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 "distance.h"
  43
  44 #include <string>
  45
  46 #include "gromacs/analysisdata/analysisdata.h"
  47 #include "gromacs/analysisdata/modules/average.h"
  48 #include "gromacs/analysisdata/modules/histogram.h"
  49 #include "gromacs/analysisdata/modules/plot.h"
  50 #include "gromacs/fileio/trx.h"
  51 #include "gromacs/math/vec.h"
  52 #include "gromacs/options/basicoptions.h"
  53 #include "gromacs/options/filenameoption.h"
  54 #include "gromacs/options/options.h"
  55 #include "gromacs/pbcutil/pbc.h"
  56 #include "gromacs/selection/selection.h"
  57 #include "gromacs/selection/selectionoption.h"
  58 #include "gromacs/trajectoryanalysis/analysissettings.h"
  59 #include "gromacs/utility/arrayref.h"
  60 #include "gromacs/utility/exceptions.h"
  61 #include "gromacs/utility/stringutil.h"
  62
  63 namespace gmx
  64 {
  65
  66 namespace analysismodules
  67 {
  68
  69 namespace
  70 {
  71
  72 class Distance : public TrajectoryAnalysisModule
  73 {
  74     public:
  75         Distance();
  76
  77         virtual void initOptions(Options                    *options,
  78                                  TrajectoryAnalysisSettings *settings);
  79         virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
  80                                   const TopologyInformation        &top);
  81
  82         virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
  83                                   TrajectoryAnalysisModuleData *pdata);
  84
  85         virtual void finishAnalysis(int nframes);
  86         virtual void writeOutput();
  87
  88     private:
  89         SelectionList                            sel_;
  90         std::string                              fnAverage_;
  91         std::string                              fnAll_;
  92         std::string                              fnXYZ_;
  93         std::string                              fnHistogram_;
  94         std::string                              fnAllStats_;
  95         double                                   meanLength_;
  96         double                                   lengthDev_;
  97         double                                   binWidth_;
  98
  99         AnalysisData                             distances_;
 100         AnalysisData                             xyz_;
 101         AnalysisDataAverageModulePointer         summaryStatsModule_;
 102         AnalysisDataAverageModulePointer         allStatsModule_;
 103         AnalysisDataFrameAverageModulePointer    averageModule_;
 104         AnalysisDataSimpleHistogramModulePointer histogramModule_;
 105
 106         // Copy and assign disallowed by base.
 107 };
 108
 109 Distance::Distance()
 110     : TrajectoryAnalysisModule(DistanceInfo::name, DistanceInfo::shortDescription),
 111       meanLength_(0.1), lengthDev_(1.0), binWidth_(0.001)
 112 {
 113     summaryStatsModule_.reset(new AnalysisDataAverageModule());
 114     summaryStatsModule_->setAverageDataSets(true);
 115     distances_.addModule(summaryStatsModule_);
 116     allStatsModule_.reset(new AnalysisDataAverageModule());
 117     distances_.addModule(allStatsModule_);
 118     averageModule_.reset(new AnalysisDataFrameAverageModule());
 119     distances_.addModule(averageModule_);
 120     histogramModule_.reset(new AnalysisDataSimpleHistogramModule());
 121     distances_.addModule(histogramModule_);
 122
 123     registerAnalysisDataset(&distances_, "dist");
 124     registerAnalysisDataset(&xyz_, "xyz");
 125     registerBasicDataset(summaryStatsModule_.get(), "stats");
 126     registerBasicDataset(allStatsModule_.get(), "allstats");
 127     registerBasicDataset(averageModule_.get(), "average");
 128     registerBasicDataset(&histogramModule_->averager(), "histogram");
 129 }
 130
 131
 132 void
 133 Distance::initOptions(Options *options, TrajectoryAnalysisSettings * /*settings*/)
 134 {
 135     static const char *const desc[] = {
 136         "[THISMODULE] calculates distances between pairs of positions",
 137         "as a function of time. Each selection specifies an independent set",
 138         "of distances to calculate. Each selection should consist of pairs",
 139         "of positions, and the distances are computed between positions 1-2,",
 140         "3-4, etc.[PAR]",
 141         "[TT]-oav[tt] writes the average distance as a function of time for",
 142         "each selection.",
 143         "[TT]-oall[tt] writes all the individual distances.",
 144         "[TT]-oxyz[tt] does the same, but the x, y, and z components of the",
 145         "distance are written instead of the norm.",
 146         "[TT]-oh[tt] writes a histogram of the distances for each selection.",
 147         "The location of the histogram is set with [TT]-len[tt] and",
 148         "[TT]-tol[tt]. Bin width is set with [TT]-binw[tt].",
 149         "[TT]-oallstat[tt] writes out the average and standard deviation for",
 150         "each individual distance, calculated over the frames."
 151     };
 152
 153     options->setDescription(desc);
 154
 155     options->addOption(FileNameOption("oav").filetype(eftPlot).outputFile()
 156                            .store(&fnAverage_).defaultBasename("distave")
 157                            .description("Average distances as function of time"));
 158     options->addOption(FileNameOption("oall").filetype(eftPlot).outputFile()
 159                            .store(&fnAll_).defaultBasename("dist")
 160                            .description("All distances as function of time"));
 161     options->addOption(FileNameOption("oxyz").filetype(eftPlot).outputFile()
 162                            .store(&fnXYZ_).defaultBasename("distxyz")
 163                            .description("Distance components as function of time"));
 164     options->addOption(FileNameOption("oh").filetype(eftPlot).outputFile()
 165                            .store(&fnHistogram_).defaultBasename("disthist")
 166                            .description("Histogram of the distances"));
 167     options->addOption(FileNameOption("oallstat").filetype(eftPlot).outputFile()
 168                            .store(&fnAllStats_).defaultBasename("diststat")
 169                            .description("Statistics for individual distances"));
 170     options->addOption(SelectionOption("select").storeVector(&sel_)
 171                            .required().dynamicMask().multiValue()
 172                            .description("Position pairs to calculate distances for"));
 173     // TODO: Extend the histogramming implementation to allow automatic
 174     // extension of the histograms to cover the data, removing the need for
 175     // the first two options.
 176     options->addOption(DoubleOption("len").store(&meanLength_)
 177                            .description("Mean distance for histogramming"));
 178     options->addOption(DoubleOption("tol").store(&lengthDev_)
 179                            .description("Width of full distribution as fraction of [TT]-len[tt]"));
 180     options->addOption(DoubleOption("binw").store(&binWidth_)
 181                            .description("Bin width for histogramming"));
 182 }
 183
 184
 185 /*! \brief
 186  * Checks that selections conform to the expectations of the tool.
 187  */
 188 void checkSelections(const SelectionList &sel)
 189 {
 190     for (size_t g = 0; g < sel.size(); ++g)
 191     {
 192         if (sel[g].posCount() % 2 != 0)
 193         {
 194             std::string message = formatString(
 195                         "Selection '%s' does not evaluate into an even number of positions "
 196                         "(there are %d positions)",
 197                         sel[g].name(), sel[g].posCount());
 198             GMX_THROW(InconsistentInputError(message));
 199         }
 200         if (sel[g].isDynamic())
 201         {
 202             for (int i = 0; i < sel[g].posCount(); i += 2)
 203             {
 204                 if (sel[g].position(i).selected() != sel[g].position(i+1).selected())
 205                 {
 206                     std::string message =
 207                         formatString("Dynamic selection %d does not select "
 208                                      "a consistent set of pairs over the frames",
 209                                      static_cast<int>(g + 1));
 210                     GMX_THROW(InconsistentInputError(message));
 211                 }
 212             }
 213         }
 214     }
 215 }
 216
 217
 218 void
 219 Distance::initAnalysis(const TrajectoryAnalysisSettings &settings,
 220                        const TopologyInformation         & /*top*/)
 221 {
 222     checkSelections(sel_);
 223
 224     distances_.setDataSetCount(sel_.size());
 225     xyz_.setDataSetCount(sel_.size());
 226     for (size_t i = 0; i < sel_.size(); ++i)
 227     {
 228         const int distCount = sel_[i].posCount() / 2;
 229         distances_.setColumnCount(i, distCount);
 230         xyz_.setColumnCount(i, distCount * 3);
 231     }
 232     const double histogramMin = (1.0 - lengthDev_) * meanLength_;
 233     const double histogramMax = (1.0 + lengthDev_) * meanLength_;
 234     histogramModule_->init(histogramFromRange(histogramMin, histogramMax)
 235                                .binWidth(binWidth_).includeAll());
 236
 237     if (!fnAverage_.empty())
 238     {
 239         AnalysisDataPlotModulePointer plotm(
 240                 new AnalysisDataPlotModule(settings.plotSettings()));
 241         plotm->setFileName(fnAverage_);
 242         plotm->setTitle("Average distance");
 243         plotm->setXAxisIsTime();
 244         plotm->setYLabel("Distance (nm)");
 245         for (size_t g = 0; g < sel_.size(); ++g)
 246         {
 247             plotm->appendLegend(sel_[g].name());
 248         }
 249         averageModule_->addModule(plotm);
 250     }
 251
 252     if (!fnAll_.empty())
 253     {
 254         AnalysisDataPlotModulePointer plotm(
 255                 new AnalysisDataPlotModule(settings.plotSettings()));
 256         plotm->setFileName(fnAll_);
 257         plotm->setTitle("Distance");
 258         plotm->setXAxisIsTime();
 259         plotm->setYLabel("Distance (nm)");
 260         // TODO: Add legends? (there can be a massive amount of columns)
 261         distances_.addModule(plotm);
 262     }
 263
 264     if (!fnXYZ_.empty())
 265     {
 266         AnalysisDataPlotModulePointer plotm(
 267                 new AnalysisDataPlotModule(settings.plotSettings()));
 268         plotm->setFileName(fnAll_);
 269         plotm->setTitle("Distance");
 270         plotm->setXAxisIsTime();
 271         plotm->setYLabel("Distance (nm)");
 272         // TODO: Add legends? (there can be a massive amount of columns)
 273         xyz_.addModule(plotm);
 274     }
 275
 276     if (!fnHistogram_.empty())
 277     {
 278         AnalysisDataPlotModulePointer plotm(
 279                 new AnalysisDataPlotModule(settings.plotSettings()));
 280         plotm->setFileName(fnHistogram_);
 281         plotm->setTitle("Distance histogram");
 282         plotm->setXLabel("Distance (nm)");
 283         plotm->setYLabel("Probability");
 284         for (size_t g = 0; g < sel_.size(); ++g)
 285         {
 286             plotm->appendLegend(sel_[g].name());
 287         }
 288         histogramModule_->averager().addModule(plotm);
 289     }
 290
 291     if (!fnAllStats_.empty())
 292     {
 293         AnalysisDataPlotModulePointer plotm(
 294                 new AnalysisDataPlotModule(settings.plotSettings()));
 295         plotm->setFileName(fnAllStats_);
 296         plotm->setErrorsAsSeparateColumn(true);
 297         plotm->setTitle("Statistics for individual distances");
 298         plotm->setXLabel("Distance index");
 299         plotm->setYLabel("Average/standard deviation (nm)");
 300         for (size_t g = 0; g < sel_.size(); ++g)
 301         {
 302             plotm->appendLegend(std::string(sel_[g].name()) + " avg");
 303             plotm->appendLegend(std::string(sel_[g].name()) + " std.dev.");
 304         }
 305         // TODO: Consider whether this output format is the best possible.
 306         allStatsModule_->addModule(plotm);
 307     }
 308 }
 309
 310
 311 void
 312 Distance::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
 313                        TrajectoryAnalysisModuleData *pdata)
 314 {
 315     AnalysisDataHandle   distHandle = pdata->dataHandle(distances_);
 316     AnalysisDataHandle   xyzHandle  = pdata->dataHandle(xyz_);
 317     const SelectionList &sel        = pdata->parallelSelections(sel_);
 318
 319     checkSelections(sel);
 320
 321     distHandle.startFrame(frnr, fr.time);
 322     xyzHandle.startFrame(frnr, fr.time);
 323     for (size_t g = 0; g < sel.size(); ++g)
 324     {
 325         distHandle.selectDataSet(g);
 326         xyzHandle.selectDataSet(g);
 327         for (int i = 0, n = 0; i < sel[g].posCount(); i += 2, ++n)
 328         {
 329             const SelectionPosition &p1 = sel[g].position(i);
 330             const SelectionPosition &p2 = sel[g].position(i+1);
 331             rvec                     dx;
 332             if (pbc != NULL)
 333             {
 334                 pbc_dx(pbc, p2.x(), p1.x(), dx);
 335             }
 336             else
 337             {
 338                 rvec_sub(p2.x(), p1.x(), dx);
 339             }
 340             real dist     = norm(dx);
 341             bool bPresent = p1.selected() && p2.selected();
 342             distHandle.setPoint(n, dist, bPresent);
 343             xyzHandle.setPoints(n*3, 3, dx);
 344         }
 345     }
 346     distHandle.finishFrame();
 347     xyzHandle.finishFrame();
 348 }
 349
 350
 351 void
 352 Distance::finishAnalysis(int /*nframes*/)
 353 {
 354     AbstractAverageHistogram &averageHistogram = histogramModule_->averager();
 355     averageHistogram.normalizeProbability();
 356     averageHistogram.done();
 357 }
 358
 359
 360 void
 361 Distance::writeOutput()
 362 {
 363     SelectionList::const_iterator sel;
 364     int                           index;
 365     for (sel = sel_.begin(), index = 0; sel != sel_.end(); ++sel, ++index)
 366     {
 367         printf("%s:\n", sel->name());
 368         printf("  Number of samples:  %d\n",
 369                summaryStatsModule_->sampleCount(index, 0));
 370         printf("  Average distance:   %-6.3f nm\n",
 371                summaryStatsModule_->average(index, 0));
 372         printf("  Standard deviation: %-6.3f nm\n",
 373                summaryStatsModule_->standardDeviation(index, 0));
 374     }
 375 }
 376
 377 }       // namespace
 378
 379 const char DistanceInfo::name[]             = "distance";
 380 const char DistanceInfo::shortDescription[] =
 381     "Calculate distances between pairs of positions";
 382
 383 TrajectoryAnalysisModulePointer DistanceInfo::create()
 384 {
 385     return TrajectoryAnalysisModulePointer(new Distance);
 386 }
 387
 388 } // namespace analysismodules
 389
 390 } // namespace gmx