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

source code

    Analysis.Analysis --+
                        |
      AngularVelocity --+
                        |
                       AngularDensityOfStates

    Sets up an Angular Density Of States analysis.

    A Subclass of nMOLDYN.Analysis.Analysis.

    Constructor: AngularDensityOfStates(|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.
            * differentiation -- an integer in [0,5] specifying the order of the differentiation used to get the velocities
                                 out of the coordinates. 0 means that the velocities are already present in the trajectory loaded
                                 for analysis.
            * 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.
            * referenceframe  -- an integer in [1,len(trajectory)] specifying which frame should be the reference.
            * stepwiserbt     -- a string being one of 'Yes' or 'No' specifying whether the reference frame for frame i should be
                                 the frame i - 1 ('Yes') or should be a fixed frame defined with |referenceframe| ('No').
            * fftwindow       -- a float in ]0.0,100.0[ specifying the width of the gaussian, in percentage of the trajectory length
                                 that will be used in the smoothing procedure.
            * group           -- a selection string specifying the groups of atoms on which the rigid body trajectory will be defined.
                                 (each group being a rigid body).
            * ados            -- 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, groupIndex, trajname) Calculates the contribution for one group. | source code
combine(self, groupIndex, 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` Inherited from `AngularVelocity`: `getAngularVelocity`, `qMatrix`

Class Variables | [hide private]
| inputParametersNames = `'trajectory', 'timeInfo', 'differentiat`...``
| shortName = `'ADOS'`
| 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: AngularVelocity.__init__

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

### calc(self, groupIndex, trajname) | source code
Calculates the contribution for one group. Parameters: `groupIndex` (integer.) - the index of the group in |self.group| list. `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 ...).

Class Variable Details | [hide private]

  ### inputParametersNames Value:
      'trajectory', 'timeInfo', 'differentiation', 'projection', 'referencef
      rame', 'stepwiserbt', 'fftwindow', 'group', 'ados', 'pyroserver',