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',