src/gromacs/trajectoryanalysis/runnercommon.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010,2011,2012,2013,2014,2015, 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 "gmxpre.h"
  43
  44 #include "runnercommon.h"
  45
  46 #include <string.h>
  47
  48 #include "gromacs/fileio/confio.h"
  49 #include "gromacs/fileio/timecontrol.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/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         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 {
 177     TrajectoryAnalysisSettings &settings = impl_->settings_;
 178
 179     // Add common file name arguments.
 180     options->addOption(FileNameOption("f")
 181                            .filetype(eftTrajectory).inputFile()
 182                            .store(&impl_->trjfile_)
 183                            .defaultBasename("traj")
 184                            .description("Input trajectory or single configuration"));
 185     options->addOption(FileNameOption("s")
 186                            .filetype(eftTopology).inputFile()
 187                            .store(&impl_->topfile_)
 188                            .defaultBasename("topol")
 189                            .description("Input structure"));
 190     options->addOption(FileNameOption("n")
 191                            .filetype(eftIndex).inputFile()
 192                            .store(&impl_->ndxfile_)
 193                            .defaultBasename("index")
 194                            .description("Extra index groups"));
 195
 196     // Add options for trajectory time control.
 197     options->addOption(DoubleOption("b")
 198                            .store(&impl_->startTime_).storeIsSet(&impl_->bStartTimeSet_)
 199                            .timeValue()
 200                            .description("First frame (%t) to read from trajectory"));
 201     options->addOption(DoubleOption("e")
 202                            .store(&impl_->endTime_).storeIsSet(&impl_->bEndTimeSet_)
 203                            .timeValue()
 204                            .description("Last frame (%t) to read from trajectory"));
 205     options->addOption(DoubleOption("dt")
 206                            .store(&impl_->deltaTime_).storeIsSet(&impl_->bDeltaTimeSet_)
 207                            .timeValue()
 208                            .description("Only use frame if t MOD dt == first time (%t)"));
 209
 210     // Add time unit option.
 211     settings.impl_->timeUnitManager.addTimeUnitOption(options, "tu");
 212
 213     // Add plot options.
 214     settings.impl_->plotSettings.initOptions(options);
 215
 216     // Add common options for trajectory processing.
 217     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
 218     {
 219         options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
 220                                .description("Make molecules whole for each frame"));
 221     }
 222     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
 223     {
 224         options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
 225                                .description("Use periodic boundary conditions for distance calculation"));
 226     }
 227
 228     options->addOption(SelectionFileOption("sf"));
 229 }
 230
 231
 232 void
 233 TrajectoryAnalysisRunnerCommon::scaleTimeOptions(Options *options)
 234 {
 235     impl_->settings_.impl_->timeUnitManager.scaleTimeOptions(options);
 236 }
 237
 238
 239 void
 240 TrajectoryAnalysisRunnerCommon::optionsFinished()
 241 {
 242     impl_->settings_.impl_->plotSettings.setTimeUnit(
 243             impl_->settings_.impl_->timeUnitManager.timeUnit());
 244
 245     if (impl_->trjfile_.empty() && impl_->topfile_.empty())
 246     {
 247         GMX_THROW(InconsistentInputError("No trajectory or topology provided, nothing to do!"));
 248     }
 249
 250     if (impl_->bStartTimeSet_)
 251     {
 252         setTimeValue(TBEGIN, impl_->startTime_);
 253     }
 254     if (impl_->bEndTimeSet_)
 255     {
 256         setTimeValue(TEND, impl_->endTime_);
 257     }
 258     if (impl_->bDeltaTimeSet_)
 259     {
 260         setTimeValue(TDELTA, impl_->deltaTime_);
 261     }
 262 }
 263
 264
 265 void
 266 TrajectoryAnalysisRunnerCommon::initIndexGroups(SelectionCollection *selections,
 267                                                 bool                 bUseDefaults)
 268 {
 269     if (impl_->ndxfile_.empty())
 270     {
 271         if (!bUseDefaults)
 272         {
 273             selections->setIndexGroups(NULL);
 274             return;
 275         }
 276         initTopology(selections);
 277     }
 278     const char *const ndxfile
 279         = (!impl_->ndxfile_.empty() ? impl_->ndxfile_.c_str() : NULL);
 280     gmx_ana_indexgrps_init(&impl_->grps_, impl_->topInfo_.topology(), ndxfile);
 281     selections->setIndexGroups(impl_->grps_);
 282 }
 283
 284
 285 void
 286 TrajectoryAnalysisRunnerCommon::doneIndexGroups(SelectionCollection *selections)
 287 {
 288     if (impl_->grps_ != NULL)
 289     {
 290         selections->setIndexGroups(NULL);
 291         gmx_ana_indexgrps_free(impl_->grps_);
 292         impl_->grps_ = NULL;
 293     }
 294 }
 295
 296
 297 void
 298 TrajectoryAnalysisRunnerCommon::initTopology(SelectionCollection *selections)
 299 {
 300     // Return immediately if the topology has already been loaded.
 301     if (impl_->topInfo_.hasTopology())
 302     {
 303         return;
 304     }
 305
 306     const TrajectoryAnalysisSettings &settings = impl_->settings_;
 307     const bool bRequireTop
 308         = settings.hasFlag(TrajectoryAnalysisSettings::efRequireTop)
 309             || selections->requiresTopology();
 310     if (bRequireTop && impl_->topfile_.empty())
 311     {
 312         GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
 313     }
 314
 315     // Load the topology if requested.
 316     if (!impl_->topfile_.empty())
 317     {
 318         char  title[STRLEN];
 319
 320         snew(impl_->topInfo_.top_, 1);
 321         impl_->topInfo_.bTop_ = read_tps_conf(impl_->topfile_.c_str(), title,
 322                                               impl_->topInfo_.top_, &impl_->topInfo_.ePBC_,
 323                                               &impl_->topInfo_.xtop_, NULL, impl_->topInfo_.boxtop_, TRUE);
 324         if (hasTrajectory()
 325             && !settings.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
 326         {
 327             sfree(impl_->topInfo_.xtop_);
 328             impl_->topInfo_.xtop_ = NULL;
 329         }
 330     }
 331
 332     // Read the first frame if we don't know the maximum number of atoms
 333     // otherwise.
 334     int  natoms = -1;
 335     if (!impl_->topInfo_.hasTopology())
 336     {
 337         initFirstFrame();
 338         natoms = impl_->fr->natoms;
 339     }
 340     selections->setTopology(impl_->topInfo_.topology(), natoms);
 341
 342     /*
 343        if (impl_->bSelDump)
 344        {
 345         gmx_ana_poscalc_coll_print_tree(stderr, impl_->pcc);
 346         fprintf(stderr, "\n");
 347        }
 348      */
 349 }
 350
 351
 352 void
 353 TrajectoryAnalysisRunnerCommon::initFirstFrame()
 354 {
 355     // Return if we have already initialized the trajectory.
 356     if (impl_->fr)
 357     {
 358         return;
 359     }
 360     time_unit_t time_unit
 361         = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
 362     output_env_init(&impl_->oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
 363
 364     int frflags = impl_->settings_.frflags();
 365     frflags |= TRX_NEED_X;
 366
 367     snew(impl_->fr, 1);
 368
 369     const TopologyInformation &top = impl_->topInfo_;
 370     if (hasTrajectory())
 371     {
 372         if (!read_first_frame(impl_->oenv_, &impl_->status_,
 373                               impl_->trjfile_.c_str(), impl_->fr, frflags))
 374         {
 375             GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
 376         }
 377         impl_->bTrajOpen_ = true;
 378
 379         if (top.hasTopology() && impl_->fr->natoms > top.topology()->atoms.nr)
 380         {
 381             GMX_THROW(InconsistentInputError(formatString(
 382                                                      "Trajectory (%d atoms) does not match topology (%d atoms)",
 383                                                      impl_->fr->natoms, top.topology()->atoms.nr)));
 384         }
 385     }
 386     else
 387     {
 388         // Prepare a frame from topology information.
 389         // TODO: Initialize more of the fields.
 390         if (frflags & (TRX_NEED_V))
 391         {
 392             GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
 393         }
 394         if (frflags & (TRX_NEED_F))
 395         {
 396             GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
 397         }
 398         impl_->fr->flags  = frflags;
 399         impl_->fr->natoms = top.topology()->atoms.nr;
 400         impl_->fr->bX     = TRUE;
 401         snew(impl_->fr->x, impl_->fr->natoms);
 402         memcpy(impl_->fr->x, top.xtop_,
 403                sizeof(*impl_->fr->x) * impl_->fr->natoms);
 404         impl_->fr->bBox   = TRUE;
 405         copy_mat(const_cast<rvec *>(top.boxtop_), impl_->fr->box);
 406     }
 407
 408     set_trxframe_ePBC(impl_->fr, top.ePBC());
 409     if (top.hasTopology() && impl_->settings_.hasRmPBC())
 410     {
 411         impl_->gpbc_ = gmx_rmpbc_init(&top.topology()->idef, top.ePBC(),
 412                                       impl_->fr->natoms);
 413     }
 414 }
 415
 416
 417 bool
 418 TrajectoryAnalysisRunnerCommon::readNextFrame()
 419 {
 420     bool bContinue = false;
 421     if (hasTrajectory())
 422     {
 423         bContinue = read_next_frame(impl_->oenv_, impl_->status_, impl_->fr);
 424     }
 425     if (!bContinue)
 426     {
 427         impl_->finishTrajectory();
 428     }
 429     return bContinue;
 430 }
 431
 432
 433 void
 434 TrajectoryAnalysisRunnerCommon::initFrame()
 435 {
 436     if (impl_->gpbc_ != NULL)
 437     {
 438         gmx_rmpbc_trxfr(impl_->gpbc_, impl_->fr);
 439     }
 440 }
 441
 442
 443 bool
 444 TrajectoryAnalysisRunnerCommon::hasTrajectory() const
 445 {
 446     return !impl_->trjfile_.empty();
 447 }
 448
 449
 450 const TopologyInformation &
 451 TrajectoryAnalysisRunnerCommon::topologyInformation() const
 452 {
 453     return impl_->topInfo_;
 454 }
 455
 456
 457 t_trxframe &
 458 TrajectoryAnalysisRunnerCommon::frame() const
 459 {
 460     GMX_RELEASE_ASSERT(impl_->fr != NULL, "Frame not available when accessed");
 461     return *impl_->fr;
 462 }
 463
 464 } // namespace gmx