#664 merge master

pybamm-team · Oct 25, 2019 · f816cde · f816cde
2 parents 8c12675 + 2af6103
commit f816cde
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diff --git a/.clang-format b/.clang-format
@@ -0,0 +1,3 @@
+# Visual Studio format
+BasedOnStyle: LLVM
+BreakBeforeBraces: Allman
diff --git a/.gitignore b/.gitignore
@@ -68,12 +68,16 @@ pyvenv.cfg
 # sundials
 sundials
 sundials4
-SuiteSparse
-SuiteSparse/.gitignore
+
+# third party
+third-party
 
 # cmakefiles
 CMakeFiles
 Makefile
-*.cmake
+cmake_install.cmake
 *.so
+*.json
+
 
+third-party/pybind11
diff --git a/.gitmodules b/.gitmodules
diff --git a/.travis.yml b/.travis.yml
@@ -14,6 +14,7 @@ addons:
     - libopenblas-dev
     - liblapack-dev
     - graphviz
+    - libsuitesparse-dev
 
 matrix:
     include:
@@ -30,10 +31,12 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.6-dev
+                - libsuitesparse-dev
           env:
             - PYBAMM_UNIT=true
             - PYBAMM_EXAMPLES=true
             - PYBAMM_SCIKITS_ODES=true
+            - PYBAMM_KLU=true
         - python: "3.7"
           addons:
             apt:
@@ -46,10 +49,12 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
+                - libsuitesparse-dev
           env:
             - PYBAMM_UNIT=true
             - PYBAMM_EXAMPLES=true
             - PYBAMM_SCIKITS_ODES=true
+            - PYBAMM_KLU=true
           if: type != cron
         # Unit testing on Python3.7 on OS/X and Ubuntu
         - os: osx
@@ -70,6 +75,7 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
+                - libsuitesparse-dev
           env:
             - PYBAMM_UNIT=true
             - PYBAMM_SCIKITS_ODES=true
@@ -86,6 +92,7 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
+                - libsuitesparse-dev
           env:
             - PYBAMM_UNIT=true
           if: type != cron
@@ -102,9 +109,11 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
+                - libsuitesparse-dev
           env:
             - PYBAMM_COVER=true
             - PYBAMM_SCIKITS_ODES=true
+            - PYBAMM_KLU=true
           if: type != cron
         - python: "3.7"
           addons:
@@ -118,6 +127,7 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
+                - libsuitesparse-dev
           env:
             - PYBAMM_DOCS=true
           if: type != cron
@@ -133,6 +143,7 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
+                - libsuitesparse-dev
           env:
             - PYBAMM_STYLE=true
           if: type != cron
@@ -149,10 +160,12 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
+                - libsuitesparse-dev
           env:
             - PYBAMM_UNIT=true
             - PYBAMM_EXAMPLES=true
             - PYBAMM_SCIKITS_ODES=true
+            - PYBAMM_KLU=true
           if: type == cron
 
 # Install graphviz for macs
@@ -190,6 +203,7 @@ install:
   - 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;
 
 before_script:
 - python --version

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@
 -   Add method to evaluate parameters more easily ([#669](https://github.com/pybamm-team/PyBaMM/pull/669))
 -   Add `Jacobian` class to reuse known Jacobians of expressions ([#665](https://github.com/pybamm-team/PyBaMM/pull/670))
 -   Add `Interpolant` class to interpolate experimental data (e.g. OCP curves) ([#661](https://github.com/pybamm-team/PyBaMM/pull/661))
+-   Added interface (via pybind11) to sundials with the IDA KLU sparse linear solver ([#657](https://github.com/pybamm-team/PyBaMM/pull/657))
 -   Allow parameters to be set by material or by specifying a particular paper ([#647](https://github.com/pybamm-team/PyBaMM/pull/647))
 -   Set relative and absolute tolerances independently in solvers ([#645](https://github.com/pybamm-team/PyBaMM/pull/645))
 -   Add some non-uniform meshes in 1D and 2D ([#617](https://github.com/pybamm-team/PyBaMM/pull/617))
@@ -19,6 +20,7 @@
 ## Bug fixes
 
 -   Fix differentiation of functions that have more than one argument
+-   Add warning if `ProcessedVariable` is called outisde its interpolation range ([#681](https://github.com/pybamm-team/PyBaMM/pull/681))
 -   Improve the way `ProcessedVariable` objects are created in higher dimensions ([#581](https://github.com/pybamm-team/PyBaMM/pull/581))
 
 # [v0.1.0](https://github.com/pybamm-team/PyBaMM/tree/v0.1.0) - 2019-10-08
@@ -66,4 +68,5 @@ with the following optional physics:
 - Scipy
 - Scikits ODE
 - Scikits DAE
+- IDA KLU sparse linear solver (Sundials)
 - Algebraic (root-finding)
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -0,0 +1,24 @@
+cmake_minimum_required(VERSION 3.10)
+project(idaklu)
+
+set (CMAKE_CXX_STANDARD 11)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+add_subdirectory(third-party/pybind11)
+pybind11_add_module(idaklu pybamm/solvers/c_solvers/idaklu.cpp)
+
+# Sundials
+set(SUNDIALS_INCLUDE "sundials4/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)
+TARGET_LINK_LIBRARIES(idaklu PRIVATE ${SUNMATSPARSE} ${IDA} ${NVECTOR} ${SUNKLU})
+
+# link suitesparse
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR})
+find_package(SuiteSparse OPTIONAL_COMPONENTS KLU AMD COLAMD BTF)
+include_directories(${SuiteSparse_INCLUDE_DIRS})
+target_link_libraries(idaklu PRIVATE ${SuiteSparse_LIBRARIES})