Package nMOLDYN :: Package Analysis :: Module NMR :: Class OrderParameter |
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# Class OrderParameter

source code

    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.

Instance Methods | [hide private]
__init__(self) The constructor. | source code
initialize(self) Initializes the analysis (e.g. | source code
calc(self, bondIndex, trajname) Calculates the contribution for one group. | source code
combine(self, bondIndex, 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', 'bond', 'atom`...``
| shortName = `'OP'`
| 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, bondIndex, trajname) | source code
Calculates the contribution for one group. Parameters: `bondIndex` (integer.) - the index of the group in |self.bond| 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', 'bond', 'atomorder', 'op', 'pyroserver',