asd

.clang-tidy

@@ -0,0 +1,148 @@
+# Generated from CLion Inspection settings
+---
+Checks: '-*,
+bugprone-argument-comment,
+bugprone-assert-side-effect,
+bugprone-bad-signal-to-kill-thread,
+bugprone-branch-clone,
+bugprone-copy-constructor-init,
+bugprone-dangling-handle,
+bugprone-dynamic-static-initializers,
+bugprone-fold-init-type,
+bugprone-forward-declaration-namespace,
+bugprone-forwarding-reference-overload,
+bugprone-inaccurate-erase,
+bugprone-incorrect-roundings,
+bugprone-integer-division,
+bugprone-lambda-function-name,
+bugprone-macro-parentheses,
+bugprone-macro-repeated-side-effects,
+bugprone-misplaced-operator-in-strlen-in-alloc,
+bugprone-misplaced-pointer-arithmetic-in-alloc,
+bugprone-misplaced-widening-cast,
+bugprone-move-forwarding-reference,
+bugprone-multiple-statement-macro,
+bugprone-no-escape,
+bugprone-not-null-terminated-result,
+bugprone-parent-virtual-call,
+bugprone-posix-return,
+bugprone-reserved-identifier,
+bugprone-sizeof-container,
+bugprone-sizeof-expression,
+bugprone-spuriously-wake-up-functions,
+bugprone-string-constructor,
+bugprone-string-integer-assignment,
+bugprone-string-literal-with-embedded-nul,
+bugprone-suspicious-enum-usage,
+bugprone-suspicious-include,
+bugprone-suspicious-memset-usage,
+bugprone-suspicious-missing-comma,
+bugprone-suspicious-semicolon,
+bugprone-suspicious-string-compare,
+bugprone-suspicious-memory-comparison,
+bugprone-suspicious-realloc-usage,
+bugprone-swapped-arguments,
+bugprone-terminating-continue,
+bugprone-throw-keyword-missing,
+bugprone-too-small-loop-variable,
+bugprone-undefined-memory-manipulation,
+bugprone-undelegated-constructor,
+bugprone-unhandled-self-assignment,
+bugprone-unused-raii,
+bugprone-unused-return-value,
+bugprone-use-after-move,
+bugprone-virtual-near-miss,
+cert-dcl21-cpp,
+cert-dcl58-cpp,
+cert-err34-c,
+cert-err52-cpp,
+cert-err60-cpp,
+cert-flp30-c,
+cert-msc50-cpp,
+cert-msc51-cpp,
+cert-str34-c,
+cppcoreguidelines-interfaces-global-init,
+cppcoreguidelines-narrowing-conversions,
+cppcoreguidelines-pro-type-member-init,
+cppcoreguidelines-pro-type-static-cast-downcast,
+cppcoreguidelines-slicing,
+google-default-arguments,
+google-explicit-constructor,
+google-runtime-operator,
+hicpp-exception-baseclass,
+hicpp-multiway-paths-covered,
+misc-misplaced-const,
+misc-new-delete-overloads,
+misc-no-recursion,
+misc-non-copyable-objects,
+misc-throw-by-value-catch-by-reference,
+misc-unconventional-assign-operator,
+misc-uniqueptr-reset-release,
+modernize-avoid-bind,
+modernize-concat-nested-namespaces,
+modernize-deprecated-headers,
+modernize-deprecated-ios-base-aliases,
+modernize-loop-convert,
+modernize-make-shared,
+modernize-make-unique,
+modernize-pass-by-value,
+modernize-raw-string-literal,
+modernize-redundant-void-arg,
+modernize-replace-auto-ptr,
+modernize-replace-disallow-copy-and-assign-macro,
+modernize-replace-random-shuffle,
+modernize-return-braced-init-list,
+modernize-shrink-to-fit,
+modernize-unary-static-assert,
+modernize-use-auto,
+modernize-use-bool-literals,
+modernize-use-emplace,
+modernize-use-equals-default,
+modernize-use-equals-delete,
+modernize-use-nodiscard,
+modernize-use-noexcept,
+modernize-use-nullptr,
+modernize-use-override,
+modernize-use-transparent-functors,
+modernize-use-uncaught-exceptions,
+mpi-buffer-deref,
+mpi-type-mismatch,
+openmp-use-default-none,
+performance-faster-string-find,
+performance-for-range-copy,
+performance-implicit-conversion-in-loop,
+performance-inefficient-algorithm,
+performance-inefficient-string-concatenation,
+performance-inefficient-vector-operation,
+performance-move-const-arg,
+performance-move-constructor-init,
+performance-no-automatic-move,
+performance-noexcept-move-constructor,
+performance-trivially-destructible,
+performance-type-promotion-in-math-fn,
+performance-unnecessary-copy-initialization,
+performance-unnecessary-value-param,
+portability-simd-intrinsics,
+readability-avoid-const-params-in-decls,
+readability-const-return-type,
+readability-container-size-empty,
+readability-convert-member-functions-to-static,
+readability-delete-null-pointer,
+readability-deleted-default,
+readability-inconsistent-declaration-parameter-name,
+readability-make-member-function-const,
+readability-misleading-indentation,
+readability-misplaced-array-index,
+readability-non-const-parameter,
+readability-redundant-control-flow,
+readability-redundant-declaration,
+readability-redundant-function-ptr-dereference,
+readability-redundant-smartptr-get,
+readability-redundant-string-cstr,
+readability-redundant-string-init,
+readability-simplify-subscript-expr,
+readability-static-accessed-through-instance,
+readability-static-definition-in-anonymous-namespace,
+readability-string-compare,
+readability-uniqueptr-delete-release,
+readability-use-anyofallof'

.github/workflows/cmake.yml

@@ -14,7 +14,7 @@ jobs:
       matrix:
         build_type : [ Release, Debug ]
         os : [ macos-latest, ubuntu-20.04 ]
-        task_backend : [Pthreads, TBB, PaRSEC]
+        task_backend : [Threads, OneTBB, PaRSEC]  # OneTBB and LegacyTBB control which version of TBB to install
         include:
           - os: ubuntu-20.04
             cxx: /usr/bin/g++-9
@@ -38,8 +38,7 @@ jobs:
         -DMPIEXEC_PREFLAGS='--bind-to;none;--allow-run-as-root'
         -DBUILD_TESTING=ON
         -DMADNESS_ENABLE_CEREAL=ON
-        -DMADNESS_TASK_BACKEND=${{ matrix.task_backend }}
-        -DMADNESS_BUILD_MADWORLD_ONLY=${{ matrix.task_backend != 'Pthreads' }}
+        -DMADNESS_BUILD_MADWORLD_ONLY=${{ matrix.task_backend != 'Threads' }}
 
     steps:
     - uses: actions/checkout@v2
@@ -49,21 +48,48 @@ jobs:
       # We'll use this as our working directory for all subsequent commands
       run: cmake -E make_directory ${{github.workspace}}/build
 
+    - name: Process task_backend
+      run: |
+        if [ "X${{ matrix.task_backend }}" = "XLegacyTBB" ]; then
+          echo "TASK_BACKEND=TBB" >> $GITHUB_ENV
+        fi
+        if [ "X${{ matrix.task_backend }}" = "XOneTBB" ]; then
+          echo "TASK_BACKEND=TBB" >> $GITHUB_ENV
+        fi
+        if [ "X${{ matrix.task_backend }}" = "XThreads" ]; then
+          echo "TASK_BACKEND=Pthreads" >> $GITHUB_ENV
+        fi
+        if [ "X${{ matrix.task_backend }}" = "XPaRSEC" ]; then
+          echo "TASK_BACKEND=PaRSEC" >> $GITHUB_ENV
+        fi
+
     - name: Install prerequisite MacOS packages
       if: ${{ matrix.os == 'macos-latest' }}
       run: |
-        brew install ninja gcc@10 boost eigen open-mpi bison tbb@2020 ccache
-        if [ "X${{ matrix.build_type }}" = "XDebug" ]; then
-          brew install cereal
+        brew install ninja gcc@10 boost eigen open-mpi bison ccache
+        if [ "X${{ matrix.task_backend }}" = "XLegacyTBB" ]; then
+          brew install tbb@2020
+          echo "TBBROOT=/usr/local/opt/tbb@2020" >> $GITHUB_ENV
+        fi
+        if [ "X${{ matrix.task_backend }}" = "XOneTBB" ]; then
+          brew install tbb
+          echo "TBBROOT=/usr/local/opt/tbb" >> $GITHUB_ENV
         fi
-        echo "TBBROOT=/usr/local/opt/tbb@2020" >> $GITHUB_ENV
-        echo "/usr/local/opt/bison/bin" >> $GITHUB_PATH
 
     - name: Install prerequisites Ubuntu packages
       if: ${{ matrix.os == 'ubuntu-20.04' }}
       run: |
         sudo apt-get update
-        sudo apt-get install ninja-build g++-9 liblapack-dev libboost-dev libboost-serialization-dev libeigen3-dev openmpi-bin libopenmpi-dev libtbb-dev ccache
+        sudo apt-get install ninja-build g++-9 liblapack-dev libboost-dev libboost-serialization-dev libeigen3-dev openmpi-bin libopenmpi-dev ccache
+        if [ "X${{ matrix.task_backend }}" = "XOneTBB" ]; then
+          wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB -O - | sudo apt-key add -
+          sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"
+          sudo apt-get install intel-oneapi-tbb-devel
+          echo "TBBROOT=/opt/intel/oneapi/tbb/latest" >> $GITHUB_ENV
+        fi
+        if [ "X${{ matrix.task_backend }}" = "XLegacyTBB" ]; then
+          sudo apt-get install libtbb-dev
+        fi
         if [ "X${{ matrix.build_type }}" = "XDebug" ]; then
           sudo apt-get install libcereal-dev
         fi
@@ -91,7 +117,7 @@ jobs:
       # Note the current convention is to use the -S and -B options here to specify source 
       # and build directories, but this is only available with CMake 3.13 and higher.  
       # The CMake binaries on the Github Actions machines are (as of this writing) 3.12
-      run: cmake $GITHUB_WORKSPACE $BUILD_CONFIG
+      run: cmake $GITHUB_WORKSPACE $BUILD_CONFIG -DMADNESS_TASK_BACKEND=$TASK_BACKEND
 
     - name: Build
       working-directory: ${{github.workspace}}/build
@@ -102,4 +128,4 @@ jobs:
     - name: Test
       working-directory: ${{github.workspace}}/build
       shell: bash
-      run: cmake --build . --target check-madness
+      run: cmake --build . --target check-short-madness

.github/workflows/make_doxygen.yml

@@ -0,0 +1,60 @@
+name: publish-doxygen
+
+# Trigger this when a pull request is merged (which implies pushing to master).
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  doxygen:
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Git Checkout
+        uses: actions/checkout@v2
+
+      - name: Create clean gh-pages branch
+        run:  git checkout -b gh-pages
+
+      - name: Install prerequisites Ubuntu packages
+        run: |
+          sudo apt-get update
+          sudo apt-get install ninja-build g++-9 liblapack-dev openmpi-bin libopenmpi-dev libtbb-dev doxygen doxygen-latex graphviz 
+
+      - name: configure
+        shell: bash
+        working-directory: ${{github.workspace}}
+        run:  |
+          cmake -E make_directory ${{github.workspace}}/build
+          cd build && cmake $GITHUB_WORKSPACE 
+
+      - name: build
+        shell: bash
+        working-directory: ${{github.workspace}}/build
+        run:
+          cd ${{github.workspace}}/build && make docs
+
+      - name: Move generated autodocs to target directory
+        working-directory: ${{github.workspace}}/build
+        run:  mv doc/html ../api-doc
+
+      - name: Add generated autodocs to Git repo in the gh-pages branch
+        working-directory: ${{github.workspace}}
+        run:  |
+          git config --global user.email "florian.bischoff@hu-berlin.de"
+          git config --global user.name  "$GITHUB_WORKFLOW GitHub action"
+          git add api-doc
+          git commit -am "Generated API doc"
+
+      - name: Publish autodocs as GitHub pages
+        run:  git push -f origin gh-pages:gh-pages
+
+      - name: Result URLs
+        run:  |
+          REPO_OWNER=$(echo $GITHUB_REPOSITORY | cut -d '/' -f 1)
+          REPO_NAME=$(echo $GITHUB_REPOSITORY | cut -d '/' -f 2)
+          echo "Formatted API docs:  https://$REPO_OWNER.github.io/$REPO_NAME/api-doc"
+          echo ""
+          echo "GitHub pages branch: $GITHUB_SERVER_URL/$GITHUB_REPOSITORY/tree/gh-pages" 

.gitignore

@@ -1,4 +1,6 @@
 build*
+cmake-build-debug*
+.history*
 
 # Compiled Object files
 *.slo
@@ -59,3 +61,7 @@ Makefile-prog.in
 compile_commands.json
 *.idx
 .clang-format
+/cmake-build-debug/.ninja_deps
+compile_commands
+.history/src/apps/molresponse/global_functions_20230530165227.cc
+.history/src/apps/molresponse/global_functions_20230530165428.cc

.readthedocs.yaml

@@ -0,0 +1,30 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: doc/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+  install:
+  - requirements: doc/requirements.txt
+