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/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     FileNameOptionManager  fileoptManager;
 111     SelectionOptionManager seloptManager(selections);
 112     Options                options(NULL, NULL);
 113     Options                moduleOptions(module_->name(), module_->description());
 114     Options                commonOptions("common", "Common analysis control");
 115     Options                selectionOptions("selection", "Common selection control");
 116
 117     options.addManager(&fileoptManager);
 118     options.addManager(&seloptManager);
 119     options.addSubSection(&commonOptions);
 120     options.addSubSection(&selectionOptions);
 121     options.addSubSection(&moduleOptions);
 122
 123     module_->initOptions(&moduleOptions, settings);
 124     common->initOptions(&commonOptions);
 125     selections->initOptions(&selectionOptions);
 126
 127     {
 128         CommandLineParser  parser(&options);
 129         // TODO: Print the help if user provides an invalid option?
 130         // Or just add a message advising the user to invoke the help?
 131         parser.parse(argc, argv);
 132         common->scaleTimeOptions(&options);
 133         options.finish();
 134     }
 135
 136     common->optionsFinished(&commonOptions);
 137     module_->optionsFinished(&moduleOptions, settings);
 138
 139     common->initIndexGroups(selections, bUseDefaultGroups_);
 140
 141     const bool bInteractive = File::standardInput().isInteractive();
 142     seloptManager.parseRequestedFromStdin(bInteractive);
 143     common->doneIndexGroups(selections);
 144
 145     common->initTopology(selections);
 146     selections->compile();
 147 }
 148
 149
 150 /********************************************************************
 151  * TrajectoryAnalysisCommandLineRunner
 152  */
 153
 154 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
 155         TrajectoryAnalysisModule *module)
 156     : impl_(new Impl(module))
 157 {
 158 }
 159
 160
 161 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
 162 {
 163 }
 164
 165
 166 void
 167 TrajectoryAnalysisCommandLineRunner::setUseDefaultGroups(bool bUseDefaults)
 168 {
 169     impl_->bUseDefaultGroups_ = bUseDefaults;
 170 }
 171
 172
 173 void
 174 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
 175 {
 176     impl_->debugLevel_ = debuglevel;
 177 }
 178
 179
 180 int
 181 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
 182 {
 183     TrajectoryAnalysisModule *module = impl_->module_;
 184
 185     SelectionCollection       selections;
 186     selections.setDebugLevel(impl_->debugLevel_);
 187
 188     TrajectoryAnalysisSettings      settings;
 189     TrajectoryAnalysisRunnerCommon  common(&settings);
 190
 191     impl_->parseOptions(&settings, &common, &selections, &argc, argv);
 192
 193     const TopologyInformation &topology = common.topologyInformation();
 194     module->initAnalysis(settings, topology);
 195
 196     // Load first frame.
 197     common.initFirstFrame();
 198     module->initAfterFirstFrame(settings, common.frame());
 199
 200     t_pbc  pbc;
 201     t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
 202
 203     int    nframes = 0;
 204     AnalysisDataParallelOptions         dataOptions;
 205     TrajectoryAnalysisModuleDataPointer pdata(
 206             module->startFrames(dataOptions, selections));
 207     do
 208     {
 209         common.initFrame();
 210         t_trxframe &frame = common.frame();
 211         if (ppbc != NULL)
 212         {
 213             set_pbc(ppbc, topology.ePBC(), frame.box);
 214         }
 215
 216         selections.evaluate(&frame, ppbc);
 217         module->analyzeFrame(nframes, frame, ppbc, pdata.get());
 218
 219         nframes++;
 220     }
 221     while (common.readNextFrame());
 222     module->finishFrames(pdata.get());
 223     if (pdata.get() != NULL)
 224     {
 225         pdata->finish();
 226     }
 227     pdata.reset();
 228
 229     if (common.hasTrajectory())
 230     {
 231         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 232                 nframes, common.frame().time);
 233     }
 234     else
 235     {
 236         fprintf(stderr, "Analyzed topology coordinates\n");
 237     }
 238
 239     // Restore the maximal groups for dynamic selections.
 240     selections.evaluateFinal(nframes);
 241
 242     module->finishAnalysis(nframes);
 243     module->writeOutput();
 244
 245     return 0;
 246 }
 247
 248
 249 void
 250 TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
 251 {
 252     // TODO: This method duplicates some code from run().
 253     // See how to best refactor it to share the common code.
 254     SelectionCollection             selections;
 255     TrajectoryAnalysisSettings      settings;
 256     TrajectoryAnalysisRunnerCommon  common(&settings);
 257
 258     SelectionOptionManager          seloptManager(&selections);
 259     Options                         options(NULL, NULL);
 260     Options                         moduleOptions(impl_->module_->name(), impl_->module_->description());
 261     Options                         commonOptions("common", "Common analysis control");
 262     Options                         selectionOptions("selection", "Common selection control");
 263
 264     options.addManager(&seloptManager);
 265     options.addSubSection(&commonOptions);
 266     options.addSubSection(&selectionOptions);
 267     options.addSubSection(&moduleOptions);
 268
 269     impl_->module_->initOptions(&moduleOptions, &settings);
 270     common.initOptions(&commonOptions);
 271     selections.initOptions(&selectionOptions);
 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 void init(CommandLineModuleSettings *settings);
 309         virtual int run(int argc, char *argv[]);
 310         virtual void writeHelp(const CommandLineHelpContext &context) const;
 311
 312     private:
 313         const char             *name_;
 314         const char             *description_;
 315         ModuleFactoryMethod     factory_;
 316
 317         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
 318 };
 319
 320 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
 321         CommandLineModuleSettings * /*settings*/)
 322 {
 323 }
 324
 325 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
 326         int argc, char *argv[])
 327 {
 328     TrajectoryAnalysisModulePointer     module(factory_());
 329     TrajectoryAnalysisCommandLineRunner runner(module.get());
 330     return runner.run(argc, argv);
 331 }
 332
 333 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
 334         const CommandLineHelpContext &context) const
 335 {
 336     TrajectoryAnalysisModulePointer     module(factory_());
 337     TrajectoryAnalysisCommandLineRunner runner(module.get());
 338     runner.writeHelp(context);
 339 }
 340
 341 // static
 342 int
 343 TrajectoryAnalysisCommandLineRunner::runAsMain(
 344         int argc, char *argv[], ModuleFactoryMethod factory)
 345 {
 346     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 347     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 348 }
 349
 350 // static
 351 void
 352 TrajectoryAnalysisCommandLineRunner::registerModule(
 353         CommandLineModuleManager *manager, const char *name,
 354         const char *description, ModuleFactoryMethod factory)
 355 {
 356     CommandLineModulePointer module(
 357             new Impl::RunnerCommandLineModule(name, description, factory));
 358     manager->addModule(move(module));
 359 }
 360
 361 } // namespace gmx