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37 #include <gromacs/trajectoryanalysis.h>
38 #include <gromacs/selection/nbsearch.h>
39 #include <gromacs/math/vec.h>
44 * Template class to serve as a basis for user analysis tools.
46 class SANS : public TrajectoryAnalysisModule
51 virtual void initOptions(IOptionsContainer *options,
52 TrajectoryAnalysisSettings *settings);
53 virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
54 const TopologyInformation &top);
56 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
57 TrajectoryAnalysisModuleData *pdata);
59 virtual void finishAnalysis(int nframes);
60 virtual void writeOutput();
65 double Gaussian(double value, double sigma, RVec Rpos, RVec Rgrid, RVec GridSpacing);
70 AnalysisNeighborhood nb_;
79 double SANS::Gaussian(double value, double sigma, RVec Rpos, RVec Rgrid, RVec GridSpacing)
81 return 2.*value*M_PI*M_PI*GridSpacing[XX]*GridSpacing[YY]*GridSpacing[ZZ]*exp(-distance2(Rpos, Rgrid)/(2*sigma*sigma))/(std::sqrt(2.0)*sigma*sigma*sigma*216.);
85 SANS::initOptions(IOptionsContainer *options,
86 TrajectoryAnalysisSettings *settings)
88 static const char *const desc[] = {
89 "Analysis tool for finding molecular core."
92 // Add the descriptive text (program help text) to the options
93 settings->setHelpText(desc);
97 SANS::initAnalysis(const TrajectoryAnalysisSettings &settings,
98 const TopologyInformation & top)
103 SANS::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
104 TrajectoryAnalysisModuleData *pdata)
106 RVec GridSpacing(0.1, 0.1, 0.1);
111 SANS::finishAnalysis(int nframes)
122 * The main function for the analysis template.
125 main(int argc, char *argv[])
127 return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<SANS>(argc, argv);