src/gromacs/trajectoryanalysis/cmdlinerunner.cpp

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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
 115     options.addManager(&fileoptManager);
 116     options.addManager(&seloptManager);
 117     if (full) {
 118             IOptionsContainer &commonOptions = options.addGroup();
 119     }
 120     IOptionsContainer &moduleOptions = options.addGroup();
 121
 122     module_->initOptions(&moduleOptions, settings);
 123     if (full) {
 124             common->initOptions(&commonOptions);
 125     }
 126     selections->initOptions(&commonOptions);
 127
 128     {
 129         CommandLineParser  parser(&options);
 130         // TODO: Print the help if user provides an invalid option?
 131         // Or just add a message advising the user to invoke the help?
 132         parser.parse(argc, argv);
 133         common->scaleTimeOptions(&options);
 134         options.finish();
 135     }
 136
 137     if (full) {
 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         TrajectoryAnalysisModule *bmodule = batch[i];
 205         batchSelections.push_back(new SelectionCollection());
 206         impls.push_back(new Impl(bmodule));
 207         std::vector<char*> modArgv = module->getArgv(i);
 208         int modArgc = modArgv.size();
 209         impls.back()->parseOptions(&settings, &common, batchSelections.back(), &modArgc, modArgv.data(), false);
 210
 211         batch[i]->initAnalysis(settings, topology);
 212     }
 213
 214     // Load first frame.
 215     common.initFirstFrame();
 216     module->initAfterFirstFrame(settings, common.frame());
 217
 218     t_pbc  pbc;
 219     t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
 220
 221     int    nframes = 0;
 222     AnalysisDataParallelOptions         dataOptions;
 223     TrajectoryAnalysisModuleDataPointer pdata(
 224             module->startFrames(dataOptions, selections));
 225
 226     std::vector<AnalysisDataParallelOptions> batchOptions;
 227     std::vector<TrajectoryAnalysisModuleDataPointer> batchDataPointers;
 228     for (size_t i = 0; i < batch.size(); i++) {
 229         batch[i]->initAfterFirstFrame(settings, common.frame());
 230
 231         batchOptions.push_back(AnalysisDataParallelOptions());
 232         batchDataPointers.push_back(batch[i]->startFrames(
 233             batchOptions.back(), *batchSelections[i]));
 234     }
 235
 236     do
 237     {
 238         common.initFrame();
 239         t_trxframe &frame = common.frame();
 240         if (ppbc != NULL)
 241         {
 242             set_pbc(ppbc, topology.ePBC(), frame.box);
 243         }
 244
 245         for (size_t i = 0; i < batch.size(); i++) {
 246             batchSelections[i]->evaluate(&frame, ppbc);
 247             batch[i]->analyzeFrame(nframes, frame, ppbc, batchDataPointers[i].get());
 248             batch[i]->finishFrameSerial(nframes);
 249         }
 250         selections.evaluate(&frame, ppbc);
 251         module->analyzeFrame(nframes, frame, ppbc, pdata.get());
 252         module->finishFrameSerial(nframes);
 253
 254         ++nframes;
 255     }
 256     while (common.readNextFrame());
 257     for (size_t i = 0; i < batch.size(); i++) {
 258         batch[i]->finishFrames(batchDataPointers[i].get());
 259         if (batchDataPointers[i].get() != NULL) {
 260             batchDataPointers[i]->finish();
 261         }
 262         batchDataPointers[i].reset();
 263     }
 264
 265     module->finishFrames(pdata.get());
 266     if (pdata.get() != NULL)
 267     {
 268         pdata->finish();
 269     }
 270     pdata.reset();
 271
 272     if (common.hasTrajectory())
 273     {
 274         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 275                 nframes, common.frame().time);
 276     }
 277     else
 278     {
 279         fprintf(stderr, "Analyzed topology coordinates\n");
 280     }
 281
 282     // Restore the maximal groups for dynamic selections.
 283     for (size_t i = 0; i < batch.size(); i++) {
 284         batchSelections[i]->evaluateFinal(nframes);
 285         batch[i]->finishAnalysis(nframes);
 286         batch[i]->writeOutput();
 287
 288         delete batchSelections[i];
 289         delete impls[i];
 290     }
 291
 292     selections.evaluateFinal(nframes);
 293
 294     module->finishAnalysis(nframes);
 295     module->writeOutput();
 296
 297     return 0;
 298 }
 299
 300
 301 void
 302 TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
 303 {
 304     // TODO: This method duplicates some code from run().
 305     // See how to best refactor it to share the common code.
 306     SelectionCollection             selections;
 307     TrajectoryAnalysisSettings      settings;
 308     TrajectoryAnalysisRunnerCommon  common(&settings);
 309
 310     SelectionOptionManager          seloptManager(&selections);
 311     Options                         options(NULL, NULL);
 312
 313     options.addManager(&seloptManager);
 314     IOptionsContainer &commonOptions = options.addGroup();
 315     IOptionsContainer &moduleOptions = options.addGroup();
 316
 317     impl_->module_->initOptions(&moduleOptions, &settings);
 318     common.initOptions(&commonOptions);
 319     selections.initOptions(&commonOptions);
 320
 321     CommandLineHelpWriter(options)
 322         .setHelpText(settings.helpText())
 323         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 324         .writeHelp(context);
 325 }
 326
 327
 328 /*! \internal \brief
 329  * Command line module for a trajectory analysis module.
 330  *
 331  * \ingroup module_trajectoryanalysis
 332  */
 333 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
 334     : public ICommandLineModule
 335 {
 336     public:
 337         /*! \brief
 338          * Constructs a module.
 339          *
 340          * \param[in] name         Name for the module.
 341          * \param[in] description  One-line description for the module.
 342          * \param[in] factory      Factory method to create the analysis module.
 343          *
 344          * Does not throw.  This is important for correct implementation of
 345          * runAsMain().
 346          */
 347         RunnerCommandLineModule(const char *name, const char *description,
 348                                 ModuleFactoryMethod factory)
 349             : name_(name), description_(description), hasFunction_(true), factory_(factory), functor_(NULL)
 350         {
 351         }
 352
 353         /*! \brief
 354          * Overloaded constructor accepting a functor instead of function pointer.
 355          */
 356         RunnerCommandLineModule(const char *name, const char *description,
 357                                 ModuleFactoryFunctor *factory)
 358             : name_(name), description_(description), hasFunction_(false), factory_(NULL), functor_(factory)
 359         {
 360         }
 361
 362         virtual const char *name() const { return name_; }
 363         virtual const char *shortDescription() const { return description_; };
 364
 365         virtual void init(CommandLineModuleSettings *settings);
 366         virtual int run(int argc, char *argv[]);
 367         virtual void writeHelp(const CommandLineHelpContext &context) const;
 368
 369     private:
 370         const char            *name_;
 371         const char            *description_;
 372         bool                   hasFunction_;
 373         ModuleFactoryMethod    factory_;
 374         ModuleFactoryFunctor   *functor_;
 375
 376         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
 377 };
 378
 379 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
 380         CommandLineModuleSettings * /*settings*/)
 381 {
 382 }
 383
 384 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
 385         int argc, char *argv[])
 386 {
 387     TrajectoryAnalysisModulePointer     module(hasFunction_? factory_() : (*functor_)());
 388     TrajectoryAnalysisCommandLineRunner runner(module.get());
 389     return runner.run(argc, argv);
 390 }
 391
 392 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
 393         const CommandLineHelpContext &context) const
 394 {
 395     TrajectoryAnalysisModulePointer     module(hasFunction_? factory_() : (*functor_)());
 396     TrajectoryAnalysisCommandLineRunner runner(module.get());
 397     runner.writeHelp(context);
 398 }
 399
 400 // static
 401 int
 402 TrajectoryAnalysisCommandLineRunner::runAsMain(
 403         int argc, char *argv[], ModuleFactoryMethod factory)
 404 {
 405     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 406     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 407 }
 408
 409 // static
 410 int
 411 TrajectoryAnalysisCommandLineRunner::runAsMain(
 412         int argc, char *argv[], ModuleFactoryFunctor *factory)
 413 {
 414     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 415     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 416 }
 417
 418 // static
 419 void
 420 TrajectoryAnalysisCommandLineRunner::registerModule(
 421         CommandLineModuleManager *manager, const char *name,
 422         const char *description, ModuleFactoryMethod factory)
 423 {
 424     CommandLineModulePointer module(
 425             new Impl::RunnerCommandLineModule(name, description, factory));
 426     manager->addModule(move(module));
 427 }
 428
 429 } // namespace gmx