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/statutil.h"
  54 #include "gromacs/legacyheaders/tpxio.h"
  55 #include "gromacs/legacyheaders/vec.h"
  56
  57 #include "gromacs/options/basicoptions.h"
  58 #include "gromacs/options/filenameoption.h"
  59 #include "gromacs/options/options.h"
  60 #include "gromacs/selection/indexutil.h"
  61 #include "gromacs/selection/selectioncollection.h"
  62 #include "gromacs/selection/selectionfileoption.h"
  63 #include "gromacs/trajectoryanalysis/analysissettings.h"
  64 #include "gromacs/utility/exceptions.h"
  65 #include "gromacs/utility/gmxassert.h"
  66 #include "gromacs/utility/stringutil.h"
  67
  68 #include "analysissettings-impl.h"
  69
  70 namespace gmx
  71 {
  72
  73 class TrajectoryAnalysisRunnerCommon::Impl
  74 {
  75     public:
  76         Impl(TrajectoryAnalysisSettings *settings);
  77         ~Impl();
  78
  79         void finishTrajectory();
  80
  81         TrajectoryAnalysisSettings &settings_;
  82         TopologyInformation         topInfo_;
  83
  84         //! Name of the trajectory file (empty if not provided).
  85         std::string                 trjfile_;
  86         //! Name of the topology file (empty if no topology provided).
  87         std::string                 topfile_;
  88         //! Name of the index file (empty if no index file provided).
  89         std::string                 ndxfile_;
  90         double                      startTime_;
  91         double                      endTime_;
  92         double                      deltaTime_;
  93
  94         gmx_ana_indexgrps_t        *grps_;
  95         bool                        bTrajOpen_;
  96         //! The current frame, or \p NULL if no frame loaded yet.
  97         t_trxframe                 *fr;
  98         gmx_rmpbc_t                 gpbc_;
  99         //! Used to store the status variable from read_first_frame().
 100         t_trxstatus                *status_;
 101         output_env_t                oenv_;
 102 };
 103
 104
 105 TrajectoryAnalysisRunnerCommon::Impl::Impl(TrajectoryAnalysisSettings *settings)
 106     : settings_(*settings),
 107       startTime_(0.0), endTime_(0.0), deltaTime_(0.0),
 108       grps_(NULL),
 109       bTrajOpen_(false), fr(NULL), gpbc_(NULL), status_(NULL), oenv_(NULL)
 110 {
 111 }
 112
 113
 114 TrajectoryAnalysisRunnerCommon::Impl::~Impl()
 115 {
 116     if (grps_ != NULL)
 117     {
 118         gmx_ana_indexgrps_free(grps_);
 119     }
 120     finishTrajectory();
 121     if (fr)
 122     {
 123         // There doesn't seem to be a function for freeing frame data
 124         sfree(fr->x);
 125         sfree(fr->v);
 126         sfree(fr->f);
 127         sfree(fr);
 128     }
 129     if (oenv_ != NULL)
 130     {
 131         output_env_done(oenv_);
 132     }
 133 }
 134
 135
 136 void
 137 TrajectoryAnalysisRunnerCommon::Impl::finishTrajectory()
 138 {
 139     if (bTrajOpen_)
 140     {
 141         close_trx(status_);
 142         bTrajOpen_ = false;
 143     }
 144     if (gpbc_ != NULL)
 145     {
 146         gmx_rmpbc_done(gpbc_);
 147         gpbc_ = NULL;
 148     }
 149 }
 150
 151 /*********************************************************************
 152  * TrajectoryAnalysisRunnerCommon
 153  */
 154
 155 TrajectoryAnalysisRunnerCommon::TrajectoryAnalysisRunnerCommon(
 156         TrajectoryAnalysisSettings *settings)
 157     : impl_(new Impl(settings))
 158 {
 159 }
 160
 161
 162 TrajectoryAnalysisRunnerCommon::~TrajectoryAnalysisRunnerCommon()
 163 {
 164 }
 165
 166
 167 void
 168 TrajectoryAnalysisRunnerCommon::initOptions(Options *options)
 169 {
 170     TrajectoryAnalysisSettings &settings = impl_->settings_;
 171
 172     // Add common file name arguments.
 173     options->addOption(FileNameOption("f")
 174                            .filetype(eftTrajectory).inputFile()
 175                            .store(&impl_->trjfile_)
 176                            .defaultBasename("traj")
 177                            .description("Input trajectory or single configuration"));
 178     options->addOption(FileNameOption("s")
 179                            .filetype(eftTopology).inputFile()
 180                            .store(&impl_->topfile_)
 181                            .defaultBasename("topol")
 182                            .description("Input structure"));
 183     options->addOption(FileNameOption("n")
 184                            .filetype(eftIndex).inputFile()
 185                            .store(&impl_->ndxfile_)
 186                            .defaultBasename("index")
 187                            .description("Extra index groups"));
 188     options->addOption(SelectionFileOption("sf"));
 189
 190     // Add options for trajectory time control.
 191     options->addOption(DoubleOption("b").store(&impl_->startTime_).timeValue()
 192                            .description("First frame (%t) to read from trajectory"));
 193     options->addOption(DoubleOption("e").store(&impl_->endTime_).timeValue()
 194                            .description("Last frame (%t) to read from trajectory"));
 195     options->addOption(DoubleOption("dt").store(&impl_->deltaTime_).timeValue()
 196                            .description("Only use frame if t MOD dt == first time (%t)"));
 197
 198     // Add time unit option.
 199     settings.impl_->timeUnitManager.addTimeUnitOption(options, "tu");
 200
 201     // Add plot options.
 202     settings.impl_->plotSettings.addOptions(options);
 203
 204     // Add common options for trajectory processing.
 205     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
 206     {
 207         options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
 208                                .description("Make molecules whole for each frame"));
 209     }
 210     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
 211     {
 212         options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
 213                                .description("Use periodic boundary conditions for distance calculation"));
 214     }
 215 }
 216
 217
 218 void
 219 TrajectoryAnalysisRunnerCommon::scaleTimeOptions(Options *options)
 220 {
 221     impl_->settings_.impl_->timeUnitManager.scaleTimeOptions(options);
 222 }
 223
 224
 225 void
 226 TrajectoryAnalysisRunnerCommon::optionsFinished(Options *options)
 227 {
 228     impl_->settings_.impl_->plotSettings.setTimeUnit(
 229             impl_->settings_.impl_->timeUnitManager.timeUnit());
 230
 231     if (impl_->trjfile_.empty() && impl_->topfile_.empty())
 232     {
 233         GMX_THROW(InconsistentInputError("No trajectory or topology provided, nothing to do!"));
 234     }
 235
 236     if (options->isSet("b"))
 237     {
 238         setTimeValue(TBEGIN, impl_->startTime_);
 239     }
 240     if (options->isSet("e"))
 241     {
 242         setTimeValue(TEND, impl_->endTime_);
 243     }
 244     if (options->isSet("dt"))
 245     {
 246         setTimeValue(TDELTA, impl_->deltaTime_);
 247     }
 248 }
 249
 250
 251 void
 252 TrajectoryAnalysisRunnerCommon::initIndexGroups(SelectionCollection *selections)
 253 {
 254     if (impl_->ndxfile_.empty())
 255     {
 256         // TODO: Initialize default selections
 257         selections->setIndexGroups(NULL);
 258     }
 259     else
 260     {
 261         gmx_ana_indexgrps_init(&impl_->grps_, NULL, impl_->ndxfile_.c_str());
 262         selections->setIndexGroups(impl_->grps_);
 263     }
 264 }
 265
 266
 267 void
 268 TrajectoryAnalysisRunnerCommon::doneIndexGroups(SelectionCollection *selections)
 269 {
 270     if (impl_->grps_ != NULL)
 271     {
 272         selections->setIndexGroups(NULL);
 273         gmx_ana_indexgrps_free(impl_->grps_);
 274         impl_->grps_ = NULL;
 275     }
 276 }
 277
 278
 279 void
 280 TrajectoryAnalysisRunnerCommon::initTopology(SelectionCollection *selections)
 281 {
 282     const TrajectoryAnalysisSettings &settings = impl_->settings_;
 283     bool bRequireTop
 284         = settings.hasFlag(TrajectoryAnalysisSettings::efRequireTop)
 285             || selections->requiresTopology();
 286     if (bRequireTop && impl_->topfile_.empty())
 287     {
 288         GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
 289     }
 290
 291     // Load the topology if requested.
 292     if (!impl_->topfile_.empty())
 293     {
 294         char  title[STRLEN];
 295
 296         snew(impl_->topInfo_.top_, 1);
 297         impl_->topInfo_.bTop_ = read_tps_conf(impl_->topfile_.c_str(), title,
 298                                               impl_->topInfo_.top_, &impl_->topInfo_.ePBC_,
 299                                               &impl_->topInfo_.xtop_, NULL, impl_->topInfo_.boxtop_, TRUE);
 300         if (hasTrajectory()
 301             && !settings.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
 302         {
 303             sfree(impl_->topInfo_.xtop_);
 304             impl_->topInfo_.xtop_ = NULL;
 305         }
 306     }
 307
 308     // Read the first frame if we don't know the maximum number of atoms
 309     // otherwise.
 310     int  natoms = -1;
 311     if (!impl_->topInfo_.hasTopology())
 312     {
 313         initFirstFrame();
 314         natoms = impl_->fr->natoms;
 315     }
 316     selections->setTopology(impl_->topInfo_.topology(), natoms);
 317
 318     /*
 319        if (impl_->bSelDump)
 320        {
 321         gmx_ana_poscalc_coll_print_tree(stderr, impl_->pcc);
 322         fprintf(stderr, "\n");
 323        }
 324      */
 325 }
 326
 327
 328 void
 329 TrajectoryAnalysisRunnerCommon::initFirstFrame()
 330 {
 331     // Return if we have already initialized the trajectory.
 332     if (impl_->fr)
 333     {
 334         return;
 335     }
 336     time_unit_t time_unit
 337         = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
 338     output_env_init(&impl_->oenv_, 0, NULL, time_unit, FALSE, exvgNONE, 0, 0);
 339
 340     int frflags = impl_->settings_.frflags();
 341     frflags |= TRX_NEED_X;
 342
 343     snew(impl_->fr, 1);
 344
 345     const TopologyInformation &top = impl_->topInfo_;
 346     if (hasTrajectory())
 347     {
 348         if (!read_first_frame(impl_->oenv_, &impl_->status_,
 349                               impl_->trjfile_.c_str(), impl_->fr, frflags))
 350         {
 351             GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
 352         }
 353         impl_->bTrajOpen_ = true;
 354
 355         if (top.hasTopology() && impl_->fr->natoms > top.topology()->atoms.nr)
 356         {
 357             GMX_THROW(InconsistentInputError(formatString(
 358                                                      "Trajectory (%d atoms) does not match topology (%d atoms)",
 359                                                      impl_->fr->natoms, top.topology()->atoms.nr)));
 360         }
 361         // TODO: Check index groups if they have been initialized based on the topology.
 362         /*
 363            if (top)
 364            {
 365             for (int i = 0; i < impl_->sel->nr(); ++i)
 366             {
 367                 gmx_ana_index_check(impl_->sel->sel(i)->indexGroup(),
 368                                     impl_->fr->natoms);
 369             }
 370            }
 371          */
 372     }
 373     else
 374     {
 375         // Prepare a frame from topology information.
 376         // TODO: Initialize more of the fields.
 377         if (frflags & (TRX_NEED_V))
 378         {
 379             GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
 380         }
 381         if (frflags & (TRX_NEED_F))
 382         {
 383             GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
 384         }
 385         impl_->fr->flags  = frflags;
 386         impl_->fr->natoms = top.topology()->atoms.nr;
 387         impl_->fr->bX     = TRUE;
 388         snew(impl_->fr->x, impl_->fr->natoms);
 389         memcpy(impl_->fr->x, top.xtop_,
 390                sizeof(*impl_->fr->x) * impl_->fr->natoms);
 391         impl_->fr->bBox   = TRUE;
 392         copy_mat(const_cast<rvec *>(top.boxtop_), impl_->fr->box);
 393     }
 394
 395     set_trxframe_ePBC(impl_->fr, top.ePBC());
 396     if (top.hasTopology() && impl_->settings_.hasRmPBC())
 397     {
 398         impl_->gpbc_ = gmx_rmpbc_init(&top.topology()->idef, top.ePBC(),
 399                                       impl_->fr->natoms);
 400     }
 401 }
 402
 403
 404 bool
 405 TrajectoryAnalysisRunnerCommon::readNextFrame()
 406 {
 407     bool bContinue = false;
 408     if (hasTrajectory())
 409     {
 410         bContinue = read_next_frame(impl_->oenv_, impl_->status_, impl_->fr);
 411     }
 412     if (!bContinue)
 413     {
 414         impl_->finishTrajectory();
 415     }
 416     return bContinue;
 417 }
 418
 419
 420 void
 421 TrajectoryAnalysisRunnerCommon::initFrame()
 422 {
 423     if (impl_->gpbc_ != NULL)
 424     {
 425         gmx_rmpbc_trxfr(impl_->gpbc_, impl_->fr);
 426     }
 427 }
 428
 429
 430 bool
 431 TrajectoryAnalysisRunnerCommon::hasTrajectory() const
 432 {
 433     return !impl_->trjfile_.empty();
 434 }
 435
 436
 437 const TopologyInformation &
 438 TrajectoryAnalysisRunnerCommon::topologyInformation() const
 439 {
 440     return impl_->topInfo_;
 441 }
 442
 443
 444 t_trxframe &
 445 TrajectoryAnalysisRunnerCommon::frame() const
 446 {
 447     GMX_RELEASE_ASSERT(impl_->fr != NULL, "Frame not available when accessed");
 448     return *impl_->fr;
 449 }
 450
 451 } // namespace gmx