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