][h] =
 534                                 fepvals->all_lambda[efptFEP][h];
 535                         }
 536                     }
 537                 }
 538             }
 539         }
 540     }
 541     else
 542     {
 543         fepvals->n_lambda     = 0;
 544         fepvals->all_lambda   = nullptr;
 545         if (fepvals->init_lambda >= 0)
 546         {
 547             fepvals->separate_dvdl[efptFEP] = TRUE;
 548         }
 549     }
 550     serializer->doReal(&fepvals->sc_alpha);
 551     serializer->doInt(&fepvals->sc_power);
 552     if (file_version >= 79)
 553     {
 554         serializer->doReal(&fepvals->sc_r_power);
 555     }
 556     else
 557     {
 558         fepvals->sc_r_power = 6.0;
 559     }
 560     serializer->doReal(&fepvals->sc_sigma);
 561     if (serializer->reading())
 562     {
 563         if (file_version >= 71)
 564         {
 565             fepvals->sc_sigma_min = fepvals->sc_sigma;
 566         }
 567         else
 568         {
 569             fepvals->sc_sigma_min = 0;
 570         }
 571     }
 572     if (file_version >= 79)
 573     {
 574         serializer->doBool(&fepvals->bScCoul);
 575     }
 576     else
 577     {
 578         fepvals->bScCoul = TRUE;
 579     }
 580     if (file_version >= 64)
 581     {
 582         serializer->doInt(&fepvals->nstdhdl);
 583     }
 584     else
 585     {
 586         fepvals->nstdhdl = 1;
 587     }
 588
 589     if (file_version >= 73)
 590     {
 591         serializer->doInt(&fepvals->separate_dhdl_file);
 592         serializer->doInt(&fepvals->dhdl_derivatives);
 593     }
 594     else
 595     {
 596         fepvals->separate_dhdl_file = esepdhdlfileYES;
 597         fepvals->dhdl_derivatives   = edhdlderivativesYES;
 598     }
 599     if (file_version >= 71)
 600     {
 601         serializer->doInt(&fepvals->dh_hist_size);
 602         serializer->doDouble(&fepvals->dh_hist_spacing);
 603     }
 604     else
 605     {
 606         fepvals->dh_hist_size    = 0;
 607         fepvals->dh_hist_spacing = 0.1;
 608     }
 609     if (file_version >= 79)
 610     {
 611         serializer->doInt(&fepvals->edHdLPrintEnergy);
 612     }
 613     else
 614     {
 615         fepvals->edHdLPrintEnergy = edHdLPrintEnergyNO;
 616     }
 617
 618     /* handle lambda_neighbors */
 619     if ((file_version >= 83 && file_version < 90) || file_version >= 92)
 620     {
 621         serializer->doInt(&fepvals->lambda_neighbors);
 622         if ( (fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0) &&
 623              (fepvals->init_lambda < 0) )
 624         {
 625             fepvals->lambda_start_n = (fepvals->init_fep_state -
 626                                        fepvals->lambda_neighbors);
 627             fepvals->lambda_stop_n = (fepvals->init_fep_state +
 628                                       fepvals->lambda_neighbors + 1);
 629             if (fepvals->lambda_start_n < 0)
 630             {
 631                 fepvals->lambda_start_n = 0;;
 632             }
 633             if (fepvals->lambda_stop_n >= fepvals->n_lambda)
 634             {
 635                 fepvals->lambda_stop_n = fepvals->n_lambda;
 636             }
 637         }
 638         else
 639         {
 640             fepvals->lambda_start_n = 0;
 641             fepvals->lambda_stop_n  = fepvals->n_lambda;
 642         }
 643     }
 644     else
 645     {
 646         fepvals->lambda_start_n = 0;
 647         fepvals->lambda_stop_n  = fepvals->n_lambda;
 648     }
 649 }
 650
 651 static void do_awhBias(gmx::ISerializer *serializer, gmx::AwhBiasParams *awhBiasParams,
 652                        int gmx_unused file_version)
 653 {
 654     serializer->doInt(&awhBiasParams->eTarget);
 655     serializer->doDouble(&awhBiasParams->targetBetaScaling);
 656     serializer->doDouble(&awhBiasParams->targetCutoff);
 657     serializer->doInt(&awhBiasParams->eGrowth);
 658     serializer->doInt(&awhBiasParams->bUserData);
 659     serializer->doDouble(&awhBiasParams->errorInitial);
 660     serializer->doInt(&awhBiasParams->ndim);
 661     serializer->doInt(&awhBiasParams->shareGroup);
 662     serializer->doBool(&awhBiasParams->equilibrateHistogram);
 663
 664     if (serializer->reading())
 665     {
 666         snew(awhBiasParams->dimParams, awhBiasParams->ndim);
 667     }
 668
 669     for (int d = 0; d < awhBiasParams->ndim; d++)
 670     {
 671         gmx::AwhDimParams *dimParams = &awhBiasParams->dimParams[d];
 672
 673         serializer->doInt(&dimParams->eCoordProvider);
 674         serializer->doInt(&dimParams->coordIndex);
 675         serializer->doDouble(&dimParams->origin);
 676         serializer->doDouble(&dimParams->end);
 677         serializer->doDouble(&dimParams->period);
 678         serializer->doDouble(&dimParams->forceConstant);
 679         serializer->doDouble(&dimParams->diffusion);
 680         serializer->doDouble(&dimParams->coordValueInit);
 681         serializer->doDouble(&dimParams->coverDiameter);
 682     }
 683 }
 684
 685 static void do_awh(gmx::ISerializer         *serializer,
 686                    gmx::AwhParams           *awhParams,
 687                    int gmx_unused            file_version)
 688 {
 689     serializer->doInt(&awhParams->numBias);
 690     serializer->doInt(&awhParams->nstOut);
 691     serializer->doInt64(&awhParams->seed);
 692     serializer->doInt(&awhParams->nstSampleCoord);
 693     serializer->doInt(&awhParams->numSamplesUpdateFreeEnergy);
 694     serializer->doInt(&awhParams->ePotential);
 695     serializer->doBool(&awhParams->shareBiasMultisim);
 696
 697     if (awhParams->numBias > 0)
 698     {
 699         if (serializer->reading())
 700         {
 701             snew(awhParams->awhBiasParams, awhParams->numBias);
 702         }
 703
 704         for (int k = 0; k < awhParams->numBias; k++)
 705         {
 706             do_awhBias(serializer, &awhParams->awhBiasParams[k], file_version);
 707         }
 708     }
 709 }
 710
 711 static void do_pull(gmx::ISerializer         *serializer,
 712                     pull_params_t            *pull,
 713                     int                       file_version,
 714                     int                       ePullOld)
 715 {
 716     int  eGeomOld = -1;
 717     ivec dimOld;
 718     int  g;
 719
 720     if (file_version >= 95)
 721     {
 722         serializer->doInt(&pull->ngroup);
 723     }
 724     serializer->doInt(&pull->ncoord);
 725     if (file_version < 95)
 726     {
 727         pull->ngroup = pull->ncoord + 1;
 728     }
 729     if (file_version < tpxv_PullCoordTypeGeom)
 730     {
 731         real dum;
 732
 733         serializer->doInt(&eGeomOld);
 734         serializer->doIvec(&dimOld);
 735         /* The inner cylinder radius, now removed */
 736         serializer->doReal(&dum);
 737     }
 738     serializer->doReal(&pull->cylinder_r);
 739     serializer->doReal(&pull->constr_tol);
 740     if (file_version >= 95)
 741     {
 742         serializer->doBool(&pull->bPrintCOM);
 743         /* With file_version < 95 this value is set below */
 744     }
 745     if (file_version >= tpxv_ReplacePullPrintCOM12)
 746     {
 747         serializer->doBool(&pull->bPrintRefValue);
 748         serializer->doBool(&pull->bPrintComp);
 749     }
 750     else if (file_version >= tpxv_PullCoordTypeGeom)
 751     {
 752         int idum;
 753         serializer->doInt(&idum); /* used to be bPrintCOM2 */
 754         serializer->doBool(&pull->bPrintRefValue);
 755         serializer->doBool(&pull->bPrintComp);
 756     }
 757     else
 758     {
 759         pull->bPrintRefValue = FALSE;
 760         pull->bPrintComp     = TRUE;
 761     }
 762     serializer->doInt(&pull->nstxout);
 763     serializer->doInt(&pull->nstfout);
 764     if (file_version >= tpxv_PullPrevStepCOMAsReference)
 765     {
 766         serializer->doBool(&pull->bSetPbcRefToPrevStepCOM);
 767     }
 768     else
 769     {
 770         pull->bSetPbcRefToPrevStepCOM = FALSE;
 771     }
 772     if (serializer->reading())
 773     {
 774         snew(pull->group, pull->ngroup);
 775         snew(pull->coord, pull->ncoord);
 776     }
 777     if (file_version < 95)
 778     {
 779         /* epullgPOS for position pulling, before epullgDIRPBC was removed */
 780         if (eGeomOld == epullgDIRPBC)
 781         {
 782             gmx_fatal(FARGS, "pull-geometry=position is no longer supported");
 783         }
 784         if (eGeomOld > epullgDIRPBC)
 785         {
 786             eGeomOld -= 1;
 787         }
 788
 789         for (g = 0; g < pull->ngroup; g++)
 790         {
 791             /* We read and ignore a pull coordinate for group 0 */
 792             do_pullgrp_tpx_pre95(serializer, &pull->group[g], &pull->coord[std::max(g-1, 0)]);
 793             if (g > 0)
 794             {
 795                 pull->coord[g-1].group[0] = 0;
 796                 pull->coord[g-1].group[1] = g;
 797             }
 798         }
 799
 800         pull->bPrintCOM = (pull->group[0].nat > 0);
 801     }
 802     else
 803     {
 804         for (g = 0; g < pull->ngroup; g++)
 805         {
 806             do_pull_group(serializer, &pull->group[g]);
 807         }
 808         for (g = 0; g < pull->ncoord; g++)
 809         {
 810             do_pull_coord(serializer, &pull->coord[g],
 811                           file_version, ePullOld, eGeomOld, dimOld);
 812         }
 813     }
 814     if (file_version >= tpxv_PullAverage)
 815     {
 816         gmx_bool v;
 817
 818         v                  = pull->bXOutAverage;
 819         serializer->doBool(&v);
 820         pull->bXOutAverage = v;
 821         v                  = pull->bFOutAverage;
 822         serializer->doBool(&v);
 823         pull->bFOutAverage = v;
 824     }
 825 }
 826
 827
 828 static void do_rotgrp(gmx::ISerializer         *serializer,
 829                       t_rotgrp                 *rotg)
 830 {
 831     serializer->doInt(&rotg->eType);
 832     serializer->doInt(&rotg->bMassW);
 833     serializer->doInt(&rotg->nat);
 834     if (serializer->reading())
 835     {
 836         snew(rotg->ind, rotg->nat);
 837     }
 838     serializer->doIntArray(rotg->ind, rotg->nat);
 839     if (serializer->reading())
 840     {
 841         snew(rotg->x_ref, rotg->nat);
 842     }
 843     serializer->doRvecArray(rotg->x_ref, rotg->nat);
 844     serializer->doRvec(&rotg->inputVec);
 845     serializer->doRvec(&rotg->pivot);
 846     serializer->doReal(&rotg->rate);
 847     serializer->doReal(&rotg->k);
 848     serializer->doReal(&rotg->slab_dist);
 849     serializer->doReal(&rotg->min_gaussian);
 850     serializer->doReal(&rotg->eps);
 851     serializer->doInt(&rotg->eFittype);
 852     serializer->doInt(&rotg->PotAngle_nstep);
 853     serializer->doReal(&rotg->PotAngle_step);
 854 }
 855
 856 static void do_rot(gmx::ISerializer         *serializer,
 857                    t_rot                    *rot)
 858 {
 859     int g;
 860
 861     serializer->doInt(&rot->ngrp);
 862     serializer->doInt(&rot->nstrout);
 863     serializer->doInt(&rot->nstsout);
 864     if (serializer->reading())
 865     {
 866         snew(rot->grp, rot->ngrp);
 867     }
 868     for (g = 0; g < rot->ngrp; g++)
 869     {
 870         do_rotgrp(serializer, &rot->grp[g]);
 871     }
 872 }
 873
 874
 875 static void do_swapgroup(gmx::ISerializer         *serializer,
 876                          t_swapGroup              *g)
 877 {
 878
 879     /* Name of the group or molecule */
 880     std::string buf;
 881     if (serializer->reading())
 882     {
 883         serializer->doString(&buf);
 884         g->molname = gmx_strdup(buf.c_str());
 885     }
 886     else
 887     {
 888         buf = g->molname;
 889         serializer->doString(&buf);
 890     }
 891
 892     /* Number of atoms in the group */
 893     serializer->doInt(&g->nat);
 894
 895     /* The group's atom indices */
 896     if (serializer->reading())
 897     {
 898         snew(g->ind, g->nat);
 899     }
 900     serializer->doIntArray(g->ind, g->nat);
 901
 902     /* Requested counts for compartments A and B */
 903     serializer->doIntArray(g->nmolReq, eCompNR);
 904 }
 905
 906 static void do_swapcoords_tpx(gmx::ISerializer         *serializer,
 907                               t_swapcoords             *swap,
 908                               int                       file_version)
 909 {
 910     /* Enums for better readability of the code */
 911     enum {
 912         eCompA = 0, eCompB
 913     };
 914     enum {
 915         eChannel0 = 0, eChannel1
 916     };
 917
 918
 919     if (file_version >= tpxv_CompElPolyatomicIonsAndMultipleIonTypes)
 920     {
 921         /* The total number of swap groups is the sum of the fixed groups
 922          * (split0, split1, solvent), and the user-defined groups (2+ types of ions)
 923          */
 924         serializer->doInt(&swap->ngrp);
 925         if (serializer->reading())
 926         {
 927             snew(swap->grp, swap->ngrp);
 928         }
 929         for (int ig = 0; ig < swap->ngrp; ig++)
 930         {
 931             do_swapgroup(serializer, &swap->grp[ig]);
 932         }
 933         serializer->doBool(&swap->massw_split[eChannel0]);
 934         serializer->doBool(&swap->massw_split[eChannel1]);
 935         serializer->doInt(&swap->nstswap);
 936         serializer->doInt(&swap->nAverage);
 937         serializer->doReal(&swap->threshold);
 938         serializer->doReal(&swap->cyl0r);
 939         serializer->doReal(&swap->cyl0u);
 940         serializer->doReal(&swap->cyl0l);
 941         serializer->doReal(&swap->cyl1r);
 942         serializer->doReal(&swap->cyl1u);
 943         serializer->doReal(&swap->cyl1l);
 944     }
 945     else
 946     {
 947         /*** Support reading older CompEl .tpr files ***/
 948
 949         /* In the original CompEl .tpr files, we always have 5 groups: */
 950         swap->ngrp = 5;
 951         snew(swap->grp, swap->ngrp);
 952
 953         swap->grp[eGrpSplit0 ].molname = gmx_strdup("split0" );  // group 0: split0
 954         swap->grp[eGrpSplit1 ].molname = gmx_strdup("split1" );  // group 1: split1
 955         swap->grp[eGrpSolvent].molname = gmx_strdup("solvent");  // group 2: solvent
 956         swap->grp[3          ].molname = gmx_strdup("anions" );  // group 3: anions
 957         swap->grp[4          ].molname = gmx_strdup("cations");  // group 4: cations
 958
 959         serializer->doInt(&swap->grp[3].nat);
 960         serializer->doInt(&swap->grp[eGrpSolvent].nat);
 961         serializer->doInt(&swap->grp[eGrpSplit0].nat);
 962         serializer->doBool(&swap->massw_split[eChannel0]);
 963         serializer->doInt(&swap->grp[eGrpSplit1].nat);
 964         serializer->doBool(&swap->massw_split[eChannel1]);
 965         serializer->doInt(&swap->nstswap);
 966         serializer->doInt(&swap->nAverage);
 967         serializer->doReal(&swap->threshold);
 968         serializer->doReal(&swap->cyl0r);
 969         serializer->doReal(&swap->cyl0u);
 970         serializer->doReal(&swap->cyl0l);
 971         serializer->doReal(&swap->cyl1r);
 972         serializer->doReal(&swap->cyl1u);
 973         serializer->doReal(&swap->cyl1l);
 974
 975         // The order[] array keeps compatibility with older .tpr files
 976         // by reading in the groups in the classic order
 977         {
 978             const int order[4] = {3, eGrpSolvent, eGrpSplit0, eGrpSplit1 };
 979
 980             for (int ig = 0; ig < 4; ig++)
 981             {
 982                 int g = order[ig];
 983                 snew(swap->grp[g].ind, swap->grp[g].nat);
 984                 serializer->doIntArray(swap->grp[g].ind, swap->grp[g].nat);
 985             }
 986         }
 987
 988         for (int j = eCompA; j <= eCompB; j++)
 989         {
 990             serializer->doInt(&swap->grp[3].nmolReq[j]); // group 3 = anions
 991             serializer->doInt(&swap->grp[4].nmolReq[j]); // group 4 = cations
 992         }
 993     }                                                    /* End support reading older CompEl .tpr files */
 994
 995     if (file_version >= tpxv_CompElWithSwapLayerOffset)
 996     {
 997         serializer->doReal(&swap->bulkOffset[eCompA]);
 998         serializer->doReal(&swap->bulkOffset[eCompB]);
 999     }
1000
1001 }
1002
1003 static void do_legacy_efield(gmx::ISerializer *serializer, gmx::KeyValueTreeObjectBuilder *root)
1004 {
1005     const char *const dimName[] = { "x", "y", "z" };
1006
1007     auto              appliedForcesObj = root->addObject("applied-forces");
1008     auto              efieldObj        = appliedForcesObj.addObject("electric-field");
1009     // The content of the tpr file for this feature has
1010     // been the same since gromacs 4.0 that was used for
1011     // developing.
1012     for (int j = 0; j < DIM; ++j)
1013     {
1014         int n, nt;
1015         serializer->doInt(&n);
1016         serializer->doInt(&nt);
1017         std::vector<real> aa(n+1), phi(nt+1), at(nt+1), phit(nt+1);
1018         serializer->doRealArray(aa.data(),  n);
1019         serializer->doRealArray(phi.data(), n);
1020         serializer->doRealArray(at.data(),  nt);
1021         serializer->doRealArray(phit.data(), nt);
1022         if (n > 0)
1023         {
1024             if (n > 1 || nt > 1)
1025             {
1026                 gmx_fatal(FARGS, "Can not handle tpr files with more than one electric field term per direction.");
1027             }
1028             auto dimObj = efieldObj.addObject(dimName[j]);
1029             dimObj.addValue<real>("E0", aa[0]);
1030             dimObj.addValue<real>("omega", at[0]);
1031             dimObj.addValue<real>("t0", phi[0]);
1032             dimObj.addValue<real>("sigma", phit[0]);
1033         }
1034     }
1035 }
1036
1037
1038 static void do_inputrec(gmx::ISerializer         *serializer,
1039                         t_inputrec               *ir,
1040                         int                       file_version)
1041 {
1042     int      i, j, k, idum = 0;
1043     real     rdum;
1044     gmx_bool bdum = false;
1045
1046     if (file_version != tpx_version)
1047     {
1048         /* Give a warning about features that are not accessible */
1049         fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n",
1050                 file_version, tpx_version);
1051     }
1052
1053     if (file_version == 0)
1054     {
1055         return;
1056     }
1057
1058     gmx::KeyValueTreeBuilder       paramsBuilder;
1059     gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
1060
1061     /* Basic inputrec stuff */
1062     serializer->doInt(&ir->eI);
1063     if (file_version >= 62)
1064     {
1065         serializer->doInt64(&ir->nsteps);
1066     }
1067     else
1068     {
1069         serializer->doInt(&idum);
1070         ir->nsteps = idum;
1071     }
1072
1073     if (file_version >= 62)
1074     {
1075         serializer->doInt64(&ir->init_step);
1076     }
1077     else
1078     {
1079         serializer->doInt(&idum);
1080         ir->init_step = idum;
1081     }
1082
1083     serializer->doInt(&ir->simulation_part);
1084
1085     if (file_version >= 67)
1086     {
1087         serializer->doInt(&ir->nstcalcenergy);
1088     }
1089     else
1090     {
1091         ir->nstcalcenergy = 1;
1092     }
1093     if (file_version >= 81)
1094     {
1095         serializer->doInt(&ir->cutoff_scheme);
1096         if (file_version < 94)
1097         {
1098             ir->cutoff_scheme = 1 - ir->cutoff_scheme;
1099         }
1100     }
1101     else
1102     {
1103         ir->cutoff_scheme = ecutsGROUP;
1104     }
1105     serializer->doInt(&ir->ns_type);
1106     serializer->doInt(&ir->nstlist);
1107     serializer->doInt(&idum); /* used to be ndelta; not used anymore */
1108
1109     serializer->doReal(&ir->rtpi);
1110
1111     serializer->doInt(&ir->nstcomm);
1112     serializer->doInt(&ir->comm_mode);
1113
1114     /* ignore nstcheckpoint */
1115     if (file_version < tpxv_RemoveObsoleteParameters1)
1116     {
1117         serializer->doInt(&idum);
1118     }
1119
1120     serializer->doInt(&ir->nstcgsteep);
1121
1122     serializer->doInt(&ir->nbfgscorr);
1123
1124     serializer->doInt(&ir->nstlog);
1125     serializer->doInt(&ir->nstxout);
1126     serializer->doInt(&ir->nstvout);
1127     serializer->doInt(&ir->nstfout);
1128     serializer->doInt(&ir->nstenergy);
1129     serializer->doInt(&ir->nstxout_compressed);
1130     if (file_version >= 59)
1131     {
1132         serializer->doDouble(&ir->init_t);
1133         serializer->doDouble(&ir->delta_t);
1134     }
1135     else
1136     {
1137         serializer->doReal(&rdum);
1138         ir->init_t = rdum;
1139         serializer->doReal(&rdum);
1140         ir->delta_t = rdum;
1141     }
1142     serializer->doReal(&ir->x_compression_precision);
1143     if (file_version >= 81)
1144     {
1145         serializer->doReal(&ir->verletbuf_tol);
1146     }
1147     else
1148     {
1149         ir->verletbuf_tol = 0;
1150     }
1151     serializer->doReal(&ir->rlist);
1152     if (file_version >= 67 && file_version < tpxv_RemoveTwinRange)
1153     {
1154         if (serializer->reading())
1155         {
1156             // Reading such a file version could invoke the twin-range
1157             // scheme, about which mdrun should give a fatal error.
1158             real dummy_rlistlong = -1;
1159             serializer->doReal(&dummy_rlistlong);
1160
1161             if (ir->rlist > 0 && (dummy_rlistlong == 0 || dummy_rlistlong > ir->rlist))
1162             {
1163                 // Get mdrun to issue an error (regardless of
1164                 // ir->cutoff_scheme).
1165                 ir->useTwinRange = true;
1166             }
1167             else
1168             {
1169                 // grompp used to set rlistlong actively. Users were
1170                 // probably also confused and set rlistlong == rlist.
1171                 // However, in all remaining cases, it is safe to let
1172                 // mdrun proceed normally.
1173                 ir->useTwinRange = false;
1174             }
1175         }
1176     }
1177     else
1178     {
1179         // No need to read or write anything
1180         ir->useTwinRange = false;
1181     }
1182     if (file_version >= 82 && file_version != 90)
1183     {
1184         // Multiple time-stepping is no longer enabled, but the old
1185         // support required the twin-range scheme, for which mdrun
1186         // already emits a fatal error.
1187         int dummy_nstcalclr = -1;
1188         serializer->doInt(&dummy_nstcalclr);
1189     }
1190     serializer->doInt(&ir->coulombtype);
1191     if (file_version >= 81)
1192     {
1193         serializer->doInt(&ir->coulomb_modifier);
1194     }
1195     else
1196     {
1197         ir->coulomb_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1198     }
1199     serializer->doReal(&ir->rcoulomb_switch);
1200     serializer->doReal(&ir->rcoulomb);
1201     serializer->doInt(&ir->vdwtype);
1202     if (file_version >= 81)
1203     {
1204         serializer->doInt(&ir->vdw_modifier);
1205     }
1206     else
1207     {
1208         ir->vdw_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1209     }
1210     serializer->doReal(&ir->rvdw_switch);
1211     serializer->doReal(&ir->rvdw);
1212     serializer->doInt(&ir->eDispCorr);
1213     serializer->doReal(&ir->epsilon_r);
1214     serializer->doReal(&ir->epsilon_rf);
1215     serializer->doReal(&ir->tabext);
1216
1217     // This permits reading a .tpr file that used implicit solvent,
1218     // and later permitting mdrun to refuse to run it.
1219     if (serializer->reading())
1220     {
1221         if (file_version < tpxv_RemoveImplicitSolvation)
1222         {
1223             serializer->doInt(&idum);
1224             serializer->doInt(&idum);
1225             serializer->doReal(&rdum);
1226             serializer->doReal(&rdum);
1227             serializer->doInt(&idum);
1228             ir->implicit_solvent = (idum > 0);
1229         }
1230         else
1231         {
1232             ir->implicit_solvent = false;
1233         }
1234         if (file_version < tpxv_RemoveImplicitSolvation)
1235         {
1236             serializer->doReal(&rdum);
1237             serializer->doReal(&rdum);
1238             serializer->doReal(&rdum);
1239             serializer->doReal(&rdum);
1240             if (file_version >= 60)
1241             {
1242                 serializer->doReal(&rdum);
1243                 serializer->doInt(&idum);
1244             }
1245             serializer->doReal(&rdum);
1246         }
1247     }
1248
1249     if (file_version >= 81)
1250     {
1251         serializer->doReal(&ir->fourier_spacing);
1252     }
1253     else
1254     {
1255         ir->fourier_spacing = 0.0;
1256     }
1257     serializer->doInt(&ir->nkx);
1258     serializer->doInt(&ir->nky);
1259     serializer->doInt(&ir->nkz);
1260     serializer->doInt(&ir->pme_order);
1261     serializer->doReal(&ir->ewald_rtol);
1262
1263     if (file_version >= 93)
1264     {
1265         serializer->doReal(&ir->ewald_rtol_lj);
1266     }
1267     else
1268     {
1269         ir->ewald_rtol_lj = ir->ewald_rtol;
1270     }
1271     serializer->doInt(&ir->ewald_geometry);
1272     serializer->doReal(&ir->epsilon_surface);
1273
1274     /* ignore bOptFFT */
1275     if (file_version < tpxv_RemoveObsoleteParameters1)
1276     {
1277         serializer->doBool(&bdum);
1278     }
1279
1280     if (file_version >= 93)
1281     {
1282         serializer->doInt(&ir->ljpme_combination_rule);
1283     }
1284     serializer->doBool(&ir->bContinuation);
1285     serializer->doInt(&ir->etc);
1286     /* before version 18, ir->etc was a gmx_bool (ir->btc),
1287      * but the values 0 and 1 still mean no and
1288      * berendsen temperature coupling, respectively.
1289      */
1290     if (file_version >= 79)
1291     {
1292         serializer->doBool(&ir->bPrintNHChains);
1293     }
1294     if (file_version >= 71)
1295     {
1296         serializer->doInt(&ir->nsttcouple);
1297     }
1298     else
1299     {
1300         ir->nsttcouple = ir->nstcalcenergy;
1301     }
1302     serializer->doInt(&ir->epc);
1303     serializer->doInt(&ir->epct);
1304     if (file_version >= 71)
1305     {
1306         serializer->doInt(&ir->nstpcouple);
1307     }
1308     else
1309     {
1310         ir->nstpcouple = ir->nstcalcenergy;
1311     }
1312     serializer->doReal(&ir->tau_p);
1313     serializer->doRvec(&ir->ref_p[XX]);
1314     serializer->doRvec(&ir->ref_p[YY]);
1315     serializer->doRvec(&ir->ref_p[ZZ]);
1316     serializer->doRvec(&ir->compress[XX]);
1317     serializer->doRvec(&ir->compress[YY]);
1318     serializer->doRvec(&ir->compress[ZZ]);
1319     serializer->doInt(&ir->refcoord_scaling);
1320     serializer->doRvec(&ir->posres_com);
1321     serializer->doRvec(&ir->posres_comB);
1322
1323     if (file_version < 79)
1324     {
1325         serializer->doInt(&ir->andersen_seed);
1326     }
1327     else
1328     {
1329         ir->andersen_seed = 0;
1330     }
1331
1332     serializer->doReal(&ir->shake_tol);
1333
1334     serializer->doInt(&ir->efep);
1335     do_fepvals(serializer, ir->fepvals, file_version);
1336
1337     if (file_version >= 79)
1338     {
1339         serializer->doBool(&ir->bSimTemp);
1340         if (ir->bSimTemp)
1341         {
1342             ir->bSimTemp = TRUE;
1343         }
1344     }
1345     else
1346     {
1347         ir->bSimTemp = FALSE;
1348     }
1349     if (ir->bSimTemp)
1350     {
1351         do_simtempvals(serializer, ir->simtempvals, ir->fepvals->n_lambda, file_version);
1352     }
1353
1354     if (file_version >= 79)
1355     {
1356         serializer->doBool(&ir->bExpanded);
1357         if (ir->bExpanded)
1358         {
1359             ir->bExpanded = TRUE;
1360         }
1361         else
1362         {
1363             ir->bExpanded = FALSE;
1364         }
1365     }
1366     if (ir->bExpanded)
1367     {
1368         do_expandedvals(serializer, ir->expandedvals, ir->fepvals, file_version);
1369     }
1370
1371     serializer->doInt(&ir->eDisre);
1372     serializer->doInt(&ir->eDisreWeighting);
1373     serializer->doBool(&ir->bDisreMixed);
1374     serializer->doReal(&ir->dr_fc);
1375     serializer->doReal(&ir->dr_tau);
1376     serializer->doInt(&ir->nstdisreout);
1377     serializer->doReal(&ir->orires_fc);
1378     serializer->doReal(&ir->orires_tau);
1379     serializer->doInt(&ir->nstorireout);
1380
1381     /* ignore dihre_fc */
1382     if (file_version < 79)
1383     {
1384         serializer->doReal(&rdum);
1385     }
1386
1387     serializer->doReal(&ir->em_stepsize);
1388     serializer->doReal(&ir->em_tol);
1389     serializer->doBool(&ir->bShakeSOR);
1390     serializer->doInt(&ir->niter);
1391     serializer->doReal(&ir->fc_stepsize);
1392     serializer->doInt(&ir->eConstrAlg);
1393     serializer->doInt(&ir->nProjOrder);
1394     serializer->doReal(&ir->LincsWarnAngle);
1395     serializer->doInt(&ir->nLincsIter);
1396     serializer->doReal(&ir->bd_fric);
1397     if (file_version >= tpxv_Use64BitRandomSeed)
1398     {
1399         serializer->doInt64(&ir->ld_seed);
1400     }
1401     else
1402     {
1403         serializer->doInt(&idum);
1404         ir->ld_seed = idum;
1405     }
1406
1407     for (i = 0; i < DIM; i++)
1408     {
1409         serializer->doRvec(&ir->deform[i]);
1410     }
1411     serializer->doReal(&ir->cos_accel);
1412
1413     serializer->doInt(&ir->userint1);
1414     serializer->doInt(&ir->userint2);
1415     serializer->doInt(&ir->userint3);
1416     serializer->doInt(&ir->userint4);
1417     serializer->doReal(&ir->userreal1);
1418     serializer->doReal(&ir->userreal2);
1419     serializer->doReal(&ir->userreal3);
1420     serializer->doReal(&ir->userreal4);
1421
1422     /* AdResS is removed, but we need to be able to read old files,
1423        and let mdrun refuse to run them */
1424     if (file_version >= 77 && file_version < tpxv_RemoveAdress)
1425     {
1426         serializer->doBool(&ir->bAdress);
1427         if (ir->bAdress)
1428         {
1429             int  idum, numThermoForceGroups, numEnergyGroups;
1430             real rdum;
1431             rvec rvecdum;
1432             serializer->doInt(&idum);
1433             serializer->doReal(&rdum);
1434             serializer->doReal(&rdum);
1435             serializer->doReal(&rdum);
1436             serializer->doInt(&idum);
1437             serializer->doInt(&idum);
1438             serializer->doRvec(&rvecdum);
1439             serializer->doInt(&numThermoForceGroups);
1440             serializer->doReal(&rdum);
1441             serializer->doInt(&numEnergyGroups);
1442             serializer->doInt(&idum);
1443
1444             if (numThermoForceGroups > 0)
1445             {
1446                 std::vector<int> idumn(numThermoForceGroups);
1447                 serializer->doIntArray(idumn.data(), idumn.size());
1448             }
1449             if (numEnergyGroups > 0)
1450             {
1451                 std::vector<int> idumn(numEnergyGroups);
1452                 serializer->doIntArray(idumn.data(), idumn.size());
1453             }
1454         }
1455     }
1456     else
1457     {
1458         ir->bAdress = FALSE;
1459     }
1460
1461     /* pull stuff */
1462     {
1463         int ePullOld = 0;
1464
1465         if (file_version >= tpxv_PullCoordTypeGeom)
1466         {
1467             serializer->doBool(&ir->bPull);
1468         }
1469         else
1470         {
1471             serializer->doInt(&ePullOld);
1472             ir->bPull = (ePullOld > 0);
1473             /* We removed the first ePull=ePullNo for the enum */
1474             ePullOld -= 1;
1475         }
1476         if (ir->bPull)
1477         {
1478             if (serializer->reading())
1479             {
1480                 snew(ir->pull, 1);
1481             }
1482             do_pull(serializer, ir->pull, file_version, ePullOld);
1483         }
1484     }
1485
1486     if (file_version >= tpxv_AcceleratedWeightHistogram)
1487     {
1488         serializer->doBool(&ir->bDoAwh);
1489
1490         if (ir->bDoAwh)
1491         {
1492             if (serializer->reading())
1493             {
1494                 snew(ir->awhParams, 1);
1495             }
1496             do_awh(serializer, ir->awhParams, file_version);
1497         }
1498     }
1499     else
1500     {
1501         ir->bDoAwh = FALSE;
1502     }
1503
1504     /* Enforced rotation */
1505     if (file_version >= 74)
1506     {
1507         serializer->doBool(&ir->bRot);
1508         if (ir->bRot)
1509         {
1510             if (serializer->reading())
1511             {
1512                 snew(ir->rot, 1);
1513             }
1514             do_rot(serializer, ir->rot);
1515         }
1516     }
1517     else
1518     {
1519         ir->bRot = FALSE;
1520     }
1521
1522     /* Interactive molecular dynamics */
1523     if (file_version >= tpxv_InteractiveMolecularDynamics)
1524     {
1525         serializer->doBool(&ir->bIMD);
1526         if (ir->bIMD)
1527         {
1528             if (serializer->reading())
1529             {
1530                 snew(ir->imd, 1);
1531             }
1532             do_imd(serializer, ir->imd);
1533         }
1534     }
1535     else
1536     {
1537         /* We don't support IMD sessions for old .tpr files */
1538         ir->bIMD = FALSE;
1539     }
1540
1541     /* grpopts stuff */
1542     serializer->doInt(&ir->opts.ngtc);
1543     if (file_version >= 69)
1544     {
1545         serializer->doInt(&ir->opts.nhchainlength);
1546     }
1547     else
1548     {
1549         ir->opts.nhchainlength = 1;
1550     }
1551     serializer->doInt(&ir->opts.ngacc);
1552     serializer->doInt(&ir->opts.ngfrz);
1553     serializer->doInt(&ir->opts.ngener);
1554
1555     if (serializer->reading())
1556     {
1557         snew(ir->opts.nrdf,   ir->opts.ngtc);
1558         snew(ir->opts.ref_t,  ir->opts.ngtc);
1559         snew(ir->opts.annealing, ir->opts.ngtc);
1560         snew(ir->opts.anneal_npoints, ir->opts.ngtc);
1561         snew(ir->opts.anneal_time, ir->opts.ngtc);
1562         snew(ir->opts.anneal_temp, ir->opts.ngtc);
1563         snew(ir->opts.tau_t,  ir->opts.ngtc);
1564         snew(ir->opts.nFreeze, ir->opts.ngfrz);
1565         snew(ir->opts.acc,    ir->opts.ngacc);
1566         snew(ir->opts.egp_flags, ir->opts.ngener*ir->opts.ngener);
1567     }
1568     if (ir->opts.ngtc > 0)
1569     {
1570         serializer->doRealArray(ir->opts.nrdf, ir->opts.ngtc);
1571         serializer->doRealArray(ir->opts.ref_t, ir->opts.ngtc);
1572         serializer->doRealArray(ir->opts.tau_t, ir->opts.ngtc);
1573     }
1574     if (ir->opts.ngfrz > 0)
1575     {
1576         serializer->doIvecArray(ir->opts.nFreeze, ir->opts.ngfrz);
1577     }
1578     if (ir->opts.ngacc > 0)
1579     {
1580         serializer->doRvecArray(ir->opts.acc, ir->opts.ngacc);
1581     }
1582     serializer->doIntArray(ir->opts.egp_flags,
1583                            ir->opts.ngener*ir->opts.ngener);
1584
1585     /* First read the lists with annealing and npoints for each group */
1586     serializer->doIntArray(ir->opts.annealing, ir->opts.ngtc);
1587     serializer->doIntArray(ir->opts.anneal_npoints, ir->opts.ngtc);
1588     for (j = 0; j < (ir->opts.ngtc); j++)
1589     {
1590         k = ir->opts.anneal_npoints[j];
1591         if (serializer->reading())
1592         {
1593             snew(ir->opts.anneal_time[j], k);
1594             snew(ir->opts.anneal_temp[j], k);
1595         }
1596         serializer->doRealArray(ir->opts.anneal_time[j], k);
1597         serializer->doRealArray(ir->opts.anneal_temp[j], k);
1598     }
1599     /* Walls */
1600     {
1601         serializer->doInt(&ir->nwall);
1602         serializer->doInt(&ir->wall_type);
1603         serializer->doReal(&ir->wall_r_linpot);
1604         serializer->doInt(&ir->wall_atomtype[0]);
1605         serializer->doInt(&ir->wall_atomtype[1]);
1606         serializer->doReal(&ir->wall_density[0]);
1607         serializer->doReal(&ir->wall_density[1]);
1608         serializer->doReal(&ir->wall_ewald_zfac);
1609     }
1610
1611     /* Cosine stuff for electric fields */
1612     if (file_version < tpxv_GenericParamsForElectricField)
1613     {
1614         do_legacy_efield(serializer, &paramsObj);
1615     }
1616
1617     /* Swap ions */
1618     if (file_version >= tpxv_ComputationalElectrophysiology)
1619     {
1620         serializer->doInt(&ir->eSwapCoords);
1621         if (ir->eSwapCoords != eswapNO)
1622         {
1623             if (serializer->reading())
1624             {
1625                 snew(ir->swap, 1);
1626             }
1627             do_swapcoords_tpx(serializer, ir->swap, file_version);
1628         }
1629     }
1630
1631     /* QMMM stuff */
1632     {
1633         serializer->doBool(&ir->bQMMM);
1634         serializer->doInt(&ir->QMMMscheme);
1635         serializer->doReal(&ir->scalefactor);
1636         serializer->doInt(&ir->opts.ngQM);
1637         if (serializer->reading())
1638         {
1639             snew(ir->opts.QMmethod,    ir->opts.ngQM);
1640             snew(ir->opts.QMbasis,     ir->opts.ngQM);
1641             snew(ir->opts.QMcharge,    ir->opts.ngQM);
1642             snew(ir->opts.QMmult,      ir->opts.ngQM);
1643             snew(ir->opts.bSH,         ir->opts.ngQM);
1644             snew(ir->opts.CASorbitals, ir->opts.ngQM);
1645             snew(ir->opts.CASelectrons, ir->opts.ngQM);
1646             snew(ir->opts.SAon,        ir->opts.ngQM);
1647             snew(ir->opts.SAoff,       ir->opts.ngQM);
1648             snew(ir->opts.SAsteps,     ir->opts.ngQM);
1649         }
1650         if (ir->opts.ngQM > 0 && ir->bQMMM)
1651         {
1652             serializer->doIntArray(ir->opts.QMmethod, ir->opts.ngQM);
1653             serializer->doIntArray(ir->opts.QMbasis, ir->opts.ngQM);
1654             serializer->doIntArray(ir->opts.QMcharge, ir->opts.ngQM);
1655             serializer->doIntArray(ir->opts.QMmult, ir->opts.ngQM);
1656             serializer->doBoolArray(ir->opts.bSH, ir->opts.ngQM);
1657             serializer->doIntArray(ir->opts.CASorbitals, ir->opts.ngQM);
1658             serializer->doIntArray(ir->opts.CASelectrons, ir->opts.ngQM);
1659             serializer->doRealArray(ir->opts.SAon, ir->opts.ngQM);
1660             serializer->doRealArray(ir->opts.SAoff, ir->opts.ngQM);
1661             serializer->doIntArray(ir->opts.SAsteps, ir->opts.ngQM);
1662             /* We leave in dummy i/o for removed parameters to avoid
1663              * changing the tpr format for every QMMM change.
1664              */
1665             std::vector<int> dummy(ir->opts.ngQM, 0);
1666             serializer->doIntArray(dummy.data(), ir->opts.ngQM);
1667             serializer->doIntArray(dummy.data(), ir->opts.ngQM);
1668         }
1669         /* end of QMMM stuff */
1670     }
1671
1672     if (file_version >= tpxv_GenericParamsForElectricField)
1673     {
1674         if (serializer->reading())
1675         {
1676             paramsObj.mergeObject(
1677                     gmx::deserializeKeyValueTree(serializer));
1678         }
1679         else
1680         {
1681             GMX_RELEASE_ASSERT(ir->params != nullptr,
1682                                "Parameters should be present when writing inputrec");
1683             gmx::serializeKeyValueTree(*ir->params, serializer);
1684         }
1685     }
1686     if (serializer->reading())
1687     {
1688         ir->params = new gmx::KeyValueTreeObject(paramsBuilder.build());
1689         // Initialize internal parameters to an empty kvt for all tpr versions
1690         ir->internalParameters = std::make_unique<gmx::KeyValueTreeObject>();
1691     }
1692
1693     if (file_version >= tpxv_GenericInternalParameters)
1694     {
1695         if (serializer->reading())
1696         {
1697             ir->internalParameters = std::make_unique<gmx::KeyValueTreeObject>(gmx::deserializeKeyValueTree(serializer));
1698         }
1699         else
1700         {
1701             GMX_RELEASE_ASSERT(ir->internalParameters != nullptr,
1702                                "Parameters should be present when writing inputrec");
1703             gmx::serializeKeyValueTree(*ir->internalParameters, serializer);
1704         }
1705     }
1706 }
1707
1708
1709 static void do_harm(gmx::ISerializer *serializer, t_iparams *iparams)
1710 {
1711     serializer->doReal(&iparams->harmonic.rA);
1712     serializer->doReal(&iparams->harmonic.krA);
1713     serializer->doReal(&iparams->harmonic.rB);
1714     serializer->doReal(&iparams->harmonic.krB);
1715 }
1716
1717 static void do_iparams(gmx::ISerializer         *serializer,
1718                        t_functype                ftype,
1719                        t_iparams                *iparams,
1720                        int                       file_version)
1721 {
1722     int      idum;
1723     real     rdum;
1724
1725     switch (ftype)
1726     {
1727         case F_ANGLES:
1728         case F_G96ANGLES:
1729         case F_BONDS:
1730         case F_G96BONDS:
1731         case F_HARMONIC:
1732         case F_IDIHS:
1733             do_harm(serializer, iparams);
1734             if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && serializer->reading())
1735             {
1736                 /* Correct incorrect storage of parameters */
1737                 iparams->pdihs.phiB = iparams->pdihs.phiA;
1738                 iparams->pdihs.cpB  = iparams->pdihs.cpA;
1739             }
1740             break;
1741         case F_RESTRANGLES:
1742             serializer->doReal(&iparams->harmonic.rA);
1743             serializer->doReal(&iparams->harmonic.krA);
1744             break;
1745         case F_LINEAR_ANGLES:
1746             serializer->doReal(&iparams->linangle.klinA);
1747             serializer->doReal(&iparams->linangle.aA);
1748             serializer->doReal(&iparams->linangle.klinB);
1749             serializer->doReal(&iparams->linangle.aB);
1750             break;
1751         case F_FENEBONDS:
1752             serializer->doReal(&iparams->fene.bm);
1753             serializer->doReal(&iparams->fene.kb);
1754             break;
1755
1756         case F_RESTRBONDS:
1757             serializer->doReal(&iparams->restraint.lowA);
1758             serializer->doReal(&iparams->restraint.up1A);
1759             serializer->doReal(&iparams->restraint.up2A);
1760             serializer->doReal(&iparams->restraint.kA);
1761             serializer->doReal(&iparams->restraint.lowB);
1762             serializer->doReal(&iparams->restraint.up1B);
1763             serializer->doReal(&iparams->restraint.up2B);
1764             serializer->doReal(&iparams->restraint.kB);
1765             break;
1766         case F_TABBONDS:
1767         case F_TABBONDSNC:
1768         case F_TABANGLES:
1769         case F_TABDIHS:
1770             serializer->doReal(&iparams->tab.kA);
1771             serializer->doInt(&iparams->tab.table);
1772             serializer->doReal(&iparams->tab.kB);
1773             break;
1774         case F_CROSS_BOND_BONDS:
1775             serializer->doReal(&iparams->cross_bb.r1e);
1776             serializer->doReal(&iparams->cross_bb.r2e);
1777             serializer->doReal(&iparams->cross_bb.krr);
1778             break;
1779         case F_CROSS_BOND_ANGLES:
1780             serializer->doReal(&iparams->cross_ba.r1e);
1781             serializer->doReal(&iparams->cross_ba.r2e);
1782             serializer->doReal(&iparams->cross_ba.r3e);
1783             serializer->doReal(&iparams->cross_ba.krt);
1784             break;
1785         case F_UREY_BRADLEY:
1786             serializer->doReal(&iparams->u_b.thetaA);
1787             serializer->doReal(&iparams->u_b.kthetaA);
1788             serializer->doReal(&iparams->u_b.r13A);
1789             serializer->doReal(&iparams->u_b.kUBA);
1790             if (file_version >= 79)
1791             {
1792                 serializer->doReal(&iparams->u_b.thetaB);
1793                 serializer->doReal(&iparams->u_b.kthetaB);
1794                 serializer->doReal(&iparams->u_b.r13B);
1795                 serializer->doReal(&iparams->u_b.kUBB);
1796             }
1797             else
1798             {
1799                 iparams->u_b.thetaB  = iparams->u_b.thetaA;
1800                 iparams->u_b.kthetaB = iparams->u_b.kthetaA;
1801                 iparams->u_b.r13B    = iparams->u_b.r13A;
1802                 iparams->u_b.kUBB    = iparams->u_b.kUBA;
1803             }
1804             break;
1805         case F_QUARTIC_ANGLES:
1806             serializer->doReal(&iparams->qangle.theta);
1807             serializer->doRealArray(iparams->qangle.c, 5);
1808             break;
1809         case F_BHAM:
1810             serializer->doReal(&iparams->bham.a);
1811             serializer->doReal(&iparams->bham.b);
1812             serializer->doReal(&iparams->bham.c);
1813             break;
1814         case F_MORSE:
1815             serializer->doReal(&iparams->morse.b0A);
1816             serializer->doReal(&iparams->morse.cbA);
1817             serializer->doReal(&iparams->morse.betaA);
1818             if (file_version >= 79)
1819             {
1820                 serializer->doReal(&iparams->morse.b0B);
1821                 serializer->doReal(&iparams->morse.cbB);
1822                 serializer->doReal(&iparams->morse.betaB);
1823             }
1824             else
1825             {
1826                 iparams->morse.b0B   = iparams->morse.b0A;
1827                 iparams->morse.cbB   = iparams->morse.cbA;
1828                 iparams->morse.betaB = iparams->morse.betaA;
1829             }
1830             break;
1831         case F_CUBICBONDS:
1832             serializer->doReal(&iparams->cubic.b0);
1833             serializer->doReal(&iparams->cubic.kb);
1834             serializer->doReal(&iparams->cubic.kcub);
1835             break;
1836         case F_CONNBONDS:
1837             break;
1838         case F_POLARIZATION:
1839             serializer->doReal(&iparams->polarize.alpha);
1840             break;
1841         case F_ANHARM_POL:
1842             serializer->doReal(&iparams->anharm_polarize.alpha);
1843             serializer->doReal(&iparams->anharm_polarize.drcut);
1844             serializer->doReal(&iparams->anharm_polarize.khyp);
1845             break;
1846         case F_WATER_POL:
1847             serializer->doReal(&iparams->wpol.al_x);
1848             serializer->doReal(&iparams->wpol.al_y);
1849             serializer->doReal(&iparams->wpol.al_z);
1850             serializer->doReal(&iparams->wpol.rOH);
1851             serializer->doReal(&iparams->wpol.rHH);
1852             serializer->doReal(&iparams->wpol.rOD);
1853             break;
1854         case F_THOLE_POL:
1855             serializer->doReal(&iparams->thole.a);
1856             serializer->doReal(&iparams->thole.alpha1);
1857             serializer->doReal(&iparams->thole.alpha2);
1858             serializer->doReal(&iparams->thole.rfac);
1859             break;
1860         case F_LJ:
1861             serializer->doReal(&iparams->lj.c6);
1862             serializer->doReal(&iparams->lj.c12);
1863             break;
1864         case F_LJ14:
1865             serializer->doReal(&iparams->lj14.c6A);
1866             serializer->doReal(&iparams->lj14.c12A);
1867             serializer->doReal(&iparams->lj14.c6B);
1868             serializer->doReal(&iparams->lj14.c12B);
1869             break;
1870         case F_LJC14_Q:
1871             serializer->doReal(&iparams->ljc14.fqq);
1872             serializer->doReal(&iparams->ljc14.qi);
1873             serializer->doReal(&iparams->ljc14.qj);
1874             serializer->doReal(&iparams->ljc14.c6);
1875             serializer->doReal(&iparams->ljc14.c12);
1876             break;
1877         case F_LJC_PAIRS_NB:
1878             serializer->doReal(&iparams->ljcnb.qi);
1879             serializer->doReal(&iparams->ljcnb.qj);
1880             serializer->doReal(&iparams->ljcnb.c6);
1881             serializer->doReal(&iparams->ljcnb.c12);
1882             break;
1883         case F_PDIHS:
1884         case F_PIDIHS:
1885         case F_ANGRES:
1886         case F_ANGRESZ:
1887             serializer->doReal(&iparams->pdihs.phiA);
1888             serializer->doReal(&iparams->pdihs.cpA);
1889             serializer->doReal(&iparams->pdihs.phiB);
1890             serializer->doReal(&iparams->pdihs.cpB);
1891             serializer->doInt(&iparams->pdihs.mult);
1892             break;
1893         case F_RESTRDIHS:
1894             serializer->doReal(&iparams->pdihs.phiA);
1895             serializer->doReal(&iparams->pdihs.cpA);
1896             break;
1897         case F_DISRES:
1898             serializer->doInt(&iparams->disres.label);
1899             serializer->doInt(&iparams->disres.type);
1900             serializer->doReal(&iparams->disres.low);
1901             serializer->doReal(&iparams->disres.up1);
1902             serializer->doReal(&iparams->disres.up2);
1903             serializer->doReal(&iparams->disres.kfac);
1904             break;
1905         case F_ORIRES:
1906             serializer->doInt(&iparams->orires.ex);
1907             serializer->doInt(&iparams->orires.label);
1908             serializer->doInt(&iparams->orires.power);
1909             serializer->doReal(&iparams->orires.c);
1910             serializer->doReal(&iparams->orires.obs);
1911             serializer->doReal(&iparams->orires.kfac);
1912             break;
1913         case F_DIHRES:
1914             if (file_version < 82)
1915             {
1916                 serializer->doInt(&idum);
1917                 serializer->doInt(&idum);
1918             }
1919             serializer->doReal(&iparams->dihres.phiA);
1920             serializer->doReal(&iparams->dihres.dphiA);
1921             serializer->doReal(&iparams->dihres.kfacA);
1922             if (file_version >= 82)
1923             {
1924                 serializer->doReal(&iparams->dihres.phiB);
1925                 serializer->doReal(&iparams->dihres.dphiB);
1926                 serializer->doReal(&iparams->dihres.kfacB);
1927             }
1928             else
1929             {
1930                 iparams->dihres.phiB  = iparams->dihres.phiA;
1931                 iparams->dihres.dphiB = iparams->dihres.dphiA;
1932                 iparams->dihres.kfacB = iparams->dihres.kfacA;
1933             }
1934             break;
1935         case F_POSRES:
1936             serializer->doRvec(&iparams->posres.pos0A);
1937             serializer->doRvec(&iparams->posres.fcA);
1938             serializer->doRvec(&iparams->posres.pos0B);
1939             serializer->doRvec(&iparams->posres.fcB);
1940             break;
1941         case F_FBPOSRES:
1942             serializer->doInt(&iparams->fbposres.geom);
1943             serializer->doRvec(&iparams->fbposres.pos0);
1944             serializer->doReal(&iparams->fbposres.r);
1945             serializer->doReal(&iparams->fbposres.k);
1946             break;
1947         case F_CBTDIHS:
1948             serializer->doRealArray(iparams->cbtdihs.cbtcA, NR_CBTDIHS);
1949             break;
1950         case F_RBDIHS:
1951             serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
1952             serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
1953             break;
1954         case F_FOURDIHS:
1955             /* Fourier dihedrals are internally represented
1956              * as Ryckaert-Bellemans since those are faster to compute.
1957              */
1958             serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
1959             serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
1960             break;
1961         case F_CONSTR:
1962         case F_CONSTRNC:
1963             serializer->doReal(&iparams->constr.dA);
1964             serializer->doReal(&iparams->constr.dB);
1965             break;
1966         case F_SETTLE:
1967             serializer->doReal(&iparams->settle.doh);
1968             serializer->doReal(&iparams->settle.dhh);
1969             break;
1970         case F_VSITE2:
1971             serializer->doReal(&iparams->vsite.a);
1972             break;
1973         case F_VSITE3:
1974         case F_VSITE3FD:
1975         case F_VSITE3FAD:
1976             serializer->doReal(&iparams->vsite.a);
1977             serializer->doReal(&iparams->vsite.b);
1978             break;
1979         case F_VSITE3OUT:
1980         case F_VSITE4FD:
1981         case F_VSITE4FDN:
1982             serializer->doReal(&iparams->vsite.a);
1983             serializer->doReal(&iparams->vsite.b);
1984             serializer->doReal(&iparams->vsite.c);
1985             break;
1986         case F_VSITEN:
1987             serializer->doInt(&iparams->vsiten.n);
1988             serializer->doReal(&iparams->vsiten.a);
1989             break;
1990         case F_GB12_NOLONGERUSED:
1991         case F_GB13_NOLONGERUSED:
1992         case F_GB14_NOLONGERUSED:
1993             // Implicit solvent parameters can still be read, but never used
1994             if (serializer->reading())
1995             {
1996                 if (file_version < 68)
1997                 {
1998                     serializer->doReal(&rdum);
1999                     serializer->doReal(&rdum);
2000                     serializer->doReal(&rdum);
2001                     serializer->doReal(&rdum);
2002                 }
2003                 if (file_version < tpxv_RemoveImplicitSolvation)
2004                 {
2005                     serializer->doReal(&rdum);
2006                     serializer->doReal(&rdum);
2007                     serializer->doReal(&rdum);
2008                     serializer->doReal(&rdum);
2009                     serializer->doReal(&rdum);
2010                 }
2011             }
2012             break;
2013         case F_CMAP:
2014             serializer->doInt(&iparams->cmap.cmapA);
2015             serializer->doInt(&iparams->cmap.cmapB);
2016             break;
2017         default:
2018             gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
2019                       ftype, interaction_function[ftype].name, __FILE__, __LINE__);
2020     }
2021 }
2022
2023 static void do_ilist(gmx::ISerializer *serializer, InteractionList *ilist)
2024 {
2025     int nr = ilist->size();
2026     serializer->doInt(&nr);
2027     if (serializer->reading())
2028     {
2029         ilist->iatoms.resize(nr);
2030     }
2031     serializer->doIntArray(ilist->iatoms.data(), ilist->size());
2032 }
2033
2034 static void do_ffparams(gmx::ISerializer         *serializer,
2035                         gmx_ffparams_t           *ffparams,
2036                         int                       file_version)
2037 {
2038     serializer->doInt(&ffparams->atnr);
2039     int numTypes = ffparams->numTypes();
2040     serializer->doInt(&numTypes);
2041     if (serializer->reading())
2042     {
2043         ffparams->functype.resize(numTypes);
2044         ffparams->iparams.resize(numTypes);
2045     }
2046     /* Read/write all the function types */
2047     serializer->doIntArray(ffparams->functype.data(), ffparams->functype.size());
2048
2049     if (file_version >= 66)
2050     {
2051         serializer->doDouble(&ffparams->reppow);
2052     }
2053     else
2054     {
2055         ffparams->reppow = 12.0;
2056     }
2057
2058     serializer->doReal(&ffparams->fudgeQQ);
2059
2060     /* Check whether all these function types are supported by the code.
2061      * In practice the code is backwards compatible, which means that the
2062      * numbering may have to be altered from old numbering to new numbering
2063      */
2064     for (int i = 0; i < ffparams->numTypes(); i++)
2065     {
2066         if (serializer->reading())
2067         {
2068             /* Loop over file versions */
2069             for (int k = 0; k < NFTUPD; k++)
2070             {
2071                 /* Compare the read file_version to the update table */
2072                 if ((file_version < ftupd[k].fvnr) &&
2073                     (ffparams->functype[i] >= ftupd[k].ftype))
2074                 {
2075                     ffparams->functype[i] += 1;
2076                 }
2077             }
2078         }
2079
2080         do_iparams(serializer, ffparams->functype[i], &ffparams->iparams[i],
2081                    file_version);
2082     }
2083 }
2084
2085 static void add_settle_atoms(InteractionList *ilist)
2086 {
2087     int i;
2088
2089     /* Settle used to only store the first atom: add the other two */
2090     ilist->iatoms.resize(2*ilist->size());
2091     for (i = ilist->size()/4 - 1; i >= 0; i--)
2092     {
2093         ilist->iatoms[4*i+0] = ilist->iatoms[2*i+0];
2094         ilist->iatoms[4*i+1] = ilist->iatoms[2*i+1];
2095         ilist->iatoms[4*i+2] = ilist->iatoms[2*i+1] + 1;
2096         ilist->iatoms[4*i+3] = ilist->iatoms[2*i+1] + 2;
2097     }
2098 }
2099
2100 static void do_ilists(gmx::ISerializer         *serializer,
2101                       InteractionLists         *ilists,
2102                       int                       file_version)
2103 {
2104     GMX_RELEASE_ASSERT(ilists, "Need a valid ilists object");
2105     GMX_RELEASE_ASSERT(ilists->size() == F_NRE, "The code needs to be in sync with InteractionLists");
2106
2107     for (int j = 0; j < F_NRE; j++)
2108     {
2109         InteractionList &ilist  = (*ilists)[j];
2110         gmx_bool         bClear = FALSE;
2111         if (serializer->reading())
2112         {
2113             for (int k = 0; k < NFTUPD; k++)
2114             {
2115                 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
2116                 {
2117                     bClear = TRUE;
2118                 }
2119             }
2120         }
2121         if (bClear)
2122         {
2123             ilist.iatoms.clear();
2124         }
2125         else
2126         {
2127             do_ilist(serializer, &ilist);
2128             if (file_version < 78 && j == F_SETTLE && ilist.size() > 0)
2129             {
2130                 add_settle_atoms(&ilist);
2131             }
2132         }
2133     }
2134 }
2135
2136 static void do_block(gmx::ISerializer *serializer, t_block *block)
2137 {
2138     serializer->doInt(&block->nr);
2139     if (serializer->reading())
2140     {
2141         if ((block->nalloc_index > 0) && (nullptr != block->index))
2142         {
2143             sfree(block->index);
2144         }
2145         block->nalloc_index = block->nr+1;
2146         snew(block->index, block->nalloc_index);
2147     }
2148     serializer->doIntArray(block->index, block->nr+1);
2149 }
2150
2151 static void do_blocka(gmx::ISerializer *serializer, t_blocka *block)
2152 {
2153     serializer->doInt(&block->nr);
2154     serializer->doInt(&block->nra);
2155     if (serializer->reading())
2156     {
2157         block->nalloc_index = block->nr+1;
2158         snew(block->index, block->nalloc_index);
2159         block->nalloc_a = block->nra;
2160         snew(block->a, block->nalloc_a);
2161     }
2162     serializer->doIntArray(block->index, block->nr+1);
2163     serializer->doIntArray(block->a, block->nra);
2164 }
2165
2166 /* This is a primitive routine to make it possible to translate atomic numbers
2167  * to element names when reading TPR files, without making the Gromacs library
2168  * directory a dependency on mdrun (which is the case if we need elements.dat).
2169  */
2170 static const char *
2171 atomicnumber_to_element(int atomicnumber)
2172 {
2173     const char * p;
2174
2175     /* This does not have to be complete, so we only include elements likely
2176      * to occur in PDB files.
2177      */
2178     switch (atomicnumber)
2179     {
2180         case 1:  p = "H";  break;
2181         case 5:  p = "B";  break;
2182         case 6:  p = "C";  break;
2183         case 7:  p = "N";  break;
2184         case 8:  p = "O";  break;
2185         case 9:  p = "F";  break;
2186         case 11: p = "Na"; break;
2187         case 12: p = "Mg"; break;
2188         case 15: p = "P";  break;
2189         case 16: p = "S";  break;
2190         case 17: p = "Cl"; break;
2191         case 18: p = "Ar"; break;
2192         case 19: p = "K";  break;
2193         case 20: p = "Ca"; break;
2194         case 25: p = "Mn"; break;
2195         case 26: p = "Fe"; break;
2196         case 28: p = "Ni"; break;
2197         case 29: p = "Cu"; break;
2198         case 30: p = "Zn"; break;
2199         case 35: p = "Br"; break;
2200         case 47: p = "Ag"; break;
2201         default: p = "";   break;
2202     }
2203     return p;
2204 }
2205
2206
2207 static void do_atom(gmx::ISerializer *serializer, t_atom *atom)
2208 {
2209     serializer->doReal(&atom->m);
2210     serializer->doReal(&atom->q);
2211     serializer->doReal(&atom->mB);
2212     serializer->doReal(&atom->qB);
2213     serializer->doUShort(&atom->type);
2214     serializer->doUShort(&atom->typeB);
2215     serializer->doInt(&atom->ptype);
2216     serializer->doInt(&atom->resind);
2217     serializer->doInt(&atom->atomnumber);
2218     if (serializer->reading())
2219     {
2220         /* Set element string from atomic number if present.
2221          * This routine returns an empty string if the name is not found.
2222          */
2223         std::strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
2224         /* avoid warnings about potentially unterminated string */
2225         atom->elem[3] = '\0';
2226     }
2227 }
2228
2229 static void do_grps(gmx::ISerializer               *serializer,
2230                     gmx::ArrayRef<AtomGroupIndices> grps)
2231 {
2232     for (auto &group : grps)
2233     {
2234         int size = group.size();
2235         serializer->doInt(&size);
2236         if (serializer->reading())
2237         {
2238             group.resize(size);
2239         }
2240         serializer->doIntArray(group.data(), size);
2241     }
2242 }
2243
2244 static void do_symstr(gmx::ISerializer *serializer, char ***nm, t_symtab *symtab)
2245 {
2246     int ls;
2247
2248     if (serializer->reading())
2249     {
2250         serializer->doInt(&ls);
2251         *nm = get_symtab_handle(symtab, ls);
2252     }
2253     else
2254     {
2255         ls = lookup_symtab(symtab, *nm);
2256         serializer->doInt(&ls);
2257     }
2258 }
2259
2260 static void do_strstr(gmx::ISerializer         *serializer,
2261                       int                       nstr,
2262                       char                   ***nm,
2263                       t_symtab                 *symtab)
2264 {
2265     int  j;
2266
2267     for (j = 0; (j < nstr); j++)
2268     {
2269         do_symstr(serializer, &(nm[j]), symtab);
2270     }
2271 }
2272
2273 static void do_resinfo(gmx::ISerializer         *serializer,
2274                        int                       n,
2275                        t_resinfo                *ri,
2276                        t_symtab                 *symtab,
2277                        int                       file_version)
2278 {
2279     int  j;
2280
2281     for (j = 0; (j < n); j++)
2282     {
2283         do_symstr(serializer, &(ri[j].name), symtab);
2284         if (file_version >= 63)
2285         {
2286             serializer->doInt(&ri[j].nr);
2287             serializer->doUChar(&ri[j].ic);
2288         }
2289         else
2290         {
2291             ri[j].nr = j + 1;
2292             ri[j].ic = ' ';
2293         }
2294     }
2295 }
2296
2297 static void do_atoms(gmx::ISerializer         *serializer,
2298                      t_atoms                  *atoms,
2299                      t_symtab                 *symtab,
2300                      int                       file_version)
2301 {
2302     int i;
2303
2304     serializer->doInt(&atoms->nr);
2305     serializer->doInt(&atoms->nres);
2306     if (serializer->reading())
2307     {
2308         /* Since we have always written all t_atom properties in the tpr file
2309          * (at least for all backward compatible versions), we don't store
2310          * but simple set the booleans here.
2311          */
2312         atoms->haveMass    = TRUE;
2313         atoms->haveCharge  = TRUE;
2314         atoms->haveType    = TRUE;
2315         atoms->haveBState  = TRUE;
2316         atoms->havePdbInfo = FALSE;
2317
2318         snew(atoms->atom, atoms->nr);
2319         snew(atoms->atomname, atoms->nr);
2320         snew(atoms->atomtype, atoms->nr);
2321         snew(atoms->atomtypeB, atoms->nr);
2322         snew(atoms->resinfo, atoms->nres);
2323         atoms->pdbinfo = nullptr;
2324     }
2325     else
2326     {
2327         GMX_RELEASE_ASSERT(atoms->haveMass && atoms->haveCharge && atoms->haveType && atoms->haveBState, "Mass, charge, atomtype and B-state parameters should be present in t_atoms when writing a tpr file");
2328     }
2329     for (i = 0; (i < atoms->nr); i++)
2330     {
2331         do_atom(serializer, &atoms->atom[i]);
2332     }
2333     do_strstr(serializer, atoms->nr, atoms->atomname, symtab);
2334     do_strstr(serializer, atoms->nr, atoms->atomtype, symtab);
2335     do_strstr(serializer, atoms->nr, atoms->atomtypeB, symtab);
2336
2337     do_resinfo(serializer, atoms->nres, atoms->resinfo, symtab, file_version);
2338 }
2339
2340 static void do_groups(gmx::ISerializer         *serializer,
2341                       SimulationGroups         *groups,
2342                       t_symtab                 *symtab)
2343 {
2344     do_grps(serializer, groups->groups);
2345     int numberOfGroupNames = groups->groupNames.size();
2346     serializer->doInt(&numberOfGroupNames);
2347     if (serializer->reading())
2348     {
2349         groups->groupNames.resize(numberOfGroupNames);
2350     }
2351     do_strstr(serializer, numberOfGroupNames, groups->groupNames.data(), symtab);
2352     for (auto group : gmx::keysOf(groups->groupNumbers))
2353     {
2354         int numberOfGroupNumbers = groups->numberOfGroupNumbers(group);
2355         serializer->doInt(&numberOfGroupNumbers);
2356         if (numberOfGroupNumbers != 0)
2357         {
2358             if (serializer->reading())
2359             {
2360                 groups->groupNumbers[group].resize(numberOfGroupNumbers);
2361             }
2362             serializer->doUCharArray(groups->groupNumbers[group].data(), numberOfGroupNumbers);
2363         }
2364     }
2365 }
2366
2367 static void do_atomtypes(gmx::ISerializer *serializer, t_atomtypes *atomtypes,
2368                          int file_version)
2369 {
2370     int      j;
2371
2372     serializer->doInt(&atomtypes->nr);
2373     j = atomtypes->nr;
2374     if (serializer->reading())
2375     {
2376         snew(atomtypes->atomnumber, j);
2377     }
2378     if (serializer->reading() && file_version < tpxv_RemoveImplicitSolvation)
2379     {
2380         std::vector<real> dummy(atomtypes->nr, 0);
2381         serializer->doRealArray(dummy.data(), dummy.size());
2382         serializer->doRealArray(dummy.data(), dummy.size());
2383         serializer->doRealArray(dummy.data(), dummy.size());
2384     }
2385     serializer->doIntArray(atomtypes->atomnumber, j);
2386
2387     if (serializer->reading() && file_version >= 60 && file_version < tpxv_RemoveImplicitSolvation)
2388     {
2389         std::vector<real> dummy(atomtypes->nr, 0);
2390         serializer->doRealArray(dummy.data(), dummy.size());
2391         serializer->doRealArray(dummy.data(), dummy.size());
2392     }
2393 }
2394
2395 static void do_symtab(gmx::ISerializer *serializer, t_symtab *symtab)
2396 {
2397     int       i, nr;
2398     t_symbuf *symbuf;
2399
2400     serializer->doInt(&symtab->nr);
2401     nr     = symtab->nr;
2402     if (serializer->reading())
2403     {
2404         snew(symtab->symbuf, 1);
2405         symbuf          = symtab->symbuf;
2406         symbuf->bufsize = nr;
2407         snew(symbuf->buf, nr);
2408         for (i = 0; (i < nr); i++)
2409         {
2410             std::string buf;
2411             serializer->doString(&buf);
2412             symbuf->buf[i] = gmx_strdup(buf.c_str());
2413         }
2414     }
2415     else
2416     {
2417         symbuf = symtab->symbuf;
2418         while (symbuf != nullptr)
2419         {
2420             for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
2421             {
2422                 std::string buf = symbuf->buf[i];
2423                 serializer->doString(&buf);
2424             }
2425             nr    -= i;
2426             symbuf = symbuf->next;
2427         }
2428         if (nr != 0)
2429         {
2430             gmx_fatal(FARGS, "nr of symtab strings left: %d", nr);
2431         }
2432     }
2433 }
2434
2435 static void do_cmap(gmx::ISerializer *serializer, gmx_cmap_t *cmap_grid)
2436 {
2437
2438     int ngrid = cmap_grid->cmapdata.size();
2439     serializer->doInt(&ngrid);
2440     serializer->doInt(&cmap_grid->grid_spacing);
2441
2442     int gs    = cmap_grid->grid_spacing;
2443     int nelem = gs * gs;
2444
2445     if (serializer->reading())
2446     {
2447         cmap_grid->cmapdata.resize(ngrid);
2448
2449         for (int i = 0; i < ngrid; i++)
2450         {
2451             cmap_grid->cmapdata[i].cmap.resize(4*nelem);
2452         }
2453     }
2454
2455     for (int i = 0; i < ngrid; i++)
2456     {
2457         for (int j = 0; j < nelem; j++)
2458         {
2459             serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4]);
2460             serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4+1]);
2461             serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4+2]);
2462             serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4+3]);
2463         }
2464     }
2465 }
2466
2467
2468 static void do_moltype(gmx::ISerializer         *serializer,
2469                        gmx_moltype_t            *molt,
2470                        t_symtab                 *symtab,
2471                        int                       file_version)
2472 {
2473     do_symstr(serializer, &(molt->name), symtab);
2474
2475     do_atoms(serializer, &molt->atoms, symtab, file_version);
2476
2477     do_ilists(serializer, &molt->ilist, file_version);
2478
2479     do_block(serializer, &molt->cgs);
2480
2481     /* This used to be in the atoms struct */
2482     do_blocka(serializer, &molt->excls);
2483 }
2484
2485 static void do_molblock(gmx::ISerializer         *serializer,
2486                         gmx_molblock_t           *molb,
2487                         int                       numAtomsPerMolecule)
2488 {
2489     serializer->doInt(&molb->type);
2490     serializer->doInt(&molb->nmol);
2491     /* To maintain forward topology reading compatibility, we store #atoms.
2492      * TODO: Change this to conditional reading of a dummy int when we
2493      *       increase tpx_generation.
2494      */
2495     serializer->doInt(&numAtomsPerMolecule);
2496     /* Position restraint coordinates */
2497     int numPosres_xA = molb->posres_xA.size();
2498     serializer->doInt(&numPosres_xA);
2499     if (numPosres_xA > 0)
2500     {
2501         if (serializer->reading())
2502         {
2503             molb->posres_xA.resize(numPosres_xA);
2504         }
2505         serializer->doRvecArray(as_rvec_array(molb->posres_xA.data()), numPosres_xA);
2506     }
2507     int numPosres_xB = molb->posres_xB.size();
2508     serializer->doInt(&numPosres_xB);
2509     if (numPosres_xB > 0)
2510     {
2511         if (serializer->reading())
2512         {
2513             molb->posres_xB.resize(numPosres_xB);
2514         }
2515         serializer->doRvecArray(as_rvec_array(molb->posres_xB.data()), numPosres_xB);
2516     }
2517
2518 }
2519
2520 static void set_disres_npair(gmx_mtop_t *mtop)
2521 {
2522     gmx_mtop_ilistloop_t     iloop;
2523     int                      nmol;
2524
2525     gmx::ArrayRef<t_iparams> ip = mtop->ffparams.iparams;
2526
2527     iloop     = gmx_mtop_ilistloop_init(mtop);
2528     while (const InteractionLists *ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
2529     {
2530         const InteractionList &il = (*ilist)[F_DISRES];
2531
2532         if (il.size() > 0)
2533         {
2534             gmx::ArrayRef<const int> a     = il.iatoms;
2535             int                      npair = 0;
2536             for (int i = 0; i < il.size(); i += 3)
2537             {
2538                 npair++;
2539                 if (i+3 == il.size() || ip[a[i]].disres.label != ip[a[i+3]].disres.label)
2540                 {
2541                     ip[a[i]].disres.npair = npair;
2542                     npair                 = 0;
2543                 }
2544             }
2545         }
2546     }
2547 }
2548
2549 static void do_mtop(gmx::ISerializer         *serializer,
2550                     gmx_mtop_t               *mtop,
2551                     int                       file_version)
2552 {
2553     do_symtab(serializer, &(mtop->symtab));
2554
2555     do_symstr(serializer, &(mtop->name), &(mtop->symtab));
2556
2557     do_ffparams(serializer, &mtop->ffparams, file_version);
2558
2559     int nmoltype = mtop->moltype.size();
2560     serializer->doInt(&nmoltype);
2561     if (serializer->reading())
2562     {
2563         mtop->moltype.resize(nmoltype);
2564     }
2565     for (gmx_moltype_t &moltype : mtop->moltype)
2566     {
2567         do_moltype(serializer, &moltype, &mtop->symtab, file_version);
2568     }
2569
2570     int nmolblock = mtop->molblock.size();
2571     serializer->doInt(&nmolblock);
2572     if (serializer->reading())
2573     {
2574         mtop->molblock.resize(nmolblock);
2575     }
2576     for (gmx_molblock_t &molblock : mtop->molblock)
2577     {
2578         int numAtomsPerMolecule = (serializer->reading() ? 0 : mtop->moltype[molblock.type].atoms.nr);
2579         do_molblock(serializer, &molblock, numAtomsPerMolecule);
2580     }
2581     serializer->doInt(&mtop->natoms);
2582
2583     if (file_version >= tpxv_IntermolecularBondeds)
2584     {
2585         serializer->doBool(&mtop->bIntermolecularInteractions);
2586         if (mtop->bIntermolecularInteractions)
2587         {
2588             if (serializer->reading())
2589             {
2590                 mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
2591             }
2592             do_ilists(serializer, mtop->intermolecular_ilist.get(), file_version);
2593         }
2594     }
2595     else
2596     {
2597         mtop->bIntermolecularInteractions = FALSE;
2598     }
2599
2600     do_atomtypes (serializer, &(mtop->atomtypes), file_version);
2601
2602     if (file_version >= 65)
2603     {
2604         do_cmap(serializer, &mtop->ffparams.cmap_grid);
2605     }
2606     else
2607     {
2608         mtop->ffparams.cmap_grid.grid_spacing = 0;
2609         mtop->ffparams.cmap_grid.cmapdata.clear();
2610     }
2611
2612     do_groups(serializer, &mtop->groups, &(mtop->symtab));
2613
2614     mtop->haveMoleculeIndices = true;
2615
2616     if (serializer->reading())
2617     {
2618         close_symtab(&(mtop->symtab));
2619     }
2620 }
2621
2622 /*! \brief
2623  * Read the first part of the TPR file to find general system information.
2624  *
2625  * If \p TopOnlyOK is true then we can read even future versions
2626  * of tpx files, provided the \p fileGeneration hasn't changed.
2627  * If it is false, we need the \p ir too, and bail out
2628  * if the file is newer than the program.
2629  *
2630  * The version and generation of the topology (see top of this file)
2631  * are returned in the two last arguments, if those arguments are non-nullptr.
2632  *
2633  * If possible, we will read the \p ir even when \p TopOnlyOK is true.
2634  *
2635  * \param[in,out] serializer The serializer used to handle header processing.
2636  * \param[in,out] tpx File header datastructure.
2637  * \param[in]     filename The name of the file being read/written
2638  * \param[in,out] fio File handle.
2639  * \param[in] TopOnlyOK If not reading \p ir is fine or not.
2640  */
2641 static void do_tpxheader(gmx::FileIOXdrSerializer *serializer,
2642                          TpxFileHeader            *tpx,
2643                          const char               *filename,
2644                          t_fileio                 *fio,
2645                          bool                      TopOnlyOK)
2646 {
2647     gmx_bool  bDouble;
2648     int       precision;
2649     int       idum = 0;
2650     real      rdum = 0;
2651
2652     /* XDR binary topology file */
2653     precision = sizeof(real);
2654     std::string buf;
2655     std::string fileTag;
2656     if (serializer->reading())
2657     {
2658         serializer->doString(&buf);
2659         if (std::strncmp(buf.c_str(), "VERSION", 7) != 0)
2660         {
2661             gmx_fatal(FARGS, "Can not read file %s,\n"
2662                       "             this file is from a GROMACS version which is older than 2.0\n"
2663                       "             Make a new one with grompp or use a gro or pdb file, if possible",
2664                       filename);
2665         }
2666         serializer->doInt(&precision);
2667         bDouble = (precision == sizeof(double));
2668         if ((precision != sizeof(float)) && !bDouble)
2669         {
2670             gmx_fatal(FARGS, "Unknown precision in file %s: real is %d bytes "
2671                       "instead of %zu or %zu",
2672                       filename, precision, sizeof(float), sizeof(double));
2673         }
2674         gmx_fio_setprecision(fio, bDouble);
2675         fprintf(stderr, "Reading file %s, %s (%s precision)\n",
2676                 filename, buf.c_str(), bDouble ? "double" : "single");
2677     }
2678     else
2679     {
2680         buf = gmx::formatString("VERSION %s", gmx_version());
2681         serializer->doString(&buf);
2682         bDouble = (precision == sizeof(double));
2683         gmx_fio_setprecision(fio, bDouble);
2684         serializer->doInt(&precision);
2685         fileTag        = gmx::formatString("%s", tpx_tag);
2686     }
2687
2688     /* Check versions! */
2689     serializer->doInt(&tpx->fileVersion);
2690
2691     /* This is for backward compatibility with development versions 77-79
2692      * where the tag was, mistakenly, placed before the generation,
2693      * which would cause a segv instead of a proper error message
2694      * when reading the topology only from tpx with <77 code.
2695      */
2696     if (tpx->fileVersion >= 77 && tpx->fileVersion <= 79)
2697     {
2698         serializer->doString(&fileTag);
2699     }
2700
2701     serializer->doInt(&tpx->fileGeneration);
2702
2703     if (tpx->fileVersion >= 81)
2704     {
2705         serializer->doString(&fileTag);
2706     }
2707     if (serializer->reading())
2708     {
2709         if (tpx->fileVersion < 77)
2710         {
2711             /* Versions before 77 don't have the tag, set it to release */
2712             fileTag = gmx::formatString("%s", TPX_TAG_RELEASE);
2713         }
2714
2715         if (fileTag != tpx_tag)
2716         {
2717             fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n",
2718                     fileTag.c_str(), tpx_tag);
2719
2720             /* We only support reading tpx files with the same tag as the code
2721              * or tpx files with the release tag and with lower version number.
2722              */
2723             if (fileTag != TPX_TAG_RELEASE && tpx->fileVersion < tpx_version)
2724             {
2725                 gmx_fatal(FARGS, "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
2726                           filename, tpx->fileVersion, fileTag.c_str(),
2727                           tpx_version, tpx_tag);
2728             }
2729         }
2730     }
2731
2732     if ((tpx->fileVersion <= tpx_incompatible_version) ||
2733         ((tpx->fileVersion > tpx_version) && !TopOnlyOK) ||
2734         (tpx->fileGeneration > tpx_generation) ||
2735         tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
2736     {
2737         gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program",
2738                   filename, tpx->fileVersion, tpx_version);
2739     }
2740
2741     serializer->doInt(&tpx->natoms);
2742     serializer->doInt(&tpx->ngtc);
2743
2744     if (tpx->fileVersion < 62)
2745     {
2746         serializer->doInt(&idum);
2747         serializer->doReal(&rdum);
2748     }
2749     if (tpx->fileVersion >= 79)
2750     {
2751         serializer->doInt(&tpx->fep_state);
2752     }
2753     serializer->doReal(&tpx->lambda);
2754     serializer->doBool(&tpx->bIr);
2755     serializer->doBool(&tpx->bTop);
2756     serializer->doBool(&tpx->bX);
2757     serializer->doBool(&tpx->bV);
2758     serializer->doBool(&tpx->bF);
2759     serializer->doBool(&tpx->bBox);
2760
2761     if ((tpx->fileGeneration > tpx_generation))
2762     {
2763         /* This can only happen if TopOnlyOK=TRUE */
2764         tpx->bIr = FALSE;
2765     }
2766 }
2767
2768 static int do_tpx_body(gmx::ISerializer *serializer,
2769                        TpxFileHeader    *tpx,
2770                        t_inputrec       *ir,
2771                        t_state          *state,
2772                        rvec             *x,
2773                        rvec             *v,
2774                        gmx_mtop_t       *mtop)
2775 {
2776     int             ePBC;
2777     gmx_bool        bPeriodicMols;
2778
2779     if (!serializer->reading())
2780     {
2781         GMX_RELEASE_ASSERT(x == nullptr && v == nullptr, "Passing separate x and v pointers to do_tpx() is not supported when writing");
2782     }
2783     else
2784     {
2785         GMX_RELEASE_ASSERT(!(x == nullptr && v != nullptr), "Passing x==NULL and v!=NULL is not supported");
2786     }
2787
2788     if (serializer->reading())
2789     {
2790         state->flags = 0;
2791         init_gtc_state(state, tpx->ngtc, 0, 0);
2792         if (x == nullptr)
2793         {
2794             // v is also nullptr by the above assertion, so we may
2795             // need to make memory in state for storing the contents
2796             // of the tpx file.
2797             if (tpx->bX)
2798             {
2799                 state->flags |= (1 << estX);
2800             }
2801             if (tpx->bV)
2802             {
2803                 state->flags |= (1 << estV);
2804             }
2805             state_change_natoms(state, tpx->natoms);
2806         }
2807     }
2808
2809     if (x == nullptr)
2810     {
2811         x = state->x.rvec_array();
2812         v = state->v.rvec_array();
2813     }
2814
2815 #define do_test(serializer, b, p) if ((serializer)->reading() && ((p) != nullptr) && !(b)) gmx_fatal(FARGS, "No %s in input file",#p)
2816
2817     do_test(serializer, tpx->bBox, state->box);
2818     if (tpx->bBox)
2819     {
2820         serializer->doRvecArray(state->box, DIM);
2821         if (tpx->fileVersion >= 51)
2822         {
2823             serializer->doRvecArray(state->box_rel, DIM);
2824         }
2825         else
2826         {
2827             /* We initialize box_rel after reading the inputrec */
2828             clear_mat(state->box_rel);
2829         }
2830         serializer->doRvecArray(state->boxv, DIM);
2831         if (tpx->fileVersion < 56)
2832         {
2833             matrix mdum;
2834             serializer->doRvecArray(mdum, DIM);
2835         }
2836     }
2837
2838     if (state->ngtc > 0)
2839     {
2840         real *dumv;
2841         snew(dumv, state->ngtc);
2842         if (tpx->fileVersion < 69)
2843         {
2844             serializer->doRealArray(dumv, state->ngtc);
2845         }
2846         /* These used to be the Berendsen tcoupl_lambda's */
2847         serializer->doRealArray(dumv, state->ngtc);
2848         sfree(dumv);
2849     }
2850
2851     do_test(serializer, tpx->bTop, mtop);
2852     if (tpx->bTop)
2853     {
2854         if (mtop)
2855         {
2856             do_mtop(serializer, mtop, tpx->fileVersion);
2857         }
2858         else
2859         {
2860             gmx_mtop_t dum_top;
2861             do_mtop(serializer, &dum_top, tpx->fileVersion);
2862         }
2863     }
2864     do_test(serializer, tpx->bX, x);
2865     if (tpx->bX)
2866     {
2867         if (serializer->reading())
2868         {
2869             state->flags |= (1<<estX);
2870         }
2871         serializer->doRvecArray(x, tpx->natoms);
2872     }
2873
2874     do_test(serializer, tpx->bV, v);
2875     if (tpx->bV)
2876     {
2877         if (serializer->reading())
2878         {
2879             state->flags |= (1<<estV);
2880         }
2881         if (!v)
2882         {
2883             std::vector<gmx::RVec> dummyVelocities(tpx->natoms);
2884             serializer->doRvecArray(as_rvec_array(dummyVelocities.data()), tpx->natoms);
2885         }
2886         else
2887         {
2888             serializer->doRvecArray(v, tpx->natoms);
2889         }
2890     }
2891
2892     // No need to run do_test when the last argument is NULL
2893     if (tpx->bF)
2894     {
2895         std::vector<gmx::RVec> dummyForces(state->natoms);
2896         serializer->doRvecArray(as_rvec_array(dummyForces.data()), tpx->natoms);
2897     }
2898
2899     /* Starting with tpx version 26, we have the inputrec
2900      * at the end of the file, so we can ignore it
2901      * if the file is never than the software (but still the
2902      * same generation - see comments at the top of this file.
2903      *
2904      *
2905      */
2906     ePBC          = -1;
2907     bPeriodicMols = FALSE;
2908
2909     do_test(serializer, tpx->bIr, ir);
2910     if (tpx->bIr)
2911     {
2912         if (tpx->fileVersion >= 53)
2913         {
2914             /* Removed the pbc info from do_inputrec, since we always want it */
2915             if (!serializer->reading())
2916             {
2917                 ePBC          = ir->ePBC;
2918                 bPeriodicMols = ir->bPeriodicMols;
2919             }
2920             serializer->doInt(&ePBC);
2921             serializer->doBool(&bPeriodicMols);
2922         }
2923         if (tpx->fileGeneration <= tpx_generation && ir)
2924         {
2925             do_inputrec(serializer, ir, tpx->fileVersion);
2926             if (tpx->fileVersion < 51)
2927             {
2928                 set_box_rel(ir, state);
2929             }
2930             if (tpx->fileVersion < 53)
2931             {
2932                 ePBC          = ir->ePBC;
2933                 bPeriodicMols = ir->bPeriodicMols;
2934             }
2935         }
2936         if (serializer->reading() && ir && tpx->fileVersion >= 53)
2937         {
2938             /* We need to do this after do_inputrec, since that initializes ir */
2939             ir->ePBC          = ePBC;
2940             ir->bPeriodicMols = bPeriodicMols;
2941         }
2942     }
2943
2944     if (serializer->reading())
2945     {
2946         if (tpx->bIr && ir)
2947         {
2948             if (state->ngtc == 0)
2949             {
2950                 /* Reading old version without tcoupl state data: set it */
2951                 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
2952             }
2953             if (tpx->bTop && mtop)
2954             {
2955                 if (tpx->fileVersion < 57)
2956                 {
2957                     if (mtop->moltype[0].ilist[F_DISRES].size() > 0)
2958                     {
2959                         ir->eDisre = edrSimple;
2960                     }
2961                     else
2962                     {
2963                         ir->eDisre = edrNone;
2964                     }
2965                 }
2966                 set_disres_npair(mtop);
2967             }
2968         }
2969
2970         if (tpx->bTop && mtop)
2971         {
2972             gmx_mtop_finalize(mtop);
2973         }
2974     }
2975
2976     return ePBC;
2977 }
2978
2979 static t_fileio *open_tpx(const char *fn, const char *mode)
2980 {
2981     return gmx_fio_open(fn, mode);
2982 }
2983
2984 static void close_tpx(t_fileio *fio)
2985 {
2986     gmx_fio_close(fio);
2987 }
2988
2989 /*! \brief
2990  * Fill information into the header only from state before writing.
2991  *
2992  * Populating the header needs to be independent from writing the information
2993  * to file to allow things like writing the raw byte stream.
2994  *
2995  * \param[in] state The current simulation state. Can't write without it.
2996  * \param[in] ir Parameter and system information.
2997  * \param[in] mtop Global topology.
2998  * \returns Fully populated header.
2999  */
3000 static TpxFileHeader populateTpxHeader(const t_state    &state,
3001                                        const t_inputrec *ir,
3002                                        const gmx_mtop_t *mtop)
3003 {
3004     TpxFileHeader header;
3005     header.natoms         = state.natoms;
3006     header.ngtc           = state.ngtc;
3007     header.fep_state      = state.fep_state;
3008     header.lambda         = state.lambda[efptFEP];
3009     header.bIr            = ir       != nullptr;
3010     header.bTop           = mtop     != nullptr;
3011     header.bX             = (state.flags & (1 << estX)) != 0;
3012     header.bV             = (state.flags & (1 << estV)) != 0;
3013     header.bF             = false;
3014     header.bBox           = true;
3015     header.fileVersion    = tpx_version;
3016     header.fileGeneration = tpx_generation;
3017
3018     return header;
3019 }
3020
3021 /************************************************************
3022  *
3023  *  The following routines are the exported ones
3024  *
3025  ************************************************************/
3026
3027 TpxFileHeader readTpxHeader(const char *fileName, bool canReadTopologyOnly)
3028 {
3029     t_fileio *fio;
3030
3031     fio = open_tpx(fileName, "r");
3032     gmx::FileIOXdrSerializer serializer(fio);
3033
3034     TpxFileHeader            tpx;
3035     do_tpxheader(&serializer, &tpx, fileName, fio, canReadTopologyOnly);
3036     close_tpx(fio);
3037     return tpx;
3038 }
3039
3040 void write_tpx_state(const char *fn,
3041                      const t_inputrec *ir, const t_state *state, const gmx_mtop_t *mtop)
3042 {
3043     t_fileio *fio;
3044
3045     fio = open_tpx(fn, "w");
3046
3047     TpxFileHeader tpx = populateTpxHeader(*state,
3048                                           ir,
3049                                           mtop);
3050
3051     gmx::FileIOXdrSerializer serializer(fio);
3052     do_tpxheader(&serializer,
3053                  &tpx,
3054                  fn,
3055                  fio,
3056                  ir == nullptr);
3057     do_tpx_body(&serializer,
3058                 &tpx,
3059                 const_cast<t_inputrec *>(ir),
3060                 const_cast<t_state *>(state), nullptr, nullptr,
3061                 const_cast<gmx_mtop_t *>(mtop));
3062     close_tpx(fio);
3063 }
3064
3065 void read_tpx_state(const char *fn,
3066                     t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
3067 {
3068     t_fileio                *fio;
3069
3070     TpxFileHeader            tpx;
3071     fio = open_tpx(fn, "r");
3072     gmx::FileIOXdrSerializer serializer(fio);
3073     do_tpxheader(&serializer,
3074                  &tpx,
3075                  fn,
3076                  fio,
3077                  ir == nullptr);
3078     do_tpx_body(&serializer,
3079                 &tpx,
3080                 ir,
3081                 state,
3082                 nullptr,
3083                 nullptr,
3084                 mtop);
3085     close_tpx(fio);
3086 }
3087
3088 int read_tpx(const char *fn,
3089              t_inputrec *ir, matrix box, int *natoms,
3090              rvec *x, rvec *v, gmx_mtop_t *mtop)
3091 {
3092     t_fileio                *fio;
3093     t_state                  state;
3094     int                      ePBC;
3095
3096     TpxFileHeader            tpx;
3097     fio     = open_tpx(fn, "r");
3098     gmx::FileIOXdrSerializer serializer(fio);
3099     do_tpxheader(&serializer,
3100                  &tpx,
3101                  fn,
3102                  fio,
3103                  ir == nullptr);
3104     ePBC    = do_tpx_body(&serializer,
3105                           &tpx,
3106                           ir, &state, x, v, mtop);
3107     close_tpx(fio);
3108     if (mtop != nullptr && natoms != nullptr)
3109     {
3110         *natoms = mtop->natoms;
3111     }
3112     if (box)
3113     {
3114         copy_mat(state.box, box);
3115     }
3116
3117     return ePBC;
3118 }
3119
3120 int read_tpx_top(const char *fn,
3121                  t_inputrec *ir, matrix box, int *natoms,
3122                  rvec *x, rvec *v, t_topology *top)
3123 {
3124     gmx_mtop_t  mtop;
3125     int         ePBC;
3126
3127     ePBC = read_tpx(fn, ir, box, natoms, x, v, &mtop);
3128
3129     *top = gmx_mtop_t_to_t_topology(&mtop, true);
3130
3131     return ePBC;
3132 }
3133
3134 gmx_bool fn2bTPX(const char *file)
3135 {
3136     return (efTPR == fn2ftp(file));
3137 }
3138
3139 void pr_tpxheader(FILE *fp, int indent, const char *title, const TpxFileHeader *sh)
3140 {
3141     if (available(fp, sh, indent, title))
3142     {
3143         indent = pr_title(fp, indent, title);
3144         pr_indent(fp, indent);
3145         fprintf(fp, "bIr    = %spresent\n", sh->bIr ? "" : "not ");
3146         pr_indent(fp, indent);
3147         fprintf(fp, "bBox   = %spresent\n", sh->bBox ? "" : "not ");
3148         pr_indent(fp, indent);
3149         fprintf(fp, "bTop   = %spresent\n", sh->bTop ? "" : "not ");
3150         pr_indent(fp, indent);
3151         fprintf(fp, "bX     = %spresent\n", sh->bX ? "" : "not ");
3152         pr_indent(fp, indent);
3153         fprintf(fp, "bV     = %spresent\n", sh->bV ? "" : "not ");
3154         pr_indent(fp, indent);
3155         fprintf(fp, "bF     = %spresent\n", sh->bF ? "" : "not ");
3156
3157         pr_indent(fp, indent);
3158         fprintf(fp, "natoms = %d\n", sh->natoms);
3159         pr_indent(fp, indent);
3160         fprintf(fp, "lambda = %e\n", sh->lambda);
3161     }
3162 }