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  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  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 };
 210 #define NFTUPD asize(ftupd)
 211
 212 /* Needed for backward compatibility */
 213 #define MAXNODES 256
 214
 215 /**************************************************************
 216  *
 217  * Now the higer level routines that do io of the structures and arrays
 218  *
 219  **************************************************************/
 220 static void do_pullgrp_tpx_pre95(gmx::ISerializer         *serializer,
 221                                  t_pull_group             *pgrp,
 222                                  t_pull_coord             *pcrd)
 223 {
 224     rvec tmp;
 225
 226     serializer->doInt(&pgrp->nat);
 227     if (serializer->reading())
 228     {
 229         snew(pgrp->ind, pgrp->nat);
 230     }
 231     serializer->doIntArray(pgrp->ind, pgrp->nat);
 232     serializer->doInt(&pgrp->nweight);
 233     if (serializer->reading())
 234     {
 235         snew(pgrp->weight, pgrp->nweight);
 236     }
 237     serializer->doRealArray(pgrp->weight, pgrp->nweight);
 238     serializer->doInt(&pgrp->pbcatom);
 239     serializer->doRvec(&pcrd->vec);
 240     clear_rvec(pcrd->origin);
 241     serializer->doRvec(&tmp);
 242     pcrd->init = tmp[0];
 243     serializer->doReal(&pcrd->rate);
 244     serializer->doReal(&pcrd->k);
 245     serializer->doReal(&pcrd->kB);
 246 }
 247
 248 static void do_pull_group(gmx::ISerializer *serializer, t_pull_group *pgrp)
 249 {
 250     serializer->doInt(&pgrp->nat);
 251     if (serializer->reading())
 252     {
 253         snew(pgrp->ind, pgrp->nat);
 254     }
 255     serializer->doIntArray(pgrp->ind, pgrp->nat);
 256     serializer->doInt(&pgrp->nweight);
 257     if (serializer->reading())
 258     {
 259         snew(pgrp->weight, pgrp->nweight);
 260     }
 261     serializer->doRealArray(pgrp->weight, pgrp->nweight);
 262     serializer->doInt(&pgrp->pbcatom);
 263 }
 264
 265 static void do_pull_coord(gmx::ISerializer *serializer,
 266                           t_pull_coord *pcrd,
 267                           int file_version,
 268                           int ePullOld, int eGeomOld, ivec dimOld)
 269 {
 270     if (file_version >= tpxv_PullCoordNGroup)
 271     {
 272         serializer->doInt(&pcrd->eType);
 273         if (file_version >= tpxv_PullExternalPotential)
 274         {
 275             if (pcrd->eType == epullEXTERNAL)
 276             {
 277                 std::string buf;
 278                 if (serializer->reading())
 279                 {
 280                     serializer->doString(&buf);
 281                     pcrd->externalPotentialProvider = gmx_strdup(buf.c_str());
 282                 }
 283                 else
 284                 {
 285                     buf = pcrd->externalPotentialProvider;
 286                     serializer->doString(&buf);
 287                 }
 288             }
 289             else
 290             {
 291                 pcrd->externalPotentialProvider = nullptr;
 292             }
 293         }
 294         else
 295         {
 296             if (serializer->reading())
 297             {
 298                 pcrd->externalPotentialProvider = nullptr;
 299             }
 300         }
 301         /* Note that we try to support adding new geometries without
 302          * changing the tpx version. This requires checks when printing the
 303          * geometry string and a check and fatal_error in init_pull.
 304          */
 305         serializer->doInt(&pcrd->eGeom);
 306         serializer->doInt(&pcrd->ngroup);
 307         if (pcrd->ngroup <= c_pullCoordNgroupMax)
 308         {
 309             serializer->doIntArray(pcrd->group, pcrd->ngroup);
 310         }
 311         else
 312         {
 313             /* More groups in file than supported, this must be a new geometry
 314              * that is not supported by our current code. Since we will not
 315              * use the groups for this coord (checks in the pull and WHAM code
 316              * ensure this), we can ignore the groups and set ngroup=0.
 317              */
 318             int *dum;
 319             snew(dum, pcrd->ngroup);
 320             serializer->doIntArray(dum, pcrd->ngroup);
 321             sfree(dum);
 322
 323             pcrd->ngroup = 0;
 324         }
 325         serializer->doIvec(&pcrd->dim);
 326     }
 327     else
 328     {
 329         pcrd->ngroup = 2;
 330         serializer->doInt(&pcrd->group[0]);
 331         serializer->doInt(&pcrd->group[1]);
 332         if (file_version >= tpxv_PullCoordTypeGeom)
 333         {
 334             pcrd->ngroup = (pcrd->eGeom == epullgDIRRELATIVE ? 4 : 2);
 335             serializer->doInt(&pcrd->eType);
 336             serializer->doInt(&pcrd->eGeom);
 337             if (pcrd->ngroup == 4)
 338             {
 339                 serializer->doInt(&pcrd->group[2]);
 340                 serializer->doInt(&pcrd->group[3]);
 341             }
 342             serializer->doIvec(&pcrd->dim);
 343         }
 344         else
 345         {
 346             pcrd->eType = ePullOld;
 347             pcrd->eGeom = eGeomOld;
 348             copy_ivec(dimOld, pcrd->dim);
 349         }
 350     }
 351     serializer->doRvec(&pcrd->origin);
 352     serializer->doRvec(&pcrd->vec);
 353     if (file_version >= tpxv_PullCoordTypeGeom)
 354     {
 355         serializer->doBool(&pcrd->bStart);
 356     }
 357     else
 358     {
 359         /* This parameter is only printed, but not actually used by mdrun */
 360         pcrd->bStart = FALSE;
 361     }
 362     serializer->doReal(&pcrd->init);
 363     serializer->doReal(&pcrd->rate);
 364     serializer->doReal(&pcrd->k);
 365     serializer->doReal(&pcrd->kB);
 366 }
 367
 368 static void do_expandedvals(gmx::ISerializer         *serializer,
 369                             t_expanded               *expand,
 370                             t_lambda                 *fepvals,
 371                             int                       file_version)
 372 {
 373     int      n_lambda = fepvals->n_lambda;
 374
 375     /* reset the lambda calculation window */
 376     fepvals->lambda_start_n = 0;
 377     fepvals->lambda_stop_n  = n_lambda;
 378     if (file_version >= 79)
 379     {
 380         if (n_lambda > 0)
 381         {
 382             if (serializer->reading())
 383             {
 384                 snew(expand->init_lambda_weights, n_lambda);
 385             }
 386             serializer->doRealArray(expand->init_lambda_weights, n_lambda);
 387             serializer->doBool(&expand->bInit_weights);
 388         }
 389
 390         serializer->doInt(&expand->nstexpanded);
 391         serializer->doInt(&expand->elmcmove);
 392         serializer->doInt(&expand->elamstats);
 393         serializer->doInt(&expand->lmc_repeats);
 394         serializer->doInt(&expand->gibbsdeltalam);
 395         serializer->doInt(&expand->lmc_forced_nstart);
 396         serializer->doInt(&expand->lmc_seed);
 397         serializer->doReal(&expand->mc_temp);
 398         serializer->doBool(&expand->bSymmetrizedTMatrix);
 399         serializer->doInt(&expand->nstTij);
 400         serializer->doInt(&expand->minvarmin);
 401         serializer->doInt(&expand->c_range);
 402         serializer->doReal(&expand->wl_scale);
 403         serializer->doReal(&expand->wl_ratio);
 404         serializer->doReal(&expand->init_wl_delta);
 405         serializer->doBool(&expand->bWLoneovert);
 406         serializer->doInt(&expand->elmceq);
 407         serializer->doInt(&expand->equil_steps);
 408         serializer->doInt(&expand->equil_samples);
 409         serializer->doInt(&expand->equil_n_at_lam);
 410         serializer->doReal(&expand->equil_wl_delta);
 411         serializer->doReal(&expand->equil_ratio);
 412     }
 413 }
 414
 415 static void do_simtempvals(gmx::ISerializer         *serializer,
 416                            t_simtemp                *simtemp,
 417                            int                       n_lambda,
 418                            int                       file_version)
 419 {
 420     if (file_version >= 79)
 421     {
 422         serializer->doInt(&simtemp->eSimTempScale);
 423         serializer->doReal(&simtemp->simtemp_high);
 424         serializer->doReal(&simtemp->simtemp_low);
 425         if (n_lambda > 0)
 426         {
 427             if (serializer->reading())
 428             {
 429                 snew(simtemp->temperatures, n_lambda);
 430             }
 431             serializer->doRealArray(simtemp->temperatures, n_lambda);
 432         }
 433     }
 434 }
 435
 436 static void do_imd(gmx::ISerializer *serializer, t_IMD *imd)
 437 {
 438     serializer->doInt(&imd->nat);
 439     if (serializer->reading())
 440     {
 441         snew(imd->ind, imd->nat);
 442     }
 443     serializer->doIntArray(imd->ind, imd->nat);
 444 }
 445
 446 static void do_fepvals(gmx::ISerializer         *serializer,
 447                        t_lambda                 *fepvals,
 448                        int                       file_version)
 449 {
 450     /* i is defined in the ndo_double macro; use g to iterate. */
 451     int      g;
 452     real     rdum;
 453
 454     /* free energy values */
 455
 456     if (file_version >= 79)
 457     {
 458         serializer->doInt(&fepvals->init_fep_state);
 459         serializer->doDouble(&fepvals->init_lambda);
 460         serializer->doDouble(&fepvals->delta_lambda);
 461     }
 462     else if (file_version >= 59)
 463     {
 464         serializer->doDouble(&fepvals->init_lambda);
 465         serializer->doDouble(&fepvals->delta_lambda);
 466     }
 467     else
 468     {
 469         serializer->doReal(&rdum);
 470         fepvals->init_lambda = rdum;
 471         serializer->doReal(&rdum);
 472         fepvals->delta_lambda = rdum;
 473     }
 474     if (file_version >= 79)
 475     {
 476         serializer->doInt(&fepvals->n_lambda);
 477         if (serializer->reading())
 478         {
 479             snew(fepvals->all_lambda, efptNR);
 480         }
 481         for (g = 0; g < efptNR; g++)
 482         {
 483             if (fepvals->n_lambda > 0)
 484             {
 485                 if (serializer->reading())
 486                 {
 487                     snew(fepvals->all_lambda[g], fepvals->n_lambda);
 488                 }
 489                 serializer->doDoubleArray(fepvals->all_lambda[g], fepvals->n_lambda);
 490                 serializer->doBoolArray(fepvals->separate_dvdl, efptNR);
 491             }
 492             else if (fepvals->init_lambda >= 0)
 493             {
 494                 fepvals->separate_dvdl[efptFEP] = TRUE;
 495             }
 496         }
 497     }
 498     else if (file_version >= 64)
 499     {
 500         serializer->doInt(&fepvals->n_lambda);
 501         if (serializer->reading())
 502         {
 503             int g;
 504
 505             snew(fepvals->all_lambda, efptNR);
 506             /* still allocate the all_lambda array's contents. */
 507             for (g = 0; g < efptNR; g++)
 508             {
 509                 if (fepvals->n_lambda > 0)
 510                 {
 511                     snew(fepvals->all_lambda[g], fepvals->n_lambda);
 512                 }
 513             }
 514         }
 515         serializer->doDoubleArray(fepvals->all_lambda[efptFEP], fepvals->n_lambda);
 516         if (fepvals->init_lambda >= 0)
 517         {
 518             int g, h;
 519
 520             fepvals->separate_dvdl[efptFEP] = TRUE;
 521
 522             if (serializer->reading())
 523             {
 524                 /* copy the contents of the efptFEP lambda component to all
 525                    the other components */
 526                 for (g = 0; g < efptNR; g++)
 527                 {
 528                     for (h = 0; h < fepvals->n_lambda; h++)
 529                     {
 530                         if (g != efptFEP)
 531                         {
 532                             fepvals->all_lambda[g][h] =
 533                                 fepvals->all_lambda[efptFEP][h];
 534                         }
 535                     }
 536                 }
 537             }
 538         }
 539     }
 540     else
 541     {
 542         fepvals->n_lambda     = 0;
 543         fepvals->all_lambda   = nullptr;
 544         if (fepvals->init_lambda >= 0)
 545         {
 546             fepvals->separate_dvdl[efptFEP] = TRUE;
 547         }
 548     }
 549     serializer->doReal(&fepvals->sc_alpha);
 550     serializer->doInt(&fepvals->sc_power);
 551     if (file_version >= 79)
 552     {
 553         serializer->doReal(&fepvals->sc_r_power);
 554     }
 555     else
 556     {
 557         fepvals->sc_r_power = 6.0;
 558     }
 559     serializer->doReal(&fepvals->sc_sigma);
 560     if (serializer->reading())
 561     {
 562         if (file_version >= 71)
 563         {
 564             fepvals->sc_sigma_min = fepvals->sc_sigma;
 565         }
 566         else
 567         {
 568             fepvals->sc_sigma_min = 0;
 569         }
 570     }
 571     if (file_version >= 79)
 572     {
 573         serializer->doBool(&fepvals->bScCoul);
 574     }
 575     else
 576     {
 577         fepvals->bScCoul = TRUE;
 578     }
 579     if (file_version >= 64)
 580     {
 581         serializer->doInt(&fepvals->nstdhdl);
 582     }
 583     else
 584     {
 585         fepvals->nstdhdl = 1;
 586     }
 587
 588     if (file_version >= 73)
 589     {
 590         serializer->doInt(&fepvals->separate_dhdl_file);
 591         serializer->doInt(&fepvals->dhdl_derivatives);
 592     }
 593     else
 594     {
 595         fepvals->separate_dhdl_file = esepdhdlfileYES;
 596         fepvals->dhdl_derivatives   = edhdlderivativesYES;
 597     }
 598     if (file_version >= 71)
 599     {
 600         serializer->doInt(&fepvals->dh_hist_size);
 601         serializer->doDouble(&fepvals->dh_hist_spacing);
 602     }
 603     else
 604     {
 605         fepvals->dh_hist_size    = 0;
 606         fepvals->dh_hist_spacing = 0.1;
 607     }
 608     if (file_version >= 79)
 609     {
 610         serializer->doInt(&fepvals->edHdLPrintEnergy);
 611     }
 612     else
 613     {
 614         fepvals->edHdLPrintEnergy = edHdLPrintEnergyNO;
 615     }
 616
 617     /* handle lambda_neighbors */
 618     if ((file_version >= 83 && file_version < 90) || file_version >= 92)
 619     {
 620         serializer->doInt(&fepvals->lambda_neighbors);
 621         if ( (fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0) &&
 622              (fepvals->init_lambda < 0) )
 623         {
 624             fepvals->lambda_start_n = (fepvals->init_fep_state -
 625                                        fepvals->lambda_neighbors);
 626             fepvals->lambda_stop_n = (fepvals->init_fep_state +
 627                                       fepvals->lambda_neighbors + 1);
 628             if (fepvals->lambda_start_n < 0)
 629             {
 630                 fepvals->lambda_start_n = 0;;
 631             }
 632             if (fepvals->lambda_stop_n >= fepvals->n_lambda)
 633             {
 634                 fepvals->lambda_stop_n = fepvals->n_lambda;
 635             }
 636         }
 637         else
 638         {
 639             fepvals->lambda_start_n = 0;
 640             fepvals->lambda_stop_n  = fepvals->n_lambda;
 641         }
 642     }
 643     else
 644     {
 645         fepvals->lambda_start_n = 0;
 646         fepvals->lambda_stop_n  = fepvals->n_lambda;
 647     }
 648 }
 649
 650 static void do_awhBias(gmx::ISerializer *serializer, gmx::AwhBiasParams *awhBiasParams,
 651                        int gmx_unused file_version)
 652 {
 653     serializer->doInt(&awhBiasParams->eTarget);
 654     serializer->doDouble(&awhBiasParams->targetBetaScaling);
 655     serializer->doDouble(&awhBiasParams->targetCutoff);
 656     serializer->doInt(&awhBiasParams->eGrowth);
 657     serializer->doInt(&awhBiasParams->bUserData);
 658     serializer->doDouble(&awhBiasParams->errorInitial);
 659     serializer->doInt(&awhBiasParams->ndim);
 660     serializer->doInt(&awhBiasParams->shareGroup);
 661     serializer->doBool(&awhBiasParams->equilibrateHistogram);
 662
 663     if (serializer->reading())
 664     {
 665         snew(awhBiasParams->dimParams, awhBiasParams->ndim);
 666     }
 667
 668     for (int d = 0; d < awhBiasParams->ndim; d++)
 669     {
 670         gmx::AwhDimParams *dimParams = &awhBiasParams->dimParams[d];
 671
 672         serializer->doInt(&dimParams->eCoordProvider);
 673         serializer->doInt(&dimParams->coordIndex);
 674         serializer->doDouble(&dimParams->origin);
 675         serializer->doDouble(&dimParams->end);
 676         serializer->doDouble(&dimParams->period);
 677         serializer->doDouble(&dimParams->forceConstant);
 678         serializer->doDouble(&dimParams->diffusion);
 679         serializer->doDouble(&dimParams->coordValueInit);
 680         serializer->doDouble(&dimParams->coverDiameter);
 681     }
 682 }
 683
 684 static void do_awh(gmx::ISerializer         *serializer,
 685                    gmx::AwhParams           *awhParams,
 686                    int gmx_unused            file_version)
 687 {
 688     serializer->doInt(&awhParams->numBias);
 689     serializer->doInt(&awhParams->nstOut);
 690     serializer->doInt64(&awhParams->seed);
 691     serializer->doInt(&awhParams->nstSampleCoord);
 692     serializer->doInt(&awhParams->numSamplesUpdateFreeEnergy);
 693     serializer->doInt(&awhParams->ePotential);
 694     serializer->doBool(&awhParams->shareBiasMultisim);
 695
 696     if (awhParams->numBias > 0)
 697     {
 698         if (serializer->reading())
 699         {
 700             snew(awhParams->awhBiasParams, awhParams->numBias);
 701         }
 702
 703         for (int k = 0; k < awhParams->numBias; k++)
 704         {
 705             do_awhBias(serializer, &awhParams->awhBiasParams[k], file_version);
 706         }
 707     }
 708 }
 709
 710 static void do_pull(gmx::ISerializer         *serializer,
 711                     pull_params_t            *pull,
 712                     int                       file_version,
 713                     int                       ePullOld)
 714 {
 715     int  eGeomOld = -1;
 716     ivec dimOld;
 717     int  g;
 718
 719     if (file_version >= 95)
 720     {
 721         serializer->doInt(&pull->ngroup);
 722     }
 723     serializer->doInt(&pull->ncoord);
 724     if (file_version < 95)
 725     {
 726         pull->ngroup = pull->ncoord + 1;
 727     }
 728     if (file_version < tpxv_PullCoordTypeGeom)
 729     {
 730         real dum;
 731
 732         serializer->doInt(&eGeomOld);
 733         serializer->doIvec(&dimOld);
 734         /* The inner cylinder radius, now removed */
 735         serializer->doReal(&dum);
 736     }
 737     serializer->doReal(&pull->cylinder_r);
 738     serializer->doReal(&pull->constr_tol);
 739     if (file_version >= 95)
 740     {
 741         serializer->doBool(&pull->bPrintCOM);
 742         /* With file_version < 95 this value is set below */
 743     }
 744     if (file_version >= tpxv_ReplacePullPrintCOM12)
 745     {
 746         serializer->doBool(&pull->bPrintRefValue);
 747         serializer->doBool(&pull->bPrintComp);
 748     }
 749     else if (file_version >= tpxv_PullCoordTypeGeom)
 750     {
 751         int idum;
 752         serializer->doInt(&idum); /* used to be bPrintCOM2 */
 753         serializer->doBool(&pull->bPrintRefValue);
 754         serializer->doBool(&pull->bPrintComp);
 755     }
 756     else
 757     {
 758         pull->bPrintRefValue = FALSE;
 759         pull->bPrintComp     = TRUE;
 760     }
 761     serializer->doInt(&pull->nstxout);
 762     serializer->doInt(&pull->nstfout);
 763     if (file_version >= tpxv_PullPrevStepCOMAsReference)
 764     {
 765         serializer->doBool(&pull->bSetPbcRefToPrevStepCOM);
 766     }
 767     else
 768     {
 769         pull->bSetPbcRefToPrevStepCOM = FALSE;
 770     }
 771     if (serializer->reading())
 772     {
 773         snew(pull->group, pull->ngroup);
 774         snew(pull->coord, pull->ncoord);
 775     }
 776     if (file_version < 95)
 777     {
 778         /* epullgPOS for position pulling, before epullgDIRPBC was removed */
 779         if (eGeomOld == epullgDIRPBC)
 780         {
 781             gmx_fatal(FARGS, "pull-geometry=position is no longer supported");
 782         }
 783         if (eGeomOld > epullgDIRPBC)
 784         {
 785             eGeomOld -= 1;
 786         }
 787
 788         for (g = 0; g < pull->ngroup; g++)
 789         {
 790             /* We read and ignore a pull coordinate for group 0 */
 791             do_pullgrp_tpx_pre95(serializer, &pull->group[g], &pull->coord[std::max(g-1, 0)]);
 792             if (g > 0)
 793             {
 794                 pull->coord[g-1].group[0] = 0;
 795                 pull->coord[g-1].group[1] = g;
 796             }
 797         }
 798
 799         pull->bPrintCOM = (pull->group[0].nat > 0);
 800     }
 801     else
 802     {
 803         for (g = 0; g < pull->ngroup; g++)
 804         {
 805             do_pull_group(serializer, &pull->group[g]);
 806         }
 807         for (g = 0; g < pull->ncoord; g++)
 808         {
 809             do_pull_coord(serializer, &pull->coord[g],
 810                           file_version, ePullOld, eGeomOld, dimOld);
 811         }
 812     }
 813     if (file_version >= tpxv_PullAverage)
 814     {
 815         gmx_bool v;
 816
 817         v                  = pull->bXOutAverage;
 818         serializer->doBool(&v);
 819         pull->bXOutAverage = v;
 820         v                  = pull->bFOutAverage;
 821         serializer->doBool(&v);
 822         pull->bFOutAverage = v;
 823     }
 824 }
 825
 826
 827 static void do_rotgrp(gmx::ISerializer         *serializer,
 828                       t_rotgrp                 *rotg)
 829 {
 830     serializer->doInt(&rotg->eType);
 831     serializer->doInt(&rotg->bMassW);
 832     serializer->doInt(&rotg->nat);
 833     if (serializer->reading())
 834     {
 835         snew(rotg->ind, rotg->nat);
 836     }
 837     serializer->doIntArray(rotg->ind, rotg->nat);
 838     if (serializer->reading())
 839     {
 840         snew(rotg->x_ref, rotg->nat);
 841     }
 842     serializer->doRvecArray(rotg->x_ref, rotg->nat);
 843     serializer->doRvec(&rotg->inputVec);
 844     serializer->doRvec(&rotg->pivot);
 845     serializer->doReal(&rotg->rate);
 846     serializer->doReal(&rotg->k);
 847     serializer->doReal(&rotg->slab_dist);
 848     serializer->doReal(&rotg->min_gaussian);
 849     serializer->doReal(&rotg->eps);
 850     serializer->doInt(&rotg->eFittype);
 851     serializer->doInt(&rotg->PotAngle_nstep);
 852     serializer->doReal(&rotg->PotAngle_step);
 853 }
 854
 855 static void do_rot(gmx::ISerializer         *serializer,
 856                    t_rot                    *rot)
 857 {
 858     int g;
 859
 860     serializer->doInt(&rot->ngrp);
 861     serializer->doInt(&rot->nstrout);
 862     serializer->doInt(&rot->nstsout);
 863     if (serializer->reading())
 864     {
 865         snew(rot->grp, rot->ngrp);
 866     }
 867     for (g = 0; g < rot->ngrp; g++)
 868     {
 869         do_rotgrp(serializer, &rot->grp[g]);
 870     }
 871 }
 872
 873
 874 static void do_swapgroup(gmx::ISerializer         *serializer,
 875                          t_swapGroup              *g)
 876 {
 877
 878     /* Name of the group or molecule */
 879     std::string buf;
 880     if (serializer->reading())
 881     {
 882         serializer->doString(&buf);
 883         g->molname = gmx_strdup(buf.c_str());
 884     }
 885     else
 886     {
 887         buf = g->molname;
 888         serializer->doString(&buf);
 889     }
 890
 891     /* Number of atoms in the group */
 892     serializer->doInt(&g->nat);
 893
 894     /* The group's atom indices */
 895     if (serializer->reading())
 896     {
 897         snew(g->ind, g->nat);
 898     }
 899     serializer->doIntArray(g->ind, g->nat);
 900
 901     /* Requested counts for compartments A and B */
 902     serializer->doIntArray(g->nmolReq, eCompNR);
 903 }
 904
 905 static void do_swapcoords_tpx(gmx::ISerializer         *serializer,
 906                               t_swapcoords             *swap,
 907                               int                       file_version)
 908 {
 909     /* Enums for better readability of the code */
 910     enum {
 911         eCompA = 0, eCompB
 912     };
 913     enum {
 914         eChannel0 = 0, eChannel1
 915     };
 916
 917
 918     if (file_version >= tpxv_CompElPolyatomicIonsAndMultipleIonTypes)
 919     {
 920         /* The total number of swap groups is the sum of the fixed groups
 921          * (split0, split1, solvent), and the user-defined groups (2+ types of ions)
 922          */
 923         serializer->doInt(&swap->ngrp);
 924         if (serializer->reading())
 925         {
 926             snew(swap->grp, swap->ngrp);
 927         }
 928         for (int ig = 0; ig < swap->ngrp; ig++)
 929         {
 930             do_swapgroup(serializer, &swap->grp[ig]);
 931         }
 932         serializer->doBool(&swap->massw_split[eChannel0]);
 933         serializer->doBool(&swap->massw_split[eChannel1]);
 934         serializer->doInt(&swap->nstswap);
 935         serializer->doInt(&swap->nAverage);
 936         serializer->doReal(&swap->threshold);
 937         serializer->doReal(&swap->cyl0r);
 938         serializer->doReal(&swap->cyl0u);
 939         serializer->doReal(&swap->cyl0l);
 940         serializer->doReal(&swap->cyl1r);
 941         serializer->doReal(&swap->cyl1u);
 942         serializer->doReal(&swap->cyl1l);
 943     }
 944     else
 945     {
 946         /*** Support reading older CompEl .tpr files ***/
 947
 948         /* In the original CompEl .tpr files, we always have 5 groups: */
 949         swap->ngrp = 5;
 950         snew(swap->grp, swap->ngrp);
 951
 952         swap->grp[eGrpSplit0 ].molname = gmx_strdup("split0" );  // group 0: split0
 953         swap->grp[eGrpSplit1 ].molname = gmx_strdup("split1" );  // group 1: split1
 954         swap->grp[eGrpSolvent].molname = gmx_strdup("solvent");  // group 2: solvent
 955         swap->grp[3          ].molname = gmx_strdup("anions" );  // group 3: anions
 956         swap->grp[4          ].molname = gmx_strdup("cations");  // group 4: cations
 957
 958         serializer->doInt(&swap->grp[3].nat);
 959         serializer->doInt(&swap->grp[eGrpSolvent].nat);
 960         serializer->doInt(&swap->grp[eGrpSplit0].nat);
 961         serializer->doBool(&swap->massw_split[eChannel0]);
 962         serializer->doInt(&swap->grp[eGrpSplit1].nat);
 963         serializer->doBool(&swap->massw_split[eChannel1]);
 964         serializer->doInt(&swap->nstswap);
 965         serializer->doInt(&swap->nAverage);
 966         serializer->doReal(&swap->threshold);
 967         serializer->doReal(&swap->cyl0r);
 968         serializer->doReal(&swap->cyl0u);
 969         serializer->doReal(&swap->cyl0l);
 970         serializer->doReal(&swap->cyl1r);
 971         serializer->doReal(&swap->cyl1u);
 972         serializer->doReal(&swap->cyl1l);
 973
 974         // The order[] array keeps compatibility with older .tpr files
 975         // by reading in the groups in the classic order
 976         {
 977             const int order[4] = {3, eGrpSolvent, eGrpSplit0, eGrpSplit1 };
 978
 979             for (int ig = 0; ig < 4; ig++)
 980             {
 981                 int g = order[ig];
 982                 snew(swap->grp[g].ind, swap->grp[g].nat);
 983                 serializer->doIntArray(swap->grp[g].ind, swap->grp[g].nat);
 984             }
 985         }
 986
 987         for (int j = eCompA; j <= eCompB; j++)
 988         {
 989             serializer->doInt(&swap->grp[3].nmolReq[j]); // group 3 = anions
 990             serializer->doInt(&swap->grp[4].nmolReq[j]); // group 4 = cations
 991         }
 992     }                                                    /* End support reading older CompEl .tpr files */
 993
 994     if (file_version >= tpxv_CompElWithSwapLayerOffset)
 995     {
 996         serializer->doReal(&swap->bulkOffset[eCompA]);
 997         serializer->doReal(&swap->bulkOffset[eCompB]);
 998     }
 999
1000 }
1001
1002 static void do_legacy_efield(gmx::ISerializer *serializer, gmx::KeyValueTreeObjectBuilder *root)
1003 {
1004     const char *const dimName[] = { "x", "y", "z" };
1005
1006     auto              appliedForcesObj = root->addObject("applied-forces");
1007     auto              efieldObj        = appliedForcesObj.addObject("electric-field");
1008     // The content of the tpr file for this feature has
1009     // been the same since gromacs 4.0 that was used for
1010     // developing.
1011     for (int j = 0; j < DIM; ++j)
1012     {
1013         int n, nt;
1014         serializer->doInt(&n);
1015         serializer->doInt(&nt);
1016         std::vector<real> aa(n+1), phi(nt+1), at(nt+1), phit(nt+1);
1017         serializer->doRealArray(aa.data(),  n);
1018         serializer->doRealArray(phi.data(), n);
1019         serializer->doRealArray(at.data(),  nt);
1020         serializer->doRealArray(phit.data(), nt);
1021         if (n > 0)
1022         {
1023             if (n > 1 || nt > 1)
1024             {
1025                 gmx_fatal(FARGS, "Can not handle tpr files with more than one electric field term per direction.");
1026             }
1027             auto dimObj = efieldObj.addObject(dimName[j]);
1028             dimObj.addValue<real>("E0", aa[0]);
1029             dimObj.addValue<real>("omega", at[0]);
1030             dimObj.addValue<real>("t0", phi[0]);
1031             dimObj.addValue<real>("sigma", phit[0]);
1032         }
1033     }
1034 }
1035
1036
1037 static void do_inputrec(gmx::ISerializer         *serializer,
1038                         t_inputrec               *ir,
1039                         int                       file_version)
1040 {
1041     int      i, j, k, idum = 0;
1042     real     rdum;
1043     gmx_bool bdum = false;
1044
1045     if (file_version != tpx_version)
1046     {
1047         /* Give a warning about features that are not accessible */
1048         fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n",
1049                 file_version, tpx_version);
1050     }
1051
1052     if (file_version == 0)
1053     {
1054         return;
1055     }
1056
1057     gmx::KeyValueTreeBuilder       paramsBuilder;
1058     gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
1059
1060     /* Basic inputrec stuff */
1061     serializer->doInt(&ir->eI);
1062     if (file_version >= 62)
1063     {
1064         serializer->doInt64(&ir->nsteps);
1065     }
1066     else
1067     {
1068         serializer->doInt(&idum);
1069         ir->nsteps = idum;
1070     }
1071
1072     if (file_version >= 62)
1073     {
1074         serializer->doInt64(&ir->init_step);
1075     }
1076     else
1077     {
1078         serializer->doInt(&idum);
1079         ir->init_step = idum;
1080     }
1081
1082     serializer->doInt(&ir->simulation_part);
1083
1084     if (file_version >= 67)
1085     {
1086         serializer->doInt(&ir->nstcalcenergy);
1087     }
1088     else
1089     {
1090         ir->nstcalcenergy = 1;
1091     }
1092     if (file_version >= 81)
1093     {
1094         serializer->doInt(&ir->cutoff_scheme);
1095         if (file_version < 94)
1096         {
1097             ir->cutoff_scheme = 1 - ir->cutoff_scheme;
1098         }
1099     }
1100     else
1101     {
1102         ir->cutoff_scheme = ecutsGROUP;
1103     }
1104     serializer->doInt(&ir->ns_type);
1105     serializer->doInt(&ir->nstlist);
1106     serializer->doInt(&idum); /* used to be ndelta; not used anymore */
1107
1108     serializer->doReal(&ir->rtpi);
1109
1110     serializer->doInt(&ir->nstcomm);
1111     serializer->doInt(&ir->comm_mode);
1112
1113     /* ignore nstcheckpoint */
1114     if (file_version < tpxv_RemoveObsoleteParameters1)
1115     {
1116         serializer->doInt(&idum);
1117     }
1118
1119     serializer->doInt(&ir->nstcgsteep);
1120
1121     serializer->doInt(&ir->nbfgscorr);
1122
1123     serializer->doInt(&ir->nstlog);
1124     serializer->doInt(&ir->nstxout);
1125     serializer->doInt(&ir->nstvout);
1126     serializer->doInt(&ir->nstfout);
1127     serializer->doInt(&ir->nstenergy);
1128     serializer->doInt(&ir->nstxout_compressed);
1129     if (file_version >= 59)
1130     {
1131         serializer->doDouble(&ir->init_t);
1132         serializer->doDouble(&ir->delta_t);
1133     }
1134     else
1135     {
1136         serializer->doReal(&rdum);
1137         ir->init_t = rdum;
1138         serializer->doReal(&rdum);
1139         ir->delta_t = rdum;
1140     }
1141     serializer->doReal(&ir->x_compression_precision);
1142     if (file_version >= 81)
1143     {
1144         serializer->doReal(&ir->verletbuf_tol);
1145     }
1146     else
1147     {
1148         ir->verletbuf_tol = 0;
1149     }
1150     serializer->doReal(&ir->rlist);
1151     if (file_version >= 67 && file_version < tpxv_RemoveTwinRange)
1152     {
1153         if (serializer->reading())
1154         {
1155             // Reading such a file version could invoke the twin-range
1156             // scheme, about which mdrun should give a fatal error.
1157             real dummy_rlistlong = -1;
1158             serializer->doReal(&dummy_rlistlong);
1159
1160             if (ir->rlist > 0 && (dummy_rlistlong == 0 || dummy_rlistlong > ir->rlist))
1161             {
1162                 // Get mdrun to issue an error (regardless of
1163                 // ir->cutoff_scheme).
1164                 ir->useTwinRange = true;
1165             }
1166             else
1167             {
1168                 // grompp used to set rlistlong actively. Users were
1169                 // probably also confused and set rlistlong == rlist.
1170                 // However, in all remaining cases, it is safe to let
1171                 // mdrun proceed normally.
1172                 ir->useTwinRange = false;
1173             }
1174         }
1175     }
1176     else
1177     {
1178         // No need to read or write anything
1179         ir->useTwinRange = false;
1180     }
1181     if (file_version >= 82 && file_version != 90)
1182     {
1183         // Multiple time-stepping is no longer enabled, but the old
1184         // support required the twin-range scheme, for which mdrun
1185         // already emits a fatal error.
1186         int dummy_nstcalclr = -1;
1187         serializer->doInt(&dummy_nstcalclr);
1188     }
1189     serializer->doInt(&ir->coulombtype);
1190     if (file_version >= 81)
1191     {
1192         serializer->doInt(&ir->coulomb_modifier);
1193     }
1194     else
1195     {
1196         ir->coulomb_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1197     }
1198     serializer->doReal(&ir->rcoulomb_switch);
1199     serializer->doReal(&ir->rcoulomb);
1200     serializer->doInt(&ir->vdwtype);
1201     if (file_version >= 81)
1202     {
1203         serializer->doInt(&ir->vdw_modifier);
1204     }
1205     else
1206     {
1207         ir->vdw_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
1208     }
1209     serializer->doReal(&ir->rvdw_switch);
1210     serializer->doReal(&ir->rvdw);
1211     serializer->doInt(&ir->eDispCorr);
1212     serializer->doReal(&ir->epsilon_r);
1213     serializer->doReal(&ir->epsilon_rf);
1214     serializer->doReal(&ir->tabext);
1215
1216     // This permits reading a .tpr file that used implicit solvent,
1217     // and later permitting mdrun to refuse to run it.
1218     if (serializer->reading())
1219     {
1220         if (file_version < tpxv_RemoveImplicitSolvation)
1221         {
1222             serializer->doInt(&idum);
1223             serializer->doInt(&idum);
1224             serializer->doReal(&rdum);
1225             serializer->doReal(&rdum);
1226             serializer->doInt(&idum);
1227             ir->implicit_solvent = (idum > 0);
1228         }
1229         else
1230         {
1231             ir->implicit_solvent = false;
1232         }
1233         if (file_version < tpxv_RemoveImplicitSolvation)
1234         {
1235             serializer->doReal(&rdum);
1236             serializer->doReal(&rdum);
1237             serializer->doReal(&rdum);
1238             serializer->doReal(&rdum);
1239             if (file_version >= 60)
1240             {
1241                 serializer->doReal(&rdum);
1242                 serializer->doInt(&idum);
1243             }
1244             serializer->doReal(&rdum);
1245         }
1246     }
1247
1248     if (file_version >= 81)
1249     {
1250         serializer->doReal(&ir->fourier_spacing);
1251     }
1252     else
1253     {
1254         ir->fourier_spacing = 0.0;
1255     }
1256     serializer->doInt(&ir->nkx);
1257     serializer->doInt(&ir->nky);
1258     serializer->doInt(&ir->nkz);
1259     serializer->doInt(&ir->pme_order);
1260     serializer->doReal(&ir->ewald_rtol);
1261
1262     if (file_version >= 93)
1263     {
1264         serializer->doReal(&ir->ewald_rtol_lj);
1265     }
1266     else
1267     {
1268         ir->ewald_rtol_lj = ir->ewald_rtol;
1269     }
1270     serializer->doInt(&ir->ewald_geometry);
1271     serializer->doReal(&ir->epsilon_surface);
1272
1273     /* ignore bOptFFT */
1274     if (file_version < tpxv_RemoveObsoleteParameters1)
1275     {
1276         serializer->doBool(&bdum);
1277     }
1278
1279     if (file_version >= 93)
1280     {
1281         serializer->doInt(&ir->ljpme_combination_rule);
1282     }
1283     serializer->doBool(&ir->bContinuation);
1284     serializer->doInt(&ir->etc);
1285     /* before version 18, ir->etc was a gmx_bool (ir->btc),
1286      * but the values 0 and 1 still mean no and
1287      * berendsen temperature coupling, respectively.
1288      */
1289     if (file_version >= 79)
1290     {
1291         serializer->doBool(&ir->bPrintNHChains);
1292     }
1293     if (file_version >= 71)
1294     {
1295         serializer->doInt(&ir->nsttcouple);
1296     }
1297     else
1298     {
1299         ir->nsttcouple = ir->nstcalcenergy;
1300     }
1301     serializer->doInt(&ir->epc);
1302     serializer->doInt(&ir->epct);
1303     if (file_version >= 71)
1304     {
1305         serializer->doInt(&ir->nstpcouple);
1306     }
1307     else
1308     {
1309         ir->nstpcouple = ir->nstcalcenergy;
1310     }
1311     serializer->doReal(&ir->tau_p);
1312     serializer->doRvec(&ir->ref_p[XX]);
1313     serializer->doRvec(&ir->ref_p[YY]);
1314     serializer->doRvec(&ir->ref_p[ZZ]);
1315     serializer->doRvec(&ir->compress[XX]);
1316     serializer->doRvec(&ir->compress[YY]);
1317     serializer->doRvec(&ir->compress[ZZ]);
1318     serializer->doInt(&ir->refcoord_scaling);
1319     serializer->doRvec(&ir->posres_com);
1320     serializer->doRvec(&ir->posres_comB);
1321
1322     if (file_version < 79)
1323     {
1324         serializer->doInt(&ir->andersen_seed);
1325     }
1326     else
1327     {
1328         ir->andersen_seed = 0;
1329     }
1330
1331     serializer->doReal(&ir->shake_tol);
1332
1333     serializer->doInt(&ir->efep);
1334     do_fepvals(serializer, ir->fepvals, file_version);
1335
1336     if (file_version >= 79)
1337     {
1338         serializer->doBool(&ir->bSimTemp);
1339         if (ir->bSimTemp)
1340         {
1341             ir->bSimTemp = TRUE;
1342         }
1343     }
1344     else
1345     {
1346         ir->bSimTemp = FALSE;
1347     }
1348     if (ir->bSimTemp)
1349     {
1350         do_simtempvals(serializer, ir->simtempvals, ir->fepvals->n_lambda, file_version);
1351     }
1352
1353     if (file_version >= 79)
1354     {
1355         serializer->doBool(&ir->bExpanded);
1356         if (ir->bExpanded)
1357         {
1358             ir->bExpanded = TRUE;
1359         }
1360         else
1361         {
1362             ir->bExpanded = FALSE;
1363         }
1364     }
1365     if (ir->bExpanded)
1366     {
1367         do_expandedvals(serializer, ir->expandedvals, ir->fepvals, file_version);
1368     }
1369
1370     serializer->doInt(&ir->eDisre);
1371     serializer->doInt(&ir->eDisreWeighting);
1372     serializer->doBool(&ir->bDisreMixed);
1373     serializer->doReal(&ir->dr_fc);
1374     serializer->doReal(&ir->dr_tau);
1375     serializer->doInt(&ir->nstdisreout);
1376     serializer->doReal(&ir->orires_fc);
1377     serializer->doReal(&ir->orires_tau);
1378     serializer->doInt(&ir->nstorireout);
1379
1380     /* ignore dihre_fc */
1381     if (file_version < 79)
1382     {
1383         serializer->doReal(&rdum);
1384     }
1385
1386     serializer->doReal(&ir->em_stepsize);
1387     serializer->doReal(&ir->em_tol);
1388     serializer->doBool(&ir->bShakeSOR);
1389     serializer->doInt(&ir->niter);
1390     serializer->doReal(&ir->fc_stepsize);
1391     serializer->doInt(&ir->eConstrAlg);
1392     serializer->doInt(&ir->nProjOrder);
1393     serializer->doReal(&ir->LincsWarnAngle);
1394     serializer->doInt(&ir->nLincsIter);
1395     serializer->doReal(&ir->bd_fric);
1396     if (file_version >= tpxv_Use64BitRandomSeed)
1397     {
1398         serializer->doInt64(&ir->ld_seed);
1399     }
1400     else
1401     {
1402         serializer->doInt(&idum);
1403         ir->ld_seed = idum;
1404     }
1405
1406     for (i = 0; i < DIM; i++)
1407     {
1408         serializer->doRvec(&ir->deform[i]);
1409     }
1410     serializer->doReal(&ir->cos_accel);
1411
1412     serializer->doInt(&ir->userint1);
1413     serializer->doInt(&ir->userint2);
1414     serializer->doInt(&ir->userint3);
1415     serializer->doInt(&ir->userint4);
1416     serializer->doReal(&ir->userreal1);
1417     serializer->doReal(&ir->userreal2);
1418     serializer->doReal(&ir->userreal3);
1419     serializer->doReal(&ir->userreal4);
1420
1421     /* AdResS is removed, but we need to be able to read old files,
1422        and let mdrun refuse to run them */
1423     if (file_version >= 77 && file_version < tpxv_RemoveAdress)
1424     {
1425         serializer->doBool(&ir->bAdress);
1426         if (ir->bAdress)
1427         {
1428             int  idum, numThermoForceGroups, numEnergyGroups;
1429             real rdum;
1430             rvec rvecdum;
1431             serializer->doInt(&idum);
1432             serializer->doReal(&rdum);
1433             serializer->doReal(&rdum);
1434             serializer->doReal(&rdum);
1435             serializer->doInt(&idum);
1436             serializer->doInt(&idum);
1437             serializer->doRvec(&rvecdum);
1438             serializer->doInt(&numThermoForceGroups);
1439             serializer->doReal(&rdum);
1440             serializer->doInt(&numEnergyGroups);
1441             serializer->doInt(&idum);
1442
1443             if (numThermoForceGroups > 0)
1444             {
1445                 std::vector<int> idumn(numThermoForceGroups);
1446                 serializer->doIntArray(idumn.data(), idumn.size());
1447             }
1448             if (numEnergyGroups > 0)
1449             {
1450                 std::vector<int> idumn(numEnergyGroups);
1451                 serializer->doIntArray(idumn.data(), idumn.size());
1452             }
1453         }
1454     }
1455     else
1456     {
1457         ir->bAdress = FALSE;
1458     }
1459
1460     /* pull stuff */
1461     {
1462         int ePullOld = 0;
1463
1464         if (file_version >= tpxv_PullCoordTypeGeom)
1465         {
1466             serializer->doBool(&ir->bPull);
1467         }
1468         else
1469         {
1470             serializer->doInt(&ePullOld);
1471             ir->bPull = (ePullOld > 0);
1472             /* We removed the first ePull=ePullNo for the enum */
1473             ePullOld -= 1;
1474         }
1475         if (ir->bPull)
1476         {
1477             if (serializer->reading())
1478             {
1479                 snew(ir->pull, 1);
1480             }
1481             do_pull(serializer, ir->pull, file_version, ePullOld);
1482         }
1483     }
1484
1485     if (file_version >= tpxv_AcceleratedWeightHistogram)
1486     {
1487         serializer->doBool(&ir->bDoAwh);
1488
1489         if (ir->bDoAwh)
1490         {
1491             if (serializer->reading())
1492             {
1493                 snew(ir->awhParams, 1);
1494             }
1495             do_awh(serializer, ir->awhParams, file_version);
1496         }
1497     }
1498     else
1499     {
1500         ir->bDoAwh = FALSE;
1501     }
1502
1503     /* Enforced rotation */
1504     if (file_version >= 74)
1505     {
1506         serializer->doBool(&ir->bRot);
1507         if (ir->bRot)
1508         {
1509             if (serializer->reading())
1510             {
1511                 snew(ir->rot, 1);
1512             }
1513             do_rot(serializer, ir->rot);
1514         }
1515     }
1516     else
1517     {
1518         ir->bRot = FALSE;
1519     }
1520
1521     /* Interactive molecular dynamics */
1522     if (file_version >= tpxv_InteractiveMolecularDynamics)
1523     {
1524         serializer->doBool(&ir->bIMD);
1525         if (ir->bIMD)
1526         {
1527             if (serializer->reading())
1528             {
1529                 snew(ir->imd, 1);
1530             }
1531             do_imd(serializer, ir->imd);
1532         }
1533     }
1534     else
1535     {
1536         /* We don't support IMD sessions for old .tpr files */
1537         ir->bIMD = FALSE;
1538     }
1539
1540     /* grpopts stuff */
1541     serializer->doInt(&ir->opts.ngtc);
1542     if (file_version >= 69)
1543     {
1544         serializer->doInt(&ir->opts.nhchainlength);
1545     }
1546     else
1547     {
1548         ir->opts.nhchainlength = 1;
1549     }
1550     serializer->doInt(&ir->opts.ngacc);
1551     serializer->doInt(&ir->opts.ngfrz);
1552     serializer->doInt(&ir->opts.ngener);
1553
1554     if (serializer->reading())
1555     {
1556         snew(ir->opts.nrdf,   ir->opts.ngtc);
1557         snew(ir->opts.ref_t,  ir->opts.ngtc);
1558         snew(ir->opts.annealing, ir->opts.ngtc);
1559         snew(ir->opts.anneal_npoints, ir->opts.ngtc);
1560         snew(ir->opts.anneal_time, ir->opts.ngtc);
1561         snew(ir->opts.anneal_temp, ir->opts.ngtc);
1562         snew(ir->opts.tau_t,  ir->opts.ngtc);
1563         snew(ir->opts.nFreeze, ir->opts.ngfrz);
1564         snew(ir->opts.acc,    ir->opts.ngacc);
1565         snew(ir->opts.egp_flags, ir->opts.ngener*ir->opts.ngener);
1566     }
1567     if (ir->opts.ngtc > 0)
1568     {
1569         serializer->doRealArray(ir->opts.nrdf, ir->opts.ngtc);
1570         serializer->doRealArray(ir->opts.ref_t, ir->opts.ngtc);
1571         serializer->doRealArray(ir->opts.tau_t, ir->opts.ngtc);
1572     }
1573     if (ir->opts.ngfrz > 0)
1574     {
1575         serializer->doIvecArray(ir->opts.nFreeze, ir->opts.ngfrz);
1576     }
1577     if (ir->opts.ngacc > 0)
1578     {
1579         serializer->doRvecArray(ir->opts.acc, ir->opts.ngacc);
1580     }
1581     serializer->doIntArray(ir->opts.egp_flags,
1582                            ir->opts.ngener*ir->opts.ngener);
1583
1584     /* First read the lists with annealing and npoints for each group */
1585     serializer->doIntArray(ir->opts.annealing, ir->opts.ngtc);
1586     serializer->doIntArray(ir->opts.anneal_npoints, ir->opts.ngtc);
1587     for (j = 0; j < (ir->opts.ngtc); j++)
1588     {
1589         k = ir->opts.anneal_npoints[j];
1590         if (serializer->reading())
1591         {
1592             snew(ir->opts.anneal_time[j], k);
1593             snew(ir->opts.anneal_temp[j], k);
1594         }
1595         serializer->doRealArray(ir->opts.anneal_time[j], k);
1596         serializer->doRealArray(ir->opts.anneal_temp[j], k);
1597     }
1598     /* Walls */
1599     {
1600         serializer->doInt(&ir->nwall);
1601         serializer->doInt(&ir->wall_type);
1602         serializer->doReal(&ir->wall_r_linpot);
1603         serializer->doInt(&ir->wall_atomtype[0]);
1604         serializer->doInt(&ir->wall_atomtype[1]);
1605         serializer->doReal(&ir->wall_density[0]);
1606         serializer->doReal(&ir->wall_density[1]);
1607         serializer->doReal(&ir->wall_ewald_zfac);
1608     }
1609
1610     /* Cosine stuff for electric fields */
1611     if (file_version < tpxv_GenericParamsForElectricField)
1612     {
1613         do_legacy_efield(serializer, &paramsObj);
1614     }
1615
1616     /* Swap ions */
1617     if (file_version >= tpxv_ComputationalElectrophysiology)
1618     {
1619         serializer->doInt(&ir->eSwapCoords);
1620         if (ir->eSwapCoords != eswapNO)
1621         {
1622             if (serializer->reading())
1623             {
1624                 snew(ir->swap, 1);
1625             }
1626             do_swapcoords_tpx(serializer, ir->swap, file_version);
1627         }
1628     }
1629
1630     /* QMMM stuff */
1631     {
1632         serializer->doBool(&ir->bQMMM);
1633         serializer->doInt(&ir->QMMMscheme);
1634         serializer->doReal(&ir->scalefactor);
1635         serializer->doInt(&ir->opts.ngQM);
1636         if (serializer->reading())
1637         {
1638             snew(ir->opts.QMmethod,    ir->opts.ngQM);
1639             snew(ir->opts.QMbasis,     ir->opts.ngQM);
1640             snew(ir->opts.QMcharge,    ir->opts.ngQM);
1641             snew(ir->opts.QMmult,      ir->opts.ngQM);
1642             snew(ir->opts.bSH,         ir->opts.ngQM);
1643             snew(ir->opts.CASorbitals, ir->opts.ngQM);
1644             snew(ir->opts.CASelectrons, ir->opts.ngQM);
1645             snew(ir->opts.SAon,        ir->opts.ngQM);
1646             snew(ir->opts.SAoff,       ir->opts.ngQM);
1647             snew(ir->opts.SAsteps,     ir->opts.ngQM);
1648         }
1649         if (ir->opts.ngQM > 0 && ir->bQMMM)
1650         {
1651             serializer->doIntArray(ir->opts.QMmethod, ir->opts.ngQM);
1652             serializer->doIntArray(ir->opts.QMbasis, ir->opts.ngQM);
1653             serializer->doIntArray(ir->opts.QMcharge, ir->opts.ngQM);
1654             serializer->doIntArray(ir->opts.QMmult, ir->opts.ngQM);
1655             serializer->doBoolArray(ir->opts.bSH, ir->opts.ngQM);
1656             serializer->doIntArray(ir->opts.CASorbitals, ir->opts.ngQM);
1657             serializer->doIntArray(ir->opts.CASelectrons, ir->opts.ngQM);
1658             serializer->doRealArray(ir->opts.SAon, ir->opts.ngQM);
1659             serializer->doRealArray(ir->opts.SAoff, ir->opts.ngQM);
1660             serializer->doIntArray(ir->opts.SAsteps, ir->opts.ngQM);
1661             /* We leave in dummy i/o for removed parameters to avoid
1662              * changing the tpr format for every QMMM change.
1663              */
1664             std::vector<int> dummy(ir->opts.ngQM, 0);
1665             serializer->doIntArray(dummy.data(), ir->opts.ngQM);
1666             serializer->doIntArray(dummy.data(), ir->opts.ngQM);
1667         }
1668         /* end of QMMM stuff */
1669     }
1670
1671     if (file_version >= tpxv_GenericParamsForElectricField)
1672     {
1673         if (serializer->reading())
1674         {
1675             paramsObj.mergeObject(
1676                     gmx::deserializeKeyValueTree(serializer));
1677         }
1678         else
1679         {
1680             GMX_RELEASE_ASSERT(ir->params != nullptr,
1681                                "Parameters should be present when writing inputrec");
1682             gmx::serializeKeyValueTree(*ir->params, serializer);
1683         }
1684     }
1685     if (serializer->reading())
1686     {
1687         ir->params = new gmx::KeyValueTreeObject(paramsBuilder.build());
1688         // Initialize internal parameters to an empty kvt for all tpr versions
1689         ir->internalParameters = std::make_unique<gmx::KeyValueTreeObject>();
1690     }
1691
1692     if (file_version >= tpxv_GenericInternalParameters)
1693     {
1694         if (serializer->reading())
1695         {
1696             ir->internalParameters = std::make_unique<gmx::KeyValueTreeObject>(gmx::deserializeKeyValueTree(serializer));
1697         }
1698         else
1699         {
1700             GMX_RELEASE_ASSERT(ir->internalParameters != nullptr,
1701                                "Parameters should be present when writing inputrec");
1702             gmx::serializeKeyValueTree(*ir->internalParameters, serializer);
1703         }
1704     }
1705 }
1706
1707
1708 static void do_harm(gmx::ISerializer *serializer, t_iparams *iparams)
1709 {
1710     serializer->doReal(&iparams->harmonic.rA);
1711     serializer->doReal(&iparams->harmonic.krA);
1712     serializer->doReal(&iparams->harmonic.rB);
1713     serializer->doReal(&iparams->harmonic.krB);
1714 }
1715
1716 static void do_iparams(gmx::ISerializer         *serializer,
1717                        t_functype                ftype,
1718                        t_iparams                *iparams,
1719                        int                       file_version)
1720 {
1721     int      idum;
1722     real     rdum;
1723
1724     switch (ftype)
1725     {
1726         case F_ANGLES:
1727         case F_G96ANGLES:
1728         case F_BONDS:
1729         case F_G96BONDS:
1730         case F_HARMONIC:
1731         case F_IDIHS:
1732             do_harm(serializer, iparams);
1733             if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && serializer->reading())
1734             {
1735                 /* Correct incorrect storage of parameters */
1736                 iparams->pdihs.phiB = iparams->pdihs.phiA;
1737                 iparams->pdihs.cpB  = iparams->pdihs.cpA;
1738             }
1739             break;
1740         case F_RESTRANGLES:
1741             serializer->doReal(&iparams->harmonic.rA);
1742             serializer->doReal(&iparams->harmonic.krA);
1743             break;
1744         case F_LINEAR_ANGLES:
1745             serializer->doReal(&iparams->linangle.klinA);
1746             serializer->doReal(&iparams->linangle.aA);
1747             serializer->doReal(&iparams->linangle.klinB);
1748             serializer->doReal(&iparams->linangle.aB);
1749             break;
1750         case F_FENEBONDS:
1751             serializer->doReal(&iparams->fene.bm);
1752             serializer->doReal(&iparams->fene.kb);
1753             break;
1754
1755         case F_RESTRBONDS:
1756             serializer->doReal(&iparams->restraint.lowA);
1757             serializer->doReal(&iparams->restraint.up1A);
1758             serializer->doReal(&iparams->restraint.up2A);
1759             serializer->doReal(&iparams->restraint.kA);
1760             serializer->doReal(&iparams->restraint.lowB);
1761             serializer->doReal(&iparams->restraint.up1B);
1762             serializer->doReal(&iparams->restraint.up2B);
1763             serializer->doReal(&iparams->restraint.kB);
1764             break;
1765         case F_TABBONDS:
1766         case F_TABBONDSNC:
1767         case F_TABANGLES:
1768         case F_TABDIHS:
1769             serializer->doReal(&iparams->tab.kA);
1770             serializer->doInt(&iparams->tab.table);
1771             serializer->doReal(&iparams->tab.kB);
1772             break;
1773         case F_CROSS_BOND_BONDS:
1774             serializer->doReal(&iparams->cross_bb.r1e);
1775             serializer->doReal(&iparams->cross_bb.r2e);
1776             serializer->doReal(&iparams->cross_bb.krr);
1777             break;
1778         case F_CROSS_BOND_ANGLES:
1779             serializer->doReal(&iparams->cross_ba.r1e);
1780             serializer->doReal(&iparams->cross_ba.r2e);
1781             serializer->doReal(&iparams->cross_ba.r3e);
1782             serializer->doReal(&iparams->cross_ba.krt);
1783             break;
1784         case F_UREY_BRADLEY:
1785             serializer->doReal(&iparams->u_b.thetaA);
1786             serializer->doReal(&iparams->u_b.kthetaA);
1787             serializer->doReal(&iparams->u_b.r13A);
1788             serializer->doReal(&iparams->u_b.kUBA);
1789             if (file_version >= 79)
1790             {
1791                 serializer->doReal(&iparams->u_b.thetaB);
1792                 serializer->doReal(&iparams->u_b.kthetaB);
1793                 serializer->doReal(&iparams->u_b.r13B);
1794                 serializer->doReal(&iparams->u_b.kUBB);
1795             }
1796             else
1797             {
1798                 iparams->u_b.thetaB  = iparams->u_b.thetaA;
1799                 iparams->u_b.kthetaB = iparams->u_b.kthetaA;
1800                 iparams->u_b.r13B    = iparams->u_b.r13A;
1801                 iparams->u_b.kUBB    = iparams->u_b.kUBA;
1802             }
1803             break;
1804         case F_QUARTIC_ANGLES:
1805             serializer->doReal(&iparams->qangle.theta);
1806             serializer->doRealArray(iparams->qangle.c, 5);
1807             break;
1808         case F_BHAM:
1809             serializer->doReal(&iparams->bham.a);
1810             serializer->doReal(&iparams->bham.b);
1811             serializer->doReal(&iparams->bham.c);
1812             break;
1813         case F_MORSE:
1814             serializer->doReal(&iparams->morse.b0A);
1815             serializer->doReal(&iparams->morse.cbA);
1816             serializer->doReal(&iparams->morse.betaA);
1817             if (file_version >= 79)
1818             {
1819                 serializer->doReal(&iparams->morse.b0B);
1820                 serializer->doReal(&iparams->morse.cbB);
1821                 serializer->doReal(&iparams->morse.betaB);
1822             }
1823             else
1824             {
1825                 iparams->morse.b0B   = iparams->morse.b0A;
1826                 iparams->morse.cbB   = iparams->morse.cbA;
1827                 iparams->morse.betaB = iparams->morse.betaA;
1828             }
1829             break;
1830         case F_CUBICBONDS:
1831             serializer->doReal(&iparams->cubic.b0);
1832             serializer->doReal(&iparams->cubic.kb);
1833             serializer->doReal(&iparams->cubic.kcub);
1834             break;
1835         case F_CONNBONDS:
1836             break;
1837         case F_POLARIZATION:
1838             serializer->doReal(&iparams->polarize.alpha);
1839             break;
1840         case F_ANHARM_POL:
1841             serializer->doReal(&iparams->anharm_polarize.alpha);
1842             serializer->doReal(&iparams->anharm_polarize.drcut);
1843             serializer->doReal(&iparams->anharm_polarize.khyp);
1844             break;
1845         case F_WATER_POL:
1846             serializer->doReal(&iparams->wpol.al_x);
1847             serializer->doReal(&iparams->wpol.al_y);
1848             serializer->doReal(&iparams->wpol.al_z);
1849             serializer->doReal(&iparams->wpol.rOH);
1850             serializer->doReal(&iparams->wpol.rHH);
1851             serializer->doReal(&iparams->wpol.rOD);
1852             break;
1853         case F_THOLE_POL:
1854             serializer->doReal(&iparams->thole.a);
1855             serializer->doReal(&iparams->thole.alpha1);
1856             serializer->doReal(&iparams->thole.alpha2);
1857             serializer->doReal(&iparams->thole.rfac);
1858             break;
1859         case F_LJ:
1860             serializer->doReal(&iparams->lj.c6);
1861             serializer->doReal(&iparams->lj.c12);
1862             break;
1863         case F_LJ14:
1864             serializer->doReal(&iparams->lj14.c6A);
1865             serializer->doReal(&iparams->lj14.c12A);
1866             serializer->doReal(&iparams->lj14.c6B);
1867             serializer->doReal(&iparams->lj14.c12B);
1868             break;
1869         case F_LJC14_Q:
1870             serializer->doReal(&iparams->ljc14.fqq);
1871             serializer->doReal(&iparams->ljc14.qi);
1872             serializer->doReal(&iparams->ljc14.qj);
1873             serializer->doReal(&iparams->ljc14.c6);
1874             serializer->doReal(&iparams->ljc14.c12);
1875             break;
1876         case F_LJC_PAIRS_NB:
1877             serializer->doReal(&iparams->ljcnb.qi);
1878             serializer->doReal(&iparams->ljcnb.qj);
1879             serializer->doReal(&iparams->ljcnb.c6);
1880             serializer->doReal(&iparams->ljcnb.c12);
1881             break;
1882         case F_PDIHS:
1883         case F_PIDIHS:
1884         case F_ANGRES:
1885         case F_ANGRESZ:
1886             serializer->doReal(&iparams->pdihs.phiA);
1887             serializer->doReal(&iparams->pdihs.cpA);
1888             serializer->doReal(&iparams->pdihs.phiB);
1889             serializer->doReal(&iparams->pdihs.cpB);
1890             serializer->doInt(&iparams->pdihs.mult);
1891             break;
1892         case F_RESTRDIHS:
1893             serializer->doReal(&iparams->pdihs.phiA);
1894             serializer->doReal(&iparams->pdihs.cpA);
1895             break;
1896         case F_DISRES:
1897             serializer->doInt(&iparams->disres.label);
1898             serializer->doInt(&iparams->disres.type);
1899             serializer->doReal(&iparams->disres.low);
1900             serializer->doReal(&iparams->disres.up1);
1901             serializer->doReal(&iparams->disres.up2);
1902             serializer->doReal(&iparams->disres.kfac);
1903             break;
1904         case F_ORIRES:
1905             serializer->doInt(&iparams->orires.ex);
1906             serializer->doInt(&iparams->orires.label);
1907             serializer->doInt(&iparams->orires.power);
1908             serializer->doReal(&iparams->orires.c);
1909             serializer->doReal(&iparams->orires.obs);
1910             serializer->doReal(&iparams->orires.kfac);
1911             break;
1912         case F_DIHRES:
1913             if (file_version < 82)
1914             {
1915                 serializer->doInt(&idum);
1916                 serializer->doInt(&idum);
1917             }
1918             serializer->doReal(&iparams->dihres.phiA);
1919             serializer->doReal(&iparams->dihres.dphiA);
1920             serializer->doReal(&iparams->dihres.kfacA);
1921             if (file_version >= 82)
1922             {
1923                 serializer->doReal(&iparams->dihres.phiB);
1924                 serializer->doReal(&iparams->dihres.dphiB);
1925                 serializer->doReal(&iparams->dihres.kfacB);
1926             }
1927             else
1928             {
1929                 iparams->dihres.phiB  = iparams->dihres.phiA;
1930                 iparams->dihres.dphiB = iparams->dihres.dphiA;
1931                 iparams->dihres.kfacB = iparams->dihres.kfacA;
1932             }
1933             break;
1934         case F_POSRES:
1935             serializer->doRvec(&iparams->posres.pos0A);
1936             serializer->doRvec(&iparams->posres.fcA);
1937             serializer->doRvec(&iparams->posres.pos0B);
1938             serializer->doRvec(&iparams->posres.fcB);
1939             break;
1940         case F_FBPOSRES:
1941             serializer->doInt(&iparams->fbposres.geom);
1942             serializer->doRvec(&iparams->fbposres.pos0);
1943             serializer->doReal(&iparams->fbposres.r);
1944             serializer->doReal(&iparams->fbposres.k);
1945             break;
1946         case F_CBTDIHS:
1947             serializer->doRealArray(iparams->cbtdihs.cbtcA, NR_CBTDIHS);
1948             break;
1949         case F_RBDIHS:
1950             serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
1951             serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
1952             break;
1953         case F_FOURDIHS:
1954             /* Fourier dihedrals are internally represented
1955              * as Ryckaert-Bellemans since those are faster to compute.
1956              */
1957             serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
1958             serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
1959             break;
1960         case F_CONSTR:
1961         case F_CONSTRNC:
1962             serializer->doReal(&iparams->constr.dA);
1963             serializer->doReal(&iparams->constr.dB);
1964             break;
1965         case F_SETTLE:
1966             serializer->doReal(&iparams->settle.doh);
1967             serializer->doReal(&iparams->settle.dhh);
1968             break;
1969         case F_VSITE2:
1970             serializer->doReal(&iparams->vsite.a);
1971             break;
1972         case F_VSITE3:
1973         case F_VSITE3FD:
1974         case F_VSITE3FAD:
1975             serializer->doReal(&iparams->vsite.a);
1976             serializer->doReal(&iparams->vsite.b);
1977             break;
1978         case F_VSITE3OUT:
1979         case F_VSITE4FD:
1980         case F_VSITE4FDN:
1981             serializer->doReal(&iparams->vsite.a);
1982             serializer->doReal(&iparams->vsite.b);
1983             serializer->doReal(&iparams->vsite.c);
1984             break;
1985         case F_VSITEN:
1986             serializer->doInt(&iparams->vsiten.n);
1987             serializer->doReal(&iparams->vsiten.a);
1988             break;
1989         case F_GB12_NOLONGERUSED:
1990         case F_GB13_NOLONGERUSED:
1991         case F_GB14_NOLONGERUSED:
1992             // Implicit solvent parameters can still be read, but never used
1993             if (serializer->reading())
1994             {
1995                 if (file_version < 68)
1996                 {
1997                     serializer->doReal(&rdum);
1998                     serializer->doReal(&rdum);
1999                     serializer->doReal(&rdum);
2000                     serializer->doReal(&rdum);
2001                 }
2002                 if (file_version < tpxv_RemoveImplicitSolvation)
2003                 {
2004                     serializer->doReal(&rdum);
2005                     serializer->doReal(&rdum);
2006                     serializer->doReal(&rdum);
2007                     serializer->doReal(&rdum);
2008                     serializer->doReal(&rdum);
2009                 }
2010             }
2011             break;
2012         case F_CMAP:
2013             serializer->doInt(&iparams->cmap.cmapA);
2014             serializer->doInt(&iparams->cmap.cmapB);
2015             break;
2016         default:
2017             gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
2018                       ftype, interaction_function[ftype].name, __FILE__, __LINE__);
2019     }
2020 }
2021
2022 static void do_ilist(gmx::ISerializer *serializer, InteractionList *ilist)
2023 {
2024     int nr = ilist->size();
2025     serializer->doInt(&nr);
2026     if (serializer->reading())
2027     {
2028         ilist->iatoms.resize(nr);
2029     }
2030     serializer->doIntArray(ilist->iatoms.data(), ilist->size());
2031 }
2032
2033 static void do_ffparams(gmx::ISerializer         *serializer,
2034                         gmx_ffparams_t           *ffparams,
2035                         int                       file_version)
2036 {
2037     serializer->doInt(&ffparams->atnr);
2038     int numTypes = ffparams->numTypes();
2039     serializer->doInt(&numTypes);
2040     if (serializer->reading())
2041     {
2042         ffparams->functype.resize(numTypes);
2043         ffparams->iparams.resize(numTypes);
2044     }
2045     /* Read/write all the function types */
2046     serializer->doIntArray(ffparams->functype.data(), ffparams->functype.size());
2047
2048     if (file_version >= 66)
2049     {
2050         serializer->doDouble(&ffparams->reppow);
2051     }
2052     else
2053     {
2054         ffparams->reppow = 12.0;
2055     }
2056
2057     serializer->doReal(&ffparams->fudgeQQ);
2058
2059     /* Check whether all these function types are supported by the code.
2060      * In practice the code is backwards compatible, which means that the
2061      * numbering may have to be altered from old numbering to new numbering
2062      */
2063     for (int i = 0; i < ffparams->numTypes(); i++)
2064     {
2065         if (serializer->reading())
2066         {
2067             /* Loop over file versions */
2068             for (int k = 0; k < NFTUPD; k++)
2069             {
2070                 /* Compare the read file_version to the update table */
2071                 if ((file_version < ftupd[k].fvnr) &&
2072                     (ffparams->functype[i] >= ftupd[k].ftype))
2073                 {
2074                     ffparams->functype[i] += 1;
2075                 }
2076             }
2077         }
2078
2079         do_iparams(serializer, ffparams->functype[i], &ffparams->iparams[i],
2080                    file_version);
2081     }
2082 }
2083
2084 static void add_settle_atoms(InteractionList *ilist)
2085 {
2086     int i;
2087
2088     /* Settle used to only store the first atom: add the other two */
2089     ilist->iatoms.resize(2*ilist->size());
2090     for (i = ilist->size()/4 - 1; i >= 0; i--)
2091     {
2092         ilist->iatoms[4*i+0] = ilist->iatoms[2*i+0];
2093         ilist->iatoms[4*i+1] = ilist->iatoms[2*i+1];
2094         ilist->iatoms[4*i+2] = ilist->iatoms[2*i+1] + 1;
2095         ilist->iatoms[4*i+3] = ilist->iatoms[2*i+1] + 2;
2096     }
2097 }
2098
2099 static void do_ilists(gmx::ISerializer         *serializer,
2100                       InteractionLists         *ilists,
2101                       int                       file_version)
2102 {
2103     GMX_RELEASE_ASSERT(ilists, "Need a valid ilists object");
2104     GMX_RELEASE_ASSERT(ilists->size() == F_NRE, "The code needs to be in sync with InteractionLists");
2105
2106     for (int j = 0; j < F_NRE; j++)
2107     {
2108         InteractionList &ilist  = (*ilists)[j];
2109         gmx_bool         bClear = FALSE;
2110         if (serializer->reading())
2111         {
2112             for (int k = 0; k < NFTUPD; k++)
2113             {
2114                 if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
2115                 {
2116                     bClear = TRUE;
2117                 }
2118             }
2119         }
2120         if (bClear)
2121         {
2122             ilist.iatoms.clear();
2123         }
2124         else
2125         {
2126             do_ilist(serializer, &ilist);
2127             if (file_version < 78 && j == F_SETTLE && ilist.size() > 0)
2128             {
2129                 add_settle_atoms(&ilist);
2130             }
2131         }
2132     }
2133 }
2134
2135 static void do_block(gmx::ISerializer *serializer, t_block *block)
2136 {
2137     serializer->doInt(&block->nr);
2138     if (serializer->reading())
2139     {
2140         if ((block->nalloc_index > 0) && (nullptr != block->index))
2141         {
2142             sfree(block->index);
2143         }
2144         block->nalloc_index = block->nr+1;
2145         snew(block->index, block->nalloc_index);
2146     }
2147     serializer->doIntArray(block->index, block->nr+1);
2148 }
2149
2150 static void do_blocka(gmx::ISerializer *serializer, t_blocka *block)
2151 {
2152     serializer->doInt(&block->nr);
2153     serializer->doInt(&block->nra);
2154     if (serializer->reading())
2155     {
2156         block->nalloc_index = block->nr+1;
2157         snew(block->index, block->nalloc_index);
2158         block->nalloc_a = block->nra;
2159         snew(block->a, block->nalloc_a);
2160     }
2161     serializer->doIntArray(block->index, block->nr+1);
2162     serializer->doIntArray(block->a, block->nra);
2163 }
2164
2165 /* This is a primitive routine to make it possible to translate atomic numbers
2166  * to element names when reading TPR files, without making the Gromacs library
2167  * directory a dependency on mdrun (which is the case if we need elements.dat).
2168  */
2169 static const char *
2170 atomicnumber_to_element(int atomicnumber)
2171 {
2172     const char * p;
2173
2174     /* This does not have to be complete, so we only include elements likely
2175      * to occur in PDB files.
2176      */
2177     switch (atomicnumber)
2178     {
2179         case 1:  p = "H";  break;
2180         case 5:  p = "B";  break;
2181         case 6:  p = "C";  break;
2182         case 7:  p = "N";  break;
2183         case 8:  p = "O";  break;
2184         case 9:  p = "F";  break;
2185         case 11: p = "Na"; break;
2186         case 12: p = "Mg"; break;
2187         case 15: p = "P";  break;
2188         case 16: p = "S";  break;
2189         case 17: p = "Cl"; break;
2190         case 18: p = "Ar"; break;
2191         case 19: p = "K";  break;
2192         case 20: p = "Ca"; break;
2193         case 25: p = "Mn"; break;
2194         case 26: p = "Fe"; break;
2195         case 28: p = "Ni"; break;
2196         case 29: p = "Cu"; break;
2197         case 30: p = "Zn"; break;
2198         case 35: p = "Br"; break;
2199         case 47: p = "Ag"; break;
2200         default: p = "";   break;
2201     }
2202     return p;
2203 }
2204
2205
2206 static void do_atom(gmx::ISerializer *serializer, t_atom *atom)
2207 {
2208     serializer->doReal(&atom->m);
2209     serializer->doReal(&atom->q);
2210     serializer->doReal(&atom->mB);
2211     serializer->doReal(&atom->qB);
2212     serializer->doUShort(&atom->type);
2213     serializer->doUShort(&atom->typeB);
2214     serializer->doInt(&atom->ptype);
2215     serializer->doInt(&atom->resind);
2216     serializer->doInt(&atom->atomnumber);
2217     if (serializer->reading())
2218     {
2219         /* Set element string from atomic number if present.
2220          * This routine returns an empty string if the name is not found.
2221          */
2222         std::strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
2223         /* avoid warnings about potentially unterminated string */
2224         atom->elem[3] = '\0';
2225     }
2226 }
2227
2228 static void do_grps(gmx::ISerializer               *serializer,
2229                     gmx::ArrayRef<AtomGroupIndices> grps)
2230 {
2231     for (auto &group : grps)
2232     {
2233         int size = group.size();
2234         serializer->doInt(&size);
2235         if (serializer->reading())
2236         {
2237             group.resize(size);
2238         }
2239         serializer->doIntArray(group.data(), size);
2240     }
2241 }
2242
2243 static void do_symstr(gmx::ISerializer *serializer, char ***nm, t_symtab *symtab)
2244 {
2245     int ls;
2246
2247     if (serializer->reading())
2248     {
2249         serializer->doInt(&ls);
2250         *nm = get_symtab_handle(symtab, ls);
2251     }
2252     else
2253     {
2254         ls = lookup_symtab(symtab, *nm);
2255         serializer->doInt(&ls);
2256     }
2257 }
2258
2259 static void do_strstr(gmx::ISerializer         *serializer,
2260                       int                       nstr,
2261                       char                   ***nm,
2262                       t_symtab                 *symtab)
2263 {
2264     int  j;
2265
2266     for (j = 0; (j < nstr); j++)
2267     {
2268         do_symstr(serializer, &(nm[j]), symtab);
2269     }
2270 }
2271
2272 static void do_resinfo(gmx::ISerializer         *serializer,
2273                        int                       n,
2274                        t_resinfo                *ri,
2275                        t_symtab                 *symtab,
2276                        int                       file_version)
2277 {
2278     int  j;
2279
2280     for (j = 0; (j < n); j++)
2281     {
2282         do_symstr(serializer, &(ri[j].name), symtab);
2283         if (file_version >= 63)
2284         {
2285             serializer->doInt(&ri[j].nr);
2286             serializer->doUChar(&ri[j].ic);
2287         }
2288         else
2289         {
2290             ri[j].nr = j + 1;
2291             ri[j].ic = ' ';
2292         }
2293     }
2294 }
2295
2296 static void do_atoms(gmx::ISerializer         *serializer,
2297                      t_atoms                  *atoms,
2298                      t_symtab                 *symtab,
2299                      int                       file_version)
2300 {
2301     int i;
2302
2303     serializer->doInt(&atoms->nr);
2304     serializer->doInt(&atoms->nres);
2305     if (serializer->reading())
2306     {
2307         /* Since we have always written all t_atom properties in the tpr file
2308          * (at least for all backward compatible versions), we don't store
2309          * but simple set the booleans here.
2310          */
2311         atoms->haveMass    = TRUE;
2312         atoms->haveCharge  = TRUE;
2313         atoms->haveType    = TRUE;
2314         atoms->haveBState  = TRUE;
2315         atoms->havePdbInfo = FALSE;
2316
2317         snew(atoms->atom, atoms->nr);
2318         snew(atoms->atomname, atoms->nr);
2319         snew(atoms->atomtype, atoms->nr);
2320         snew(atoms->atomtypeB, atoms->nr);
2321         snew(atoms->resinfo, atoms->nres);
2322         atoms->pdbinfo = nullptr;
2323     }
2324     else
2325     {
2326         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");
2327     }
2328     for (i = 0; (i < atoms->nr); i++)
2329     {
2330         do_atom(serializer, &atoms->atom[i]);
2331     }
2332     do_strstr(serializer, atoms->nr, atoms->atomname, symtab);
2333     do_strstr(serializer, atoms->nr, atoms->atomtype, symtab);
2334     do_strstr(serializer, atoms->nr, atoms->atomtypeB, symtab);
2335
2336     do_resinfo(serializer, atoms->nres, atoms->resinfo, symtab, file_version);
2337 }
2338
2339 static void do_groups(gmx::ISerializer         *serializer,
2340                       SimulationGroups         *groups,
2341                       t_symtab                 *symtab)
2342 {
2343     do_grps(serializer, groups->groups);
2344     int numberOfGroupNames = groups->groupNames.size();
2345     serializer->doInt(&numberOfGroupNames);
2346     if (serializer->reading())
2347     {
2348         groups->groupNames.resize(numberOfGroupNames);
2349     }
2350     do_strstr(serializer, numberOfGroupNames, groups->groupNames.data(), symtab);
2351     for (auto group : gmx::keysOf(groups->groupNumbers))
2352     {
2353         int numberOfGroupNumbers = groups->numberOfGroupNumbers(group);
2354         serializer->doInt(&numberOfGroupNumbers);
2355         if (numberOfGroupNumbers != 0)
2356         {
2357             if (serializer->reading())
2358             {
2359                 groups->groupNumbers[group].resize(numberOfGroupNumbers);
2360             }
2361             serializer->doUCharArray(groups->groupNumbers[group].data(), numberOfGroupNumbers);
2362         }
2363     }
2364 }
2365
2366 static void do_atomtypes(gmx::ISerializer *serializer, t_atomtypes *atomtypes,
2367                          int file_version)
2368 {
2369     int      j;
2370
2371     serializer->doInt(&atomtypes->nr);
2372     j = atomtypes->nr;
2373     if (serializer->reading())
2374     {
2375         snew(atomtypes->atomnumber, j);
2376     }
2377     if (serializer->reading() && file_version < tpxv_RemoveImplicitSolvation)
2378     {
2379         std::vector<real> dummy(atomtypes->nr, 0);
2380         serializer->doRealArray(dummy.data(), dummy.size());
2381         serializer->doRealArray(dummy.data(), dummy.size());
2382         serializer->doRealArray(dummy.data(), dummy.size());
2383     }
2384     serializer->doIntArray(atomtypes->atomnumber, j);
2385
2386     if (serializer->reading() && file_version >= 60 && file_version < tpxv_RemoveImplicitSolvation)
2387     {
2388         std::vector<real> dummy(atomtypes->nr, 0);
2389         serializer->doRealArray(dummy.data(), dummy.size());
2390         serializer->doRealArray(dummy.data(), dummy.size());
2391     }
2392 }
2393
2394 static void do_symtab(gmx::ISerializer *serializer, t_symtab *symtab)
2395 {
2396     int       i, nr;
2397     t_symbuf *symbuf;
2398
2399     serializer->doInt(&symtab->nr);
2400     nr     = symtab->nr;
2401     if (serializer->reading())
2402     {
2403         snew(symtab->symbuf, 1);
2404         symbuf          = symtab->symbuf;
2405         symbuf->bufsize = nr;
2406         snew(symbuf->buf, nr);
2407         for (i = 0; (i < nr); i++)
2408         {
2409             std::string buf;
2410             serializer->doString(&buf);
2411             symbuf->buf[i] = gmx_strdup(buf.c_str());
2412         }
2413     }
2414     else
2415     {
2416         symbuf = symtab->symbuf;
2417         while (symbuf != nullptr)
2418         {
2419             for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
2420             {
2421                 std::string buf = symbuf->buf[i];
2422                 serializer->doString(&buf);
2423             }
2424             nr    -= i;
2425             symbuf = symbuf->next;
2426         }
2427         if (nr != 0)
2428         {
2429             gmx_fatal(FARGS, "nr of symtab strings left: %d", nr);
2430         }
2431     }
2432 }
2433
2434 static void do_cmap(gmx::ISerializer *serializer, gmx_cmap_t *cmap_grid)
2435 {
2436
2437     int ngrid = cmap_grid->cmapdata.size();
2438     serializer->doInt(&ngrid);
2439     serializer->doInt(&cmap_grid->grid_spacing);
2440
2441     int gs    = cmap_grid->grid_spacing;
2442     int nelem = gs * gs;
2443
2444     if (serializer->reading())
2445     {
2446         cmap_grid->cmapdata.resize(ngrid);
2447
2448         for (int i = 0; i < ngrid; i++)
2449         {
2450             cmap_grid->cmapdata[i].cmap.resize(4*nelem);
2451         }
2452     }
2453
2454     for (int i = 0; i < ngrid; i++)
2455     {
2456         for (int j = 0; j < nelem; j++)
2457         {
2458             serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4]);
2459             serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4+1]);
2460             serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4+2]);
2461             serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4+3]);
2462         }
2463     }
2464 }
2465
2466
2467 static void do_moltype(gmx::ISerializer         *serializer,
2468                        gmx_moltype_t            *molt,
2469                        t_symtab                 *symtab,
2470                        int                       file_version)
2471 {
2472     do_symstr(serializer, &(molt->name), symtab);
2473
2474     do_atoms(serializer, &molt->atoms, symtab, file_version);
2475
2476     do_ilists(serializer, &molt->ilist, file_version);
2477
2478     do_block(serializer, &molt->cgs);
2479
2480     /* This used to be in the atoms struct */
2481     do_blocka(serializer, &molt->excls);
2482 }
2483
2484 static void do_molblock(gmx::ISerializer         *serializer,
2485                         gmx_molblock_t           *molb,
2486                         int                       numAtomsPerMolecule)
2487 {
2488     serializer->doInt(&molb->type);
2489     serializer->doInt(&molb->nmol);
2490     /* To maintain forward topology reading compatibility, we store #atoms.
2491      * TODO: Change this to conditional reading of a dummy int when we
2492      *       increase tpx_generation.
2493      */
2494     serializer->doInt(&numAtomsPerMolecule);
2495     /* Position restraint coordinates */
2496     int numPosres_xA = molb->posres_xA.size();
2497     serializer->doInt(&numPosres_xA);
2498     if (numPosres_xA > 0)
2499     {
2500         if (serializer->reading())
2501         {
2502             molb->posres_xA.resize(numPosres_xA);
2503         }
2504         serializer->doRvecArray(as_rvec_array(molb->posres_xA.data()), numPosres_xA);
2505     }
2506     int numPosres_xB = molb->posres_xB.size();
2507     serializer->doInt(&numPosres_xB);
2508     if (numPosres_xB > 0)
2509     {
2510         if (serializer->reading())
2511         {
2512             molb->posres_xB.resize(numPosres_xB);
2513         }
2514         serializer->doRvecArray(as_rvec_array(molb->posres_xB.data()), numPosres_xB);
2515     }
2516
2517 }
2518
2519 static void set_disres_npair(gmx_mtop_t *mtop)
2520 {
2521     gmx_mtop_ilistloop_t     iloop;
2522     int                      nmol;
2523
2524     gmx::ArrayRef<t_iparams> ip = mtop->ffparams.iparams;
2525
2526     iloop     = gmx_mtop_ilistloop_init(mtop);
2527     while (const InteractionLists *ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
2528     {
2529         const InteractionList &il = (*ilist)[F_DISRES];
2530
2531         if (il.size() > 0)
2532         {
2533             gmx::ArrayRef<const int> a     = il.iatoms;
2534             int                      npair = 0;
2535             for (int i = 0; i < il.size(); i += 3)
2536             {
2537                 npair++;
2538                 if (i+3 == il.size() || ip[a[i]].disres.label != ip[a[i+3]].disres.label)
2539                 {
2540                     ip[a[i]].disres.npair = npair;
2541                     npair                 = 0;
2542                 }
2543             }
2544         }
2545     }
2546 }
2547
2548 static void do_mtop(gmx::ISerializer         *serializer,
2549                     gmx_mtop_t               *mtop,
2550                     int                       file_version)
2551 {
2552     do_symtab(serializer, &(mtop->symtab));
2553
2554     do_symstr(serializer, &(mtop->name), &(mtop->symtab));
2555
2556     do_ffparams(serializer, &mtop->ffparams, file_version);
2557
2558     int nmoltype = mtop->moltype.size();
2559     serializer->doInt(&nmoltype);
2560     if (serializer->reading())
2561     {
2562         mtop->moltype.resize(nmoltype);
2563     }
2564     for (gmx_moltype_t &moltype : mtop->moltype)
2565     {
2566         do_moltype(serializer, &moltype, &mtop->symtab, file_version);
2567     }
2568
2569     int nmolblock = mtop->molblock.size();
2570     serializer->doInt(&nmolblock);
2571     if (serializer->reading())
2572     {
2573         mtop->molblock.resize(nmolblock);
2574     }
2575     for (gmx_molblock_t &molblock : mtop->molblock)
2576     {
2577         int numAtomsPerMolecule = (serializer->reading() ? 0 : mtop->moltype[molblock.type].atoms.nr);
2578         do_molblock(serializer, &molblock, numAtomsPerMolecule);
2579     }
2580     serializer->doInt(&mtop->natoms);
2581
2582     if (file_version >= tpxv_IntermolecularBondeds)
2583     {
2584         serializer->doBool(&mtop->bIntermolecularInteractions);
2585         if (mtop->bIntermolecularInteractions)
2586         {
2587             if (serializer->reading())
2588             {
2589                 mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
2590             }
2591             do_ilists(serializer, mtop->intermolecular_ilist.get(), file_version);
2592         }
2593     }
2594     else
2595     {
2596         mtop->bIntermolecularInteractions = FALSE;
2597     }
2598
2599     do_atomtypes (serializer, &(mtop->atomtypes), file_version);
2600
2601     if (file_version >= 65)
2602     {
2603         do_cmap(serializer, &mtop->ffparams.cmap_grid);
2604     }
2605     else
2606     {
2607         mtop->ffparams.cmap_grid.grid_spacing = 0;
2608         mtop->ffparams.cmap_grid.cmapdata.clear();
2609     }
2610
2611     do_groups(serializer, &mtop->groups, &(mtop->symtab));
2612
2613     mtop->haveMoleculeIndices = true;
2614
2615     if (serializer->reading())
2616     {
2617         close_symtab(&(mtop->symtab));
2618     }
2619 }
2620
2621 /*! \brief
2622  * Read the first part of the TPR file to find general system information.
2623  *
2624  * If \p TopOnlyOK is true then we can read even future versions
2625  * of tpx files, provided the \p fileGeneration hasn't changed.
2626  * If it is false, we need the \p ir too, and bail out
2627  * if the file is newer than the program.
2628  *
2629  * The version and generation of the topology (see top of this file)
2630  * are returned in the two last arguments, if those arguments are non-nullptr.
2631  *
2632  * If possible, we will read the \p ir even when \p TopOnlyOK is true.
2633  *
2634  * \param[in,out] serializer The serializer used to handle header processing.
2635  * \param[in,out] tpx File header datastructure.
2636  * \param[in]     filename The name of the file being read/written
2637  * \param[in,out] fio File handle.
2638  * \param[in] TopOnlyOK If not reading \p ir is fine or not.
2639  */
2640 static void do_tpxheader(gmx::FileIOXdrSerializer *serializer,
2641                          TpxFileHeader            *tpx,
2642                          const char               *filename,
2643                          t_fileio                 *fio,
2644                          bool                      TopOnlyOK)
2645 {
2646     gmx_bool  bDouble;
2647     int       precision;
2648     int       idum = 0;
2649     real      rdum = 0;
2650
2651     /* XDR binary topology file */
2652     precision = sizeof(real);
2653     std::string buf;
2654     std::string fileTag;
2655     if (serializer->reading())
2656     {
2657         serializer->doString(&buf);
2658         if (std::strncmp(buf.c_str(), "VERSION", 7) != 0)
2659         {
2660             gmx_fatal(FARGS, "Can not read file %s,\n"
2661                       "             this file is from a GROMACS version which is older than 2.0\n"
2662                       "             Make a new one with grompp or use a gro or pdb file, if possible",
2663                       filename);
2664         }
2665         serializer->doInt(&precision);
2666         bDouble = (precision == sizeof(double));
2667         if ((precision != sizeof(float)) && !bDouble)
2668         {
2669             gmx_fatal(FARGS, "Unknown precision in file %s: real is %d bytes "
2670                       "instead of %zu or %zu",
2671                       filename, precision, sizeof(float), sizeof(double));
2672         }
2673         gmx_fio_setprecision(fio, bDouble);
2674         fprintf(stderr, "Reading file %s, %s (%s precision)\n",
2675                 filename, buf.c_str(), bDouble ? "double" : "single");
2676     }
2677     else
2678     {
2679         buf = gmx::formatString("VERSION %s", gmx_version());
2680         serializer->doString(&buf);
2681         bDouble = (precision == sizeof(double));
2682         gmx_fio_setprecision(fio, bDouble);
2683         serializer->doInt(&precision);
2684         fileTag        = gmx::formatString("%s", tpx_tag);
2685     }
2686
2687     /* Check versions! */
2688     serializer->doInt(&tpx->fileVersion);
2689
2690     /* This is for backward compatibility with development versions 77-79
2691      * where the tag was, mistakenly, placed before the generation,
2692      * which would cause a segv instead of a proper error message
2693      * when reading the topology only from tpx with <77 code.
2694      */
2695     if (tpx->fileVersion >= 77 && tpx->fileVersion <= 79)
2696     {
2697         serializer->doString(&fileTag);
2698     }
2699
2700     serializer->doInt(&tpx->fileGeneration);
2701
2702     if (tpx->fileVersion >= 81)
2703     {
2704         serializer->doString(&fileTag);
2705     }
2706     if (serializer->reading())
2707     {
2708         if (tpx->fileVersion < 77)
2709         {
2710             /* Versions before 77 don't have the tag, set it to release */
2711             fileTag = gmx::formatString("%s", TPX_TAG_RELEASE);
2712         }
2713
2714         if (fileTag != tpx_tag)
2715         {
2716             fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n",
2717                     fileTag.c_str(), tpx_tag);
2718
2719             /* We only support reading tpx files with the same tag as the code
2720              * or tpx files with the release tag and with lower version number.
2721              */
2722             if (fileTag != TPX_TAG_RELEASE && tpx->fileVersion < tpx_version)
2723             {
2724                 gmx_fatal(FARGS, "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
2725                           filename, tpx->fileVersion, fileTag.c_str(),
2726                           tpx_version, tpx_tag);
2727             }
2728         }
2729     }
2730
2731     if ((tpx->fileVersion <= tpx_incompatible_version) ||
2732         ((tpx->fileVersion > tpx_version) && !TopOnlyOK) ||
2733         (tpx->fileGeneration > tpx_generation) ||
2734         tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
2735     {
2736         gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program",
2737                   filename, tpx->fileVersion, tpx_version);
2738     }
2739
2740     serializer->doInt(&tpx->natoms);
2741     serializer->doInt(&tpx->ngtc);
2742
2743     if (tpx->fileVersion < 62)
2744     {
2745         serializer->doInt(&idum);
2746         serializer->doReal(&rdum);
2747     }
2748     if (tpx->fileVersion >= 79)
2749     {
2750         serializer->doInt(&tpx->fep_state);
2751     }
2752     serializer->doReal(&tpx->lambda);
2753     serializer->doBool(&tpx->bIr);
2754     serializer->doBool(&tpx->bTop);
2755     serializer->doBool(&tpx->bX);
2756     serializer->doBool(&tpx->bV);
2757     serializer->doBool(&tpx->bF);
2758     serializer->doBool(&tpx->bBox);
2759
2760     if ((tpx->fileGeneration > tpx_generation))
2761     {
2762         /* This can only happen if TopOnlyOK=TRUE */
2763         tpx->bIr = FALSE;
2764     }
2765 }
2766
2767 static int do_tpx_body(gmx::ISerializer *serializer,
2768                        TpxFileHeader    *tpx,
2769                        t_inputrec       *ir,
2770                        t_state          *state,
2771                        rvec             *x,
2772                        rvec             *v,
2773                        gmx_mtop_t       *mtop)
2774 {
2775     int             ePBC;
2776     gmx_bool        bPeriodicMols;
2777
2778     if (!serializer->reading())
2779     {
2780         GMX_RELEASE_ASSERT(x == nullptr && v == nullptr, "Passing separate x and v pointers to do_tpx() is not supported when writing");
2781     }
2782     else
2783     {
2784         GMX_RELEASE_ASSERT(!(x == nullptr && v != nullptr), "Passing x==NULL and v!=NULL is not supported");
2785     }
2786
2787     if (serializer->reading())
2788     {
2789         state->flags = 0;
2790         init_gtc_state(state, tpx->ngtc, 0, 0);
2791         if (x == nullptr)
2792         {
2793             // v is also nullptr by the above assertion, so we may
2794             // need to make memory in state for storing the contents
2795             // of the tpx file.
2796             if (tpx->bX)
2797             {
2798                 state->flags |= (1 << estX);
2799             }
2800             if (tpx->bV)
2801             {
2802                 state->flags |= (1 << estV);
2803             }
2804             state_change_natoms(state, tpx->natoms);
2805         }
2806     }
2807
2808     if (x == nullptr)
2809     {
2810         x = state->x.rvec_array();
2811         v = state->v.rvec_array();
2812     }
2813
2814 #define do_test(serializer, b, p) if ((serializer)->reading() && ((p) != nullptr) && !(b)) gmx_fatal(FARGS, "No %s in input file",#p)
2815
2816     do_test(serializer, tpx->bBox, state->box);
2817     if (tpx->bBox)
2818     {
2819         serializer->doRvecArray(state->box, DIM);
2820         if (tpx->fileVersion >= 51)
2821         {
2822             serializer->doRvecArray(state->box_rel, DIM);
2823         }
2824         else
2825         {
2826             /* We initialize box_rel after reading the inputrec */
2827             clear_mat(state->box_rel);
2828         }
2829         serializer->doRvecArray(state->boxv, DIM);
2830         if (tpx->fileVersion < 56)
2831         {
2832             matrix mdum;
2833             serializer->doRvecArray(mdum, DIM);
2834         }
2835     }
2836
2837     if (state->ngtc > 0)
2838     {
2839         real *dumv;
2840         snew(dumv, state->ngtc);
2841         if (tpx->fileVersion < 69)
2842         {
2843             serializer->doRealArray(dumv, state->ngtc);
2844         }
2845         /* These used to be the Berendsen tcoupl_lambda's */
2846         serializer->doRealArray(dumv, state->ngtc);
2847         sfree(dumv);
2848     }
2849
2850     do_test(serializer, tpx->bTop, mtop);
2851     if (tpx->bTop)
2852     {
2853         if (mtop)
2854         {
2855             do_mtop(serializer, mtop, tpx->fileVersion);
2856         }
2857         else
2858         {
2859             gmx_mtop_t dum_top;
2860             do_mtop(serializer, &dum_top, tpx->fileVersion);
2861         }
2862     }
2863     do_test(serializer, tpx->bX, x);
2864     if (tpx->bX)
2865     {
2866         if (serializer->reading())
2867         {
2868             state->flags |= (1<<estX);
2869         }
2870         serializer->doRvecArray(x, tpx->natoms);
2871     }
2872
2873     do_test(serializer, tpx->bV, v);
2874     if (tpx->bV)
2875     {
2876         if (serializer->reading())
2877         {
2878             state->flags |= (1<<estV);
2879         }
2880         if (!v)
2881         {
2882             std::vector<gmx::RVec> dummyVelocities(tpx->natoms);
2883             serializer->doRvecArray(as_rvec_array(dummyVelocities.data()), tpx->natoms);
2884         }
2885         else
2886         {
2887             serializer->doRvecArray(v, tpx->natoms);
2888         }
2889     }
2890
2891     // No need to run do_test when the last argument is NULL
2892     if (tpx->bF)
2893     {
2894         std::vector<gmx::RVec> dummyForces(state->natoms);
2895         serializer->doRvecArray(as_rvec_array(dummyForces.data()), tpx->natoms);
2896     }
2897
2898     /* Starting with tpx version 26, we have the inputrec
2899      * at the end of the file, so we can ignore it
2900      * if the file is never than the software (but still the
2901      * same generation - see comments at the top of this file.
2902      *
2903      *
2904      */
2905     ePBC          = -1;
2906     bPeriodicMols = FALSE;
2907
2908     do_test(serializer, tpx->bIr, ir);
2909     if (tpx->bIr)
2910     {
2911         if (tpx->fileVersion >= 53)
2912         {
2913             /* Removed the pbc info from do_inputrec, since we always want it */
2914             if (!serializer->reading())
2915             {
2916                 ePBC          = ir->ePBC;
2917                 bPeriodicMols = ir->bPeriodicMols;
2918             }
2919             serializer->doInt(&ePBC);
2920             serializer->doBool(&bPeriodicMols);
2921         }
2922         if (tpx->fileGeneration <= tpx_generation && ir)
2923         {
2924             do_inputrec(serializer, ir, tpx->fileVersion);
2925             if (tpx->fileVersion < 51)
2926             {
2927                 set_box_rel(ir, state);
2928             }
2929             if (tpx->fileVersion < 53)
2930             {
2931                 ePBC          = ir->ePBC;
2932                 bPeriodicMols = ir->bPeriodicMols;
2933             }
2934         }
2935         if (serializer->reading() && ir && tpx->fileVersion >= 53)
2936         {
2937             /* We need to do this after do_inputrec, since that initializes ir */
2938             ir->ePBC          = ePBC;
2939             ir->bPeriodicMols = bPeriodicMols;
2940         }
2941     }
2942
2943     if (serializer->reading())
2944     {
2945         if (tpx->bIr && ir)
2946         {
2947             if (state->ngtc == 0)
2948             {
2949                 /* Reading old version without tcoupl state data: set it */
2950                 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
2951             }
2952             if (tpx->bTop && mtop)
2953             {
2954                 if (tpx->fileVersion < 57)
2955                 {
2956                     if (mtop->moltype[0].ilist[F_DISRES].size() > 0)
2957                     {
2958                         ir->eDisre = edrSimple;
2959                     }
2960                     else
2961                     {
2962                         ir->eDisre = edrNone;
2963                     }
2964                 }
2965                 set_disres_npair(mtop);
2966             }
2967         }
2968
2969         if (tpx->bTop && mtop)
2970         {
2971             gmx_mtop_finalize(mtop);
2972         }
2973     }
2974
2975     return ePBC;
2976 }
2977
2978 static t_fileio *open_tpx(const char *fn, const char *mode)
2979 {
2980     return gmx_fio_open(fn, mode);
2981 }
2982
2983 static void close_tpx(t_fileio *fio)
2984 {
2985     gmx_fio_close(fio);
2986 }
2987
2988 /*! \brief
2989  * Fill information into the header only from state before writing.
2990  *
2991  * Populating the header needs to be independent from writing the information
2992  * to file to allow things like writing the raw byte stream.
2993  *
2994  * \param[in] state The current simulation state. Can't write without it.
2995  * \param[in] ir Parameter and system information.
2996  * \param[in] mtop Global topology.
2997  * \returns Fully populated header.
2998  */
2999 static TpxFileHeader populateTpxHeader(const t_state    &state,
3000                                        const t_inputrec *ir,
3001                                        const gmx_mtop_t *mtop)
3002 {
3003     TpxFileHeader header;
3004     header.natoms         = state.natoms;
3005     header.ngtc           = state.ngtc;
3006     header.fep_state      = state.fep_state;
3007     header.lambda         = state.lambda[efptFEP];
3008     header.bIr            = ir       != nullptr;
3009     header.bTop           = mtop     != nullptr;
3010     header.bX             = (state.flags & (1 << estX)) != 0;
3011     header.bV             = (state.flags & (1 << estV)) != 0;
3012     header.bF             = false;
3013     header.bBox           = true;
3014     header.fileVersion    = tpx_version;
3015     header.fileGeneration = tpx_generation;
3016
3017     return header;
3018 }
3019
3020 /************************************************************
3021  *
3022  *  The following routines are the exported ones
3023  *
3024  ************************************************************/
3025
3026 TpxFileHeader readTpxHeader(const char *fileName, bool canReadTopologyOnly)
3027 {
3028     t_fileio *fio;
3029
3030     fio = open_tpx(fileName, "r");
3031     gmx::FileIOXdrSerializer serializer(fio);
3032
3033     TpxFileHeader            tpx;
3034     do_tpxheader(&serializer, &tpx, fileName, fio, canReadTopologyOnly);
3035     close_tpx(fio);
3036     return tpx;
3037 }
3038
3039 void write_tpx_state(const char *fn,
3040                      const t_inputrec *ir, const t_state *state, const gmx_mtop_t *mtop)
3041 {
3042     t_fileio *fio;
3043
3044     fio = open_tpx(fn, "w");
3045
3046     TpxFileHeader tpx = populateTpxHeader(*state,
3047                                           ir,
3048                                           mtop);
3049
3050     gmx::FileIOXdrSerializer serializer(fio);
3051     do_tpxheader(&serializer,
3052                  &tpx,
3053                  fn,
3054                  fio,
3055                  ir == nullptr);
3056     do_tpx_body(&serializer,
3057                 &tpx,
3058                 const_cast<t_inputrec *>(ir),
3059                 const_cast<t_state *>(state), nullptr, nullptr,
3060                 const_cast<gmx_mtop_t *>(mtop));
3061     close_tpx(fio);
3062 }
3063
3064 void read_tpx_state(const char *fn,
3065                     t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
3066 {
3067     t_fileio                *fio;
3068
3069     TpxFileHeader            tpx;
3070     fio = open_tpx(fn, "r");
3071     gmx::FileIOXdrSerializer serializer(fio);
3072     do_tpxheader(&serializer,
3073                  &tpx,
3074                  fn,
3075                  fio,
3076                  ir == nullptr);
3077     do_tpx_body(&serializer,
3078                 &tpx,
3079                 ir,
3080                 state,
3081                 nullptr,
3082                 nullptr,
3083                 mtop);
3084     close_tpx(fio);
3085 }
3086
3087 int read_tpx(const char *fn,
3088              t_inputrec *ir, matrix box, int *natoms,
3089              rvec *x, rvec *v, gmx_mtop_t *mtop)
3090 {
3091     t_fileio                *fio;
3092     t_state                  state;
3093     int                      ePBC;
3094
3095     TpxFileHeader            tpx;
3096     fio     = open_tpx(fn, "r");
3097     gmx::FileIOXdrSerializer serializer(fio);
3098     do_tpxheader(&serializer,
3099                  &tpx,
3100                  fn,
3101                  fio,
3102                  ir == nullptr);
3103     ePBC    = do_tpx_body(&serializer,
3104                           &tpx,
3105                           ir, &state, x, v, mtop);
3106     close_tpx(fio);
3107     if (mtop != nullptr && natoms != nullptr)
3108     {
3109         *natoms = mtop->natoms;
3110     }
3111     if (box)
3112     {
3113         copy_mat(state.box, box);
3114     }
3115
3116     return ePBC;
3117 }
3118
3119 int read_tpx_top(const char *fn,
3120                  t_inputrec *ir, matrix box, int *natoms,
3121                  rvec *x, rvec *v, t_topology *top)
3122 {
3123     gmx_mtop_t  mtop;
3124     int         ePBC;
3125
3126     ePBC = read_tpx(fn, ir, box, natoms, x, v, &mtop);
3127
3128     *top = gmx_mtop_t_to_t_topology(&mtop, true);
3129
3130     return ePBC;
3131 }
3132
3133 gmx_bool fn2bTPX(const char *file)
3134 {
3135     return (efTPR == fn2ftp(file));
3136 }
3137
3138 void pr_tpxheader(FILE *fp, int indent, const char *title, const TpxFileHeader *sh)
3139 {
3140     if (available(fp, sh, indent, title))
3141     {
3142         indent = pr_title(fp, indent, title);
3143         pr_indent(fp, indent);
3144         fprintf(fp, "bIr    = %spresent\n", sh->bIr ? "" : "not ");
3145         pr_indent(fp, indent);
3146         fprintf(fp, "bBox   = %spresent\n", sh->bBox ? "" : "not ");
3147         pr_indent(fp, indent);
3148         fprintf(fp, "bTop   = %spresent\n", sh->bTop ? "" : "not ");
3149         pr_indent(fp, indent);
3150         fprintf(fp, "bX     = %spresent\n", sh->bX ? "" : "not ");
3151         pr_indent(fp, indent);
3152         fprintf(fp, "bV     = %spresent\n", sh->bV ? "" : "not ");
3153         pr_indent(fp, indent);
3154         fprintf(fp, "bF     = %spresent\n", sh->bF ? "" : "not ");
3155
3156         pr_indent(fp, indent);
3157         fprintf(fp, "natoms = %d\n", sh->natoms);
3158         pr_indent(fp, indent);
3159         fprintf(fp, "lambda = %e\n", sh->lambda);
3160     }
3161 }