PotentialEnergy.py

from .Base import Base
 
class PotentialEnergy(Base):
    """
    Class for analysis of potential energies.
    """
 
    def __init__(self, run):
        """
        The constructor.
 
        @param[in] run
                   The run to analyze, as an instance of `Run`.
        """
 
        super(PotentialEnergy, self).__init__(run)
 
 
    def getMPLAxesForValueAsFunctionOfTime(self):
        """
        Returns a `matplotlib.axes.Axes` object that contains a plot of the
        potential energy, with the horizontal axis showing the simulation
        time `t`, and the vertical axis showing the potential energy at that
        point in time.
        """
 
        import matplotlib.figure
 
        figure = matplotlib.figure.Figure()
        axes = figure.add_subplot(1, 1, 1)
        lines = []
        legendLabels = []
 
        data = self.getValueAsFunctionOfTime()
        _line, = axes.plot(data.keys(), data.values())
        lines.append(_line)
        legendLabels.append("Potential Energy")
 
        axes.legend(lines, legendLabels)
 
        axes.set_title("Star Polymer Potential Energy")
        axes.set_xlabel("Simulation Time t")
        axes.set_ylabel("Potential Energy")
 
        return axes
 
 
    def _computeValueAsFunctionOfTime(self):
        """
        Takes the raw simulation output, and computes the potential energy 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"]
 
        lastTimestepAnalyzed = -9e9
        while True:
            time += timestep
 
            particles = snapshots.readTimestep()
 
            if time - lastTimestepAnalyzed < self._getAnalysisTimestep():
                continue
            lastTimestepAnalyzed = time
 
 
            if particles.isEmpty():
                break
 
            starPolymers.setParticles(particles)
 
            ret[time] = starPolymers.getPotentialEnergy()
 
        return ret
 
 
    def _getCacheFilename(self):
        """
        Returns the filename where cached data is (expected to be) saved to.
        """
 
        return "potentialEnergy.txt"
 
 
    def _getCacheMetadata(self):
        """
        Returns the cache metadata.
        """
 
        cacheVersion = 1
 
        metadata = \
            {
                "cacheVersion": cacheVersion,
                "analysisTimestep": self._getAnalysisTimestep()
            }
        return metadata
 
 
    def _getAnalysisTimestep(self):
        """
        Returns the timestep between to analysis points.
        """
 
        return 100