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/cmdlinemodulemanager.h"
  48 #include "gromacs/commandline/cmdlineoptionsmodule.h"
  49 #include "gromacs/options/ioptionscontainer.h"
  50 #include "gromacs/options/timeunitmanager.h"
  51 #include "gromacs/pbcutil/pbc.h"
  52 #include "gromacs/selection/selectioncollection.h"
  53 #include "gromacs/selection/selectionoptionbehavior.h"
  54 #include "gromacs/trajectory/trajectoryframe.h"
  55 #include "gromacs/trajectoryanalysis/analysismodule.h"
  56 #include "gromacs/trajectoryanalysis/analysissettings.h"
  57 #include "gromacs/trajectoryanalysis/topologyinformation.h"
  58 #include "gromacs/utility/exceptions.h"
  59 #include "gromacs/utility/filestream.h"
  60 #include "gromacs/utility/gmxassert.h"
  61
  62 #include "runnercommon.h"
  63
  64 namespace gmx
  65 {
  66
  67 namespace
  68 {
  69
  70 /********************************************************************
  71  * RunnerModule
  72  */
  73
  74 class RunnerModule : public ICommandLineOptionsModule
  75 {
  76     public:
  77         explicit RunnerModule(TrajectoryAnalysisModulePointer module)
  78             : module_(std::move(module)), common_(&settings_)
  79         {
  80         }
  81
  82         void init(CommandLineModuleSettings * /*settings*/) override {}
  83         void initOptions(IOptionsContainer                 *options,
  84                          ICommandLineOptionsModuleSettings *settings) override;
  85         void optionsFinished() override;
  86         int run() override;
  87
  88         TrajectoryAnalysisModulePointer module_;
  89         TrajectoryAnalysisSettings      settings_;
  90         TrajectoryAnalysisRunnerCommon  common_;
  91         SelectionCollection             selections_;
  92 };
  93
  94 void RunnerModule::initOptions(
  95         IOptionsContainer *options, ICommandLineOptionsModuleSettings *settings)
  96 {
  97     std::shared_ptr<TimeUnitBehavior>        timeUnitBehavior(
  98             new TimeUnitBehavior());
  99     std::shared_ptr<SelectionOptionBehavior> selectionOptionBehavior(
 100             new SelectionOptionBehavior(&selections_,
 101                                         common_.topologyProvider()));
 102     settings->addOptionsBehavior(timeUnitBehavior);
 103     settings->addOptionsBehavior(selectionOptionBehavior);
 104     IOptionsContainer &commonOptions = options->addGroup();
 105     IOptionsContainer &moduleOptions = options->addGroup();
 106
 107     settings_.setOptionsModuleSettings(settings);
 108     module_->initOptions(&moduleOptions, &settings_);
 109     settings_.setOptionsModuleSettings(nullptr);
 110     common_.initOptions(&commonOptions, timeUnitBehavior.get());
 111     selectionOptionBehavior->initOptions(&commonOptions);
 112 }
 113
 114 void RunnerModule::optionsFinished()
 115 {
 116     common_.optionsFinished();
 117     module_->optionsFinished(&settings_);
 118 }
 119
 120 int RunnerModule::run()
 121 {
 122     common_.initTopology();
 123     const TopologyInformation &topology = common_.topologyInformation();
 124     module_->initAnalysis(settings_, topology);
 125
 126     // Load first frame.
 127     common_.initFirstFrame();
 128     common_.initFrameIndexGroup();
 129     module_->initAfterFirstFrame(settings_, common_.frame());
 130
 131     t_pbc  pbc;
 132     t_pbc *ppbc = settings_.hasPBC() ? &pbc : nullptr;
 133
 134     int    nframes = 0;
 135     AnalysisDataParallelOptions         dataOptions;
 136     TrajectoryAnalysisModuleDataPointer pdata(
 137             module_->startFrames(dataOptions, selections_));
 138     do
 139     {
 140         common_.initFrame();
 141         t_trxframe &frame = common_.frame();
 142         if (ppbc != nullptr)
 143         {
 144             set_pbc(ppbc, topology.ePBC(), frame.box);
 145         }
 146
 147         selections_.evaluate(&frame, ppbc);
 148         module_->analyzeFrame(nframes, frame, ppbc, pdata.get());
 149         module_->finishFrameSerial(nframes);
 150
 151         ++nframes;
 152     }
 153     while (common_.readNextFrame());
 154     module_->finishFrames(pdata.get());
 155     if (pdata.get() != nullptr)
 156     {
 157         pdata->finish();
 158     }
 159     pdata.reset();
 160
 161     if (common_.hasTrajectory())
 162     {
 163         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 164                 nframes, common_.frame().time);
 165     }
 166     else
 167     {
 168         fprintf(stderr, "Analyzed topology coordinates\n");
 169     }
 170
 171     // Restore the maximal groups for dynamic selections.
 172     selections_.evaluateFinal(nframes);
 173
 174     module_->finishAnalysis(nframes);
 175     module_->writeOutput();
 176
 177     return 0;
 178 }
 179
 180 }   // namespace
 181
 182 /********************************************************************
 183  * TrajectoryAnalysisCommandLineRunner
 184  */
 185
 186 // static
 187 int
 188 TrajectoryAnalysisCommandLineRunner::runAsMain(
 189         int argc, char *argv[], const ModuleFactoryMethod &factory)
 190 {
 191     auto runnerFactory = [factory]
 192     {
 193         return createModule(factory());
 194     };
 195     return ICommandLineOptionsModule::runAsMain(argc, argv, nullptr, nullptr, runnerFactory);
 196 }
 197
 198 // static
 199 void
 200 TrajectoryAnalysisCommandLineRunner::registerModule(
 201         CommandLineModuleManager *manager, const char *name,
 202         const char *description, const ModuleFactoryMethod &factory)
 203 {
 204     auto runnerFactory = [factory]
 205     {
 206         return createModule(factory());
 207     };
 208     ICommandLineOptionsModule::registerModuleFactory(
 209             manager, name, description, runnerFactory);
 210 }
 211
 212 // static
 213 std::unique_ptr<ICommandLineOptionsModule>
 214 TrajectoryAnalysisCommandLineRunner::createModule(
 215         TrajectoryAnalysisModulePointer module)
 216 {
 217     return ICommandLineOptionsModulePointer(new RunnerModule(std::move(module)));
 218 }
 219
 220 } // namespace gmx