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                                                 bool                 bUseDefaults)
 255 {
 256     if (impl_->ndxfile_.empty())
 257     {
 258         if (!bUseDefaults)
 259         {
 260             selections->setIndexGroups(NULL);
 261             return;
 262         }
 263         initTopology(selections);
 264     }
 265     const char *const ndxfile
 266         = (!impl_->ndxfile_.empty() ? impl_->ndxfile_.c_str() : NULL);
 267     gmx_ana_indexgrps_init(&impl_->grps_, impl_->topInfo_.topology(), ndxfile);
 268     selections->setIndexGroups(impl_->grps_);
 269 }
 270
 271
 272 void
 273 TrajectoryAnalysisRunnerCommon::doneIndexGroups(SelectionCollection *selections)
 274 {
 275     if (impl_->grps_ != NULL)
 276     {
 277         selections->setIndexGroups(NULL);
 278         gmx_ana_indexgrps_free(impl_->grps_);
 279         impl_->grps_ = NULL;
 280     }
 281 }
 282
 283
 284 void
 285 TrajectoryAnalysisRunnerCommon::initTopology(SelectionCollection *selections)
 286 {
 287     // Return immediately if the topology has already been loaded.
 288     if (impl_->topInfo_.hasTopology())
 289     {
 290         return;
 291     }
 292
 293     const TrajectoryAnalysisSettings &settings = impl_->settings_;
 294     const bool bRequireTop
 295         = settings.hasFlag(TrajectoryAnalysisSettings::efRequireTop)
 296             || selections->requiresTopology();
 297     if (bRequireTop && impl_->topfile_.empty())
 298     {
 299         GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
 300     }
 301
 302     // Load the topology if requested.
 303     if (!impl_->topfile_.empty())
 304     {
 305         char  title[STRLEN];
 306
 307         snew(impl_->topInfo_.top_, 1);
 308         impl_->topInfo_.bTop_ = read_tps_conf(impl_->topfile_.c_str(), title,
 309                                               impl_->topInfo_.top_, &impl_->topInfo_.ePBC_,
 310                                               &impl_->topInfo_.xtop_, NULL, impl_->topInfo_.boxtop_, TRUE);
 311         if (hasTrajectory()
 312             && !settings.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
 313         {
 314             sfree(impl_->topInfo_.xtop_);
 315             impl_->topInfo_.xtop_ = NULL;
 316         }
 317     }
 318
 319     // Read the first frame if we don't know the maximum number of atoms
 320     // otherwise.
 321     int  natoms = -1;
 322     if (!impl_->topInfo_.hasTopology())
 323     {
 324         initFirstFrame();
 325         natoms = impl_->fr->natoms;
 326     }
 327     selections->setTopology(impl_->topInfo_.topology(), natoms);
 328
 329     /*
 330        if (impl_->bSelDump)
 331        {
 332         gmx_ana_poscalc_coll_print_tree(stderr, impl_->pcc);
 333         fprintf(stderr, "\n");
 334        }
 335      */
 336 }
 337
 338
 339 void
 340 TrajectoryAnalysisRunnerCommon::initFirstFrame()
 341 {
 342     // Return if we have already initialized the trajectory.
 343     if (impl_->fr)
 344     {
 345         return;
 346     }
 347     time_unit_t time_unit
 348         = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
 349     output_env_init(&impl_->oenv_, 0, NULL, time_unit, FALSE, exvgNONE, 0, 0);
 350
 351     int frflags = impl_->settings_.frflags();
 352     frflags |= TRX_NEED_X;
 353
 354     snew(impl_->fr, 1);
 355
 356     const TopologyInformation &top = impl_->topInfo_;
 357     if (hasTrajectory())
 358     {
 359         if (!read_first_frame(impl_->oenv_, &impl_->status_,
 360                               impl_->trjfile_.c_str(), impl_->fr, frflags))
 361         {
 362             GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
 363         }
 364         impl_->bTrajOpen_ = true;
 365
 366         if (top.hasTopology() && impl_->fr->natoms > top.topology()->atoms.nr)
 367         {
 368             GMX_THROW(InconsistentInputError(formatString(
 369                                                      "Trajectory (%d atoms) does not match topology (%d atoms)",
 370                                                      impl_->fr->natoms, top.topology()->atoms.nr)));
 371         }
 372         // TODO: Check index groups if they have been initialized based on the topology.
 373         /*
 374            if (top)
 375            {
 376             for (int i = 0; i < impl_->sel->nr(); ++i)
 377             {
 378                 gmx_ana_index_check(impl_->sel->sel(i)->indexGroup(),
 379                                     impl_->fr->natoms);
 380             }
 381            }
 382          */
 383     }
 384     else
 385     {
 386         // Prepare a frame from topology information.
 387         // TODO: Initialize more of the fields.
 388         if (frflags & (TRX_NEED_V))
 389         {
 390             GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
 391         }
 392         if (frflags & (TRX_NEED_F))
 393         {
 394             GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
 395         }
 396         impl_->fr->flags  = frflags;
 397         impl_->fr->natoms = top.topology()->atoms.nr;
 398         impl_->fr->bX     = TRUE;
 399         snew(impl_->fr->x, impl_->fr->natoms);
 400         memcpy(impl_->fr->x, top.xtop_,
 401                sizeof(*impl_->fr->x) * impl_->fr->natoms);
 402         impl_->fr->bBox   = TRUE;
 403         copy_mat(const_cast<rvec *>(top.boxtop_), impl_->fr->box);
 404     }
 405
 406     set_trxframe_ePBC(impl_->fr, top.ePBC());
 407     if (top.hasTopology() && impl_->settings_.hasRmPBC())
 408     {
 409         impl_->gpbc_ = gmx_rmpbc_init(&top.topology()->idef, top.ePBC(),
 410                                       impl_->fr->natoms);
 411     }
 412 }
 413
 414
 415 bool
 416 TrajectoryAnalysisRunnerCommon::readNextFrame()
 417 {
 418     bool bContinue = false;
 419     if (hasTrajectory())
 420     {
 421         bContinue = read_next_frame(impl_->oenv_, impl_->status_, impl_->fr);
 422     }
 423     if (!bContinue)
 424     {
 425         impl_->finishTrajectory();
 426     }
 427     return bContinue;
 428 }
 429
 430
 431 void
 432 TrajectoryAnalysisRunnerCommon::initFrame()
 433 {
 434     if (impl_->gpbc_ != NULL)
 435     {
 436         gmx_rmpbc_trxfr(impl_->gpbc_, impl_->fr);
 437     }
 438 }
 439
 440
 441 bool
 442 TrajectoryAnalysisRunnerCommon::hasTrajectory() const
 443 {
 444     return !impl_->trjfile_.empty();
 445 }
 446
 447
 448 const TopologyInformation &
 449 TrajectoryAnalysisRunnerCommon::topologyInformation() const
 450 {
 451     return impl_->topInfo_;
 452 }
 453
 454
 455 t_trxframe &
 456 TrajectoryAnalysisRunnerCommon::frame() const
 457 {
 458     GMX_RELEASE_ASSERT(impl_->fr != NULL, "Frame not available when accessed");
 459     return *impl_->fr;
 460 }
 461
 462 } // namespace gmx