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37 * Declares trajectory analysis module for distance calculations.
39 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
40 * \ingroup module_trajectoryanalysis
42 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_FREEVOLUME_H
43 #define GMX_TRAJECTORYANALYSIS_MODULES_FREEVOLUME_H
46 #include "gromacs/legacyheaders/gmx_random.h"
47 #include "../analysismodule.h"
48 #include "gromacs/selection/nbsearch.h"
49 #include "gromacs/selection/indexutil.h"
50 #include "gromacs/analysisdata/analysisdata.h"
51 #include "gromacs/analysisdata/modules/average.h"
52 #include "gromacs/selection/selection.h"
57 namespace analysismodules
61 * Class used to compute free volume in a simulations box.
63 * Inherits TrajectoryAnalysisModule and all functions from there.
64 * Does not implement any new functionality.
67 * \ingroup module_trajectoryanalysis
69 class FreeVolume : public TrajectoryAnalysisModule
73 static const char name[];
75 //! One line description
76 static const char shortDescription[];
82 virtual ~FreeVolume();
84 //! Set the options and setting
85 virtual void initOptions(Options *options,
86 TrajectoryAnalysisSettings *settings);
88 //! First routine called by the analysis frame work
89 virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
90 const TopologyInformation &top);
92 //! Call for each frame of the trajectory
93 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
94 TrajectoryAnalysisModuleData *pdata);
96 //! Last routine called by the analysis frame work
97 virtual void finishAnalysis(int nframes);
99 //! Routine to write output, that is additional over the built-in
100 virtual void writeOutput();
103 std::string fnFreevol_;
106 AnalysisDataAverageModulePointer adata_;
114 gmx_ana_nbsearch_t *nbsearch_;
115 //! The van der Waals radius per atom
116 std::vector<double> vdw_radius_;
118 // Copy and assign disallowed by base.
121 } // namespace analysismodules