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 "gmxpre.h"
  43
  44 #include "runnercommon.h"
  45
  46 #include <cstring>
  47
  48 #include <algorithm>
  49 #include <string>
  50
  51 #include "gromacs/fileio/oenv.h"
  52 #include "gromacs/fileio/timecontrol.h"
  53 #include "gromacs/fileio/trxio.h"
  54 #include "gromacs/math/vec.h"
  55 #include "gromacs/options/basicoptions.h"
  56 #include "gromacs/options/filenameoption.h"
  57 #include "gromacs/options/ioptionscontainer.h"
  58 #include "gromacs/pbcutil/rmpbc.h"
  59 #include "gromacs/selection/selection.h"
  60 #include "gromacs/selection/selectioncollection.h"
  61 #include "gromacs/selection/selectionoption.h"
  62 #include "gromacs/selection/selectionoptionbehavior.h"
  63 #include "gromacs/topology/topology.h"
  64 #include "gromacs/trajectory/trajectoryframe.h"
  65 #include "gromacs/trajectoryanalysis/analysissettings.h"
  66 #include "gromacs/trajectoryanalysis/topologyinformation.h"
  67 #include "gromacs/utility/cstringutil.h"
  68 #include "gromacs/utility/exceptions.h"
  69 #include "gromacs/utility/gmxassert.h"
  70 #include "gromacs/utility/programcontext.h"
  71 #include "gromacs/utility/smalloc.h"
  72 #include "gromacs/utility/stringutil.h"
  73
  74 #include "analysissettings-impl.h"
  75
  76 namespace gmx
  77 {
  78
  79 class TrajectoryAnalysisRunnerCommon::Impl : public ITopologyProvider
  80 {
  81     public:
  82         explicit Impl(TrajectoryAnalysisSettings *settings);
  83         ~Impl();
  84
  85         bool hasTrajectory() const { return !trjfile_.empty(); }
  86
  87         void initTopology(bool required);
  88         void initFirstFrame();
  89         void initFrameIndexGroup();
  90         void finishTrajectory();
  91
  92         // From ITopologyProvider
  93         virtual gmx_mtop_t *getTopology(bool required)
  94         {
  95             initTopology(required);
  96             return topInfo_.mtop_.get();
  97         }
  98         virtual int getAtomCount()
  99         {
 100             if (!topInfo_.hasTopology())
 101             {
 102                 if (trajectoryGroup_.isValid())
 103                 {
 104                     GMX_THROW(InconsistentInputError("-fgroup is only supported when -s is also specified"));
 105                 }
 106                 // Read the first frame if we don't know the maximum number of
 107                 // atoms otherwise.
 108                 initFirstFrame();
 109                 return fr->natoms;
 110             }
 111             return -1;
 112         }
 113
 114         TrajectoryAnalysisSettings &settings_;
 115         TopologyInformation         topInfo_;
 116
 117         //! Name of the trajectory file (empty if not provided).
 118         std::string                 trjfile_;
 119         //! Name of the topology file (empty if no topology provided).
 120         std::string                 topfile_;
 121         Selection                   trajectoryGroup_;
 122         double                      startTime_;
 123         double                      endTime_;
 124         double                      deltaTime_;
 125         bool                        bStartTimeSet_;
 126         bool                        bEndTimeSet_;
 127         bool                        bDeltaTimeSet_;
 128
 129         bool                        bTrajOpen_;
 130         //! The current frame, or \p NULL if no frame loaded yet.
 131         t_trxframe                 *fr;
 132         gmx_rmpbc_t                 gpbc_;
 133         //! Used to store the status variable from read_first_frame().
 134         t_trxstatus                *status_;
 135         gmx_output_env_t           *oenv_;
 136 };
 137
 138
 139 TrajectoryAnalysisRunnerCommon::Impl::Impl(TrajectoryAnalysisSettings *settings)
 140     : settings_(*settings),
 141       startTime_(0.0), endTime_(0.0), deltaTime_(0.0),
 142       bStartTimeSet_(false), bEndTimeSet_(false), bDeltaTimeSet_(false),
 143       bTrajOpen_(false), fr(nullptr), gpbc_(nullptr), status_(nullptr), oenv_(nullptr)
 144 {
 145 }
 146
 147
 148 TrajectoryAnalysisRunnerCommon::Impl::~Impl()
 149 {
 150     finishTrajectory();
 151     if (fr != nullptr)
 152     {
 153         // There doesn't seem to be a function for freeing frame data
 154         sfree(fr->x);
 155         sfree(fr->v);
 156         sfree(fr->f);
 157         sfree(fr->index);
 158         sfree(fr);
 159     }
 160     if (oenv_ != nullptr)
 161     {
 162         output_env_done(oenv_);
 163     }
 164 }
 165
 166 void
 167 TrajectoryAnalysisRunnerCommon::Impl::initTopology(bool required)
 168 {
 169     // Return immediately if the topology has already been loaded.
 170     if (topInfo_.hasTopology())
 171     {
 172         return;
 173     }
 174
 175     if (required && topfile_.empty())
 176     {
 177         GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
 178     }
 179
 180     // Load the topology if requested.
 181     if (!topfile_.empty())
 182     {
 183         topInfo_.fillFromInputFile(topfile_);
 184         if (hasTrajectory()
 185             && !settings_.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
 186         {
 187             sfree(topInfo_.xtop_);
 188             topInfo_.xtop_ = nullptr;
 189         }
 190     }
 191 }
 192
 193 void
 194 TrajectoryAnalysisRunnerCommon::Impl::initFirstFrame()
 195 {
 196     // Return if we have already initialized the trajectory.
 197     if (fr != nullptr)
 198     {
 199         return;
 200     }
 201     time_unit_t time_unit
 202         = static_cast<time_unit_t>(settings_.timeUnit() + 1); // NOLINT(misc-misplaced-widening-cast)
 203     output_env_init(&oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
 204
 205     int frflags = settings_.frflags();
 206     frflags |= TRX_NEED_X;
 207
 208     snew(fr, 1);
 209
 210     if (hasTrajectory())
 211     {
 212         if (!read_first_frame(oenv_, &status_, trjfile_.c_str(), fr, frflags))
 213         {
 214             GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
 215         }
 216         bTrajOpen_ = true;
 217
 218         if (topInfo_.hasTopology())
 219         {
 220             const int topologyAtomCount = topInfo_.topology()->atoms.nr;
 221             if (fr->natoms > topologyAtomCount)
 222             {
 223                 const std::string message
 224                     = formatString("Trajectory (%d atoms) does not match topology (%d atoms)",
 225                                    fr->natoms, topologyAtomCount);
 226                 GMX_THROW(InconsistentInputError(message));
 227             }
 228         }
 229     }
 230     else
 231     {
 232         // Prepare a frame from topology information.
 233         // TODO: Initialize more of the fields.
 234         if (frflags & (TRX_NEED_V))
 235         {
 236             GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
 237         }
 238         if (frflags & (TRX_NEED_F))
 239         {
 240             GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
 241         }
 242         fr->natoms = topInfo_.topology()->atoms.nr;
 243         fr->bX     = TRUE;
 244         snew(fr->x, fr->natoms);
 245         memcpy(fr->x, topInfo_.xtop_,
 246                sizeof(*fr->x) * fr->natoms);
 247         fr->bBox   = TRUE;
 248         copy_mat(topInfo_.boxtop_, fr->box);
 249     }
 250
 251     set_trxframe_ePBC(fr, topInfo_.ePBC());
 252     if (topInfo_.hasTopology() && settings_.hasRmPBC())
 253     {
 254         gpbc_ = gmx_rmpbc_init(&topInfo_.topology()->idef, topInfo_.ePBC(),
 255                                fr->natoms);
 256     }
 257 }
 258
 259 void
 260 TrajectoryAnalysisRunnerCommon::Impl::initFrameIndexGroup()
 261 {
 262     if (!trajectoryGroup_.isValid())
 263     {
 264         return;
 265     }
 266     GMX_RELEASE_ASSERT(bTrajOpen_,
 267                        "Trajectory index only makes sense with a real trajectory");
 268     if (trajectoryGroup_.atomCount() != fr->natoms)
 269     {
 270         const std::string message = formatString(
 271                     "Selection specified with -fgroup has %d atoms, but "
 272                     "the trajectory (-f) has %d atoms.",
 273                     trajectoryGroup_.atomCount(), fr->natoms);
 274         GMX_THROW(InconsistentInputError(message));
 275     }
 276     fr->bIndex = TRUE;
 277     snew(fr->index, trajectoryGroup_.atomCount());
 278     std::copy(trajectoryGroup_.atomIndices().begin(),
 279               trajectoryGroup_.atomIndices().end(),
 280               fr->index);
 281 }
 282
 283 void
 284 TrajectoryAnalysisRunnerCommon::Impl::finishTrajectory()
 285 {
 286     if (bTrajOpen_)
 287     {
 288         close_trx(status_);
 289         bTrajOpen_ = false;
 290     }
 291     if (gpbc_ != nullptr)
 292     {
 293         gmx_rmpbc_done(gpbc_);
 294         gpbc_ = nullptr;
 295     }
 296 }
 297
 298 /*********************************************************************
 299  * TrajectoryAnalysisRunnerCommon
 300  */
 301
 302 TrajectoryAnalysisRunnerCommon::TrajectoryAnalysisRunnerCommon(
 303         TrajectoryAnalysisSettings *settings)
 304     : impl_(new Impl(settings))
 305 {
 306 }
 307
 308
 309 TrajectoryAnalysisRunnerCommon::~TrajectoryAnalysisRunnerCommon()
 310 {
 311 }
 312
 313
 314 ITopologyProvider *
 315 TrajectoryAnalysisRunnerCommon::topologyProvider()
 316 {
 317     return impl_.get();
 318 }
 319
 320
 321 void
 322 TrajectoryAnalysisRunnerCommon::initOptions(IOptionsContainer *options,
 323                                             TimeUnitBehavior  *timeUnitBehavior)
 324 {
 325     TrajectoryAnalysisSettings &settings = impl_->settings_;
 326
 327     // Add common file name arguments.
 328     options->addOption(FileNameOption("f")
 329                            .filetype(eftTrajectory).inputFile()
 330                            .store(&impl_->trjfile_)
 331                            .defaultBasename("traj")
 332                            .description("Input trajectory or single configuration"));
 333     options->addOption(FileNameOption("s")
 334                            .filetype(eftTopology).inputFile()
 335                            .store(&impl_->topfile_)
 336                            .defaultBasename("topol")
 337                            .description("Input structure"));
 338
 339     // Add options for trajectory time control.
 340     options->addOption(DoubleOption("b")
 341                            .store(&impl_->startTime_).storeIsSet(&impl_->bStartTimeSet_)
 342                            .timeValue()
 343                            .description("First frame (%t) to read from trajectory"));
 344     options->addOption(DoubleOption("e")
 345                            .store(&impl_->endTime_).storeIsSet(&impl_->bEndTimeSet_)
 346                            .timeValue()
 347                            .description("Last frame (%t) to read from trajectory"));
 348     options->addOption(DoubleOption("dt")
 349                            .store(&impl_->deltaTime_).storeIsSet(&impl_->bDeltaTimeSet_)
 350                            .timeValue()
 351                            .description("Only use frame if t MOD dt == first time (%t)"));
 352
 353     // Add time unit option.
 354     timeUnitBehavior->setTimeUnitFromEnvironment();
 355     timeUnitBehavior->addTimeUnitOption(options, "tu");
 356     timeUnitBehavior->setTimeUnitStore(&impl_->settings_.impl_->timeUnit);
 357
 358     options->addOption(SelectionOption("fgroup")
 359                            .store(&impl_->trajectoryGroup_)
 360                            .onlySortedAtoms().onlyStatic()
 361                            .description("Atoms stored in the trajectory file "
 362                                         "(if not set, assume first N atoms)"));
 363
 364     // Add plot options.
 365     settings.impl_->plotSettings.initOptions(options);
 366
 367     // Add common options for trajectory processing.
 368     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
 369     {
 370         options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
 371                                .description("Make molecules whole for each frame"));
 372     }
 373     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
 374     {
 375         options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
 376                                .description("Use periodic boundary conditions for distance calculation"));
 377     }
 378 }
 379
 380
 381 void
 382 TrajectoryAnalysisRunnerCommon::optionsFinished()
 383 {
 384     if (impl_->trjfile_.empty() && impl_->topfile_.empty())
 385     {
 386         GMX_THROW(InconsistentInputError("No trajectory or topology provided, nothing to do!"));
 387     }
 388
 389     if (impl_->trajectoryGroup_.isValid() && impl_->trjfile_.empty())
 390     {
 391         GMX_THROW(InconsistentInputError("-fgroup only makes sense together with a trajectory (-f)"));
 392     }
 393
 394     impl_->settings_.impl_->plotSettings.setTimeUnit(impl_->settings_.timeUnit());
 395
 396     if (impl_->bStartTimeSet_)
 397     {
 398         setTimeValue(TBEGIN, impl_->startTime_);
 399     }
 400     if (impl_->bEndTimeSet_)
 401     {
 402         setTimeValue(TEND, impl_->endTime_);
 403     }
 404     if (impl_->bDeltaTimeSet_)
 405     {
 406         setTimeValue(TDELTA, impl_->deltaTime_);
 407     }
 408 }
 409
 410
 411 void
 412 TrajectoryAnalysisRunnerCommon::initTopology()
 413 {
 414     const bool topologyRequired =
 415         impl_->settings_.hasFlag(TrajectoryAnalysisSettings::efRequireTop);
 416     impl_->initTopology(topologyRequired);
 417 }
 418
 419
 420 void
 421 TrajectoryAnalysisRunnerCommon::initFirstFrame()
 422 {
 423     impl_->initFirstFrame();
 424 }
 425
 426
 427 void
 428 TrajectoryAnalysisRunnerCommon::initFrameIndexGroup()
 429 {
 430     impl_->initFrameIndexGroup();
 431 }
 432
 433
 434 bool
 435 TrajectoryAnalysisRunnerCommon::readNextFrame()
 436 {
 437     bool bContinue = false;
 438     if (hasTrajectory())
 439     {
 440         bContinue = read_next_frame(impl_->oenv_, impl_->status_, impl_->fr);
 441     }
 442     if (!bContinue)
 443     {
 444         impl_->finishTrajectory();
 445     }
 446     return bContinue;
 447 }
 448
 449
 450 void
 451 TrajectoryAnalysisRunnerCommon::initFrame()
 452 {
 453     if (impl_->gpbc_ != nullptr)
 454     {
 455         gmx_rmpbc_trxfr(impl_->gpbc_, impl_->fr);
 456     }
 457 }
 458
 459
 460 bool
 461 TrajectoryAnalysisRunnerCommon::hasTrajectory() const
 462 {
 463     return impl_->hasTrajectory();
 464 }
 465
 466
 467 const TopologyInformation &
 468 TrajectoryAnalysisRunnerCommon::topologyInformation() const
 469 {
 470     return impl_->topInfo_;
 471 }
 472
 473
 474 t_trxframe &
 475 TrajectoryAnalysisRunnerCommon::frame() const
 476 {
 477     GMX_RELEASE_ASSERT(impl_->fr != nullptr, "Frame not available when accessed");
 478     return *impl_->fr;
 479 }
 480
 481 } // namespace gmx