src/gromacs/trajectoryanalysis/runnercommon.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements gmx::TrajectoryAnalysisRunnerCommon.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_trajectoryanalysis
  41  */
  42 #include "runnercommon.h"
  43
  44 #ifdef HAVE_CONFIG_H
  45 #include "config.h"
  46 #endif
  47
  48 #include <string.h>
  49
  50 #include "gromacs/legacyheaders/oenv.h"
  51 #include "gromacs/legacyheaders/rmpbc.h"
  52 #include "gromacs/legacyheaders/smalloc.h"
  53 #include "gromacs/legacyheaders/statutil.h"
  54 #include "gromacs/legacyheaders/tpxio.h"
  55 #include "gromacs/legacyheaders/vec.h"
  56
  57 #include "gromacs/options/basicoptions.h"
  58 #include "gromacs/options/filenameoption.h"
  59 #include "gromacs/options/options.h"
  60 #include "gromacs/selection/indexutil.h"
  61 #include "gromacs/selection/selectioncollection.h"
  62 #include "gromacs/selection/selectionfileoption.h"
  63 #include "gromacs/trajectoryanalysis/analysissettings.h"
  64 #include "gromacs/utility/exceptions.h"
  65 #include "gromacs/utility/gmxassert.h"
  66 #include "gromacs/utility/stringutil.h"
  67
  68 #include "analysissettings-impl.h"
  69
  70 namespace gmx
  71 {
  72
  73 class TrajectoryAnalysisRunnerCommon::Impl
  74 {
  75     public:
  76         Impl(TrajectoryAnalysisSettings *settings);
  77         ~Impl();
  78
  79         void finishTrajectory();
  80
  81         TrajectoryAnalysisSettings &settings_;
  82         TopologyInformation         topInfo_;
  83
  84         bool                        bHelp_;
  85         bool                        bShowHidden_;
  86         bool                        bQuiet_;
  87         //! Name of the trajectory file (empty if not provided).
  88         std::string                 trjfile_;
  89         //! Name of the topology file (empty if no topology provided).
  90         std::string                 topfile_;
  91         //! Name of the index file (empty if no index file provided).
  92         std::string                 ndxfile_;
  93         double                      startTime_;
  94         double                      endTime_;
  95         double                      deltaTime_;
  96
  97         gmx_ana_indexgrps_t        *grps_;
  98         bool                        bTrajOpen_;
  99         //! The current frame, or \p NULL if no frame loaded yet.
 100         t_trxframe                 *fr;
 101         gmx_rmpbc_t                 gpbc_;
 102         //! Used to store the status variable from read_first_frame().
 103         t_trxstatus                *status_;
 104         output_env_t                oenv_;
 105 };
 106
 107
 108 TrajectoryAnalysisRunnerCommon::Impl::Impl(TrajectoryAnalysisSettings *settings)
 109     : settings_(*settings),
 110       bHelp_(false), bShowHidden_(false), bQuiet_(false),
 111       startTime_(0.0), endTime_(0.0), deltaTime_(0.0),
 112       grps_(NULL),
 113       bTrajOpen_(false), fr(NULL), gpbc_(NULL), status_(NULL), oenv_(NULL)
 114 {
 115 }
 116
 117
 118 TrajectoryAnalysisRunnerCommon::Impl::~Impl()
 119 {
 120     if (grps_ != NULL)
 121     {
 122         gmx_ana_indexgrps_free(grps_);
 123     }
 124     finishTrajectory();
 125     if (fr)
 126     {
 127         // There doesn't seem to be a function for freeing frame data
 128         sfree(fr->x);
 129         sfree(fr->v);
 130         sfree(fr->f);
 131         sfree(fr);
 132     }
 133     if (oenv_ != NULL)
 134     {
 135         output_env_done(oenv_);
 136     }
 137 }
 138
 139
 140 void
 141 TrajectoryAnalysisRunnerCommon::Impl::finishTrajectory()
 142 {
 143     if (bTrajOpen_)
 144     {
 145         close_trx(status_);
 146         bTrajOpen_ = false;
 147     }
 148     if (gpbc_ != NULL)
 149     {
 150         gmx_rmpbc_done(gpbc_);
 151         gpbc_ = NULL;
 152     }
 153 }
 154
 155 /*********************************************************************
 156  * TrajectoryAnalysisRunnerCommon
 157  */
 158
 159 TrajectoryAnalysisRunnerCommon::TrajectoryAnalysisRunnerCommon(
 160         TrajectoryAnalysisSettings *settings)
 161     : impl_(new Impl(settings))
 162 {
 163 }
 164
 165
 166 TrajectoryAnalysisRunnerCommon::~TrajectoryAnalysisRunnerCommon()
 167 {
 168 }
 169
 170
 171 void
 172 TrajectoryAnalysisRunnerCommon::initOptions(Options *options)
 173 {
 174     TrajectoryAnalysisSettings &settings = impl_->settings_;
 175
 176     // Add options for help.
 177     options->addOption(BooleanOption("h").store(&impl_->bHelp_)
 178                            .description("Print help and quit"));
 179     options->addOption(BooleanOption("hidden").store(&impl_->bShowHidden_)
 180                            .hidden()
 181                            .description("Show hidden options"));
 182     options->addOption(BooleanOption("quiet").store(&impl_->bQuiet_)
 183                            .hidden()
 184                            .description("Hide options in normal run"));
 185
 186     // Add common file name arguments.
 187     options->addOption(FileNameOption("f")
 188                            .filetype(eftTrajectory).inputFile()
 189                            .store(&impl_->trjfile_)
 190                            .defaultBasename("traj")
 191                            .description("Input trajectory or single configuration"));
 192     options->addOption(FileNameOption("s")
 193                            .filetype(eftTopology).inputFile()
 194                            .store(&impl_->topfile_)
 195                            .defaultBasename("topol")
 196                            .description("Input structure"));
 197     options->addOption(FileNameOption("n")
 198                            .filetype(eftIndex).inputFile()
 199                            .store(&impl_->ndxfile_)
 200                            .defaultBasename("index")
 201                            .description("Extra index groups"));
 202     options->addOption(SelectionFileOption("sf"));
 203
 204     // Add options for trajectory time control.
 205     options->addOption(DoubleOption("b").store(&impl_->startTime_).timeValue()
 206                            .description("First frame (%t) to read from trajectory"));
 207     options->addOption(DoubleOption("e").store(&impl_->endTime_).timeValue()
 208                            .description("Last frame (%t) to read from trajectory"));
 209     options->addOption(DoubleOption("dt").store(&impl_->deltaTime_).timeValue()
 210                            .description("Only use frame if t MOD dt == first time (%t)"));
 211
 212     // Add time unit option.
 213     settings.impl_->timeUnitManager.addTimeUnitOption(options, "tu");
 214
 215     // Add plot options.
 216     settings.impl_->plotSettings.addOptions(options);
 217
 218     // Add common options for trajectory processing.
 219     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
 220     {
 221         options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
 222                                .description("Make molecules whole for each frame"));
 223     }
 224     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
 225     {
 226         options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
 227                                .description("Use periodic boundary conditions for distance calculation"));
 228     }
 229 }
 230
 231
 232 void
 233 TrajectoryAnalysisRunnerCommon::scaleTimeOptions(Options *options)
 234 {
 235     impl_->settings_.impl_->timeUnitManager.scaleTimeOptions(options);
 236 }
 237
 238
 239 bool
 240 TrajectoryAnalysisRunnerCommon::optionsFinished(Options *options)
 241 {
 242     if (impl_->bHelp_)
 243     {
 244         return false;
 245     }
 246
 247     impl_->settings_.impl_->plotSettings.setTimeUnit(
 248             impl_->settings_.impl_->timeUnitManager.timeUnit());
 249
 250     if (impl_->trjfile_.empty() && impl_->topfile_.empty())
 251     {
 252         GMX_THROW(InconsistentInputError("No trajectory or topology provided, nothing to do!"));
 253     }
 254
 255     if (options->isSet("b"))
 256     {
 257         setTimeValue(TBEGIN, impl_->startTime_);
 258     }
 259     if (options->isSet("e"))
 260     {
 261         setTimeValue(TEND, impl_->endTime_);
 262     }
 263     if (options->isSet("dt"))
 264     {
 265         setTimeValue(TDELTA, impl_->deltaTime_);
 266     }
 267
 268     return true;
 269 }
 270
 271
 272 void
 273 TrajectoryAnalysisRunnerCommon::initIndexGroups(SelectionCollection *selections)
 274 {
 275     if (impl_->ndxfile_.empty())
 276     {
 277         // TODO: Initialize default selections
 278         selections->setIndexGroups(NULL);
 279     }
 280     else
 281     {
 282         gmx_ana_indexgrps_init(&impl_->grps_, NULL, impl_->ndxfile_.c_str());
 283         selections->setIndexGroups(impl_->grps_);
 284     }
 285 }
 286
 287
 288 void
 289 TrajectoryAnalysisRunnerCommon::doneIndexGroups(SelectionCollection *selections)
 290 {
 291     if (impl_->grps_ != NULL)
 292     {
 293         selections->setIndexGroups(NULL);
 294         gmx_ana_indexgrps_free(impl_->grps_);
 295         impl_->grps_ = NULL;
 296     }
 297 }
 298
 299
 300 void
 301 TrajectoryAnalysisRunnerCommon::initTopology(SelectionCollection *selections)
 302 {
 303     const TrajectoryAnalysisSettings &settings = impl_->settings_;
 304     bool bRequireTop
 305         = settings.hasFlag(TrajectoryAnalysisSettings::efRequireTop)
 306             || selections->requiresTopology();
 307     if (bRequireTop && impl_->topfile_.empty())
 308     {
 309         GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
 310     }
 311
 312     // Load the topology if requested.
 313     if (!impl_->topfile_.empty())
 314     {
 315         char  title[STRLEN];
 316
 317         snew(impl_->topInfo_.top_, 1);
 318         impl_->topInfo_.bTop_ = read_tps_conf(impl_->topfile_.c_str(), title,
 319                                               impl_->topInfo_.top_, &impl_->topInfo_.ePBC_,
 320                                               &impl_->topInfo_.xtop_, NULL, impl_->topInfo_.boxtop_, TRUE);
 321         if (hasTrajectory()
 322             && !settings.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
 323         {
 324             sfree(impl_->topInfo_.xtop_);
 325             impl_->topInfo_.xtop_ = NULL;
 326         }
 327     }
 328
 329     // Read the first frame if we don't know the maximum number of atoms
 330     // otherwise.
 331     int  natoms = -1;
 332     if (!impl_->topInfo_.hasTopology())
 333     {
 334         initFirstFrame();
 335         natoms = impl_->fr->natoms;
 336     }
 337     selections->setTopology(impl_->topInfo_.topology(), natoms);
 338
 339     /*
 340        if (impl_->bSelDump)
 341        {
 342         gmx_ana_poscalc_coll_print_tree(stderr, impl_->pcc);
 343         fprintf(stderr, "\n");
 344        }
 345      */
 346 }
 347
 348
 349 void
 350 TrajectoryAnalysisRunnerCommon::initFirstFrame()
 351 {
 352     // Return if we have already initialized the trajectory.
 353     if (impl_->fr)
 354     {
 355         return;
 356     }
 357     time_unit_t time_unit
 358         = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
 359     output_env_init(&impl_->oenv_, 0, NULL, time_unit, FALSE, exvgNONE, 0, 0);
 360
 361     int frflags = impl_->settings_.frflags();
 362     frflags |= TRX_NEED_X;
 363
 364     snew(impl_->fr, 1);
 365
 366     const TopologyInformation &top = impl_->topInfo_;
 367     if (hasTrajectory())
 368     {
 369         if (!read_first_frame(impl_->oenv_, &impl_->status_,
 370                               impl_->trjfile_.c_str(), impl_->fr, frflags))
 371         {
 372             GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
 373         }
 374         impl_->bTrajOpen_ = true;
 375
 376         if (top.hasTopology() && impl_->fr->natoms > top.topology()->atoms.nr)
 377         {
 378             GMX_THROW(InconsistentInputError(formatString(
 379                                                      "Trajectory (%d atoms) does not match topology (%d atoms)",
 380                                                      impl_->fr->natoms, top.topology()->atoms.nr)));
 381         }
 382         // Check index groups if they have been initialized based on the topology.
 383         /*
 384            if (top)
 385            {
 386             for (int i = 0; i < impl_->sel->nr(); ++i)
 387             {
 388                 gmx_ana_index_check(impl_->sel->sel(i)->indexGroup(),
 389                                     impl_->fr->natoms);
 390             }
 391            }
 392          */
 393     }
 394     else
 395     {
 396         // Prepare a frame from topology information.
 397         // TODO: Initialize more of the fields.
 398         if (frflags & (TRX_NEED_V))
 399         {
 400             GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
 401         }
 402         if (frflags & (TRX_NEED_F))
 403         {
 404             GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
 405         }
 406         impl_->fr->flags  = frflags;
 407         impl_->fr->natoms = top.topology()->atoms.nr;
 408         impl_->fr->bX     = TRUE;
 409         snew(impl_->fr->x, impl_->fr->natoms);
 410         memcpy(impl_->fr->x, top.xtop_,
 411                sizeof(*impl_->fr->x) * impl_->fr->natoms);
 412         impl_->fr->bBox   = TRUE;
 413         copy_mat(const_cast<rvec *>(top.boxtop_), impl_->fr->box);
 414     }
 415
 416     set_trxframe_ePBC(impl_->fr, top.ePBC());
 417     if (top.hasTopology() && impl_->settings_.hasRmPBC())
 418     {
 419         impl_->gpbc_ = gmx_rmpbc_init(&top.topology()->idef, top.ePBC(),
 420                                       impl_->fr->natoms, impl_->fr->box);
 421     }
 422 }
 423
 424
 425 bool
 426 TrajectoryAnalysisRunnerCommon::readNextFrame()
 427 {
 428     bool bContinue = false;
 429     if (hasTrajectory())
 430     {
 431         bContinue = read_next_frame(impl_->oenv_, impl_->status_, impl_->fr);
 432     }
 433     if (!bContinue)
 434     {
 435         impl_->finishTrajectory();
 436     }
 437     return bContinue;
 438 }
 439
 440
 441 void
 442 TrajectoryAnalysisRunnerCommon::initFrame()
 443 {
 444     if (impl_->gpbc_ != NULL)
 445     {
 446         gmx_rmpbc_trxfr(impl_->gpbc_, impl_->fr);
 447     }
 448 }
 449
 450
 451 TrajectoryAnalysisRunnerCommon::HelpFlags
 452 TrajectoryAnalysisRunnerCommon::helpFlags() const
 453 {
 454     HelpFlags flags = 0;
 455
 456     if (!impl_->bQuiet_)
 457     {
 458         flags |= efHelpShowOptions;
 459         if (impl_->bHelp_)
 460         {
 461             flags |= efHelpShowDescriptions;
 462         }
 463         if (impl_->bShowHidden_)
 464         {
 465             flags |= efHelpShowHidden;
 466         }
 467     }
 468     return flags;
 469 }
 470
 471 bool
 472 TrajectoryAnalysisRunnerCommon::hasTrajectory() const
 473 {
 474     return !impl_->trjfile_.empty();
 475 }
 476
 477
 478 const TopologyInformation &
 479 TrajectoryAnalysisRunnerCommon::topologyInformation() const
 480 {
 481     return impl_->topInfo_;
 482 }
 483
 484
 485 t_trxframe &
 486 TrajectoryAnalysisRunnerCommon::frame() const
 487 {
 488     GMX_RELEASE_ASSERT(impl_->fr != NULL, "Frame not available when accessed");
 489     return *impl_->fr;
 490 }
 491
 492 } // namespace gmx