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