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/analysisdata/paralleloptions.h"
  49 #include "gromacs/commandline/cmdlinehelpcontext.h"
  50 #include "gromacs/commandline/cmdlinehelpwriter.h"
  51 #include "gromacs/commandline/cmdlinemodule.h"
  52 #include "gromacs/commandline/cmdlinemodulemanager.h"
  53 #include "gromacs/commandline/cmdlineparser.h"
  54 #include "gromacs/fileio/trx.h"
  55 #include "gromacs/options/options.h"
  56 #include "gromacs/pbcutil/pbc.h"
  57 #include "gromacs/selection/selectioncollection.h"
  58 #include "gromacs/selection/selectionoptionmanager.h"
  59 #include "gromacs/trajectoryanalysis/analysismodule.h"
  60 #include "gromacs/trajectoryanalysis/analysissettings.h"
  61 #include "gromacs/trajectoryanalysis/runnercommon.h"
  62 #include "gromacs/utility/exceptions.h"
  63 #include "gromacs/utility/file.h"
  64 #include "gromacs/utility/gmxassert.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[]);
  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[])
 110 {
 111     Options options(NULL, NULL);
 112     Options moduleOptions(module_->name(), module_->description());
 113     Options commonOptions("common", "Common analysis control");
 114     Options selectionOptions("selection", "Common selection control");
 115     module_->initOptions(&moduleOptions, settings);
 116     common->initOptions(&commonOptions);
 117     selections->initOptions(&selectionOptions);
 118
 119     options.addSubSection(&commonOptions);
 120     options.addSubSection(&selectionOptions);
 121     options.addSubSection(&moduleOptions);
 122
 123     SelectionOptionManager seloptManager(selections);
 124     setManagerForSelectionOptions(&options, &seloptManager);
 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     common->optionsFinished(&commonOptions);
 136     module_->optionsFinished(&moduleOptions, settings);
 137
 138     common->initIndexGroups(selections, bUseDefaultGroups_);
 139
 140     const bool bInteractive = File::standardInput().isInteractive();
 141     seloptManager.parseRequestedFromStdin(bInteractive);
 142     common->doneIndexGroups(selections);
 143
 144     common->initTopology(selections);
 145     selections->compile();
 146 }
 147
 148
 149 /********************************************************************
 150  * TrajectoryAnalysisCommandLineRunner
 151  */
 152
 153 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
 154         TrajectoryAnalysisModule *module)
 155     : impl_(new Impl(module))
 156 {
 157 }
 158
 159
 160 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
 161 {
 162 }
 163
 164
 165 void
 166 TrajectoryAnalysisCommandLineRunner::setUseDefaultGroups(bool bUseDefaults)
 167 {
 168     impl_->bUseDefaultGroups_ = bUseDefaults;
 169 }
 170
 171
 172 void
 173 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
 174 {
 175     impl_->debugLevel_ = debuglevel;
 176 }
 177
 178
 179 int
 180 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
 181 {
 182     TrajectoryAnalysisModule *module = impl_->module_;
 183
 184     SelectionCollection       selections;
 185     selections.setDebugLevel(impl_->debugLevel_);
 186
 187     TrajectoryAnalysisSettings      settings;
 188     TrajectoryAnalysisRunnerCommon  common(&settings);
 189
 190     impl_->parseOptions(&settings, &common, &selections, &argc, argv);
 191
 192     const TopologyInformation &topology = common.topologyInformation();
 193     module->initAnalysis(settings, topology);
 194
 195     // Load first frame.
 196     common.initFirstFrame();
 197     module->initAfterFirstFrame(common.frame());
 198
 199     t_pbc  pbc;
 200     t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
 201
 202     int    nframes = 0;
 203     AnalysisDataParallelOptions         dataOptions;
 204     TrajectoryAnalysisModuleDataPointer pdata(
 205             module->startFrames(dataOptions, selections));
 206     do
 207     {
 208         common.initFrame();
 209         t_trxframe &frame = common.frame();
 210         if (ppbc != NULL)
 211         {
 212             set_pbc(ppbc, topology.ePBC(), frame.box);
 213         }
 214
 215         selections.evaluate(&frame, ppbc);
 216         module->analyzeFrame(nframes, frame, ppbc, pdata.get());
 217
 218         nframes++;
 219     }
 220     while (common.readNextFrame());
 221     module->finishFrames(pdata.get());
 222     if (pdata.get() != NULL)
 223     {
 224         pdata->finish();
 225     }
 226     pdata.reset();
 227
 228     if (common.hasTrajectory())
 229     {
 230         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 231                 nframes, common.frame().time);
 232     }
 233     else
 234     {
 235         fprintf(stderr, "Analyzed topology coordinates\n");
 236     }
 237
 238     // Restore the maximal groups for dynamic selections.
 239     selections.evaluateFinal(nframes);
 240
 241     module->finishAnalysis(nframes);
 242     module->writeOutput();
 243
 244     return 0;
 245 }
 246
 247
 248 void
 249 TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
 250 {
 251     // TODO: This method duplicates some code from run().
 252     // See how to best refactor it to share the common code.
 253     SelectionCollection             selections;
 254     TrajectoryAnalysisSettings      settings;
 255     TrajectoryAnalysisRunnerCommon  common(&settings);
 256
 257     Options options(NULL, NULL);
 258     Options moduleOptions(impl_->module_->name(), impl_->module_->description());
 259     Options commonOptions("common", "Common analysis control");
 260     Options selectionOptions("selection", "Common selection control");
 261
 262     impl_->module_->initOptions(&moduleOptions, &settings);
 263     common.initOptions(&commonOptions);
 264     selections.initOptions(&selectionOptions);
 265
 266     options.addSubSection(&commonOptions);
 267     options.addSubSection(&selectionOptions);
 268     options.addSubSection(&moduleOptions);
 269
 270     SelectionOptionManager seloptManager(&selections);
 271     setManagerForSelectionOptions(&options, &seloptManager);
 272
 273     CommandLineHelpWriter(options)
 274         .setShowDescriptions(true)
 275         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 276         .writeHelp(context);
 277 }
 278
 279
 280 /*! \internal \brief
 281  * Command line module for a trajectory analysis module.
 282  *
 283  * \ingroup module_trajectoryanalysis
 284  */
 285 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
 286     : public CommandLineModuleInterface
 287 {
 288     public:
 289         /*! \brief
 290          * Constructs a module.
 291          *
 292          * \param[in] name         Name for the module.
 293          * \param[in] description  One-line description for the module.
 294          * \param[in] factory      Factory method to create the analysis module.
 295          *
 296          * Does not throw.  This is important for correct implementation of
 297          * runAsMain().
 298          */
 299         RunnerCommandLineModule(const char *name, const char *description,
 300                                 ModuleFactoryMethod factory)
 301             : name_(name), description_(description), factory_(factory)
 302         {
 303         }
 304
 305         virtual const char *name() const { return name_; }
 306         virtual const char *shortDescription() const { return description_; };
 307
 308         virtual int run(int argc, char *argv[]);
 309         virtual void writeHelp(const CommandLineHelpContext &context) const;
 310
 311     private:
 312         const char             *name_;
 313         const char             *description_;
 314         ModuleFactoryMethod     factory_;
 315
 316         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
 317 };
 318
 319 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
 320         int argc, char *argv[])
 321 {
 322     TrajectoryAnalysisModulePointer     module(factory_());
 323     TrajectoryAnalysisCommandLineRunner runner(module.get());
 324     return runner.run(argc, argv);
 325 }
 326
 327 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
 328         const CommandLineHelpContext &context) const
 329 {
 330     TrajectoryAnalysisModulePointer     module(factory_());
 331     TrajectoryAnalysisCommandLineRunner runner(module.get());
 332     runner.writeHelp(context);
 333 }
 334
 335 // static
 336 int
 337 TrajectoryAnalysisCommandLineRunner::runAsMain(
 338         int argc, char *argv[], ModuleFactoryMethod factory)
 339 {
 340     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 341     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 342 }
 343
 344 // static
 345 void
 346 TrajectoryAnalysisCommandLineRunner::registerModule(
 347         CommandLineModuleManager *manager, const char *name,
 348         const char *description, ModuleFactoryMethod factory)
 349 {
 350     CommandLineModulePointer module(
 351             new Impl::RunnerCommandLineModule(name, description, factory));
 352     manager->addModule(move(module));
 353 }
 354
 355 } // namespace gmx