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

source code

    Analysis.Analysis --+
                        |
                       MeanSquareDisplacement

    Sets up a Mean Square Displacement analysis.

    A Subclass of nMOLDYN.Analysis.Analysis.

    Constructor: MeanSquareDisplacement(|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.
            * projection  -- a string of the form 'vx,vy,vz' specifying the vector along which the analysis
                             will be computed. 'vx', 'vy', and 'vz' are floats specifying respectively the x, y and z value
                             of that vector.
            * 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.
            * msd         -- 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 algorithm is based on the Fast Correlation Algorithm (FCA) algorithm

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
Numpy array |
atomicMSD(self, atom, series) Returns the atomic Mean-Square-Displacement. | 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', 'projection',`...``
| shortName = `'MSD'`
| 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.

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

### atomicMSD(self, atom, series) | source code
Returns the atomic Mean-Square-Displacement. Parameters: `atom` (an instance of MMTK.Atom class.) - the atom on which the atomic MSD has been calculated. `series` (NumPy array) - a array of dimension (self.nFrames,3) specifying the coordinates of atom |atom| for the selected frames. Returns: Numpy array the MSD computed for atom |atom| with trajectory |series|.

Class Variable Details | [hide private]

  ### inputParametersNames Value:
      'trajectory', 'timeinfo', 'projection', 'subset', 'deuteration', 'weig
      hts', 'msd', 'pyroserver',