#546 merge #923

pybamm-team · Mar 28, 2020 · 6500ac9 · 6500ac9
2 parents d71cd6b + aae9402
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,8 +19,14 @@
 -   Added `CasadiAlgebraicSolver` for solving algebraic systems with CasADi ([#868](https://github.com/pybamm-team/PyBaMM/pull/868))
 -   Added electrolyte functions from Landesfeind ([#860](https://github.com/pybamm-team/PyBaMM/pull/860))
 
+## Optimizations
+
+-   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))
 -   Fixed bug raised if function returns a scalar ([#919](https://github.com/pybamm-team/PyBaMM/pull/919))
 -   Fixed event handling in `ScipySolver` ([#905](https://github.com/pybamm-team/PyBaMM/pull/905))
 -   Made input handling clearer in solvers ([#905](https://github.com/pybamm-team/PyBaMM/pull/905))

diff --git a/docs/source/expression_tree/operations/index.rst b/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
diff --git a/docs/source/expression_tree/operations/unpack_symbol.rst b/docs/source/expression_tree/operations/unpack_symbol.rst
@@ -0,0 +1,5 @@
+Symbol Unpacker
+===============
+
+.. autoclass:: pybamm.SymbolUnpacker
+  :members:
diff --git a/docs/source/models/submodels/electrolyte/index.rst b/docs/source/models/submodels/electrolyte/index.rst
diff --git a/...ls/electrolyte/stefan_maxwell/conductivity/base_stefan_maxwell_conductivity.rst b/...ls/electrolyte/stefan_maxwell/conductivity/base_stefan_maxwell_conductivity.rst
diff --git a/...ectrolyte/stefan_maxwell/conductivity/composite_stefan_maxwell_conductivity.rst b/...ectrolyte/stefan_maxwell/conductivity/composite_stefan_maxwell_conductivity.rst
diff --git a/...ls/electrolyte/stefan_maxwell/conductivity/full_stefan_maxwell_conductivity.rst b/...ls/electrolyte/stefan_maxwell/conductivity/full_stefan_maxwell_conductivity.rst
diff --git a/docs/source/models/submodels/electrolyte/stefan_maxwell/conductivity/index.rst b/docs/source/models/submodels/electrolyte/stefan_maxwell/conductivity/index.rst
diff --git a/...electrolyte/stefan_maxwell/conductivity/leading_stefan_maxwell_conductivity.rst b/...electrolyte/stefan_maxwell/conductivity/leading_stefan_maxwell_conductivity.rst
diff --git a/...ell/conductivity/surface_form/full_surface_form_stefan_maxwell_conductivity.rst b/...ell/conductivity/surface_form/full_surface_form_stefan_maxwell_conductivity.rst
diff --git a/.../conductivity/surface_form/leading_surface_form_stefan_maxwell_conductivity.rst b/.../conductivity/surface_form/leading_surface_form_stefan_maxwell_conductivity.rst
diff --git a/...ubmodels/electrolyte/stefan_maxwell/diffusion/base_stefan_maxwell_diffusion.rst b/...ubmodels/electrolyte/stefan_maxwell/diffusion/base_stefan_maxwell_diffusion.rst
diff --git a/...els/electrolyte/stefan_maxwell/diffusion/composite_stefan_maxwell_diffusion.rst b/...els/electrolyte/stefan_maxwell/diffusion/composite_stefan_maxwell_diffusion.rst
diff --git a/...dels/electrolyte/stefan_maxwell/diffusion/constant_stefan_maxwell_diffusion.rst b/...dels/electrolyte/stefan_maxwell/diffusion/constant_stefan_maxwell_diffusion.rst
diff --git a/...s/electrolyte/stefan_maxwell/diffusion/first_order_stefan_maxwell_diffusion.rst b/...s/electrolyte/stefan_maxwell/diffusion/first_order_stefan_maxwell_diffusion.rst
diff --git a/...ubmodels/electrolyte/stefan_maxwell/diffusion/full_stefan_maxwell_diffusion.rst b/...ubmodels/electrolyte/stefan_maxwell/diffusion/full_stefan_maxwell_diffusion.rst
diff --git a/docs/source/models/submodels/electrolyte/stefan_maxwell/diffusion/index.rst b/docs/source/models/submodels/electrolyte/stefan_maxwell/diffusion/index.rst
diff --git a/...odels/electrolyte/stefan_maxwell/diffusion/leading_stefan_maxwell_diffusion.rst b/...odels/electrolyte/stefan_maxwell/diffusion/leading_stefan_maxwell_diffusion.rst
diff --git a/docs/source/models/submodels/electrolyte/stefan_maxwell/index.rst b/docs/source/models/submodels/electrolyte/stefan_maxwell/index.rst
diff --git a/...trolyte/base_electrolyte_conductivity.rst → ...ctivity/base_electrolyte_conductivity.rst b/...trolyte/base_electrolyte_conductivity.rst → ...ctivity/base_electrolyte_conductivity.rst
@@ -1,6 +1,6 @@
 Base Electrolyte Conductivity Submodel
 ======================================
 
-.. autoclass:: pybamm.electrolyte.BaseElectrolyteConductivity
+.. autoclass:: pybamm.electrolyte_conductivity.BaseElectrolyteConductivity
     :members:
 
diff --git a/docs/source/models/submodels/electrolyte_conductivity/composite_conductivity.rst b/docs/source/models/submodels/electrolyte_conductivity/composite_conductivity.rst
@@ -0,0 +1,5 @@
+Composite Model
+===============
+
+.. autoclass:: pybamm.electrolyte_conductivity.Composite
+    :members:
diff --git a/docs/source/models/submodels/electrolyte_conductivity/full_conductivity.rst b/docs/source/models/submodels/electrolyte_conductivity/full_conductivity.rst
@@ -0,0 +1,7 @@
+Full Model
+==========
+
+.. autoclass:: pybamm.electrolyte_conductivity.Full
+    :members:
+    :inherited-members:
+
diff --git a/docs/source/models/submodels/electrolyte_conductivity/index.rst b/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
diff --git a/...source/models/submodels/electrolyte_conductivity/leading_order_conductivity.rst b/...source/models/submodels/electrolyte_conductivity/leading_order_conductivity.rst
@@ -0,0 +1,6 @@
+Leading Order Model
+===================
+
+.. autoclass:: pybamm.electrolyte_conductivity.LeadingOrder
+    :members:
+
diff --git a/...yte_conductivity/surface_form/full_surface_form_stefan_maxwell_conductivity.rst b/...yte_conductivity/surface_form/full_surface_form_stefan_maxwell_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:
diff --git a/...xwell/conductivity/surface_form/index.rst → ...olyte_conductivity/surface_form/index.rst b/...xwell/conductivity/surface_form/index.rst → ...olyte_conductivity/surface_form/index.rst
diff --git a/..._conductivity/surface_form/leading_surface_form_stefan_maxwell_conductivity.rst b/..._conductivity/surface_form/leading_surface_form_stefan_maxwell_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:
diff --git a/...lectrolyte/base_electrolyte_diffusion.rst → ..._diffusion/base_electrolyte_diffusion.rst b/...lectrolyte/base_electrolyte_diffusion.rst → ..._diffusion/base_electrolyte_diffusion.rst
@@ -1,5 +1,5 @@
 Base Electrolyte Diffusion Submodel
 ====================================
 
-.. autoclass:: pybamm.electrolyte.BaseElectrolyteDiffusion
+.. autoclass:: pybamm.electrolyte_diffusion.BaseElectrolyteDiffusion
     :members:
diff --git a/docs/source/models/submodels/electrolyte_diffusion/composite_diffusion.rst b/docs/source/models/submodels/electrolyte_diffusion/composite_diffusion.rst
@@ -0,0 +1,5 @@
+Composite Model
+===============
+
+.. autoclass:: pybamm.electrolyte_diffusion.Composite
+    :members:
diff --git a/docs/source/models/submodels/electrolyte_diffusion/constant_concentration.rst b/docs/source/models/submodels/electrolyte_diffusion/constant_concentration.rst
@@ -0,0 +1,6 @@
+Constant Concentration
+=======================
+
+.. autoclass:: pybamm.electrolyte_diffusion.ConstantConcentration
+    :members:
+
diff --git a/docs/source/models/submodels/electrolyte_diffusion/full_diffusion.rst b/docs/source/models/submodels/electrolyte_diffusion/full_diffusion.rst
@@ -0,0 +1,6 @@
+Full Model
+==========
+
+.. autoclass:: pybamm.electrolyte_diffusion.Full
+    :members:
+
diff --git a/docs/source/models/submodels/electrolyte_diffusion/index.rst b/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
diff --git a/docs/source/models/submodels/electrolyte_diffusion/leading_order_diffusion.rst b/docs/source/models/submodels/electrolyte_diffusion/leading_order_diffusion.rst
@@ -0,0 +1,7 @@
+Leading Order Model
+===================
+
+.. autoclass:: pybamm.electrolyte_diffusion.LeadingOrder
+    :members:
+
+
diff --git a/docs/source/models/submodels/index.rst b/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

diff --git a/examples/notebooks/models/spm1.png b/examples/notebooks/models/spm1.png
diff --git a/examples/notebooks/spatial_methods/finite-volumes.ipynb b/examples/notebooks/spatial_methods/finite-volumes.ipynb
diff --git a/examples/notebooks/using-submodels.ipynb b/examples/notebooks/using-submodels.ipynb
diff --git a/examples/scripts/compare_lead_acid.py b/examples/scripts/compare_lead_acid.py
@@ -17,9 +17,9 @@
 
 # load models
 models = [
-    pybamm.lead_acid.LOQS(),
-    # pybamm.lead_acid.FOQS(),
-    pybamm.lead_acid.Composite(),
+    # pybamm.lead_acid.LOQS(),
+    # # pybamm.lead_acid.FOQS(),
+    # pybamm.lead_acid.Composite(),
     pybamm.lead_acid.Full(),
 ]
 

diff --git a/examples/scripts/custom_model.py b/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()

diff --git a/pybamm/__init__.py b/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,

diff --git a/pybamm/expression_tree/functions.py b/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(