src/gromacs/trajectoryanalysis/runnercommon.cpp

   1 /*
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  31 /*! \internal \file
  32  * \brief
  33  * Implements gmx::TrajectoryAnalysisRunnerCommon.
  34  *
  35  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
  36  * \ingroup module_trajectoryanalysis
  37  */
  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include <string.h>
  43
  44 #include "oenv.h"
  45 #include "rmpbc.h"
  46 #include "smalloc.h"
  47 #include "statutil.h"
  48 #include "tpxio.h"
  49 #include "vec.h"
  50
  51 #include "gromacs/options/basicoptions.h"
  52 #include "gromacs/options/filenameoption.h"
  53 #include "gromacs/options/options.h"
  54 #include "gromacs/selection/indexutil.h"
  55 #include "gromacs/selection/selectioncollection.h"
  56 #include "gromacs/selection/selectionfileoption.h"
  57 #include "gromacs/trajectoryanalysis/analysissettings.h"
  58 #include "gromacs/trajectoryanalysis/runnercommon.h"
  59 #include "gromacs/utility/exceptions.h"
  60 #include "gromacs/utility/gmxassert.h"
  61 #include "gromacs/utility/stringutil.h"
  62
  63 #include "analysissettings-impl.h"
  64
  65 namespace gmx
  66 {
  67
  68 class TrajectoryAnalysisRunnerCommon::Impl
  69 {
  70     public:
  71         Impl(TrajectoryAnalysisSettings *settings);
  72         ~Impl();
  73
  74         void finishTrajectory();
  75
  76         TrajectoryAnalysisSettings &settings_;
  77         TopologyInformation     topInfo_;
  78
  79         bool                    bHelp_;
  80         bool                    bShowHidden_;
  81         bool                    bQuiet_;
  82         //! Name of the trajectory file (empty if not provided).
  83         std::string             trjfile_;
  84         //! Name of the topology file (empty if no topology provided).
  85         std::string             topfile_;
  86         //! Name of the index file (empty if no index file provided).
  87         std::string             ndxfile_;
  88         double                  startTime_;
  89         double                  endTime_;
  90         double                  deltaTime_;
  91
  92         gmx_ana_indexgrps_t    *grps_;
  93         bool                    bTrajOpen_;
  94         //! The current frame, or \p NULL if no frame loaded yet.
  95         t_trxframe          *fr;
  96         gmx_rmpbc_t             gpbc_;
  97         //! Used to store the status variable from read_first_frame().
  98         t_trxstatus            *status_;
  99         output_env_t            oenv_;
 100 };
 101
 102
 103 TrajectoryAnalysisRunnerCommon::Impl::Impl(TrajectoryAnalysisSettings *settings)
 104     : settings_(*settings),
 105       bHelp_(false), bShowHidden_(false), bQuiet_(false),
 106       startTime_(0.0), endTime_(0.0), deltaTime_(0.0),
 107       grps_(NULL),
 108       bTrajOpen_(false), fr(NULL), gpbc_(NULL), status_(NULL), oenv_(NULL)
 109 {
 110 }
 111
 112
 113 TrajectoryAnalysisRunnerCommon::Impl::~Impl()
 114 {
 115     if (grps_ != NULL)
 116     {
 117         gmx_ana_indexgrps_free(grps_);
 118     }
 119     finishTrajectory();
 120     if (fr)
 121     {
 122         // There doesn't seem to be a function for freeing frame data
 123         sfree(fr->x);
 124         sfree(fr->v);
 125         sfree(fr->f);
 126         sfree(fr);
 127     }
 128     if (oenv_ != NULL)
 129     {
 130         output_env_done(oenv_);
 131     }
 132 }
 133
 134
 135 void
 136 TrajectoryAnalysisRunnerCommon::Impl::finishTrajectory()
 137 {
 138     if (bTrajOpen_)
 139     {
 140         close_trx(status_);
 141         bTrajOpen_ = false;
 142     }
 143     if (gpbc_ != NULL)
 144     {
 145         gmx_rmpbc_done(gpbc_);
 146         gpbc_ = NULL;
 147     }
 148 }
 149
 150 /*********************************************************************
 151  * TrajectoryAnalysisRunnerCommon
 152  */
 153
 154 TrajectoryAnalysisRunnerCommon::TrajectoryAnalysisRunnerCommon(
 155         TrajectoryAnalysisSettings *settings)
 156     : impl_(new Impl(settings))
 157 {
 158 }
 159
 160
 161 TrajectoryAnalysisRunnerCommon::~TrajectoryAnalysisRunnerCommon()
 162 {
 163 }
 164
 165
 166 void
 167 TrajectoryAnalysisRunnerCommon::initOptions(Options *options)
 168 {
 169     TrajectoryAnalysisSettings &settings = impl_->settings_;
 170
 171     // Add options for help.
 172     options->addOption(BooleanOption("h").store(&impl_->bHelp_)
 173                            .description("Print help and quit"));
 174     options->addOption(BooleanOption("hidden").store(&impl_->bShowHidden_)
 175                            .hidden()
 176                            .description("Show hidden options"));
 177     options->addOption(BooleanOption("quiet").store(&impl_->bQuiet_)
 178                            .hidden()
 179                            .description("Hide options in normal run"));
 180
 181     // Add common file name arguments.
 182     options->addOption(FileNameOption("f")
 183                            .filetype(eftTrajectory).inputFile()
 184                            .store(&impl_->trjfile_)
 185                            .defaultBasename("traj")
 186                            .description("Input trajectory or single configuration"));
 187     options->addOption(FileNameOption("s")
 188                            .filetype(eftTopology).inputFile()
 189                            .store(&impl_->topfile_)
 190                            .defaultBasename("topol")
 191                            .description("Input structure"));
 192     options->addOption(FileNameOption("n")
 193                            .filetype(eftIndex).inputFile()
 194                            .store(&impl_->ndxfile_)
 195                            .defaultBasename("index")
 196                            .description("Extra index groups"));
 197     options->addOption(SelectionFileOption("sf"));
 198
 199     // Add options for trajectory time control.
 200     options->addOption(DoubleOption("b").store(&impl_->startTime_).timeValue()
 201                            .description("First frame (%t) to read from trajectory"));
 202     options->addOption(DoubleOption("e").store(&impl_->endTime_).timeValue()
 203                            .description("Last frame (%t) to read from trajectory"));
 204     options->addOption(DoubleOption("dt").store(&impl_->deltaTime_).timeValue()
 205                            .description("Only use frame if t MOD dt == first time (%t)"));
 206
 207     // Add time unit option.
 208     settings.impl_->timeUnitManager.addTimeUnitOption(options, "tu");
 209
 210     // Add plot options.
 211     settings.impl_->plotSettings.addOptions(options);
 212
 213     // Add common options for trajectory processing.
 214     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
 215     {
 216         options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
 217                                .description("Make molecules whole for each frame"));
 218     }
 219     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
 220     {
 221         options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
 222                                .description("Use periodic boundary conditions for distance calculation"));
 223     }
 224 }
 225
 226
 227 void
 228 TrajectoryAnalysisRunnerCommon::scaleTimeOptions(Options *options)
 229 {
 230     impl_->settings_.impl_->timeUnitManager.scaleTimeOptions(options);
 231 }
 232
 233
 234 bool
 235 TrajectoryAnalysisRunnerCommon::optionsFinished(Options *options)
 236 {
 237     if (impl_->bHelp_)
 238     {
 239         return false;
 240     }
 241
 242     impl_->settings_.impl_->plotSettings.setTimeUnit(
 243             impl_->settings_.impl_->timeUnitManager.timeUnit());
 244
 245     if (impl_->trjfile_.empty() && impl_->topfile_.empty())
 246     {
 247         GMX_THROW(InconsistentInputError("No trajectory or topology provided, nothing to do!"));
 248     }
 249
 250     if (options->isSet("b"))
 251         setTimeValue(TBEGIN, impl_->startTime_);
 252     if (options->isSet("e"))
 253         setTimeValue(TEND, impl_->endTime_);
 254     if (options->isSet("dt"))
 255         setTimeValue(TDELTA, impl_->deltaTime_);
 256
 257     return true;
 258 }
 259
 260
 261 void
 262 TrajectoryAnalysisRunnerCommon::initIndexGroups(SelectionCollection *selections)
 263 {
 264     if (impl_->ndxfile_.empty())
 265     {
 266         // TODO: Initialize default selections
 267         selections->setIndexGroups(NULL);
 268     }
 269     else
 270     {
 271         gmx_ana_indexgrps_init(&impl_->grps_, NULL, impl_->ndxfile_.c_str());
 272         selections->setIndexGroups(impl_->grps_);
 273     }
 274 }
 275
 276
 277 void
 278 TrajectoryAnalysisRunnerCommon::doneIndexGroups(SelectionCollection *selections)
 279 {
 280     if (impl_->grps_ != NULL)
 281     {
 282         selections->setIndexGroups(NULL);
 283         gmx_ana_indexgrps_free(impl_->grps_);
 284         impl_->grps_ = NULL;
 285     }
 286 }
 287
 288
 289 void
 290 TrajectoryAnalysisRunnerCommon::initTopology(SelectionCollection *selections)
 291 {
 292     const TrajectoryAnalysisSettings &settings = impl_->settings_;
 293     bool bRequireTop
 294         = settings.hasFlag(TrajectoryAnalysisSettings::efRequireTop)
 295           || selections->requiresTopology();
 296     if (bRequireTop && impl_->topfile_.empty())
 297     {
 298         GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
 299     }
 300
 301     // Load the topology if requested.
 302     if (!impl_->topfile_.empty())
 303     {
 304         char  title[STRLEN];
 305
 306         snew(impl_->topInfo_.top_, 1);
 307         impl_->topInfo_.bTop_ = read_tps_conf(impl_->topfile_.c_str(), title,
 308                 impl_->topInfo_.top_, &impl_->topInfo_.ePBC_,
 309                 &impl_->topInfo_.xtop_, NULL, impl_->topInfo_.boxtop_, TRUE);
 310         if (hasTrajectory()
 311             && !settings.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
 312         {
 313             sfree(impl_->topInfo_.xtop_);
 314             impl_->topInfo_.xtop_ = NULL;
 315         }
 316     }
 317
 318     // Read the first frame if we don't know the maximum number of atoms
 319     // otherwise.
 320     int  natoms = -1;
 321     if (!impl_->topInfo_.hasTopology())
 322     {
 323         initFirstFrame();
 324         natoms = impl_->fr->natoms;
 325     }
 326     selections->setTopology(impl_->topInfo_.topology(), natoms);
 327
 328     /*
 329     if (impl_->bSelDump)
 330     {
 331         gmx_ana_poscalc_coll_print_tree(stderr, impl_->pcc);
 332         fprintf(stderr, "\n");
 333     }
 334     */
 335 }
 336
 337
 338 void
 339 TrajectoryAnalysisRunnerCommon::initFirstFrame()
 340 {
 341     // Return if we have already initialized the trajectory.
 342     if (impl_->fr)
 343     {
 344         return;
 345     }
 346     time_unit_t time_unit
 347         = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
 348     output_env_init(&impl_->oenv_, 0, NULL, time_unit, FALSE, exvgNONE, 0, 0);
 349
 350     int frflags = impl_->settings_.frflags();
 351     frflags |= TRX_NEED_X;
 352
 353     snew(impl_->fr, 1);
 354
 355     const TopologyInformation &top = impl_->topInfo_;
 356     if (hasTrajectory())
 357     {
 358         if (!read_first_frame(impl_->oenv_, &impl_->status_,
 359                               impl_->trjfile_.c_str(), impl_->fr, frflags))
 360         {
 361             GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
 362         }
 363         impl_->bTrajOpen_ = true;
 364
 365         if (top.hasTopology() && impl_->fr->natoms > top.topology()->atoms.nr)
 366         {
 367             GMX_THROW(InconsistentInputError(formatString(
 368                       "Trajectory (%d atoms) does not match topology (%d atoms)",
 369                       impl_->fr->natoms, top.topology()->atoms.nr)));
 370         }
 371         // Check index groups if they have been initialized based on the topology.
 372         /*
 373         if (top)
 374         {
 375             for (int i = 0; i < impl_->sel->nr(); ++i)
 376             {
 377                 gmx_ana_index_check(impl_->sel->sel(i)->indexGroup(),
 378                                     impl_->fr->natoms);
 379             }
 380         }
 381         */
 382     }
 383     else
 384     {
 385         // Prepare a frame from topology information.
 386         // TODO: Initialize more of the fields.
 387         if (frflags & (TRX_NEED_V))
 388         {
 389             GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
 390         }
 391         if (frflags & (TRX_NEED_F))
 392         {
 393             GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
 394         }
 395         impl_->fr->flags  = frflags;
 396         impl_->fr->natoms = top.topology()->atoms.nr;
 397         impl_->fr->bX     = TRUE;
 398         snew(impl_->fr->x, impl_->fr->natoms);
 399         memcpy(impl_->fr->x, top.xtop_,
 400                sizeof(*impl_->fr->x) * impl_->fr->natoms);
 401         impl_->fr->bBox   = TRUE;
 402         copy_mat(const_cast<rvec *>(top.boxtop_), impl_->fr->box);
 403     }
 404
 405     set_trxframe_ePBC(impl_->fr, top.ePBC());
 406     if (top.hasTopology() && impl_->settings_.hasRmPBC())
 407     {
 408         impl_->gpbc_ = gmx_rmpbc_init(&top.topology()->idef, top.ePBC(),
 409                                       impl_->fr->natoms, impl_->fr->box);
 410     }
 411 }
 412
 413
 414 bool
 415 TrajectoryAnalysisRunnerCommon::readNextFrame()
 416 {
 417     bool bContinue = false;
 418     if (hasTrajectory())
 419     {
 420         bContinue = read_next_frame(impl_->oenv_, impl_->status_, impl_->fr);
 421     }
 422     if (!bContinue)
 423     {
 424         impl_->finishTrajectory();
 425     }
 426     return bContinue;
 427 }
 428
 429
 430 void
 431 TrajectoryAnalysisRunnerCommon::initFrame()
 432 {
 433     if (impl_->gpbc_ != NULL)
 434     {
 435         gmx_rmpbc_trxfr(impl_->gpbc_, impl_->fr);
 436     }
 437 }
 438
 439
 440 TrajectoryAnalysisRunnerCommon::HelpFlags
 441 TrajectoryAnalysisRunnerCommon::helpFlags() const
 442 {
 443     HelpFlags flags = 0;
 444
 445     if (!impl_->bQuiet_)
 446     {
 447         flags |= efHelpShowOptions;
 448         if (impl_->bHelp_)
 449         {
 450             flags |= efHelpShowDescriptions;
 451         }
 452         if (impl_->bShowHidden_)
 453         {
 454             flags |= efHelpShowHidden;
 455         }
 456     }
 457     return flags;
 458 }
 459
 460 bool
 461 TrajectoryAnalysisRunnerCommon::hasTrajectory() const
 462 {
 463     return !impl_->trjfile_.empty();
 464 }
 465
 466
 467 const TopologyInformation &
 468 TrajectoryAnalysisRunnerCommon::topologyInformation() const
 469 {
 470     return impl_->topInfo_;
 471 }
 472
 473
 474 t_trxframe &
 475 TrajectoryAnalysisRunnerCommon::frame() const
 476 {
 477     GMX_RELEASE_ASSERT(impl_->fr != NULL, "Frame not available when accessed");
 478     return *impl_->fr;
 479 }
 480
 481 } // namespace gmx