Package nMOLDYN :: Package Analysis :: Module Dynamics :: Class RootMeanSquareDeviation |
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# Class RootMeanSquareDeviation

source code

    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.

Instance Methods | [hide private]
__init__(self) The constructor. | source code
initialize(self) Initializes the analysis (e.g. | source code
calc(self, atom, trajname) Calculates the atomic term. | source code
combine(self, atom, x) | source code
finalize(self) Finalizes the calculations (e.g. | source code
Inherited from `Analysis.Analysis`: `analysisTime`, `buildJobInfo`, `buildTimeInfo`, `deuterationSelection`, `groupSelection`, `parseInputParameters`, `preLoadTrajectory`, `runAnalysis`, `saveAnalysis`, `setInputParameters`, `subsetSelection`, `updateJobProgress`, `weightingScheme`

Class Variables | [hide private]
| inputParametersNames = `'trajectory', 'timeinfo', 'referencefra`...``
| shortName = `'RMSD'`
| canBeEstimated = `True`

Method Details | [hide private]

### __init__(self) (Constructor) | source code
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__

### initialize(self) | source code
Initializes the analysis (e.g. parses and checks input parameters, set some variables ...).

### calc(self, atom, trajname) | source code
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. 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))

### finalize(self) | source code
Finalizes the calculations (e.g. averaging the total term, output files creations ...)

Class Variable Details | [hide private]

  ### inputParametersNames Value:
      'trajectory', 'timeinfo', 'referenceframe', 'subset', 'deuteration', '
      weights', 'rmsd', 'pyroserver',