#247 merge master

pybamm-team · Feb 5, 2020 · 5d5db8f · 5d5db8f
2 parents 50980b5 + 93b3b25
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diff --git a/.gitignore b/.gitignore
@@ -4,6 +4,7 @@
 *.png
 /local/
 *.DS_Store
+*.mat
 
 # don't ignore important .txt files
 !requirements*

diff --git a/.requirements-docs.txt b/.requirements-docs.txt
@@ -8,3 +8,4 @@ scikit-fem>=0.2.0
 casadi>=3.5.0
 guzzle-sphinx-theme
 sphinx>=1.5
+python-Levenshtein>=0.12.0
diff --git a/.travis.yml b/.travis.yml
@@ -79,7 +79,8 @@ matrix:
           env:
             - PYBAMM_UNIT=true
             - PYBAMM_SCIKITS_ODES=true
-        # Unit testing on Python3.7 on Ubuntu without scikit odes
+            - PYBAMM_KLU=true
+        # Unit and example testing on Python3.7 on Ubuntu without optional dependencies
         - python: "3.7"
           addons:
             apt:
@@ -95,6 +96,7 @@ matrix:
                 - libsuitesparse-dev
           env:
             - PYBAMM_UNIT=true
+            - PYBAMM_EXAMPLES=true
           if: type != cron
         # Cover, docs and style checking, latest Python version only
         - python: "3.7"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,19 @@
 
 ## Features
 
+-   Added capacitance effects to lithium-ion models ()
+-   Added fuzzy string matching for parameters and variables ([#796](https://github.com/pybamm-team/PyBaMM/pull/796))
+-   Changed ParameterValues to raise an error when a parameter that wasn't previously defined is updated ([#796](https://github.com/pybamm-team/PyBaMM/pull/796))
+-   Added some basic models (BasicSPM and BasicDFN) in order to clearly demonstrate the PyBaMM model structure for battery models ([#795](https://github.com/pybamm-team/PyBaMM/pull/795))
+-   Added the harmonic mean to the Finite Volume method, which is now used when computing fluxes ([#783](https://github.com/pybamm-team/PyBaMM/pull/783))
+-   Refactored `Solution` to make it a dictionary that contains all of the solution variables. This automatically creates `ProcessedVariable` objects when required, so that the solution can be obtained much more easily. ([#781](https://github.com/pybamm-team/PyBaMM/pull/781))
+-   Added notebook to explain broadcasts ([#776](https://github.com/pybamm-team/PyBaMM/pull/776))
+-   Added a step to discretisation that automatically compute the inverse of the mass matrix of the differential part of the problem so that the underlying DAEs can be provided in semi-explicit form, as required by the CasADi solver ([#769](https://github.com/pybamm-team/PyBaMM/pull/769))
+-   Added the gradient operation for the Finite Element Method ([#767](https://github.com/pybamm-team/PyBaMM/pull/767))
+-   Added `InputParameter` node for quickly changing parameter values ([#752](https://github.com/pybamm-team/PyBaMM/pull/752))
+-   Added submodels for operating modes other than current-controlled ([#751](https://github.com/pybamm-team/PyBaMM/pull/751))
+-   Changed finite volume discretisation to use exact values provided by Neumann boundary conditions when computing the gradient instead of adding ghost nodes([#748](https://github.com/pybamm-team/PyBaMM/pull/748))
+-   Added optional R(x) distribution in particle models ([#745](https://github.com/pybamm-team/PyBaMM/pull/745))
 -   Generalized importing of external variables ([#728](https://github.com/pybamm-team/PyBaMM/pull/728))
 -   Separated active and inactive material volume fractions ([#726](https://github.com/pybamm-team/PyBaMM/pull/726))
 -   Added submodels for tortuosity ([#726](https://github.com/pybamm-team/PyBaMM/pull/726))
@@ -24,13 +37,20 @@
 
 ## Optimizations
 
+-   Simplified solver interface ([#800](https://github.com/pybamm-team/PyBaMM/pull/800))
+-   Added caching for shape evaluation, used during discretisation ([#780](https://github.com/pybamm-team/PyBaMM/pull/780))
 -   Added an option to skip model checks during discretisation, which could be slow for large models ([#739](https://github.com/pybamm-team/PyBaMM/pull/739))
 -   Use CasADi's automatic differentation algorithms by default when solving a model ([#714](https://github.com/pybamm-team/PyBaMM/pull/714))
 -   Avoid re-checking size when making a copy of an `Index` object ([#656](https://github.com/pybamm-team/PyBaMM/pull/656))
 -   Avoid recalculating `_evaluation_array` when making a copy of a `StateVector` object ([#653](https://github.com/pybamm-team/PyBaMM/pull/653))
 
 ## Bug fixes
 
+-   Fixed examples to run with basic pip installation ([#800](https://github.com/pybamm-team/PyBaMM/pull/800))
+-   Added events for CasADi solver when stepping ([#800](https://github.com/pybamm-team/PyBaMM/pull/800))
+-   Improved implementation of broadcasts ([#776](https://github.com/pybamm-team/PyBaMM/pull/776))
+-   Fixed a bug which meant that the Ohmic heating in the current collectors was incorrect if using the Finite Element Method ([#767](https://github.com/pybamm-team/PyBaMM/pull/767))
+-   Improved automatic broadcasting ([#747](https://github.com/pybamm-team/PyBaMM/pull/747))
 -   Fixed bug with wrong temperature in initial conditions ([#737](https://github.com/pybamm-team/PyBaMM/pull/737))
 -   Improved flexibility of parameter values so that parameters (such as diffusivity or current) can be set as functions or scalars ([#723](https://github.com/pybamm-team/PyBaMM/pull/723))
 -   Fixed a bug where boundary conditions were sometimes handled incorrectly in 1+1D models ([#713](https://github.com/pybamm-team/PyBaMM/pull/713))
@@ -43,9 +63,12 @@
 
 ## Breaking changes
 
+-   Removed `Outer` and `Kron` nodes as no longer used ([#777](https://github.com/pybamm-team/PyBaMM/pull/777))
+-   Moved `results` to separate repositories ([#761](https://github.com/pybamm-team/PyBaMM/pull/761))
 -   The parameters "Bruggeman coefficient" must now be specified separately as "Bruggeman coefficient (electrolyte)" and "Bruggeman coefficient (electrode)"
 -   The current classes (`GetConstantCurrent`, `GetUserCurrent` and `GetUserData`) have now been removed. Please refer to the [`change-input-current` notebook](https://github.com/pybamm-team/PyBaMM/blob/master/examples/notebooks/change-input-current.ipynb) for information on how to specify an input current
 -   Parameter functions must now use pybamm functions instead of numpy functions (e.g. `pybamm.exp` instead of `numpy.exp`), as these are then used to construct the expression tree directly. Generally, pybamm syntax follows numpy syntax; please get in touch if a function you need is missing.
+-   The current must now be updated by changing "Current function [A]" or "C-rate" instead of "Typical current [A]"
 
 
 # [v0.1.0](https://github.com/pybamm-team/PyBaMM/tree/v0.1.0) - 2019-10-08

diff --git a/INSTALL-LINUX.md b/INSTALL-LINUX.md
@@ -94,25 +94,25 @@ Before installing scikits.odes, you need to have installed:
 - Fortran compiler (e.g. gfortran)
 - BLAS/LAPACK install (OpenBLAS is recommended by the scikits.odes developers)
 - CMake (for building Sundials)
-- Sundials 4.1.0
+- Sundials 5.0.0
 
 You can install these on Ubuntu or Debian using apt-get:
 
 ```bash
 sudo apt-get install python3-dev gfortran gcc cmake libopenblas-dev
 ```
 
-To install Sundials 4.1.0, on the command-line type:
+To install Sundials 5.0.0, on the command-line type:
 
 ```bash
 INSTALL_DIR=`pwd`/sundials
-wget https://computation.llnl.gov/projects/sundials/download/sundials-4.1.0.tar.gz
-tar -xvf sundials-4.1.0.tar.gz
-mkdir build-sundials-4.1.0
-cd build-sundials-4.1.0/
-cmake -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_TYPE=int32_t -DBUILD_ARKODE:BOOL=OFF -DEXAMPLES_ENABLE:BOOL=OFF -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR ../sundials-4.1.0/
+wget https://computation.llnl.gov/projects/sundials/download/sundials-5.0.0.tar.gz
+tar -xvf sundials-5.0.0.tar.gz
+mkdir build-sundials-5.0.0
+cd build-sundials-5.0.0/
+cmake -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_TYPE=int32_t -DBUILD_ARKODE:BOOL=OFF -DEXAMPLES_ENABLE:BOOL=OFF -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR ../sundials-5.0.0/
 make install
-rm -r ../sundials-4.1.0
+rm -r ../sundials-5.0.0
 ```
 
 Then install [scikits.odes](https://github.com/bmcage/odes), letting it know the sundials install location:

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright (c) 2017-2019, University of Oxford (University of Oxford means the Chancellor, Masters and Scholars of the University of Oxford, having an administrative office at Wellington Square, Oxford OX1 2JD, UK).
+Copyright (c) 2018-2020, University of Oxford (University of Oxford means the Chancellor, Masters and Scholars of the University of Oxford, having an administrative office at Wellington Square, Oxford OX1 2JD, UK).
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/README.md b/README.md
@@ -29,6 +29,8 @@ hosted on [Read The Docs](readthedocs.io). A set of slides giving an overview of
 can be found
 [here](https://github.com/pybamm-team/pybamm_summary_slides/blob/master/pybamm.pdf).
 
+For further examples, see the list of repositories that use PyBaMM [here](https://github.com/pybamm-team/pybamm-example-results)
+
 ## How can I obtain & install PyBaMM?
 
 ### Linux

diff --git a/docs/source/expression_tree/binary_operator.rst b/docs/source/expression_tree/binary_operator.rst
@@ -25,15 +25,7 @@ Binary Operators
 .. autoclass:: pybamm.Inner
   :members:
 
-.. autoclass:: pybamm.Outer
-  :members:
-
-.. autoclass:: pybamm.Kron
-  :members:
-
 .. autoclass:: pybamm.Heaviside
   :members:
 
-.. autofunction:: pybamm.outer
-
 .. autofunction:: pybamm.source
diff --git a/docs/source/expression_tree/broadcasts.rst b/docs/source/expression_tree/broadcasts.rst
@@ -9,3 +9,6 @@ Broadcasting Operators
 
 .. autoclass:: pybamm.PrimaryBroadcast
   :members:
+
+.. autoclass:: pybamm.SecondaryBroadcast
+  :members:
diff --git a/docs/source/expression_tree/index.rst b/docs/source/expression_tree/index.rst
@@ -16,5 +16,6 @@ Expression Tree
   concatenations
   broadcasts
   functions
+  input_parameter
   interpolant
   operations/index
diff --git a/docs/source/expression_tree/input_parameter.rst b/docs/source/expression_tree/input_parameter.rst
@@ -0,0 +1,5 @@
+Input Parameter
+===============
+
+.. autoclass:: pybamm.InputParameter
+  :members:
diff --git a/docs/source/expression_tree/variable.rst b/docs/source/expression_tree/variable.rst
@@ -3,3 +3,6 @@ Variable
 
 .. autoclass:: pybamm.Variable
   :members:
+
+.. autoclass:: pybamm.ExternalVariable
+  :members:
diff --git a/docs/source/models/lithium_ion/dfn.rst b/docs/source/models/lithium_ion/dfn.rst
@@ -3,3 +3,6 @@ Doyle-Fuller-Newman (DFN)
 
 .. autoclass:: pybamm.lithium_ion.DFN
     :members:
+
+.. autoclass:: pybamm.lithium_ion.BasicDFN
+    :members:
diff --git a/docs/source/models/lithium_ion/spm.rst b/docs/source/models/lithium_ion/spm.rst
@@ -3,3 +3,6 @@ Single Particle Model (SPM)
 
 .. autoclass:: pybamm.lithium_ion.SPM
     :members:
+
+.. autoclass:: pybamm.lithium_ion.BasicSPM
+    :members:
diff --git a/docs/source/models/submodels/current_collector/index.rst b/docs/source/models/submodels/current_collector/index.rst
@@ -10,5 +10,4 @@ Current Collector
   homogeneous_current_collector
   potential_pair
   quite_conductive_potential_pair
-  single_particle_potential_pair
   set_potential_single_particle
diff --git a/docs/source/models/submodels/current_collector/single_particle_potential_pair.rst b/docs/source/models/submodels/current_collector/single_particle_potential_pair.rst
diff --git a/docs/source/models/submodels/external_circuit/current_control_external_circuit.rst b/docs/source/models/submodels/external_circuit/current_control_external_circuit.rst
@@ -0,0 +1,6 @@
+Current control external circuit
+================================
+
+.. autoclass:: pybamm.external_circuit.CurrentControl
+    :members:
+
diff --git a/.../source/models/submodels/external_circuit/function_control_external_circuit.rst b/.../source/models/submodels/external_circuit/function_control_external_circuit.rst
@@ -0,0 +1,11 @@
+Function control external circuit
+=================================
+
+.. autoclass:: pybamm.external_circuit.FunctionControl
+    :members:
+
+.. autoclass:: pybamm.external_circuit.VoltageFunctionControl
+    :members:
+
+.. autoclass:: pybamm.external_circuit.PowerFunctionControl
+    :members:
diff --git a/docs/source/models/submodels/external_circuit/index.rst b/docs/source/models/submodels/external_circuit/index.rst
@@ -0,0 +1,15 @@
+External circuit
+================
+
+Models to enforce different boundary conditions (as imposed by an imaginary external
+circuit) such as constant current, constant voltage, constant power, or any other
+relationship between the current and voltage. "Current control" enforces these directly
+through boundary conditions, while "Function control"
+submodels add an algebraic equation (for the current) and hence can be used to set any
+variable to be constant.
+
+.. toctree::
+  :maxdepth: 1
+
+  current_control_external_circuit
+  function_control_external_circuit
diff --git a/docs/source/models/submodels/index.rst b/docs/source/models/submodels/index.rst
@@ -9,6 +9,7 @@ Submodels
     convection/index
     electrode/index
     electrolyte/index
+    external_circuit/index
     interface/index
     oxygen_diffusion/index
     particle/index

diff --git a/docs/source/processed_variable.rst b/docs/source/processed_variable.rst
@@ -1,7 +1,5 @@
 Post-Process Variables
 ======================
 
-.. autofunction:: pybamm.post_process_variables
-
 .. autoclass:: pybamm.ProcessedVariable
   :members:
diff --git a/docs/source/solvers/base_solvers.rst b/docs/source/solvers/base_solvers.rst
@@ -3,9 +3,3 @@ Base Solvers
 
 .. autoclass:: pybamm.BaseSolver
   :members:
-
-.. autoclass:: pybamm.OdeSolver
-  :members:
-
-.. autoclass:: pybamm.DaeSolver
-  :members:
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,6 +4,7 @@ @@
     *.png
     /local/
     *.DS_Store
+    *.mat
     # don't ignore important .txt files
     !requirements*
@@ Expand Down @@