src/gromacs/trajectoryanalysis/cmdlinerunner.cpp

   1 /*
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   4  * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
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  35 /*! \internal \file
  36  * \brief
  37  * Implements gmx::TrajectoryAnalysisCommandLineRunner.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_trajectoryanalysis
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "cmdlinerunner.h"
  45
  46 #include "gromacs/analysisdata/paralleloptions.h"
  47 #include "gromacs/commandline/cmdlinehelpcontext.h"
  48 #include "gromacs/commandline/cmdlinehelpwriter.h"
  49 #include "gromacs/commandline/cmdlinemodule.h"
  50 #include "gromacs/commandline/cmdlinemodulemanager.h"
  51 #include "gromacs/commandline/cmdlineparser.h"
  52 #include "gromacs/fileio/trx.h"
  53 #include "gromacs/options/filenameoptionmanager.h"
  54 #include "gromacs/options/options.h"
  55 #include "gromacs/pbcutil/pbc.h"
  56 #include "gromacs/selection/selectioncollection.h"
  57 #include "gromacs/selection/selectionoptionmanager.h"
  58 #include "gromacs/trajectoryanalysis/analysismodule.h"
  59 #include "gromacs/trajectoryanalysis/analysissettings.h"
  60 #include "gromacs/utility/exceptions.h"
  61 #include "gromacs/utility/filestream.h"
  62 #include "gromacs/utility/gmxassert.h"
  63
  64 #include "runnercommon.h"
  65
  66 namespace gmx
  67 {
  68
  69 /********************************************************************
  70  * TrajectoryAnalysisCommandLineRunner::Impl
  71  */
  72
  73 class TrajectoryAnalysisCommandLineRunner::Impl
  74 {
  75     public:
  76         class RunnerCommandLineModule;
  77
  78         Impl(TrajectoryAnalysisModule *module);
  79         ~Impl();
  80
  81         void parseOptions(TrajectoryAnalysisSettings *settings,
  82                           TrajectoryAnalysisRunnerCommon *common,
  83                           SelectionCollection *selections,
  84                           int *argc, char *argv[], bool full = true);
  85
  86         TrajectoryAnalysisModule *module_;
  87         bool                      bUseDefaultGroups_;
  88         int                       debugLevel_;
  89 };
  90
  91
  92 TrajectoryAnalysisCommandLineRunner::Impl::Impl(
  93         TrajectoryAnalysisModule *module)
  94     : module_(module), bUseDefaultGroups_(true), debugLevel_(0)
  95 {
  96 }
  97
  98
  99 TrajectoryAnalysisCommandLineRunner::Impl::~Impl()
 100 {
 101 }
 102
 103
 104 void
 105 TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
 106         TrajectoryAnalysisSettings *settings,
 107         TrajectoryAnalysisRunnerCommon *common,
 108         SelectionCollection *selections,
 109         int *argc, char *argv[], bool full)
 110 {
 111     FileNameOptionManager  fileoptManager;
 112     SelectionOptionManager seloptManager(selections);
 113     Options                options(NULL, NULL);
 114     IOptionsContainer     &commonOptions = options.addGroup();
 115     IOptionsContainer     &moduleOptions = options.addGroup();
 116
 117     options.addManager(&fileoptManager);
 118     options.addManager(&seloptManager);
 119
 120     module_->initOptions(&moduleOptions, settings);
 121     if (full)
 122     {
 123         common->initOptions(&commonOptions);
 124     }
 125     selections->initOptions(&commonOptions);
 126
 127     {
 128         CommandLineParser  parser(&options);
 129         // TODO: Print the help if user provides an invalid option?
 130         // Or just add a message advising the user to invoke the help?
 131         parser.parse(argc, argv);
 132         common->scaleTimeOptions(&options);
 133         options.finish();
 134     }
 135
 136     if (full)
 137     {
 138         common->optionsFinished();
 139     }
 140     module_->optionsFinished(settings);
 141
 142     common->initIndexGroups(selections, bUseDefaultGroups_);
 143
 144     const bool bInteractive = StandardInputStream::instance().isInteractive();
 145     seloptManager.parseRequestedFromStdin(bInteractive);
 146
 147     common->doneIndexGroups(selections);
 148     common->initTopology(selections);
 149
 150     selections->compile();
 151 }
 152
 153
 154 /********************************************************************
 155  * TrajectoryAnalysisCommandLineRunner
 156  */
 157
 158 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
 159         TrajectoryAnalysisModule *module)
 160     : impl_(new Impl(module))
 161 {
 162 }
 163
 164
 165 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
 166 {
 167 }
 168
 169
 170 void
 171 TrajectoryAnalysisCommandLineRunner::setUseDefaultGroups(bool bUseDefaults)
 172 {
 173     impl_->bUseDefaultGroups_ = bUseDefaults;
 174 }
 175
 176
 177 void
 178 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
 179 {
 180     impl_->debugLevel_ = debuglevel;
 181 }
 182
 183
 184 int
 185 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
 186 {
 187     TrajectoryAnalysisModule *module = impl_->module_;
 188
 189     SelectionCollection       selections;
 190     selections.setDebugLevel(impl_->debugLevel_);
 191
 192     TrajectoryAnalysisSettings      settings;
 193     TrajectoryAnalysisRunnerCommon  common(&settings);
 194
 195     impl_->parseOptions(&settings, &common, &selections, &argc, argv);
 196
 197     const TopologyInformation &topology = common.topologyInformation();
 198     module->initAnalysis(settings, topology);
 199
 200     TrajectoryAnalysisModule::Batch   batch = module->getBatch();
 201     std::vector<SelectionCollection*> batchSelections;
 202     std::vector<Impl*>                impls;
 203     for (size_t i = 0; i < batch.size(); i++)
 204     {
 205         TrajectoryAnalysisModule *bmodule = batch[i];
 206         batchSelections.push_back(new SelectionCollection());
 207         impls.push_back(new Impl(bmodule));
 208         std::vector<char*> modArgv = module->getArgv(i);
 209         int                modArgc = modArgv.size();
 210         impls.back()->parseOptions(&settings, &common, batchSelections.back(), &modArgc, modArgv.data(), false);
 211
 212         batch[i]->initAnalysis(settings, topology);
 213     }
 214
 215     // Load first frame.
 216     common.initFirstFrame();
 217     module->initAfterFirstFrame(settings, common.frame());
 218
 219     t_pbc  pbc;
 220     t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
 221
 222     int    nframes = 0;
 223     AnalysisDataParallelOptions         dataOptions;
 224     TrajectoryAnalysisModuleDataPointer pdata(
 225             module->startFrames(dataOptions, selections));
 226
 227     std::vector<AnalysisDataParallelOptions>         batchOptions;
 228     std::vector<TrajectoryAnalysisModuleDataPointer> batchDataPointers;
 229     for (size_t i = 0; i < batch.size(); i++)
 230     {
 231         batch[i]->initAfterFirstFrame(settings, common.frame());
 232
 233         batchOptions.push_back(AnalysisDataParallelOptions());
 234         batchDataPointers.push_back(batch[i]->startFrames(
 235                                             batchOptions.back(), *batchSelections[i]));
 236     }
 237
 238     do
 239     {
 240         common.initFrame();
 241         t_trxframe &frame = common.frame();
 242         if (ppbc != NULL)
 243         {
 244             set_pbc(ppbc, topology.ePBC(), frame.box);
 245         }
 246
 247         for (size_t i = 0; i < batch.size(); i++)
 248         {
 249             batchSelections[i]->evaluate(&frame, ppbc);
 250             batch[i]->analyzeFrame(nframes, frame, ppbc, batchDataPointers[i].get());
 251             batch[i]->finishFrameSerial(nframes);
 252         }
 253         selections.evaluate(&frame, ppbc);
 254         module->analyzeFrame(nframes, frame, ppbc, pdata.get());
 255         module->finishFrameSerial(nframes);
 256
 257         ++nframes;
 258     }
 259     while (common.readNextFrame());
 260     for (size_t i = 0; i < batch.size(); i++)
 261     {
 262         batch[i]->finishFrames(batchDataPointers[i].get());
 263         if (batchDataPointers[i].get() != NULL)
 264         {
 265             batchDataPointers[i]->finish();
 266         }
 267         batchDataPointers[i].reset();
 268     }
 269
 270     module->finishFrames(pdata.get());
 271     if (pdata.get() != NULL)
 272     {
 273         pdata->finish();
 274     }
 275     pdata.reset();
 276
 277     if (common.hasTrajectory())
 278     {
 279         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 280                 nframes, common.frame().time);
 281     }
 282     else
 283     {
 284         fprintf(stderr, "Analyzed topology coordinates\n");
 285     }
 286
 287     // Restore the maximal groups for dynamic selections.
 288     for (size_t i = 0; i < batch.size(); i++)
 289     {
 290         batchSelections[i]->evaluateFinal(nframes);
 291         batch[i]->finishAnalysis(nframes);
 292         batch[i]->writeOutput();
 293
 294         delete batchSelections[i];
 295         delete impls[i];
 296     }
 297
 298     selections.evaluateFinal(nframes);
 299
 300     module->finishAnalysis(nframes);
 301     module->writeOutput();
 302
 303     return 0;
 304 }
 305
 306
 307 void
 308 TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
 309 {
 310     // TODO: This method duplicates some code from run().
 311     // See how to best refactor it to share the common code.
 312     SelectionCollection             selections;
 313     TrajectoryAnalysisSettings      settings;
 314     TrajectoryAnalysisRunnerCommon  common(&settings);
 315
 316     SelectionOptionManager          seloptManager(&selections);
 317     Options                         options(NULL, NULL);
 318
 319     options.addManager(&seloptManager);
 320     IOptionsContainer &commonOptions = options.addGroup();
 321     IOptionsContainer &moduleOptions = options.addGroup();
 322
 323     impl_->module_->initOptions(&moduleOptions, &settings);
 324     common.initOptions(&commonOptions);
 325     selections.initOptions(&commonOptions);
 326
 327     CommandLineHelpWriter(options)
 328         .setHelpText(settings.helpText())
 329         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 330         .writeHelp(context);
 331 }
 332
 333
 334 /*! \internal \brief
 335  * Command line module for a trajectory analysis module.
 336  *
 337  * \ingroup module_trajectoryanalysis
 338  */
 339 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
 340     : public ICommandLineModule
 341 {
 342     public:
 343         /*! \brief
 344          * Constructs a module.
 345          *
 346          * \param[in] name         Name for the module.
 347          * \param[in] description  One-line description for the module.
 348          * \param[in] factory      Factory method to create the analysis module.
 349          *
 350          * Does not throw.  This is important for correct implementation of
 351          * runAsMain().
 352          */
 353         RunnerCommandLineModule(const char *name, const char *description,
 354                                 ModuleFactoryMethod factory)
 355             : name_(name), description_(description), hasFunction_(true), factory_(factory), functor_(NULL)
 356         {
 357         }
 358
 359         /*! \brief
 360          * Overloaded constructor accepting a functor instead of function pointer.
 361          */
 362         RunnerCommandLineModule(const char *name, const char *description,
 363                                 ModuleFactoryFunctor *factory)
 364             : name_(name), description_(description), hasFunction_(false), factory_(NULL), functor_(factory)
 365         {
 366         }
 367
 368         virtual const char *name() const { return name_; }
 369         virtual const char *shortDescription() const { return description_; };
 370
 371         virtual void init(CommandLineModuleSettings *settings);
 372         virtual int run(int argc, char *argv[]);
 373         virtual void writeHelp(const CommandLineHelpContext &context) const;
 374
 375     private:
 376         const char             *name_;
 377         const char             *description_;
 378         bool                    hasFunction_;
 379         ModuleFactoryMethod     factory_;
 380         ModuleFactoryFunctor   *functor_;
 381
 382         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
 383 };
 384
 385 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
 386         CommandLineModuleSettings * /*settings*/)
 387 {
 388 }
 389
 390 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
 391         int argc, char *argv[])
 392 {
 393     TrajectoryAnalysisModulePointer     module(hasFunction_ ? factory_() : (*functor_)());
 394     TrajectoryAnalysisCommandLineRunner runner(module.get());
 395     return runner.run(argc, argv);
 396 }
 397
 398 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
 399         const CommandLineHelpContext &context) const
 400 {
 401     TrajectoryAnalysisModulePointer     module(hasFunction_ ? factory_() : (*functor_)());
 402     TrajectoryAnalysisCommandLineRunner runner(module.get());
 403     runner.writeHelp(context);
 404 }
 405
 406 // static
 407 int
 408 TrajectoryAnalysisCommandLineRunner::runAsMain(
 409         int argc, char *argv[], ModuleFactoryMethod factory)
 410 {
 411     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 412     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 413 }
 414
 415 // static
 416 int
 417 TrajectoryAnalysisCommandLineRunner::runAsMain(
 418         int argc, char *argv[], ModuleFactoryFunctor *factory)
 419 {
 420     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 421     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 422 }
 423
 424 // static
 425 void
 426 TrajectoryAnalysisCommandLineRunner::registerModule(
 427         CommandLineModuleManager *manager, const char *name,
 428         const char *description, ModuleFactoryMethod factory)
 429 {
 430     CommandLineModulePointer module(
 431             new Impl::RunnerCommandLineModule(name, description, factory));
 432     manager->addModule(move(module));
 433 }
 434
 435 } // namespace gmx