def setUp(self):
ensembleSize=3
esim = EnsembleSimulation("ensemble",ensembleSize)
print "ensemble size", esim.size(),"running on",esim.numThreads(),"processors."
dyn = ivm.IVM(esim)
protocol.torsionTopology(dyn)
potList = PotList("test pot list")
pot = PyEnsemblePot('test ensemble pot')
potList.append(pot)
protocol.initDynamics(dyn,
bathTemp=400,
initVelocities=1,
potList=potList,
finalTime=1,
numSteps=1,
printInterval=0)
dyn.run()
# Give atoms uniform weights, except for the anisotropy axis
#
protocol.massSetup()
# IVM setup
# the IVM is used for performing dynamics and minimization in torsion-angle
# space, and in Cartesian space.
#
from ivm import IVM
dyn = IVM()
# reset ivm topology for torsion-angle dynamics
#
dyn.reset()
protocol.torsionTopology(dyn)
# minc used for final cartesian minimization
#
minc = IVM()
protocol.initMinimize(minc)
protocol.cartesianTopology(minc)
# object which performs simulated annealing
#
from simulationTools import AnnealIVM
init_t = 3000. # Need high temp and slow annealing to converge
cool = AnnealIVM(initTemp=init_t,
finalTemp=25,
tempStep=12.5,
#
protocol.massSetup()
# IVM setup
# the IVM is used for performing dynamics and minimization in torsion-angle
# space, and in Cartesian space.
#
dyn = IVM()
# initialize ivm topology for torsion-angle dynamics
#for m in media.values():
# m.setFreedom("fixDa, fixRh") #fix tensor Rh, Da, vary orientation
## m.setFreedom("varyDa, varyRh") #vary tensor Rh, Da, vary orientation
protocol.torsionTopology(dyn)
# minc used for final cartesian minimization
#
minc = IVM()
protocol.initMinimize(minc)
#for m in media.values():
# m.setFreedom("varyDa, varyRh") #allow all tensor parameters float here
# pass
protocol.cartesianTopology(minc)
# object which performs simulated annealing
#