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Analysis.Analysis --+ | RootMeanSquareDeviation
Sets up a Root Mean Square Deviation analysis. A Subclass of nMOLDYN.Analysis.Analysis. Constructor: RootMeanSquareDeviation(|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. * referenceframe -- an integer in [1,len(trajectory)] specifying which frame should be the reference. * 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. * rmsd -- 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.
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Inherited from |
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inputParametersNames = 'trajectory', 'timeinfo', 'referencefra
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shortName = 'RMSD'
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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.
Note: an atom-by-atom implementation was prefered than a frame-by-frame implementation of the type: msd = t.configuration[frame] - t.configuration[self.referenceFrame] msd = self.weights * msd * msd self.RMSD[frameIndex] = N.sqrt(N.add.reduce(msd)) |
Finalizes the calculations (e.g. averaging the total term, output files creations ...) |
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inputParametersNames
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