Gromacs
5.1.3
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Class used to compute free volume in a simulations box.
Inherits TrajectoryAnalysisModule and all functions from there. Does not implement any new functionality.
Public Member Functions | |
FreeVolume () | |
Constructor. | |
virtual | ~FreeVolume () |
Destructor. | |
virtual void | initOptions (Options *options, TrajectoryAnalysisSettings *settings) |
Set the options and setting. | |
virtual void | initAnalysis (const TrajectoryAnalysisSettings &settings, const TopologyInformation &top) |
First routine called by the analysis framework. | |
virtual void | analyzeFrame (int frnr, const t_trxframe &fr, t_pbc *pbc, TrajectoryAnalysisModuleData *pdata) |
Call for each frame of the trajectory. | |
virtual void | finishAnalysis (int nframes) |
Last routine called by the analysis framework. | |
virtual void | writeOutput () |
Routine to write output, that is additional over the built-in. | |
Public Member Functions inherited from gmx::TrajectoryAnalysisModule | |
virtual void | optionsFinished (Options *options, TrajectoryAnalysisSettings *settings) |
Called after all option values have been set. More... | |
virtual void | initAfterFirstFrame (const TrajectoryAnalysisSettings &settings, const t_trxframe &fr) |
Performs additional initialization after reading the first frame. More... | |
virtual TrajectoryAnalysisModuleDataPointer | startFrames (const AnalysisDataParallelOptions &opt, const SelectionCollection &selections) |
Starts the analysis of frames. More... | |
virtual void | finishFrames (TrajectoryAnalysisModuleData *pdata) |
Finishes the analysis of frames. More... | |
const char * | name () const |
Returns the name of the analysis module. More... | |
const char * | description () const |
Returns short description for the analysis module. More... | |
int | datasetCount () const |
Returns the number of datasets provided by the module. More... | |
const std::vector< std::string > & | datasetNames () const |
Returns a vector with the names of datasets provided by the module. More... | |
AbstractAnalysisData & | datasetFromIndex (int index) const |
Returns a pointer to the data set index . More... | |
AbstractAnalysisData & | datasetFromName (const char *name) const |
Returns a pointer to the data set with name name . More... | |
void | finishFrameSerial (int frameIndex) |
Processes data in AnalysisData objects in serial for each frame. More... | |
Additional Inherited Members | |
Protected Member Functions inherited from gmx::TrajectoryAnalysisModule | |
TrajectoryAnalysisModule (const char *name, const char *description) | |
Initializes the dataset registration mechanism. More... | |
void | registerBasicDataset (AbstractAnalysisData *data, const char *name) |
Registers a dataset that exports data. More... | |
void | registerAnalysisDataset (AnalysisData *data, const char *name) |
Registers a parallelized dataset that exports data. More... | |