Merge pull request #29 from Battery-Intelligence-Lab/chebyshev

Chebyshev

.github/workflows/ubuntu-unit.yml

@@ -27,6 +27,9 @@ jobs:
           - CC: gcc-12
             CXX: g++-12
             compiler: gcc-12 g++-12
+          - CC: gcc-13
+            CXX: g++-13
+            compiler: gcc-13 g++-13
           - CC: clang-12
             CXX: clang++-12
             compiler: clang-12
@@ -36,7 +39,15 @@ jobs:
           - CC: clang-14
             CXX: clang++-14
             compiler: clang-14
-
+          - CC: clang-15
+            CXX: clang++-15
+            compiler: clang-15
+          - CC: clang-16
+            CXX: clang++-16
+            compiler: clang-16
+          - CC: clang-17
+            CXX: clang++-17
+            compiler: clang-17
     steps:
       - uses: actions/checkout@v3
 

CMakeLists.txt

@@ -1,15 +1,14 @@
-cmake_minimum_required(VERSION 3.17)
+cmake_minimum_required(VERSION 3.21)
 
 # include(cmake/ProjectSettings.cmake)
 project(SLIDE VERSION "3.0.0"
   DESCRIPTION "A simulator for lithium-ion battery degradation"
   HOMEPAGE_URL https://github.com/Battery-Intelligence-Lab/SLIDE/
   LANGUAGES CXX)
 
-
-
 include(cmake/StandardProjectSettings.cmake)
 include(cmake/PreventInSourceBuilds.cmake)
+include(cmake/Dependencies.cmake) # Include external projects
 
 # Link this 'library' to use the warnings specified in CompilerWarnings.cmake
 add_library(project_warnings INTERFACE)
@@ -20,20 +19,17 @@ target_compile_features(project_options INTERFACE cxx_std_20)
 
 enable_testing()
 add_subdirectory(src bin)
-add_subdirectory(external/eigen)
-
-target_link_libraries(src PUBLIC eigen)
 
 include(cmake/Coverage.cmake)
 add_subdirectory(tests)
 
-
+target_link_libraries(src PUBLIC Eigen3::Eigen range-v3 fmt) # Link dependencies to the src library.
+# glaze::glaze  -> maybe in future. 
 
 add_executable(slide
   src/main.cpp
 )
 
-
 target_link_libraries(slide
   PRIVATE
   src
@@ -46,8 +42,6 @@ target_include_directories(slide
   data
 )
 
-
-
 # message(STATUS "Project: ${PROJECT_NAME} version ${PROJECT_HOMEPAGE_URL}")
 
 # cmake --build ./build/ --parallel $(($(nproc)-1))
@@ -97,40 +91,11 @@ target_link_libraries(${LIB_NAME}
 )
 
 # # install header
-# install(FILES "src/slide.hpp" DESTINATION include)
 include(GNUInstallDirs)
 
 install(TARGETS ${LIB_NAME} EXPORT ${LIB_NAME}Targets
   ARCHIVE DESTINATION lib
   LIBRARY DESTINATION lib
   RUNTIME DESTINATION bin
   INCLUDES DESTINATION include
-)
-
-# install(EXPORT MyProject-targets DESTINATION lib/cmake/MyProject)
-
-# # # install the library
-# # install(TARGETS MyProject
-# # 	EXPORT MyProject-targets
-# # 	LIBRARY DESTINATION lib
-# # 	ARCHIVE DESTINATION lib
-# # )
-
-# # # install export target and config for find_package
-# # install(EXPORT ${LIB_NAME}Targets DESTINATION lib/cmake/${LIB_NAME})
-# # include(CMakePackageConfigHelpers)
-# # configure_package_config_file(
-# # 	"MyProjectConfig.cmake.in" "${CMAKE_CURRENT_BINARY_DIR}/MyProjectConfig.cmake"
-# # 	INSTALL_DESTINATION "lib/cmake/${LIB_NAME}"
-# # )
-# # install(FILES "${CMAKE_CURRENT_BINARY_DIR}/MyProjectConfig.cmake" DESTINATION "lib/cmake/${LIB_NAME}")
-
-# # defines targets and sources CMAKE_BUILD_PARALLEL_LEVEL -> Try this to see if it gets better than -j
-# add_subdirectory(src)
-
-# install(TARGETS slide_v3
-# CONFIGURATIONS Debug
-# RUNTIME DESTINATION Debug/bin)
-# install(TARGETS slide_v3
-# CONFIGURATIONS Release
-# RUNTIME DESTINATION Release/bin)
+)

cmake/CompilerWarnings.cmake

@@ -80,6 +80,7 @@ function(set_project_warnings project_name)
       /wd4273 # QtAlignedMalloc, inconsistent DLL linkage
       /wd4324 # structure was padded due to declspec(align())
       /wd4503 # decorated name length exceeded, name was truncated
+      /Zc:preprocessor 
   )
 
   if(MSVC)

cmake/Coverage.cmake

@@ -2,7 +2,7 @@ option (SLIDE_ENABLE_COVERAGE "Enable coverage reporting for GCC or Clang" OFF)
 # Setup macro for coverage testing for GCC or Clang
 macro(add_executable_with_coverage_and_test TARGET_NAME CPP_FILE_NAME)
     add_executable(${TARGET_NAME} ${CPP_FILE_NAME})
-    target_link_libraries(${TARGET_NAME} PRIVATE src)
+    target_link_libraries(${TARGET_NAME} PRIVATE src Catch2::Catch2WithMain)
     add_test(NAME ${TARGET_NAME} COMMAND ${TARGET_NAME} WORKING_DIRECTORY bin)
     if (SLIDE_ENABLE_COVERAGE)
         if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU" OR ${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")

cmake/Dependencies.cmake

@@ -0,0 +1,40 @@
+# This cmake file is to add external dependency projects.
+# Adapted from https://github.com/cpp-best-practices/cmake_template/tree/main
+list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake/recipes/")
+
+include(cmake/recipes/CPM.cmake)
+
+# Range-v3 library:
+CPMAddPackage(
+  NAME range-v3
+  URL "https://github.com/ericniebler/range-v3/archive/refs/tags/0.12.0.tar.gz"
+  DOWNLOAD_ONLY YES
+)
+
+include(eigen)
+
+add_library(range-v3 INTERFACE)
+target_include_directories(range-v3 SYSTEM INTERFACE ${range-v3_SOURCE_DIR}/include)
+
+# Catch2 library:
+if(NOT TARGET Catch2::Catch2WithMain)
+  CPMAddPackage(
+    NAME Catch2
+    URL "https://github.com/catchorg/Catch2/archive/refs/tags/v3.3.2.tar.gz"
+  )
+endif()
+
+
+# CPMAddPackage("gh:fmtlib/fmt#10.1.1") #fmt library
+# fmt library:
+CPMAddPackage(
+  NAME fmt
+  URL "https://github.com/fmtlib/fmt/archive/refs/tags/10.1.1.tar.gz"
+)
+
+
+# # Glaze library:
+# CPMAddPackage(
+#   NAME glaze
+#   URL "https://github.com/stephenberry/glaze/archive/refs/tags/v1.3.4.tar.gz"
+# )

cmake/readme.md

@@ -1,5 +1,7 @@
-The files in this folder are taken and adapted from: 
+The files in this folder are mostly taken and adapted from: 
 
 https://github.com/lefticus/cpp_weekly/tree/master/cmake
 
-Currently, they may or may not be in use. 
+Currently, they may or may not be in use. 
+
+CPM is obtained from https://github.com/cpm-cmake/CPM.cmake

cmake/recipes/CPM.cmake

@@ -0,0 +1,22 @@
+# SPDX-License-Identifier: MIT
+# SPDX-FileCopyrightText: Copyright (c) 2019-2023 Lars Melchior and contributors
+set(CPM_DOWNLOAD_VERSION 0.40.0)
+set(CPM_HASH_SUM "7b354f3a5976c4626c876850c93944e52c83ec59a159ae5de5be7983f0e17a2a")
+
+if(CPM_SOURCE_CACHE)
+  set(CPM_DOWNLOAD_LOCATION "${CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
+elseif(DEFINED ENV{CPM_SOURCE_CACHE})
+  set(CPM_DOWNLOAD_LOCATION "$ENV{CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
+else()
+  set(CPM_DOWNLOAD_LOCATION "${CMAKE_BINARY_DIR}/cmake/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
+endif()
+
+# Expand relative path. This is important if the provided path contains a tilde (~)
+get_filename_component(CPM_DOWNLOAD_LOCATION ${CPM_DOWNLOAD_LOCATION} ABSOLUTE)
+
+file(DOWNLOAD
+     https://github.com/cpm-cmake/CPM.cmake/releases/download/v${CPM_DOWNLOAD_VERSION}/CPM.cmake
+     ${CPM_DOWNLOAD_LOCATION} EXPECTED_HASH SHA256=${CPM_HASH_SUM}
+)
+
+include(${CPM_DOWNLOAD_LOCATION})

cmake/recipes/eigen.cmake

@@ -0,0 +1,68 @@
+# Obtained: https://github.com/polyfem/polysolve/tree/main/cmake/recipes
+# Copyright 2019 Adobe. All rights reserved.
+# This file is licensed to you under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License. You may obtain a copy
+# of the License at http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software distributed under
+# the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR REPRESENTATIONS
+# OF ANY KIND, either express or implied. See the License for the specific language
+# governing permissions and limitations under the License.
+#
+if(TARGET Eigen3::Eigen)
+    return()
+endif()
+
+option(EIGEN_WITH_MKL "Use Eigen with MKL" OFF)
+option(EIGEN_DONT_VECTORIZE "Disable Eigen vectorization" OFF)
+option(EIGEN_MPL2_ONLY "Enable Eigen MPL2 license only" OFF)
+
+message(STATUS "Third-party: creating target 'Eigen3::Eigen'")
+
+include(CPM)
+# Eigen library:
+CPMAddPackage(
+  NAME eigen
+  URL "https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz"
+  DOWNLOAD_ONLY YES
+)
+
+add_library(Eigen3_Eigen INTERFACE)
+add_library(Eigen3::Eigen ALIAS Eigen3_Eigen)
+
+include(GNUInstallDirs)
+target_include_directories(Eigen3_Eigen SYSTEM INTERFACE
+    $<BUILD_INTERFACE:${eigen_SOURCE_DIR}>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
+
+if(EIGEN_MPL2_ONLY)
+    target_compile_definitions(Eigen3_Eigen INTERFACE EIGEN_MPL2_ONLY)
+endif()
+
+if(EIGEN_DONT_VECTORIZE)
+    target_compile_definitions(Eigen3_Eigen INTERFACE EIGEN_DONT_VECTORIZE)
+endif()
+
+if(EIGEN_WITH_MKL)
+    #TODO : Checks that, on 64bits systems, `mkl::mkl` is using the LP64 interface
+    # (by looking at the compile definition of the target)
+    include(mkl)
+    target_link_libraries(Eigen3_Eigen INTERFACE mkl::mkl)
+    target_compile_definitions(Eigen3_Eigen INTERFACE
+        EIGEN_USE_MKL_ALL
+        EIGEN_USE_LAPACKE_STRICT
+    )
+endif()
+
+# On Windows, enable natvis files to improve debugging experience
+if(WIN32 AND eigen_SOURCE_DIR)
+    target_sources(Eigen3_Eigen INTERFACE $<BUILD_INTERFACE:${eigen_SOURCE_DIR}/debug/msvc/eigen.natvis>)
+endif()
+
+# Install rules
+set(CMAKE_INSTALL_DEFAULT_COMPONENT_NAME eigen)
+set_target_properties(Eigen3_Eigen PROPERTIES EXPORT_NAME Eigen)
+install(DIRECTORY ${eigen_SOURCE_DIR} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+install(TARGETS Eigen3_Eigen EXPORT Eigen_Targets)
+install(EXPORT Eigen_Targets DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/eigen NAMESPACE Eigen3::)

deprecated/src/BasicCycler.cpp

@@ -10,7 +10,7 @@
  *
  * Copyright (c) 2019, The Chancellor, Masters and Scholars of the University
  * of Oxford, VITO nv, and the 'Slide' Developers.
- * See the licence file LICENCE.txt for more information.
+ * See the licence file LICENSE for more information.
  */
 
 #include <filesystem>

deprecated/src/BasicCycler.hpp

@@ -7,7 +7,7 @@
  *
  * Copyright (c) 2019, The Chancellor, Masters and Scholars of the University
  * of Oxford, VITO nv, and the 'Slide' Developers.
- * See the licence file LICENCE.txt for more information.
+ * See the licence file LICENSE for more information.
  */
 
 #pragma once

deprecated/src/CyclerOld.cpp

@@ -11,7 +11,7 @@
  *
  * Copyright (c) 2019, The Chancellor, Masters and Scholars of the University
  * of Oxford, VITO nv, and the 'Slide' Developers.
- * See the licence file LICENCE.txt for more information.
+ * See the licence file LICENSE for more information.
  */
 
 #include "CyclerOld.hpp"

deprecated/src/CyclerOld.hpp

@@ -9,7 +9,7 @@
  *
  * Copyright (c) 2019, The Chancellor, Masters and Scholars of the University
  * of Oxford, VITO nv, and the 'Slide' Developers.
- * See the licence file LICENCE.txt for more information.
+ * See the licence file LICENSE for more information.
  */
 
 #pragma once

develop/TODO.md

@@ -16,13 +16,13 @@
   - [ ] There are classes with completely capital? Which one? 
   - [ ] SUNDIALS is pretty quick. 
   - [ ] Automated tests against PyBAMM 
-  - [ ] Catch2 library for testing. 
+  - [x] Catch2 library for testing. 
   - [ ] Snapshot testing. 
   - [ ] Template projects in OxRSE template-project-cpp
   - [ ] gui_starter_library Jason Turner. 
   - [ ] clang-tidy 
   - [ ] codecov. 
-  - [ ] Doxygen. 
+  - [x] Doxygen. 
   - [ ] CPack
 
 
@@ -35,10 +35,23 @@
 - [x] sp - sn question 
 - [x] cps - cns question: dOCV_neg and dOCV_tot are taking zp_surf as input due to our data. Very important. 
 - [ ] Should capacity check also contain a CV phase? 
+- [ ] Chebyshev discretisation only works for nch = 5. Need to see why.
 
 
 ### Current priority:
-
+- [ ] Module_data is deleted but look for it and bring it back.
+- [ ] State always holds cumulative variables. 
+- [ ] Fix INTERFACE library problem in C++. Cannot include <DataFrame.hpp> and others! 
+- [ ] DataFrame class is added for named columns.
+- [ ] Create Module_p_ApproxPI 
+- [ ] PTHREADS definition
+- [ ] inline namespaces for literals. 
+- [ ] Make Eigen-based calculations for Matrix-vector multiplications. 
+- [ ] Electrode-based calculations? 
+- [x] cmake_minimum_required(VERSION 3.17) -> 3.21
+- [x] CPM package manager is adopted. 
+- [ ] Renew matlab scripts to read results. 
+- [ ] Matio and parquet data types. 
 - [ ] In `test_specificDeg` in `Procedure_test.cpp` there is a weak cell.
 - [ ] What to do if one of the series cells reach maximum voltage? 
 - [ ] CCCV for ageing CV should be done with the remaining voltage. 
@@ -120,6 +133,7 @@
 - [ ] setSUs and assigning unique pointers then testing individually is very difficult. Clearly a design problem.
 - [ ] getNSUs may slow down time to time. 
 - [ ] std::vector<double> Iolds in Module_p.cpp
+- [ ] Use just one memory allocation, dynamically allocated memory space for Model_SPM. 
 
 
 ### From SLIDE v2: