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     Options                moduleOptions(module_->name(), module_->description());
 115     Options                commonOptions("common", "Common analysis control");
 116     Options                selectionOptions("selection", "Common selection control");
 117
 118     options.addManager(&fileoptManager);
 119     options.addManager(&seloptManager);
 120     options.addSubSection(&commonOptions);
 121     options.addSubSection(&selectionOptions);
 122     options.addSubSection(&moduleOptions);
 123
 124     module_->initOptions(&moduleOptions, settings);
 125     common->initOptions(&commonOptions);
 126     selections->initOptions(&selectionOptions);
 127
 128     {
 129         CommandLineParser  parser(&options);
 130         // TODO: Print the help if user provides an invalid option?
 131         // Or just add a message advising the user to invoke the help?
 132         parser.parse(argc, argv);
 133         common->scaleTimeOptions(&options);
 134         options.finish();
 135     }
 136
 137     common->optionsFinished(&commonOptions);
 138     module_->optionsFinished(&moduleOptions, settings);
 139
 140     common->initIndexGroups(selections, bUseDefaultGroups_);
 141
 142     const bool bInteractive = StandardInputStream::instance().isInteractive();
 143     seloptManager.parseRequestedFromStdin(bInteractive);
 144     common->doneIndexGroups(selections);
 145
 146     common->initTopology(selections);
 147     selections->compile();
 148 }
 149
 150
 151 /********************************************************************
 152  * TrajectoryAnalysisCommandLineRunner
 153  */
 154
 155 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
 156         TrajectoryAnalysisModule *module)
 157     : impl_(new Impl(module))
 158 {
 159 }
 160
 161
 162 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
 163 {
 164 }
 165
 166
 167 void
 168 TrajectoryAnalysisCommandLineRunner::setUseDefaultGroups(bool bUseDefaults)
 169 {
 170     impl_->bUseDefaultGroups_ = bUseDefaults;
 171 }
 172
 173
 174 void
 175 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
 176 {
 177     impl_->debugLevel_ = debuglevel;
 178 }
 179
 180
 181 int
 182 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
 183 {
 184     TrajectoryAnalysisModule *module = impl_->module_;
 185
 186     SelectionCollection       selections;
 187     selections.setDebugLevel(impl_->debugLevel_);
 188
 189     TrajectoryAnalysisSettings      settings;
 190     TrajectoryAnalysisRunnerCommon  common(&settings);
 191
 192     impl_->parseOptions(&settings, &common, &selections, &argc, argv);
 193
 194     const TopologyInformation &topology = common.topologyInformation();
 195     module->initAnalysis(settings, topology);
 196
 197     // Load first frame.
 198     common.initFirstFrame();
 199     module->initAfterFirstFrame(settings, common.frame());
 200
 201     t_pbc  pbc;
 202     t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
 203
 204     int    nframes = 0;
 205     AnalysisDataParallelOptions         dataOptions;
 206     TrajectoryAnalysisModuleDataPointer pdata(
 207             module->startFrames(dataOptions, selections));
 208     do
 209     {
 210         common.initFrame();
 211         t_trxframe &frame = common.frame();
 212         if (ppbc != NULL)
 213         {
 214             set_pbc(ppbc, topology.ePBC(), frame.box);
 215         }
 216
 217         selections.evaluate(&frame, ppbc);
 218         module->analyzeFrame(nframes, frame, ppbc, pdata.get());
 219         module->finishFrameSerial(nframes);
 220
 221         ++nframes;
 222     }
 223     while (common.readNextFrame());
 224     module->finishFrames(pdata.get());
 225     if (pdata.get() != NULL)
 226     {
 227         pdata->finish();
 228     }
 229     pdata.reset();
 230
 231     if (common.hasTrajectory())
 232     {
 233         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 234                 nframes, common.frame().time);
 235     }
 236     else
 237     {
 238         fprintf(stderr, "Analyzed topology coordinates\n");
 239     }
 240
 241     // Restore the maximal groups for dynamic selections.
 242     selections.evaluateFinal(nframes);
 243
 244     module->finishAnalysis(nframes);
 245     module->writeOutput();
 246
 247     return 0;
 248 }
 249
 250
 251 void
 252 TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
 253 {
 254     // TODO: This method duplicates some code from run().
 255     // See how to best refactor it to share the common code.
 256     SelectionCollection             selections;
 257     TrajectoryAnalysisSettings      settings;
 258     TrajectoryAnalysisRunnerCommon  common(&settings);
 259
 260     SelectionOptionManager          seloptManager(&selections);
 261     Options                         options(NULL, NULL);
 262     Options                         moduleOptions(impl_->module_->name(), impl_->module_->description());
 263     Options                         commonOptions("common", "Common analysis control");
 264     Options                         selectionOptions("selection", "Common selection control");
 265
 266     options.addManager(&seloptManager);
 267     options.addSubSection(&commonOptions);
 268     options.addSubSection(&selectionOptions);
 269     options.addSubSection(&moduleOptions);
 270
 271     impl_->module_->initOptions(&moduleOptions, &settings);
 272     common.initOptions(&commonOptions);
 273     selections.initOptions(&selectionOptions);
 274
 275     CommandLineHelpWriter(options)
 276         .setShowDescriptions(true)
 277         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 278         .writeHelp(context);
 279 }
 280
 281
 282 /*! \internal \brief
 283  * Command line module for a trajectory analysis module.
 284  *
 285  * \ingroup module_trajectoryanalysis
 286  */
 287 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
 288     : public CommandLineModuleInterface
 289 {
 290     public:
 291         /*! \brief
 292          * Constructs a module.
 293          *
 294          * \param[in] name         Name for the module.
 295          * \param[in] description  One-line description for the module.
 296          * \param[in] factory      Factory method to create the analysis module.
 297          *
 298          * Does not throw.  This is important for correct implementation of
 299          * runAsMain().
 300          */
 301         RunnerCommandLineModule(const char *name, const char *description,
 302                                 ModuleFactoryMethod factory)
 303             : name_(name), description_(description), factory_(factory)
 304         {
 305         }
 306
 307         virtual const char *name() const { return name_; }
 308         virtual const char *shortDescription() const { return description_; };
 309
 310         virtual void init(CommandLineModuleSettings *settings);
 311         virtual int run(int argc, char *argv[]);
 312         virtual void writeHelp(const CommandLineHelpContext &context) const;
 313
 314     private:
 315         const char             *name_;
 316         const char             *description_;
 317         ModuleFactoryMethod     factory_;
 318
 319         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
 320 };
 321
 322 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
 323         CommandLineModuleSettings * /*settings*/)
 324 {
 325 }
 326
 327 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
 328         int argc, char *argv[])
 329 {
 330     TrajectoryAnalysisModulePointer     module(factory_());
 331     TrajectoryAnalysisCommandLineRunner runner(module.get());
 332     return runner.run(argc, argv);
 333 }
 334
 335 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
 336         const CommandLineHelpContext &context) const
 337 {
 338     TrajectoryAnalysisModulePointer     module(factory_());
 339     TrajectoryAnalysisCommandLineRunner runner(module.get());
 340     runner.writeHelp(context);
 341 }
 342
 343 // static
 344 int
 345 TrajectoryAnalysisCommandLineRunner::runAsMain(
 346         int argc, char *argv[], ModuleFactoryMethod factory)
 347 {
 348     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 349     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 350 }
 351
 352 // static
 353 void
 354 TrajectoryAnalysisCommandLineRunner::registerModule(
 355         CommandLineModuleManager *manager, const char *name,
 356         const char *description, ModuleFactoryMethod factory)
 357 {
 358     CommandLineModulePointer module(
 359             new Impl::RunnerCommandLineModule(name, description, factory));
 360     manager->addModule(move(module));
 361 }
 362
 363 } // namespace gmx