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/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[]);
  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     FileNameOptionManager  fileoptManager;
 112     SelectionOptionManager seloptManager(selections);
 113     Options                options(NULL, NULL);
 114
 115     options.addManager(&fileoptManager);
 116     options.addManager(&seloptManager);
 117     IOptionsContainer &commonOptions = options.addGroup();
 118     IOptionsContainer &moduleOptions = options.addGroup();
 119
 120     module_->initOptions(&moduleOptions, settings);
 121     common->initOptions(&commonOptions);
 122     selections->initOptions(&commonOptions);
 123
 124     {
 125         CommandLineParser  parser(&options);
 126         // TODO: Print the help if user provides an invalid option?
 127         // Or just add a message advising the user to invoke the help?
 128         parser.parse(argc, argv);
 129         common->scaleTimeOptions(&options);
 130         options.finish();
 131     }
 132
 133     common->optionsFinished();
 134     module_->optionsFinished(settings);
 135
 136     common->initIndexGroups(selections, bUseDefaultGroups_);
 137
 138     const bool bInteractive = StandardInputStream::instance().isInteractive();
 139     seloptManager.parseRequestedFromStdin(bInteractive);
 140     common->doneIndexGroups(selections);
 141
 142     common->initTopology(selections);
 143     selections->compile();
 144 }
 145
 146
 147 /********************************************************************
 148  * TrajectoryAnalysisCommandLineRunner
 149  */
 150
 151 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
 152         TrajectoryAnalysisModule *module)
 153     : impl_(new Impl(module))
 154 {
 155 }
 156
 157
 158 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
 159 {
 160 }
 161
 162
 163 void
 164 TrajectoryAnalysisCommandLineRunner::setUseDefaultGroups(bool bUseDefaults)
 165 {
 166     impl_->bUseDefaultGroups_ = bUseDefaults;
 167 }
 168
 169
 170 void
 171 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
 172 {
 173     impl_->debugLevel_ = debuglevel;
 174 }
 175
 176
 177 int
 178 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
 179 {
 180     TrajectoryAnalysisModule *module = impl_->module_;
 181
 182     SelectionCollection       selections;
 183     selections.setDebugLevel(impl_->debugLevel_);
 184
 185     TrajectoryAnalysisSettings      settings;
 186     TrajectoryAnalysisRunnerCommon  common(&settings);
 187
 188     impl_->parseOptions(&settings, &common, &selections, &argc, argv);
 189
 190     const TopologyInformation &topology = common.topologyInformation();
 191     module->initAnalysis(settings, topology);
 192
 193     // Load first frame.
 194     common.initFirstFrame();
 195     module->initAfterFirstFrame(settings, common.frame());
 196
 197     t_pbc  pbc;
 198     t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
 199
 200     int    nframes = 0;
 201     AnalysisDataParallelOptions         dataOptions;
 202     TrajectoryAnalysisModuleDataPointer pdata(
 203             module->startFrames(dataOptions, selections));
 204     do
 205     {
 206         common.initFrame();
 207         t_trxframe &frame = common.frame();
 208         if (ppbc != NULL)
 209         {
 210             set_pbc(ppbc, topology.ePBC(), frame.box);
 211         }
 212
 213         selections.evaluate(&frame, ppbc);
 214         module->analyzeFrame(nframes, frame, ppbc, pdata.get());
 215         module->finishFrameSerial(nframes);
 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     SelectionOptionManager          seloptManager(&selections);
 257     Options                         options(NULL, NULL);
 258
 259     options.addManager(&seloptManager);
 260     IOptionsContainer &commonOptions = options.addGroup();
 261     IOptionsContainer &moduleOptions = options.addGroup();
 262
 263     impl_->module_->initOptions(&moduleOptions, &settings);
 264     common.initOptions(&commonOptions);
 265     selections.initOptions(&commonOptions);
 266
 267     CommandLineHelpWriter(options)
 268         .setHelpText(settings.helpText())
 269         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 270         .writeHelp(context);
 271 }
 272
 273
 274 /*! \internal \brief
 275  * Command line module for a trajectory analysis module.
 276  *
 277  * \ingroup module_trajectoryanalysis
 278  */
 279 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
 280     : public ICommandLineModule
 281 {
 282     public:
 283         /*! \brief
 284          * Constructs a module.
 285          *
 286          * \param[in] name         Name for the module.
 287          * \param[in] description  One-line description for the module.
 288          * \param[in] factory      Factory method to create the analysis module.
 289          *
 290          * Does not throw.  This is important for correct implementation of
 291          * runAsMain().
 292          */
 293         RunnerCommandLineModule(const char *name, const char *description,
 294                                 ModuleFactoryMethod factory)
 295             : name_(name), description_(description), factory_(factory)
 296         {
 297         }
 298
 299         virtual const char *name() const { return name_; }
 300         virtual const char *shortDescription() const { return description_; };
 301
 302         virtual void init(CommandLineModuleSettings *settings);
 303         virtual int run(int argc, char *argv[]);
 304         virtual void writeHelp(const CommandLineHelpContext &context) const;
 305
 306     private:
 307         const char             *name_;
 308         const char             *description_;
 309         ModuleFactoryMethod     factory_;
 310
 311         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
 312 };
 313
 314 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
 315         CommandLineModuleSettings * /*settings*/)
 316 {
 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