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/cmdlinehelpcontext.h"
  48 #include "gromacs/commandline/cmdlinehelpwriter.h"
  49 #include "gromacs/commandline/cmdlineoptionsmodule.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"
  63
  64 #include "runnercommon.h"
  65
  66 namespace gmx
  67 {
  68
  69 /********************************************************************
  70  * TrajectoryAnalysisCommandLineRunner::Impl
  71  */
  72
  73 class TrajectoryAnalysisCommandLineRunner::Impl
  74 {
  75     public:
  76         Impl(TrajectoryAnalysisModulePointer module);
  77         ~Impl();
  78
  79         TrajectoryAnalysisModulePointer module_;
  80         bool                            bUseDefaultGroups_;
  81         int                             debugLevel_;
  82         SelectionCollection             selections_;
  83         SelectionOptionManager          selOptManager_;
  84         TrajectoryAnalysisSettings      settings_;
  85         TrajectoryAnalysisRunnerCommon  common_;
  86 };
  87
  88
  89 TrajectoryAnalysisCommandLineRunner::Impl::Impl(
  90         TrajectoryAnalysisModulePointer module)
  91     : module_(module), bUseDefaultGroups_(true), debugLevel_(0),
  92       selOptManager_(&selections_), common_(&settings_)
  93 {
  94 }
  95
  96
  97 TrajectoryAnalysisCommandLineRunner::Impl::~Impl()
  98 {
  99     module_.reset();
 100 }
 101
 102
 103 /********************************************************************
 104  * TrajectoryAnalysisCommandLineRunner
 105  */
 106
 107 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
 108         TrajectoryAnalysisCommandLineRunner::ModuleFactoryMethod factory)
 109     : impl_(new Impl(factory()))
 110 {
 111 }
 112
 113 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
 114         TrajectoryAnalysisCommandLineRunner::ModuleFactoryFunctor *functor)
 115     : impl_(new Impl((*functor)()))
 116 {
 117 }
 118
 119 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
 120 {
 121 }
 122
 123
 124 void
 125 TrajectoryAnalysisCommandLineRunner::setUseDefaultGroups(bool bUseDefaults)
 126 {
 127     impl_->bUseDefaultGroups_ = bUseDefaults;
 128 }
 129
 130
 131 void
 132 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
 133 {
 134     impl_->debugLevel_ = debuglevel;
 135 }
 136
 137 void TrajectoryAnalysisCommandLineRunner::init(CommandLineModuleSettings * /*settings*/)
 138 {
 139 }
 140
 141 void
 142 TrajectoryAnalysisCommandLineRunner::initOptions(IOptionsContainer                 *options,
 143                                                  ICommandLineOptionsModuleSettings *settings)
 144 {
 145     impl_->selections_.setDebugLevel(impl_->debugLevel_);
 146
 147     options->addManager(&impl_->selOptManager_);
 148
 149     IOptionsContainer &commonOptions = options->addGroup();
 150     IOptionsContainer &moduleOptions = options->addGroup();
 151
 152     impl_->module_->initOptions(&moduleOptions, &impl_->settings_);
 153     impl_->common_.initOptions(&commonOptions);
 154     impl_->selections_.initOptions(&commonOptions);
 155
 156     const char *help[] = { impl_->settings_.helpText().data() };
 157     settings->setHelpText(help);
 158 }
 159
 160 void
 161 TrajectoryAnalysisCommandLineRunner::optionsFinished()
 162 {
 163     // TODO: scaleTimeOptions? (maybe pass options here too, with default arg)
 164     impl_->common_.optionsFinished();
 165     impl_->module_->optionsFinished(&impl_->settings_);
 166
 167     impl_->common_.initIndexGroups(&impl_->selections_, impl_->bUseDefaultGroups_);
 168
 169     const bool bInteractive = StandardInputStream::instance().isInteractive();
 170     impl_->selOptManager_.parseRequestedFromStdin(bInteractive);
 171     impl_->common_.doneIndexGroups(&impl_->selections_);
 172
 173     impl_->common_.initTopology(&impl_->selections_);
 174     impl_->selections_.compile();
 175 }
 176
 177
 178 int
 179 TrajectoryAnalysisCommandLineRunner::run()
 180 {
 181     const TopologyInformation &topology = impl_->common_.topologyInformation();
 182     impl_->module_->initAnalysis(impl_->settings_, topology);
 183
 184     // Load first frame.
 185     impl_->common_.initFirstFrame();
 186     impl_->module_->initAfterFirstFrame(impl_->settings_, impl_->common_.frame());
 187
 188     t_pbc  pbc;
 189     t_pbc *ppbc = impl_->settings_.hasPBC() ? &pbc : NULL;
 190
 191     int    nframes = 0;
 192     AnalysisDataParallelOptions         dataOptions;
 193     TrajectoryAnalysisModuleDataPointer pdata(
 194             impl_->module_->startFrames(dataOptions, impl_->selections_));
 195     do
 196     {
 197         impl_->common_.initFrame();
 198         t_trxframe &frame = impl_->common_.frame();
 199         if (ppbc != NULL)
 200         {
 201             set_pbc(ppbc, topology.ePBC(), frame.box);
 202         }
 203
 204         impl_->selections_.evaluate(&frame, ppbc);
 205         impl_->module_->analyzeFrame(nframes, frame, ppbc, pdata.get());
 206         impl_->module_->finishFrameSerial(nframes);
 207
 208         ++nframes;
 209     }
 210     while (impl_->common_.readNextFrame());
 211     impl_->module_->finishFrames(pdata.get());
 212     if (pdata.get() != NULL)
 213     {
 214         pdata->finish();
 215     }
 216     pdata.reset();
 217
 218     if (impl_->common_.hasTrajectory())
 219     {
 220         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 221                 nframes, impl_->common_.frame().time);
 222     }
 223     else
 224     {
 225         fprintf(stderr, "Analyzed topology coordinates\n");
 226     }
 227
 228     // Restore the maximal groups for dynamic selections.
 229     impl_->selections_.evaluateFinal(nframes);
 230
 231     impl_->module_->finishAnalysis(nframes);
 232     impl_->module_->writeOutput();
 233     return 0;
 234 }
 235
 236 // static
 237 int
 238 TrajectoryAnalysisCommandLineRunner::runAsMain(
 239         int argc, char *argv[], ModuleFactoryMethod factory)
 240 {
 241     TrajectoryAnalysisCommandLineRunner *module = new TrajectoryAnalysisCommandLineRunner(factory);
 242     return ICommandLineOptionsModule::runAsMain(argc, argv, module);
 243 }
 244
 245 // static
 246 int
 247 TrajectoryAnalysisCommandLineRunner::runAsMain(
 248         int argc, char *argv[], ModuleFactoryFunctor *factory)
 249 {
 250     TrajectoryAnalysisCommandLineRunner *module = new TrajectoryAnalysisCommandLineRunner(factory);
 251     return ICommandLineOptionsModule::runAsMain(argc, argv, module);
 252 }
 253
 254 // static
 255 void
 256 TrajectoryAnalysisCommandLineRunner::registerModule(
 257         CommandLineModuleManager *manager, const char *name,
 258         const char *description, ModuleFactoryMethod factory)
 259 {
 260     ICommandLineOptionsModule::registerModule(manager, name, description,
 261         new TrajectoryAnalysisCommandLineRunner(factory));
 262 }
 263
 264 } // namespace gmx