Merge pull request #386 from Warwick-Plasma/4.18-devel

Updating to EPOCH 4.18

.github/workflows/auto_pr.yml

@@ -0,0 +1,42 @@
+name: auto-pr
+
+on:
+  push:
+    branches:
+    - 4.*-devel
+
+jobs:
+  pull-request:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Set branch variables
+      run: BASE_REF=$(echo $GITHUB_REF | cut -f3- -d\/);
+           major=$(echo $BASE_REF | cut -f1 -d\.);
+           minor=$(echo $BASE_REF | cut -f2 -d\. | cut -f1 -d\-);
+           DEST_BRANCH=$major.$((minor+1))-devel;
+           git branch -a | grep "origin/$DEST_BRANCH" || {
+             DEST_BRANCH=$((major+1)).0-devel;
+             git branch -a | grep "origin/$DEST_BRANCH" || exit 1;
+           };
+           echo "BASE_REF=$BASE_REF" >> $GITHUB_ENV;
+           echo "DEST_BRANCH=$DEST_BRANCH" >> $GITHUB_ENV;
+
+    - name: Create Pull Request
+      id: open-pr
+      uses: repo-sync/pull-request@v2
+      with:
+        destination_branch: ${{ env.DEST_BRANCH }}
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        pr_title: "Pull $BASE_REF into $DEST_BRANCH"
+        pr_label: "auto-pr"
+
+    - name: Auto approve
+      uses: hmarr/auto-approve-action@v2
+      with:
+        github-token: ${{ secrets.GH_APPROVE }}
+        pull-request-number: ${{ steps.open-pr.outputs.pr_number }}

.github/workflows/automerge.yml

@@ -0,0 +1,18 @@
+name: automerge
+
+# Controls when the action will run.
+on:
+  pull_request_review:
+    branches:
+    - main
+    - '*-devel'
+
+jobs:
+  automerge:
+    if: contains(github.event.pull_request.labels.*.name, 'auto-pr')
+    runs-on: ubuntu-20.04
+    steps:
+    - name: Auto merge
+      uses: alexwilson/enable-github-automerge-action@1.0.0
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/build_test.yml

@@ -2,16 +2,22 @@ name: CI
 
 # Controls when the action will run.
 on:
-  push:
-    branches: [ main, '*-devel' ]
   pull_request:
-    branches: [ main, '*-devel' ]
+    branches:
+    - main
+    - '*-devel'
+  pull_request_review:
+    branches:
+    - main
+    - '*-devel'
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
 jobs:
   build_and_test:
+    if: github.event_name != 'pull_request_review' ||
+        contains(github.event.pull_request.labels.*.name, 'auto-pr')
     # The type of runner that the job will run on
     runs-on: ubuntu-20.04
     strategy:
@@ -37,36 +43,38 @@ jobs:
       MPIPROCS: 2
       MODE: ${{ matrix.mode }}
       DEFINE: ${{ matrix.define }}
+      GH_BASE: ${{ github.event.pull_request.base.ref }}
+      GH_HEAD: ${{ github.event.pull_request.head.ref }}
+      GH_SHA: ${{ github.event.pull_request.head.sha }}
 
     steps:
-      - name: Install dependencies
-        run: sudo apt update &&
-             sudo apt install -y
-                 python3-dev
-                 python3-numpy
-                 python3-nose
-                 python3-matplotlib
-                 libpython3-dev
-                 mpich
+    - name: Install dependencies
+      run: sudo apt update &&
+           sudo apt install -y
+               python3-dev
+               python3-numpy
+               python3-nose
+               python3-matplotlib
+               libpython3-dev
+               mpich
 
-      - name: Checkout code
-        uses: actions/checkout@v2
-        with:
-          submodules: recursive
-          fetch-depth: 0
+    - name: Checkout code
+      uses: actions/checkout@v2
+      with:
+        submodules: recursive
+        fetch-depth: 0
 
-      - name: Merge branch
-        if: github.event_name == 'pull_request'
-        run: git config user.email "test@example.com" &&
-             git config user.name "test" &&
-             git checkout -b $GITHUB_HEAD_REF $GITHUB_SHA &&
-             git checkout -b $GITHUB_BASE_REF origin/$GITHUB_BASE_REF &&
-             git merge --no-ff $GITHUB_HEAD_REF
+    - name: Merge branch
+      run: git config user.email "test@example.com" &&
+           git config user.name "test" &&
+           git checkout -b $GH_HEAD $GH_SHA &&
+           git checkout -b $GH_BASE origin/$GH_BASE &&
+           git merge --no-ff $GH_HEAD
 
-      - name: Cleanup
-        run: cd epoch1d && make cleanall &&
-             cd ../epoch2d && make cleanall &&
-             cd ../epoch3d && make cleanall
+    - name: Cleanup
+      run: cd epoch1d && make cleanall &&
+           cd ../epoch2d && make cleanall &&
+           cd ../epoch3d && make cleanall
 
-      - name: Compile and run tests
-        run: ./scripts/run-tests-epoch-all.sh ${{ matrix.flag }}
+    - name: Compile and run tests
+      run: ./scripts/run-tests-epoch-all.sh ${{ matrix.flag }}

CHANGELOG.md

@@ -1,3 +1,23 @@
+## v4.17.0 to v4.18.0
+
+ * PIC loop re-organised to ensure output files are dumped at the correct 
+   time-step.
+
+ * Fixed over-flow bug in dist_fn.
+
+ * Input deck can now store logical constants (value T or F).
+
+ * Added new n_coll_steps parameter to collisions block. This sub-cycles the
+   collisions, running them once every n steps. Collisions are run assuming a
+   time-step of n*dt, to retain the same physical behaviour.
+
+ * Added use_bremsstrahlung_scatter parameter to bremsstrahlung block. This
+   samples photon emission angle from the bremsstrahlung angular distribution. 
+   The model comes from the Geant4 Physics Reference Manual, which parametrises 
+   Tsai 1974, DOI: https://doi.org/10.1103/RevModPhys.46.815
+
+ * Fixed bug in non-relativistic bremsstrahlung cross-sections.
+
 ## v4.16.0 to v4.17.0
 
  * Added volume correction sampling Zenitani 2015 DOI 10.1063/1.4919383

epoch1d/Makefile

@@ -446,7 +446,7 @@ balance.o: balance.F90 boundary.o constants.o mpi_subtype_control.o \
   redblack_module.o timer.o utilities.o
 boundary.o: boundary.F90 injectors.o laser.o mpi_subtype_control.o \
   particle_id_hash.o particle_temperature.o partlist.o utilities.o
-bremsstrahlung.o: bremsstrahlung.F90 calc_df.o partlist.o setup.o
+bremsstrahlung.o: bremsstrahlung.F90 calc_df.o particles.o partlist.o setup.o
 calc_df.o: calc_df.F90 boundary.o
 collisions.o: collisions.F90 calc_df.o prefetch.o
 constants.o: constants.F90 $(SDFMOD)

epoch1d/example_decks/electron_ion_equilibration.deck

@@ -0,0 +1,65 @@
+begin:constant
+
+  dl = 7.4e-10
+
+end:constant
+
+begin:control
+
+  x_min = 0.0
+  x_max = 100*dl
+  nx = 5
+  t_end = 20e-12
+  stdout_frequency = 1000
+  print_eta_string = T
+  smooth_currents = T
+
+end:control
+
+begin:boundaries
+
+  bc_x_max = periodic
+  bc_x_min = periodic
+
+end:boundaries
+
+begin:species
+
+  name = protons
+  charge = 1
+  mass = 1836
+  temp_ev = 50
+  npart_per_cell = 5000
+  density = 1e22/cc
+
+end:species
+
+begin:species
+
+  name = electrons
+  charge = -1
+  mass = 1
+  temp_ev = 100
+  npart_per_cell = 5000
+  density = 1e22/cc
+
+end:species
+
+begin:collisions
+
+  use_collisions = T
+  coulomb_log = 5
+  collide = all
+  use_nanbu = T
+
+end:collisions
+
+begin:output
+
+  nstep_snapshot = 1000
+  grid = always
+  temperature = always + species
+  number_density = always + species
+  ekbar = always + species
+
+end:output

epoch1d/example_decks/electron_isotropisation.deck

@@ -0,0 +1,57 @@
+begin:constant
+
+  dl = 7.4e-10
+
+end:constant
+
+begin:control
+
+  x_min = 0.0
+  x_max = 100*dl 
+  nx = 10
+  t_end = 5e-14
+  stdout_frequency = 1000
+  print_eta_string = T
+  smooth_currents = T
+
+end:control
+
+begin:boundaries
+  bc_x_max = periodic
+  bc_x_min = periodic
+end:boundaries	
+
+begin:species
+
+  name = electrons
+  charge = -1
+  mass = 1
+  temp_x_ev = 150
+  temp_y_ev = 50
+  temp_z_ev = 50
+  npart_per_cell = 5000
+  density = 1e22/cc
+
+end:species
+
+begin:collisions
+
+  use_collisions = T
+  coulomb_log = 5
+  collide = all
+  use_nanbu = T
+
+end:collisions
+
+begin:output
+
+  nstep_snapshot = 10
+  grid = always
+  temperature = always + species
+  number_density = always + species
+  ekbar = always + species
+  temperature_x = always + species
+  temperature_y = always + species
+  temperature_z = always + species
+
+end:output