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() override;
  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         gmx_mtop_t *getTopology(bool required) override
  94         {
  95             initTopology(required);
  96             return topInfo_.mtop_.get();
  97         }
  98         int getAtomCount() override
  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             topInfo_.xtop_.clear();
 188         }
 189         if (hasTrajectory()
 190             && !settings_.hasFlag(TrajectoryAnalysisSettings::efUseTopV))
 191         {
 192             topInfo_.vtop_.clear();
 193         }
 194     }
 195 }
 196
 197 void
 198 TrajectoryAnalysisRunnerCommon::Impl::initFirstFrame()
 199 {
 200     // Return if we have already initialized the trajectory.
 201     if (fr != nullptr)
 202     {
 203         return;
 204     }
 205     time_unit_t time_unit
 206         = static_cast<time_unit_t>(settings_.timeUnit() + 1); // NOLINT(bugprone-misplaced-widening-cast)
 207     output_env_init(&oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
 208
 209     int frflags = settings_.frflags();
 210     frflags |= TRX_NEED_X;
 211
 212     snew(fr, 1);
 213
 214     if (hasTrajectory())
 215     {
 216         if (!read_first_frame(oenv_, &status_, trjfile_.c_str(), fr, frflags))
 217         {
 218             GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
 219         }
 220         bTrajOpen_ = true;
 221
 222         if (topInfo_.hasTopology())
 223         {
 224             const int topologyAtomCount = topInfo_.mtop()->natoms;
 225             if (fr->natoms > topologyAtomCount)
 226             {
 227                 const std::string message
 228                     = formatString("Trajectory (%d atoms) does not match topology (%d atoms)",
 229                                    fr->natoms, topologyAtomCount);
 230                 GMX_THROW(InconsistentInputError(message));
 231             }
 232         }
 233     }
 234     else
 235     {
 236         // Prepare a frame from topology information.
 237         if (frflags & (TRX_NEED_F))
 238         {
 239             GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
 240         }
 241         fr->natoms = topInfo_.mtop()->natoms;
 242         fr->bX     = TRUE;
 243         snew(fr->x, fr->natoms);
 244         memcpy(fr->x, topInfo_.xtop_.data(),
 245                sizeof(*fr->x) * fr->natoms);
 246         if (frflags & (TRX_NEED_V))
 247         {
 248             if (topInfo_.vtop_.empty())
 249             {
 250                 GMX_THROW(InvalidInputError("Velocities were required, but could not be read from the topology file"));
 251             }
 252             fr->bV = TRUE;
 253             snew(fr->v, fr->natoms);
 254             memcpy(fr->v, topInfo_.vtop_.data(),
 255                    sizeof(*fr->v) * fr->natoms);
 256         }
 257         fr->bBox   = TRUE;
 258         copy_mat(topInfo_.boxtop_, fr->box);
 259     }
 260
 261     set_trxframe_ePBC(fr, topInfo_.ePBC());
 262     if (topInfo_.hasTopology() && settings_.hasRmPBC())
 263     {
 264         gpbc_             = gmx_rmpbc_init(topInfo_);
 265     }
 266 }
 267
 268 void
 269 TrajectoryAnalysisRunnerCommon::Impl::initFrameIndexGroup()
 270 {
 271     if (!trajectoryGroup_.isValid())
 272     {
 273         return;
 274     }
 275     GMX_RELEASE_ASSERT(bTrajOpen_,
 276                        "Trajectory index only makes sense with a real trajectory");
 277     if (trajectoryGroup_.atomCount() != fr->natoms)
 278     {
 279         const std::string message = formatString(
 280                     "Selection specified with -fgroup has %d atoms, but "
 281                     "the trajectory (-f) has %d atoms.",
 282                     trajectoryGroup_.atomCount(), fr->natoms);
 283         GMX_THROW(InconsistentInputError(message));
 284     }
 285     fr->bIndex = TRUE;
 286     snew(fr->index, trajectoryGroup_.atomCount());
 287     std::copy(trajectoryGroup_.atomIndices().begin(),
 288               trajectoryGroup_.atomIndices().end(),
 289               fr->index);
 290 }
 291
 292 void
 293 TrajectoryAnalysisRunnerCommon::Impl::finishTrajectory()
 294 {
 295     if (bTrajOpen_)
 296     {
 297         close_trx(status_);
 298         bTrajOpen_ = false;
 299     }
 300     if (gpbc_ != nullptr)
 301     {
 302         gmx_rmpbc_done(gpbc_);
 303         gpbc_ = nullptr;
 304     }
 305 }
 306
 307 /*********************************************************************
 308  * TrajectoryAnalysisRunnerCommon
 309  */
 310
 311 TrajectoryAnalysisRunnerCommon::TrajectoryAnalysisRunnerCommon(
 312         TrajectoryAnalysisSettings *settings)
 313     : impl_(new Impl(settings))
 314 {
 315 }
 316
 317
 318 TrajectoryAnalysisRunnerCommon::~TrajectoryAnalysisRunnerCommon()
 319 {
 320 }
 321
 322
 323 ITopologyProvider *
 324 TrajectoryAnalysisRunnerCommon::topologyProvider()
 325 {
 326     return impl_.get();
 327 }
 328
 329
 330 void
 331 TrajectoryAnalysisRunnerCommon::initOptions(IOptionsContainer *options,
 332                                             TimeUnitBehavior  *timeUnitBehavior)
 333 {
 334     TrajectoryAnalysisSettings &settings = impl_->settings_;
 335
 336     // Add common file name arguments.
 337     options->addOption(FileNameOption("f")
 338                            .filetype(eftTrajectory).inputFile()
 339                            .store(&impl_->trjfile_)
 340                            .defaultBasename("traj")
 341                            .description("Input trajectory or single configuration"));
 342     options->addOption(FileNameOption("s")
 343                            .filetype(eftTopology).inputFile()
 344                            .store(&impl_->topfile_)
 345                            .defaultBasename("topol")
 346                            .description("Input structure"));
 347
 348     // Add options for trajectory time control.
 349     options->addOption(DoubleOption("b")
 350                            .store(&impl_->startTime_).storeIsSet(&impl_->bStartTimeSet_)
 351                            .timeValue()
 352                            .description("First frame (%t) to read from trajectory"));
 353     options->addOption(DoubleOption("e")
 354                            .store(&impl_->endTime_).storeIsSet(&impl_->bEndTimeSet_)
 355                            .timeValue()
 356                            .description("Last frame (%t) to read from trajectory"));
 357     options->addOption(DoubleOption("dt")
 358                            .store(&impl_->deltaTime_).storeIsSet(&impl_->bDeltaTimeSet_)
 359                            .timeValue()
 360                            .description("Only use frame if t MOD dt == first time (%t)"));
 361
 362     // Add time unit option.
 363     timeUnitBehavior->setTimeUnitFromEnvironment();
 364     timeUnitBehavior->addTimeUnitOption(options, "tu");
 365     timeUnitBehavior->setTimeUnitStore(&impl_->settings_.impl_->timeUnit);
 366
 367     options->addOption(SelectionOption("fgroup")
 368                            .store(&impl_->trajectoryGroup_)
 369                            .onlySortedAtoms().onlyStatic()
 370                            .description("Atoms stored in the trajectory file "
 371                                         "(if not set, assume first N atoms)"));
 372
 373     // Add plot options.
 374     settings.impl_->plotSettings.initOptions(options);
 375
 376     // Add common options for trajectory processing.
 377     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
 378     {
 379         options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
 380                                .description("Make molecules whole for each frame"));
 381     }
 382     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
 383     {
 384         options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
 385                                .description("Use periodic boundary conditions for distance calculation"));
 386     }
 387 }
 388
 389
 390 void
 391 TrajectoryAnalysisRunnerCommon::optionsFinished()
 392 {
 393     if (impl_->trjfile_.empty() && impl_->topfile_.empty())
 394     {
 395         GMX_THROW(InconsistentInputError("No trajectory or topology provided, nothing to do!"));
 396     }
 397
 398     if (impl_->trajectoryGroup_.isValid() && impl_->trjfile_.empty())
 399     {
 400         GMX_THROW(InconsistentInputError("-fgroup only makes sense together with a trajectory (-f)"));
 401     }
 402
 403     impl_->settings_.impl_->plotSettings.setTimeUnit(impl_->settings_.timeUnit());
 404
 405     if (impl_->bStartTimeSet_)
 406     {
 407         setTimeValue(TBEGIN, impl_->startTime_);
 408     }
 409     if (impl_->bEndTimeSet_)
 410     {
 411         setTimeValue(TEND, impl_->endTime_);
 412     }
 413     if (impl_->bDeltaTimeSet_)
 414     {
 415         setTimeValue(TDELTA, impl_->deltaTime_);
 416     }
 417 }
 418
 419
 420 void
 421 TrajectoryAnalysisRunnerCommon::initTopology()
 422 {
 423     const bool topologyRequired =
 424         impl_->settings_.hasFlag(TrajectoryAnalysisSettings::efRequireTop);
 425     impl_->initTopology(topologyRequired);
 426 }
 427
 428
 429 void
 430 TrajectoryAnalysisRunnerCommon::initFirstFrame()
 431 {
 432     impl_->initFirstFrame();
 433 }
 434
 435
 436 void
 437 TrajectoryAnalysisRunnerCommon::initFrameIndexGroup()
 438 {
 439     impl_->initFrameIndexGroup();
 440 }
 441
 442
 443 bool
 444 TrajectoryAnalysisRunnerCommon::readNextFrame()
 445 {
 446     bool bContinue = false;
 447     if (hasTrajectory())
 448     {
 449         bContinue = read_next_frame(impl_->oenv_, impl_->status_, impl_->fr);
 450     }
 451     if (!bContinue)
 452     {
 453         impl_->finishTrajectory();
 454     }
 455     return bContinue;
 456 }
 457
 458
 459 void
 460 TrajectoryAnalysisRunnerCommon::initFrame()
 461 {
 462     if (impl_->gpbc_ != nullptr)
 463     {
 464         gmx_rmpbc_trxfr(impl_->gpbc_, impl_->fr);
 465     }
 466 }
 467
 468
 469 bool
 470 TrajectoryAnalysisRunnerCommon::hasTrajectory() const
 471 {
 472     return impl_->hasTrajectory();
 473 }
 474
 475
 476 const TopologyInformation &
 477 TrajectoryAnalysisRunnerCommon::topologyInformation() const
 478 {
 479     return impl_->topInfo_;
 480 }
 481
 482
 483 t_trxframe &
 484 TrajectoryAnalysisRunnerCommon::frame() const
 485 {
 486     GMX_RELEASE_ASSERT(impl_->fr != nullptr, "Frame not available when accessed");
 487     return *impl_->fr;
 488 }
 489
 490 } // namespace gmx