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