################################
# Equilibration exercise
################################

################################
# Import Digital Material 
#
# ListOfAtoms
# Initializers
# Transformers
# Observers
# NeighborLocators
# BoundaryConditions
# Potentials
# Movers
#
################################

import DigitalMaterial as DM
import imp
imp.reload(DM)

################################
# Dimension of space
################################

DM.dim = 3

################################
# Transfer other libraries from DM
################################

vi = DM.vi 			# Visual Python
pylab = DM.pylab

################################
# Set up pieces of simulation
################################


class EquilibrationTest (DM.MDSystem):
    """
    Appropriate potentials and stuff for watching random walks of gas molecules
    """
    #
    def __init__(self, atoms=None, nAtoms=10, T=1.0, L=4., minDist=1.0):
	potential = \
		DM.LennardJonesCutPotential()
	boundaryConditions = DM.PeriodicBoundaryConditions(L)
	neighborLocator = DM.SimpleNeighborLocator(potential.cutoff,
							boundaryConditions)
	if atoms is None:
    	    atoms = DM.RandomNonoverlappingListOfAtoms(L, neighborLocator,
	    			minDist=1.0, nAtoms=nAtoms, temperature=T)
	# Remove center-of-mass momentum from gas
	atoms.velocities -= DM.scipy.sum(atoms.velocities)/len(atoms.velocities)
	self.displayObserver = DM.VisualDisplayAtomsObserver(atoms,L)
	self.velocityTrajectoryObserver = DM.VelocityTrajectoryObserver()
	observers = [self.displayObserver, self.velocityTrajectoryObserver]
	mover = DM.RunVelocityVerlet;
	DM.MDSystem.__init__(self, L, atoms, observers, neighborLocator,
			     boundaryConditions, potential, mover)
    #
    def PlotHistograms(self, nHists=6, factorBetweenHists=4):
    	"""
	Plots velocity histograms for nHists time intervals growing by factor
	(Equals momentum histogram if m=1)
	"""
	for h in range(nHists):
	   nSteps = factorBetweenHists**h
	   self.Run(nSteps=nSteps)
	   pylab.figure(h+1)
	   pylab.hist(self.velocityTrajectoryObserver.vTrajectory, 
				normed=1.0, bins=50)
	   pylab.show()
	   self.velocityTrajectoryObserver.Reset()


def demo():
    """Demonstrates solution for exercise: example of usage"""
    print("Equilibration demo")
    sys = EquilibrationTest()
    sys.PlotHistograms()
    

if __name__=="__main__":
    demo()


# Copyright (C) Cornell University
# All rights reserved.
# Apache License, Version 2.0