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 <string.h>
  47
  48 #include <algorithm>
  49 #include <string>
  50
  51 #include "gromacs/compat/make_unique.h"
  52 #include "gromacs/fileio/confio.h"
  53 #include "gromacs/fileio/oenv.h"
  54 #include "gromacs/fileio/timecontrol.h"
  55 #include "gromacs/fileio/trxio.h"
  56 #include "gromacs/math/vec.h"
  57 #include "gromacs/options/basicoptions.h"
  58 #include "gromacs/options/filenameoption.h"
  59 #include "gromacs/options/ioptionscontainer.h"
  60 #include "gromacs/pbcutil/rmpbc.h"
  61 #include "gromacs/selection/selection.h"
  62 #include "gromacs/selection/selectioncollection.h"
  63 #include "gromacs/selection/selectionoption.h"
  64 #include "gromacs/selection/selectionoptionbehavior.h"
  65 #include "gromacs/topology/topology.h"
  66 #include "gromacs/trajectory/trajectoryframe.h"
  67 #include "gromacs/trajectoryanalysis/analysissettings.h"
  68 #include "gromacs/utility/cstringutil.h"
  69 #include "gromacs/utility/exceptions.h"
  70 #include "gromacs/utility/gmxassert.h"
  71 #include "gromacs/utility/programcontext.h"
  72 #include "gromacs/utility/smalloc.h"
  73 #include "gromacs/utility/stringutil.h"
  74
  75 #include "analysissettings-impl.h"
  76
  77 namespace gmx
  78 {
  79
  80 class TrajectoryAnalysisRunnerCommon::Impl : public ITopologyProvider
  81 {
  82     public:
  83         explicit Impl(TrajectoryAnalysisSettings *settings);
  84         ~Impl();
  85
  86         bool hasTrajectory() const { return !trjfile_.empty(); }
  87
  88         void initTopology(bool required);
  89         void initFirstFrame();
  90         void initFrameIndexGroup();
  91         void finishTrajectory();
  92
  93         // From ITopologyProvider
  94         virtual gmx_mtop_t *getTopology(bool required)
  95         {
  96             initTopology(required);
  97             return topInfo_.mtop_.get();
  98         }
  99         virtual int getAtomCount()
 100         {
 101             if (!topInfo_.hasTopology())
 102             {
 103                 if (trajectoryGroup_.isValid())
 104                 {
 105                     GMX_THROW(InconsistentInputError("-fgroup is only supported when -s is also specified"));
 106                 }
 107                 // Read the first frame if we don't know the maximum number of
 108                 // atoms otherwise.
 109                 initFirstFrame();
 110                 return fr->natoms;
 111             }
 112             return -1;
 113         }
 114
 115         TrajectoryAnalysisSettings &settings_;
 116         TopologyInformation         topInfo_;
 117
 118         //! Name of the trajectory file (empty if not provided).
 119         std::string                 trjfile_;
 120         //! Name of the topology file (empty if no topology provided).
 121         std::string                 topfile_;
 122         Selection                   trajectoryGroup_;
 123         double                      startTime_;
 124         double                      endTime_;
 125         double                      deltaTime_;
 126         bool                        bStartTimeSet_;
 127         bool                        bEndTimeSet_;
 128         bool                        bDeltaTimeSet_;
 129
 130         bool                        bTrajOpen_;
 131         //! The current frame, or \p NULL if no frame loaded yet.
 132         t_trxframe                 *fr;
 133         gmx_rmpbc_t                 gpbc_;
 134         //! Used to store the status variable from read_first_frame().
 135         t_trxstatus                *status_;
 136         gmx_output_env_t           *oenv_;
 137 };
 138
 139
 140 TrajectoryAnalysisRunnerCommon::Impl::Impl(TrajectoryAnalysisSettings *settings)
 141     : settings_(*settings),
 142       startTime_(0.0), endTime_(0.0), deltaTime_(0.0),
 143       bStartTimeSet_(false), bEndTimeSet_(false), bDeltaTimeSet_(false),
 144       bTrajOpen_(false), fr(nullptr), gpbc_(nullptr), status_(nullptr), oenv_(nullptr)
 145 {
 146 }
 147
 148
 149 TrajectoryAnalysisRunnerCommon::Impl::~Impl()
 150 {
 151     finishTrajectory();
 152     if (fr != nullptr)
 153     {
 154         // There doesn't seem to be a function for freeing frame data
 155         sfree(fr->x);
 156         sfree(fr->v);
 157         sfree(fr->f);
 158         sfree(fr->index);
 159         sfree(fr);
 160     }
 161     if (oenv_ != nullptr)
 162     {
 163         output_env_done(oenv_);
 164     }
 165 }
 166
 167 void
 168 TrajectoryAnalysisRunnerCommon::Impl::initTopology(bool required)
 169 {
 170     // Return immediately if the topology has already been loaded.
 171     if (topInfo_.hasTopology())
 172     {
 173         return;
 174     }
 175
 176     if (required && topfile_.empty())
 177     {
 178         GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
 179     }
 180
 181     // Load the topology if requested.
 182     if (!topfile_.empty())
 183     {
 184         topInfo_.mtop_ = gmx::compat::make_unique<gmx_mtop_t>();
 185         readConfAndTopology(topfile_.c_str(), &topInfo_.bTop_, topInfo_.mtop_.get(),
 186                             &topInfo_.ePBC_, &topInfo_.xtop_, nullptr,
 187                             topInfo_.boxtop_);
 188         // TODO: Only load this here if the tool actually needs it; selections
 189         // take care of themselves.
 190         for (gmx_moltype_t &moltype : topInfo_.mtop_->moltype)
 191         {
 192             if (!moltype.atoms.haveMass)
 193             {
 194                 // Try to read masses from database, be silent about missing masses
 195                 atomsSetMassesBasedOnNames(&moltype.atoms, FALSE);
 196             }
 197         }
 198         if (hasTrajectory()
 199             && !settings_.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
 200         {
 201             sfree(topInfo_.xtop_);
 202             topInfo_.xtop_ = nullptr;
 203         }
 204     }
 205 }
 206
 207 void
 208 TrajectoryAnalysisRunnerCommon::Impl::initFirstFrame()
 209 {
 210     // Return if we have already initialized the trajectory.
 211     if (fr != nullptr)
 212     {
 213         return;
 214     }
 215     time_unit_t time_unit
 216         = static_cast<time_unit_t>(settings_.timeUnit() + 1);
 217     output_env_init(&oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
 218
 219     int frflags = settings_.frflags();
 220     frflags |= TRX_NEED_X;
 221
 222     snew(fr, 1);
 223
 224     if (hasTrajectory())
 225     {
 226         if (!read_first_frame(oenv_, &status_, trjfile_.c_str(), fr, frflags))
 227         {
 228             GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
 229         }
 230         bTrajOpen_ = true;
 231
 232         if (topInfo_.hasTopology())
 233         {
 234             const int topologyAtomCount = topInfo_.topology()->atoms.nr;
 235             if (fr->natoms > topologyAtomCount)
 236             {
 237                 const std::string message
 238                     = formatString("Trajectory (%d atoms) does not match topology (%d atoms)",
 239                                    fr->natoms, topologyAtomCount);
 240                 GMX_THROW(InconsistentInputError(message));
 241             }
 242         }
 243     }
 244     else
 245     {
 246         // Prepare a frame from topology information.
 247         // TODO: Initialize more of the fields.
 248         if (frflags & (TRX_NEED_V))
 249         {
 250             GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
 251         }
 252         if (frflags & (TRX_NEED_F))
 253         {
 254             GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
 255         }
 256         fr->natoms = topInfo_.topology()->atoms.nr;
 257         fr->bX     = TRUE;
 258         snew(fr->x, fr->natoms);
 259         memcpy(fr->x, topInfo_.xtop_,
 260                sizeof(*fr->x) * fr->natoms);
 261         fr->bBox   = TRUE;
 262         copy_mat(topInfo_.boxtop_, fr->box);
 263     }
 264
 265     set_trxframe_ePBC(fr, topInfo_.ePBC());
 266     if (topInfo_.hasTopology() && settings_.hasRmPBC())
 267     {
 268         gpbc_ = gmx_rmpbc_init(&topInfo_.topology()->idef, topInfo_.ePBC(),
 269                                fr->natoms);
 270     }
 271 }
 272
 273 void
 274 TrajectoryAnalysisRunnerCommon::Impl::initFrameIndexGroup()
 275 {
 276     if (!trajectoryGroup_.isValid())
 277     {
 278         return;
 279     }
 280     GMX_RELEASE_ASSERT(bTrajOpen_,
 281                        "Trajectory index only makes sense with a real trajectory");
 282     if (trajectoryGroup_.atomCount() != fr->natoms)
 283     {
 284         const std::string message = formatString(
 285                     "Selection specified with -fgroup has %d atoms, but "
 286                     "the trajectory (-f) has %d atoms.",
 287                     trajectoryGroup_.atomCount(), fr->natoms);
 288         GMX_THROW(InconsistentInputError(message));
 289     }
 290     fr->bIndex = TRUE;
 291     snew(fr->index, trajectoryGroup_.atomCount());
 292     std::copy(trajectoryGroup_.atomIndices().begin(),
 293               trajectoryGroup_.atomIndices().end(),
 294               fr->index);
 295 }
 296
 297 void
 298 TrajectoryAnalysisRunnerCommon::Impl::finishTrajectory()
 299 {
 300     if (bTrajOpen_)
 301     {
 302         close_trx(status_);
 303         bTrajOpen_ = false;
 304     }
 305     if (gpbc_ != nullptr)
 306     {
 307         gmx_rmpbc_done(gpbc_);
 308         gpbc_ = nullptr;
 309     }
 310 }
 311
 312 /*********************************************************************
 313  * TrajectoryAnalysisRunnerCommon
 314  */
 315
 316 TrajectoryAnalysisRunnerCommon::TrajectoryAnalysisRunnerCommon(
 317         TrajectoryAnalysisSettings *settings)
 318     : impl_(new Impl(settings))
 319 {
 320 }
 321
 322
 323 TrajectoryAnalysisRunnerCommon::~TrajectoryAnalysisRunnerCommon()
 324 {
 325 }
 326
 327
 328 ITopologyProvider *
 329 TrajectoryAnalysisRunnerCommon::topologyProvider()
 330 {
 331     return impl_.get();
 332 }
 333
 334
 335 void
 336 TrajectoryAnalysisRunnerCommon::initOptions(IOptionsContainer *options,
 337                                             TimeUnitBehavior  *timeUnitBehavior)
 338 {
 339     TrajectoryAnalysisSettings &settings = impl_->settings_;
 340
 341     // Add common file name arguments.
 342     options->addOption(FileNameOption("f")
 343                            .filetype(eftTrajectory).inputFile()
 344                            .store(&impl_->trjfile_)
 345                            .defaultBasename("traj")
 346                            .description("Input trajectory or single configuration"));
 347     options->addOption(FileNameOption("s")
 348                            .filetype(eftTopology).inputFile()
 349                            .store(&impl_->topfile_)
 350                            .defaultBasename("topol")
 351                            .description("Input structure"));
 352
 353     // Add options for trajectory time control.
 354     options->addOption(DoubleOption("b")
 355                            .store(&impl_->startTime_).storeIsSet(&impl_->bStartTimeSet_)
 356                            .timeValue()
 357                            .description("First frame (%t) to read from trajectory"));
 358     options->addOption(DoubleOption("e")
 359                            .store(&impl_->endTime_).storeIsSet(&impl_->bEndTimeSet_)
 360                            .timeValue()
 361                            .description("Last frame (%t) to read from trajectory"));
 362     options->addOption(DoubleOption("dt")
 363                            .store(&impl_->deltaTime_).storeIsSet(&impl_->bDeltaTimeSet_)
 364                            .timeValue()
 365                            .description("Only use frame if t MOD dt == first time (%t)"));
 366
 367     // Add time unit option.
 368     timeUnitBehavior->setTimeUnitFromEnvironment();
 369     timeUnitBehavior->addTimeUnitOption(options, "tu");
 370     timeUnitBehavior->setTimeUnitStore(&impl_->settings_.impl_->timeUnit);
 371
 372     options->addOption(SelectionOption("fgroup")
 373                            .store(&impl_->trajectoryGroup_)
 374                            .onlySortedAtoms().onlyStatic()
 375                            .description("Atoms stored in the trajectory file "
 376                                         "(if not set, assume first N atoms)"));
 377
 378     // Add plot options.
 379     settings.impl_->plotSettings.initOptions(options);
 380
 381     // Add common options for trajectory processing.
 382     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
 383     {
 384         options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
 385                                .description("Make molecules whole for each frame"));
 386     }
 387     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
 388     {
 389         options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
 390                                .description("Use periodic boundary conditions for distance calculation"));
 391     }
 392 }
 393
 394
 395 void
 396 TrajectoryAnalysisRunnerCommon::optionsFinished()
 397 {
 398     if (impl_->trjfile_.empty() && impl_->topfile_.empty())
 399     {
 400         GMX_THROW(InconsistentInputError("No trajectory or topology provided, nothing to do!"));
 401     }
 402
 403     if (impl_->trajectoryGroup_.isValid() && impl_->trjfile_.empty())
 404     {
 405         GMX_THROW(InconsistentInputError("-fgroup only makes sense together with a trajectory (-f)"));
 406     }
 407
 408     impl_->settings_.impl_->plotSettings.setTimeUnit(impl_->settings_.timeUnit());
 409
 410     if (impl_->bStartTimeSet_)
 411     {
 412         setTimeValue(TBEGIN, impl_->startTime_);
 413     }
 414     if (impl_->bEndTimeSet_)
 415     {
 416         setTimeValue(TEND, impl_->endTime_);
 417     }
 418     if (impl_->bDeltaTimeSet_)
 419     {
 420         setTimeValue(TDELTA, impl_->deltaTime_);
 421     }
 422 }
 423
 424
 425 void
 426 TrajectoryAnalysisRunnerCommon::initTopology()
 427 {
 428     const bool topologyRequired =
 429         impl_->settings_.hasFlag(TrajectoryAnalysisSettings::efRequireTop);
 430     impl_->initTopology(topologyRequired);
 431 }
 432
 433
 434 void
 435 TrajectoryAnalysisRunnerCommon::initFirstFrame()
 436 {
 437     impl_->initFirstFrame();
 438 }
 439
 440
 441 void
 442 TrajectoryAnalysisRunnerCommon::initFrameIndexGroup()
 443 {
 444     impl_->initFrameIndexGroup();
 445 }
 446
 447
 448 bool
 449 TrajectoryAnalysisRunnerCommon::readNextFrame()
 450 {
 451     bool bContinue = false;
 452     if (hasTrajectory())
 453     {
 454         bContinue = read_next_frame(impl_->oenv_, impl_->status_, impl_->fr);
 455     }
 456     if (!bContinue)
 457     {
 458         impl_->finishTrajectory();
 459     }
 460     return bContinue;
 461 }
 462
 463
 464 void
 465 TrajectoryAnalysisRunnerCommon::initFrame()
 466 {
 467     if (impl_->gpbc_ != nullptr)
 468     {
 469         gmx_rmpbc_trxfr(impl_->gpbc_, impl_->fr);
 470     }
 471 }
 472
 473
 474 bool
 475 TrajectoryAnalysisRunnerCommon::hasTrajectory() const
 476 {
 477     return impl_->hasTrajectory();
 478 }
 479
 480
 481 const TopologyInformation &
 482 TrajectoryAnalysisRunnerCommon::topologyInformation() const
 483 {
 484     return impl_->topInfo_;
 485 }
 486
 487
 488 t_trxframe &
 489 TrajectoryAnalysisRunnerCommon::frame() const
 490 {
 491     GMX_RELEASE_ASSERT(impl_->fr != nullptr, "Frame not available when accessed");
 492     return *impl_->fr;
 493 }
 494
 495 } // namespace gmx