Traceback errors in Python that I don't understand why I'm getting











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I'm getting traceback issues with my kmc.time_step(), self.evolve(events_index, dt) and my ran_int = randint(len(index)) saying that zip has no length but have no clue how to go about solving this.



Im trying to model a kinetic monte carlo simulation by checking nearest neighbours of an array to see if they have any occupied states and then either "diffusing" through if they aren't occupied (moving to the unoccupied point). If the point is occupied then diffusion cant happen so aggregation occurs. I have a bunch of conditional if statements to check these but then why I try to run I get traceback errors and have no clue why.



from numpy import *
# from scipy.signal import correlate2d
from numpy.random import randint, choice, uniform
from matplotlib.pyplot import *


class KineticMonteCarlo(object):

def __init__(self, Model):

"""Initialise a Kinetic Monte Carlo evolution method for
the given model. The model object requires the following
vectorised methods:

Model.evolve : <method>
evolves model according to given events
Model.get_rates : <method>
returns event rates
"""

# reference state
self.Model = Model
self.state = Model.state

# event rates and evolution rule
self.evolve = Model.evolve
self.get_rates = Model.get_rates

def time_step(self):
"""Perform parallel Kinetic Monte-Carlo update on model"""

# calculate transition rate fractions
rates = self.get_rates() # a k-dimensional array
probabilities = cumsum(rates, axis=0) # a k-dim array

total_rate = probabilities[-1]
probabilities /= total_rate

# choose events according to rates
u = uniform(0, 1)
events_index = sum(probabilities < u)

# generate waiting time
v = uniform(0, 1)
dt = -log(v)/total_rate

# carry out events
self.evolve(events_index, dt)


class LatticeGas(object):

def __init__(self, n_sites, density):

# initialisation of lattice gas with given density
self.size = 2*int(ceil(sqrt(n_sites)/2))
self.state = choice([0, 1], size=(self.size, self.size), p=[1-density, density])
self.time = 0.
self.aggcnt = 0
self.diffcnt = 0
self.n = 0

''' this return a a matrix of 0 and 1; 1 for occupied sites'''

def get_rates(self):
temp = 100
kb = 1.38
beta = 1/(kb * temp)
ads_rate = 0.001 * exp(- beta * 0.01)
des_rate = 0.001 * exp(- beta * 0.01)
diff_rate = 0.1 * exp(- beta * 0.35)

return array([ads_rate, des_rate, diff_rate])

def evolve(self, events_index, dt):
non_zero_m = self.state != 0
non_zeroi, non_zeroj = where(non_zero_m)
index = zip(non_zeroi, non_zeroj)

ran_ind = randint(len(index))
randi, randj = index[ran_ind]

n1 = (randi - 1) % self.size
n2 = (randj - 2) % self.size
e1 = (randj + 1) % self.size
e2 = (randj + 2) % self.size
w1 = (randj - 1) % self.size
w2 = (randj - 2) % self.size
s1 = (randi + 1) % self.size
s2 = (randi + 2) % self.size

if events_index == 0:
self.state[index[randint(len(index))]]

elif events_index == 1:
index = zip(*where(self.state == 0))
self.state[index[randint(len(index))]]

elif events_index == 2:
while True:
rand_direc = randint(4)

if rand_direc == 3 and self.state[n1, randj] == 0:
self.state[n1, randj] = 1
self.state[randi, randj] = 0
if self.state[n2, randj % self.size == 0] and self.state[n1, w1] == 0 and self.state[n1, e1] == 0:
self.diffcnt += 1
else:
self.aggcnt == 1
break

if rand_direc == 2 and self.state[randi, e1] == 0:
self.state[randi, e1] = 1
self.state[randi, randj] = 0
if self.state[n1, e1] and self.state[s1, e1] == 0 and self.state[randi, e2] == 0:
self.diffcnt += 1
else:
self.aggcnt += 1
break

elif rand_direc == 1 and self.state[s1, randj] == 0:
self.state[s1, randj] = 1
self.state[randi, randj] = 0
if self.state[s1, e1] == 0 and self.state[s1, w1] == 0 and self.state[s2, randj] == 0:
self.diffcnt += 1
else:
self.aggcount += 1
break

elif rand_direc == 0 and self.state[randi, w1] == 0:
self.state[randi, w1] = 1
self.state[randi, randj] = 0
if self.state[n1, w1] == 0 and self.state[s1, w1] == 0 and self.state[randi, w2] == 0:
self.diffcnt += 1
else:
self.aggcnt += 1
break

def show(self):
# Display current lattice configuration, with black
# and white representing whether there is a particle or not

figure(figsize=(5, 5))
imshow(self.state, interpolation="none", cmap='bone_r', vmin=0, vmax=1)
axis('off')
show()


# example of how code should work
model = LatticeGas(50, 0.1)
kmc = KineticMonteCarlo(model)
steps = 100

for i in range(steps):
kmc.time_step()
model.show()









share|improve this question




















  • 5




    You should show the traceback of the errors.
    – b-fg
    Nov 11 at 12:13










  • Welcome to stackoverflow! Please take the tour and read the help pages. Helpful may be "how to ask good questions" and this question checklist. Users here are way more ready to help if you provide minimal, complete, and verifiable example with some input and the desired output.
    – Mikhail Stepanov
    Nov 11 at 13:11










  • Yeah sorry about that, finally figured out that I coded this in Python 2.7 at university and then at home I have Python 3 so bits of coding didn't work like they did before I think. As when I went to uni and used Python 2.7 it was fine. Thanks for giving advice on how to try and improve my post though, appreciate it.
    – Neel Patel
    Nov 11 at 13:28















up vote
-1
down vote

favorite












I'm getting traceback issues with my kmc.time_step(), self.evolve(events_index, dt) and my ran_int = randint(len(index)) saying that zip has no length but have no clue how to go about solving this.



Im trying to model a kinetic monte carlo simulation by checking nearest neighbours of an array to see if they have any occupied states and then either "diffusing" through if they aren't occupied (moving to the unoccupied point). If the point is occupied then diffusion cant happen so aggregation occurs. I have a bunch of conditional if statements to check these but then why I try to run I get traceback errors and have no clue why.



from numpy import *
# from scipy.signal import correlate2d
from numpy.random import randint, choice, uniform
from matplotlib.pyplot import *


class KineticMonteCarlo(object):

def __init__(self, Model):

"""Initialise a Kinetic Monte Carlo evolution method for
the given model. The model object requires the following
vectorised methods:

Model.evolve : <method>
evolves model according to given events
Model.get_rates : <method>
returns event rates
"""

# reference state
self.Model = Model
self.state = Model.state

# event rates and evolution rule
self.evolve = Model.evolve
self.get_rates = Model.get_rates

def time_step(self):
"""Perform parallel Kinetic Monte-Carlo update on model"""

# calculate transition rate fractions
rates = self.get_rates() # a k-dimensional array
probabilities = cumsum(rates, axis=0) # a k-dim array

total_rate = probabilities[-1]
probabilities /= total_rate

# choose events according to rates
u = uniform(0, 1)
events_index = sum(probabilities < u)

# generate waiting time
v = uniform(0, 1)
dt = -log(v)/total_rate

# carry out events
self.evolve(events_index, dt)


class LatticeGas(object):

def __init__(self, n_sites, density):

# initialisation of lattice gas with given density
self.size = 2*int(ceil(sqrt(n_sites)/2))
self.state = choice([0, 1], size=(self.size, self.size), p=[1-density, density])
self.time = 0.
self.aggcnt = 0
self.diffcnt = 0
self.n = 0

''' this return a a matrix of 0 and 1; 1 for occupied sites'''

def get_rates(self):
temp = 100
kb = 1.38
beta = 1/(kb * temp)
ads_rate = 0.001 * exp(- beta * 0.01)
des_rate = 0.001 * exp(- beta * 0.01)
diff_rate = 0.1 * exp(- beta * 0.35)

return array([ads_rate, des_rate, diff_rate])

def evolve(self, events_index, dt):
non_zero_m = self.state != 0
non_zeroi, non_zeroj = where(non_zero_m)
index = zip(non_zeroi, non_zeroj)

ran_ind = randint(len(index))
randi, randj = index[ran_ind]

n1 = (randi - 1) % self.size
n2 = (randj - 2) % self.size
e1 = (randj + 1) % self.size
e2 = (randj + 2) % self.size
w1 = (randj - 1) % self.size
w2 = (randj - 2) % self.size
s1 = (randi + 1) % self.size
s2 = (randi + 2) % self.size

if events_index == 0:
self.state[index[randint(len(index))]]

elif events_index == 1:
index = zip(*where(self.state == 0))
self.state[index[randint(len(index))]]

elif events_index == 2:
while True:
rand_direc = randint(4)

if rand_direc == 3 and self.state[n1, randj] == 0:
self.state[n1, randj] = 1
self.state[randi, randj] = 0
if self.state[n2, randj % self.size == 0] and self.state[n1, w1] == 0 and self.state[n1, e1] == 0:
self.diffcnt += 1
else:
self.aggcnt == 1
break

if rand_direc == 2 and self.state[randi, e1] == 0:
self.state[randi, e1] = 1
self.state[randi, randj] = 0
if self.state[n1, e1] and self.state[s1, e1] == 0 and self.state[randi, e2] == 0:
self.diffcnt += 1
else:
self.aggcnt += 1
break

elif rand_direc == 1 and self.state[s1, randj] == 0:
self.state[s1, randj] = 1
self.state[randi, randj] = 0
if self.state[s1, e1] == 0 and self.state[s1, w1] == 0 and self.state[s2, randj] == 0:
self.diffcnt += 1
else:
self.aggcount += 1
break

elif rand_direc == 0 and self.state[randi, w1] == 0:
self.state[randi, w1] = 1
self.state[randi, randj] = 0
if self.state[n1, w1] == 0 and self.state[s1, w1] == 0 and self.state[randi, w2] == 0:
self.diffcnt += 1
else:
self.aggcnt += 1
break

def show(self):
# Display current lattice configuration, with black
# and white representing whether there is a particle or not

figure(figsize=(5, 5))
imshow(self.state, interpolation="none", cmap='bone_r', vmin=0, vmax=1)
axis('off')
show()


# example of how code should work
model = LatticeGas(50, 0.1)
kmc = KineticMonteCarlo(model)
steps = 100

for i in range(steps):
kmc.time_step()
model.show()









share|improve this question




















  • 5




    You should show the traceback of the errors.
    – b-fg
    Nov 11 at 12:13










  • Welcome to stackoverflow! Please take the tour and read the help pages. Helpful may be "how to ask good questions" and this question checklist. Users here are way more ready to help if you provide minimal, complete, and verifiable example with some input and the desired output.
    – Mikhail Stepanov
    Nov 11 at 13:11










  • Yeah sorry about that, finally figured out that I coded this in Python 2.7 at university and then at home I have Python 3 so bits of coding didn't work like they did before I think. As when I went to uni and used Python 2.7 it was fine. Thanks for giving advice on how to try and improve my post though, appreciate it.
    – Neel Patel
    Nov 11 at 13:28













up vote
-1
down vote

favorite









up vote
-1
down vote

favorite











I'm getting traceback issues with my kmc.time_step(), self.evolve(events_index, dt) and my ran_int = randint(len(index)) saying that zip has no length but have no clue how to go about solving this.



Im trying to model a kinetic monte carlo simulation by checking nearest neighbours of an array to see if they have any occupied states and then either "diffusing" through if they aren't occupied (moving to the unoccupied point). If the point is occupied then diffusion cant happen so aggregation occurs. I have a bunch of conditional if statements to check these but then why I try to run I get traceback errors and have no clue why.



from numpy import *
# from scipy.signal import correlate2d
from numpy.random import randint, choice, uniform
from matplotlib.pyplot import *


class KineticMonteCarlo(object):

def __init__(self, Model):

"""Initialise a Kinetic Monte Carlo evolution method for
the given model. The model object requires the following
vectorised methods:

Model.evolve : <method>
evolves model according to given events
Model.get_rates : <method>
returns event rates
"""

# reference state
self.Model = Model
self.state = Model.state

# event rates and evolution rule
self.evolve = Model.evolve
self.get_rates = Model.get_rates

def time_step(self):
"""Perform parallel Kinetic Monte-Carlo update on model"""

# calculate transition rate fractions
rates = self.get_rates() # a k-dimensional array
probabilities = cumsum(rates, axis=0) # a k-dim array

total_rate = probabilities[-1]
probabilities /= total_rate

# choose events according to rates
u = uniform(0, 1)
events_index = sum(probabilities < u)

# generate waiting time
v = uniform(0, 1)
dt = -log(v)/total_rate

# carry out events
self.evolve(events_index, dt)


class LatticeGas(object):

def __init__(self, n_sites, density):

# initialisation of lattice gas with given density
self.size = 2*int(ceil(sqrt(n_sites)/2))
self.state = choice([0, 1], size=(self.size, self.size), p=[1-density, density])
self.time = 0.
self.aggcnt = 0
self.diffcnt = 0
self.n = 0

''' this return a a matrix of 0 and 1; 1 for occupied sites'''

def get_rates(self):
temp = 100
kb = 1.38
beta = 1/(kb * temp)
ads_rate = 0.001 * exp(- beta * 0.01)
des_rate = 0.001 * exp(- beta * 0.01)
diff_rate = 0.1 * exp(- beta * 0.35)

return array([ads_rate, des_rate, diff_rate])

def evolve(self, events_index, dt):
non_zero_m = self.state != 0
non_zeroi, non_zeroj = where(non_zero_m)
index = zip(non_zeroi, non_zeroj)

ran_ind = randint(len(index))
randi, randj = index[ran_ind]

n1 = (randi - 1) % self.size
n2 = (randj - 2) % self.size
e1 = (randj + 1) % self.size
e2 = (randj + 2) % self.size
w1 = (randj - 1) % self.size
w2 = (randj - 2) % self.size
s1 = (randi + 1) % self.size
s2 = (randi + 2) % self.size

if events_index == 0:
self.state[index[randint(len(index))]]

elif events_index == 1:
index = zip(*where(self.state == 0))
self.state[index[randint(len(index))]]

elif events_index == 2:
while True:
rand_direc = randint(4)

if rand_direc == 3 and self.state[n1, randj] == 0:
self.state[n1, randj] = 1
self.state[randi, randj] = 0
if self.state[n2, randj % self.size == 0] and self.state[n1, w1] == 0 and self.state[n1, e1] == 0:
self.diffcnt += 1
else:
self.aggcnt == 1
break

if rand_direc == 2 and self.state[randi, e1] == 0:
self.state[randi, e1] = 1
self.state[randi, randj] = 0
if self.state[n1, e1] and self.state[s1, e1] == 0 and self.state[randi, e2] == 0:
self.diffcnt += 1
else:
self.aggcnt += 1
break

elif rand_direc == 1 and self.state[s1, randj] == 0:
self.state[s1, randj] = 1
self.state[randi, randj] = 0
if self.state[s1, e1] == 0 and self.state[s1, w1] == 0 and self.state[s2, randj] == 0:
self.diffcnt += 1
else:
self.aggcount += 1
break

elif rand_direc == 0 and self.state[randi, w1] == 0:
self.state[randi, w1] = 1
self.state[randi, randj] = 0
if self.state[n1, w1] == 0 and self.state[s1, w1] == 0 and self.state[randi, w2] == 0:
self.diffcnt += 1
else:
self.aggcnt += 1
break

def show(self):
# Display current lattice configuration, with black
# and white representing whether there is a particle or not

figure(figsize=(5, 5))
imshow(self.state, interpolation="none", cmap='bone_r', vmin=0, vmax=1)
axis('off')
show()


# example of how code should work
model = LatticeGas(50, 0.1)
kmc = KineticMonteCarlo(model)
steps = 100

for i in range(steps):
kmc.time_step()
model.show()









share|improve this question















I'm getting traceback issues with my kmc.time_step(), self.evolve(events_index, dt) and my ran_int = randint(len(index)) saying that zip has no length but have no clue how to go about solving this.



Im trying to model a kinetic monte carlo simulation by checking nearest neighbours of an array to see if they have any occupied states and then either "diffusing" through if they aren't occupied (moving to the unoccupied point). If the point is occupied then diffusion cant happen so aggregation occurs. I have a bunch of conditional if statements to check these but then why I try to run I get traceback errors and have no clue why.



from numpy import *
# from scipy.signal import correlate2d
from numpy.random import randint, choice, uniform
from matplotlib.pyplot import *


class KineticMonteCarlo(object):

def __init__(self, Model):

"""Initialise a Kinetic Monte Carlo evolution method for
the given model. The model object requires the following
vectorised methods:

Model.evolve : <method>
evolves model according to given events
Model.get_rates : <method>
returns event rates
"""

# reference state
self.Model = Model
self.state = Model.state

# event rates and evolution rule
self.evolve = Model.evolve
self.get_rates = Model.get_rates

def time_step(self):
"""Perform parallel Kinetic Monte-Carlo update on model"""

# calculate transition rate fractions
rates = self.get_rates() # a k-dimensional array
probabilities = cumsum(rates, axis=0) # a k-dim array

total_rate = probabilities[-1]
probabilities /= total_rate

# choose events according to rates
u = uniform(0, 1)
events_index = sum(probabilities < u)

# generate waiting time
v = uniform(0, 1)
dt = -log(v)/total_rate

# carry out events
self.evolve(events_index, dt)


class LatticeGas(object):

def __init__(self, n_sites, density):

# initialisation of lattice gas with given density
self.size = 2*int(ceil(sqrt(n_sites)/2))
self.state = choice([0, 1], size=(self.size, self.size), p=[1-density, density])
self.time = 0.
self.aggcnt = 0
self.diffcnt = 0
self.n = 0

''' this return a a matrix of 0 and 1; 1 for occupied sites'''

def get_rates(self):
temp = 100
kb = 1.38
beta = 1/(kb * temp)
ads_rate = 0.001 * exp(- beta * 0.01)
des_rate = 0.001 * exp(- beta * 0.01)
diff_rate = 0.1 * exp(- beta * 0.35)

return array([ads_rate, des_rate, diff_rate])

def evolve(self, events_index, dt):
non_zero_m = self.state != 0
non_zeroi, non_zeroj = where(non_zero_m)
index = zip(non_zeroi, non_zeroj)

ran_ind = randint(len(index))
randi, randj = index[ran_ind]

n1 = (randi - 1) % self.size
n2 = (randj - 2) % self.size
e1 = (randj + 1) % self.size
e2 = (randj + 2) % self.size
w1 = (randj - 1) % self.size
w2 = (randj - 2) % self.size
s1 = (randi + 1) % self.size
s2 = (randi + 2) % self.size

if events_index == 0:
self.state[index[randint(len(index))]]

elif events_index == 1:
index = zip(*where(self.state == 0))
self.state[index[randint(len(index))]]

elif events_index == 2:
while True:
rand_direc = randint(4)

if rand_direc == 3 and self.state[n1, randj] == 0:
self.state[n1, randj] = 1
self.state[randi, randj] = 0
if self.state[n2, randj % self.size == 0] and self.state[n1, w1] == 0 and self.state[n1, e1] == 0:
self.diffcnt += 1
else:
self.aggcnt == 1
break

if rand_direc == 2 and self.state[randi, e1] == 0:
self.state[randi, e1] = 1
self.state[randi, randj] = 0
if self.state[n1, e1] and self.state[s1, e1] == 0 and self.state[randi, e2] == 0:
self.diffcnt += 1
else:
self.aggcnt += 1
break

elif rand_direc == 1 and self.state[s1, randj] == 0:
self.state[s1, randj] = 1
self.state[randi, randj] = 0
if self.state[s1, e1] == 0 and self.state[s1, w1] == 0 and self.state[s2, randj] == 0:
self.diffcnt += 1
else:
self.aggcount += 1
break

elif rand_direc == 0 and self.state[randi, w1] == 0:
self.state[randi, w1] = 1
self.state[randi, randj] = 0
if self.state[n1, w1] == 0 and self.state[s1, w1] == 0 and self.state[randi, w2] == 0:
self.diffcnt += 1
else:
self.aggcnt += 1
break

def show(self):
# Display current lattice configuration, with black
# and white representing whether there is a particle or not

figure(figsize=(5, 5))
imshow(self.state, interpolation="none", cmap='bone_r', vmin=0, vmax=1)
axis('off')
show()


# example of how code should work
model = LatticeGas(50, 0.1)
kmc = KineticMonteCarlo(model)
steps = 100

for i in range(steps):
kmc.time_step()
model.show()






python simulation lattice






share|improve this question















share|improve this question













share|improve this question




share|improve this question








edited Nov 11 at 13:26

























asked Nov 11 at 11:16









Neel Patel

11




11








  • 5




    You should show the traceback of the errors.
    – b-fg
    Nov 11 at 12:13










  • Welcome to stackoverflow! Please take the tour and read the help pages. Helpful may be "how to ask good questions" and this question checklist. Users here are way more ready to help if you provide minimal, complete, and verifiable example with some input and the desired output.
    – Mikhail Stepanov
    Nov 11 at 13:11










  • Yeah sorry about that, finally figured out that I coded this in Python 2.7 at university and then at home I have Python 3 so bits of coding didn't work like they did before I think. As when I went to uni and used Python 2.7 it was fine. Thanks for giving advice on how to try and improve my post though, appreciate it.
    – Neel Patel
    Nov 11 at 13:28














  • 5




    You should show the traceback of the errors.
    – b-fg
    Nov 11 at 12:13










  • Welcome to stackoverflow! Please take the tour and read the help pages. Helpful may be "how to ask good questions" and this question checklist. Users here are way more ready to help if you provide minimal, complete, and verifiable example with some input and the desired output.
    – Mikhail Stepanov
    Nov 11 at 13:11










  • Yeah sorry about that, finally figured out that I coded this in Python 2.7 at university and then at home I have Python 3 so bits of coding didn't work like they did before I think. As when I went to uni and used Python 2.7 it was fine. Thanks for giving advice on how to try and improve my post though, appreciate it.
    – Neel Patel
    Nov 11 at 13:28








5




5




You should show the traceback of the errors.
– b-fg
Nov 11 at 12:13




You should show the traceback of the errors.
– b-fg
Nov 11 at 12:13












Welcome to stackoverflow! Please take the tour and read the help pages. Helpful may be "how to ask good questions" and this question checklist. Users here are way more ready to help if you provide minimal, complete, and verifiable example with some input and the desired output.
– Mikhail Stepanov
Nov 11 at 13:11




Welcome to stackoverflow! Please take the tour and read the help pages. Helpful may be "how to ask good questions" and this question checklist. Users here are way more ready to help if you provide minimal, complete, and verifiable example with some input and the desired output.
– Mikhail Stepanov
Nov 11 at 13:11












Yeah sorry about that, finally figured out that I coded this in Python 2.7 at university and then at home I have Python 3 so bits of coding didn't work like they did before I think. As when I went to uni and used Python 2.7 it was fine. Thanks for giving advice on how to try and improve my post though, appreciate it.
– Neel Patel
Nov 11 at 13:28




Yeah sorry about that, finally figured out that I coded this in Python 2.7 at university and then at home I have Python 3 so bits of coding didn't work like they did before I think. As when I went to uni and used Python 2.7 it was fine. Thanks for giving advice on how to try and improve my post though, appreciate it.
– Neel Patel
Nov 11 at 13:28

















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