Class DynamicIncoherentStructureFactor
source code
Analysis.Analysis --+
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DynamicIncoherentStructureFactor
Sets up an Dynamic Incoherent Structure Factor analysis.
A Subclass of nMOLDYN.Analysis.Analysis.
Constructor: DynamicIncoherentStructureFactorARModel(|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.
* disf -- 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.
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Inherited from Analysis.Analysis :
analysisTime ,
buildJobInfo ,
buildTimeInfo ,
deuterationSelection ,
groupSelection ,
parseInputParameters ,
preLoadTrajectory ,
runAnalysis ,
saveAnalysis ,
setInputParameters ,
subsetSelection ,
updateJobProgress ,
weightingScheme
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inputParametersNames = 'trajectory', 'timeinfo', 'qshellvalues...
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default = {'weights': 'incoherent'}
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shortName = 'DISF'
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canBeEstimated = True
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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__
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Initializes the analysis (e.g. parses and checks input parameters, set
some variables ...).
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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.
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Finalizes the calculations (e.g. averaging the total term, output
files creations ...)
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inputParametersNames
- Value:
'trajectory', 'timeinfo', 'qshellvalues', 'qshellwidth', 'qvectorspers
hell', 'qvectorsgenerator', 'qvectorsdirection', 'fftwindow', 'subset'
, 'deuteration', 'weights', 'disf', 'pyroserver',
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