src/gromacs/trajectoryanalysis/runnercommon.cpp

   1 /*
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  31 /*! \internal \file
  32  * \brief
  33  * Implements gmx::TrajectoryAnalysisRunnerCommon.
  34  *
  35  * \author Teemu Murtola <teemu.murtola@gmail.com>
  36  * \ingroup module_trajectoryanalysis
  37  */
  38 #include "runnercommon.h"
  39
  40 #ifdef HAVE_CONFIG_H
  41 #include "config.h"
  42 #endif
  43
  44 #include <string.h>
  45
  46 #include "gromacs/legacyheaders/oenv.h"
  47 #include "gromacs/legacyheaders/rmpbc.h"
  48 #include "gromacs/legacyheaders/smalloc.h"
  49 #include "gromacs/legacyheaders/statutil.h"
  50 #include "gromacs/legacyheaders/tpxio.h"
  51 #include "gromacs/legacyheaders/vec.h"
  52
  53 #include "gromacs/options/basicoptions.h"
  54 #include "gromacs/options/filenameoption.h"
  55 #include "gromacs/options/options.h"
  56 #include "gromacs/selection/indexutil.h"
  57 #include "gromacs/selection/selectioncollection.h"
  58 #include "gromacs/selection/selectionfileoption.h"
  59 #include "gromacs/trajectoryanalysis/analysissettings.h"
  60 #include "gromacs/utility/exceptions.h"
  61 #include "gromacs/utility/gmxassert.h"
  62 #include "gromacs/utility/stringutil.h"
  63
  64 #include "analysissettings-impl.h"
  65
  66 namespace gmx
  67 {
  68
  69 class TrajectoryAnalysisRunnerCommon::Impl
  70 {
  71     public:
  72         Impl(TrajectoryAnalysisSettings *settings);
  73         ~Impl();
  74
  75         void finishTrajectory();
  76
  77         TrajectoryAnalysisSettings &settings_;
  78         TopologyInformation         topInfo_;
  79
  80         bool                        bHelp_;
  81         bool                        bShowHidden_;
  82         bool                        bQuiet_;
  83         //! Name of the trajectory file (empty if not provided).
  84         std::string                 trjfile_;
  85         //! Name of the topology file (empty if no topology provided).
  86         std::string                 topfile_;
  87         //! Name of the index file (empty if no index file provided).
  88         std::string                 ndxfile_;
  89         double                      startTime_;
  90         double                      endTime_;
  91         double                      deltaTime_;
  92
  93         gmx_ana_indexgrps_t        *grps_;
  94         bool                        bTrajOpen_;
  95         //! The current frame, or \p NULL if no frame loaded yet.
  96         t_trxframe                 *fr;
  97         gmx_rmpbc_t                 gpbc_;
  98         //! Used to store the status variable from read_first_frame().
  99         t_trxstatus                *status_;
 100         output_env_t                oenv_;
 101 };
 102
 103
 104 TrajectoryAnalysisRunnerCommon::Impl::Impl(TrajectoryAnalysisSettings *settings)
 105     : settings_(*settings),
 106       bHelp_(false), bShowHidden_(false), bQuiet_(false),
 107       startTime_(0.0), endTime_(0.0), deltaTime_(0.0),
 108       grps_(NULL),
 109       bTrajOpen_(false), fr(NULL), gpbc_(NULL), status_(NULL), oenv_(NULL)
 110 {
 111 }
 112
 113
 114 TrajectoryAnalysisRunnerCommon::Impl::~Impl()
 115 {
 116     if (grps_ != NULL)
 117     {
 118         gmx_ana_indexgrps_free(grps_);
 119     }
 120     finishTrajectory();
 121     if (fr)
 122     {
 123         // There doesn't seem to be a function for freeing frame data
 124         sfree(fr->x);
 125         sfree(fr->v);
 126         sfree(fr->f);
 127         sfree(fr);
 128     }
 129     if (oenv_ != NULL)
 130     {
 131         output_env_done(oenv_);
 132     }
 133 }
 134
 135
 136 void
 137 TrajectoryAnalysisRunnerCommon::Impl::finishTrajectory()
 138 {
 139     if (bTrajOpen_)
 140     {
 141         close_trx(status_);
 142         bTrajOpen_ = false;
 143     }
 144     if (gpbc_ != NULL)
 145     {
 146         gmx_rmpbc_done(gpbc_);
 147         gpbc_ = NULL;
 148     }
 149 }
 150
 151 /*********************************************************************
 152  * TrajectoryAnalysisRunnerCommon
 153  */
 154
 155 TrajectoryAnalysisRunnerCommon::TrajectoryAnalysisRunnerCommon(
 156         TrajectoryAnalysisSettings *settings)
 157     : impl_(new Impl(settings))
 158 {
 159 }
 160
 161
 162 TrajectoryAnalysisRunnerCommon::~TrajectoryAnalysisRunnerCommon()
 163 {
 164 }
 165
 166
 167 void
 168 TrajectoryAnalysisRunnerCommon::initOptions(Options *options)
 169 {
 170     TrajectoryAnalysisSettings &settings = impl_->settings_;
 171
 172     // Add options for help.
 173     options->addOption(BooleanOption("h").store(&impl_->bHelp_)
 174                            .description("Print help and quit"));
 175     options->addOption(BooleanOption("hidden").store(&impl_->bShowHidden_)
 176                            .hidden()
 177                            .description("Show hidden options"));
 178     options->addOption(BooleanOption("quiet").store(&impl_->bQuiet_)
 179                            .hidden()
 180                            .description("Hide options in normal run"));
 181
 182     // Add common file name arguments.
 183     options->addOption(FileNameOption("f")
 184                            .filetype(eftTrajectory).inputFile()
 185                            .store(&impl_->trjfile_)
 186                            .defaultBasename("traj")
 187                            .description("Input trajectory or single configuration"));
 188     options->addOption(FileNameOption("s")
 189                            .filetype(eftTopology).inputFile()
 190                            .store(&impl_->topfile_)
 191                            .defaultBasename("topol")
 192                            .description("Input structure"));
 193     options->addOption(FileNameOption("n")
 194                            .filetype(eftIndex).inputFile()
 195                            .store(&impl_->ndxfile_)
 196                            .defaultBasename("index")
 197                            .description("Extra index groups"));
 198     options->addOption(SelectionFileOption("sf"));
 199
 200     // Add options for trajectory time control.
 201     options->addOption(DoubleOption("b").store(&impl_->startTime_).timeValue()
 202                            .description("First frame (%t) to read from trajectory"));
 203     options->addOption(DoubleOption("e").store(&impl_->endTime_).timeValue()
 204                            .description("Last frame (%t) to read from trajectory"));
 205     options->addOption(DoubleOption("dt").store(&impl_->deltaTime_).timeValue()
 206                            .description("Only use frame if t MOD dt == first time (%t)"));
 207
 208     // Add time unit option.
 209     settings.impl_->timeUnitManager.addTimeUnitOption(options, "tu");
 210
 211     // Add plot options.
 212     settings.impl_->plotSettings.addOptions(options);
 213
 214     // Add common options for trajectory processing.
 215     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
 216     {
 217         options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
 218                                .description("Make molecules whole for each frame"));
 219     }
 220     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
 221     {
 222         options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
 223                                .description("Use periodic boundary conditions for distance calculation"));
 224     }
 225 }
 226
 227
 228 void
 229 TrajectoryAnalysisRunnerCommon::scaleTimeOptions(Options *options)
 230 {
 231     impl_->settings_.impl_->timeUnitManager.scaleTimeOptions(options);
 232 }
 233
 234
 235 bool
 236 TrajectoryAnalysisRunnerCommon::optionsFinished(Options *options)
 237 {
 238     if (impl_->bHelp_)
 239     {
 240         return false;
 241     }
 242
 243     impl_->settings_.impl_->plotSettings.setTimeUnit(
 244             impl_->settings_.impl_->timeUnitManager.timeUnit());
 245
 246     if (impl_->trjfile_.empty() && impl_->topfile_.empty())
 247     {
 248         GMX_THROW(InconsistentInputError("No trajectory or topology provided, nothing to do!"));
 249     }
 250
 251     if (options->isSet("b"))
 252     {
 253         setTimeValue(TBEGIN, impl_->startTime_);
 254     }
 255     if (options->isSet("e"))
 256     {
 257         setTimeValue(TEND, impl_->endTime_);
 258     }
 259     if (options->isSet("dt"))
 260     {
 261         setTimeValue(TDELTA, impl_->deltaTime_);
 262     }
 263
 264     return true;
 265 }
 266
 267
 268 void
 269 TrajectoryAnalysisRunnerCommon::initIndexGroups(SelectionCollection *selections)
 270 {
 271     if (impl_->ndxfile_.empty())
 272     {
 273         // TODO: Initialize default selections
 274         selections->setIndexGroups(NULL);
 275     }
 276     else
 277     {
 278         gmx_ana_indexgrps_init(&impl_->grps_, NULL, impl_->ndxfile_.c_str());
 279         selections->setIndexGroups(impl_->grps_);
 280     }
 281 }
 282
 283
 284 void
 285 TrajectoryAnalysisRunnerCommon::doneIndexGroups(SelectionCollection *selections)
 286 {
 287     if (impl_->grps_ != NULL)
 288     {
 289         selections->setIndexGroups(NULL);
 290         gmx_ana_indexgrps_free(impl_->grps_);
 291         impl_->grps_ = NULL;
 292     }
 293 }
 294
 295
 296 void
 297 TrajectoryAnalysisRunnerCommon::initTopology(SelectionCollection *selections)
 298 {
 299     const TrajectoryAnalysisSettings &settings = impl_->settings_;
 300     bool bRequireTop
 301         = settings.hasFlag(TrajectoryAnalysisSettings::efRequireTop)
 302             || selections->requiresTopology();
 303     if (bRequireTop && impl_->topfile_.empty())
 304     {
 305         GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
 306     }
 307
 308     // Load the topology if requested.
 309     if (!impl_->topfile_.empty())
 310     {
 311         char  title[STRLEN];
 312
 313         snew(impl_->topInfo_.top_, 1);
 314         impl_->topInfo_.bTop_ = read_tps_conf(impl_->topfile_.c_str(), title,
 315                                               impl_->topInfo_.top_, &impl_->topInfo_.ePBC_,
 316                                               &impl_->topInfo_.xtop_, NULL, impl_->topInfo_.boxtop_, TRUE);
 317         if (hasTrajectory()
 318             && !settings.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
 319         {
 320             sfree(impl_->topInfo_.xtop_);
 321             impl_->topInfo_.xtop_ = NULL;
 322         }
 323     }
 324
 325     // Read the first frame if we don't know the maximum number of atoms
 326     // otherwise.
 327     int  natoms = -1;
 328     if (!impl_->topInfo_.hasTopology())
 329     {
 330         initFirstFrame();
 331         natoms = impl_->fr->natoms;
 332     }
 333     selections->setTopology(impl_->topInfo_.topology(), natoms);
 334
 335     /*
 336        if (impl_->bSelDump)
 337        {
 338         gmx_ana_poscalc_coll_print_tree(stderr, impl_->pcc);
 339         fprintf(stderr, "\n");
 340        }
 341      */
 342 }
 343
 344
 345 void
 346 TrajectoryAnalysisRunnerCommon::initFirstFrame()
 347 {
 348     // Return if we have already initialized the trajectory.
 349     if (impl_->fr)
 350     {
 351         return;
 352     }
 353     time_unit_t time_unit
 354         = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
 355     output_env_init(&impl_->oenv_, 0, NULL, time_unit, FALSE, exvgNONE, 0, 0);
 356
 357     int frflags = impl_->settings_.frflags();
 358     frflags |= TRX_NEED_X;
 359
 360     snew(impl_->fr, 1);
 361
 362     const TopologyInformation &top = impl_->topInfo_;
 363     if (hasTrajectory())
 364     {
 365         if (!read_first_frame(impl_->oenv_, &impl_->status_,
 366                               impl_->trjfile_.c_str(), impl_->fr, frflags))
 367         {
 368             GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
 369         }
 370         impl_->bTrajOpen_ = true;
 371
 372         if (top.hasTopology() && impl_->fr->natoms > top.topology()->atoms.nr)
 373         {
 374             GMX_THROW(InconsistentInputError(formatString(
 375                                                      "Trajectory (%d atoms) does not match topology (%d atoms)",
 376                                                      impl_->fr->natoms, top.topology()->atoms.nr)));
 377         }
 378         // Check index groups if they have been initialized based on the topology.
 379         /*
 380            if (top)
 381            {
 382             for (int i = 0; i < impl_->sel->nr(); ++i)
 383             {
 384                 gmx_ana_index_check(impl_->sel->sel(i)->indexGroup(),
 385                                     impl_->fr->natoms);
 386             }
 387            }
 388          */
 389     }
 390     else
 391     {
 392         // Prepare a frame from topology information.
 393         // TODO: Initialize more of the fields.
 394         if (frflags & (TRX_NEED_V))
 395         {
 396             GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
 397         }
 398         if (frflags & (TRX_NEED_F))
 399         {
 400             GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
 401         }
 402         impl_->fr->flags  = frflags;
 403         impl_->fr->natoms = top.topology()->atoms.nr;
 404         impl_->fr->bX     = TRUE;
 405         snew(impl_->fr->x, impl_->fr->natoms);
 406         memcpy(impl_->fr->x, top.xtop_,
 407                sizeof(*impl_->fr->x) * impl_->fr->natoms);
 408         impl_->fr->bBox   = TRUE;
 409         copy_mat(const_cast<rvec *>(top.boxtop_), impl_->fr->box);
 410     }
 411
 412     set_trxframe_ePBC(impl_->fr, top.ePBC());
 413     if (top.hasTopology() && impl_->settings_.hasRmPBC())
 414     {
 415         impl_->gpbc_ = gmx_rmpbc_init(&top.topology()->idef, top.ePBC(),
 416                                       impl_->fr->natoms, impl_->fr->box);
 417     }
 418 }
 419
 420
 421 bool
 422 TrajectoryAnalysisRunnerCommon::readNextFrame()
 423 {
 424     bool bContinue = false;
 425     if (hasTrajectory())
 426     {
 427         bContinue = read_next_frame(impl_->oenv_, impl_->status_, impl_->fr);
 428     }
 429     if (!bContinue)
 430     {
 431         impl_->finishTrajectory();
 432     }
 433     return bContinue;
 434 }
 435
 436
 437 void
 438 TrajectoryAnalysisRunnerCommon::initFrame()
 439 {
 440     if (impl_->gpbc_ != NULL)
 441     {
 442         gmx_rmpbc_trxfr(impl_->gpbc_, impl_->fr);
 443     }
 444 }
 445
 446
 447 TrajectoryAnalysisRunnerCommon::HelpFlags
 448 TrajectoryAnalysisRunnerCommon::helpFlags() const
 449 {
 450     HelpFlags flags = 0;
 451
 452     if (!impl_->bQuiet_)
 453     {
 454         flags |= efHelpShowOptions;
 455         if (impl_->bHelp_)
 456         {
 457             flags |= efHelpShowDescriptions;
 458         }
 459         if (impl_->bShowHidden_)
 460         {
 461             flags |= efHelpShowHidden;
 462         }
 463     }
 464     return flags;
 465 }
 466
 467 bool
 468 TrajectoryAnalysisRunnerCommon::hasTrajectory() const
 469 {
 470     return !impl_->trjfile_.empty();
 471 }
 472
 473
 474 const TopologyInformation &
 475 TrajectoryAnalysisRunnerCommon::topologyInformation() const
 476 {
 477     return impl_->topInfo_;
 478 }
 479
 480
 481 t_trxframe &
 482 TrajectoryAnalysisRunnerCommon::frame() const
 483 {
 484     GMX_RELEASE_ASSERT(impl_->fr != NULL, "Frame not available when accessed");
 485     return *impl_->fr;
 486 }
 487
 488 } // namespace gmx