Corrections for symmetry factor feature in GRChombo (#26)

* Corrections for symmetry factor feature in GRChombo

Corrected the params files and any uses of AMRReductions in
both of the Examples, to account for the integral symmetry factor
feature in GRChombo (see GRChombo Issue No. 197). Specifically:

1. Added the symmetry_correction flag to the params files
(under the Boundary Condition parameters)
2. Provided the chombo parameter storing the symmetry factor
to every instance of the norm and sum AMRReductions functions,
in the specificPostTimeStep() function for each example.

Note that the symmetry factor is calculated entirely in the
ChomboParameters.h file of the main GRChombo repo.

* Corrections for symmetry factor feature in GRChombo

Added the symmetry factor flag to params for both examples,
enabling calls to AMRReductions the ability to correct for
symmetry factor associated with reflective boundary conditions
(see Issue 197).

* Removed symmetry factor from amr_reductions

* Removed symmetry_correction flag

* Update intel test, as in GRChombo

* Small changes in tests

* Revert "Small changes in tests"

This reverts commit ac53bf2.

* Small changes to tests

* Remove output path in aparams and symmetry factors in conservation plots

* Remove mpi matrix

* typo fix

* Comment out max_steps line

---------

Co-authored-by: dinatraykova <dina.traykova@aei.mpg.de>

.github/workflows/joss-paper.yaml

@@ -16,7 +16,7 @@ jobs:
           # This should be the path to the paper within your repo.
           paper-path: paper/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled

.github/workflows/run-grdzhadzha-tests-intel.yml

@@ -4,7 +4,7 @@ on: [push]
 
 jobs:
   build-and-test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     env:
       CHOMBO_HOME: ${{ github.workspace }}/Chombo/lib
       OMP_NUM_THREADS: 1
@@ -34,12 +34,13 @@ jobs:
         sudo apt-get update
         sudo apt-get -y --no-install-recommends install csh libgetopt-complete-perl
 
-    - name: Install Intel compilers/MPI
+    - name: Install Intel compilers
       run: |
-        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
-        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
-        sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"
-        sudo apt-get -y install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-compiler-fortran intel-oneapi-mkl intel-oneapi-mpi intel-oneapi-mpi-devel intel-oneapi-openmp
+        wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \
+        | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
+        echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+        sudo apt-get update
+        sudo apt-get -y install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2023.2.4 intel-oneapi-compiler-fortran-2023.2.4 intel-oneapi-mkl-2023.2.0 intel-oneapi-openmp-2023.2.4 intel-oneapi-mpi intel-oneapi-mpi-devel
       working-directory: /tmp
 
     - name: Build Chombo

Examples/BoostedBHComplexScalar/params.txt

@@ -7,7 +7,7 @@
 verbosity = 0
 
 # location / naming of output files
-# output_path = "" # Main path for all files. Must exist!
+output_path = "" # Main path for all files. Must exist!
 chk_prefix = BoostedBH_
 plot_prefix = BoostedBHp_
 # restart_file = BoostedBH_000000.3d.hdf5
@@ -122,7 +122,7 @@ lo_boundary = 3 2 2
 vars_parity            = 0 0 0 0   #phi and Pi (Re and Im)
 vars_parity_diagnostic = 0 0 0     #chi, rhoLinMom and rhoEnergy
 		         0 0 0     #fluxLinMom, fluxEnergy and sourceLinMom
-			 
+
 # if sommerfeld boundaries selected, must select
 # non zero asymptotic values
 num_nonzero_asymptotic_vars = 0
@@ -143,7 +143,7 @@ extrapolation_order = 0
 # dt will be dx*dt_multiplier on each grid level
 dt_multiplier = 0.1
 stop_time = 250.0
-# max_steps = 4
+#max_steps = 4
 
 nan_check = 1
 

Examples/BoostedBHComplexScalar/plot_conservation.py

@@ -12,15 +12,13 @@
 plt.rcParams.update({'figure.figsize'    :  '6, 4.2'})
 plt.rcParams.update({'figure.autolayout': True})
 
-symmetry = 4.0
-
 EMS = np.loadtxt('data/EnergyIntegrals.dat')
 F = np.loadtxt('data/FluxIntegrals.dat')
 timedata = EMS[:,0][1:]
 dt = timedata[1] - timedata[0]
-E = EMS[:,1][1:]*symmetry
-M = EMS[:,2][1:]*symmetry
-S = EMS[:,3][1:]*symmetry
+E = EMS[:,1][1:]
+M = EMS[:,2][1:]
+S = EMS[:,3][1:]
 E0 = E-E[0]
 M0 = M-M[0]
 FEi = F[:,1]

Examples/KerrBHScalarField/params.txt

@@ -119,7 +119,7 @@ lo_boundary = 1 1 2
 vars_parity            = 0 0 0 0   #phi and Pi (Re and Im)
 vars_parity_diagnostic = 0 0 0     #chi, rhoEnergy and rhoAngMom
 		         0 0 0     #sourceAngMom, fluxAngMom and fluxEnergy
-			 
+
 # if sommerfeld boundaries selected, must select
 # non zero asymptotic values
 num_nonzero_asymptotic_vars = 0

Examples/KerrBHScalarField/plot_conservation.py

@@ -12,14 +12,12 @@
 plt.rcParams.update({'figure.figsize'    :  '6, 4.2'})
 plt.rcParams.update({'figure.autolayout': True})
 
-symmetry = 2.0
-
 EMS = np.loadtxt('data/EnergyIntegrals.dat')
 F = np.loadtxt('data/FluxIntegrals.dat')
 timedata = EMS[:,0][1:]
 dt = timedata[1] - timedata[0]
-E = EMS[:,1][1:]*symmetry
-M = EMS[:,2][1:]*symmetry
+E = EMS[:,1][1:]
+M = EMS[:,2][1:]
 E0 = E-E[0]
 M0 = M-M[0]
 FEi = F[:,1]