Error out of memory

Errors
1

Screenshot from 2022-06-06 23-21-28
Screenshot from 2022-06-06 23-21-28751×168 6.27 KB

Hi,I have just started to learn fenics. I want to solve the given system of pde with the help of fenics and want to draw a picture of solution. When I am solving it on a mesh of dimension 1800x600 by finite difference method, I am getting a spiral pattern. But when I am trying to solve it by use of fenics on the given size of mesh I am getting an error OUT OF MEMORY.
this is my code-
from fenics import *
import matplotlib.pyplot as plt
#final time
T = 85

#number of time steps
num_steps = 70

#time step size
dt = T / num_steps

#Generate Mesh
x_lim = 100
y_lim = 100
mesh = RectangleMesh (Point(0,0),Point(x_lim,y_lim), x_lim, y_lim)
plot(mesh)
plt.show()

#Define function space for given system of pde
P1 = FiniteElement(‘P’, triangle, 1)
element = MixedElement([P1, P1])
V = FunctionSpace(mesh, element)

#Define test functions
v_1, v_2 = TestFunctions(V)

#Define functions for system
u = Function(V)
u_n = Function(V)

#Define Initial Condition
u_0 = Expression ((‘6.69-(1.25pow(10,-18))(x[0]-1600)(x[1]-800)-(0.1875pow(10,-10))(x[0]-2)(x[1]-300)’, ‘1.19-(0.3pow(10,-8))(x[0]-1500)-(1.5pow(10,-8))(x[1]-50)’), degree = 1)
u_n = project(u_0,V)

#Split system functions to access components
u_1, u_2 = split(u)
u_n1, u_n2= split(u_n)

#Define source terms
f_1 = Constant(0)
f_2 = Constant(0)

#Parameter values
d = 1.2
alpha = 1.30039
beta = 1.3
rho = 0.24
kappa = 42
xi = 0.110013
mu = 0.4614
k = Constant(dt)

F = ((u_1 - u_n1) / k)v_1dx -rhou_1(1-(u_1/kappa))v_1dx+((betau_1u_2)/(1+u_1))v_1dx+dot( grad(u_1),grad(v_1))*dx\

  • ((u_2 - u_n2) / k)v_2dx - mu*(((alphau_1u_2)/(1+u_1))-u_2-xiu_2u_2)v_2dx+d*dot(grad(u_2),grad(v_2))*dx \
  • f_1v_1dx - f_2v_2dx

#Create VTK files for visualization output
vtkfile_u_1 = File(‘Pattern formation_system/u_1.pvd’)
vtkfile_u_2 = File(‘Pattern_formation/u_2.pvd’)

#Create progress bar
progress = Progress(‘Time-stepping’)
set_log_level(LogLevel.PROGRESS)

#Time-stepping
t = 0

for n in range(num_steps):
#Update current time
t += dt

#Solve variational problem for time step
solve(F == 0, u)

print(t)
plot(u_1)
plt.show()
plot(u_2)
plt.show()

#Save solution to file (VTK)
_u_1, _u_2= u.split()
vtkfile_u_1 << (_u_1, t)
vtkfile_u_2 << (_u_2, t)

#Update previous solution
u_n.assign(u)
Boundary Conditions are nuemann boundary conditions.
Also the initial condition is given.
PLease check it. I will be very thankful to you for any suggestion.

2

Please format your code using markdown syntax, see: Problem with bool in solve() - #3 by kamensky for details.

It would also help if you could include the whole error message, and in particular which line is causing out of memory error.

Note that your system is fairly small, so I’m curious as to how much RAM you have available on your system.

Also note that we advice new users to use DOLFINx instead of Dolfin, see: The new DOLFINx solver is now recommended over DOLFIN

You can also pick up various tips on setting appropriate solver options from Default absolute tolerance and relative tolerance - #4 by nate

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