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37 * Implements gmx::analysismodules::Distance.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_trajectoryanalysis
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/fileio/trx.h"
53 #include "gromacs/math/vec.h"
54 #include "gromacs/options/basicoptions.h"
55 #include "gromacs/options/filenameoption.h"
56 #include "gromacs/options/options.h"
57 #include "gromacs/pbcutil/pbc.h"
58 #include "gromacs/selection/selection.h"
59 #include "gromacs/selection/selectionoption.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"
68 namespace analysismodules
74 class Distance : public TrajectoryAnalysisModule
79 virtual void initOptions(Options *options,
80 TrajectoryAnalysisSettings *settings);
81 virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
82 const TopologyInformation &top);
84 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
85 TrajectoryAnalysisModuleData *pdata);
87 virtual void finishAnalysis(int nframes);
88 virtual void writeOutput();
92 std::string fnAverage_;
95 std::string fnHistogram_;
96 std::string fnAllStats_;
101 AnalysisData distances_;
103 AnalysisDataAverageModulePointer summaryStatsModule_;
104 AnalysisDataAverageModulePointer allStatsModule_;
105 AnalysisDataFrameAverageModulePointer averageModule_;
106 AnalysisDataSimpleHistogramModulePointer histogramModule_;
108 // Copy and assign disallowed by base.
112 : TrajectoryAnalysisModule(DistanceInfo::name, DistanceInfo::shortDescription),
113 meanLength_(0.1), lengthDev_(1.0), binWidth_(0.001)
115 summaryStatsModule_.reset(new AnalysisDataAverageModule());
116 summaryStatsModule_->setAverageDataSets(true);
117 distances_.addModule(summaryStatsModule_);
118 allStatsModule_.reset(new AnalysisDataAverageModule());
119 distances_.addModule(allStatsModule_);
120 averageModule_.reset(new AnalysisDataFrameAverageModule());
121 distances_.addModule(averageModule_);
122 histogramModule_.reset(new AnalysisDataSimpleHistogramModule());
123 distances_.addModule(histogramModule_);
125 registerAnalysisDataset(&distances_, "dist");
126 registerAnalysisDataset(&xyz_, "xyz");
127 registerBasicDataset(summaryStatsModule_.get(), "stats");
128 registerBasicDataset(allStatsModule_.get(), "allstats");
129 registerBasicDataset(averageModule_.get(), "average");
130 registerBasicDataset(&histogramModule_->averager(), "histogram");
135 Distance::initOptions(Options *options, TrajectoryAnalysisSettings * /*settings*/)
137 static const char *const desc[] = {
138 "[THISMODULE] calculates distances between pairs of positions",
139 "as a function of time. Each selection specifies an independent set",
140 "of distances to calculate. Each selection should consist of pairs",
141 "of positions, and the distances are computed between positions 1-2,",
143 "[TT]-oav[tt] writes the average distance as a function of time for",
145 "[TT]-oall[tt] writes all the individual distances.",
146 "[TT]-oxyz[tt] does the same, but the x, y, and z components of the",
147 "distance are written instead of the norm.",
148 "[TT]-oh[tt] writes a histogram of the distances for each selection.",
149 "The location of the histogram is set with [TT]-len[tt] and",
150 "[TT]-tol[tt]. Bin width is set with [TT]-binw[tt].",
151 "[TT]-oallstat[tt] writes out the average and standard deviation for",
152 "each individual distance, calculated over the frames."
155 options->setDescription(desc);
157 options->addOption(FileNameOption("oav").filetype(eftPlot).outputFile()
158 .store(&fnAverage_).defaultBasename("distave")
159 .description("Average distances as function of time"));
160 options->addOption(FileNameOption("oall").filetype(eftPlot).outputFile()
161 .store(&fnAll_).defaultBasename("dist")
162 .description("All distances as function of time"));
163 options->addOption(FileNameOption("oxyz").filetype(eftPlot).outputFile()
164 .store(&fnXYZ_).defaultBasename("distxyz")
165 .description("Distance components as function of time"));
166 options->addOption(FileNameOption("oh").filetype(eftPlot).outputFile()
167 .store(&fnHistogram_).defaultBasename("disthist")
168 .description("Histogram of the distances"));
169 options->addOption(FileNameOption("oallstat").filetype(eftPlot).outputFile()
170 .store(&fnAllStats_).defaultBasename("diststat")
171 .description("Statistics for individual distances"));
172 options->addOption(SelectionOption("select").storeVector(&sel_)
173 .required().dynamicMask().multiValue()
174 .description("Position pairs to calculate distances for"));
175 // TODO: Extend the histogramming implementation to allow automatic
176 // extension of the histograms to cover the data, removing the need for
177 // the first two options.
178 options->addOption(DoubleOption("len").store(&meanLength_)
179 .description("Mean distance for histogramming"));
180 options->addOption(DoubleOption("tol").store(&lengthDev_)
181 .description("Width of full distribution as fraction of [TT]-len[tt]"));
182 options->addOption(DoubleOption("binw").store(&binWidth_)
183 .description("Bin width for histogramming"));
188 * Checks that selections conform to the expectations of the tool.
190 void checkSelections(const SelectionList &sel)
192 for (size_t g = 0; g < sel.size(); ++g)
194 if (sel[g].posCount() % 2 != 0)
196 std::string message = formatString(
197 "Selection '%s' does not evaluate into an even number of positions "
198 "(there are %d positions)",
199 sel[g].name(), sel[g].posCount());
200 GMX_THROW(InconsistentInputError(message));
202 if (sel[g].isDynamic())
204 for (int i = 0; i < sel[g].posCount(); i += 2)
206 if (sel[g].position(i).selected() != sel[g].position(i+1).selected())
208 std::string message =
209 formatString("Dynamic selection %d does not select "
210 "a consistent set of pairs over the frames",
211 static_cast<int>(g + 1));
212 GMX_THROW(InconsistentInputError(message));
221 Distance::initAnalysis(const TrajectoryAnalysisSettings &settings,
222 const TopologyInformation & /*top*/)
224 checkSelections(sel_);
226 distances_.setDataSetCount(sel_.size());
227 xyz_.setDataSetCount(sel_.size());
228 for (size_t i = 0; i < sel_.size(); ++i)
230 const int distCount = sel_[i].posCount() / 2;
231 distances_.setColumnCount(i, distCount);
232 xyz_.setColumnCount(i, distCount * 3);
234 const double histogramMin = (1.0 - lengthDev_) * meanLength_;
235 const double histogramMax = (1.0 + lengthDev_) * meanLength_;
236 histogramModule_->init(histogramFromRange(histogramMin, histogramMax)
237 .binWidth(binWidth_).includeAll());
239 if (!fnAverage_.empty())
241 AnalysisDataPlotModulePointer plotm(
242 new AnalysisDataPlotModule(settings.plotSettings()));
243 plotm->setFileName(fnAverage_);
244 plotm->setTitle("Average distance");
245 plotm->setXAxisIsTime();
246 plotm->setYLabel("Distance (nm)");
247 for (size_t g = 0; g < sel_.size(); ++g)
249 plotm->appendLegend(sel_[g].name());
251 averageModule_->addModule(plotm);
256 AnalysisDataPlotModulePointer plotm(
257 new AnalysisDataPlotModule(settings.plotSettings()));
258 plotm->setFileName(fnAll_);
259 plotm->setTitle("Distance");
260 plotm->setXAxisIsTime();
261 plotm->setYLabel("Distance (nm)");
262 // TODO: Add legends? (there can be a massive amount of columns)
263 distances_.addModule(plotm);
268 AnalysisDataPlotModulePointer plotm(
269 new AnalysisDataPlotModule(settings.plotSettings()));
270 plotm->setFileName(fnAll_);
271 plotm->setTitle("Distance");
272 plotm->setXAxisIsTime();
273 plotm->setYLabel("Distance (nm)");
274 // TODO: Add legends? (there can be a massive amount of columns)
275 xyz_.addModule(plotm);
278 if (!fnHistogram_.empty())
280 AnalysisDataPlotModulePointer plotm(
281 new AnalysisDataPlotModule(settings.plotSettings()));
282 plotm->setFileName(fnHistogram_);
283 plotm->setTitle("Distance histogram");
284 plotm->setXLabel("Distance (nm)");
285 plotm->setYLabel("Probability");
286 for (size_t g = 0; g < sel_.size(); ++g)
288 plotm->appendLegend(sel_[g].name());
290 histogramModule_->averager().addModule(plotm);
293 if (!fnAllStats_.empty())
295 AnalysisDataPlotModulePointer plotm(
296 new AnalysisDataPlotModule(settings.plotSettings()));
297 plotm->setFileName(fnAllStats_);
298 plotm->setErrorsAsSeparateColumn(true);
299 plotm->setTitle("Statistics for individual distances");
300 plotm->setXLabel("Distance index");
301 plotm->setYLabel("Average/standard deviation (nm)");
302 for (size_t g = 0; g < sel_.size(); ++g)
304 plotm->appendLegend(std::string(sel_[g].name()) + " avg");
305 plotm->appendLegend(std::string(sel_[g].name()) + " std.dev.");
307 // TODO: Consider whether this output format is the best possible.
308 allStatsModule_->addModule(plotm);
314 Distance::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
315 TrajectoryAnalysisModuleData *pdata)
317 AnalysisDataHandle distHandle = pdata->dataHandle(distances_);
318 AnalysisDataHandle xyzHandle = pdata->dataHandle(xyz_);
319 const SelectionList &sel = pdata->parallelSelections(sel_);
321 checkSelections(sel);
323 distHandle.startFrame(frnr, fr.time);
324 xyzHandle.startFrame(frnr, fr.time);
325 for (size_t g = 0; g < sel.size(); ++g)
327 distHandle.selectDataSet(g);
328 xyzHandle.selectDataSet(g);
329 for (int i = 0, n = 0; i < sel[g].posCount(); i += 2, ++n)
331 const SelectionPosition &p1 = sel[g].position(i);
332 const SelectionPosition &p2 = sel[g].position(i+1);
336 pbc_dx(pbc, p2.x(), p1.x(), dx);
340 rvec_sub(p2.x(), p1.x(), dx);
342 real dist = norm(dx);
343 bool bPresent = p1.selected() && p2.selected();
344 distHandle.setPoint(n, dist, bPresent);
345 xyzHandle.setPoints(n*3, 3, dx);
348 distHandle.finishFrame();
349 xyzHandle.finishFrame();
354 Distance::finishAnalysis(int /*nframes*/)
356 AbstractAverageHistogram &averageHistogram = histogramModule_->averager();
357 averageHistogram.normalizeProbability();
358 averageHistogram.done();
363 Distance::writeOutput()
365 SelectionList::const_iterator sel;
367 for (sel = sel_.begin(), index = 0; sel != sel_.end(); ++sel, ++index)
369 printf("%s:\n", sel->name());
370 printf(" Number of samples: %d\n",
371 summaryStatsModule_->sampleCount(index, 0));
372 printf(" Average distance: %-8.5f nm\n",
373 summaryStatsModule_->average(index, 0));
374 printf(" Standard deviation: %-8.5f nm\n",
375 summaryStatsModule_->standardDeviation(index, 0));
381 const char DistanceInfo::name[] = "distance";
382 const char DistanceInfo::shortDescription[] =
383 "Calculate distances between pairs of positions";
385 TrajectoryAnalysisModulePointer DistanceInfo::create()
387 return TrajectoryAnalysisModulePointer(new Distance);
390 } // namespace analysismodules