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