src/gromacs/trajectoryanalysis/cmdlinerunner.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
   5  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
   6  * others, as listed in the AUTHORS file in the top-level source
   7  * directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  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/pbc.h"
  49 #include "gromacs/legacyheaders/rmpbc.h"
  50 #include "gromacs/legacyheaders/statutil.h"
  51
  52 #include "gromacs/analysisdata/paralleloptions.h"
  53 #include "gromacs/commandline/cmdlinehelpwriter.h"
  54 #include "gromacs/commandline/cmdlinemodule.h"
  55 #include "gromacs/commandline/cmdlinemodulemanager.h"
  56 #include "gromacs/commandline/cmdlineparser.h"
  57 #include "gromacs/onlinehelp/helpwritercontext.h"
  58 #include "gromacs/options/options.h"
  59 #include "gromacs/selection/selectioncollection.h"
  60 #include "gromacs/selection/selectionoptionmanager.h"
  61 #include "gromacs/trajectoryanalysis/analysismodule.h"
  62 #include "gromacs/trajectoryanalysis/analysissettings.h"
  63 #include "gromacs/trajectoryanalysis/runnercommon.h"
  64 #include "gromacs/utility/exceptions.h"
  65 #include "gromacs/utility/file.h"
  66 #include "gromacs/utility/gmxassert.h"
  67 #include "gromacs/utility/programinfo.h"
  68
  69 namespace gmx
  70 {
  71
  72 /********************************************************************
  73  * TrajectoryAnalysisCommandLineRunner::Impl
  74  */
  75
  76 class TrajectoryAnalysisCommandLineRunner::Impl
  77 {
  78     public:
  79         class RunnerCommandLineModule;
  80
  81         Impl(TrajectoryAnalysisModule *module);
  82         ~Impl();
  83
  84         void printHelp(const Options                        &options,
  85                        const TrajectoryAnalysisSettings     &settings,
  86                        const TrajectoryAnalysisRunnerCommon &common);
  87         bool parseOptions(TrajectoryAnalysisSettings *settings,
  88                           TrajectoryAnalysisRunnerCommon *common,
  89                           SelectionCollection *selections,
  90                           int *argc, char *argv[]);
  91
  92         TrajectoryAnalysisModule *module_;
  93         int                       debugLevel_;
  94 };
  95
  96
  97 TrajectoryAnalysisCommandLineRunner::Impl::Impl(
  98         TrajectoryAnalysisModule *module)
  99     : module_(module), debugLevel_(0)
 100 {
 101 }
 102
 103
 104 TrajectoryAnalysisCommandLineRunner::Impl::~Impl()
 105 {
 106 }
 107
 108
 109 void
 110 TrajectoryAnalysisCommandLineRunner::Impl::printHelp(
 111         const Options                        &options,
 112         const TrajectoryAnalysisSettings     &settings,
 113         const TrajectoryAnalysisRunnerCommon &common)
 114 {
 115     TrajectoryAnalysisRunnerCommon::HelpFlags flags = common.helpFlags();
 116     if (flags != 0)
 117     {
 118         HelpWriterContext context(&File::standardError(),
 119                                   eHelpOutputFormat_Console);
 120         CommandLineHelpWriter(options)
 121             .setShowDescriptions(flags & TrajectoryAnalysisRunnerCommon::efHelpShowDescriptions)
 122             .setShowHidden(flags & TrajectoryAnalysisRunnerCommon::efHelpShowHidden)
 123             .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 124             .writeHelp(context);
 125     }
 126 }
 127
 128
 129 bool
 130 TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
 131         TrajectoryAnalysisSettings *settings,
 132         TrajectoryAnalysisRunnerCommon *common,
 133         SelectionCollection *selections,
 134         int *argc, char *argv[])
 135 {
 136     Options options(NULL, NULL);
 137     Options moduleOptions(module_->name(), module_->description());
 138     Options commonOptions("common", "Common analysis control");
 139     Options selectionOptions("selection", "Common selection control");
 140     module_->initOptions(&moduleOptions, settings);
 141     common->initOptions(&commonOptions);
 142     selections->initOptions(&selectionOptions);
 143
 144     options.addSubSection(&commonOptions);
 145     options.addSubSection(&selectionOptions);
 146     options.addSubSection(&moduleOptions);
 147
 148     SelectionOptionManager seloptManager(selections);
 149     setManagerForSelectionOptions(&options, &seloptManager);
 150
 151     {
 152         CommandLineParser  parser(&options);
 153         try
 154         {
 155             parser.parse(argc, argv);
 156         }
 157         catch (const UserInputError &ex)
 158         {
 159             printHelp(options, *settings, *common);
 160             throw;
 161         }
 162         printHelp(options, *settings, *common);
 163         common->scaleTimeOptions(&options);
 164         options.finish();
 165     }
 166
 167     if (!common->optionsFinished(&commonOptions))
 168     {
 169         return false;
 170     }
 171     module_->optionsFinished(&moduleOptions, settings);
 172
 173     common->initIndexGroups(selections);
 174
 175     // TODO: Check whether the input is a pipe.
 176     bool bInteractive = true;
 177     seloptManager.parseRequestedFromStdin(bInteractive);
 178     common->doneIndexGroups(selections);
 179
 180     return true;
 181 }
 182
 183
 184 /********************************************************************
 185  * TrajectoryAnalysisCommandLineRunner
 186  */
 187
 188 TrajectoryAnalysisCommandLineRunner::TrajectoryAnalysisCommandLineRunner(
 189         TrajectoryAnalysisModule *module)
 190     : impl_(new Impl(module))
 191 {
 192 }
 193
 194
 195 TrajectoryAnalysisCommandLineRunner::~TrajectoryAnalysisCommandLineRunner()
 196 {
 197 }
 198
 199
 200 void
 201 TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
 202 {
 203     impl_->debugLevel_ = 1;
 204 }
 205
 206
 207 int
 208 TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
 209 {
 210     TrajectoryAnalysisModule *module = impl_->module_;
 211
 212     SelectionCollection  selections;
 213     selections.setDebugLevel(impl_->debugLevel_);
 214
 215     TrajectoryAnalysisSettings      settings;
 216     TrajectoryAnalysisRunnerCommon  common(&settings);
 217
 218     if (!impl_->parseOptions(&settings, &common, &selections, &argc, argv))
 219     {
 220         return 0;
 221     }
 222
 223     common.initTopology(&selections);
 224     selections.compile();
 225
 226     const TopologyInformation &topology = common.topologyInformation();
 227     module->initAnalysis(settings, topology);
 228
 229     // Load first frame.
 230     common.initFirstFrame();
 231     module->initAfterFirstFrame(common.frame());
 232
 233     t_pbc  pbc;
 234     t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
 235
 236     int    nframes = 0;
 237     AnalysisDataParallelOptions         dataOptions;
 238     TrajectoryAnalysisModuleDataPointer pdata(
 239             module->startFrames(dataOptions, selections));
 240     do
 241     {
 242         common.initFrame();
 243         t_trxframe &frame = common.frame();
 244         if (ppbc != NULL)
 245         {
 246             set_pbc(ppbc, topology.ePBC(), frame.box);
 247         }
 248
 249         selections.evaluate(&frame, ppbc);
 250         module->analyzeFrame(nframes, frame, ppbc, pdata.get());
 251
 252         nframes++;
 253     }
 254     while (common.readNextFrame());
 255     module->finishFrames(pdata.get());
 256     if (pdata.get() != NULL)
 257     {
 258         pdata->finish();
 259     }
 260     pdata.reset();
 261
 262     if (common.hasTrajectory())
 263     {
 264         fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
 265                 nframes, common.frame().time);
 266     }
 267     else
 268     {
 269         fprintf(stderr, "Analyzed topology coordinates\n");
 270     }
 271
 272     // Restore the maximal groups for dynamic selections.
 273     selections.evaluateFinal(nframes);
 274
 275     module->finishAnalysis(nframes);
 276     module->writeOutput();
 277
 278     return 0;
 279 }
 280
 281
 282 void
 283 TrajectoryAnalysisCommandLineRunner::writeHelp(const HelpWriterContext &context)
 284 {
 285     // TODO: This method duplicates some code from run() and Impl::printHelp().
 286     // See how to best refactor it to share the common code.
 287     SelectionCollection             selections;
 288     TrajectoryAnalysisSettings      settings;
 289     TrajectoryAnalysisRunnerCommon  common(&settings);
 290
 291     Options options(NULL, NULL);
 292     Options moduleOptions(impl_->module_->name(), impl_->module_->description());
 293     Options commonOptions("common", "Common analysis control");
 294     Options selectionOptions("selection", "Common selection control");
 295
 296     impl_->module_->initOptions(&moduleOptions, &settings);
 297     common.initOptions(&commonOptions);
 298     selections.initOptions(&selectionOptions);
 299
 300     options.addSubSection(&commonOptions);
 301     options.addSubSection(&selectionOptions);
 302     options.addSubSection(&moduleOptions);
 303
 304     SelectionOptionManager seloptManager(&selections);
 305     setManagerForSelectionOptions(&options, &seloptManager);
 306
 307     CommandLineHelpWriter(options)
 308         .setShowDescriptions(true)
 309         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
 310         .writeHelp(context);
 311 }
 312
 313
 314 /*! \internal \brief
 315  * Command line module for a trajectory analysis module.
 316  *
 317  * \ingroup module_trajectoryanalysis
 318  */
 319 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
 320     : public CommandLineModuleInterface
 321 {
 322     public:
 323         /*! \brief
 324          * Constructs a module.
 325          *
 326          * \param[in] name         Name for the module.
 327          * \param[in] description  One-line description for the module.
 328          * \param[in] factory      Factory method to create the analysis module.
 329          *
 330          * Does not throw.  This is important for correct implementation of
 331          * runAsMain().
 332          */
 333         RunnerCommandLineModule(const char *name, const char *description,
 334                                 ModuleFactoryMethod factory)
 335             : name_(name), description_(description), factory_(factory)
 336         {
 337         }
 338
 339         virtual const char *name() const { return name_; }
 340         virtual const char *shortDescription() const { return description_; };
 341
 342         virtual int run(int argc, char *argv[]);
 343         virtual void writeHelp(const HelpWriterContext &context) const;
 344
 345     private:
 346         const char             *name_;
 347         const char             *description_;
 348         ModuleFactoryMethod     factory_;
 349
 350         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
 351 };
 352
 353 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
 354         int argc, char *argv[])
 355 {
 356     TrajectoryAnalysisModulePointer     module(factory_());
 357     TrajectoryAnalysisCommandLineRunner runner(module.get());
 358     return runner.run(argc, argv);
 359 }
 360
 361 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
 362         const HelpWriterContext &context) const
 363 {
 364     TrajectoryAnalysisModulePointer     module(factory_());
 365     TrajectoryAnalysisCommandLineRunner runner(module.get());
 366     runner.writeHelp(context);
 367 }
 368
 369 // static
 370 int
 371 TrajectoryAnalysisCommandLineRunner::runAsMain(
 372         int argc, char *argv[], ModuleFactoryMethod factory)
 373 {
 374     Impl::RunnerCommandLineModule module(NULL, NULL, factory);
 375     return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
 376 }
 377
 378 // static
 379 void
 380 TrajectoryAnalysisCommandLineRunner::registerModule(
 381         CommandLineModuleManager *manager, const char *name,
 382         const char *description, ModuleFactoryMethod factory)
 383 {
 384     CommandLineModulePointer module(
 385             new Impl::RunnerCommandLineModule(name, description, factory));
 386     manager->addModule(move(module));
 387 }
 388
 389 } // namespace gmx