def run_exit_times(statePair, runs):
np.random.seed()
asympot = potentials.asym3Dpotential(scalefactor=2.0)
r1 = np.array(np.zeros(3))
p1 = mrd.particle(r1, 1.0)
sphereboundary = mrd.reflectiveSphere(4.)
integrator = integrators.brownianDynamicsSp(asympot, sphereboundary, p1,
0.001, 1.0)
sim = mrd.simulation(integrator)
exitTimes = []
exitPositions = []
fpts = []
exits = 0
run = 0
totalRuns = 0
while run < runs:
integrator.pa.position = np.array(minima[statePair[0]])
integrator.clock = 0.
totalRuns += 1
while True:
sim.integrator.integrate()
if np.linalg.norm(minima[statePair[1]] -
integrator.pa.position) < 0.2:
fpts.append(integrator.clock)
run += 1
break
elif np.linalg.norm(integrator.pa.position) > R:
exits += 1
exitTimes.append(integrator.clock)
exitPositions.append(integrator.pa.position)
break
print str(statePair[0]) + ' to ' + str(statePair[1])
return [np.array(fpts), totalRuns, exitTimes, exitPositions]
def run_mfpts_to_bath(state, runs, scalef, dt, runbound):
global MFPTS, minima
np.random.seed()
asympot3D = potentials.asym3Dpotential(scalefactor = scalef)
p1 = mrd.particle(np.zeros(3), 1.0)
sphereboundary = mrd.reflectiveSphere(4.0)
integrator = integrators.brownianDynamicsSp(asympot3D, sphereboundary, p1, dt, 1.0)
sim = mrd.simulation(integrator)
fpts = []
for run in range(runs):
integrator.pa.position = np.array(minima[state])
fpts.append(sim.run_mfpt(runbound))
print 'state '+str(state)+' done'
return np.array(fpts)
def run_mfpts_from_bath(bathRad, numpoints, scalefactor, dt):
np.random.seed()
asympot3D = potentials.asym3Dpotential(scalefactor=scalefactor)
p1 = mrd.particle(np.zeros(3), 1.0)
sphereboundary = mrd.reflectiveSphere(bathRad)
integrator = integrators.brownianDynamicsSp(asympot3D, sphereboundary, p1,
dt, 1.0)
sim = mrd.simulation(integrator)
startpoints = get_startpoints(numpoints, bathRad - radiusThreshold)
fpts = []
for startpoint in startpoints:
integrator.pa.position = startpoint
integrator.clock = 0.
fpts.append(sim.run_mfpt_points(np.array(minima), 0.2))
print 'bath to ' + str(bathRad)
return np.array(fpts)
def run_mfpts_from_bath(startPosition, bathRad, dt):
np.random.seed()
p1 = mrd.particle(np.zeros(3), D_CO)
msm = mrd.MSM(T, minima)
msm.exitStates = []
boundary = mrd.reflectiveSphere(bathRad)
integrator = integrators.MSMRDtruncTrajs3D(msm, bathRad, p1, dt,
interactionRadius, boundary,
model)
sim = mrd.simulation(integrator)
integrator.particle.position = startPosition
integrator.clock = 0.
integrator.transition = False
integrator.MSM.state = -1
integrator.MSMactive = False
integrator.MSM.exit = False
return sim.run_mfpt_state(boundState)
def run_mfpts_to_bath(state, runs, dt = 0.1):
p1 = mrd.particle(np.zeros(3), D_CO)
msm = mrd.MSM(T, minima)
msm.exitStates = []
boundary = mrd.reflectiveSphere(2.*interactionRadius)
integrator = integrators.MSMRDtruncTrajs3D(msm, 2.*interactionRadius, p1, dt, interactionRadius, boundary, model)
sim = mrd.simulation(integrator)
fpts = []
for run in range(runs):
integrator.particle.position = np.zeros(3)
integrator.clock = 0.
integrator.MSM.state = state
integrator.lastState = state
integrator.lastStateTime = 0
integrator.transition = True
integrator.MSMactive = True
integrator.MSM.exit = False
fpts.append(sim.run_mfpt(40.))
print str(state)+' to bath'
return np.array(fpts)
def run_mfpts_to_bath(state, runs, dt=0.001):
p1 = mrd.particle(np.zeros(2), 1.0)
msm = mrd.MSM(T, minima)
msm.exitStates = []
boundary = mrd.reflectiveSphere(4.)
integrator = integrators.MSMRDtruncTrajs(msm, 4.0, p1, 0.001, model, 2.5)
sim = mrd.simulation(integrator)
fpts = []
for run in range(runs):
integrator.p.position = np.zeros(2)
integrator.clock = 0.
integrator.MSM.state = state
integrator.lastState = state
integrator.lastStateTime = 0
integrator.transition = True
integrator.MSMactive = True
integrator.MSM.exit = False
fpts.append(sim.run_mfpt(2.7))
print str(state) + ' to bath'
return np.array(fpts)
def run_mfpts_from_bath(bathRad, numpoints, dt):
np.random.seed()
p1 = mrd.particle(np.zeros(2), 1.0)
msm = mrd.MSM(T, minima)
msm.exitStates = []
boundary = mrd.reflectiveSphere(bathRad)
integrator = integrators.MSMRDtruncTrajs(msm, bathRad, p1, 0.001, model,
2.5)
sim = mrd.simulation(integrator)
fpts = []
startpoints = get_startpoints(numpoints, bathRad - radiusThreshold)
for startpoint in startpoints:
integrator.p.position = startpoint
integrator.clock = 0.
integrator.transition = False
integrator.MSM.state = -1
integrator.MSMactive = False
integrator.MSM.exit = False
fpts.append(sim.run_mfpt_states())
print 'bath to ' + str(bathRad)
return np.array(fpts)
def run_exit_times(statePair, runs):
np.random.seed()
r1 = np.array(np.zeros(3))
p1 = mrd.particle(r1, 1.0)
msm = mrd.MSM(T, minima)
msm.exitStates = []
boundary = mrd.reflectiveSphere(4.)
integrator = integrators.MSMRDtruncTrajs3D(msm, 4.0, p1, 0.001, 2.5, boundary, model)
sim = mrd.simulation(integrator)
exitTimes = []
exitPositions = []
fpts = []
exits = 0
run = 0
totalRuns = 0
while run < runs:
integrator.particle.position = np.array(np.zeros(3))
integrator.clock = 0.
integrator.MSM.state = statePair[0]
integrator.lastState = statePair[0]
integrator.transition = True
integrator.MSMactive = True
totalRuns += 1
while True:
sim.integrator.integrate()
if integrator.MSM.state == statePair[1]:
fpts.append(integrator.clock)
run += 1
break
elif not integrator.MSMactive:
exits += 1
exitTimes.append(integrator.clock)
exitPositions.append(integrator.particle.position)
break
print str(statePair[0])+' to ' + str(statePair[1])
return [np.array(fpts), totalRuns, exitTimes, exitPositions]