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37 * Implements gmx::analysismodules::Distance.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_trajectoryanalysis
46 #include "gromacs/legacyheaders/pbc.h"
47 #include "gromacs/legacyheaders/vec.h"
49 #include "gromacs/analysisdata/analysisdata.h"
50 #include "gromacs/analysisdata/modules/average.h"
51 #include "gromacs/analysisdata/modules/histogram.h"
52 #include "gromacs/analysisdata/modules/plot.h"
53 #include "gromacs/options/basicoptions.h"
54 #include "gromacs/options/filenameoption.h"
55 #include "gromacs/options/options.h"
56 #include "gromacs/selection/selection.h"
57 #include "gromacs/selection/selectionoption.h"
58 #include "gromacs/trajectoryanalysis/analysissettings.h"
59 #include "gromacs/utility/exceptions.h"
60 #include "gromacs/utility/stringutil.h"
65 namespace analysismodules
71 class Distance : public TrajectoryAnalysisModule
76 virtual void initOptions(Options *options,
77 TrajectoryAnalysisSettings *settings);
78 virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
79 const TopologyInformation &top);
81 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
82 TrajectoryAnalysisModuleData *pdata);
84 virtual void finishAnalysis(int nframes);
85 virtual void writeOutput();
89 std::string fnAverage_;
92 std::string fnHistogram_;
93 std::string fnAllStats_;
98 AnalysisData distances_;
100 AnalysisDataAverageModulePointer summaryStatsModule_;
101 AnalysisDataAverageModulePointer allStatsModule_;
102 AnalysisDataFrameAverageModulePointer averageModule_;
103 AnalysisDataSimpleHistogramModulePointer histogramModule_;
105 // Copy and assign disallowed by base.
109 : TrajectoryAnalysisModule(DistanceInfo::name, DistanceInfo::shortDescription),
110 meanLength_(0.1), lengthDev_(1.0), binWidth_(0.001)
112 summaryStatsModule_.reset(new AnalysisDataAverageModule());
113 summaryStatsModule_->setAverageDataSets(true);
114 distances_.addModule(summaryStatsModule_);
115 allStatsModule_.reset(new AnalysisDataAverageModule());
116 distances_.addModule(allStatsModule_);
117 averageModule_.reset(new AnalysisDataFrameAverageModule());
118 distances_.addModule(averageModule_);
119 histogramModule_.reset(new AnalysisDataSimpleHistogramModule());
120 distances_.addModule(histogramModule_);
122 registerAnalysisDataset(&distances_, "dist");
123 registerAnalysisDataset(&xyz_, "xyz");
124 registerBasicDataset(summaryStatsModule_.get(), "stats");
125 registerBasicDataset(allStatsModule_.get(), "allstats");
126 registerBasicDataset(averageModule_.get(), "average");
127 registerBasicDataset(&histogramModule_->averager(), "histogram");
132 Distance::initOptions(Options *options, TrajectoryAnalysisSettings * /*settings*/)
134 static const char *const desc[] = {
135 "[TT]gmx distance[tt] calculates distances between pairs of positions",
136 "as a function of time. Each selection specifies an independent set",
137 "of distances to calculate. Each selection should consist of pairs",
138 "of positions, and the distances are computed between positions 1-2,",
140 "[TT]-oav[tt] writes the average distance as a function of time for",
142 "[TT]-oall[tt] writes all the individual distances.",
143 "[TT]-oxyz[tt] does the same, but the x, y, and z components of the",
144 "distance are written instead of the norm.",
145 "[TT]-oh[tt] writes a histogram of the distances for each selection.",
146 "The location of the histogram is set with [TT]-len[tt] and",
147 "[TT]-tol[tt]. Bin width is set with [TT]-binw[tt].",
148 "[TT]-oallstat[tt] writes out the average and standard deviation for",
149 "each individual distance, calculated over the frames."
152 options->setDescription(concatenateStrings(desc));
154 options->addOption(FileNameOption("oav").filetype(eftPlot).outputFile()
155 .store(&fnAverage_).defaultBasename("distave")
156 .description("Average distances as function of time"));
157 options->addOption(FileNameOption("oall").filetype(eftPlot).outputFile()
158 .store(&fnAll_).defaultBasename("dist")
159 .description("All distances as function of time"));
160 options->addOption(FileNameOption("oxyz").filetype(eftPlot).outputFile()
161 .store(&fnXYZ_).defaultBasename("distxyz")
162 .description("Distance components as function of time"));
163 options->addOption(FileNameOption("oh").filetype(eftPlot).outputFile()
164 .store(&fnHistogram_).defaultBasename("disthist")
165 .description("Histogram of the distances"));
166 options->addOption(FileNameOption("oallstat").filetype(eftPlot).outputFile()
167 .store(&fnAllStats_).defaultBasename("diststat")
168 .description("Statistics for individual distances"));
169 options->addOption(SelectionOption("select").storeVector(&sel_)
170 .required().dynamicMask().multiValue()
171 .description("Position pairs to calculate distances for"));
172 // TODO: Extend the histogramming implementation to allow automatic
173 // extension of the histograms to cover the data, removing the need for
174 // the first two options.
175 options->addOption(DoubleOption("len").store(&meanLength_)
176 .description("Mean distance for histogramming"));
177 options->addOption(DoubleOption("tol").store(&lengthDev_)
178 .description("Width of full distribution as fraction of [TT]-len[tt]"));
179 options->addOption(DoubleOption("binw").store(&binWidth_)
180 .description("Bin width for histogramming"));
185 * Checks that selections conform to the expectations of the tool.
187 void checkSelections(const SelectionList &sel)
189 for (size_t g = 0; g < sel.size(); ++g)
191 if (sel[g].posCount() % 2 != 0)
193 std::string message = formatString(
194 "Selection '%s' does not evaluate into an even number of positions "
195 "(there are %d positions)",
196 sel[g].name(), sel[g].posCount());
197 GMX_THROW(InconsistentInputError(message));
199 if (sel[g].isDynamic())
201 for (int i = 0; i < sel[g].posCount(); i += 2)
203 if (sel[g].position(i).selected() != sel[g].position(i+1).selected())
205 std::string message =
206 formatString("Dynamic selection %d does not select "
207 "a consistent set of pairs over the frames",
208 static_cast<int>(g + 1));
209 GMX_THROW(InconsistentInputError(message));
218 Distance::initAnalysis(const TrajectoryAnalysisSettings &settings,
219 const TopologyInformation & /*top*/)
221 checkSelections(sel_);
223 distances_.setDataSetCount(sel_.size());
224 xyz_.setDataSetCount(sel_.size());
225 for (size_t i = 0; i < sel_.size(); ++i)
227 const int distCount = sel_[i].posCount() / 2;
228 distances_.setColumnCount(i, distCount);
229 xyz_.setColumnCount(i, distCount * 3);
231 const double histogramMin = (1.0 - lengthDev_) * meanLength_;
232 const double histogramMax = (1.0 + lengthDev_) * meanLength_;
233 histogramModule_->init(histogramFromRange(histogramMin, histogramMax)
234 .binWidth(binWidth_).includeAll());
236 if (!fnAverage_.empty())
238 AnalysisDataPlotModulePointer plotm(
239 new AnalysisDataPlotModule(settings.plotSettings()));
240 plotm->setFileName(fnAverage_);
241 plotm->setTitle("Average distance");
242 plotm->setXAxisIsTime();
243 plotm->setYLabel("Distance (nm)");
244 for (size_t g = 0; g < sel_.size(); ++g)
246 plotm->appendLegend(sel_[g].name());
248 averageModule_->addModule(plotm);
253 AnalysisDataPlotModulePointer plotm(
254 new AnalysisDataPlotModule(settings.plotSettings()));
255 plotm->setFileName(fnAll_);
256 plotm->setTitle("Distance");
257 plotm->setXAxisIsTime();
258 plotm->setYLabel("Distance (nm)");
259 // TODO: Add legends? (there can be a massive amount of columns)
260 distances_.addModule(plotm);
265 AnalysisDataPlotModulePointer plotm(
266 new AnalysisDataPlotModule(settings.plotSettings()));
267 plotm->setFileName(fnAll_);
268 plotm->setTitle("Distance");
269 plotm->setXAxisIsTime();
270 plotm->setYLabel("Distance (nm)");
271 // TODO: Add legends? (there can be a massive amount of columns)
272 xyz_.addModule(plotm);
275 if (!fnHistogram_.empty())
277 AnalysisDataPlotModulePointer plotm(
278 new AnalysisDataPlotModule(settings.plotSettings()));
279 plotm->setFileName(fnHistogram_);
280 plotm->setTitle("Distance histogram");
281 plotm->setXLabel("Distance (nm)");
282 plotm->setYLabel("Probability");
283 for (size_t g = 0; g < sel_.size(); ++g)
285 plotm->appendLegend(sel_[g].name());
287 histogramModule_->averager().addModule(plotm);
290 if (!fnAllStats_.empty())
292 AnalysisDataPlotModulePointer plotm(
293 new AnalysisDataPlotModule(settings.plotSettings()));
294 plotm->setFileName(fnAllStats_);
295 plotm->setErrorsAsSeparateColumn(true);
296 plotm->setTitle("Statistics for individual distances");
297 plotm->setXLabel("Distance index");
298 plotm->setYLabel("Average/standard deviation (nm)");
299 for (size_t g = 0; g < sel_.size(); ++g)
301 plotm->appendLegend(std::string(sel_[g].name()) + " avg");
302 plotm->appendLegend(std::string(sel_[g].name()) + " std.dev.");
304 // TODO: Consider whether this output format is the best possible.
305 allStatsModule_->addModule(plotm);
311 Distance::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
312 TrajectoryAnalysisModuleData *pdata)
314 AnalysisDataHandle distHandle = pdata->dataHandle(distances_);
315 AnalysisDataHandle xyzHandle = pdata->dataHandle(xyz_);
316 const SelectionList &sel = pdata->parallelSelections(sel_);
318 checkSelections(sel);
320 distHandle.startFrame(frnr, fr.time);
321 xyzHandle.startFrame(frnr, fr.time);
322 for (size_t g = 0; g < sel.size(); ++g)
324 distHandle.selectDataSet(g);
325 xyzHandle.selectDataSet(g);
326 for (int i = 0, n = 0; i < sel[g].posCount(); i += 2, ++n)
328 const SelectionPosition &p1 = sel[g].position(i);
329 const SelectionPosition &p2 = sel[g].position(i+1);
333 pbc_dx(pbc, p2.x(), p1.x(), dx);
337 rvec_sub(p2.x(), p1.x(), dx);
339 real dist = norm(dx);
340 bool bPresent = p1.selected() && p2.selected();
341 distHandle.setPoint(n, dist, bPresent);
342 xyzHandle.setPoints(n*3, 3, dx);
345 distHandle.finishFrame();
346 xyzHandle.finishFrame();
351 Distance::finishAnalysis(int /*nframes*/)
353 AbstractAverageHistogram &averageHistogram = histogramModule_->averager();
354 averageHistogram.normalizeProbability();
355 averageHistogram.done();
360 Distance::writeOutput()
362 SelectionList::const_iterator sel;
364 for (sel = sel_.begin(), index = 0; sel != sel_.end(); ++sel, ++index)
366 printf("%s:\n", sel->name());
367 printf(" Number of samples: %d\n",
368 summaryStatsModule_->sampleCount(index, 0));
369 printf(" Average distance: %-6.3f nm\n",
370 summaryStatsModule_->average(index, 0));
371 printf(" Standard deviation: %-6.3f nm\n",
372 summaryStatsModule_->standardDeviation(index, 0));
378 const char DistanceInfo::name[] = "distance";
379 const char DistanceInfo::shortDescription[] =
380 "Calculate distances between pairs of positions";
382 TrajectoryAnalysisModulePointer DistanceInfo::create()
384 return TrajectoryAnalysisModulePointer(new Distance);
387 } // namespace analysismodules