Package nMOLDYN :: Package Analysis :: Module Structure :: Class CoordinationNumber |
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[frames] | no frames]

# Class CoordinationNumber

source code

    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.

Instance Methods | [hide private]
__init__(self) The constructor. | source code
initialize(self) Initializes the analysis (e.g. | source code
calc(self, frameIndex, trajname) Calculates the contribution for one frame. | source code
combine(self, frameIndex, x) | source code
finalize(self) Finalizes the calculations (e.g. | source code
Inherited from `Analysis.Analysis`: `analysisTime`, `buildJobInfo`, `buildTimeInfo`, `deuterationSelection`, `groupSelection`, `parseInputParameters`, `preLoadTrajectory`, `runAnalysis`, `saveAnalysis`, `setInputParameters`, `subsetSelection`, `updateJobProgress`, `weightingScheme`

Class Variables | [hide private]
| inputParametersNames = `'trajectory', 'timeinfo', 'rvalues', 'g`...``
| shortName = `'CN'`
| canBeEstimated = `True`

Method Details | [hide private]

### __init__(self) (Constructor) | source code
The constructor. Insures that the class can not be instanciated directly from here. Parameters: `parameters` - a dictionnary that contains parameters of the selected analysis. `statusBar` - if not None, an instance of nMOLDYN.GUI.Widgets.StatusBar. Will attach a status bar to the selected analysis. Overrides: Analysis.Analysis.__init__

### initialize(self) | source code
Initializes the analysis (e.g. parses and checks input parameters, set some variables ...).

### calc(self, frameIndex, trajname) | source code
Calculates the contribution for one frame. Parameters: `frameIndex` (integer.) - the index of the frame in |self.frameIndexes| array. `trajname` (string) - the name of the trajectory file name.

### finalize(self) | source code
Finalizes the calculations (e.g. averaging the total term, output files creations ...).

Class Variable Details | [hide private]

  ### inputParametersNames Value:
      'trajectory', 'timeinfo', 'rvalues', 'group', 'subset', 'deuteration',
       'cn', 'pyroserver',