def __init__(self):
#do everything in the constructor.
#this way, when we instantiate the object below, the whole
#simulation will automatically run
print "Initializing simulation"
self.sim = CustomSimulation(rng)
self.sim.setTemperature(0.5)
#self.sim.setDragCoefficient(2.5)
#self.sim.setTimestep(0.05)
tpsgraphics.pefield(self.sim, tn, -3., 3.0, -1.5, 3.5, 0, 2, 0.150)
tn.write("scale by 0.5\n")
tn.write("rotate x by -20\n")
tn.write("mol new\n")
self.sim.setParticlePosition(-1, 0)
print "Done Initializing simulation"
q1 = TpsTestPeSurf2dOrderParamX(3)
q2 = TpsTestPeSurf2dOrderParamY(3)
q = TpsOrderParameterAggregate()
q.addOrderParameter(q1)
q.addOrderParameter(q2)
trj = TpsTrajectoryUniformStep(self.sim, 500, 5)
self.tpe = TpsTrajectoryEnsemble(trj)
working_traj = self.tpe.getTrajectory(-1)
self.sim.setPathEnsemble(self.tpe)
print "Initializing"
self.sim.show = 1
TpsAlgorithmBruteForce.__init__(self, self.tpe, rng, q)
#writer.analyze(self.tpe.getLastTrajectory())
self.sim.setTemperature(0.15)
self.nstep = 0
print "starting path sampling:"
for i in range(1, 501):
print i
self.doStep()
var = raw_input("Return/Enter to EXIT ")
tn.write("exit\n")
exit(1)
def __init__(self):
#do everything in the constructor.
#this way, when we instantiate the object below, the whole
#simulation will automatically run
print "Initializing simulation"
self.sim = CustomSimulation(rng)
self.sim.setTemperature(0.5)
#self.sim.setDragCoefficient(2.5)
#self.sim.setTimestep(0.05)
tpsgraphics.pefield(self.sim, tn, -3., 3.0, -1.5, 3.5, 0, 2, 0.150)
tn.write("scale by 0.5\n")
tn.write("rotate x by -20\n")
tn.write("mol new\n")
self.sim.setParticlePosition(-1, 0)
print "Done Initializing simulation"
q1 = TpsTestPeSurf2dOrderParamX(3)
q2 = TpsTestPeSurf2dOrderParamY(3)
q = TpsOrderParameterAggregate()
q.addOrderParameter(q1)
q.addOrderParameter(q2)
init = TpsInitializerBruteForce()
trj = TpsTrajectoryUniformStep(self.sim, 500, 5)
self.tpe = TpsTrajectoryEnsemble(trj)
working_traj = self.tpe.getTrajectory(-1)
self.sim.setPathEnsemble(self.tpe)
print "Initializing"
self.sim.show = 0
TpsAlgorithmTPS.__init__(self, self.tpe, rng, q, init)
writer.analyze(self.tpe.getLastTrajectory())
#dv = TpsTimesliceModifierPerturbVelocities(0.0001, 1.0, 1, 1)
self.shift = TpsTrialMoveShift(50, 400)
self.fshot = TpsTrialMoveShotForward()
self.bshot = TpsTrialMoveShotBackward()
self.shot = TpsTrialMoveShot()
self.flex = TpsTrialMoveShotFlexible(500)
self.ashot = TpsTrialMoveShotAimless(5)
self.addTrialMove(self.ashot)
#self.addTrialMove(fshot)
#self.addTrialMove(bshot)
#self.addTrialMove(shift)
self.sim.setTemperature(0.15)
self.sim.show = 0
self.nstep = 0
print "starting path sampling:"
for i in range(1, 501):
print i
self.doStep()
for i in range(1, 1000):
self.doStepCustom()
var = raw_input("Return/Enter to EXIT ")
tn.write("exit\n")
exit(1)
def __init__(self):
#do everything in the constructor.
#this way, when we instantiate the object below, the whole
#simulation will automatically run
print "Initializing simulation"
self.sim = CustomSimulation(rng)
self.sim.setTemperature(0.5)
#self.sim.setDragCoefficient(2.5)
#self.sim.setTimestep(0.05)
tpsgraphics.pefield(self.sim, tn, -3., 3.0, -1.5, 3.5, 0, 2, 0.150)
tn.write("scale by 0.5\n")
tn.write("rotate x by -20\n")
tn.write("mol new\n")
self.sim.setParticlePosition(-1, 0)
print "Done Initializing simulation"
q1 = TpsTestPeSurf2dOrderParamX(3)
q2 = TpsTestPeSurf2dOrderParamY(3)
q = TpsOrderParameterAggregate()
q.addOrderParameter(q1)
q.addOrderParameter(q2)
init = TpsInitializerBruteForce()
trj = TpsTrajectoryUniformStep(self.sim, 500, 5)
self.tpe = TpsTrajectoryEnsemble(trj)
working_traj = self.tpe.getTrajectory(-1)
self.sim.setPathEnsemble(self.tpe)
print "Initializing"
self.sim.show = 0
TpsAlgorithmTPS.__init__(self, self.tpe, rng, q, init)
writer.analyze(self.tpe.getLastTrajectory())
#dv = TpsTimesliceModifierPerturbVelocities(0.0001, 1.0, 1, 1)
self.shift = TpsTrialMoveShift(50, 400)
self.fshot = TpsTrialMoveShotForward()
self.bshot = TpsTrialMoveShotBackward()
self.shot = TpsTrialMoveShot()
self.flex = TpsTrialMoveShotFlexible(500)
self.ashot = TpsTrialMoveShotAimless(5)
self.addTrialMove(self.ashot)
#self.addTrialMove(fshot)
#self.addTrialMove(bshot)
#self.addTrialMove(shift)
self.sim.setTemperature(0.15)
self.sim.show = 0
self.nstep = 0
print "starting path sampling:"
for i in range(1, 501):
print i
self.doStep()
for i in range(1, 1000):
self.doStepCustom()
var = raw_input("Return/Enter to EXIT ")
tn.write("exit\n")
exit(1)