src/gromacs/trajectoryanalysis/runnercommon.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, 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 <algorithm>
  49 #include <string>
  50
  51 #include "gromacs/fileio/confio.h"
  52 #include "gromacs/fileio/oenv.h"
  53 #include "gromacs/fileio/timecontrol.h"
  54 #include "gromacs/fileio/trxio.h"
  55 #include "gromacs/math/vec.h"
  56 #include "gromacs/options/basicoptions.h"
  57 #include "gromacs/options/filenameoption.h"
  58 #include "gromacs/options/ioptionscontainer.h"
  59 #include "gromacs/pbcutil/rmpbc.h"
  60 #include "gromacs/selection/selection.h"
  61 #include "gromacs/selection/selectioncollection.h"
  62 #include "gromacs/selection/selectionoption.h"
  63 #include "gromacs/selection/selectionoptionbehavior.h"
  64 #include "gromacs/topology/topology.h"
  65 #include "gromacs/trajectory/trajectoryframe.h"
  66 #include "gromacs/trajectoryanalysis/analysissettings.h"
  67 #include "gromacs/utility/cstringutil.h"
  68 #include "gromacs/utility/exceptions.h"
  69 #include "gromacs/utility/gmxassert.h"
  70 #include "gromacs/utility/programcontext.h"
  71 #include "gromacs/utility/smalloc.h"
  72 #include "gromacs/utility/stringutil.h"
  73
  74 #include "analysissettings-impl.h"
  75
  76 namespace gmx
  77 {
  78
  79 class TrajectoryAnalysisRunnerCommon::Impl : public ITopologyProvider
  80 {
  81     public:
  82         explicit Impl(TrajectoryAnalysisSettings *settings);
  83         ~Impl();
  84
  85         bool hasTrajectory() const { return !trjfile_.empty(); }
  86
  87         void initTopology(bool required);
  88         void initFirstFrame();
  89         void initFrameIndexGroup();
  90         void finishTrajectory();
  91
  92         // From ITopologyProvider
  93         virtual t_topology *getTopology(bool required)
  94         {
  95             initTopology(required);
  96             return topInfo_.topology();
  97         }
  98         virtual int getAtomCount()
  99         {
 100             if (!topInfo_.hasTopology())
 101             {
 102                 if (trajectoryGroup_.isValid())
 103                 {
 104                     GMX_THROW(InconsistentInputError("-fgroup is only supported when -s is also specified"));
 105                 }
 106                 // Read the first frame if we don't know the maximum number of
 107                 // atoms otherwise.
 108                 initFirstFrame();
 109                 return fr->natoms;
 110             }
 111             return -1;
 112         }
 113
 114         TrajectoryAnalysisSettings &settings_;
 115         TopologyInformation         topInfo_;
 116
 117         //! Name of the trajectory file (empty if not provided).
 118         std::string                 trjfile_;
 119         //! Name of the topology file (empty if no topology provided).
 120         std::string                 topfile_;
 121         Selection                   trajectoryGroup_;
 122         double                      startTime_;
 123         double                      endTime_;
 124         double                      deltaTime_;
 125         bool                        bStartTimeSet_;
 126         bool                        bEndTimeSet_;
 127         bool                        bDeltaTimeSet_;
 128
 129         bool                        bTrajOpen_;
 130         //! The current frame, or \p NULL if no frame loaded yet.
 131         t_trxframe                 *fr;
 132         gmx_rmpbc_t                 gpbc_;
 133         //! Used to store the status variable from read_first_frame().
 134         t_trxstatus                *status_;
 135         gmx_output_env_t           *oenv_;
 136 };
 137
 138
 139 TrajectoryAnalysisRunnerCommon::Impl::Impl(TrajectoryAnalysisSettings *settings)
 140     : settings_(*settings),
 141       startTime_(0.0), endTime_(0.0), deltaTime_(0.0),
 142       bStartTimeSet_(false), bEndTimeSet_(false), bDeltaTimeSet_(false),
 143       bTrajOpen_(false), fr(NULL), gpbc_(NULL), status_(NULL), oenv_(NULL)
 144 {
 145 }
 146
 147
 148 TrajectoryAnalysisRunnerCommon::Impl::~Impl()
 149 {
 150     finishTrajectory();
 151     if (fr != nullptr)
 152     {
 153         // There doesn't seem to be a function for freeing frame data
 154         sfree(fr->x);
 155         sfree(fr->v);
 156         sfree(fr->f);
 157         sfree(fr->index);
 158         sfree(fr);
 159     }
 160     if (oenv_ != nullptr)
 161     {
 162         output_env_done(oenv_);
 163     }
 164 }
 165
 166 void
 167 TrajectoryAnalysisRunnerCommon::Impl::initTopology(bool required)
 168 {
 169     // Return immediately if the topology has already been loaded.
 170     if (topInfo_.hasTopology())
 171     {
 172         return;
 173     }
 174
 175     if (required && topfile_.empty())
 176     {
 177         GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
 178     }
 179
 180     // Load the topology if requested.
 181     if (!topfile_.empty())
 182     {
 183         snew(topInfo_.top_, 1);
 184         topInfo_.bTop_ = read_tps_conf(topfile_.c_str(), topInfo_.top_, &topInfo_.ePBC_,
 185                                        &topInfo_.xtop_, NULL, topInfo_.boxtop_, FALSE);
 186         if (!topInfo_.top_->atoms.haveMass)
 187         {
 188             // Try to read masses from database, be silent about missing masses
 189             atomsSetMassesBasedOnNames(&topInfo_.top_->atoms, FALSE);
 190         }
 191         if (hasTrajectory()
 192             && !settings_.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
 193         {
 194             sfree(topInfo_.xtop_);
 195             topInfo_.xtop_ = NULL;
 196         }
 197     }
 198 }
 199
 200 void
 201 TrajectoryAnalysisRunnerCommon::Impl::initFirstFrame()
 202 {
 203     // Return if we have already initialized the trajectory.
 204     if (fr != NULL)
 205     {
 206         return;
 207     }
 208     time_unit_t time_unit
 209         = static_cast<time_unit_t>(settings_.timeUnit() + 1);
 210     output_env_init(&oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
 211
 212     int frflags = settings_.frflags();
 213     frflags |= TRX_NEED_X;
 214
 215     snew(fr, 1);
 216
 217     if (hasTrajectory())
 218     {
 219         if (!read_first_frame(oenv_, &status_, trjfile_.c_str(), fr, frflags))
 220         {
 221             GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
 222         }
 223         bTrajOpen_ = true;
 224
 225         if (topInfo_.hasTopology())
 226         {
 227             const int topologyAtomCount = topInfo_.topology()->atoms.nr;
 228             if (fr->natoms > topologyAtomCount)
 229             {
 230                 const std::string message
 231                     = formatString("Trajectory (%d atoms) does not match topology (%d atoms)",
 232                                    fr->natoms, topologyAtomCount);
 233                 GMX_THROW(InconsistentInputError(message));
 234             }
 235         }
 236     }
 237     else
 238     {
 239         // Prepare a frame from topology information.
 240         // TODO: Initialize more of the fields.
 241         if (frflags & (TRX_NEED_V))
 242         {
 243             GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
 244         }
 245         if (frflags & (TRX_NEED_F))
 246         {
 247             GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
 248         }
 249         fr->natoms = topInfo_.topology()->atoms.nr;
 250         fr->bX     = TRUE;
 251         snew(fr->x, fr->natoms);
 252         memcpy(fr->x, topInfo_.xtop_,
 253                sizeof(*fr->x) * fr->natoms);
 254         fr->bBox   = TRUE;
 255         copy_mat(topInfo_.boxtop_, fr->box);
 256     }
 257
 258     set_trxframe_ePBC(fr, topInfo_.ePBC());
 259     if (topInfo_.hasTopology() && settings_.hasRmPBC())
 260     {
 261         gpbc_ = gmx_rmpbc_init(&topInfo_.topology()->idef, topInfo_.ePBC(),
 262                                fr->natoms);
 263     }
 264 }
 265
 266 void
 267 TrajectoryAnalysisRunnerCommon::Impl::initFrameIndexGroup()
 268 {
 269     if (!trajectoryGroup_.isValid())
 270     {
 271         return;
 272     }
 273     GMX_RELEASE_ASSERT(bTrajOpen_,
 274                        "Trajectory index only makes sense with a real trajectory");
 275     if (trajectoryGroup_.atomCount() != fr->natoms)
 276     {
 277         const std::string message = formatString(
 278                     "Selection specified with -fgroup has %d atoms, but "
 279                     "the trajectory (-f) has %d atoms.",
 280                     trajectoryGroup_.atomCount(), fr->natoms);
 281         GMX_THROW(InconsistentInputError(message));
 282     }
 283     fr->bIndex = TRUE;
 284     snew(fr->index, trajectoryGroup_.atomCount());
 285     std::copy(trajectoryGroup_.atomIndices().begin(),
 286               trajectoryGroup_.atomIndices().end(),
 287               fr->index);
 288 }
 289
 290 void
 291 TrajectoryAnalysisRunnerCommon::Impl::finishTrajectory()
 292 {
 293     if (bTrajOpen_)
 294     {
 295         close_trx(status_);
 296         bTrajOpen_ = false;
 297     }
 298     if (gpbc_ != NULL)
 299     {
 300         gmx_rmpbc_done(gpbc_);
 301         gpbc_ = NULL;
 302     }
 303 }
 304
 305 /*********************************************************************
 306  * TrajectoryAnalysisRunnerCommon
 307  */
 308
 309 TrajectoryAnalysisRunnerCommon::TrajectoryAnalysisRunnerCommon(
 310         TrajectoryAnalysisSettings *settings)
 311     : impl_(new Impl(settings))
 312 {
 313 }
 314
 315
 316 TrajectoryAnalysisRunnerCommon::~TrajectoryAnalysisRunnerCommon()
 317 {
 318 }
 319
 320
 321 ITopologyProvider *
 322 TrajectoryAnalysisRunnerCommon::topologyProvider()
 323 {
 324     return impl_.get();
 325 }
 326
 327
 328 void
 329 TrajectoryAnalysisRunnerCommon::initOptions(IOptionsContainer *options,
 330                                             TimeUnitBehavior  *timeUnitBehavior)
 331 {
 332     TrajectoryAnalysisSettings &settings = impl_->settings_;
 333
 334     // Add common file name arguments.
 335     options->addOption(FileNameOption("f")
 336                            .filetype(eftTrajectory).inputFile()
 337                            .store(&impl_->trjfile_)
 338                            .defaultBasename("traj")
 339                            .description("Input trajectory or single configuration"));
 340     options->addOption(FileNameOption("s")
 341                            .filetype(eftTopology).inputFile()
 342                            .store(&impl_->topfile_)
 343                            .defaultBasename("topol")
 344                            .description("Input structure"));
 345
 346     // Add options for trajectory time control.
 347     options->addOption(DoubleOption("b")
 348                            .store(&impl_->startTime_).storeIsSet(&impl_->bStartTimeSet_)
 349                            .timeValue()
 350                            .description("First frame (%t) to read from trajectory"));
 351     options->addOption(DoubleOption("e")
 352                            .store(&impl_->endTime_).storeIsSet(&impl_->bEndTimeSet_)
 353                            .timeValue()
 354                            .description("Last frame (%t) to read from trajectory"));
 355     options->addOption(DoubleOption("dt")
 356                            .store(&impl_->deltaTime_).storeIsSet(&impl_->bDeltaTimeSet_)
 357                            .timeValue()
 358                            .description("Only use frame if t MOD dt == first time (%t)"));
 359
 360     // Add time unit option.
 361     timeUnitBehavior->setTimeUnitFromEnvironment();
 362     timeUnitBehavior->addTimeUnitOption(options, "tu");
 363     timeUnitBehavior->setTimeUnitStore(&impl_->settings_.impl_->timeUnit);
 364
 365     options->addOption(SelectionOption("fgroup")
 366                            .store(&impl_->trajectoryGroup_)
 367                            .onlySortedAtoms().onlyStatic()
 368                            .description("Atoms stored in the trajectory file "
 369                                         "(if not set, assume first N atoms)"));
 370
 371     // Add plot options.
 372     settings.impl_->plotSettings.initOptions(options);
 373
 374     // Add common options for trajectory processing.
 375     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
 376     {
 377         options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
 378                                .description("Make molecules whole for each frame"));
 379     }
 380     if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
 381     {
 382         options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
 383                                .description("Use periodic boundary conditions for distance calculation"));
 384     }
 385 }
 386
 387
 388 void
 389 TrajectoryAnalysisRunnerCommon::optionsFinished()
 390 {
 391     if (impl_->trjfile_.empty() && impl_->topfile_.empty())
 392     {
 393         GMX_THROW(InconsistentInputError("No trajectory or topology provided, nothing to do!"));
 394     }
 395
 396     if (impl_->trajectoryGroup_.isValid() && impl_->trjfile_.empty())
 397     {
 398         GMX_THROW(InconsistentInputError("-fgroup only makes sense together with a trajectory (-f)"));
 399     }
 400
 401     impl_->settings_.impl_->plotSettings.setTimeUnit(impl_->settings_.timeUnit());
 402
 403     if (impl_->bStartTimeSet_)
 404     {
 405         setTimeValue(TBEGIN, impl_->startTime_);
 406     }
 407     if (impl_->bEndTimeSet_)
 408     {
 409         setTimeValue(TEND, impl_->endTime_);
 410     }
 411     if (impl_->bDeltaTimeSet_)
 412     {
 413         setTimeValue(TDELTA, impl_->deltaTime_);
 414     }
 415 }
 416
 417
 418 void
 419 TrajectoryAnalysisRunnerCommon::initTopology()
 420 {
 421     const bool topologyRequired =
 422         impl_->settings_.hasFlag(TrajectoryAnalysisSettings::efRequireTop);
 423     impl_->initTopology(topologyRequired);
 424 }
 425
 426
 427 void
 428 TrajectoryAnalysisRunnerCommon::initFirstFrame()
 429 {
 430     impl_->initFirstFrame();
 431 }
 432
 433
 434 void
 435 TrajectoryAnalysisRunnerCommon::initFrameIndexGroup()
 436 {
 437     impl_->initFrameIndexGroup();
 438 }
 439
 440
 441 bool
 442 TrajectoryAnalysisRunnerCommon::readNextFrame()
 443 {
 444     bool bContinue = false;
 445     if (hasTrajectory())
 446     {
 447         bContinue = read_next_frame(impl_->oenv_, impl_->status_, impl_->fr);
 448     }
 449     if (!bContinue)
 450     {
 451         impl_->finishTrajectory();
 452     }
 453     return bContinue;
 454 }
 455
 456
 457 void
 458 TrajectoryAnalysisRunnerCommon::initFrame()
 459 {
 460     if (impl_->gpbc_ != NULL)
 461     {
 462         gmx_rmpbc_trxfr(impl_->gpbc_, impl_->fr);
 463     }
 464 }
 465
 466
 467 bool
 468 TrajectoryAnalysisRunnerCommon::hasTrajectory() const
 469 {
 470     return impl_->hasTrajectory();
 471 }
 472
 473
 474 const TopologyInformation &
 475 TrajectoryAnalysisRunnerCommon::topologyInformation() const
 476 {
 477     return impl_->topInfo_;
 478 }
 479
 480
 481 t_trxframe &
 482 TrajectoryAnalysisRunnerCommon::frame() const
 483 {
 484     GMX_RELEASE_ASSERT(impl_->fr != NULL, "Frame not available when accessed");
 485     return *impl_->fr;
 486 }
 487
 488 } // namespace gmx