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

source code

    Analysis.Analysis --+
                        |
                       QuasiHarmonicAnalysis

    Sets up a Quasi Harmonic Analysis analysis.

    A Subclass of nMOLDYN.Analysis.Analysis.

    Constructor: QuasiHarmonicAnalysis(|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.
            * temperature -- the temperature at which the MD was performed.
            * subset      -- a selection string specifying the atoms to consider for the analysis.
            * qha         -- the output NetCDF file name.

    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 analysis is used to get effective modes of vibration from fluctuations calculated by an MD simulation.
          The results of such an analysis can be seen by generating pseudo-trajectories reproducing the vibrations along
          a vibration mode.
        - For more details: Brooks et al., J. Comp. Chem. 1995, 16, 1522-1542.

Instance Methods | [hide private]
__init__(self) The constructor. | source code
initialize(self) Initializes the analysis (e.g. | source code
internalRun(self) Runs the analysis. | 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', 'temperature'`...``
| shortName = `'QHA'`
| canBeEstimated = `False`

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 ...).

Class Variable Details | [hide private]

  ### inputParametersNames Value:
      'trajectory', 'timeinfo', 'temperature', 'subset', 'qha'