| Home | Trees | Indices | Help |
|
|---|
|
|
Analysis.Analysis --+
|
CoordinationNumber
Sets up a Coordination Number analysis.
A Subclass of nMOLDYN.Analysis.Analysis.
Constructor: CoordinationNumber(|parameters| = None)
Arguments:
- |parameters| -- a dictionnary of the input parameters, or 'None' to set up the analysis without parameters.
* trajectory -- a trajectory file name or an instance of MMTK.Trajectory.Trajectory class.
* timeinfo -- a string of the form 'first:last:step' where 'first' is an integer specifying the first frame
number to consider, 'last' is an integer specifying the last frame number to consider and
'step' is an integer specifying the step number between two frames.
* rvalues -- a string of the form 'rmin:rmax:dr' where 'rmin' is a float specifying the minimum distance to
consider, 'rmax' is a float specifying the maximum distance value to consider and 'dr' is a float
specifying the distance increment.
* group -- a selection string specifying the groups of atoms that will be used to define the points around which
the coordination number will be computed. For each group, there is one point defined as the center of
gravity of the group.
* subset -- a selection string specifying the atoms to consider for the analysis.
* deuteration -- a selection string specifying the hydrogen atoms whose atomic parameters will be those of the deuterium.
* cn -- the output NetCDF file name. A CDL version of this file will also be generated with the '.cdl' extension
instead of the '.nc' extension.
* pyroserver -- a string specifying if Pyro will be used and how to run the analysis.
Running modes:
- To run the analysis do: a.runAnalysis() where a is the analysis object.
- To estimate the analysis do: a.estimateAnalysis() where a is the analysis object.
- To save the analysis to 'file' file name do: a.saveAnalysis(file) where a is the analysis object.
Comments:
- This code contains a pyrex function for the distance histogram calculation than enhances significantly its
performance.
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
Inherited from |
|||
|
|||
inputParametersNames = 'trajectory', 'timeinfo', 'rvalues', 'g
|
|||
shortName = 'CN'
|
|||
canBeEstimated = True
|
|||
|
|||
The constructor. Insures that the class can not be instanciated directly from here.
|
Initializes the analysis (e.g. parses and checks input parameters, set some variables ...). |
Calculates the contribution for one frame.
|
Finalizes the calculations (e.g. averaging the total term, output files creations ...). |
|
|||
inputParametersNames
|
| Home | Trees | Indices | Help |
|
|---|
| Generated by Epydoc 3.0.1 on Thu Oct 8 16:56:57 2009 | http://epydoc.sourceforge.net |