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37 * Implements gmx::TrajectoryAnalysisCommandLineRunner.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_trajectoryanalysis
44 #include "cmdlinerunner.h"
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/fileio/trx.h"
55 #include "gromacs/options/filenameoptionmanager.h"
56 #include "gromacs/options/options.h"
57 #include "gromacs/pbcutil/pbc.h"
58 #include "gromacs/selection/selectioncollection.h"
59 #include "gromacs/selection/selectionoptionmanager.h"
60 #include "gromacs/trajectoryanalysis/analysismodule.h"
61 #include "gromacs/trajectoryanalysis/analysissettings.h"
62 #include "gromacs/trajectoryanalysis/runnercommon.h"
63 #include "gromacs/utility/exceptions.h"
64 #include "gromacs/utility/file.h"
65 #include "gromacs/utility/gmxassert.h"
70 /********************************************************************
71 * TrajectoryAnalysisCommandLineRunner::Impl
74 class TrajectoryAnalysisCommandLineRunner::Impl
77 class RunnerCommandLineModule;
79 Impl(TrajectoryAnalysisModule *module);
82 void parseOptions(TrajectoryAnalysisSettings *settings,
83 TrajectoryAnalysisRunnerCommon *common,
84 SelectionCollection *selections,
85 int *argc, char *argv[]);
87 TrajectoryAnalysisModule *module_;
88 bool bUseDefaultGroups_;
93 TrajectoryAnalysisCommandLineRunner::Impl::Impl(
94 TrajectoryAnalysisModule *module)
95 : module_(module), bUseDefaultGroups_(true), debugLevel_(0)
100 TrajectoryAnalysisCommandLineRunner::Impl::~Impl()
106 TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
107 TrajectoryAnalysisSettings *settings,
108 TrajectoryAnalysisRunnerCommon *common,
109 SelectionCollection *selections,
110 int *argc, char *argv[])
112 FileNameOptionManager fileoptManager;
113 SelectionOptionManager seloptManager(selections);
114 Options options(NULL, NULL);
115 Options moduleOptions(module_->name(), module_->description());
116 Options commonOptions("common", "Common analysis control");
117 Options selectionOptions("selection", "Common selection control");
119 options.addManager(&fileoptManager);
120 options.addManager(&seloptManager);
121 options.addSubSection(&commonOptions);
122 options.addSubSection(&selectionOptions);
123 options.addSubSection(&moduleOptions);
125 module_->initOptions(&moduleOptions, settings);
126 common->initOptions(&commonOptions);
127 selections->initOptions(&selectionOptions);
130 CommandLineParser parser(&options);
131 // TODO: Print the help if user provides an invalid option?
132 // Or just add a message advising the user to invoke the help?
133 parser.parse(argc, argv);
134 common->scaleTimeOptions(&options);
138 common->optionsFinished(&commonOptions);
139 module_->optionsFinished(&moduleOptions, settings);
141 common->initIndexGroups(selections, bUseDefaultGroups_);
143 const bool bInteractive = File::standardInput().isInteractive();
144 seloptManager.parseRequestedFromStdin(bInteractive);
145 common->doneIndexGroups(selections);
147 common->initTopology(selections);
148 selections->compile();
152 /********************************************************************
153 * TrajectoryAnalysisCommandLineRunner
156 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
157 TrajectoryAnalysisModule *module)
158 : impl_(new Impl(module))
163 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
169 TrajectoryAnalysisCommandLineRunner::setUseDefaultGroups(bool bUseDefaults)
171 impl_->bUseDefaultGroups_ = bUseDefaults;
176 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
178 impl_->debugLevel_ = debuglevel;
183 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
185 TrajectoryAnalysisModule *module = impl_->module_;
187 SelectionCollection selections;
188 selections.setDebugLevel(impl_->debugLevel_);
190 TrajectoryAnalysisSettings settings;
191 TrajectoryAnalysisRunnerCommon common(&settings);
193 impl_->parseOptions(&settings, &common, &selections, &argc, argv);
195 const TopologyInformation &topology = common.topologyInformation();
196 module->initAnalysis(settings, topology);
199 common.initFirstFrame();
200 module->initAfterFirstFrame(settings, common.frame());
203 t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
206 AnalysisDataParallelOptions dataOptions;
207 TrajectoryAnalysisModuleDataPointer pdata(
208 module->startFrames(dataOptions, selections));
212 t_trxframe &frame = common.frame();
215 set_pbc(ppbc, topology.ePBC(), frame.box);
218 selections.evaluate(&frame, ppbc);
219 module->analyzeFrame(nframes, frame, ppbc, pdata.get());
223 while (common.readNextFrame());
224 module->finishFrames(pdata.get());
225 if (pdata.get() != NULL)
231 if (common.hasTrajectory())
233 fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
234 nframes, common.frame().time);
238 fprintf(stderr, "Analyzed topology coordinates\n");
241 // Restore the maximal groups for dynamic selections.
242 selections.evaluateFinal(nframes);
244 module->finishAnalysis(nframes);
245 module->writeOutput();
252 TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
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);
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");
266 options.addManager(&seloptManager);
267 options.addSubSection(&commonOptions);
268 options.addSubSection(&selectionOptions);
269 options.addSubSection(&moduleOptions);
271 impl_->module_->initOptions(&moduleOptions, &settings);
272 common.initOptions(&commonOptions);
273 selections.initOptions(&selectionOptions);
275 CommandLineHelpWriter(options)
276 .setShowDescriptions(true)
277 .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
283 * Command line module for a trajectory analysis module.
285 * \ingroup module_trajectoryanalysis
287 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
288 : public CommandLineModuleInterface
292 * Constructs a module.
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.
298 * Does not throw. This is important for correct implementation of
301 RunnerCommandLineModule(const char *name, const char *description,
302 ModuleFactoryMethod factory)
303 : name_(name), description_(description), factory_(factory)
307 virtual const char *name() const { return name_; }
308 virtual const char *shortDescription() const { return description_; };
310 virtual void init(CommandLineModuleSettings *settings);
311 virtual int run(int argc, char *argv[]);
312 virtual void writeHelp(const CommandLineHelpContext &context) const;
316 const char *description_;
317 ModuleFactoryMethod factory_;
319 GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
322 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
323 CommandLineModuleSettings * /*settings*/)
327 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
328 int argc, char *argv[])
330 TrajectoryAnalysisModulePointer module(factory_());
331 TrajectoryAnalysisCommandLineRunner runner(module.get());
332 return runner.run(argc, argv);
335 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
336 const CommandLineHelpContext &context) const
338 TrajectoryAnalysisModulePointer module(factory_());
339 TrajectoryAnalysisCommandLineRunner runner(module.get());
340 runner.writeHelp(context);
345 TrajectoryAnalysisCommandLineRunner::runAsMain(
346 int argc, char *argv[], ModuleFactoryMethod factory)
348 Impl::RunnerCommandLineModule module(NULL, NULL, factory);
349 return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
354 TrajectoryAnalysisCommandLineRunner::registerModule(
355 CommandLineModuleManager *manager, const char *name,
356 const char *description, ModuleFactoryMethod factory)
358 CommandLineModulePointer module(
359 new Impl::RunnerCommandLineModule(name, description, factory));
360 manager->addModule(move(module));