Package nMOLDYN :: Package Analysis :: Module Structure :: Class PairDistributionFunction
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Class PairDistributionFunction

source code

Analysis.Analysis --+
                    |
                   PairDistributionFunction

Sets up a Pair Distribution Function analysis.

A Subclass of nMOLDYN.Analysis.Analysis. 

Constructor: PairDistributionFunction(|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. 
        * 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.
        * weights     -- a string equal to 'equal', 'mass', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting
                         scheme to use.
        * pdf         -- 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 that is based on a FORTRAN code 
      written by Miguel Gonzalez, Insitut Laue Langevin, Grenoble, France.

Instance Methods [hide private]
 
__init__(self)
The constructor.
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initialize(self)
Initializes the analysis (e.g.
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calc(self, frameIndex, trajname)
Calculates the contribution for one frame.
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combine(self, frameIndex, x) source code
 
finalize(self)
Finalizes the calculations (e.g.
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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', 's...
  shortName = 'PDF'
  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)

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Initializes the analysis (e.g. parses and checks input parameters, set some variables ...).

calc(self, frameIndex, trajname)

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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)

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Finalizes the calculations (e.g. averaging the total term, output files creations ...).


Class Variable Details [hide private]

inputParametersNames

Value:
'trajectory', 'timeinfo', 'rvalues', 'subset', 'deuteration', 'weights\
', 'pdf', 'pyroserver',