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37 * Implements gmx::TrajectoryAnalysisCommandLineRunner.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_trajectoryanalysis
44 #include "cmdlinerunner.h"
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"
64 #include "runnercommon.h"
69 /********************************************************************
70 * TrajectoryAnalysisCommandLineRunner::Impl
73 class TrajectoryAnalysisCommandLineRunner::Impl
76 class RunnerCommandLineModule;
78 Impl(TrajectoryAnalysisModule *module);
81 void parseOptions(TrajectoryAnalysisSettings *settings,
82 TrajectoryAnalysisRunnerCommon *common,
83 SelectionCollection *selections,
84 int *argc, char *argv[], bool full=true);
86 TrajectoryAnalysisModule *module_;
87 bool bUseDefaultGroups_;
92 TrajectoryAnalysisCommandLineRunner::Impl::Impl(
93 TrajectoryAnalysisModule *module)
94 : module_(module), bUseDefaultGroups_(true), debugLevel_(0)
99 TrajectoryAnalysisCommandLineRunner::Impl::~Impl()
105 TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
106 TrajectoryAnalysisSettings *settings,
107 TrajectoryAnalysisRunnerCommon *common,
108 SelectionCollection *selections,
109 int *argc, char *argv[], bool full)
111 FileNameOptionManager fileoptManager;
112 SelectionOptionManager seloptManager(selections);
113 Options options(NULL, NULL);
115 options.addManager(&fileoptManager);
116 options.addManager(&seloptManager);
118 IOptionsContainer &commonOptions = options.addGroup();
120 IOptionsContainer &moduleOptions = options.addGroup();
122 module_->initOptions(&moduleOptions, settings);
124 common->initOptions(&commonOptions);
126 selections->initOptions(&commonOptions);
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);
138 common->optionsFinished();
140 module_->optionsFinished(settings);
142 common->initIndexGroups(selections, bUseDefaultGroups_);
144 const bool bInteractive = StandardInputStream::instance().isInteractive();
145 seloptManager.parseRequestedFromStdin(bInteractive);
147 common->doneIndexGroups(selections);
148 common->initTopology(selections);
150 selections->compile();
154 /********************************************************************
155 * TrajectoryAnalysisCommandLineRunner
158 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
159 TrajectoryAnalysisModule *module)
160 : impl_(new Impl(module))
165 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
171 TrajectoryAnalysisCommandLineRunner::setUseDefaultGroups(bool bUseDefaults)
173 impl_->bUseDefaultGroups_ = bUseDefaults;
178 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
180 impl_->debugLevel_ = debuglevel;
185 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
187 TrajectoryAnalysisModule *module = impl_->module_;
189 SelectionCollection selections;
190 selections.setDebugLevel(impl_->debugLevel_);
192 TrajectoryAnalysisSettings settings;
193 TrajectoryAnalysisRunnerCommon common(&settings);
195 impl_->parseOptions(&settings, &common, &selections, &argc, argv);
197 const TopologyInformation &topology = common.topologyInformation();
198 module->initAnalysis(settings, topology);
200 TrajectoryAnalysisModule::Batch batch = module->getBatch();
201 std::vector<SelectionCollection*> batchSelections;
202 std::vector<Impl*> impls;
203 for (size_t i = 0; i < batch.size(); i++) {
204 TrajectoryAnalysisModule *bmodule = batch[i];
205 batchSelections.push_back(new SelectionCollection());
206 impls.push_back(new Impl(bmodule));
207 std::vector<char*> modArgv = module->getArgv(i);
208 int modArgc = modArgv.size();
209 impls.back()->parseOptions(&settings, &common, batchSelections.back(), &modArgc, modArgv.data(), false);
211 batch[i]->initAnalysis(settings, topology);
215 common.initFirstFrame();
216 module->initAfterFirstFrame(settings, common.frame());
219 t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
222 AnalysisDataParallelOptions dataOptions;
223 TrajectoryAnalysisModuleDataPointer pdata(
224 module->startFrames(dataOptions, selections));
226 std::vector<AnalysisDataParallelOptions> batchOptions;
227 std::vector<TrajectoryAnalysisModuleDataPointer> batchDataPointers;
228 for (size_t i = 0; i < batch.size(); i++) {
229 batch[i]->initAfterFirstFrame(settings, common.frame());
231 batchOptions.push_back(AnalysisDataParallelOptions());
232 batchDataPointers.push_back(batch[i]->startFrames(
233 batchOptions.back(), *batchSelections[i]));
239 t_trxframe &frame = common.frame();
242 set_pbc(ppbc, topology.ePBC(), frame.box);
245 for (size_t i = 0; i < batch.size(); i++) {
246 batchSelections[i]->evaluate(&frame, ppbc);
247 batch[i]->analyzeFrame(nframes, frame, ppbc, batchDataPointers[i].get());
248 batch[i]->finishFrameSerial(nframes);
250 selections.evaluate(&frame, ppbc);
251 module->analyzeFrame(nframes, frame, ppbc, pdata.get());
252 module->finishFrameSerial(nframes);
256 while (common.readNextFrame());
257 for (size_t i = 0; i < batch.size(); i++) {
258 batch[i]->finishFrames(batchDataPointers[i].get());
259 if (batchDataPointers[i].get() != NULL) {
260 batchDataPointers[i]->finish();
262 batchDataPointers[i].reset();
265 module->finishFrames(pdata.get());
266 if (pdata.get() != NULL)
272 if (common.hasTrajectory())
274 fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
275 nframes, common.frame().time);
279 fprintf(stderr, "Analyzed topology coordinates\n");
282 // Restore the maximal groups for dynamic selections.
283 for (size_t i = 0; i < batch.size(); i++) {
284 batchSelections[i]->evaluateFinal(nframes);
285 batch[i]->finishAnalysis(nframes);
286 batch[i]->writeOutput();
288 delete batchSelections[i];
292 selections.evaluateFinal(nframes);
294 module->finishAnalysis(nframes);
295 module->writeOutput();
302 TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
304 // TODO: This method duplicates some code from run().
305 // See how to best refactor it to share the common code.
306 SelectionCollection selections;
307 TrajectoryAnalysisSettings settings;
308 TrajectoryAnalysisRunnerCommon common(&settings);
310 SelectionOptionManager seloptManager(&selections);
311 Options options(NULL, NULL);
313 options.addManager(&seloptManager);
314 IOptionsContainer &commonOptions = options.addGroup();
315 IOptionsContainer &moduleOptions = options.addGroup();
317 impl_->module_->initOptions(&moduleOptions, &settings);
318 common.initOptions(&commonOptions);
319 selections.initOptions(&commonOptions);
321 CommandLineHelpWriter(options)
322 .setHelpText(settings.helpText())
323 .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
329 * Command line module for a trajectory analysis module.
331 * \ingroup module_trajectoryanalysis
333 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
334 : public ICommandLineModule
338 * Constructs a module.
340 * \param[in] name Name for the module.
341 * \param[in] description One-line description for the module.
342 * \param[in] factory Factory method to create the analysis module.
344 * Does not throw. This is important for correct implementation of
347 RunnerCommandLineModule(const char *name, const char *description,
348 ModuleFactoryMethod factory)
349 : name_(name), description_(description), hasFunction_(true), factory_(factory), functor_(NULL)
354 * Overloaded constructor accepting a functor instead of function pointer.
356 RunnerCommandLineModule(const char *name, const char *description,
357 ModuleFactoryFunctor *factory)
358 : name_(name), description_(description), hasFunction_(false), factory_(NULL), functor_(factory)
362 virtual const char *name() const { return name_; }
363 virtual const char *shortDescription() const { return description_; };
365 virtual void init(CommandLineModuleSettings *settings);
366 virtual int run(int argc, char *argv[]);
367 virtual void writeHelp(const CommandLineHelpContext &context) const;
371 const char *description_;
373 ModuleFactoryMethod factory_;
374 ModuleFactoryFunctor *functor_;
376 GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
379 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
380 CommandLineModuleSettings * /*settings*/)
384 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
385 int argc, char *argv[])
387 TrajectoryAnalysisModulePointer module(hasFunction_? factory_() : (*functor_)());
388 TrajectoryAnalysisCommandLineRunner runner(module.get());
389 return runner.run(argc, argv);
392 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
393 const CommandLineHelpContext &context) const
395 TrajectoryAnalysisModulePointer module(hasFunction_? factory_() : (*functor_)());
396 TrajectoryAnalysisCommandLineRunner runner(module.get());
397 runner.writeHelp(context);
402 TrajectoryAnalysisCommandLineRunner::runAsMain(
403 int argc, char *argv[], ModuleFactoryMethod factory)
405 Impl::RunnerCommandLineModule module(NULL, NULL, factory);
406 return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
411 TrajectoryAnalysisCommandLineRunner::runAsMain(
412 int argc, char *argv[], ModuleFactoryFunctor *factory)
414 Impl::RunnerCommandLineModule module(NULL, NULL, factory);
415 return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
420 TrajectoryAnalysisCommandLineRunner::registerModule(
421 CommandLineModuleManager *manager, const char *name,
422 const char *description, ModuleFactoryMethod factory)
424 CommandLineModulePointer module(
425 new Impl::RunnerCommandLineModule(name, description, factory));
426 manager->addModule(move(module));