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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.
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Inherited from |
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inputParametersNames = 'trajectory', 'timeinfo', 'qshellvalues
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default = {'weights': 'coherent'}
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shortName = 'SSCSF'
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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 contribution for one frame.
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Finalizes the calculations (e.g. averaging the total term, output files creations ...). |
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inputParametersNames
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