Issue 923 reformat electrolyte

CHANGELOG.md

@@ -1,8 +1,14 @@
-# [Unreleased](https://github.com/pybamm-team/PyBaMM)
+# [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
-## Features
+## Optimizations
 
 -   Made `QuickPlot` compatible with Google Colab ([#935](https://github.com/pybamm-team/PyBaMM/pull/935))
+-   Sped up model building ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
+-   Changed default solver for lead-acid to `CasadiSolver` ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
+
+## Bug fixes
+
+-   Reformatted electrolyte submodels ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
 
 # [v0.2.1](https://github.com/pybamm-team/PyBaMM/tree/v0.2.1) - 2020-03-31
 

docs/source/expression_tree/operations/index.rst

@@ -9,3 +9,4 @@ Classes and functions that operate on the expression tree
   evaluate
   jacobian
   convert_to_casadi
+  unpack_symbol

docs/source/expression_tree/operations/unpack_symbol.rst

@@ -0,0 +1,5 @@
+Symbol Unpacker
+===============
+
+.. autoclass:: pybamm.SymbolUnpacker
+  :members:

docs/source/models/submodels/electrolyte/base_electrolyte_conductivity.rst → docs/source/models/submodels/electrolyte_conductivity/base_electrolyte_conductivity.rst

@@ -1,6 +1,6 @@
 Base Electrolyte Conductivity Submodel
 ======================================
 
-.. autoclass:: pybamm.electrolyte.BaseElectrolyteConductivity
+.. autoclass:: pybamm.electrolyte_conductivity.BaseElectrolyteConductivity
     :members:
 

docs/source/models/submodels/electrolyte_conductivity/composite_conductivity.rst

@@ -0,0 +1,5 @@
+Composite Model
+===============
+
+.. autoclass:: pybamm.electrolyte_conductivity.Composite
+    :members:

docs/source/models/submodels/electrolyte_conductivity/full_conductivity.rst

@@ -0,0 +1,7 @@
+Full Model
+==========
+
+.. autoclass:: pybamm.electrolyte_conductivity.Full
+    :members:
+    :inherited-members:
+

docs/source/models/submodels/electrolyte_conductivity/index.rst

@@ -0,0 +1,11 @@
+Electrolyte Conductivity
+========================
+
+.. toctree::
+    :maxdepth: 1
+
+    base_electrolyte_conductivity
+    leading_order_conductivity
+    composite_conductivity
+    full_conductivity
+    surface_form/index

docs/source/models/submodels/electrolyte_conductivity/leading_order_conductivity.rst

@@ -0,0 +1,6 @@
+Leading Order Model
+===================
+
+.. autoclass:: pybamm.electrolyte_conductivity.LeadingOrder
+    :members:
+

docs/source/models/submodels/electrolyte_conductivity/surface_form/full_surface_form_conductivity.rst

@@ -0,0 +1,8 @@
+Full Model
+===========
+
+.. autoclass:: pybamm.electrolyte_conductivity.surface_potential_form.FullDifferential
+    :members:
+
+.. autoclass:: pybamm.electrolyte_conductivity.surface_potential_form.FullAlgebraic
+    :members:

docs/source/models/submodels/electrolyte_conductivity/surface_form/index.rst

@@ -0,0 +1,7 @@
+Surface Form
+=============
+
+.. toctree::
+
+  full_surface_form_conductivity
+  leading_surface_form_conductivity

docs/source/models/submodels/electrolyte_conductivity/surface_form/leading_surface_form_conductivity.rst

@@ -0,0 +1,8 @@
+Leading Order Model
+====================
+
+.. autoclass:: pybamm.electrolyte_conductivity.surface_potential_form.LeadingOrderDifferential
+    :members:
+
+.. autoclass:: pybamm.electrolyte_conductivity.surface_potential_form.LeadingOrderAlgebraic
+    :members:

docs/source/models/submodels/electrolyte/base_electrolyte_diffusion.rst → docs/source/models/submodels/electrolyte_diffusion/base_electrolyte_diffusion.rst

@@ -1,5 +1,5 @@
 Base Electrolyte Diffusion Submodel
 ====================================
 
-.. autoclass:: pybamm.electrolyte.BaseElectrolyteDiffusion
+.. autoclass:: pybamm.electrolyte_diffusion.BaseElectrolyteDiffusion
     :members:

docs/source/models/submodels/electrolyte_diffusion/composite_diffusion.rst

@@ -0,0 +1,5 @@
+Composite Model
+===============
+
+.. autoclass:: pybamm.electrolyte_diffusion.Composite
+    :members:

docs/source/models/submodels/electrolyte_diffusion/constant_concentration.rst

@@ -0,0 +1,6 @@
+Constant Concentration
+=======================
+
+.. autoclass:: pybamm.electrolyte_diffusion.ConstantConcentration
+    :members:
+

docs/source/models/submodels/electrolyte_diffusion/full_diffusion.rst

@@ -0,0 +1,6 @@
+Full Model
+==========
+
+.. autoclass:: pybamm.electrolyte_diffusion.Full
+    :members:
+

docs/source/models/submodels/electrolyte_diffusion/index.rst

@@ -0,0 +1,10 @@
+Electrolyte Diffusion
+=====================
+
+.. toctree::
+
+  base_electrolyte_diffusion
+  constant_concentration
+  leading_order_diffusion
+  composite_diffusion
+  full_diffusion

docs/source/models/submodels/electrolyte_diffusion/leading_order_diffusion.rst

@@ -0,0 +1,7 @@
+Leading Order Model
+===================
+
+.. autoclass:: pybamm.electrolyte_diffusion.LeadingOrder
+    :members:
+
+

docs/source/models/submodels/index.rst

@@ -8,7 +8,8 @@ Submodels
     current_collector/index
     convection/index
     electrode/index
-    electrolyte/index
+    electrolyte_conductivity/index
+    electrolyte_diffusion/index
     external_circuit/index
     interface/index
     oxygen_diffusion/index

examples/scripts/compare_lead_acid.py

@@ -18,14 +18,14 @@
 # load models
 models = [
     pybamm.lead_acid.LOQS(),
-    # pybamm.lead_acid.FOQS(),
-    pybamm.lead_acid.Composite(),
+    pybamm.lead_acid.FOQS(),
+    pybamm.lead_acid.CompositeExtended(),
     pybamm.lead_acid.Full(),
 ]
 
 # load parameter values and process models and geometry
 param = models[0].default_parameter_values
-param.update({"Current function [A]": 10, "Initial State of Charge": 1})
+param.update({"Current function [A]": 85, "Initial State of Charge": 1})
 for model in models:
     param.process_model(model)
 

examples/scripts/custom_model.py

@@ -34,13 +34,12 @@
 model.submodels["positive interface"] = pybamm.interface.InverseButlerVolmer(
     model.param, "Positive", "lithium-ion main"
 )
-electrolyte = pybamm.electrolyte.stefan_maxwell
-model.submodels["electrolyte diffusion"] = electrolyte.diffusion.ConstantConcentration(
-    model.param
-)
-model.submodels["electrolyte conductivity"] = electrolyte.conductivity.LeadingOrder(
-    model.param
-)
+model.submodels[
+    "electrolyte diffusion"
+] = pybamm.electrolyte_diffusion.ConstantConcentration(model.param)
+model.submodels[
+    "electrolyte conductivity"
+] = pybamm.electrolyte_conductivity.LeadingOrder(model.param)
 
 # build model
 model.build_model()

pybamm/__init__.py

@@ -101,6 +101,7 @@ def version(formatted=False):
 )
 from .expression_tree.operations.jacobian import Jacobian
 from .expression_tree.operations.convert_to_casadi import CasadiConverter
+from .expression_tree.operations.unpack_symbols import SymbolUnpacker
 
 #
 # Model classes
@@ -123,7 +124,8 @@ def version(formatted=False):
 from .models.submodels import (
     convection,
     current_collector,
-    electrolyte,
+    electrolyte_conductivity,
+    electrolyte_diffusion,
     electrode,
     external_circuit,
     interface,

pybamm/expression_tree/broadcasts.py

@@ -252,8 +252,8 @@ class FullBroadcast(Broadcast):
     "A class for full broadcasts"
 
     def __init__(self, child, broadcast_domain, auxiliary_domains, name=None):
-        if auxiliary_domains == "current collector":
-            auxiliary_domains = {"secondary": "current collector"}
+        if isinstance(auxiliary_domains, str):
+            auxiliary_domains = {"secondary": auxiliary_domains}
         super().__init__(
             child,
             broadcast_domain,

pybamm/expression_tree/functions.py

@@ -86,7 +86,7 @@ def diff(self, variable):
             children = self.orphans
             partial_derivatives = [None] * len(children)
             for i, child in enumerate(self.children):
-                # if variable appears in the function,use autograd to differentiate
+                # if variable appears in the function, differentiate
                 # function, and apply chain rule
                 if variable.id in [symbol.id for symbol in child.pre_order()]:
                     partial_derivatives[i] = self._function_diff(