#646 merge master

.gitignore

@@ -4,6 +4,7 @@
 *.png
 /local/
 *.DS_Store
+*.mat
 
 # don't ignore important .txt files
 !requirements*
@@ -69,6 +70,12 @@ pyvenv.cfg
 # sundials
 sundials
 sundials4
+sundials-*
+SuiteSparse-*
+build_sundials
+
+# downloads
+*.gz
 
 # third party
 third-party

.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

.travis.yml

@@ -82,7 +82,7 @@ matrix:
             - PYBAMM_UNIT=true
             - PYBAMM_SCIKITS_ODES=true
             - PYBAMM_KLU=true
-        # Unit testing on Python3.7 on Ubuntu without scikit odes
+        # Unit and example testing on Python3.7 on Ubuntu without optional dependencies
         - python: "3.7"
           addons:
             apt:
@@ -98,6 +98,7 @@ 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"
@@ -203,12 +204,28 @@ before_install: |
 #       without the packages from -dev and -doc!
 install:
   - pip install --upgrade pip
+  # In order to download SUNDIALS and SuiteSparse
+  - pip install wget
   - pip install .
   - if [[ $PYBAMM_DOCS == true ]]; then pip install -e .[docs]; fi;
   - if [[ $PYBAMM_STYLE == true || $PYBAMM_EXAMPLES ]]; then pip install -e .[dev]; fi;
   - if [[ $PYBAMM_COVER == true ]]; then pip install coverage codecov; fi;
-  - if [[ $PYBAMM_SCIKITS_ODES == true ]]; then source scripts/install_scikits_odes.sh; fi;
-  - if [[ $PYBAMM_KLU == true ]]; then source scripts/install_sundials_4.1.0.sh; fi;
+  - |
+    if [[ $PYBAMM_SCIKITS_ODES == true ]]; then
+      python setup.py install_odes -f;
+      export LD_LIBRARY_PATH=sundials/lib:$LD_LIBRARY_PATH
+    fi;
+  - |
+    if [[ $PYBAMM_KLU == true ]]; then
+      mkdir -p third-party;
+      cd third-party;
+      rm -rf pybind11;
+      git clone https://github.com/pybind/pybind11.git;
+      cd ../;
+      python setup.py install_klu -f;
+      export LD_LIBRARY_PATH=sundials/lib:$LD_LIBRARY_PATH
+      export LD_LIBRARY_PATH=SuiteSparse-5.6.0/lib:$LD_LIBRARY_PATH
+    fi;
 
 before_script:
 - python --version

CHANGELOG.md

@@ -2,6 +2,18 @@
 
 ## Features
 
+-   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 +36,21 @@
 
 ## Optimizations
 
+-   Now simplifying objects that are constant as soon as they are created ([#801](https://github.com/pybamm-team/PyBaMM/pull/801))
+-   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))
@@ -44,9 +64,12 @@
 
 ## 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

CMakeLists.txt

@@ -8,17 +8,18 @@ add_subdirectory(third-party/pybind11)
 pybind11_add_module(idaklu pybamm/solvers/c_solvers/idaklu.cpp)
 
 # Sundials
-set(SUNDIALS_INCLUDE "sundials4/include")
+set(SUNDIALS_INCLUDE "sundials/include")
 TARGET_INCLUDE_DIRECTORIES(idaklu PRIVATE ${SUNDIALS_INCLUDE})
 
-find_library(SUNMATSPARSE sundials_sunmatrixsparse PATHS "sundials4/lib" NO_DEFAULT_PATH)
-find_library(IDA sundials_ida PATHS "sundials4/lib" NO_DEFAULT_PATH)
-find_library(NVECTOR sundials_nvecserial PATHS "sundials4/lib" NO_DEFAULT_PATH)
-find_library(SUNKLU sundials_sunlinsolklu PATHS "sundials4/lib" NO_DEFAULT_PATH)
+find_library(SUNMATSPARSE sundials_sunmatrixsparse PATHS "sundials/lib" NO_DEFAULT_PATH)
+find_library(IDA sundials_ida PATHS "sundials/lib" NO_DEFAULT_PATH)
+find_library(NVECTOR sundials_nvecserial PATHS "sundials/lib" NO_DEFAULT_PATH)
+find_library(SUNKLU sundials_sunlinsolklu PATHS "sundials/lib" NO_DEFAULT_PATH)
 TARGET_LINK_LIBRARIES(idaklu PRIVATE ${SUNMATSPARSE} ${IDA} ${NVECTOR} ${SUNKLU})
 
 # link suitesparse
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR})
+set(SuiteSparse_ROOT SuiteSparse-5.6.0)
 find_package(SuiteSparse OPTIONAL_COMPONENTS KLU AMD COLAMD BTF)
 include_directories(${SuiteSparse_INCLUDE_DIRS})
 target_link_libraries(idaklu PRIVATE ${SuiteSparse_LIBRARIES})