src/gromacs/trajectoryanalysis/modules/distance.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements gmx::analysismodules::Distance.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_trajectoryanalysis
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "distance.h"
  45
  46 #include <string>
  47
  48 #include "gromacs/analysisdata/analysisdata.h"
  49 #include "gromacs/analysisdata/modules/average.h"
  50 #include "gromacs/analysisdata/modules/histogram.h"
  51 #include "gromacs/analysisdata/modules/plot.h"
  52 #include "gromacs/math/vec.h"
  53 #include "gromacs/options/basicoptions.h"
  54 #include "gromacs/options/filenameoption.h"
  55 #include "gromacs/options/ioptionscontainer.h"
  56 #include "gromacs/pbcutil/pbc.h"
  57 #include "gromacs/selection/selection.h"
  58 #include "gromacs/selection/selectionoption.h"
  59 #include "gromacs/trajectory/trajectoryframe.h"
  60 #include "gromacs/trajectoryanalysis/analysissettings.h"
  61 #include "gromacs/utility/arrayref.h"
  62 #include "gromacs/utility/exceptions.h"
  63 #include "gromacs/utility/stringutil.h"
  64
  65 namespace gmx
  66 {
  67
  68 namespace analysismodules
  69 {
  70
  71 namespace
  72 {
  73
  74 class Distance : public TrajectoryAnalysisModule
  75 {
  76     public:
  77         Distance();
  78
  79         virtual void initOptions(IOptionsContainer          *options,
  80                                  TrajectoryAnalysisSettings *settings);
  81         virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
  82                                   const TopologyInformation        &top);
  83
  84         virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
  85                                   TrajectoryAnalysisModuleData *pdata);
  86
  87         virtual void finishAnalysis(int nframes);
  88         virtual void writeOutput();
  89
  90     private:
  91         SelectionList                            sel_;
  92         std::string                              fnAverage_;
  93         std::string                              fnAll_;
  94         std::string                              fnXYZ_;
  95         std::string                              fnHistogram_;
  96         std::string                              fnAllStats_;
  97         double                                   meanLength_;
  98         double                                   lengthDev_;
  99         double                                   binWidth_;
 100
 101         AnalysisData                             distances_;
 102         AnalysisData                             xyz_;
 103         AnalysisDataAverageModulePointer         summaryStatsModule_;
 104         AnalysisDataAverageModulePointer         allStatsModule_;
 105         AnalysisDataFrameAverageModulePointer    averageModule_;
 106         AnalysisDataSimpleHistogramModulePointer histogramModule_;
 107
 108         // Copy and assign disallowed by base.
 109 };
 110
 111 Distance::Distance()
 112     : meanLength_(0.1), lengthDev_(1.0), binWidth_(0.001)
 113 {
 114     summaryStatsModule_.reset(new AnalysisDataAverageModule());
 115     summaryStatsModule_->setAverageDataSets(true);
 116     distances_.addModule(summaryStatsModule_);
 117     allStatsModule_.reset(new AnalysisDataAverageModule());
 118     distances_.addModule(allStatsModule_);
 119     averageModule_.reset(new AnalysisDataFrameAverageModule());
 120     distances_.addModule(averageModule_);
 121     histogramModule_.reset(new AnalysisDataSimpleHistogramModule());
 122     distances_.addModule(histogramModule_);
 123
 124     registerAnalysisDataset(&distances_, "dist");
 125     registerAnalysisDataset(&xyz_, "xyz");
 126     registerBasicDataset(summaryStatsModule_.get(), "stats");
 127     registerBasicDataset(allStatsModule_.get(), "allstats");
 128     registerBasicDataset(averageModule_.get(), "average");
 129     registerBasicDataset(&histogramModule_->averager(), "histogram");
 130 }
 131
 132
 133 void
 134 Distance::initOptions(IOptionsContainer *options, TrajectoryAnalysisSettings *settings)
 135 {
 136     static const char *const desc[] = {
 137         "[THISMODULE] calculates distances between pairs of positions",
 138         "as a function of time. Each selection specifies an independent set",
 139         "of distances to calculate. Each selection should consist of pairs",
 140         "of positions, and the distances are computed between positions 1-2,",
 141         "3-4, etc.[PAR]",
 142         "[TT]-oav[tt] writes the average distance as a function of time for",
 143         "each selection.",
 144         "[TT]-oall[tt] writes all the individual distances.",
 145         "[TT]-oxyz[tt] does the same, but the x, y, and z components of the",
 146         "distance are written instead of the norm.",
 147         "[TT]-oh[tt] writes a histogram of the distances for each selection.",
 148         "The location of the histogram is set with [TT]-len[tt] and",
 149         "[TT]-tol[tt]. Bin width is set with [TT]-binw[tt].",
 150         "[TT]-oallstat[tt] writes out the average and standard deviation for",
 151         "each individual distance, calculated over the frames.[PAR]",
 152         "Note that [THISMODULE] calculates distances between fixed pairs",
 153         "(1-2, 3-4, etc.) within a single selection.  To calculate distances",
 154         "between two selections, including minimum, maximum, and pairwise",
 155         "distances, use [gmx-pairdist]."
 156     };
 157
 158     settings->setHelpText(desc);
 159
 160     options->addOption(FileNameOption("oav").filetype(eftPlot).outputFile()
 161                            .store(&fnAverage_).defaultBasename("distave")
 162                            .description("Average distances as function of time"));
 163     options->addOption(FileNameOption("oall").filetype(eftPlot).outputFile()
 164                            .store(&fnAll_).defaultBasename("dist")
 165                            .description("All distances as function of time"));
 166     options->addOption(FileNameOption("oxyz").filetype(eftPlot).outputFile()
 167                            .store(&fnXYZ_).defaultBasename("distxyz")
 168                            .description("Distance components as function of time"));
 169     options->addOption(FileNameOption("oh").filetype(eftPlot).outputFile()
 170                            .store(&fnHistogram_).defaultBasename("disthist")
 171                            .description("Histogram of the distances"));
 172     options->addOption(FileNameOption("oallstat").filetype(eftPlot).outputFile()
 173                            .store(&fnAllStats_).defaultBasename("diststat")
 174                            .description("Statistics for individual distances"));
 175     options->addOption(SelectionOption("select").storeVector(&sel_)
 176                            .required().dynamicMask().multiValue()
 177                            .description("Position pairs to calculate distances for"));
 178     // TODO: Extend the histogramming implementation to allow automatic
 179     // extension of the histograms to cover the data, removing the need for
 180     // the first two options.
 181     options->addOption(DoubleOption("len").store(&meanLength_)
 182                            .description("Mean distance for histogramming"));
 183     options->addOption(DoubleOption("tol").store(&lengthDev_)
 184                            .description("Width of full distribution as fraction of [TT]-len[tt]"));
 185     options->addOption(DoubleOption("binw").store(&binWidth_)
 186                            .description("Bin width for histogramming"));
 187 }
 188
 189
 190 /*! \brief
 191  * Checks that selections conform to the expectations of the tool.
 192  */
 193 void checkSelections(const SelectionList &sel)
 194 {
 195     for (size_t g = 0; g < sel.size(); ++g)
 196     {
 197         if (sel[g].posCount() % 2 != 0)
 198         {
 199             std::string message = formatString(
 200                         "Selection '%s' does not evaluate into an even number of positions "
 201                         "(there are %d positions)",
 202                         sel[g].name(), sel[g].posCount());
 203             GMX_THROW(InconsistentInputError(message));
 204         }
 205         if (sel[g].isDynamic())
 206         {
 207             for (int i = 0; i < sel[g].posCount(); i += 2)
 208             {
 209                 if (sel[g].position(i).selected() != sel[g].position(i+1).selected())
 210                 {
 211                     std::string message =
 212                         formatString("Dynamic selection %d does not select "
 213                                      "a consistent set of pairs over the frames",
 214                                      static_cast<int>(g + 1));
 215                     GMX_THROW(InconsistentInputError(message));
 216                 }
 217             }
 218         }
 219     }
 220 }
 221
 222
 223 void
 224 Distance::initAnalysis(const TrajectoryAnalysisSettings &settings,
 225                        const TopologyInformation         & /*top*/)
 226 {
 227     checkSelections(sel_);
 228
 229     distances_.setDataSetCount(sel_.size());
 230     xyz_.setDataSetCount(sel_.size());
 231     for (size_t i = 0; i < sel_.size(); ++i)
 232     {
 233         const int distCount = sel_[i].posCount() / 2;
 234         distances_.setColumnCount(i, distCount);
 235         xyz_.setColumnCount(i, distCount * 3);
 236     }
 237     const double histogramMin = (1.0 - lengthDev_) * meanLength_;
 238     const double histogramMax = (1.0 + lengthDev_) * meanLength_;
 239     histogramModule_->init(histogramFromRange(histogramMin, histogramMax)
 240                                .binWidth(binWidth_).includeAll());
 241
 242     if (!fnAverage_.empty())
 243     {
 244         AnalysisDataPlotModulePointer plotm(
 245                 new AnalysisDataPlotModule(settings.plotSettings()));
 246         plotm->setFileName(fnAverage_);
 247         plotm->setTitle("Average distance");
 248         plotm->setXAxisIsTime();
 249         plotm->setYLabel("Distance (nm)");
 250         for (size_t g = 0; g < sel_.size(); ++g)
 251         {
 252             plotm->appendLegend(sel_[g].name());
 253         }
 254         averageModule_->addModule(plotm);
 255     }
 256
 257     if (!fnAll_.empty())
 258     {
 259         AnalysisDataPlotModulePointer plotm(
 260                 new AnalysisDataPlotModule(settings.plotSettings()));
 261         plotm->setFileName(fnAll_);
 262         plotm->setTitle("Distance");
 263         plotm->setXAxisIsTime();
 264         plotm->setYLabel("Distance (nm)");
 265         // TODO: Add legends? (there can be a massive amount of columns)
 266         distances_.addModule(plotm);
 267     }
 268
 269     if (!fnXYZ_.empty())
 270     {
 271         AnalysisDataPlotModulePointer plotm(
 272                 new AnalysisDataPlotModule(settings.plotSettings()));
 273         plotm->setFileName(fnXYZ_);
 274         plotm->setTitle("Distance");
 275         plotm->setXAxisIsTime();
 276         plotm->setYLabel("Distance (nm)");
 277         // TODO: Add legends? (there can be a massive amount of columns)
 278         xyz_.addModule(plotm);
 279     }
 280
 281     if (!fnHistogram_.empty())
 282     {
 283         AnalysisDataPlotModulePointer plotm(
 284                 new AnalysisDataPlotModule(settings.plotSettings()));
 285         plotm->setFileName(fnHistogram_);
 286         plotm->setTitle("Distance histogram");
 287         plotm->setXLabel("Distance (nm)");
 288         plotm->setYLabel("Probability");
 289         for (size_t g = 0; g < sel_.size(); ++g)
 290         {
 291             plotm->appendLegend(sel_[g].name());
 292         }
 293         histogramModule_->averager().addModule(plotm);
 294     }
 295
 296     if (!fnAllStats_.empty())
 297     {
 298         AnalysisDataPlotModulePointer plotm(
 299                 new AnalysisDataPlotModule(settings.plotSettings()));
 300         plotm->setFileName(fnAllStats_);
 301         plotm->setErrorsAsSeparateColumn(true);
 302         plotm->setTitle("Statistics for individual distances");
 303         plotm->setXLabel("Distance index");
 304         plotm->setYLabel("Average/standard deviation (nm)");
 305         for (size_t g = 0; g < sel_.size(); ++g)
 306         {
 307             plotm->appendLegend(std::string(sel_[g].name()) + " avg");
 308             plotm->appendLegend(std::string(sel_[g].name()) + " std.dev.");
 309         }
 310         // TODO: Consider whether this output format is the best possible.
 311         allStatsModule_->addModule(plotm);
 312     }
 313 }
 314
 315
 316 void
 317 Distance::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
 318                        TrajectoryAnalysisModuleData *pdata)
 319 {
 320     AnalysisDataHandle   distHandle = pdata->dataHandle(distances_);
 321     AnalysisDataHandle   xyzHandle  = pdata->dataHandle(xyz_);
 322     const SelectionList &sel        = pdata->parallelSelections(sel_);
 323
 324     checkSelections(sel);
 325
 326     distHandle.startFrame(frnr, fr.time);
 327     xyzHandle.startFrame(frnr, fr.time);
 328     for (size_t g = 0; g < sel.size(); ++g)
 329     {
 330         distHandle.selectDataSet(g);
 331         xyzHandle.selectDataSet(g);
 332         for (int i = 0, n = 0; i < sel[g].posCount(); i += 2, ++n)
 333         {
 334             const SelectionPosition &p1 = sel[g].position(i);
 335             const SelectionPosition &p2 = sel[g].position(i+1);
 336             rvec                     dx;
 337             if (pbc != NULL)
 338             {
 339                 pbc_dx(pbc, p2.x(), p1.x(), dx);
 340             }
 341             else
 342             {
 343                 rvec_sub(p2.x(), p1.x(), dx);
 344             }
 345             real dist     = norm(dx);
 346             bool bPresent = p1.selected() && p2.selected();
 347             distHandle.setPoint(n, dist, bPresent);
 348             xyzHandle.setPoints(n*3, 3, dx, bPresent);
 349         }
 350     }
 351     distHandle.finishFrame();
 352     xyzHandle.finishFrame();
 353 }
 354
 355
 356 void
 357 Distance::finishAnalysis(int /*nframes*/)
 358 {
 359     AbstractAverageHistogram &averageHistogram = histogramModule_->averager();
 360     averageHistogram.normalizeProbability();
 361     averageHistogram.done();
 362 }
 363
 364
 365 void
 366 Distance::writeOutput()
 367 {
 368     SelectionList::const_iterator sel;
 369     int                           index;
 370     for (sel = sel_.begin(), index = 0; sel != sel_.end(); ++sel, ++index)
 371     {
 372         printf("%s:\n", sel->name());
 373         printf("  Number of samples:  %d\n",
 374                summaryStatsModule_->sampleCount(index, 0));
 375         printf("  Average distance:   %-8.5f nm\n",
 376                summaryStatsModule_->average(index, 0));
 377         printf("  Standard deviation: %-8.5f nm\n",
 378                summaryStatsModule_->standardDeviation(index, 0));
 379     }
 380 }
 381
 382 }       // namespace
 383
 384 const char DistanceInfo::name[]             = "distance";
 385 const char DistanceInfo::shortDescription[] =
 386     "Calculate distances between pairs of positions";
 387
 388 TrajectoryAnalysisModulePointer DistanceInfo::create()
 389 {
 390     return TrajectoryAnalysisModulePointer(new Distance);
 391 }
 392
 393 } // namespace analysismodules
 394
 395 } // namespace gmx