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37 * Implements gmx::analysismodules::Distance.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_trajectoryanalysis
44 #include "gromacs/legacyheaders/pbc.h"
45 #include "gromacs/legacyheaders/vec.h"
47 #include "gromacs/analysisdata/analysisdata.h"
48 #include "gromacs/analysisdata/modules/plot.h"
49 #include "gromacs/options/basicoptions.h"
50 #include "gromacs/options/filenameoption.h"
51 #include "gromacs/options/options.h"
52 #include "gromacs/selection/selection.h"
53 #include "gromacs/selection/selectionoption.h"
54 #include "gromacs/trajectoryanalysis/analysissettings.h"
55 #include "gromacs/utility/exceptions.h"
56 #include "gromacs/utility/stringutil.h"
61 namespace analysismodules
64 const char Distance::name[] = "distance";
65 const char Distance::shortDescription[] =
66 "Calculate distances";
69 : TrajectoryAnalysisModule(name, shortDescription),
70 avem_(new AnalysisDataAverageModule())
72 data_.setColumnCount(4);
73 registerAnalysisDataset(&data_, "distance");
83 Distance::initOptions(Options *options, TrajectoryAnalysisSettings * /*settings*/)
85 static const char *const desc[] = {
86 "g_dist can calculate the distance between two positions as",
87 "a function of time. The total distance and its",
88 "x, y and z components are plotted."
91 options->setDescription(concatenateStrings(desc));
93 options->addOption(FileNameOption("o").filetype(eftPlot).outputFile()
94 .store(&fnDist_).defaultBasename("dist")
95 .description("Computed distances"));
96 options->addOption(SelectionOption("select").required().valueCount(2)
102 Distance::initAnalysis(const TrajectoryAnalysisSettings &settings,
103 const TopologyInformation & /*top*/)
105 if (sel_[0].posCount() != 1)
107 GMX_THROW(InvalidInputError("The first selection does not define a single position"));
109 if (sel_[1].posCount() != 1)
111 GMX_THROW(InvalidInputError("The second selection does not define a single position"));
114 data_.addModule(avem_);
115 AnalysisDataPlotModulePointer plotm_(new AnalysisDataPlotModule());
116 plotm_->setSettings(settings.plotSettings());
117 plotm_->setFileName(fnDist_);
118 plotm_->setTitle("Distance");
119 plotm_->setXAxisIsTime();
120 plotm_->setYLabel("Distance (nm)");
121 data_.addModule(plotm_);
126 Distance::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
127 TrajectoryAnalysisModuleData *pdata)
129 AnalysisDataHandle dh = pdata->dataHandle(data_);
130 const Selection &sel1 = pdata->parallelSelection(sel_[0]);
131 const Selection &sel2 = pdata->parallelSelection(sel_[1]);
134 const SelectionPosition &p1 = sel1.position(0);
135 const SelectionPosition &p2 = sel2.position(0);
139 pbc_dx(pbc, p1.x(), p2.x(), dx);
143 rvec_sub(p1.x(), p2.x(), dx);
146 dh.startFrame(frnr, fr.time);
148 dh.setPoints(1, 3, dx);
154 Distance::finishAnalysis(int /*nframes*/)
160 Distance::writeOutput()
162 fprintf(stderr, "Average distance: %f\n", avem_->average(0));
163 fprintf(stderr, "Std. deviation: %f\n", avem_->stddev(0));
166 } // namespace analysismodules