834 merge #933

Author: valentinsulzer

.gitignore

@@ -96,3 +96,6 @@ cmake_install.cmake
 
 
 third-party/pybind11
+
+# Build dependencies/
+KLU_module_deps

.travis.yml

@@ -14,7 +14,6 @@ addons:
     - libopenblas-dev
     - liblapack-dev
     - graphviz
-    - libsuitesparse-dev
 
 matrix:
     include:
@@ -31,7 +30,6 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.6-dev
-                - libsuitesparse-dev
           env:
             - PYBAMM_UNIT=true
             - PYBAMM_EXAMPLES=true
@@ -49,7 +47,6 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
-                - libsuitesparse-dev
           env:
             - PYBAMM_UNIT=true
             - PYBAMM_EXAMPLES=true
@@ -76,7 +73,6 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
-                - libsuitesparse-dev
           env:
             - PYBAMM_UNIT=true
             - PYBAMM_SCIKITS_ODES=true
@@ -94,7 +90,6 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
-                - libsuitesparse-dev
           env:
             - PYBAMM_UNIT=true
             - PYBAMM_EXAMPLES=true
@@ -112,7 +107,6 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
-                - libsuitesparse-dev
           env:
             - PYBAMM_COVER=true
             - PYBAMM_SCIKITS_ODES=true
@@ -130,7 +124,6 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
-                - libsuitesparse-dev
           env:
             - PYBAMM_DOCS=true
           if: type != cron
@@ -146,7 +139,6 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
-                - libsuitesparse-dev
           env:
             - PYBAMM_STYLE=true
           if: type != cron
@@ -163,7 +155,6 @@ matrix:
                 - liblapack-dev
                 - graphviz
                 - python3.7-dev
-                - libsuitesparse-dev
           env:
             - PYBAMM_UNIT=true
             - PYBAMM_EXAMPLES=true
@@ -195,6 +186,7 @@ before_install: |
     source venv/bin/activate;
     # A manual check that the correct version of Python is running.
     python --version;
+    pip install wheel;
   fi
 
 # Install dependencies
@@ -203,27 +195,24 @@ 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 -e .
   - 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 [[ $PYBAMM_SCIKITS_ODES == true ]]; then
-      python setup.py install_odes -f;
-      export LD_LIBRARY_PATH=sundials/lib:$LD_LIBRARY_PATH
+      pip install wget;
+      pybamm_install_odes --install-sundials;
+      export LD_LIBRARY_PATH=scikits.odes/sundials5/lib:$LD_LIBRARY_PATH;
     fi;
   - |
     if [[ $PYBAMM_KLU == true ]]; then
-      mkdir -p third-party;
-      cd third-party;
+      pip install wget
+      python scripts/setup_KLU_module_build.py
+      export LD_LIBRARY_PATH=$(HOME)/.local/lib:$LD_LIBRARY_PATH
       rm -rf pybind11;
       git clone https://github.com/pybind/pybind11.git;
-      cd ../;
-      python setup.py install_klu -f;
-      export LD_LIBRARY_PATH=sundials/lib:$LD_LIBRARY_PATH
-      export LD_LIBRARY_PATH=SuiteSparse-5.6.0/lib:$LD_LIBRARY_PATH
+      pip install -e .
     fi;
 
 before_script:

CHANGELOG.md

@@ -2,6 +2,9 @@
 
 ## Features
 
+-   Added functionality to solver to automatically discretise a 0D model ([#947](https://github.com/pybamm-team/PyBaMM/pull/947))
+-   Added sensitivity to `CasadiAlgebraicSolver` ([#940](https://github.com/pybamm-team/PyBaMM/pull/940))
+-   Added `ProcessedSymbolicVariable` class, which can handle symbolic variables (i.e. variables for which the inputs are symbolic) ([#940](https://github.com/pybamm-team/PyBaMM/pull/940))
 -   Made `QuickPlot` compatible with Google Colab ([#935](https://github.com/pybamm-team/PyBaMM/pull/935))
 -   Added `BasicFull` model for lead-acid ([#932](https://github.com/pybamm-team/PyBaMM/pull/932))
 
@@ -12,11 +15,19 @@
 
 ## Bug fixes
 
+-   Fixed `Interpolant` ids to allow processing ([#962](https://github.com/pybamm-team/PyBaMM/pull/962)
+-   Changed simulation attributes to assign copies rather than the objects themselves ([#952](https://github.com/pybamm-team/PyBaMM/pull/952)
+-   Added default values to base model so that it works with the `Simulation` class ([#952](https://github.com/pybamm-team/PyBaMM/pull/952)
+-   Fixed solver to recompute initial conditions when inputs are changed ([#951](https://github.com/pybamm-team/PyBaMM/pull/951)
+-   Reformatted thermal submodels ([#938](https://github.com/pybamm-team/PyBaMM/pull/938)
 -   Reformatted electrolyte submodels ([#927](https://github.com/pybamm-team/PyBaMM/pull/927))
+-   Reformatted convection submodels ([#635](https://github.com/pybamm-team/PyBaMM/pull/635))
 
 ## Breaking changes
 
 -   Removed some inputs like `T_inf`, `R_g` and activation energies to some of the standard function parameters. This is because each of those inputs is specific to a particular function (e.g. the reference temperature at which the function was measured). To change a property such as the activation energy, users should create a new function, specifying the relevant property as a `Parameter` or `InputParameter` ([#942](https://github.com/pybamm-team/PyBaMM/pull/942))
+-   The thermal option 'xyz-lumped' has been removed. The option 'thermal current collector' has also been removed ([#938](https://github.com/pybamm-team/PyBaMM/pull/938)
+-   The 'C-rate' parameter has been deprecated. Use 'Current function [A]' instead. The cell capacity can be accessed as 'Cell capacity [A.h]', and used to calculate current from C-rate ([#952](https://github.com/pybamm-team/PyBaMM/pull/952)
 
 # [v0.2.1](https://github.com/pybamm-team/PyBaMM/tree/v0.2.1) - 2020-03-31
 
@@ -45,7 +56,7 @@ New expression tree node types, models, parameter sets and solvers, as well as g
 
 ## Bug fixes
 
--   Filter out discontinuities that occur after solve times 
+-   Filter out discontinuities that occur after solve times
     ([#941](https://github.com/pybamm-team/PyBaMM/pull/945))
 -   Fixed tight layout for QuickPlot in jupyter notebooks ([#930](https://github.com/pybamm-team/PyBaMM/pull/930))
 -   Fixed bug raised if function returns a scalar ([#919](https://github.com/pybamm-team/PyBaMM/pull/919))

CMakeBuild.py

@@ -0,0 +1,107 @@
+import os
+import sys
+import subprocess
+from pathlib import Path
+from platform import system
+
+try:
+    from setuptools.command.build_ext import build_ext
+except ImportError:
+    from distutils.command.build_ext import build_ext
+
+default_lib_dir = (
+    "" if system() == "Windows" else os.path.join(os.getenv("HOME"), ".local")
+)
+
+
+class CMakeBuild(build_ext):
+    user_options = build_ext.user_options + [
+        ("suitesparse-root=", None, "suitesparse source location"),
+        ("sundials-root=", None, "sundials source location"),
+    ]
+
+    def initialize_options(self):
+        build_ext.initialize_options(self)
+        self.suitesparse_root = None
+        self.sundials_root = None
+
+    def finalize_options(self):
+        build_ext.finalize_options(self)
+        # Determine the calling command to get the
+        # undefined options from.
+        # If build_ext was called directly then this
+        # doesn't matter.
+        try:
+            self.get_finalized_command("install", create=0)
+            calling_cmd = "install"
+        except AttributeError:
+            calling_cmd = "bdist_wheel"
+        self.set_undefined_options(
+            calling_cmd,
+            ("suitesparse_root", "suitesparse_root"),
+            ("sundials_root", "sundials_root"),
+        )
+        if not self.suitesparse_root:
+            self.suitesparse_root = os.path.join(default_lib_dir)
+        if not self.sundials_root:
+            self.sundials_root = os.path.join(default_lib_dir)
+
+    def run(self):
+        if not self.extensions:
+            return
+
+        cmake_args = ["-DPYTHON_EXECUTABLE={}".format(sys.executable)]
+        if self.suitesparse_root:
+            cmake_args.append(
+                "-DSuiteSparse_ROOT={}".format(os.path.abspath(self.suitesparse_root))
+            )
+        if self.sundials_root:
+            cmake_args.append(
+                "-DSUNDIALS_ROOT={}".format(os.path.abspath(self.sundials_root))
+            )
+
+        if not os.path.exists(self.build_temp):
+            os.makedirs(self.build_temp)
+
+        # The CMakeError.log file is generated by cmake is the configure step
+        # encounters error. In the following the existence of this file is used
+        # to determine whether or not the cmake configure step went smoothly.
+        # So must make sure this file does not remain from a previous failed build.
+        if os.path.isfile(os.path.join(self.build_temp, "CMakeError.log")):
+            os.remove(os.path.join(self.build_temp, "CMakeError.log"))
+
+        cmake_list_dir = os.path.abspath(os.path.dirname(__file__))
+        print("-" * 10, "Running CMake for idaklu solver", "-" * 40)
+        subprocess.run(["cmake", cmake_list_dir] + cmake_args, cwd=self.build_temp)
+
+        if os.path.isfile(os.path.join(self.build_temp, "CMakeError.log")):
+            msg = (
+                "cmake configuration steps encountered errors, and the idaklu module"
+                " could not be built. Make sure dependencies are correctly "
+                "installed. See "
+                "https://github.com/pybamm-team/PyBaMM/blob/develop/"
+                "INSTALL-LINUX-MAC.md"
+            )
+            raise RuntimeError(msg)
+        else:
+            print("-" * 10, "Building idaklu module", "-" * 40)
+            subprocess.run(["cmake", "--build", "."], cwd=self.build_temp)
+
+            # Move from build temp to final position
+            for ext in self.extensions:
+                self.move_output(ext)
+
+    def move_output(self, ext):
+        # Copy built module to dist/ directory
+        build_temp = Path(self.build_temp).resolve()
+        source_path = build_temp / self.get_ext_filename(ext.name)
+        # Get destination location
+        # self.get_ext_fullpath(ext.name) -->
+        # build/lib.linux-x86_64-3.5/idaklu.cpython-37m-x86_64-linux-gnu.so
+        # using resolve() with python < 3.6 will result in a FileNotFoundError
+        # since the location does not yet exists.
+        dest_path = Path(self.get_ext_fullpath(ext.name)).resolve()
+        source_path = build_temp / self.get_ext_filename(ext.name)
+        dest_directory = dest_path.parents[0]
+        dest_directory.mkdir(parents=True, exist_ok=True)
+        self.copy_file(source_path, dest_path)

CMakeLists.txt

@@ -4,22 +4,20 @@ project(idaklu)
 set (CMAKE_CXX_STANDARD 11)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
-add_subdirectory(third-party/pybind11)
+if(NOT PYBIND11_DIR)
+  set(PYBIND11_DIR pybind11)
+endif()
+
+add_subdirectory(${PYBIND11_DIR})
 pybind11_add_module(idaklu pybamm/solvers/c_solvers/idaklu.cpp)
 
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR})
 # Sundials
-set(SUNDIALS_INCLUDE "sundials/include")
-TARGET_INCLUDE_DIRECTORIES(idaklu PRIVATE ${SUNDIALS_INCLUDE})
-
-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})
+find_package(SUNDIALS)
+target_include_directories(idaklu PRIVATE ${SUNDIALS_INCLUDE_DIR})
+target_link_libraries(idaklu PRIVATE ${SUNDIALS_LIBRARIES})
 
 # 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})

FindSUNDIALS.cmake

@@ -0,0 +1,81 @@
+# This module is adapted from that in CADET (`<https://github.com/modsim/CADET)>`_):
+
+# .. cmake_module::
+
+#    Find SUNDIALS, the SUite of Nonlinear and DIfferential/ALgebraic equation Solvers.
+#
+#    The module looks for the following sundials components
+#
+#    * sundials_ida
+#    * sundials_sunlinsolklu
+#    * sundials_sunmatrix_sparse
+#    * sundials_nvecserial
+#
+#    To provide the module with a hint about where to find your SUNDIALS installation,
+#    you can set the environment variable :code:`SUNDIALS_ROOT`. The FindSUNDIALS module will
+#    then look in this path when searching for SUNDIALS paths and libraries.
+#    This behavior is defined in CMake >= 3.12, see policy CMP0074.
+#    It is replicated for older versions by adding the :code:`SUNDIALS_ROOT` variable to the
+#    :code:`PATHS` entry.
+#
+#    This module will define the following variables:
+#    :code:`SUNDIALS_INCLUDE_DIRS` - Location of the SUNDIALS includes
+#    :code:`SUNDIALS_LIBRARIES` - Required libraries for all requested components
+
+# List of the valid SUNDIALS components
+
+# find the SUNDIALS include directories
+find_path(SUNDIALS_INCLUDE_DIR
+  NAMES
+    ida/ida.h
+    sundials/sundials_math.h
+    sundials/sundials_types.h
+    sunlinsol/sunlinsol_klu.h
+    sunmatrix/sunmatrix_sparse.h
+  PATH_SUFFIXES
+    include
+  PATHS
+    ${SUNDIALS_ROOT}
+  )
+
+set(SUNDIALS_WANT_COMPONENTS
+  sundials_ida
+  sundials_sunlinsolklu
+  sundials_sunmatrixsparse
+  sundials_nvecserial
+  )
+
+# find the SUNDIALS libraries
+foreach(LIB ${SUNDIALS_WANT_COMPONENTS})
+    if (UNIX AND SUNDIALS_PREFER_STATIC_LIBRARIES)
+        # According to bug 1643 on the CMake bug tracker, this is the
+        # preferred method for searching for a static library.
+        # See http://www.cmake.org/Bug/view.php?id=1643.  We search
+        # first for the full static library name, but fall back to a
+        # generic search on the name if the static search fails.
+        set(THIS_LIBRARY_SEARCH lib${LIB}.a ${LIB})
+    else()
+        set(THIS_LIBRARY_SEARCH ${LIB})
+    endif()
+
+    find_library(SUNDIALS_${LIB}_LIBRARY
+        NAMES ${THIS_LIBRARY_SEARCH}
+        PATH_SUFFIXES
+            lib
+            Lib
+	PATHS
+	    ${SUNDIALS_ROOT}
+    )
+
+    set(SUNDIALS_${LIB}_FOUND FALSE)
+    if (SUNDIALS_${LIB}_LIBRARY)
+      list(APPEND SUNDIALS_LIBRARIES ${SUNDIALS_${LIB}_LIBRARY})
+      set(SUNDIALS_${LIB}_FOUND TRUE)
+    endif()
+    mark_as_advanced(SUNDIALS_${LIB}_LIBRARY)
+endforeach()
+
+mark_as_advanced(
+    SUNDIALS_LIBRARIES
+    SUNDIALS_INCLUDE_DIR
+)