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