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