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