src/gromacs/trajectoryanalysis/runnercommon.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  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 "runnercommon.h"
  43
  44 #include "config.h"
  45
  46 #include <string.h>
  47
  48 #include "gromacs/legacyheaders/oenv.h"
  49
  50 #include "gromacs/fileio/timecontrol.h"
  51 #include "gromacs/fileio/tpxio.h"
  52 #include "gromacs/fileio/trx.h"
  53 #include "gromacs/fileio/trxio.h"
  54 #include "gromacs/math/vec.h"
  55 #include "gromacs/options/basicoptions.h"
  56 #include "gromacs/options/filenameoption.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/exceptions.h"
  65 #include "gromacs/utility/gmxassert.h"
  66 #include "gromacs/utility/programcontext.h"
  67 #include "gromacs/utility/smalloc.h"
  68 #include "gromacs/utility/stringutil.h"
  69
  70 #include "analysissettings-impl.h"
  71
  72 namespace gmx
  73 {
  74
  75 class TrajectoryAnalysisRunnerCommon::Impl
  76 {
  77     public:
  78         Impl(TrajectoryAnalysisSettings *settings);
  79         ~Impl();
  80
  81         void finishTrajectory();
  82
  83         TrajectoryAnalysisSettings &settings_;
  84         TopologyInformation         topInfo_;
  85
  86         //! Name of the trajectory file (empty if not provided).
  87         std::string                 trjfile_;
  88         //! Name of the topology file (empty if no topology provided).
  89         std::string                 topfile_;
  90         //! Name of the index file (empty if no index file provided).
  91         std::string                 ndxfile_;
  92         double                      startTime_;
  93         double                      endTime_;
  94         double                      deltaTime_;
  95
  96         gmx_ana_indexgrps_t        *grps_;
  97         bool                        bTrajOpen_;
  98         //! The current frame, or \p NULL if no frame loaded yet.
  99         t_trxframe                 *fr;
 100         gmx_rmpbc_t                 gpbc_;
 101         //! Used to store the status variable from read_first_frame().
 102         t_trxstatus                *status_;
 103         output_env_t                oenv_;
 104 };
 105
 106
 107 TrajectoryAnalysisRunnerCommon::Impl::Impl(TrajectoryAnalysisSettings *settings)
 108     : settings_(*settings),
 109       startTime_(0.0), endTime_(0.0), deltaTime_(0.0),
 110       grps_(NULL),
 111       bTrajOpen_(false), fr(NULL), gpbc_(NULL), status_(NULL), oenv_(NULL)
 112 {
 113 }
 114
 115
 116 TrajectoryAnalysisRunnerCommon::Impl::~Impl()
 117 {
 118     if (grps_ != NULL)
 119     {
 120         gmx_ana_indexgrps_free(grps_);
 121     }
 122     finishTrajectory();
 123     if (fr)
 124     {
 125         // There doesn't seem to be a function for freeing frame data
 126         sfree(fr->x);
 127         sfree(fr->v);
 128         sfree(fr->f);
 129         sfree(fr);
 130     }
 131     if (oenv_ != NULL)
 132     {
 133         output_env_done(oenv_);
 134     }
 135 }
 136
 137
 138 void
 139 TrajectoryAnalysisRunnerCommon::Impl::finishTrajectory()
 140 {
 141     if (bTrajOpen_)
 142     {
 143         close_trx(status_);
 144         bTrajOpen_ = false;
 145     }
 146     if (gpbc_ != NULL)
 147     {
 148         gmx_rmpbc_done(gpbc_);
 149         gpbc_ = NULL;
 150     }
 151 }
 152
 153 /*********************************************************************
 154  * TrajectoryAnalysisRunnerCommon
 155  */
 156
 157 TrajectoryAnalysisRunnerCommon::TrajectoryAnalysisRunnerCommon(
 158         TrajectoryAnalysisSettings *settings)
 159     : impl_(new Impl(settings))
 160 {
 161 }
 162
 163
 164 TrajectoryAnalysisRunnerCommon::~TrajectoryAnalysisRunnerCommon()
 165 {
 166 }
 167
 168
 169 void
 170 TrajectoryAnalysisRunnerCommon::initOptions(Options *options)
 171 {
 172     TrajectoryAnalysisSettings &settings = impl_->settings_;
 173
 174     // Add common file name arguments.
 175     options->addOption(FileNameOption("f")
 176                            .filetype(eftTrajectory).inputFile()
 177                            .store(&impl_->trjfile_)
 178                            .defaultBasename("traj")
 179                            .description("Input trajectory or single configuration"));
 180     options->addOption(FileNameOption("s")
 181                            .filetype(eftTopology).inputFile()
 182                            .store(&impl_->topfile_)
 183                            .defaultBasename("topol")
 184                            .description("Input structure"));
 185     options->addOption(FileNameOption("n")
 186                            .filetype(eftIndex).inputFile()
 187                            .store(&impl_->ndxfile_)
 188                            .defaultBasename("index")
 189                            .description("Extra index groups"));
 190
 191     // Add options for trajectory time control.
 192     options->addOption(DoubleOption("b").store(&impl_->startTime_).timeValue()
 193                            .description("First frame (%t) to read from trajectory"));
 194     options->addOption(DoubleOption("e").store(&impl_->endTime_).timeValue()
 195                            .description("Last frame (%t) to read from trajectory"));
 196     options->addOption(DoubleOption("dt").store(&impl_->deltaTime_).timeValue()
 197                            .description("Only use frame if t MOD dt == first time (%t)"));
 198
 199     // Add time unit option.
 200     settings.impl_->timeUnitManager.addTimeUnitOption(options, "tu");
 201
 202     // Add plot options.
 203     settings.impl_->plotSettings.addOptions(options);
 204
 205     // Add common options for trajectory processing.
 206     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
 207     {
 208         options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
 209                                .description("Make molecules whole for each frame"));
 210     }
 211     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
 212     {
 213         options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
 214                                .description("Use periodic boundary conditions for distance calculation"));
 215     }
 216
 217     options->addOption(SelectionFileOption("sf"));
 218 }
 219
 220
 221 void
 222 TrajectoryAnalysisRunnerCommon::scaleTimeOptions(Options *options)
 223 {
 224     impl_->settings_.impl_->timeUnitManager.scaleTimeOptions(options);
 225 }
 226
 227
 228 void
 229 TrajectoryAnalysisRunnerCommon::optionsFinished(Options *options)
 230 {
 231     impl_->settings_.impl_->plotSettings.setTimeUnit(
 232             impl_->settings_.impl_->timeUnitManager.timeUnit());
 233
 234     if (impl_->trjfile_.empty() && impl_->topfile_.empty())
 235     {
 236         GMX_THROW(InconsistentInputError("No trajectory or topology provided, nothing to do!"));
 237     }
 238
 239     if (options->isSet("b"))
 240     {
 241         setTimeValue(TBEGIN, impl_->startTime_);
 242     }
 243     if (options->isSet("e"))
 244     {
 245         setTimeValue(TEND, impl_->endTime_);
 246     }
 247     if (options->isSet("dt"))
 248     {
 249         setTimeValue(TDELTA, impl_->deltaTime_);
 250     }
 251 }
 252
 253
 254 void
 255 TrajectoryAnalysisRunnerCommon::initIndexGroups(SelectionCollection *selections,
 256                                                 bool                 bUseDefaults)
 257 {
 258     if (impl_->ndxfile_.empty())
 259     {
 260         if (!bUseDefaults)
 261         {
 262             selections->setIndexGroups(NULL);
 263             return;
 264         }
 265         initTopology(selections);
 266     }
 267     const char *const ndxfile
 268         = (!impl_->ndxfile_.empty() ? impl_->ndxfile_.c_str() : NULL);
 269     gmx_ana_indexgrps_init(&impl_->grps_, impl_->topInfo_.topology(), ndxfile);
 270     selections->setIndexGroups(impl_->grps_);
 271 }
 272
 273
 274 void
 275 TrajectoryAnalysisRunnerCommon::doneIndexGroups(SelectionCollection *selections)
 276 {
 277     if (impl_->grps_ != NULL)
 278     {
 279         selections->setIndexGroups(NULL);
 280         gmx_ana_indexgrps_free(impl_->grps_);
 281         impl_->grps_ = NULL;
 282     }
 283 }
 284
 285
 286 void
 287 TrajectoryAnalysisRunnerCommon::initTopology(SelectionCollection *selections)
 288 {
 289     // Return immediately if the topology has already been loaded.
 290     if (impl_->topInfo_.hasTopology())
 291     {
 292         return;
 293     }
 294
 295     const TrajectoryAnalysisSettings &settings = impl_->settings_;
 296     const bool bRequireTop
 297         = settings.hasFlag(TrajectoryAnalysisSettings::efRequireTop)
 298             || selections->requiresTopology();
 299     if (bRequireTop && impl_->topfile_.empty())
 300     {
 301         GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
 302     }
 303
 304     // Load the topology if requested.
 305     if (!impl_->topfile_.empty())
 306     {
 307         char  title[STRLEN];
 308
 309         snew(impl_->topInfo_.top_, 1);
 310         impl_->topInfo_.bTop_ = read_tps_conf(impl_->topfile_.c_str(), title,
 311                                               impl_->topInfo_.top_, &impl_->topInfo_.ePBC_,
 312                                               &impl_->topInfo_.xtop_, NULL, impl_->topInfo_.boxtop_, TRUE);
 313         if (hasTrajectory()
 314             && !settings.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
 315         {
 316             sfree(impl_->topInfo_.xtop_);
 317             impl_->topInfo_.xtop_ = NULL;
 318         }
 319     }
 320
 321     // Read the first frame if we don't know the maximum number of atoms
 322     // otherwise.
 323     int  natoms = -1;
 324     if (!impl_->topInfo_.hasTopology())
 325     {
 326         initFirstFrame();
 327         natoms = impl_->fr->natoms;
 328     }
 329     selections->setTopology(impl_->topInfo_.topology(), natoms);
 330
 331     /*
 332        if (impl_->bSelDump)
 333        {
 334         gmx_ana_poscalc_coll_print_tree(stderr, impl_->pcc);
 335         fprintf(stderr, "\n");
 336        }
 337      */
 338 }
 339
 340
 341 void
 342 TrajectoryAnalysisRunnerCommon::initFirstFrame()
 343 {
 344     // Return if we have already initialized the trajectory.
 345     if (impl_->fr)
 346     {
 347         return;
 348     }
 349     time_unit_t time_unit
 350         = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
 351     output_env_init(&impl_->oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
 352
 353     int frflags = impl_->settings_.frflags();
 354     frflags |= TRX_NEED_X;
 355
 356     snew(impl_->fr, 1);
 357
 358     const TopologyInformation &top = impl_->topInfo_;
 359     if (hasTrajectory())
 360     {
 361         if (!read_first_frame(impl_->oenv_, &impl_->status_,
 362                               impl_->trjfile_.c_str(), impl_->fr, frflags))
 363         {
 364             GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
 365         }
 366         impl_->bTrajOpen_ = true;
 367
 368         if (top.hasTopology() && impl_->fr->natoms > top.topology()->atoms.nr)
 369         {
 370             GMX_THROW(InconsistentInputError(formatString(
 371                                                      "Trajectory (%d atoms) does not match topology (%d atoms)",
 372                                                      impl_->fr->natoms, top.topology()->atoms.nr)));
 373         }
 374     }
 375     else
 376     {
 377         // Prepare a frame from topology information.
 378         // TODO: Initialize more of the fields.
 379         if (frflags & (TRX_NEED_V))
 380         {
 381             GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
 382         }
 383         if (frflags & (TRX_NEED_F))
 384         {
 385             GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
 386         }
 387         impl_->fr->flags  = frflags;
 388         impl_->fr->natoms = top.topology()->atoms.nr;
 389         impl_->fr->bX     = TRUE;
 390         snew(impl_->fr->x, impl_->fr->natoms);
 391         memcpy(impl_->fr->x, top.xtop_,
 392                sizeof(*impl_->fr->x) * impl_->fr->natoms);
 393         impl_->fr->bBox   = TRUE;
 394         copy_mat(const_cast<rvec *>(top.boxtop_), impl_->fr->box);
 395     }
 396
 397     set_trxframe_ePBC(impl_->fr, top.ePBC());
 398     if (top.hasTopology() && impl_->settings_.hasRmPBC())
 399     {
 400         impl_->gpbc_ = gmx_rmpbc_init(&top.topology()->idef, top.ePBC(),
 401                                       impl_->fr->natoms);
 402     }
 403 }
 404
 405
 406 bool
 407 TrajectoryAnalysisRunnerCommon::readNextFrame()
 408 {
 409     bool bContinue = false;
 410     if (hasTrajectory())
 411     {
 412         bContinue = read_next_frame(impl_->oenv_, impl_->status_, impl_->fr);
 413     }
 414     if (!bContinue)
 415     {
 416         impl_->finishTrajectory();
 417     }
 418     return bContinue;
 419 }
 420
 421
 422 void
 423 TrajectoryAnalysisRunnerCommon::initFrame()
 424 {
 425     if (impl_->gpbc_ != NULL)
 426     {
 427         gmx_rmpbc_trxfr(impl_->gpbc_, impl_->fr);
 428     }
 429 }
 430
 431
 432 bool
 433 TrajectoryAnalysisRunnerCommon::hasTrajectory() const
 434 {
 435     return !impl_->trjfile_.empty();
 436 }
 437
 438
 439 const TopologyInformation &
 440 TrajectoryAnalysisRunnerCommon::topologyInformation() const
 441 {
 442     return impl_->topInfo_;
 443 }
 444
 445
 446 t_trxframe &
 447 TrajectoryAnalysisRunnerCommon::frame() const
 448 {
 449     GMX_RELEASE_ASSERT(impl_->fr != NULL, "Frame not available when accessed");
 450     return *impl_->fr;
 451 }
 452
 453 } // namespace gmx