How to use snow_2 output with FickianDiffusion algorithm

[ryanvolpi]

Hello! I'd like to use the FickianDiffusion algorithm on a network I extract using snow2 but I can't seem to find an example which lays out the steps in a way that works in the current version of openpnm. I think my issue is related to getting the network geometry, but I am not sure. As an example of what I am trying, see below. Any direction would be greatly appreciated!

import porespy as ps
import openpnm as op

im = ps.generators.blobs(shape=[50, 50, 50], porosity=0.6)
snow_output = ps.networks.snow2(im.astype(int), boundary_width = [[0,0],[0,0],[3,0]])
#create empty dummy network
pn = op.network.GenericNetwork()
#update openpnm pore network
pn.update(snow_output.network)
#prj = pn.project

air = op.phases.GenericPhase(network=pn)
f = op.models.phases.diffusivity.fuller
air.add_model(propname='pore.diffusivity',
              model=f,
              MA=0.032, MB=0.028, vA=16.6, vB=17.9)

phys = op.physics.GenericPhysics(network=pn, phase=air)#, geometry=geo
f = op.models.physics.diffusive_conductance.ordinary_diffusion
phys.add_model(propname='throat.diffusive_conductance',
               model=f)

fd = op.algorithms.FickianDiffusion(network=pn, phase=air)
fd.set_value_BC(pores=pn.pores('boundary'), values=1)
fd.set_value_BC(pores=[p for p in pn.pores() if not p in pn.pores('boundary')], values=0)
fd.run()
#print(fd.rate(pores=pn.pores('left')))

C:\Users\volpir\PycharmProjects\Computer Vision Playground\venv\lib\site-packages\numba\np\ufunc\parallel.py:365: NumbaWarning: The TBB threading layer requires TBB version 2019.5 or later i.e., TBB_INTERFACE_VERSION >= 11005. Found TBB_INTERFACE_VERSION = 11004. The TBB threading layer is disabled.
warnings.warn(problem)
WARNING : No Geometry provided, phys_01 will not be associated with any locations
SOURCE : openpnm.physics.GenericPhysics.init
TIME STAMP : 2021-05-19 16:34:37,814

ERROR : throat.diffusive_conductance was not run since the following property is
missing: 'pore.area'
SOURCE : openpnm.core.ModelsMixin._regen
TIME STAMP : 2021-05-19 16:34:37,817

KeyError Traceback (most recent call last)
in
27 fd.set_value_BC(pores=pn.pores('boundary'), values=1)
28 fd.set_value_BC(pores=[p for p in pn.pores() if not p in pn.pores('boundary')], values=0)
---> 29 fd.run()
30 #print(fd.rate(pores=pn.pores('left')))

~\PycharmProjects\Computer Vision Playground\venv\lib\site-packages\openpnm\algorithms\ReactiveTransport.py in run(self, x0)
152 self._validate_settings()
153 # Check if A and b are well-defined
--> 154 self._validate_data_health()
155 quantity = self.settings['quantity']
156 logger.info('Running ReactiveTransport')

~\PycharmProjects\Computer Vision Playground\venv\lib\site-packages\openpnm\algorithms\GenericTransport.py in _validate_data_health(self)
790
791 # Short-circuit subsequent checks if data are healthy
--> 792 if np.isfinite(self.A.data).all() and np.isfinite(self.b).all():
793 return True
794 # Validate network topology health

~\PycharmProjects\Computer Vision Playground\venv\lib\site-packages\openpnm\algorithms\GenericTransport.py in _get_A(self)
487 def _get_A(self):
488 if self._A is None:
--> 489 self._build_A()
490 return self._A
491

~\PycharmProjects\Computer Vision Playground\venv\lib\site-packages\openpnm\algorithms\GenericTransport.py in _build_A(self)
466 except KeyError:
467 raise Exception('Phase has not been defined for algorithm')
--> 468 g = phase[gvals]
469 am = network.create_adjacency_matrix(weights=g, fmt='coo')
470 self._pure_A = spgr.laplacian(am).astype(float)

~\PycharmProjects\Computer Vision Playground\venv\lib\site-packages\openpnm\phases\GenericPhase.py in getitem(self, key)
97 prop=not_el + '.' + prop,
98 mode='mean')
---> 99 vals = super().getitem(key)
100 return vals

~\PycharmProjects\Computer Vision Playground\venv\lib\site-packages\openpnm\core\Base.py in getitem(self, key)
275 vals = super().getitem(key)
276 else:
--> 277 raise KeyError(key)
278 return vals
279

KeyError: 'throat.diffusive_conductance'

[jgostick]

The 'dev' version of Porespy (which I assume you're using since you have used snow2) is not quite compatible with OpenPNM. We are in the midst converting PoreSpy to V2, and then OpenPNM to V3, but everything takes longer than it was supposed to. For now, I suggest you use the 'conda' or 'pip' versions of both packages, which are compatible with each other.

[ryanvolpi]

Oh, of course, that makes sense! Thank you.