Adding short description for examples

examples/BMCSL.py

@@ -3,7 +3,12 @@
 
 @author: Nitish Govindarajan
 
+Simple example for the BMCSL model for finite size ion effects
+
 Code to reproduce Figure 1 from doi:10.1016/j.jcis.2007.08.006
+Biesheuvel, P.M. and Van Soestbergen, M., 2007. Counterion volume effects in
+mixed electrical double layers. Journal of Colloid and Interface Science,
+316(2), pp.490-499.
 """
 
 # Import required libraries

examples/bicarb.py

@@ -5,7 +5,8 @@
 class CarbonateSolver(EchemSolver):
     def __init__(self):
         """
-        Bicarbonate example reproduced from:
+        Flow past an electrode with bicarbonate bulk reactions and linear CO2 electrolysis
+        Example reproduced from:
         Lin, T.Y., Baker, S.E., Duoss, E.B. and Beck, V.A., 2021. Analysis of
         the Reactive CO2 Surface Flux in Electrocatalytic Aqueous Flow
         Reactors. Industrial & Engineering Chemistry Research, 60(31),

examples/bicarb_Ag_Cu_tandem_example.py

@@ -11,19 +11,19 @@
 comm = MPI.COMM_WORLD
 rank = comm.Get_rank()
 
-##Description:
-#This example case runs a tandem electrode system, with an Ag catalyst placed
-#in front of a Cu catalyst, at a Peclet number of 1E3. 
-#The advection/diffusion/migration/electroneutrality equations are solved 
-#for the bulk electrolyte, and a Tafel description is applied for the surface 
-#catalyst reactions.
+"""
+This example case runs a tandem electrode system, with an Ag catalyst placed
+in front of a Cu catalyst, at a Peclet number of 1E3. 
+The advection/diffusion/migration/electroneutrality equations are solved 
+for the bulk electrolyte, and a Tafel description is applied for the surface 
+catalyst reactions.
 
-#Assumed products of Cu catalyst are C2H4, C2H6O, and H2.
-#Assumed products of Ag catalysis are CO and H2.
+Assumed products of Cu catalyst are C2H4, C2H6O, and H2.
+Assumed products of Ag catalysis are CO and H2.
+
+--------------------------------------------------------------------------
+list of references
 
-##--------------------------------------------------------------------------
-#list of references
-"""
 Bicarbonate flow reactor setup given in:
 Lin, T.Y., Baker, S.E., Duoss, E.B. and Beck, V.A., 2021. Analysis of
 the Reactive CO2 Surface Flux in Electrocatalytic Aqueous Flow
@@ -53,10 +53,9 @@
 Microkinetics with Continuum Transport Models to Understand Electrochemical 
 CO2 Reduction in Flow Reactors. PRX Energy, 2(3), pp.033010.
 
+--------------------------------------------------------------------------
+end of list of references
 """
-##--------------------------------------------------------------------------
-#end of list of references
-
 
 
 #---------------------------------------------------------------------------

examples/bortels_threeion.py

@@ -7,6 +7,20 @@
 parser.add_argument("--family", type=str, default='DG')
 args, _ = parser.parse_known_args()
 
+"""
+2D Flow-plate reactor with electroneutral Nernst-Planck. Using a custom gmsh
+mesh with refinement close to the electrodes. GMSH is used to get the mesh file
+from the .geo file as follows:
+
+    gmsh -2 bortels_structuredquad.geo
+
+Three ion case taken from: 
+Bortels, L., Deconinck, J. and Van Den Bossche, B., 1996. The multi-dimensional
+upwinding method as a new simulation tool for the analysis of multi-ion
+electrolytes controlled by diffusion, convection and migration. Part 1. Steady
+state analysis of a parallel plane flow channel. Journal of Electroanalytical
+Chemistry, 404(1), pp.15-26.
+"""
 
 class BortelsSolver(EchemSolver):
     def __init__(self):

examples/bortels_threeion_extruded_3D_nondim.py

@@ -8,6 +8,24 @@
 
 set_log_level(DEBUG)
 
+"""
+3D Flow-plate reactor with electroneutral Nernst-Planck. Using a custom gmsh
+mesh with refinement close to the electrodes. The mesh is then extruded in the
+z-direction. Custom block preconditioners are used. The file submitter.pl can
+be adapted to launch slurm jobs using perl.
+
+Three ion case adapted from the 2D case in: 
+Bortels, L., Deconinck, J. and Van Den Bossche, B., 1996. The multi-dimensional
+upwinding method as a new simulation tool for the analysis of multi-ion
+electrolytes controlled by diffusion, convection and migration. Part 1. Steady
+state analysis of a parallel plane flow channel. Journal of Electroanalytical
+Chemistry, 404(1), pp.15-26.
+
+Nondimensionalization and preconditioning from:
+Roy, T., Andrej, J. and Beck, V.A., 2023. A scalable DG solver for the
+electroneutral Nernst-Planck equations. Journal of Computational Physics, 475,
+p.111859.
+"""
 
 parser = argparse.ArgumentParser()
 parser.add_argument('-ref_levels', type=int, default=0)
@@ -55,6 +73,7 @@ def coarsen_form(self, form, args):
 class BortelsSolver(EchemSolver):
     def __init__(self):
         # Create an initial coarse mesh
+        # Note: will need to use "gmsh -2 mesh_name.geo" command to convert to .msh format
         if args.mesh == 'structured':
             plane_mesh = Mesh('bortels_structuredquad_nondim_coarse1664.msh')
             layers = 8
@@ -197,7 +216,6 @@ def set_velocity(self):
 
 # Custom solver parameters
 
-
 class CoarsenPenaltyPMGPC(P1PC):
     def coarsen_form(self, form, replace_dict):
         k = 1

examples/bortels_threeion_nondim.py

@@ -1,6 +1,25 @@
 from firedrake import *
 from echemflow import EchemSolver
 
+"""
+2D Flow-plate reactor with electroneutral Nernst-Planck. Using a custom gmsh
+mesh with refinement close to the electrodes. GMSH is used to get the mesh file
+from the .geo file as follows:
+
+    gmsh -2 bortels_structuredquad_nondim.geo
+
+Three ion case taken from: 
+Bortels, L., Deconinck, J. and Van Den Bossche, B., 1996. The multi-dimensional
+upwinding method as a new simulation tool for the analysis of multi-ion
+electrolytes controlled by diffusion, convection and migration. Part 1. Steady
+state analysis of a parallel plane flow channel. Journal of Electroanalytical
+Chemistry, 404(1), pp.15-26.
+
+Nondimensionalization from:
+Roy, T., Andrej, J. and Beck, V.A., 2023. A scalable DG solver for the
+electroneutral Nernst-Planck equations. Journal of Computational Physics, 475,
+p.111859.
+"""
 
 class BortelsSolver(EchemSolver):
     def __init__(self):

examples/bortels_twoion.py

@@ -5,6 +5,20 @@
 parser.add_argument("--family", type=str, default='DG')
 args, _ = parser.parse_known_args()
 
+"""
+2D Flow-plate reactor with electroneutral Nernst-Planck. Using a custom GMSH
+mesh with refinement close to the electrodes. GMSH is used to get the mesh file
+from the .geo file as follows:
+
+    gmsh -2 bortels_structuredquad.geo
+
+Two ion case taken from: 
+Bortels, L., Deconinck, J. and Van Den Bossche, B., 1996. The multi-dimensional
+upwinding method as a new simulation tool for the analysis of multi-ion
+electrolytes controlled by diffusion, convection and migration. Part 1. Steady
+state analysis of a parallel plane flow channel. Journal of Electroanalytical
+Chemistry, 404(1), pp.15-26.
+"""
 
 class BortelsSolver(EchemSolver):
     def __init__(self):

examples/bortels_twoion_nondim.py

@@ -1,6 +1,25 @@
 from firedrake import *
 from echemfem import EchemSolver
 
+"""
+2D Flow-plate reactor with electroneutral Nernst-Planck. Using a custom gmsh
+mesh with refinement close to the electrodes. GMSH is used to get the mesh file
+from the .geo file as follows:
+
+    gmsh -2 bortels_structuredquad_nondim.geo
+
+Two ion case taken from: 
+Bortels, L., Deconinck, J. and Van Den Bossche, B., 1996. The multi-dimensional
+upwinding method as a new simulation tool for the analysis of multi-ion
+electrolytes controlled by diffusion, convection and migration. Part 1. Steady
+state analysis of a parallel plane flow channel. Journal of Electroanalytical
+Chemistry, 404(1), pp.15-26.
+
+Nondimensionalization from:
+Roy, T., Andrej, J. and Beck, V.A., 2023. A scalable DG solver for the
+electroneutral Nernst-Planck equations. Journal of Computational Physics, 475,
+p.111859.
+"""
 
 class BortelsSolver(EchemSolver):
     def __init__(self):

examples/carbonate.py

@@ -1,20 +1,24 @@
 from firedrake import *
 from echemfem import EchemSolver, IntervalBoundaryLayerMesh
 
+"""
+A 1D example of diffusion-reaction for CO2 electrolysis with bicarbonate bulk
+reactions. The bulk reactions and charge-transfer reactions are implemented by
+hand.
+
+Steady-state version of example from
+Gupta, N., Gattrell, M. and MacDougall, B., 2006. Calculation for the
+cathode surface concentrations in the electrochemical reduction of CO2 in
+KHCO3 solutions. Journal of applied electrochemistry, 36(2), pp.161-172.
+
+Using the bicarbonate bulk reactions from
+Schulz, K.G., Riebesell, U., Rost, B., Thoms, S. and Zeebe, R.E., 2006.
+Determination of the rate constants for the carbon dioxide to bicarbonate
+inter-conversion in pH-buffered seawater systems. Marine chemistry,
+100(1-2), pp.53-65.
+"""
 
 class CarbonateSolver(EchemSolver):
-    """
-    Steady-state version of example from
-    Gupta, N., Gattrell, M. and MacDougall, B., 2006. Calculation for the
-    cathode surface concentrations in the electrochemical reduction of CO2 in
-    KHCO3 solutions. Journal of applied electrochemistry, 36(2), pp.161-172.
-    but using the bicarbonate bulk reactions from
-    Schulz, K.G., Riebesell, U., Rost, B., Thoms, S. and Zeebe, R.E., 2006.
-    Determination of the rate constants for the carbon dioxide to bicarbonate
-    inter-conversion in pH-buffered seawater systems. Marine chemistry,
-    100(1-2), pp.53-65.
-    """
-
     def __init__(self):
 
         delta = 0.0001
@@ -115,6 +119,9 @@ def set_boundary_markers(self):
 solver = CarbonateSolver()
 solver.setup_solver()
 solver.solve()
+
+### Plotting
+
 C_CO2, C_OH, C_H, C_CO3, C_HCO3 = solver.u.subfunctions
 # OH boundary layer
 x = solver.mesh.coordinates

examples/carbonate_homog_params.py

@@ -1,20 +1,24 @@
 from firedrake import *
 from echemfem import EchemSolver, IntervalBoundaryLayerMesh
 
+"""
+A 1D example of diffusion-reaction for CO2 electrolysis with bicarbonate bulk
+reactions. The charge-transfer reactions are implemented by hand but the bulk
+reactions are implemented using the homog_params interface.
+
+Steady-state version of example from
+Gupta, N., Gattrell, M. and MacDougall, B., 2006. Calculation for the
+cathode surface concentrations in the electrochemical reduction of CO2 in
+KHCO3 solutions. Journal of applied electrochemistry, 36(2), pp.161-172.
+
+Using the bicarbonate bulk reactions from
+Schulz, K.G., Riebesell, U., Rost, B., Thoms, S. and Zeebe, R.E., 2006.
+Determination of the rate constants for the carbon dioxide to bicarbonate
+inter-conversion in pH-buffered seawater systems. Marine chemistry,
+100(1-2), pp.53-65.
+"""
 
 class CarbonateSolver(EchemSolver):
-    """
-    Steady-state version of example from
-    Gupta, N., Gattrell, M. and MacDougall, B., 2006. Calculation for the
-    cathode surface concentrations in the electrochemical reduction of CO2 in
-    KHCO3 solutions. Journal of applied electrochemistry, 36(2), pp.161-172.
-    but using the bicarbonate bulk reactions from
-    Schulz, K.G., Riebesell, U., Rost, B., Thoms, S. and Zeebe, R.E., 2006.
-    Determination of the rate constants for the carbon dioxide to bicarbonate
-    inter-conversion in pH-buffered seawater systems. Marine chemistry,
-    100(1-2), pp.53-65.
-    """
-
     def __init__(self):
 
         delta = 0.0001
@@ -142,6 +146,9 @@ def set_boundary_markers(self):
 solver = CarbonateSolver()
 solver.setup_solver()
 solver.solve()
+
+### Plotting
+
 C_CO2, C_OH, C_H, C_CO3, C_HCO3 = solver.u.subfunctions
 # OH boundary layer
 x = solver.mesh.coordinates

examples/catalyst_layer_Cu.py

@@ -6,7 +6,10 @@
 import csv
 import pdb
 """
-Model fromn
+1D model for the CO2 electrolysis in a copper catalyst layer of a gas diffusion
+electrode (GDE). The model uses electroneutral Nernst-Planck in a porous
+medium.
+
 Corral D, Lee DU, Ehlinger VM, Nitopi S, Acosta JE, Wang L, King AJ, Feaster JT, 
 Lin YR, Weber AZ, Baker SE. Bridging knowledge gaps in liquid-and vapor-fed CO2 
 electrolysis through active electrode area. Chem Catalysis. 2022 Oct 12.
@@ -240,6 +243,9 @@ def set_boundary_markers(self):
     solver.U_app.assign(Vs)
     print("V = %d mV" % (Vs * 1000))
     solver.solve()
+
+    ## Plotting
+
     cCO2, cOH, cH, cCO3, cHCO3, phi2, phi1 = solver.u.subfunctions
     cK = Function(solver.V).assign(2 * cCO3 + cOH + cHCO3 - cH)
 

examples/catalyst_layer_Cu_full.py

@@ -5,7 +5,12 @@
 import numpy as np
 import csv
 """
-Model fromn
+1D model for the CO2 electrolysis in a copper catalyst layer of a gas diffusion
+electrode (GDE). The model uses electroneutral Nernst-Planck in a porous
+medium. This version of the code does not eliminate a species by substituting
+the electroneutrality equation, but rather explicitly solves for
+electroneutrality.
+
 Corral D, Lee DU, Ehlinger VM, Nitopi S, Acosta JE, Wang L, King AJ, Feaster JT, 
 Lin YR, Weber AZ, Baker SE. Bridging knowledge gaps in liquid-and vapor-fed CO2 
 electrolysis through active electrode area. Chem Catalysis. 2022 Oct 12.
@@ -240,6 +245,9 @@ def set_boundary_markers(self):
     solver.U_app.assign(Vs)
     print("V = %d mV" % (Vs * 1000))
     solver.solve()
+
+    ## Plotting
+
     cCO2, cOH, cH, cCO3, cHCO3, cK, phi2, phi1 = solver.u.subfunctions
 
     x_ = Function(V).interpolate(solver.mesh.coordinates[0]).vector().dat.data

examples/cylindrical_pore.py

@@ -2,7 +2,9 @@
 from echemfem import EchemSolver
 import numpy as np
 """
-Model from
+A symmetric cylindrical pore model for CO2 electrolysis using electroneutral
+Nernst-Planck and simplified bicarbonate bulk reactions.
+
 Elucidating Mass Transport Regimes in Gas Diffusion Electrodes for CO2 Electroreduction
 Thomas Moore, Xiaoxing Xia, Sarah E. Baker, Eric B. Duoss, and Victor A. Beck
 ACS Energy Letters 2021 6 (10), 3600-3606
@@ -170,18 +172,18 @@ def set_boundary_markers(self):
 solver.save_solutions = False
 solver.solve()
 
+## Plotting
+
 # getting active region
 _, Z = SpatialCoordinate(solver.mesh)
 active = conditional(le(Z, 5e-6), 1., 0.)
 
-
 def get_boundary_dofs(V, i):
     u = Function(V)
     bc = DirichletBC(V, active, i)
     bc.apply(u)
     return np.where(u.vector()[:] == 1)
 
-
 dofs = get_boundary_dofs(solver.V, 2)
 Z_cat = Function(solver.V).interpolate(Z).dat.data[dofs]
 

examples/gupta.py

@@ -4,6 +4,9 @@
 
 class GuptaSolver(EchemSolver):
     """
+    A 1D example of diffusion-reaction for CO2 electrolysis with bicarbonate bulk
+    reactions.
+
     Steady-state version of example from
     Gupta, N., Gattrell, M. and MacDougall, B., 2006. Calculation for the
     cathode surface concentrations in the electrochemical reduction of CO2 in
@@ -94,6 +97,9 @@ def set_boundary_markers(self):
 solver = GuptaSolver()
 solver.setup_solver()
 solver.solve()
+
+## Plotting
+
 C_CO2, C_HCO3, C_CO3, C_OH = solver.u.subfunctions
 # OH boundary layer
 x = solver.mesh.coordinates