Good day everybody,
I am a beginner at using FEniCS, I use the latets version of FEniCS installed with Docker on Windows 10. I have the following problem:
I would like to solve a transient diffusion PDE with homogeneous Dirichlet and Neumann BCs with an arbitrary initial condition that I import from a .mat file. In the end, the goal is to export the solution back to Matlab for postprocessing. At the end is a (hopefully) minimal example of my code.
My question is about the initial condition:
Based on an older answer to a similar question (From an older question (https://fenicsproject.org/qa/465/interpolate-function-given-matrix-on-finite-element-basis/) I tried to define my initial condition in the same way, but the resulting initial state was still wrong, looking scrambled. The problem seems to be the mapping of the content of the .mat file to correct vertices of the mesh, but i am unaware how to properly do that in the current version, since the solutions in the linked question (
parameters['reorder_dofs_serial'] = False and
psi.vector()[:] = phi_vector[V.dofmap().vertex_to_dof_map(mesh)]) both didn’t work for me, the end result after exporting the data still looked scrambled.
In the example below I pretty much only set the IC and then export it, here I would like to know how to properly set the IC so that the exported file looks the same as the imported one.
from __future__ import print_function from fenics import * import numpy as np from scipy.io import loadmat, savemat T = 0.5 # final time X = 0.5 Y = 1.0 # Subdomains class Inlet(SubDomain): Y = Y; def inside(self, x, on_boundary): return x > Y - DOLFIN_EPS and on_boundary class Outlet(SubDomain): def inside(self, x, on_boundary): return x < DOLFIN_EPS and on_boundary class Walls(SubDomain): def inside(self, x, on_boundary): return on_boundary # Create mesh and define function space nx = ny = 5 mesh = RectangleMesh(Point(0,0),Point(X,Y),nx,ny) V = FunctionSpace(mesh, 'CG', 1) # Subdomains sub_domains = MeshFunction("size_t", mesh, mesh.topology().dim() - 1); walls = Walls() inlet = Inlet() outlet = Outlet() u_Diri = Constant('0') bc_Inlet = DirichletBC(V, u_Diri, inlet) bc_Outlet = DirichletBC(V, u_Diri, outlet) bcs = [bc_Inlet,bc_Outlet] # Define initial value u_Ini = Function(V) # Load Initial State from .mat ini_cont = loadmat('example.mat') ini = ini_cont['M'] ini_vector = (ini[:,:]).reshape((nx+1)*(ny+1)) u_Ini.vector()[:] = ini_vector[vertex_to_dof_map(V)] u_n = interpolate(u_Ini, V) t = 0 hdf = HDF5File(mesh.mpi_comm(),'InitialState.h5','w') # Export the first step hdf.write(u_n,'fun',t) # Calculations are excluded here... ... ... ... # Export the coordinates in a separate .csv file Coord = V.tabulate_dof_coordinates() Coord.resize((V.dim(), 2)) x = Coord[:,0] z = Coord[:,1] np.savetxt("Results/Coords.csv", np.c_[x, z], delimiter=",")