11 clean up fenics and kratos example (#14)

* Restructure Kratos example

* clean-up

* Clean up docs

* Remove Neumann bc from fenics-example

* Move benchmarks to sub-directories

* Add benchmarks in new directory

* Update github actions

* Remove the defaults channel

* Add README for each benchmark

* Add comments to Kratos mesh conversion

* Move files according to joergfunger suggestion

* fix github workflow

Author: srosenbu

.github/workflows/run-benchmark.yml

@@ -40,13 +40,13 @@ jobs:
       - name: run-fenics-benchmarks
         shell: bash -l {0}
         run: |
-          cd $GITHUB_WORKSPACE/benchmarks/linear-elasticity-plate-with-hole/
+          cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/FEniCS/
           snakemake --use-conda --force --cores 'all'
       
       - name: run-Kratos-benchmarks
         shell: bash -l {0}
         run: |
-          cd $GITHUB_WORKSPACE/benchmarks/linear-elasticity-plate-with-hole-Kratos/
+          cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/Kratos/
           snakemake --use-conda --force --cores 'all'
 
       #- name: run-optimization-workflow
@@ -66,12 +66,12 @@ jobs:
         with:
             name: fenics-output
             path: |
-              benchmarks/linear-elasticity-plate-with-hole/data
+              benchmarks/linear-elastic-plate-with-hole/FEniCS/data
       
       - name: Archive kratos data
         uses: actions/upload-artifact@v4
         with:
             name: kratos-output
             path: |
-              benchmarks/linear-elasticity-plate-with-hole-Kratos/data
+              benchmarks/linear-elastic-plate-with-hole/Kratos/data
               

benchmarks/linear-elastic-plate-with-hole/FEniCS/README.md

@@ -0,0 +1,9 @@
+# Infinite plate with hole benchmark in FEniCSx
+
+This directory contains:
+
+* `Snakefile`: A snakefile to run the benchmark.
+* `run_simulation.py`: The main script to run the benchmark.
+* `create_input_files.py`: A script to create the input files for the benchmark.
+* `environment.yml`: A conda environment file to create the environment needed to run the benchmark.
+* `parameters_*.json`: A set of parameters files for the benchmark. Each file will create a new instance of the benchmark with different parameters.

…ear-elasticity-plate-with-hole/Snakefile …elastic-plate-with-hole/FEniCS/Snakefilebenchmarks/linear-elasticity-plate-with-hole/Snakefile renamed to benchmarks/linear-elastic-plate-with-hole/FEniCS/Snakefile benchmarks/linear-elasticity-plate-with-hole/Snakefile renamed to benchmarks/linear-elastic-plate-with-hole/FEniCS/Snakefile

@@ -27,7 +27,7 @@
     .to_base_units()
     .magnitude
 )
-# create mesh
+# create mesh with gmsh python api
 """
 4---------3
 |         |