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