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/file.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 = File::standardInput().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
 220         nframes++;
 221     }
 222     while (common.readNextFrame());
 223     module->finishFrames(pdata.get());
 224     if (pdata.get() != NULL)
 225     {
 226         pdata->finish();
 227     }
 228     pdata.reset();
 229
 230     if (common.hasTrajectory())
 231     {
 232         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 233                 nframes, common.frame().time);
 234     }
 235     else
 236     {
 237         fprintf(stderr, "Analyzed topology coordinates\n");
 238     }
 239
 240     // Restore the maximal groups for dynamic selections.
 241     selections.evaluateFinal(nframes);
 242
 243     module->finishAnalysis(nframes);
 244     module->writeOutput();
 245
 246     return 0;
 247 }
 248
 249
 250 void
 251 TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
 252 {
 253     // TODO: This method duplicates some code from run().
 254     // See how to best refactor it to share the common code.
 255     SelectionCollection             selections;
 256     TrajectoryAnalysisSettings      settings;
 257     TrajectoryAnalysisRunnerCommon  common(&settings);
 258
 259     SelectionOptionManager          seloptManager(&selections);
 260     Options                         options(NULL, NULL);
 261     Options                         moduleOptions(impl_->module_->name(), impl_->module_->description());
 262     Options                         commonOptions("common", "Common analysis control");
 263     Options                         selectionOptions("selection", "Common selection control");
 264
 265     options.addManager(&seloptManager);
 266     options.addSubSection(&commonOptions);
 267     options.addSubSection(&selectionOptions);
 268     options.addSubSection(&moduleOptions);
 269
 270     impl_->module_->initOptions(&moduleOptions, &settings);
 271     common.initOptions(&commonOptions);
 272     selections.initOptions(&selectionOptions);
 273
 274     CommandLineHelpWriter(options)
 275         .setShowDescriptions(true)
 276         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 277         .writeHelp(context);
 278 }
 279
 280
 281 /*! \internal \brief
 282  * Command line module for a trajectory analysis module.
 283  *
 284  * \ingroup module_trajectoryanalysis
 285  */
 286 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
 287     : public CommandLineModuleInterface
 288 {
 289     public:
 290         /*! \brief
 291          * Constructs a module.
 292          *
 293          * \param[in] name         Name for the module.
 294          * \param[in] description  One-line description for the module.
 295          * \param[in] factory      Factory method to create the analysis module.
 296          *
 297          * Does not throw.  This is important for correct implementation of
 298          * runAsMain().
 299          */
 300         RunnerCommandLineModule(const char *name, const char *description,
 301                                 ModuleFactoryMethod factory)
 302             : name_(name), description_(description), factory_(factory)
 303         {
 304         }
 305
 306         virtual const char *name() const { return name_; }
 307         virtual const char *shortDescription() const { return description_; };
 308
 309         virtual void init(CommandLineModuleSettings *settings);
 310         virtual int run(int argc, char *argv[]);
 311         virtual void writeHelp(const CommandLineHelpContext &context) const;
 312
 313     private:
 314         const char             *name_;
 315         const char             *description_;
 316         ModuleFactoryMethod     factory_;
 317
 318         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
 319 };
 320
 321 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
 322         CommandLineModuleSettings * /*settings*/)
 323 {
 324 }
 325
 326 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
 327         int argc, char *argv[])
 328 {
 329     TrajectoryAnalysisModulePointer     module(factory_());
 330     TrajectoryAnalysisCommandLineRunner runner(module.get());
 331     return runner.run(argc, argv);
 332 }
 333
 334 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
 335         const CommandLineHelpContext &context) const
 336 {
 337     TrajectoryAnalysisModulePointer     module(factory_());
 338     TrajectoryAnalysisCommandLineRunner runner(module.get());
 339     runner.writeHelp(context);
 340 }
 341
 342 // static
 343 int
 344 TrajectoryAnalysisCommandLineRunner::runAsMain(
 345         int argc, char *argv[], ModuleFactoryMethod factory)
 346 {
 347     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 348     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 349 }
 350
 351 // static
 352 void
 353 TrajectoryAnalysisCommandLineRunner::registerModule(
 354         CommandLineModuleManager *manager, const char *name,
 355         const char *description, ModuleFactoryMethod factory)
 356 {
 357     CommandLineModulePointer module(
 358             new Impl::RunnerCommandLineModule(name, description, factory));
 359     manager->addModule(move(module));
 360 }
 361
 362 } // namespace gmx