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 "cmdlinerunner.h"
  43
  44 #ifdef HAVE_CONFIG_H
  45 #include "config.h"
  46 #endif
  47
  48 #include "gromacs/legacyheaders/pbc.h"
  49 #include "gromacs/legacyheaders/rmpbc.h"
  50 #include "gromacs/legacyheaders/statutil.h"
  51
  52 #include "gromacs/analysisdata/paralleloptions.h"
  53 #include "gromacs/commandline/cmdlinehelpcontext.h"
  54 #include "gromacs/commandline/cmdlinehelpwriter.h"
  55 #include "gromacs/commandline/cmdlinemodule.h"
  56 #include "gromacs/commandline/cmdlinemodulemanager.h"
  57 #include "gromacs/commandline/cmdlineparser.h"
  58 #include "gromacs/onlinehelp/helpwritercontext.h"
  59 #include "gromacs/options/options.h"
  60 #include "gromacs/selection/selectioncollection.h"
  61 #include "gromacs/selection/selectionoptionmanager.h"
  62 #include "gromacs/trajectoryanalysis/analysismodule.h"
  63 #include "gromacs/trajectoryanalysis/analysissettings.h"
  64 #include "gromacs/trajectoryanalysis/runnercommon.h"
  65 #include "gromacs/utility/exceptions.h"
  66 #include "gromacs/utility/file.h"
  67 #include "gromacs/utility/gmxassert.h"
  68 #include "gromacs/utility/programinfo.h"
  69
  70 namespace gmx
  71 {
  72
  73 /********************************************************************
  74  * TrajectoryAnalysisCommandLineRunner::Impl
  75  */
  76
  77 class TrajectoryAnalysisCommandLineRunner::Impl
  78 {
  79     public:
  80         class RunnerCommandLineModule;
  81
  82         Impl(TrajectoryAnalysisModule *module);
  83         ~Impl();
  84
  85         void printHelp(const Options                        &options,
  86                        const TrajectoryAnalysisSettings     &settings,
  87                        const TrajectoryAnalysisRunnerCommon &common);
  88         bool parseOptions(TrajectoryAnalysisSettings *settings,
  89                           TrajectoryAnalysisRunnerCommon *common,
  90                           SelectionCollection *selections,
  91                           int *argc, char *argv[]);
  92
  93         TrajectoryAnalysisModule *module_;
  94         int                       debugLevel_;
  95 };
  96
  97
  98 TrajectoryAnalysisCommandLineRunner::Impl::Impl(
  99         TrajectoryAnalysisModule *module)
 100     : module_(module), debugLevel_(0)
 101 {
 102 }
 103
 104
 105 TrajectoryAnalysisCommandLineRunner::Impl::~Impl()
 106 {
 107 }
 108
 109
 110 void
 111 TrajectoryAnalysisCommandLineRunner::Impl::printHelp(
 112         const Options                        &options,
 113         const TrajectoryAnalysisSettings     &settings,
 114         const TrajectoryAnalysisRunnerCommon &common)
 115 {
 116     TrajectoryAnalysisRunnerCommon::HelpFlags flags = common.helpFlags();
 117     if (flags != 0)
 118     {
 119         CommandLineHelpContext context(&File::standardError(),
 120                                        eHelpOutputFormat_Console);
 121         CommandLineHelpWriter(options)
 122             .setShowDescriptions(flags & TrajectoryAnalysisRunnerCommon::efHelpShowDescriptions)
 123             .setShowHidden(flags & TrajectoryAnalysisRunnerCommon::efHelpShowHidden)
 124             .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 125             .writeHelp(context);
 126     }
 127 }
 128
 129
 130 bool
 131 TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
 132         TrajectoryAnalysisSettings *settings,
 133         TrajectoryAnalysisRunnerCommon *common,
 134         SelectionCollection *selections,
 135         int *argc, char *argv[])
 136 {
 137     Options options(NULL, NULL);
 138     Options moduleOptions(module_->name(), module_->description());
 139     Options commonOptions("common", "Common analysis control");
 140     Options selectionOptions("selection", "Common selection control");
 141     module_->initOptions(&moduleOptions, settings);
 142     common->initOptions(&commonOptions);
 143     selections->initOptions(&selectionOptions);
 144
 145     options.addSubSection(&commonOptions);
 146     options.addSubSection(&selectionOptions);
 147     options.addSubSection(&moduleOptions);
 148
 149     SelectionOptionManager seloptManager(selections);
 150     setManagerForSelectionOptions(&options, &seloptManager);
 151
 152     {
 153         CommandLineParser  parser(&options);
 154         try
 155         {
 156             parser.parse(argc, argv);
 157         }
 158         catch (const UserInputError &ex)
 159         {
 160             printHelp(options, *settings, *common);
 161             throw;
 162         }
 163         printHelp(options, *settings, *common);
 164         common->scaleTimeOptions(&options);
 165         options.finish();
 166     }
 167
 168     if (!common->optionsFinished(&commonOptions))
 169     {
 170         return false;
 171     }
 172     module_->optionsFinished(&moduleOptions, settings);
 173
 174     common->initIndexGroups(selections);
 175
 176     // TODO: Check whether the input is a pipe.
 177     bool bInteractive = true;
 178     seloptManager.parseRequestedFromStdin(bInteractive);
 179     common->doneIndexGroups(selections);
 180
 181     return true;
 182 }
 183
 184
 185 /********************************************************************
 186  * TrajectoryAnalysisCommandLineRunner
 187  */
 188
 189 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
 190         TrajectoryAnalysisModule *module)
 191     : impl_(new Impl(module))
 192 {
 193 }
 194
 195
 196 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
 197 {
 198 }
 199
 200
 201 void
 202 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
 203 {
 204     impl_->debugLevel_ = 1;
 205 }
 206
 207
 208 int
 209 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
 210 {
 211     TrajectoryAnalysisModule *module = impl_->module_;
 212
 213     SelectionCollection       selections;
 214     selections.setDebugLevel(impl_->debugLevel_);
 215
 216     TrajectoryAnalysisSettings      settings;
 217     TrajectoryAnalysisRunnerCommon  common(&settings);
 218
 219     if (!impl_->parseOptions(&settings, &common, &selections, &argc, argv))
 220     {
 221         return 0;
 222     }
 223
 224     common.initTopology(&selections);
 225     selections.compile();
 226
 227     const TopologyInformation &topology = common.topologyInformation();
 228     module->initAnalysis(settings, topology);
 229
 230     // Load first frame.
 231     common.initFirstFrame();
 232     module->initAfterFirstFrame(common.frame());
 233
 234     t_pbc  pbc;
 235     t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
 236
 237     int    nframes = 0;
 238     AnalysisDataParallelOptions         dataOptions;
 239     TrajectoryAnalysisModuleDataPointer pdata(
 240             module->startFrames(dataOptions, selections));
 241     do
 242     {
 243         common.initFrame();
 244         t_trxframe &frame = common.frame();
 245         if (ppbc != NULL)
 246         {
 247             set_pbc(ppbc, topology.ePBC(), frame.box);
 248         }
 249
 250         selections.evaluate(&frame, ppbc);
 251         module->analyzeFrame(nframes, frame, ppbc, pdata.get());
 252
 253         nframes++;
 254     }
 255     while (common.readNextFrame());
 256     module->finishFrames(pdata.get());
 257     if (pdata.get() != NULL)
 258     {
 259         pdata->finish();
 260     }
 261     pdata.reset();
 262
 263     if (common.hasTrajectory())
 264     {
 265         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 266                 nframes, common.frame().time);
 267     }
 268     else
 269     {
 270         fprintf(stderr, "Analyzed topology coordinates\n");
 271     }
 272
 273     // Restore the maximal groups for dynamic selections.
 274     selections.evaluateFinal(nframes);
 275
 276     module->finishAnalysis(nframes);
 277     module->writeOutput();
 278
 279     return 0;
 280 }
 281
 282
 283 void
 284 TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
 285 {
 286     // TODO: This method duplicates some code from run() and Impl::printHelp().
 287     // See how to best refactor it to share the common code.
 288     SelectionCollection             selections;
 289     TrajectoryAnalysisSettings      settings;
 290     TrajectoryAnalysisRunnerCommon  common(&settings);
 291
 292     Options options(NULL, NULL);
 293     Options moduleOptions(impl_->module_->name(), impl_->module_->description());
 294     Options commonOptions("common", "Common analysis control");
 295     Options selectionOptions("selection", "Common selection control");
 296
 297     impl_->module_->initOptions(&moduleOptions, &settings);
 298     common.initOptions(&commonOptions);
 299     selections.initOptions(&selectionOptions);
 300
 301     options.addSubSection(&commonOptions);
 302     options.addSubSection(&selectionOptions);
 303     options.addSubSection(&moduleOptions);
 304
 305     SelectionOptionManager seloptManager(&selections);
 306     setManagerForSelectionOptions(&options, &seloptManager);
 307
 308     CommandLineHelpWriter(options)
 309         .setShowDescriptions(true)
 310         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 311         .writeHelp(context);
 312 }
 313
 314
 315 /*! \internal \brief
 316  * Command line module for a trajectory analysis module.
 317  *
 318  * \ingroup module_trajectoryanalysis
 319  */
 320 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
 321     : public CommandLineModuleInterface
 322 {
 323     public:
 324         /*! \brief
 325          * Constructs a module.
 326          *
 327          * \param[in] name         Name for the module.
 328          * \param[in] description  One-line description for the module.
 329          * \param[in] factory      Factory method to create the analysis module.
 330          *
 331          * Does not throw.  This is important for correct implementation of
 332          * runAsMain().
 333          */
 334         RunnerCommandLineModule(const char *name, const char *description,
 335                                 ModuleFactoryMethod factory)
 336             : name_(name), description_(description), factory_(factory)
 337         {
 338         }
 339
 340         virtual const char *name() const { return name_; }
 341         virtual const char *shortDescription() const { return description_; };
 342
 343         virtual int run(int argc, char *argv[]);
 344         virtual void writeHelp(const CommandLineHelpContext &context) const;
 345
 346     private:
 347         const char             *name_;
 348         const char             *description_;
 349         ModuleFactoryMethod     factory_;
 350
 351         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
 352 };
 353
 354 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
 355         int argc, char *argv[])
 356 {
 357     TrajectoryAnalysisModulePointer     module(factory_());
 358     TrajectoryAnalysisCommandLineRunner runner(module.get());
 359     return runner.run(argc, argv);
 360 }
 361
 362 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
 363         const CommandLineHelpContext &context) const
 364 {
 365     // TODO: Implement #969.
 366     if (context.writerContext().outputFormat() != eHelpOutputFormat_Console)
 367     {
 368         return;
 369     }
 370     TrajectoryAnalysisModulePointer     module(factory_());
 371     TrajectoryAnalysisCommandLineRunner runner(module.get());
 372     runner.writeHelp(context);
 373 }
 374
 375 // static
 376 int
 377 TrajectoryAnalysisCommandLineRunner::runAsMain(
 378         int argc, char *argv[], ModuleFactoryMethod factory)
 379 {
 380     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 381     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 382 }
 383
 384 // static
 385 void
 386 TrajectoryAnalysisCommandLineRunner::registerModule(
 387         CommandLineModuleManager *manager, const char *name,
 388         const char *description, ModuleFactoryMethod factory)
 389 {
 390     CommandLineModulePointer module(
 391             new Impl::RunnerCommandLineModule(name, description, factory));
 392     manager->addModule(move(module));
 393 }
 394
 395 } // namespace gmx