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Analysis.Analysis --+ | OrderParameter
Sets up an order parameter analysis. A Subclass of nMOLDYN.Analysis.Analysis. Constructor: OrderParameter(|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. * group -- a selection string specifying the groups of atoms that will define the vectors on which the analysis will be computed. Each group must contain two and only two atoms. * atomorder -- a string of the form 'atom1,atom2,atom3' where 'atom1', 'atom2' and 'atom3' are respectively the MMTK atom names of the atoms in the way they should be ordered. * op -- 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: - This code is based on a first implementation made by Vania Calandrini.
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Inherited from |
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inputParametersNames = 'trajectory', 'timeinfo', 'bond', 'atom
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shortName = 'OP'
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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 group.
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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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