Updating the new_geometries branch (#14)

* Apply latest developments to the photo_dev branch (#7) * Added new printing option * Added ability to write contributions Contributions into a single band can be written to a qe matrix file * Added more printing in QE matrix file * Added extra output print and comments * Allow user to set max # of layers * Tested the code to work properly * Removed bug in MPI parallelisation for IMFP * Changed the order of printing for MPI * Rewrote distribute qe-matrix output The new version is more ram intensive, but keeps us from having to open and close the file many times to write from the different MPI processes. * Ran fprettify on all files * Update projection_utils.f90 * Update .gitignore * Update .gitignore * Update make.system * Update jdos_utils.f90 * Update optics.f90 * Removed extra gitignore file * Create docs_to_pages * Rename docs_to_pages to docs_to_pages.yml * Update docs_to_pages.yml * Update docs_to_pages.yml * Update docs_to_pages.yml * Ran pre-commit * Update main.yml Made sure that optados.x is created to run the tests in the test-suite * Update main.yml Made sure optados.mpi is created and available for the test-suite * Update main.yml * Corrected .gitignore files * Reformulated and corrected qe_mat mpi test * Update docs_to_pages.yml * Updating to latest version in dev version (#12) * Added new printing option * Added ability to write contributions Contributions into a single band can be written to a qe matrix file * Added more printing in QE matrix file * Added extra output print and comments * Allow user to set max # of layers * Tested the code to work properly * Removed bug in MPI parallelisation for IMFP * Changed the order of printing for MPI * Rewrote distribute qe-matrix output The new version is more ram intensive, but keeps us from having to open and close the file many times to write from the different MPI processes. * Ran fprettify on all files * Finish Merge photo_dev * Removed trailing spaces in the user_guide.tex * Merging into develop (#8) * Create docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Delete docs.yml * Merge the created GH action into the development branch (#9) * Create docs_to_pages * Rename docs_to_pages to docs_to_pages.yml * Update docs_to_pages.yml * Update docs_to_pages.yml * Update docs_to_pages.yml * Merge old default branch into new default (#10) * Create docs_to_pages * Rename docs_to_pages to docs_to_pages.yml * Update docs_to_pages.yml * Update docs_to_pages.yml * Update docs_to_pages.yml * Ran pre-commit * Update main.yml Made sure that optados.x is created to run the tests in the test-suite * Update main.yml Made sure optados.mpi is created and available for the test-suite * Update main.yml * Corrected .gitignore files * Reformulated and corrected qe_mat mpi test * Update docs_to_pages.yml * Update docs_to_pages.yml * Update photo.f90 Removed extra character in formatting description * Removed off by one error for energy indices * Added final state printing * Corrected extra printing statements * Added layer volume calc and more * Projected jdos (#13) * Added first implementation of projected jdos * Corrected calculating projected_jdos * Changed band of pdos weight applied to jdos This change allows the calculated jdos to be independent of cell size Likely problem with the calculation of the the weighted jdos, as this will probably make it dependent on the cell again * Simplified proj_PDOS calculation * Removed faulty import * Troubleshot errors with memalloc + scope problems * Added latest changes * Added new printing option * Added ability to write contributions Contributions into a single band can be written to a qe matrix file * Added more printing in QE matrix file * Added extra output print and comments * Allow user to set max # of layers * Tested the code to work properly * Removed bug in MPI parallelisation for IMFP * Changed the order of printing for MPI * Rewrote distribute qe-matrix output The new version is more ram intensive, but keeps us from having to open and close the file many times to write from the different MPI processes. * Ran fprettify on all files * Finish Merge photo_dev * Removed trailing spaces in the user_guide.tex * Merging into develop (#8) * Create docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Update docs.yml * Delete docs.yml * Merge the created GH action into the development branch (#9) * Create docs_to_pages * Rename docs_to_pages to docs_to_pages.yml * Update docs_to_pages.yml * Update docs_to_pages.yml * Update docs_to_pages.yml * Merge old default branch into new default (#10) * Create docs_to_pages * Rename docs_to_pages to docs_to_pages.yml * Update docs_to_pages.yml * Update docs_to_pages.yml * Update docs_to_pages.yml * Ran pre-commit * Update main.yml Made sure that optados.x is created to run the tests in the test-suite * Update main.yml Made sure optados.mpi is created and available for the test-suite * Update main.yml * Corrected .gitignore files * Reformulated and corrected qe_mat mpi test * Update docs_to_pages.yml * Update docs_to_pages.yml * Update photo.f90 Removed extra character in formatting description * Removed off by one error for energy indices * Added final state printing * Corrected extra printing statements * Started to implement proj wJDOS * Added printing for photoemission * Implemented atom based printing * Removed superfluous code * Added atom volume in optics calc * Fixed writing statements for mpi program * Added printing to output file for optics * Fixed mpi printing * Removed projected jdos from jdos utils * Changed single comment
wuppersaver · Oct 30, 2023 · 073edd4 · 073edd4
1 parent cf27dd6
commit 073edd4
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Showing 52 changed files with 807 additions and 5,996 deletions.
diff --git a/.github/workflows/docs_to_pages.yml b/.github/workflows/docs_to_pages.yml
@@ -0,0 +1,40 @@
+# This is a basic workflow to help you get started with Actions
+
+name: Docs to Pages
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the "photo_dev" branch
+  push:
+    branches: [ "develop" ]
+  pull_request:
+    branches: [ "develop" ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: built
+        uses: wuppersaver/ford-build@v1.0
+        with:
+          project_file: /optados/
+      - name: Deploy to GitHub Pages
+        if: success()
+        uses: crazy-max/ghaction-github-pages@v3
+        with:
+          target_branch: gh-pages
+          build_dir: ./optados/auto_doc/
+          verbose: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -16,16 +16,16 @@ on:
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   pre-commit:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      - uses: pre-commit/action@v2.0.0
+      - uses: actions/checkout@v3.5.3
+      - uses: actions/setup-python@v4.7.0
+      - uses: pre-commit/action@v3.0.0
 
 
   build:
     # The type of runner that the job will run on
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
@@ -50,11 +50,14 @@ jobs:
             matplotlib  \
       - name: build
         run:  |
-          cd optados 
+          cd optados
+          sed -i "s/.*BUILD :=.*/BUILD := fast/" make.system
           make 
           make tools
+          sed -i "s/.*COMMS_ARCH :=.*/COMMS_ARCH := mpi/" make.system
+          make
       - name: run tests
         run: |
           cd optados/test-suite
-          ./run_tests -v --category=default 
+          ./run_tests -n 1 -v --category=default 
 
diff --git a/.gitignore b/.gitignore
diff --git a/optados/documents/photoemission/user_guide.tex b/optados/documents/photoemission/user_guide.tex
diff --git a/optados/make.system b/optados/make.system
@@ -39,7 +39,7 @@ ifeq ($(SYSTEM), gfortran)
    FFLAGS= -fconvert=big-endian -fPIC
    FFLAGS_PARALLEL=  -DMPI
    FFLAGS_FAST= -O3
-   FFLAGS_DEBUG= -O0  -g -fcheck=all -ffpe-trap=zero
+   FFLAGS_DEBUG= -O0  -g -fcheck=all -ffpe-trap=invalid
    EXTENSION=.gfortran
 endif