src/gromacs/trajectoryanalysis/cmdlinerunner.cpp

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  36 /*! \internal \file
  37  * \brief
  38  * Implements gmx::TrajectoryAnalysisCommandLineRunner.
  39  *
  40  * \author Teemu Murtola <teemu.murtola@gmail.com>
  41  * \ingroup module_trajectoryanalysis
  42  */
  43 #include "gmxpre.h"
  44
  45 #include "cmdlinerunner.h"
  46
  47 #include "gromacs/analysisdata/paralleloptions.h"
  48 #include "gromacs/commandline/cmdlinemodulemanager.h"
  49 #include "gromacs/commandline/cmdlineoptionsmodule.h"
  50 #include "gromacs/options/ioptionscontainer.h"
  51 #include "gromacs/options/timeunitmanager.h"
  52 #include "gromacs/pbcutil/pbc.h"
  53 #include "gromacs/selection/selectioncollection.h"
  54 #include "gromacs/selection/selectionoptionbehavior.h"
  55 #include "gromacs/trajectory/trajectoryframe.h"
  56 #include "gromacs/trajectoryanalysis/analysismodule.h"
  57 #include "gromacs/trajectoryanalysis/analysissettings.h"
  58 #include "gromacs/trajectoryanalysis/topologyinformation.h"
  59 #include "gromacs/utility/exceptions.h"
  60 #include "gromacs/utility/filestream.h"
  61 #include "gromacs/utility/gmxassert.h"
  62
  63 #include "runnercommon.h"
  64
  65 namespace gmx
  66 {
  67
  68 namespace
  69 {
  70
  71 /********************************************************************
  72  * RunnerModule
  73  */
  74
  75 class RunnerModule : public ICommandLineOptionsModule
  76 {
  77 public:
  78     explicit RunnerModule(TrajectoryAnalysisModulePointer module) :
  79         module_(std::move(module)),
  80         common_(&settings_)
  81     {
  82     }
  83
  84     void init(CommandLineModuleSettings* /*settings*/) override {}
  85     void initOptions(IOptionsContainer* options, ICommandLineOptionsModuleSettings* settings) override;
  86     void optionsFinished() override;
  87     int  run() override;
  88
  89     TrajectoryAnalysisModulePointer module_;
  90     TrajectoryAnalysisSettings      settings_;
  91     TrajectoryAnalysisRunnerCommon  common_;
  92     SelectionCollection             selections_;
  93 };
  94
  95 void RunnerModule::initOptions(IOptionsContainer* options, ICommandLineOptionsModuleSettings* settings)
  96 {
  97     std::shared_ptr<TimeUnitBehavior>        timeUnitBehavior(new TimeUnitBehavior());
  98     std::shared_ptr<SelectionOptionBehavior> selectionOptionBehavior(
  99             new SelectionOptionBehavior(&selections_, common_.topologyProvider()));
 100     settings->addOptionsBehavior(timeUnitBehavior);
 101     settings->addOptionsBehavior(selectionOptionBehavior);
 102     IOptionsContainer& commonOptions = options->addGroup();
 103     IOptionsContainer& moduleOptions = options->addGroup();
 104
 105     settings_.setOptionsModuleSettings(settings);
 106     module_->initOptions(&moduleOptions, &settings_);
 107     settings_.setOptionsModuleSettings(nullptr);
 108     common_.initOptions(&commonOptions, timeUnitBehavior.get());
 109     selectionOptionBehavior->initOptions(&commonOptions);
 110 }
 111
 112 void RunnerModule::optionsFinished()
 113 {
 114     common_.optionsFinished();
 115     module_->optionsFinished(&settings_);
 116 }
 117
 118 int RunnerModule::run()
 119 {
 120     common_.initTopology();
 121     const TopologyInformation& topology = common_.topologyInformation();
 122     module_->initAnalysis(settings_, topology);
 123
 124     // Load first frame.
 125     common_.initFirstFrame();
 126     common_.initFrameIndexGroup();
 127     module_->initAfterFirstFrame(settings_, common_.frame());
 128
 129     t_pbc  pbc;
 130     t_pbc* ppbc = settings_.hasPBC() ? &pbc : nullptr;
 131
 132     int                                 nframes = 0;
 133     AnalysisDataParallelOptions         dataOptions;
 134     TrajectoryAnalysisModuleDataPointer pdata(module_->startFrames(dataOptions, selections_));
 135     do
 136     {
 137         common_.initFrame();
 138         t_trxframe& frame = common_.frame();
 139         if (ppbc != nullptr)
 140         {
 141             set_pbc(ppbc, topology.pbcType(), frame.box);
 142         }
 143
 144         selections_.evaluate(&frame, ppbc);
 145         module_->analyzeFrame(nframes, frame, ppbc, pdata.get());
 146         module_->finishFrameSerial(nframes);
 147
 148         ++nframes;
 149     } while (common_.readNextFrame());
 150     module_->finishFrames(pdata.get());
 151     if (pdata.get() != nullptr)
 152     {
 153         pdata->finish();
 154     }
 155     pdata.reset();
 156
 157     if (common_.hasTrajectory())
 158     {
 159         fprintf(stderr, "Analyzed %d frames, last time %.3f\n", nframes, common_.frame().time);
 160     }
 161     else
 162     {
 163         fprintf(stderr, "Analyzed topology coordinates\n");
 164     }
 165
 166     // Restore the maximal groups for dynamic selections.
 167     selections_.evaluateFinal(nframes);
 168
 169     module_->finishAnalysis(nframes);
 170     module_->writeOutput();
 171
 172     return 0;
 173 }
 174
 175 } // namespace
 176
 177 /********************************************************************
 178  * TrajectoryAnalysisCommandLineRunner
 179  */
 180
 181 // static
 182 int TrajectoryAnalysisCommandLineRunner::runAsMain(int argc, char* argv[], const ModuleFactoryMethod& factory)
 183 {
 184     auto runnerFactory = [factory] { return createModule(factory()); };
 185     return ICommandLineOptionsModule::runAsMain(argc, argv, nullptr, nullptr, runnerFactory);
 186 }
 187
 188 // static
 189 void TrajectoryAnalysisCommandLineRunner::registerModule(CommandLineModuleManager*  manager,
 190                                                          const char*                name,
 191                                                          const char*                description,
 192                                                          const ModuleFactoryMethod& factory)
 193 {
 194     auto runnerFactory = [factory] { return createModule(factory()); };
 195     ICommandLineOptionsModule::registerModuleFactory(manager, name, description, runnerFactory);
 196 }
 197
 198 // static
 199 std::unique_ptr<ICommandLineOptionsModule>
 200 TrajectoryAnalysisCommandLineRunner::createModule(TrajectoryAnalysisModulePointer module)
 201 {
 202     return ICommandLineOptionsModulePointer(new RunnerModule(std::move(module)));
 203 }
 204
 205 } // namespace gmx