Api fixes

.github/workflows/nightly.yaml

@@ -16,30 +16,50 @@ jobs:
     strategy:
       fail-fast: false
     steps:
-      - name: checkout testapp
+      - name: checkout this repo
         uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
       - name: checkout opensn
         uses: actions/checkout@v4
         with:
           repository: Open-Sn/opensn
           path: opensn
+      - name: clean build directories
+        shell: bash
+        run: |
+          rm -rf opensn/build opensn/install ROM/build diffusion/build
       - name: install opensn
         shell: bash
         run: |
           module load opensn/gcc/14 python3/3.12.3
           cd opensn && mkdir build && mkdir install && cd build 
           cmake -DCMAKE_INSTALL_PREFIX=../install .. && make -j && make install
-      - name: compile app
+      - name: compile rom
         shell: bash
         run: |
           module load opensn/gcc/14 python3/3.12.3 libROM/1.0.0
           export OpenSn_DIR=$PWD/opensn/install
           cd ROM 
           mkdir build && cd build && cmake .. && make -j
-      - name: test examples
+      - name: test rom
         shell: bash
         run: |
           module load opensn/gcc/14 python3/3.12.3 libROM/1.0.0
           cd ROM
           export PYTHONPATH=$PWD/python
           cd examples/reed && python3 run_rom_reed.py --exe ../../build/rom_app_exec
+      - name: compile diffusion
+        shell: bash
+        run: |
+          module load opensn/gcc/14 python3/3.12.3
+          export OpenSn_DIR=$PWD/opensn/install
+          cd diffusion
+          mkdir build && cd build && cmake .. && make -j
+      - name: test diffusion
+        shell: bash
+        run: |
+          module load opensn/gcc/14 python3/3.12.3
+          cd diffusion
+          export PYTHONPATH=$PWD/python
+          test/run_tests -d test/diffusion

.gitignore

@@ -4,19 +4,10 @@ cmake-build-debug
 .idea
 bin
 build*/
-doc/documentation
-doc/HTMLdocs
-doc/whitepages
 
 # root Makefile is generated by CMake automatically
 Makefile
 
-resources/Dependencies/lua-5.3.5/
-resources/Dependencies/ncurses/
-resources/Dependencies/readline/
-resources/Dependencies/triangle/
-resources/Dependencies/glew-2.1.0/
-
 # Latex compile files
 *.aux
 *.lof
@@ -29,21 +20,10 @@ resources/Dependencies/glew-2.1.0/
 # All vtk mesh files
 /*.vtu
 /*.pvtu
-test/**/*.pvtu
-test/**/*.vtu
-test/modules/linear_boltzmann_solvers/dsa/SimTest_92b_DSA_PWLC.pvtu
-test/modules/linear_boltzmann_solvers/dsa/SimTest_92b_DSA_PWLC_0.vtu
-test/**/*.csv
-
-tests/BigTests/*/solutions/
 
 # All exodus files
 /*.e
 
-resources/Dependencies/.DS_Store
-
-resources/.DS_Store
-
 # python files
 .DS_Store
 ._.DS_Store
@@ -54,14 +34,10 @@ __pycache__
 
 *-private.sh
 
-#Documentation
-doc/generated_files
-
 #visual studio code files
 .vscode/
 
 test/**/out/
-tutorials/**/out/
 
 #Scratch directory
 scratch/
@@ -91,4 +67,4 @@ tutorials/**/*.py
 examples/*/basis/*
 examples/*/data/*
 examples/*/output/*
-examples/*/results/*
+examples/*/results/*

README.md

@@ -3,5 +3,5 @@
 This repository contains example application that extend the capabilities of OpenSn.
 A short description of each example is given below:
 
-- [ROM](./ROM/README.md):
-    Reduced-Order Modeling Application
+- **ROM**: Reduced-Order Modeling Application
+- **Diffusion**: Diffusion Application (CFEM/DFEM)

ROM/src/rom/steady_state_rom_solver.cc

@@ -63,8 +63,6 @@ SteadyStateROMSolver::Execute()
       }
     }
 
-    lbs_problem_->UpdateFieldFunctions();
-
     rom_problem_->TakeSample(rom_options.param_id);
   }
   if (rom_options.phase == Phase::MERGE)

diffusion/.clang-format

@@ -0,0 +1,34 @@
+---
+BasedOnStyle: LLVM
+AlignTrailingComments: 'true'
+AllowShortBlocksOnASingleLine: 'true'
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLoopsOnASingleLine: 'false'
+AlwaysBreakTemplateDeclarations: 'Yes'
+AttributeMacros:
+  - __host__
+  - __device__
+  - __global__
+  - __shared__
+  - __managed__
+BinPackArguments: 'false'
+BinPackParameters: 'false'
+BreakBeforeBraces: Allman
+ColumnLimit: '100'
+CommentPragmas: ''' ?[\\@][a-zA-Z].*$'''
+ConstructorInitializerAllOnOneLineOrOnePerLine: 'true'
+ConstructorInitializerIndentWidth: '2'
+ContinuationIndentWidth: '2'
+FixNamespaceComments: 'true'
+IndentCaseLabels: 'true'
+PointerAlignment: Left
+ReflowComments: 'true'
+SortIncludes: 'false'
+SpaceBeforeParens: ControlStatements
+SpacesBeforeTrailingComments: '1'
+TabWidth: '2'
+UseTab: Never
+AlwaysBreakAfterReturnType: TopLevelDefinitions
+AllowShortFunctionsOnASingleLine: InlineOnly
+
+...

diffusion/.clang-tidy

@@ -0,0 +1,68 @@
+---
+Checks: "*,
+        -abseil-*,
+        -altera-*,
+        -android-*,
+        -boost-*,
+        -objc-*,
+        -darwin-*,
+        -fuchsia-*,
+        -google-*,
+        -hicpp-*,
+        -linuxkernel-*,
+        -llvm*,
+        -mpi-*,
+        -zircon-*,
+        -cert-*,
+        -clang-analyzer-optin.mpi.MPI-Checker,
+        -bugprone-easily-swappable-parameters,
+        -cppcoreguidelines-avoid-magic-numbers,
+        -cppcoreguidelines-avoid-non-const-global-variables,
+        -cppcoreguidelines-non-private-member-variables-in-classes,
+        -cppcoreguidelines-pro-bounds-array-to-pointer-decay,
+        -cppcoreguidelines-pro-bounds-pointer-arithmetic,
+        -cppcoreguidelines-avoid-c-arrays,
+        -cppcoreguidelines-pro-bounds-constant-array-index,
+        -cppcoreguidelines-special-member-functions,
+        -cppcoreguidelines-avoid-const-or-ref-data-members,
+        -cppcoreguidelines-use-default-member-init,
+        -cppcoreguidelines-macro-usage,
+        -cppcoreguidelines-use-enum-class,
+        -misc-non-private-member-variables-in-classes,
+        -misc-unused-parameters,
+        -misc-include-cleaner,
+        -misc-const-correctness,
+        -misc-use-anonymous-namespace,
+        -misc-no-recursion,
+        -modernize-avoid-c-arrays,
+        -modernize-use-trailing-return-type,
+        -modernize-use-nodiscard,
+        -modernize-use-ranges,
+        -modernize-use-constraints,
+        -modernize-use-std-numbers,
+        -modernize-use-default-member-init,
+        -modernize-loop-convert,
+        -modernize-use-designated-initializers,
+        -performance-avoid-endl,
+        -performance-enum-size,
+        -performance-unnecessary-value-param,
+        -portability-avoid-pragma-once,
+        -portability-template-virtual-member-function,
+        -readability-magic-numbers,
+        -readability-braces-around-statements,
+        -readability-identifier-length,
+        -readability-function-cognitive-complexity,
+        -readability-else-after-return,
+        -readability-implicit-bool-conversion,
+        -readability-isolate-declaration,
+        -readability-redundant-member-init,
+        -readability-math-missing-parentheses,
+        -readability-convert-member-functions-to-static,
+        -readability-use-anyofallof,
+        -readability-container-contains,
+        -readability-redundant-access-specifiers,
+        -readability-avoid-nested-conditional-operator,
+"
+WarningsAsErrors: ''
+HeaderFilterRegex: ''
+FormatStyle:     none

diffusion/CMakeLists.txt

@@ -0,0 +1,58 @@
+cmake_minimum_required(VERSION 3.14)
+project(OpenSnApp LANGUAGES C CXX)
+
+set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+find_package(MPI REQUIRED)
+find_package(VTK REQUIRED COMPONENTS
+  CommonCore
+  CommonDataModel
+  IOLegacy
+  IOCore
+  IOXML
+  ParallelCore
+  IOParallelXML
+  FiltersCore
+  IOEnSight
+  IOExodus
+)
+
+include(CMakeFindDependencyMacro)
+
+find_package(OpenSn REQUIRED)
+
+message(STATUS "Found OpenSn ${OpenSn_VERSION} (from: ${OpenSn_DIR})")
+
+find_package(pybind11 REQUIRED)
+
+find_package(caliper REQUIRED)
+
+find_package(Python REQUIRED COMPONENTS Interpreter Development)
+
+file(GLOB_RECURSE DIFFUSION_SRCS CONFIGURE_DEPENDS ${PROJECT_SOURCE_DIR}/src/diffusion/*.cc)
+
+add_executable(
+  diff_app_exec
+  src/main.cc
+  src/diff_py_app.cc
+  src/diffusion.cc
+  ${DIFFUSION_SRCS}
+)
+
+target_include_directories(diff_app_exec PRIVATE
+  ${PROJECT_SOURCE_DIR}/src
+  ${OpenSn_INSTALL_PREFIX}/include
+  ${PROJECT_SOURCE_DIR}/blah/opensn/external
+)
+
+target_link_libraries(diff_app_exec PRIVATE
+  opensn::opensn
+  opensn::libopensnpy
+  MPI::MPI_CXX
+  caliper
+  pybind11::embed
+  Python::Python
+)