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     Options                moduleOptions(module_->name(), module_->description());
 115     Options                commonOptions("common", "Common analysis control");
 116     Options                selectionOptions("selection", "Common selection control");
 117
 118     options.addManager(&fileoptManager);
 119     options.addManager(&seloptManager);
 120     if (full) {
 121         options.addSubSection(&commonOptions);
 122     }
 123     options.addSubSection(&selectionOptions);
 124     options.addSubSection(&moduleOptions);
 125
 126     module_->initOptions(&moduleOptions, settings);
 127     if (full) {
 128         common->initOptions(&commonOptions);
 129     }
 130     selections->initOptions(&selectionOptions);
 131
 132     {
 133         CommandLineParser  parser(&options);
 134         // TODO: Print the help if user provides an invalid option?
 135         // Or just add a message advising the user to invoke the help?
 136         parser.parse(argc, argv);
 137         common->scaleTimeOptions(&options);
 138         options.finish();
 139     }
 140
 141     if (full) {
 142         common->optionsFinished(&commonOptions);
 143     }
 144     module_->optionsFinished(&moduleOptions, settings);
 145
 146     common->initIndexGroups(selections, bUseDefaultGroups_);
 147
 148     const bool bInteractive = StandardInputStream::instance().isInteractive();
 149     seloptManager.parseRequestedFromStdin(bInteractive);
 150
 151     common->doneIndexGroups(selections);
 152     common->initTopology(selections);
 153
 154     selections->compile();
 155 }
 156
 157
 158 /********************************************************************
 159  * TrajectoryAnalysisCommandLineRunner
 160  */
 161
 162 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
 163         TrajectoryAnalysisModule *module)
 164     : impl_(new Impl(module))
 165 {
 166 }
 167
 168
 169 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
 170 {
 171 }
 172
 173
 174 void
 175 TrajectoryAnalysisCommandLineRunner::setUseDefaultGroups(bool bUseDefaults)
 176 {
 177     impl_->bUseDefaultGroups_ = bUseDefaults;
 178 }
 179
 180
 181 void
 182 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
 183 {
 184     impl_->debugLevel_ = debuglevel;
 185 }
 186
 187
 188 int
 189 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
 190 {
 191     TrajectoryAnalysisModule *module = impl_->module_;
 192
 193     SelectionCollection       selections;
 194     selections.setDebugLevel(impl_->debugLevel_);
 195
 196     TrajectoryAnalysisSettings      settings;
 197     TrajectoryAnalysisRunnerCommon  common(&settings);
 198
 199     impl_->parseOptions(&settings, &common, &selections, &argc, argv);
 200
 201     const TopologyInformation &topology = common.topologyInformation();
 202     module->initAnalysis(settings, topology);
 203
 204     TrajectoryAnalysisModule::Batch batch = module->getBatch();
 205     std::vector<SelectionCollection*> batchSelections;
 206     std::vector<Impl*> impls;
 207     for (size_t i = 0; i < batch.size(); i++) {
 208         TrajectoryAnalysisModule *bmodule = batch[i];
 209         batchSelections.push_back(new SelectionCollection());
 210         impls.push_back(new Impl(bmodule));
 211         std::vector<char*> modArgv = module->getArgv(i);
 212         int modArgc = modArgv.size();
 213         impls.back()->parseOptions(&settings, &common, batchSelections.back(), &modArgc, modArgv.data(), false);
 214
 215         batch[i]->initAnalysis(settings, topology);
 216     }
 217
 218     // Load first frame.
 219     common.initFirstFrame();
 220     module->initAfterFirstFrame(settings, common.frame());
 221
 222     t_pbc  pbc;
 223     t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
 224
 225     int    nframes = 0;
 226     AnalysisDataParallelOptions         dataOptions;
 227     TrajectoryAnalysisModuleDataPointer pdata(
 228             module->startFrames(dataOptions, selections));
 229
 230     std::vector<AnalysisDataParallelOptions> batchOptions;
 231     std::vector<TrajectoryAnalysisModuleDataPointer> batchDataPointers;
 232     for (size_t i = 0; i < batch.size(); i++) {
 233         batch[i]->initAfterFirstFrame(settings, common.frame());
 234
 235         batchOptions.push_back(AnalysisDataParallelOptions());
 236         batchDataPointers.push_back(batch[i]->startFrames(
 237             batchOptions.back(), *batchSelections[i]));
 238     }
 239
 240     do
 241     {
 242         common.initFrame();
 243         t_trxframe &frame = common.frame();
 244         if (ppbc != NULL)
 245         {
 246             set_pbc(ppbc, topology.ePBC(), frame.box);
 247         }
 248
 249         for (size_t i = 0; i < batch.size(); i++) {
 250             batchSelections[i]->evaluate(&frame, ppbc);
 251             batch[i]->analyzeFrame(nframes, frame, ppbc, batchDataPointers[i].get());
 252             batch[i]->finishFrameSerial(nframes);
 253         }
 254         selections.evaluate(&frame, ppbc);
 255         module->analyzeFrame(nframes, frame, ppbc, pdata.get());
 256         module->finishFrameSerial(nframes);
 257
 258         ++nframes;
 259     }
 260     while (common.readNextFrame());
 261     for (size_t i = 0; i < batch.size(); i++) {
 262         batch[i]->finishFrames(batchDataPointers[i].get());
 263         if (batchDataPointers[i].get() != NULL) {
 264             batchDataPointers[i]->finish();
 265         }
 266         batchDataPointers[i].reset();
 267     }
 268
 269     module->finishFrames(pdata.get());
 270     if (pdata.get() != NULL)
 271     {
 272         pdata->finish();
 273     }
 274     pdata.reset();
 275
 276     if (common.hasTrajectory())
 277     {
 278         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 279                 nframes, common.frame().time);
 280     }
 281     else
 282     {
 283         fprintf(stderr, "Analyzed topology coordinates\n");
 284     }
 285
 286     // Restore the maximal groups for dynamic selections.
 287     for (size_t i = 0; i < batch.size(); i++) {
 288         batchSelections[i]->evaluateFinal(nframes);
 289         batch[i]->finishAnalysis(nframes);
 290         batch[i]->writeOutput();
 291
 292         delete batchSelections[i];
 293         delete impls[i];
 294     }
 295
 296     selections.evaluateFinal(nframes);
 297
 298     module->finishAnalysis(nframes);
 299     module->writeOutput();
 300
 301     return 0;
 302 }
 303
 304
 305 void
 306 TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
 307 {
 308     // TODO: This method duplicates some code from run().
 309     // See how to best refactor it to share the common code.
 310     SelectionCollection             selections;
 311     TrajectoryAnalysisSettings      settings;
 312     TrajectoryAnalysisRunnerCommon  common(&settings);
 313
 314     SelectionOptionManager          seloptManager(&selections);
 315     Options                         options(NULL, NULL);
 316     Options                         moduleOptions(impl_->module_->name(), impl_->module_->description());
 317     Options                         commonOptions("common", "Common analysis control");
 318     Options                         selectionOptions("selection", "Common selection control");
 319
 320     options.addManager(&seloptManager);
 321     options.addSubSection(&commonOptions);
 322     options.addSubSection(&selectionOptions);
 323     options.addSubSection(&moduleOptions);
 324
 325     impl_->module_->initOptions(&moduleOptions, &settings);
 326     common.initOptions(&commonOptions);
 327     selections.initOptions(&selectionOptions);
 328
 329     CommandLineHelpWriter(options)
 330         .setHelpText(settings.helpText())
 331         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 332         .writeHelp(context);
 333 }
 334
 335
 336 /*! \internal \brief
 337  * Command line module for a trajectory analysis module.
 338  *
 339  * \ingroup module_trajectoryanalysis
 340  */
 341 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
 342     : public ICommandLineModule
 343 {
 344     public:
 345         /*! \brief
 346          * Constructs a module.
 347          *
 348          * \param[in] name         Name for the module.
 349          * \param[in] description  One-line description for the module.
 350          * \param[in] factory      Factory method to create the analysis module.
 351          *
 352          * Does not throw.  This is important for correct implementation of
 353          * runAsMain().
 354          */
 355         RunnerCommandLineModule(const char *name, const char *description,
 356                                 ModuleFactoryMethod factory)
 357             : name_(name), description_(description), hasFunction_(true), factory_(factory), functor_(NULL)
 358         {
 359         }
 360
 361         /*! \brief
 362          * Overloaded constructor accepting a functor instead of function pointer.
 363          */
 364         RunnerCommandLineModule(const char *name, const char *description,
 365                                 ModuleFactoryFunctor *factory)
 366             : name_(name), description_(description), hasFunction_(false), factory_(NULL), functor_(factory)
 367         {
 368         }
 369
 370         virtual const char *name() const { return name_; }
 371         virtual const char *shortDescription() const { return description_; };
 372
 373         virtual void init(CommandLineModuleSettings *settings);
 374         virtual int run(int argc, char *argv[]);
 375         virtual void writeHelp(const CommandLineHelpContext &context) const;
 376
 377     private:
 378         const char            *name_;
 379         const char            *description_;
 380         bool                   hasFunction_;
 381         ModuleFactoryMethod    factory_;
 382         ModuleFactoryFunctor   *functor_;
 383
 384         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
 385 };
 386
 387 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
 388         CommandLineModuleSettings * /*settings*/)
 389 {
 390 }
 391
 392 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
 393         int argc, char *argv[])
 394 {
 395     TrajectoryAnalysisModulePointer     module(hasFunction_? factory_() : (*functor_)());
 396     TrajectoryAnalysisCommandLineRunner runner(module.get());
 397     return runner.run(argc, argv);
 398 }
 399
 400 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
 401         const CommandLineHelpContext &context) const
 402 {
 403     TrajectoryAnalysisModulePointer     module(hasFunction_? factory_() : (*functor_)());
 404     TrajectoryAnalysisCommandLineRunner runner(module.get());
 405     runner.writeHelp(context);
 406 }
 407
 408 // static
 409 int
 410 TrajectoryAnalysisCommandLineRunner::runAsMain(
 411         int argc, char *argv[], ModuleFactoryMethod factory)
 412 {
 413     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 414     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 415 }
 416
 417 // static
 418 int
 419 TrajectoryAnalysisCommandLineRunner::runAsMain(
 420         int argc, char *argv[], ModuleFactoryFunctor *factory)
 421 {
 422     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 423     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 424 }
 425
 426 // static
 427 void
 428 TrajectoryAnalysisCommandLineRunner::registerModule(
 429         CommandLineModuleManager *manager, const char *name,
 430         const char *description, ModuleFactoryMethod factory)
 431 {
 432     CommandLineModulePointer module(
 433             new Impl::RunnerCommandLineModule(name, description, factory));
 434     manager->addModule(move(module));
 435 }
 436
 437 } // namespace gmx