Package nMOLDYN :: Package Analysis :: Module Scattering :: Class DynamicIncoherentStructureFactorGaussian |
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# Class DynamicIncoherentStructureFactorGaussian

source code

    Analysis.Analysis --+
                        |
                       DynamicIncoherentStructureFactorGaussian

    Sets up an Dynamic Incoherent Structure Factor analysis within Gaussian approximation.

    A Subclass of nMOLDYN.Analysis.Analysis.

    Constructor: DynamicIncoherentStructureFactorGaussian(|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.
            * qshellvalues -- a string of the form 'qmin1:qmax1:dq1;qmin2:qmax2:dq2...' where 'qmin1', 'qmin2' ... ,
                              'qmax1', 'qmax2' ... and 'dq1', 'dq2' ... are floats that represents respectively
                              the q minimum, the q maximum and the q steps for q interval 1, 2 ...
            * fftwindow    -- a float in ]0.0,100.0[ specifying the width of the gaussian, in percentage of the trajectory length
                              that will be used in the smoothing procedure.
            * 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.
            * disfg        -- the output NetCDF file name for the intermediate scattering function.
            * 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.

Instance Methods | [hide private]
__init__(self) The constructor. | source code
initialize(self) Initializes the analysis (e.g. | source code
calc(self, atom, trajname) Calculates the atomic term. | source code
combine(self, atom, x) | source code
finalize(self) Finalizes the calculations (e.g. | source code
getMSD(self, series) Computes the atomic component of the Mean-Square-Displacement. | 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', 'qshellvalues`...``
| default = `{'weights': 'incoherent'}`
| shortName = `'DISFG'`
| 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, atom, trajname) | source code
Calculates the atomic term. Parameters: `atom` (an instance of MMTK.Atom class.) - the atom on which the atomic term has been calculated. `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 ...)

### getMSD(self, series) | source code
Computes the atomic component of the Mean-Square-Displacement. This is the exact copy of the version written in nMOLDYN.Simulations.Dynamics but rewritten here for to keep the module Scattering independant from module Dynamics.

Class Variable Details | [hide private]

  ### inputParametersNames Value:
      'trajectory', 'timeinfo', 'qshellvalues', 'fftwindow', 'subset', 'deut
      eration', 'weights', 'disfg', 'pyroserver',