src/gromacs/trajectoryanalysis/cmdlinerunner.cpp

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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         common->initOptions(&commonOptions);
 123     }
 124     selections->initOptions(&commonOptions);
 125
 126     {
 127         CommandLineParser  parser(&options);
 128         // TODO: Print the help if user provides an invalid option?
 129         // Or just add a message advising the user to invoke the help?
 130         parser.parse(argc, argv);
 131         common->scaleTimeOptions(&options);
 132         options.finish();
 133     }
 134
 135     if (full) {
 136         common->optionsFinished();
 137     }
 138     module_->optionsFinished(settings);
 139
 140     common->initIndexGroups(selections, bUseDefaultGroups_);
 141
 142     const bool bInteractive = StandardInputStream::instance().isInteractive();
 143     seloptManager.parseRequestedFromStdin(bInteractive);
 144
 145     common->doneIndexGroups(selections);
 146     common->initTopology(selections);
 147
 148     selections->compile();
 149 }
 150
 151
 152 /********************************************************************
 153  * TrajectoryAnalysisCommandLineRunner
 154  */
 155
 156 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
 157         TrajectoryAnalysisModule *module)
 158     : impl_(new Impl(module))
 159 {
 160 }
 161
 162
 163 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
 164 {
 165 }
 166
 167
 168 void
 169 TrajectoryAnalysisCommandLineRunner::setUseDefaultGroups(bool bUseDefaults)
 170 {
 171     impl_->bUseDefaultGroups_ = bUseDefaults;
 172 }
 173
 174
 175 void
 176 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
 177 {
 178     impl_->debugLevel_ = debuglevel;
 179 }
 180
 181
 182 int
 183 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
 184 {
 185     TrajectoryAnalysisModule *module = impl_->module_;
 186
 187     SelectionCollection       selections;
 188     selections.setDebugLevel(impl_->debugLevel_);
 189
 190     TrajectoryAnalysisSettings      settings;
 191     TrajectoryAnalysisRunnerCommon  common(&settings);
 192
 193     impl_->parseOptions(&settings, &common, &selections, &argc, argv);
 194
 195     const TopologyInformation &topology = common.topologyInformation();
 196     module->initAnalysis(settings, topology);
 197
 198     TrajectoryAnalysisModule::Batch batch = module->getBatch();
 199     std::vector<SelectionCollection*> batchSelections;
 200     std::vector<Impl*> impls;
 201     for (size_t i = 0; i < batch.size(); i++) {
 202         TrajectoryAnalysisModule *bmodule = batch[i];
 203         batchSelections.push_back(new SelectionCollection());
 204         impls.push_back(new Impl(bmodule));
 205         std::vector<char*> modArgv = module->getArgv(i);
 206         int modArgc = modArgv.size();
 207         impls.back()->parseOptions(&settings, &common, batchSelections.back(), &modArgc, modArgv.data(), false);
 208
 209         batch[i]->initAnalysis(settings, topology);
 210     }
 211
 212     // Load first frame.
 213     common.initFirstFrame();
 214     module->initAfterFirstFrame(settings, common.frame());
 215
 216     t_pbc  pbc;
 217     t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
 218
 219     int    nframes = 0;
 220     AnalysisDataParallelOptions         dataOptions;
 221     TrajectoryAnalysisModuleDataPointer pdata(
 222             module->startFrames(dataOptions, selections));
 223
 224     std::vector<AnalysisDataParallelOptions> batchOptions;
 225     std::vector<TrajectoryAnalysisModuleDataPointer> batchDataPointers;
 226     for (size_t i = 0; i < batch.size(); i++) {
 227         batch[i]->initAfterFirstFrame(settings, common.frame());
 228
 229         batchOptions.push_back(AnalysisDataParallelOptions());
 230         batchDataPointers.push_back(batch[i]->startFrames(
 231             batchOptions.back(), *batchSelections[i]));
 232     }
 233
 234     do
 235     {
 236         common.initFrame();
 237         t_trxframe &frame = common.frame();
 238         if (ppbc != NULL)
 239         {
 240             set_pbc(ppbc, topology.ePBC(), frame.box);
 241         }
 242
 243         for (size_t i = 0; i < batch.size(); i++) {
 244             batchSelections[i]->evaluate(&frame, ppbc);
 245             batch[i]->analyzeFrame(nframes, frame, ppbc, batchDataPointers[i].get());
 246             batch[i]->finishFrameSerial(nframes);
 247         }
 248         selections.evaluate(&frame, ppbc);
 249         module->analyzeFrame(nframes, frame, ppbc, pdata.get());
 250         module->finishFrameSerial(nframes);
 251
 252         ++nframes;
 253     }
 254     while (common.readNextFrame());
 255     for (size_t i = 0; i < batch.size(); i++) {
 256         batch[i]->finishFrames(batchDataPointers[i].get());
 257         if (batchDataPointers[i].get() != NULL) {
 258             batchDataPointers[i]->finish();
 259         }
 260         batchDataPointers[i].reset();
 261     }
 262
 263     module->finishFrames(pdata.get());
 264     if (pdata.get() != NULL)
 265     {
 266         pdata->finish();
 267     }
 268     pdata.reset();
 269
 270     if (common.hasTrajectory())
 271     {
 272         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 273                 nframes, common.frame().time);
 274     }
 275     else
 276     {
 277         fprintf(stderr, "Analyzed topology coordinates\n");
 278     }
 279
 280     // Restore the maximal groups for dynamic selections.
 281     for (size_t i = 0; i < batch.size(); i++) {
 282         batchSelections[i]->evaluateFinal(nframes);
 283         batch[i]->finishAnalysis(nframes);
 284         batch[i]->writeOutput();
 285
 286         delete batchSelections[i];
 287         delete impls[i];
 288     }
 289
 290     selections.evaluateFinal(nframes);
 291
 292     module->finishAnalysis(nframes);
 293     module->writeOutput();
 294
 295     return 0;
 296 }
 297
 298
 299 void
 300 TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
 301 {
 302     // TODO: This method duplicates some code from run().
 303     // See how to best refactor it to share the common code.
 304     SelectionCollection             selections;
 305     TrajectoryAnalysisSettings      settings;
 306     TrajectoryAnalysisRunnerCommon  common(&settings);
 307
 308     SelectionOptionManager          seloptManager(&selections);
 309     Options                         options(NULL, NULL);
 310
 311     options.addManager(&seloptManager);
 312     IOptionsContainer &commonOptions = options.addGroup();
 313     IOptionsContainer &moduleOptions = options.addGroup();
 314
 315     impl_->module_->initOptions(&moduleOptions, &settings);
 316     common.initOptions(&commonOptions);
 317     selections.initOptions(&commonOptions);
 318
 319     CommandLineHelpWriter(options)
 320         .setHelpText(settings.helpText())
 321         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 322         .writeHelp(context);
 323 }
 324
 325
 326 /*! \internal \brief
 327  * Command line module for a trajectory analysis module.
 328  *
 329  * \ingroup module_trajectoryanalysis
 330  */
 331 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
 332     : public ICommandLineModule
 333 {
 334     public:
 335         /*! \brief
 336          * Constructs a module.
 337          *
 338          * \param[in] name         Name for the module.
 339          * \param[in] description  One-line description for the module.
 340          * \param[in] factory      Factory method to create the analysis module.
 341          *
 342          * Does not throw.  This is important for correct implementation of
 343          * runAsMain().
 344          */
 345         RunnerCommandLineModule(const char *name, const char *description,
 346                                 ModuleFactoryMethod factory)
 347             : name_(name), description_(description), hasFunction_(true), factory_(factory), functor_(NULL)
 348         {
 349         }
 350
 351         /*! \brief
 352          * Overloaded constructor accepting a functor instead of function pointer.
 353          */
 354         RunnerCommandLineModule(const char *name, const char *description,
 355                                 ModuleFactoryFunctor *factory)
 356             : name_(name), description_(description), hasFunction_(false), factory_(NULL), functor_(factory)
 357         {
 358         }
 359
 360         virtual const char *name() const { return name_; }
 361         virtual const char *shortDescription() const { return description_; };
 362
 363         virtual void init(CommandLineModuleSettings *settings);
 364         virtual int run(int argc, char *argv[]);
 365         virtual void writeHelp(const CommandLineHelpContext &context) const;
 366
 367     private:
 368         const char            *name_;
 369         const char            *description_;
 370         bool                   hasFunction_;
 371         ModuleFactoryMethod    factory_;
 372         ModuleFactoryFunctor   *functor_;
 373
 374         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
 375 };
 376
 377 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
 378         CommandLineModuleSettings * /*settings*/)
 379 {
 380 }
 381
 382 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
 383         int argc, char *argv[])
 384 {
 385     TrajectoryAnalysisModulePointer     module(hasFunction_? factory_() : (*functor_)());
 386     TrajectoryAnalysisCommandLineRunner runner(module.get());
 387     return runner.run(argc, argv);
 388 }
 389
 390 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
 391         const CommandLineHelpContext &context) const
 392 {
 393     TrajectoryAnalysisModulePointer     module(hasFunction_? factory_() : (*functor_)());
 394     TrajectoryAnalysisCommandLineRunner runner(module.get());
 395     runner.writeHelp(context);
 396 }
 397
 398 // static
 399 int
 400 TrajectoryAnalysisCommandLineRunner::runAsMain(
 401         int argc, char *argv[], ModuleFactoryMethod factory)
 402 {
 403     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 404     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 405 }
 406
 407 // static
 408 int
 409 TrajectoryAnalysisCommandLineRunner::runAsMain(
 410         int argc, char *argv[], ModuleFactoryFunctor *factory)
 411 {
 412     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 413     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 414 }
 415
 416 // static
 417 void
 418 TrajectoryAnalysisCommandLineRunner::registerModule(
 419         CommandLineModuleManager *manager, const char *name,
 420         const char *description, ModuleFactoryMethod factory)
 421 {
 422     CommandLineModulePointer module(
 423             new Impl::RunnerCommandLineModule(name, description, factory));
 424     manager->addModule(move(module));
 425 }
 426
 427 } // namespace gmx