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

source code

    Analysis.Analysis --+
                        |
                       StaticCoherentStructureFactor

    Sets up a Coherent Structure Factor analysis.

    A Subclass of nMOLDYN.Analysis.Analysis.

    Constructor: StaticCoherentStructureFactor(|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 ...
            * qshellwidth       -- a float specifying the width of the q shells.
            * qvectorspershell  -- a float specifying the number of q vectors to generate per q shell.
            * qvectorsgenerator -- a string being one of 'isotropic', 'anisotropic' or 'explicit' specifying the way the q vectors
                                   will be generated.
            * qvectorsdirection -- a string of the form 'v1x,v1y,v1z;v2x,v2y,v2z...' where 'v1x', 'v2x' ..., 'v1y', 'v2y' ... and
                                   'v1z', 'v2z' ... are floats that represents respectively the x, y and z values of the vectord along
                                   which the q vectors should be generated.
            * 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.
            * csf               -- 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, qIndex, trajname) Calculates the contribution for one Q-shell. | source code
combine(self, qIndex, 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', 'qshellvalues`...``
| default = `{'weights': 'coherent'}`
| shortName = `'SCSF'`
| canBeEstimated = `False`

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, qIndex, trajname) | source code
Calculates the contribution for one Q-shell. Parameters: `qIndex` (integer.) - the index of the Q-shell in |self.qRadii| list. `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', 'qshellvalues', 'qshellwidth', 'qvectorspers
      hell', 'qvectorsgenerator', 'qvectorsdirection', 'subset', 'deuteratio
      n', 'weights', 'scsf', 'pyroserver',