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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.
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Inherited from |
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inputParametersNames = 'trajectory', 'timeinfo', 'qshellvalues
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default = {'weights': 'incoherent'}
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shortName = 'DISFG'
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canBeEstimated = True
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The constructor. Insures that the class can not be instanciated directly from here.
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Initializes the analysis (e.g. parses and checks input parameters, set some variables ...). |
Calculates the atomic term.
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Finalizes the calculations (e.g. averaging the total term, output files creations ...) |
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. |
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inputParametersNames
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