Merge pull request #218 from jotelha/pep-8-electrochemistry

MAINT: Remodel electrochemistry module interface API to adhere to PEP-8 conventions

.github/workflows/tests.yml

@@ -6,6 +6,8 @@ on:
       - '**'
     tags:
       - '**'
+  pull_request:
+    branches: [ master ]
 
 jobs:
   tests:
@@ -24,6 +26,14 @@ jobs:
           # Upgrade to latest meson and ninja
           sudo pip install --upgrade meson ninja
 
+      # needs fenics only to run test_poisson_nernst_planck_solver_fenics
+      - name: install_fenics
+        run: |
+          sudo apt-get install -y --no-install-recommends software-properties-common
+          sudo add-apt-repository -y ppa:fenics-packages/fenics
+          sudo apt-get update -qy
+          sudo apt-get install -y fenics python3-dolfin python3-mshr
+
       - name: build_c
         run: |
           sudo pip install .[test]

docs/applications/electrochemistry_1.py

@@ -55,10 +55,10 @@
 pnp = PoissonNernstPlanckSystem(c=c, z=z, L=L, delta_u=delta_u)
 
 # %% [markdown]
-# The method `useStandardInterfaceBC` will apply boundary conditions as shown in <a hef="#figure1">Figure 1</a>, with Dirichlet boundary conditions on the potential and zero total flux boundary conditions on ion diffusion and electromigration.
+# The method `use_standard_interface_bc` will apply boundary conditions as shown in <a hef="#figure1">Figure 1</a>, with Dirichlet boundary conditions on the potential and zero total flux boundary conditions on ion diffusion and electromigration.
 
 # %%
-pnp.useStandardInterfaceBC()
+pnp.use_standard_interface_bc()
 ui, nij, _ = pnp.solve()
 
 # %% [markdown]
@@ -188,7 +188,7 @@ def make_patch_spines_invisible(ax):
 # The only difference is the application of another set of predefined boundary conditions.
 
 # %%
-pnp.useStandardCellBC()
+pnp.use_standard_cell_bc()
 
 # %% [markdown]
 # These boundary conditions assume no Stern layer, i.e. $\lambda_S = 0$
@@ -309,7 +309,7 @@ def make_patch_spines_invisible(ax):
 # The following applies zero flux and, particularly, Robin boundary conditions as shown in <a href="#figure2">Figure 2</a>.
 
 # %%
-pnp.useSternLayerCellBC()
+pnp.use_stern_layer_cell_bc()
 
 pnp.output = True
 xij = pnp.solve()

docs/applications/electrochemistry_2.py

@@ -63,12 +63,12 @@ def make_patch_spines_invisible(ax):
     c, z, L, delta_u=delta_u, N=N,
     solver="hybr", options={'xtol':1e-12})
 
-pnp['std_interface'].useStandardInterfaceBC()
+pnp['std_interface'].use_standard_interface_bc()
 uij, nij, lamj = pnp['std_interface'].solve()
 
 # define desired system
 pnp['fenics_interface'] = PoissonNernstPlanckSystemFEniCS(c, z, L, delta_u=delta_u, N=N)
-pnp['fenics_interface'].useStandardInterfaceBC()
+pnp['fenics_interface'].use_standard_interface_bc()
 uij, nij, _ = pnp['fenics_interface'].solve()
 
 # %% [markdown]
@@ -184,15 +184,15 @@ def make_patch_spines_invisible(ax):
 pnp['std_interface_high_potential'] = PoissonNernstPlanckSystem(
     c, z, L, delta_u=delta_u,N=N,
     solver="hybr", options={'xtol':1e-14})
-pnp['std_interface_high_potential'].useStandardInterfaceBC()
+pnp['std_interface_high_potential'].use_standard_interface_bc()
 uij, nij, lamj = pnp['std_interface_high_potential'].solve()
 
 # %% [markdown]
 # Apparently, the `PoissonNernstPlanckSystem` controlled-volumes solver does not converge ...
 
 # %%
 pnp['fenics_interface_high_potential'] = PoissonNernstPlanckSystemFEniCS(c, z, L, delta_u=delta_u, N=200)
-pnp['fenics_interface_high_potential'].useStandardInterfaceBC()
+pnp['fenics_interface_high_potential'].use_standard_interface_bc()
 uij, nij, _ = pnp['fenics_interface_high_potential'].solve()
 
 # %% [markdown]

matscipy/cli/electrochemistry/poisson_nernst_planck_solver_cli.py

@@ -164,6 +164,37 @@ class ArgumentDefaultsAndRawDescriptionHelpFormatter(
     logger = logging.getLogger()
     logger.setLevel(loglevel)
 
+    # use FEniCS finite element solver if available,
+    # otherwise own controlled volume scheme
+    try:
+        import fenics
+        from matscipy.electrochemistry.poisson_nernst_planck_solver_fenics \
+            import PoissonNernstPlanckSystemFEniCS as PoissonNernstPlanckSystem
+        import dolfin
+        import ffc
+        dolfin.cpp.log.set_log_level(loglevel)
+
+        if not args.outfile:
+            # fenics writes some log messages to stdout. If we pipe the output,
+            # we don't want that, hence here we have to suppress fenics logging
+            # if no output file has been specified
+            ffc.log.set_level(logging.ERROR)
+            fenics.set_log_level(logging.ERROR)
+            fenics.set_log_active(False)
+            dolfin.cpp.log.set_log_level(logging.ERROR)
+            dolfin.cpp.log.set_log_active(False)
+
+            logging.getLogger('UFL').setLevel(logging.ERROR)
+            logging.getLogger('FFC').setLevel(logging.ERROR)
+
+        logger.info("Will use FEniCS finite element solver.")
+    except ModuleNotFoundError:
+        logger.warning(
+            "No FEniCS finite element solver found,"
+            " falling back to internal controlled-volume implementation."
+            " ATTENTION: Number conservation not exact.")
+        from matscipy.electrochemistry import PoissonNernstPlanckSystem
+
     # remove all handlers
     for h in logger.handlers:
         logger.removeHandler(h)
@@ -181,22 +212,6 @@ class ArgumentDefaultsAndRawDescriptionHelpFormatter(
         fh.setLevel(loglevel)
         logger.addHandler(fh)
 
-    # use FEniCS finite element solver if available,
-    # otherwise own controlled volume scheme
-    try:
-        import fenics
-        from matscipy.electrochemistry.poisson_nernst_planck_solver_fenics \
-            import PoissonNernstPlanckSystemFEniCS as PoissonNernstPlanckSystem
-        import dolfin
-        dolfin.cpp.log.set_log_level(loglevel)
-        logger.info("Will use FEniCS finite element solver.")
-    except ModuleNotFoundError:
-        logger.warning(
-            "No FEniCS finite element solver found,"
-            " falling back to internal controlled-volume implementation."
-            " ATTENTION: Number conservation not exact.")
-        from matscipy.electrochemistry import PoissonNernstPlanckSystem
-
     # set up system
     pnp = PoissonNernstPlanckSystem(
         c=np.array(args.concentrations, dtype=float),
@@ -211,22 +226,16 @@ class ArgumentDefaultsAndRawDescriptionHelpFormatter(
         relative_permittivity=float(args.relative_permittivity))
 
     if args.boundary_conditions in ('cell-robin') and float(args.lambda_S) > 0:
-        pnp.useSternLayerCellBC()
+        pnp.use_stern_layer_cell_bc()
     elif ((args.boundary_conditions in ('cell-robin') and float(args.lambda_S) == 0)
             or args.boundary_conditions == 'cell'):
-        pnp.useStandardCellBC()
+        pnp.use_standard_cell_bc()
     elif args.boundary_conditions == 'interface':
-        pnp.useStandardInterfaceBC()
+        pnp.use_standard_interface_bc()
     else:
         raise ValueError("Boundary conditions '{}' not implemented!".format(
                          args.boundary_conditions))
 
-    if not args.outfile:
-        # fenics writes some log messages to stdout. If we pipe the output,
-        # we don't want that, hence here we have to suppress fenics logging
-        # if no output file has been specified
-        dolfin.cpp.log.set_log_active(False)
-
     pnp.solve()
 
     extra_kwargs = {}

matscipy/electrochemistry/continuous2discrete.py

@@ -289,7 +289,7 @@ def generate_structure(distribution, box=np.array([50, 50, 100]), count=100, n_g
             Z, _ = integrate.quad(d, support[-1][0], support[-1][1])
         else:  # discrete support
             support.append(np.linspace(0, box[k], n_gridpoints[k]))
-            Z = np.sum(d(support[-1])) # Normalization constant
+            Z = np.sum(d(support[-1]))  # Normalization constant
 
         logger.info("Normalizing 'distribution' {} by {}.".format(d, Z))
         normalized_distribution.append(

matscipy/electrochemistry/poisson_boltzmann_distribution.py

@@ -86,8 +86,7 @@ def debye(c, z,
     lambda_D : float
         Debye length, sqrt( epsR*eps*R*T/(2*F^2*I) ) [m]
     """
-    I = ionic_strength(c, z)
-    return np.sqrt(relative_permittivity*vacuum_permittivity*R*T/(2.0*F**2*I))
+    return np.sqrt(relative_permittivity*vacuum_permittivity*R*T/(2.0*F**2*ionic_strength(c, z)))
 
 
 def gamma(u, T=298.15):