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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/file.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);
114 Options moduleOptions(module_->name(), module_->description());
115 Options commonOptions("common", "Common analysis control");
116 Options selectionOptions("selection", "Common selection control");
118 options.addManager(&fileoptManager);
119 options.addManager(&seloptManager);
121 options.addSubSection(&commonOptions);
123 options.addSubSection(&selectionOptions);
124 options.addSubSection(&moduleOptions);
126 module_->initOptions(&moduleOptions, settings);
128 common->initOptions(&commonOptions);
130 selections->initOptions(&selectionOptions);
133 CommandLineParser parser(&options);
134 // TODO: Print the help if user provides an invalid option?
135 // Or just add a message advising the user to invoke the help?
136 parser.parse(argc, argv);
137 common->scaleTimeOptions(&options);
142 common->optionsFinished(&commonOptions);
144 module_->optionsFinished(&moduleOptions, settings);
146 common->initIndexGroups(selections, bUseDefaultGroups_);
148 const bool bInteractive = File::standardInput().isInteractive();
149 seloptManager.parseRequestedFromStdin(bInteractive);
151 common->doneIndexGroups(selections);
152 common->initTopology(selections);
154 selections->compile();
158 /********************************************************************
159 * TrajectoryAnalysisCommandLineRunner
162 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
163 TrajectoryAnalysisModule *module)
164 : impl_(new Impl(module))
169 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
175 TrajectoryAnalysisCommandLineRunner::setUseDefaultGroups(bool bUseDefaults)
177 impl_->bUseDefaultGroups_ = bUseDefaults;
182 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
184 impl_->debugLevel_ = debuglevel;
189 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
191 TrajectoryAnalysisModule *module = impl_->module_;
193 SelectionCollection selections;
194 selections.setDebugLevel(impl_->debugLevel_);
196 TrajectoryAnalysisSettings settings;
197 TrajectoryAnalysisRunnerCommon common(&settings);
199 impl_->parseOptions(&settings, &common, &selections, &argc, argv);
201 const TopologyInformation &topology = common.topologyInformation();
202 module->initAnalysis(settings, topology);
204 TrajectoryAnalysisModule::Batch batch = module->getBatch();
205 std::vector<SelectionCollection*> batchSelections;
206 std::vector<Impl*> impls;
207 for (size_t i = 0; i < batch.size(); i++) {
208 TrajectoryAnalysisModule *bmodule = batch[i];
209 batchSelections.push_back(new SelectionCollection());
210 impls.push_back(new Impl(bmodule));
211 std::vector<char*> modArgv = module->getArgv(i);
212 int modArgc = modArgv.size();
213 impls.back()->parseOptions(&settings, &common, batchSelections.back(), &modArgc, modArgv.data(), false);
215 batch[i]->initAnalysis(settings, topology);
219 common.initFirstFrame();
220 module->initAfterFirstFrame(settings, common.frame());
223 t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
226 AnalysisDataParallelOptions dataOptions;
227 TrajectoryAnalysisModuleDataPointer pdata(
228 module->startFrames(dataOptions, selections));
230 std::vector<AnalysisDataParallelOptions> batchOptions;
231 std::vector<TrajectoryAnalysisModuleDataPointer> batchDataPointers;
232 for (size_t i = 0; i < batch.size(); i++) {
233 batch[i]->initAfterFirstFrame(settings, common.frame());
235 batchOptions.push_back(AnalysisDataParallelOptions());
236 batchDataPointers.push_back(batch[i]->startFrames(
237 batchOptions.back(), *batchSelections[i]));
243 t_trxframe &frame = common.frame();
246 set_pbc(ppbc, topology.ePBC(), frame.box);
249 for (size_t i = 0; i < batch.size(); i++) {
250 batchSelections[i]->evaluate(&frame, ppbc);
251 batch[i]->analyzeFrame(nframes, frame, ppbc, batchDataPointers[i].get());
252 batch[i]->finishFrameSerial(nframes);
254 selections.evaluate(&frame, ppbc);
255 module->analyzeFrame(nframes, frame, ppbc, pdata.get());
256 module->finishFrameSerial(nframes);
260 while (common.readNextFrame());
261 for (size_t i = 0; i < batch.size(); i++) {
262 batch[i]->finishFrames(batchDataPointers[i].get());
263 if (batchDataPointers[i].get() != NULL) {
264 batchDataPointers[i]->finish();
266 batchDataPointers[i].reset();
269 module->finishFrames(pdata.get());
270 if (pdata.get() != NULL)
276 if (common.hasTrajectory())
278 fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
279 nframes, common.frame().time);
283 fprintf(stderr, "Analyzed topology coordinates\n");
286 // Restore the maximal groups for dynamic selections.
287 for (size_t i = 0; i < batch.size(); i++) {
288 batchSelections[i]->evaluateFinal(nframes);
289 batch[i]->finishAnalysis(nframes);
290 batch[i]->writeOutput();
292 delete batchSelections[i];
296 selections.evaluateFinal(nframes);
298 module->finishAnalysis(nframes);
299 module->writeOutput();
306 TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
308 // TODO: This method duplicates some code from run().
309 // See how to best refactor it to share the common code.
310 SelectionCollection selections;
311 TrajectoryAnalysisSettings settings;
312 TrajectoryAnalysisRunnerCommon common(&settings);
314 SelectionOptionManager seloptManager(&selections);
315 Options options(NULL, NULL);
316 Options moduleOptions(impl_->module_->name(), impl_->module_->description());
317 Options commonOptions("common", "Common analysis control");
318 Options selectionOptions("selection", "Common selection control");
320 options.addManager(&seloptManager);
321 options.addSubSection(&commonOptions);
322 options.addSubSection(&selectionOptions);
323 options.addSubSection(&moduleOptions);
325 impl_->module_->initOptions(&moduleOptions, &settings);
326 common.initOptions(&commonOptions);
327 selections.initOptions(&selectionOptions);
329 CommandLineHelpWriter(options)
330 .setShowDescriptions(true)
331 .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
337 * Command line module for a trajectory analysis module.
339 * \ingroup module_trajectoryanalysis
341 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
342 : public CommandLineModuleInterface
346 * Constructs a module.
348 * \param[in] name Name for the module.
349 * \param[in] description One-line description for the module.
350 * \param[in] factory Factory method to create the analysis module.
352 * Does not throw. This is important for correct implementation of
355 RunnerCommandLineModule(const char *name, const char *description,
356 ModuleFactoryMethod factory)
357 : name_(name), description_(description), hasFunction_(true), factory_(factory), functor_(NULL)
362 * Overloaded constructor accepting a functor instead of function pointer.
364 RunnerCommandLineModule(const char *name, const char *description,
365 ModuleFactoryFunctor *factory)
366 : name_(name), description_(description), hasFunction_(false), factory_(NULL), functor_(factory)
370 virtual const char *name() const { return name_; }
371 virtual const char *shortDescription() const { return description_; };
373 virtual void init(CommandLineModuleSettings *settings);
374 virtual int run(int argc, char *argv[]);
375 virtual void writeHelp(const CommandLineHelpContext &context) const;
379 const char *description_;
381 ModuleFactoryMethod factory_;
382 ModuleFactoryFunctor *functor_;
384 GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
387 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
388 CommandLineModuleSettings * /*settings*/)
392 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
393 int argc, char *argv[])
395 TrajectoryAnalysisModulePointer module(hasFunction_? factory_() : (*functor_)());
396 TrajectoryAnalysisCommandLineRunner runner(module.get());
397 return runner.run(argc, argv);
400 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
401 const CommandLineHelpContext &context) const
403 TrajectoryAnalysisModulePointer module(hasFunction_? factory_() : (*functor_)());
404 TrajectoryAnalysisCommandLineRunner runner(module.get());
405 runner.writeHelp(context);
410 TrajectoryAnalysisCommandLineRunner::runAsMain(
411 int argc, char *argv[], ModuleFactoryMethod factory)
413 Impl::RunnerCommandLineModule module(NULL, NULL, factory);
414 return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
419 TrajectoryAnalysisCommandLineRunner::runAsMain(
420 int argc, char *argv[], ModuleFactoryFunctor *factory)
422 Impl::RunnerCommandLineModule module(NULL, NULL, factory);
423 return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
428 TrajectoryAnalysisCommandLineRunner::registerModule(
429 CommandLineModuleManager *manager, const char *name,
430 const char *description, ModuleFactoryMethod factory)
432 CommandLineModulePointer module(
433 new Impl::RunnerCommandLineModule(name, description, factory));
434 manager->addModule(move(module));