src/gromacs/trajectoryanalysis/cmdlinerunner.cpp

   1 /*
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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 "cmdlinerunner.h"
  43
  44 #ifdef HAVE_CONFIG_H
  45 #include "config.h"
  46 #endif
  47
  48 #include "gromacs/legacyheaders/copyrite.h"
  49 #include "gromacs/legacyheaders/pbc.h"
  50 #include "gromacs/legacyheaders/rmpbc.h"
  51 #include "gromacs/legacyheaders/statutil.h"
  52
  53 #include "gromacs/analysisdata/paralleloptions.h"
  54 #include "gromacs/commandline/cmdlinehelpwriter.h"
  55 #include "gromacs/commandline/cmdlineparser.h"
  56 #include "gromacs/onlinehelp/helpwritercontext.h"
  57 #include "gromacs/options/options.h"
  58 #include "gromacs/selection/selectioncollection.h"
  59 #include "gromacs/selection/selectionoptionmanager.h"
  60 #include "gromacs/trajectoryanalysis/analysismodule.h"
  61 #include "gromacs/trajectoryanalysis/analysissettings.h"
  62 #include "gromacs/trajectoryanalysis/runnercommon.h"
  63 #include "gromacs/utility/exceptions.h"
  64 #include "gromacs/utility/file.h"
  65 #include "gromacs/utility/gmxassert.h"
  66
  67 namespace gmx
  68 {
  69
  70 /********************************************************************
  71  * TrajectoryAnalysisCommandLineRunner::Impl
  72  */
  73
  74 class TrajectoryAnalysisCommandLineRunner::Impl
  75 {
  76     public:
  77         Impl(TrajectoryAnalysisModule *module);
  78         ~Impl();
  79
  80         void printHelp(const Options                        &options,
  81                        const TrajectoryAnalysisSettings     &settings,
  82                        const TrajectoryAnalysisRunnerCommon &common);
  83         bool parseOptions(TrajectoryAnalysisSettings *settings,
  84                           TrajectoryAnalysisRunnerCommon *common,
  85                           SelectionCollection *selections,
  86                           int *argc, char *argv[]);
  87
  88         TrajectoryAnalysisModule *module_;
  89         int                       debugLevel_;
  90         bool                      bPrintCopyright_;
  91 };
  92
  93
  94 TrajectoryAnalysisCommandLineRunner::Impl::Impl(
  95         TrajectoryAnalysisModule *module)
  96     : module_(module), debugLevel_(0), bPrintCopyright_(true)
  97 {
  98 }
  99
 100
 101 TrajectoryAnalysisCommandLineRunner::Impl::~Impl()
 102 {
 103 }
 104
 105
 106 void
 107 TrajectoryAnalysisCommandLineRunner::Impl::printHelp(
 108         const Options                        &options,
 109         const TrajectoryAnalysisSettings     &settings,
 110         const TrajectoryAnalysisRunnerCommon &common)
 111 {
 112     TrajectoryAnalysisRunnerCommon::HelpFlags flags = common.helpFlags();
 113     if (flags != 0)
 114     {
 115         HelpWriterContext context(&File::standardError(),
 116                                   eHelpOutputFormat_Console);
 117         CommandLineHelpWriter(options)
 118             .setShowDescriptions(flags & TrajectoryAnalysisRunnerCommon::efHelpShowDescriptions)
 119             .setShowHidden(flags & TrajectoryAnalysisRunnerCommon::efHelpShowHidden)
 120             .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 121             .writeHelp(context);
 122     }
 123 }
 124
 125
 126 bool
 127 TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
 128         TrajectoryAnalysisSettings *settings,
 129         TrajectoryAnalysisRunnerCommon *common,
 130         SelectionCollection *selections,
 131         int *argc, char *argv[])
 132 {
 133     Options options(NULL, NULL);
 134     Options moduleOptions(module_->name(), module_->description());
 135     Options commonOptions("common", "Common analysis control");
 136     Options selectionOptions("selection", "Common selection control");
 137     module_->initOptions(&moduleOptions, settings);
 138     common->initOptions(&commonOptions);
 139     selections->initOptions(&selectionOptions);
 140
 141     options.addSubSection(&commonOptions);
 142     options.addSubSection(&selectionOptions);
 143     options.addSubSection(&moduleOptions);
 144
 145     SelectionOptionManager seloptManager(selections);
 146     setManagerForSelectionOptions(&options, &seloptManager);
 147
 148     {
 149         CommandLineParser  parser(&options);
 150         try
 151         {
 152             parser.parse(argc, argv);
 153         }
 154         catch (const UserInputError &ex)
 155         {
 156             printHelp(options, *settings, *common);
 157             throw;
 158         }
 159         printHelp(options, *settings, *common);
 160         common->scaleTimeOptions(&options);
 161         options.finish();
 162     }
 163
 164     if (!common->optionsFinished(&commonOptions))
 165     {
 166         return false;
 167     }
 168     module_->optionsFinished(&moduleOptions, settings);
 169
 170     common->initIndexGroups(selections);
 171
 172     // TODO: Check whether the input is a pipe.
 173     bool bInteractive = true;
 174     seloptManager.parseRequestedFromStdin(bInteractive);
 175     common->doneIndexGroups(selections);
 176
 177     return true;
 178 }
 179
 180
 181 /********************************************************************
 182  * TrajectoryAnalysisCommandLineRunner
 183  */
 184
 185 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
 186         TrajectoryAnalysisModule *module)
 187     : impl_(new Impl(module))
 188 {
 189 }
 190
 191
 192 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
 193 {
 194 }
 195
 196
 197 void
 198 TrajectoryAnalysisCommandLineRunner::setPrintCopyright(bool bPrint)
 199 {
 200     impl_->bPrintCopyright_ = bPrint;
 201 }
 202
 203
 204 void
 205 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
 206 {
 207     impl_->debugLevel_ = 1;
 208 }
 209
 210
 211 int
 212 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
 213 {
 214     TrajectoryAnalysisModule *module = impl_->module_;
 215
 216     if (impl_->bPrintCopyright_)
 217     {
 218         CopyRight(stderr, argv[0]);
 219     }
 220
 221     SelectionCollection  selections;
 222     selections.setDebugLevel(impl_->debugLevel_);
 223
 224     TrajectoryAnalysisSettings      settings;
 225     TrajectoryAnalysisRunnerCommon  common(&settings);
 226
 227     if (!impl_->parseOptions(&settings, &common, &selections, &argc, argv))
 228     {
 229         return 0;
 230     }
 231
 232     common.initTopology(&selections);
 233     selections.compile();
 234
 235     const TopologyInformation &topology = common.topologyInformation();
 236     module->initAnalysis(settings, topology);
 237
 238     // Load first frame.
 239     common.initFirstFrame();
 240     module->initAfterFirstFrame(common.frame());
 241
 242     t_pbc  pbc;
 243     t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
 244
 245     int    nframes = 0;
 246     AnalysisDataParallelOptions         dataOptions;
 247     TrajectoryAnalysisModuleDataPointer pdata(
 248             module->startFrames(dataOptions, selections));
 249     do
 250     {
 251         common.initFrame();
 252         t_trxframe &frame = common.frame();
 253         if (ppbc != NULL)
 254         {
 255             set_pbc(ppbc, topology.ePBC(), frame.box);
 256         }
 257
 258         selections.evaluate(&frame, ppbc);
 259         module->analyzeFrame(nframes, frame, ppbc, pdata.get());
 260
 261         nframes++;
 262     }
 263     while (common.readNextFrame());
 264     module->finishFrames(pdata.get());
 265     if (pdata.get() != NULL)
 266     {
 267         pdata->finish();
 268     }
 269     pdata.reset();
 270
 271     if (common.hasTrajectory())
 272     {
 273         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 274                 nframes, common.frame().time);
 275     }
 276     else
 277     {
 278         fprintf(stderr, "Analyzed topology coordinates\n");
 279     }
 280
 281     // Restore the maximal groups for dynamic selections.
 282     selections.evaluateFinal(nframes);
 283
 284     module->finishAnalysis(nframes);
 285     module->writeOutput();
 286
 287     return 0;
 288 }
 289
 290
 291 void
 292 TrajectoryAnalysisCommandLineRunner::writeHelp(const HelpWriterContext &context)
 293 {
 294     // TODO: This method duplicates some code from run() and Impl::printHelp().
 295     // See how to best refactor it to share the common code.
 296     SelectionCollection             selections;
 297     TrajectoryAnalysisSettings      settings;
 298     TrajectoryAnalysisRunnerCommon  common(&settings);
 299
 300     Options options(NULL, NULL);
 301     Options moduleOptions(impl_->module_->name(), impl_->module_->description());
 302     Options commonOptions("common", "Common analysis control");
 303     Options selectionOptions("selection", "Common selection control");
 304
 305     impl_->module_->initOptions(&moduleOptions, &settings);
 306     common.initOptions(&commonOptions);
 307     selections.initOptions(&selectionOptions);
 308
 309     options.addSubSection(&commonOptions);
 310     options.addSubSection(&selectionOptions);
 311     options.addSubSection(&moduleOptions);
 312
 313     SelectionOptionManager seloptManager(&selections);
 314     setManagerForSelectionOptions(&options, &seloptManager);
 315
 316     CommandLineHelpWriter(options)
 317         .setShowDescriptions(true)
 318         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 319         .writeHelp(context);
 320 }
 321
 322 } // namespace gmx