Package nMOLDYN :: Package Analysis :: Module Scattering :: Class SmoothedStaticCoherentStructureFactor
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Class SmoothedStaticCoherentStructureFactor

source code

Analysis.Analysis --+
                    |
                   SmoothedStaticCoherentStructureFactor

Sets up an Smoothed Static Coherent Structure Factor.

A Subclass of nMOLDYN.Analysis.Analysis. 

Constructor: SmoothedStaticCoherentStructureFactor(|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 ...
        * 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.
        * scsf              -- 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:
    
    - The analysis is based on the angular averaged coherent static structure factor formula where the
      summation over the q vectors is replaced by an integral over the q space. The formula used is taken 
      from equation 2.35 of Fischer et al. Rep. Prog. Phys. 69 (2006) 233-299.
    

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', 'qshellvalues...
  default = {'weights': 'coherent'}
  shortName = 'SSCSF'
  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', 'qshellvalues', 'subset', 'deuteration', 'we\
ights', 'sscsf', 'pyroserver',