EckartAngularVelocityVector.py

from .Base import Base
 
class EckartAngularVelocityVector(Base):
    """
    Class for analysis of Eckart-frame angular velocity vectors, as defined in
    `MPCDAnalysis.EckartSystem`.
    """
 
    def __init__(self, run):
        """
        The constructor.
 
        @param[in] run
                   The run to analyze, as an instance of `Run`.
        """
 
        super(EckartAngularVelocityVector, self).__init__(run)
 
 
    def getMPLAxesForValueAsFunctionOfTime(self):
        """
        Returns a `matplotlib.axes.Axes` object that contains a plot of the
        Eckart angular velocities of star polymer, with the horizontal axis
        showing the simulation time `t`, and the Cartesian components of the
        Eckart angular velocity vector, in radians per time unit.
        """
 
        import matplotlib.figure
 
        figure = matplotlib.figure.Figure()
        axes = figure.add_subplot(1, 1, 1)
        lines = []
        legendLabels = []
 
        data = self.getValueAsFunctionOfTime()
        frequencies = [[], [], []]
        for datum in data.values():
            for i in [0, 1, 2]:
                frequencies[i].append(datum[i])
 
        _line, = axes.plot(data.keys(), frequencies[0])
        lines.append(_line)
        legendLabels.append("Eckart Angular Velocity: x Component")
 
        _line, = axes.plot(data.keys(), frequencies[1])
        lines.append(_line)
        legendLabels.append("Eckart Angular Velocity: y Component")
 
        _line, = axes.plot(data.keys(), frequencies[2])
        lines.append(_line)
        legendLabels.append("Eckart Angular Velocity: z Component")
 
        axes.legend(lines, legendLabels)
 
        axes.set_title("Star Polymer Eckart Angular Velocity")
        axes.set_xlabel("Simulation Time t")
        axes.set_ylabel("Eckart Angular Velocity [rad/T]")
 
        return axes
 
 
    def _computeValueAsFunctionOfTime(self):
        """
        Takes the raw simulation output, and computes the Eckart angular
        velocity vector as a function of time. The result is returned as an
        `collcections.OrderedDict`.
        """
 
        from collections import OrderedDict
 
 
        config = self.getRun().getConfiguration()
        snapshots = self._getSnapshots()
        starPolymers = self._getStarPolymers()
 
        ret = OrderedDict()
        timestep = config["mpc.timestep"]
        time = timestep * config["mpc.warmupSteps"]
 
        eckartSystem = None
        while True:
            time += timestep
 
            particles = snapshots.readTimestep()
            particles.setUniformMass(starPolymers.getParticleMass())
 
            if particles.isEmpty():
                break
 
            if eckartSystem is None:
                from MPCDAnalysis.EckartSystem import EckartSystem
                eckartSystem = EckartSystem(particles)
 
            ret[time] = eckartSystem.getEckartAngularVelocityVector(particles)
 
        return ret
 
 
    def _getCacheFilename(self):
        """
        Returns the filename where cached data is (expected to be) saved to.
        """
 
        return "eckartAngularVelocityVectors.txt"
 
 
    def _getCacheValueInterpreter(self):
        """
        Returns what is to be used as the `valueInterpreter` argument to
        `Cache.getDataOrderedDict`.
        """
 
        def valueInterpreter(string):
            import ast
            return ast.literal_eval(string)
 
        return valueInterpreter