Merged v4 into main (#751)

* Change version to v4 for all files (#686)

* Removed GH actions.

* Changed version to v4 for all files.

* Verified totals for DASimpleFoam (#715)

* Added first lib with test yml.

* Fixed a bug in the test script.

* Added the first v4 test.

* Added the missing DAOption Make.

* Added test codecov

* Update and rename codecov.yml to code_cov.yml

* Added unit_test verification mechanism

* Unify the incompressible and compressible libs.

* Added more libs.

* Renamed DAObjFunc to DAFunction.

* More renames.

* Re-structue the DAFunction.

* Added more libs and delete unused DAPart and DAJac sub classes.

* DASOlver compiled.

* Re-organized coloring util.

* Re-organized pyDASolvers.

* Fixed the unit test setup file.

* Added the DAInput and DAOutput classes.

* Added -w to all the options files to disable warnings.

* Changed the interfaces for many classes.

* Changed the Allmake files.

* Changed init file.

* Changed mphys and pyDAFoam python layers.

* Changed DASolver and add calcJacTVecProduct function.

* Fixed an issue in init file.

* DAOutput uses its own dicts.

* Added the missing pip install for tests.

* Total accurate for DASimpleFoam.

* Enabled new build modes (#723)

* Fixed a bug for the distributed flag for functions

* Fixed all the Make files.

* Changed the AD -D name to CODI_NO_AD, CODI_ADR and CODI_ADF.

* Changed the cython lib compilation method.

* Changed the pre and post-processing build.

* Changed the python files to new build.

* Added a new libs folder for the cython libs.

* Changed the github action files.

* Added the ADR build in the github action.

* Fixed a bug in the GH action file.

* Fixed the unit test script.

* Added regression, unit, and coverage test templates (#724)

* Fixed a bug for the distributed flag for functions

* Added DASimpleFoam test.

* Fixed codecov test.

* Fixed a bug in codecov

* Added Python coverage.

* Added more tracking files.

* Fixed a codecov typo

* Changed the all run script for test such that it will run all the tests.

* Added checkMesh and printRes to primals.

* Added DARhoSimpleFoam (#726)

* Fixed a bug for the distributed flag for functions

* Made printInterval and maxRes class-wide vars.

* Added the DARhoSimpleFoam tests.

* Fixed test files.

* Added the missing file.

* Enabled forward model and verified adjoint accuracy (#727)

* Fixed a bug for the distributed flag for functions

* Enabled forward mode AD. Verified machine-precision accurate adjoint for DASimpleFoam

* Added new interfaces for inputs (#733)

* Removed 2> log for test files.

* Re-organize input and output. Added patchVelocity

* Added dF back for patchVelocity.

* Enabled CD and CL based on AOA.

* Enabled auto make mode.

* Print info for DAInput and calcJac.

* Changed designVar to solverInput and re-organized all partial calls.

* Added more solvers and functions. (#734)

* Removed the distributed arg for calcJac.

* Added DARhoSimpleCFoam.

* Added DAHeatTransferFoam and related functions.

* Added the missing files.

* Fixed the DATurb order.

* Used mpicc to auto-detect include and lib paths.

* Added DASimpleTFoam and related functions.

* Added the missing files.

* Added kOmegaSST and moved Coloring into DASolver.

* Fixed the code cov.

* Re-organized new turbModel structure and added Fv3 and laminar models.

* Added the moment function.

* Fixed an issue to avoid computing all dF partials.

* Removed un-used funcs in Python layer.

* Removed unused funcs in DASolver.

* Removed parts for DAFunction and re-organized codes.

* Added pimple adjoint and verified totals  (#737)

* Added DAPimpleFoam and primal working.

* Updated the pimple ref.

* Added pimple and verified derivs

* Fixed a critical bug about normRes.

* Added the updatePC call back.

* Updated ref.

* Updated simpleFoam refs.

* Added shape var for pimple. Totals not accurate yet.

* Tested pimple shape with forward and the totals are accurate.

* Added forward tests and changed function interfaces (#741)

* Added DATimeOp and re-organized evalFunctions.

* Added forward AD test.

* Added flags to compile forward mode.

* Renamed the test refs

* Moved old test files.

* Added forward tests and FD refs.

* Add pimpleDym primal (#744)

* Added pimpleDyM.

* Added the docker deploy yml.

* Change pimpledym test file name

* Enabled ADF for docker build

* Fixed an issue in the docker build yml

* Added more inputs, changed solverInto to inputInfo, and added aerothermal (#745)

* Added field input and verifed its totals.

* Added tests for vector field.

* Added the patchVar input.

* Added CHT.

* Added the missing files.

* Added the missing flag.

* Added regModel to pimple (#746)

* Enabled regression par as dv.

* Deleted DAMotion and DARegDb classes

* Removed regDb dependencies.

* Deleted unused models.

* Renamed models to DAMisc

* Moved boundaryConditions to DAMisc.

* Changed the test file name

* Added variance func.

* Added regModel for pimple with a test.

* Removed outdated codes (#747)

* Allowed empty function.

* Removed outdated codes.

* Renamed thermalVar to thermalCoupling.

* Updated the aerothermal test script.

* Fixed aerothermal.

* Added aerostructural (#748)

* Added forceCoupling for FSI.

* Verified the AeroStruct total.

* Removed the masks, aeroProp, and acoustics in mphys_dafoam.

* Adjusted the aero-struct tolerance.

* Added all solvers and functions back (#750)

* Deleted Laplacian and Piso.

* Deleted scalarTransport

* Added turboFoam and mass flow rate func.

* Deleted outdated functions and added all functions back.

* Deleted outdated res and stateInfo.

* Added rhoPimple

* Added all turb models.

* Changed the primalMaxRes calculation.

* Added more tests and fixed issues.

* Added more tests.

.github/workflows/code_cov.yml

@@ -0,0 +1,36 @@
+name: codecov
+
+on: [push, pull_request]
+
+env:
+  REPO_NAME: 'dafoam'
+  DOCKER_WORKING_DIR: '/home/dafoamuser/dafoam/$REPO_NAME'
+  DOCKER_MOUNT_DIR: '/home/dafoamuser/mount/$REPO_NAME'
+  DOCKER_TAG: 'v4'
+  DOCKER_ENV_FILE: '/home/dafoamuser/dafoam/loadDAFoam.sh'
+  DOCKER_OF_ADF_BASHRC: '/home/dafoamuser/dafoam/OpenFOAM/OpenFOAM-v1812-ADF/etc/bashrc'
+  DOCKER_OF_ADR_BASHRC: '/home/dafoamuser/dafoam/OpenFOAM/OpenFOAM-v1812-ADR/etc/bashrc'
+
+jobs:
+  code_coverage:
+    runs-on: ubuntu-20.04
+    name: Codecov
+    steps:
+    - uses: actions/checkout@main
+    - name: Create the docker container and run the tests
+      run: |
+        docker pull dafoam/opt-packages:${{env.DOCKER_TAG}}
+        docker run -i -d -u dafoamuser --name regtest -v $GITHUB_WORKSPACE:${{env.DOCKER_MOUNT_DIR}} dafoam/opt-packages:${{env.DOCKER_TAG}} /bin/bash
+        docker exec -i regtest /bin/bash -c "rm -rf ${{env.DOCKER_WORKING_DIR}} && cp -r ${{env.DOCKER_MOUNT_DIR}} ${{env.DOCKER_WORKING_DIR}}"
+        docker exec -i regtest /bin/bash -c ". ${{env.DOCKER_ENV_FILE}} && cd ${{env.DOCKER_WORKING_DIR}}/src && . ./.add_coverage_flag.sh"
+        docker exec -i -e COMPILE_DAFOAM_ADF=1 regtest /bin/bash -c ". ${{env.DOCKER_ENV_FILE}} && cd ${{env.DOCKER_WORKING_DIR}} && ./Allmake"
+        docker exec -i -e DF_CHECK_COVERAGE=1 regtest /bin/bash -c ". ${{env.DOCKER_ENV_FILE}} && cd ${{env.DOCKER_WORKING_DIR}}/tests && ./Allrun"
+        docker exec -i regtest /bin/bash -c ". ${{env.DOCKER_ENV_FILE}} && cd ${{env.DOCKER_WORKING_DIR}}/tests && coverage combine && coverage xml && echo dafoamuser | sudo -S cp -r coverage.xml ${{env.DOCKER_MOUNT_DIR}}/"
+        docker exec -i regtest /bin/bash -c ". ${{env.DOCKER_ENV_FILE}} && cd ${{env.DOCKER_WORKING_DIR}} && lcov --capture --directory . --output-file coverage.info && echo dafoamuser | sudo -S cp -r coverage.info ${{env.DOCKER_MOUNT_DIR}}/"
+    - name: Upload
+      uses: codecov/codecov-action@v4
+      with:
+        fail_ci_if_error: true 
+        files: ./coverage.info 
+        token: ${{secrets.CODECOV_TOKEN}}
+        verbose: true

.github/workflows/docker.yml

@@ -3,12 +3,10 @@ name: docker
 on:
   push:
     branches:
-      - main
+      - v4
 
 env:
   DOCKER_ENV_FILE: '/home/dafoamuser/dafoam/loadDAFoam.sh'
-  DOCKER_OF_ADF_BASHRC: '/home/dafoamuser/dafoam/OpenFOAM/OpenFOAM-v1812-ADF/etc/bashrc'
-  DOCKER_OF_ADR_BASHRC: '/home/dafoamuser/dafoam/OpenFOAM/OpenFOAM-v1812-ADR/etc/bashrc'
 
 jobs:
   push_to_registry:
@@ -19,11 +17,11 @@ jobs:
     - name: Build and push
       run: |
         echo ${{ secrets.DOCKER_PASSWORD }} | docker login -u dafoam --password-stdin
-        docker pull dafoam/opt-packages:latest
-        docker run -i -d -u dafoamuser --name build_latest dafoam/opt-packages:latest /bin/bash
-        docker exec -i -e DAFOAM_NO_WARNINGS=1 build_latest /bin/bash -c ". ${{env.DOCKER_ENV_FILE}} && cd /home/dafoamuser/dafoam/repos && git clone https://github.com/mdolab/dafoam && cd dafoam && ./Allmake && . ${{env.DOCKER_OF_ADR_BASHRC}} && ./Allclean && ./Allmake && . ${{env.DOCKER_OF_ADF_BASHRC}} && ./Allclean && ./Allmake && pip install . && cd .. && rm -rf /home/dafoamuser/dafoam/repos/dafoam"
-        docker export build_latest > build_latest.tar
+        docker pull dafoam/opt-packages:v4
+        docker run -i -d -u dafoamuser --name build_v4 dafoam/opt-packages:v4 /bin/bash
+        docker exec -e COMPILE_DAFOAM_ADF=1 -i build_v4 /bin/bash -c ". ${{env.DOCKER_ENV_FILE}} && cd /home/dafoamuser/dafoam/repos && rm -rf dafoam && git clone https://github.com/mdolab/dafoam && cd dafoam && git checkout v4 && ./Allmake"
+        docker export build_v4 > build_v4.tar
         docker rm -f $(docker ps -a -q)
-        docker rmi -f dafoam/opt-packages:latest
-        docker import build_latest.tar dafoam/opt-packages:latest
-        docker push dafoam/opt-packages:latest
+        docker rmi -f dafoam/opt-packages:v4
+        docker import build_v4.tar dafoam/opt-packages:v4
+        docker push dafoam/opt-packages:v4

.github/workflows/tests.yml

@@ -0,0 +1,27 @@
+name: tests
+
+on: [push, pull_request]
+
+env:
+  REPO_NAME: 'dafoam'
+  DOCKER_WORKING_DIR: '/home/dafoamuser/dafoam/$REPO_NAME'
+  DOCKER_MOUNT_DIR: '/home/dafoamuser/mount/$REPO_NAME'
+  DOCKER_TAG: 'v4'
+  DOCKER_ENV_FILE: '/home/dafoamuser/dafoam/loadDAFoam.sh'
+  DOCKER_OF_ADF_BASHRC: '/home/dafoamuser/dafoam/OpenFOAM/OpenFOAM-v1812-ADF/etc/bashrc'
+  DOCKER_OF_ADR_BASHRC: '/home/dafoamuser/dafoam/OpenFOAM/OpenFOAM-v1812-ADR/etc/bashrc'
+
+jobs:
+
+  reg_tests:
+    runs-on: ubuntu-20.04
+    name: Tests
+    steps:
+    - uses: actions/checkout@v3
+    - name: Create the docker container and run the tests
+      run: |
+        docker pull dafoam/opt-packages:${{env.DOCKER_TAG}}
+        docker run -i -d -u dafoamuser --name regtest -v $GITHUB_WORKSPACE:${{env.DOCKER_MOUNT_DIR}} dafoam/opt-packages:${{env.DOCKER_TAG}} /bin/bash
+        docker exec -i regtest /bin/bash -c "rm -rf ${{env.DOCKER_WORKING_DIR}} && cp -r ${{env.DOCKER_MOUNT_DIR}} ${{env.DOCKER_WORKING_DIR}}"
+        docker exec -i -e COMPILE_DAFOAM_ADF=1 regtest /bin/bash -c ". ${{env.DOCKER_ENV_FILE}} && cd ${{env.DOCKER_WORKING_DIR}} && ./Allmake"
+        docker exec -i regtest /bin/bash -c ". ${{env.DOCKER_ENV_FILE}} && cd ${{env.DOCKER_WORKING_DIR}}/tests && ./Allrun"

Allclean

@@ -5,9 +5,36 @@ if [ -z "$WM_PROJECT" ]; then
   exit 1
 fi
 
-cd src/adjoint && ./Allclean && cd -
-cd src/pyDASolvers && ./Allclean && cd -
-cd src/utilities/coloring && ./Allclean && cd -
-cd src/utilities/postProcessing && ./Allclean && cd -
-cd src/utilities/preProcessing && ./Allclean && cd -
-cd tests && ./Allclean && cd -
+function cleanDAFoam()
+{ 
+  cd src/adjoint && rm -rf lnInclude && cd -
+  cd src/adjoint && ./Allclean && cd -
+  cd src/newTurbModels && ./Allclean && cd -
+  cd src/pyUnitTests && ./Allclean && cd -
+  cd src/pyDASolvers && ./Allclean && cd -
+  cd src/utilities/preProcessing && ./Allclean && cd -
+}
+
+# clean original mode
+echo "***************** Cleaning original mode **************"
+. $DAFOAM_ROOT_PATH/loadDAFoam.sh
+cleanDAFoam
+# clean ADR mode
+echo "***************** Cleaning ADR mode **************"
+. $DAFOAM_ROOT_PATH/loadDAFoam.sh
+. $DAFOAM_ROOT_PATH/OpenFOAM/OpenFOAM-v1812-ADR/etc/bashrc
+cleanDAFoam
+# if COMPILE_DAFOAM_ADF is set, compile ADF mode
+if [ -z "$COMPILE_DAFOAM_ADF" ]; then
+  echo "COMPILE_DAFOAM_ADF is not set. skip the ADF mode"
+else
+  echo "***************** Cleaning ADF mode **************"
+  . $DAFOAM_ROOT_PATH/loadDAFoam.sh
+  . $DAFOAM_ROOT_PATH/OpenFOAM/OpenFOAM-v1812-ADF/etc/bashrc
+  cleanDAFoam
+fi
+
+# reset the OpenFOAM environment to the original mode
+. $DAFOAM_ROOT_PATH/loadDAFoam.sh
+
+

Allmake

@@ -1,22 +1,46 @@
 #!/usr/bin/env bash
 
-# the script will exit if there is any error
-set -e
-
 if [ -z "$WM_PROJECT" ]; then
   echo "OpenFOAM environment not found, forgot to source the OpenFOAM bashrc?"
   exit 1
 fi
 
-if [ -z "$1" ]; then
-  echo "Argument not found. Using the default value: opt"
-  argm="opt"
+function makeDAFoam()
+{ 
+  # the script will exit if there is any error
+  set -e
+  wmakeLnInclude src/adjoint
+  cd src/adjoint && ./Allmake && cd -
+  cd src/newTurbModels && ./Allmake && cd -
+  cd src/pyUnitTests && ./Allmake && cd -
+  cd src/pyDASolvers && ./Allmake && cd -
+  cd src/utilities/preProcessing && ./Allmake && cd -
+  # disable the -e flag
+  set +e
+}
+
+# compile original mode
+echo "***************** Compiling original mode **************"
+. $DAFOAM_ROOT_PATH/loadDAFoam.sh
+makeDAFoam
+# compile ADR mode
+echo "***************** Compiling ADR mode **************"
+. $DAFOAM_ROOT_PATH/loadDAFoam.sh
+. $DAFOAM_ROOT_PATH/OpenFOAM/OpenFOAM-v1812-ADR/etc/bashrc
+makeDAFoam
+# if COMPILE_DAFOAM_ADF is set, compile ADF mode
+if [ -z "$COMPILE_DAFOAM_ADF" ]; then
+  echo "COMPILE_DAFOAM_ADF is not set. skip the ADF mode"
 else
-  argm="$1"
+  echo "***************** Compiling ADF mode **************"
+  . $DAFOAM_ROOT_PATH/loadDAFoam.sh
+  . $DAFOAM_ROOT_PATH/OpenFOAM/OpenFOAM-v1812-ADF/etc/bashrc
+  makeDAFoam
 fi
 
-cd src/adjoint && ./Allmake $argm && cd -
-cd src/pyDASolvers && ./Allmake $argm && cd -
-cd src/utilities/coloring && ./Allmake $argm && cd -
-cd src/utilities/postProcessing && ./Allmake $argm && cd -
-cd src/utilities/preProcessing && ./Allmake $argm && cd -
+# reset the OpenFOAM environment to the original mode
+. $DAFOAM_ROOT_PATH/loadDAFoam.sh
+
+pip install .
+
+ls -R dafoam/libs && echo " " && echo "*** Build Successful! ***" && echo " "

dafoam/libs/ADF/__init__.py

@@ -0,0 +1 @@
+# empty_file

dafoam/libs/ADR/__init__.py

@@ -0,0 +1 @@
+# empty_file

dafoam/libs/__init__.py

@@ -0,0 +1 @@
+# empty_file