#858 merge develop

pybamm-team · Mar 15, 2020 · ff5e810 · ff5e810
2 parents 00990f9 + 986ff2c
commit ff5e810
Show file tree

Hide file tree

Showing 175 changed files with 4,169 additions and 3,016 deletions.
diff --git a/.gitignore b/.gitignore
@@ -36,6 +36,9 @@ input/*
 !input/comsol_results/
 !input/drive_cycles
 
+# keep images required by notebooks
+!examples/notebooks/Creating%20Models/SEI.png
+
 # simulation outputs
 out/
 config.py
@@ -59,6 +62,7 @@ htmlcov/
 pyproject.toml
 
 # virtual enviroment
+env/
 venv/
 venv3.5/
 PyBaMM-env/

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,25 @@
+# [Unreleased](https://github.com/pybamm-team/PyBaMM)
+
+## Features
+
+-   Added additional notebooks showing how to create and compare models ([#877](https://github.com/pybamm-team/PyBaMM/pull/877))
+-   Added `Minimum`, `Maximum` and `Sign` operators ([#876](https://github.com/pybamm-team/PyBaMM/pull/876))
+-   Added a search feature to `FuzzyDict` ([#875](https://github.com/pybamm-team/PyBaMM/pull/875))
+-   Add ambient temperature as a function of time ([#872](https://github.com/pybamm-team/PyBaMM/pull/872))
+-   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))
+
+## Bug fixes
+
+-   Reformatted external circuit submodels ([#879](https://github.com/pybamm-team/PyBaMM/pull/879))
+-   Some bug fixes to generalize specifying models that aren't battery models, see [#846](https://github.com/pybamm-team/PyBaMM/issues/846)
+-   Reformatted interface submodels to be more readable ([#866](https://github.com/pybamm-team/PyBaMM/pull/866))
+-   Removed double-counted "number of electrodes connected in parallel" from simulation ([#864](https://github.com/pybamm-team/PyBaMM/pull/864))
+
+## Breaking changes
+
+-   Removed "set external temperature" and "set external potential" options. Use "external submodels" option instead ([#862](https://github.com/pybamm-team/PyBaMM/pull/862))
+
 # [v0.2.0](https://github.com/pybamm-team/PyBaMM/tree/v0.2.0) - 2020-02-26
 
 This release introduces many new features and optimizations. All models can now be solved using the pip installation - in particular, the DFN can be solved in around 0.1s. Other highlights include an improved user interface, simulations of experimental protocols (GITT, CCCV, etc), new parameter sets for NCA and LGM50, drive cycles, "input parameters" and "external variables" for quickly solving models with different parameter values and coupling with external software, and general bug fixes and optimizations.

diff --git a/docs/source/expression_tree/binary_operator.rst b/docs/source/expression_tree/binary_operator.rst
@@ -28,4 +28,20 @@ Binary Operators
 .. autoclass:: pybamm.Heaviside
   :members:
 
+.. autoclass:: pybamm.EqualHeaviside
+  :members:
+
+.. autoclass:: pybamm.NotEqualHeaviside
+  :members:
+
+.. autoclass:: pybamm.Minimum
+  :members:
+
+.. autoclass:: pybamm.Maximum
+  :members:
+
+.. autofunction:: pybamm.minimum
+
+.. autofunction:: pybamm.maximum
+
 .. autofunction:: pybamm.source
diff --git a/docs/source/expression_tree/unary_operator.rst b/docs/source/expression_tree/unary_operator.rst
@@ -10,6 +10,9 @@ Unary Operators
 .. autoclass:: pybamm.AbsoluteValue
   :members:
 
+.. autoclass:: pybamm.Sign
+  :members:
+
 .. autoclass:: pybamm.Index
   :members:
 
@@ -67,4 +70,12 @@ Unary Operators
 
 .. autofunction:: pybamm.x_average
 
+.. autofunction:: pybamm.r_average
+
+.. autofunction:: pybamm.z_average
+
+.. autofunction:: pybamm.yz_average
+
 .. autofunction:: pybamm.boundary_value
+
+.. autofunction:: pybamm.sign
diff --git a/docs/source/models/submodels/current_collector/index.rst b/docs/source/models/submodels/current_collector/index.rst
@@ -10,4 +10,3 @@ Current Collector
   homogeneous_current_collector
   potential_pair
   quite_conductive_potential_pair
-  set_potential_single_particle
diff --git a/docs/source/models/submodels/current_collector/set_potential_single_particle.rst b/docs/source/models/submodels/current_collector/set_potential_single_particle.rst
diff --git a/docs/source/models/submodels/interface/diffusion_limited.rst b/docs/source/models/submodels/interface/diffusion_limited.rst
@@ -0,0 +1,5 @@
+Diffusion-limited
+=================
+
+.. autoclass:: pybamm.interface.DiffusionLimited
+    :members:
diff --git a/.../source/models/submodels/interface/diffusion_limited/base_diffusion_limited.rst b/.../source/models/submodels/interface/diffusion_limited/base_diffusion_limited.rst
diff --git a/.../source/models/submodels/interface/diffusion_limited/full_diffusion_limited.rst b/.../source/models/submodels/interface/diffusion_limited/full_diffusion_limited.rst
diff --git a/docs/source/models/submodels/interface/diffusion_limited/index.rst b/docs/source/models/submodels/interface/diffusion_limited/index.rst
diff --git a/...urce/models/submodels/interface/diffusion_limited/leading_diffusion_limited.rst b/...urce/models/submodels/interface/diffusion_limited/leading_diffusion_limited.rst
diff --git a/...source/models/submodels/interface/first_order_kinetics/first_order_kinetics.rst b/...source/models/submodels/interface/first_order_kinetics/first_order_kinetics.rst
@@ -0,0 +1,5 @@
+First-order Kinetics
+====================
+
+.. autoclass:: pybamm.interface.FirstOrderKinetics
+    :members:
diff --git a/docs/source/models/submodels/interface/first_order_kinetics/index.rst b/docs/source/models/submodels/interface/first_order_kinetics/index.rst
@@ -0,0 +1,8 @@
+First-order Kinetics
+====================
+
+.. toctree::
+  :maxdepth: 1
+
+  inverse_first_order_kinetics
+  first_order_kinetics
diff --git a/...ics/base_inverse_first_order_kinetics.rst → ...kinetics/inverse_first_order_kinetics.rst b/...ics/base_inverse_first_order_kinetics.rst → ...kinetics/inverse_first_order_kinetics.rst
@@ -1,5 +1,5 @@
 Base Inverse First-order Kinetics
 =================================
 
-.. autoclass:: pybamm.interface.inverse_kinetics.BaseInverseFirstOrderKinetics
+.. autoclass:: pybamm.interface.InverseFirstOrderKinetics
     :members:
diff --git a/docs/source/models/submodels/interface/index.rst b/docs/source/models/submodels/interface/index.rst
@@ -5,8 +5,7 @@ Interface
   :maxdepth: 1
 
   base_interface
-  diffusion_limited/index
-  inverse_kinetics/index
   kinetics/index
-  lead_acid
-  lithium_ion
+  inverse_kinetics/index
+  first_order_kinetics/index
+  diffusion_limited
diff --git a/docs/source/models/submodels/interface/inverse_kinetics/base_inverse_kinetics.rst b/docs/source/models/submodels/interface/inverse_kinetics/base_inverse_kinetics.rst
diff --git a/docs/source/models/submodels/interface/inverse_kinetics/index.rst b/docs/source/models/submodels/interface/inverse_kinetics/index.rst
@@ -4,6 +4,4 @@ Inverse Interface Kinetics
 .. toctree::
   :maxdepth: 1
 
-  base_inverse_first_order_kinetics
-  base_inverse_kinetics
   inverse_butler_volmer
diff --git a/docs/source/models/submodels/interface/kinetics/base_first_order_kinetics.rst b/docs/source/models/submodels/interface/kinetics/base_first_order_kinetics.rst
diff --git a/docs/source/models/submodels/interface/kinetics/base_kinetics.rst b/docs/source/models/submodels/interface/kinetics/base_kinetics.rst
@@ -1,5 +1,5 @@
 Base Kinetics
 =============
 
-.. autoclass:: pybamm.interface.kinetics.BaseModel
+.. autoclass:: pybamm.interface.BaseKinetics
     :members:
diff --git a/docs/source/models/submodels/interface/kinetics/butler_volmer.rst b/docs/source/models/submodels/interface/kinetics/butler_volmer.rst
@@ -1,8 +1,5 @@
 Butler-Volmer
 =============
 
-.. autoclass:: pybamm.interface.kinetics.ButlerVolmer
-    :members:
-
-.. autoclass:: pybamm.interface.kinetics.FirstOrderButlerVolmer
+.. autoclass:: pybamm.interface.ButlerVolmer
     :members:
diff --git a/docs/source/models/submodels/interface/kinetics/index.rst b/docs/source/models/submodels/interface/kinetics/index.rst
@@ -5,7 +5,6 @@ Interface Kinetics
   :maxdepth: 1
 
   base_kinetics
-  base_first_order_kinetics
   butler_volmer
   no_reaction
   tafel
diff --git a/docs/source/models/submodels/interface/kinetics/no_reaction.rst b/docs/source/models/submodels/interface/kinetics/no_reaction.rst
@@ -1,5 +1,5 @@
 No Reaction
 ===========
 
-.. autoclass:: pybamm.interface.kinetics.NoReaction
+.. autoclass:: pybamm.interface.NoReaction
     :members:
diff --git a/docs/source/models/submodels/interface/kinetics/tafel.rst b/docs/source/models/submodels/interface/kinetics/tafel.rst
@@ -1,11 +1,8 @@
 Tafel
 =====
 
-.. autoclass:: pybamm.interface.kinetics.ForwardTafel
-    :members:
-
-.. autoclass:: pybamm.interface.kinetics.FirstOrderForwardTafel
+.. autoclass:: pybamm.interface.ForwardTafel
     :members:
 
-.. autoclass:: pybamm.interface.kinetics.BackwardTafel
+.. autoclass:: pybamm.interface.BackwardTafel
     :members:
diff --git a/docs/source/models/submodels/interface/lead_acid.rst b/docs/source/models/submodels/interface/lead_acid.rst
diff --git a/docs/source/models/submodels/interface/lithium_ion.rst b/docs/source/models/submodels/interface/lithium_ion.rst
diff --git a/docs/source/models/submodels/thermal/x_lumped/index.rst b/docs/source/models/submodels/thermal/x_lumped/index.rst
@@ -9,4 +9,3 @@ X-lumped
   x_lumped_0D_current_collector
   x_lumped_1D_current_collector
   x_lumped_2D_current_collector
-  x_lumped_1D_set_temperature
diff --git a/docs/source/models/submodels/thermal/x_lumped/x_lumped_1D_set_temperature.rst b/docs/source/models/submodels/thermal/x_lumped/x_lumped_1D_set_temperature.rst
diff --git a/docs/source/solvers/algebraic_solvers.rst b/docs/source/solvers/algebraic_solvers.rst
@@ -3,3 +3,6 @@ Algebraic Solvers
 
 .. autoclass:: pybamm.AlgebraicSolver
   :members:
+
+.. autoclass:: pybamm.CasadiAlgebraicSolver
+  :members: