Problem while performing Stokes flow with a PN extracted with porespy

[falvlima]

Hi,

I am facing some problems while performing stokes flow through a pore network extracted with porespy.

I could perform, for example, an injection algorithm, but when I use the stokes algorithm the following error appears.

Any guess regarding the problem?

sf_x.run()
Traceback (most recent call last):

  File "C:\Users\FERNAN~1\AppData\Local\Temp/ipykernel_5496/2468941576.py", line 1, in <module>
    sf_x.run()

  File "C:\ProgramData\Anaconda3\envs\py38\lib\site-packages\openpnm\algorithms\ReactiveTransport.py", line 159, in run
    x = self._run_reactive(x0)

  File "C:\ProgramData\Anaconda3\envs\py38\lib\site-packages\openpnm\algorithms\ReactiveTransport.py", line 361, in _run_reactive
    self[quantity] = x = self._solve(x0=x) * w + x * (1 - w)

  File "C:\ProgramData\Anaconda3\envs\py38\lib\site-packages\openpnm\algorithms\GenericTransport.py", line 621, in _solve
    x = solver(A, b, atol=atol, rtol=rtol, max_it=max_it, x0=x0)

  File "C:\ProgramData\Anaconda3\envs\py38\lib\site-packages\openpnm\algorithms\GenericTransport.py", line 680, in solver
    x = pypardiso.spsolve(A=A, b=b)

  File "C:\ProgramData\Anaconda3\envs\py38\lib\site-packages\pypardiso\scipy_aliases.py", line 44, in spsolve
    solver._check_A(A)

  File "C:\ProgramData\Anaconda3\envs\py38\lib\site-packages\pypardiso\pardiso_wrapper.py", line 224, in _check_A
    raise ValueError('Matrix A is singular, because it contains empty {}(s)'.format(row_col))

ValueError: Matrix A is singular, because it contains empty row(s)

[jgostick]

This is almost certainly because you have disconnected pores from your extraction. You can either clean up the image before extraction by applying fill_blind_pores to your image, or you can trim disconnected pores from the network once you have it in openpnm. If you run net.check_network_health() it will return a dictionary with several arrays, one of which is a list of pores to that should probably be trimmed.