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