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