Update restart files of application tests for p4est 2.3.6 (#1181)

Description
deal.II changed the version of the dependancy p4est to 2.3.6 for their docker master-focal (the one we use for our CI with deal.II version master). We were using p4est 2.3.2, which makes some of our application-test restart files not compatible with the new p4est version.
Unfortunately, the previous restart files were generated a long time ago (> 9 months). The .prm has not been updated since then and they were a bit all over the place.

Solution
Update the .prm files with the proper parameter names.
Update the restart files that were failling.
Gather the .prm for the lethe-fluid-particles and lethe-fluid-vans .prm generator in the generator folder.
If the .prm restart generator file was not there, new ones have been created trying to replicated it.

Testing
All tests pass on CI with deal.II version master and they are now disabled with deal.II version 9.5.0.

Documentation
The next PR will modify the installation doc according to p4est 2.3.6

Former-commit-id: 4dd53b3

.github/PULL_REQUEST_TEMPLATE/pull_request_template_bug-fix.md

@@ -35,7 +35,7 @@ See [this page](https://chaos-polymtl.github.io/lethe/documentation/contributing
 Code related list:
 - [ ] All in-code documentation related to this PR is up to date (Doxygen format)
 - [ ] Lethe documentation is up to date
-- [ ] Fix has unit test(s) (preferred) or application test(s)
+- [ ] Fix has unit test(s) (preferred) or application test(s), and restart files are in the generator folder
 - [ ] The branch is rebased onto master
 - [ ] Changelog (CHANGELOG.md) is up to date
 - [ ] Code is indented with indent-all and .prm files (examples and tests) with prm-indent

.github/PULL_REQUEST_TEMPLATE/pull_request_template_new-feature.md

@@ -32,7 +32,7 @@ See [this page](https://chaos-polymtl.github.io/lethe/documentation/contributing
 Code related list:
 - [ ] All in-code documentation related to this PR is up to date (Doxygen format)
 - [ ] Lethe documentation is up to date
-- [ ] New feature has unit test(s) (preferred) or application test(s)
+- [ ] New feature has unit test(s) (preferred) or application test(s), and restart files are in the generator folder
 - [ ] The branch is rebased onto master
 - [ ] Changelog (CHANGELOG.md) is up to date
 - [ ] Code is indented with indent-all and .prm files (examples and tests) with prm-indent

.github/workflows/main_release.yml

@@ -63,7 +63,10 @@ jobs:
           make -j${{ env.COMPILE_JOBS }}
 
       # These tests require a single core each so we will run them in parallel
+      # Only run tests on deal.ii master version
+      # Restart files are not compatible with deal.ii v9.5.0
       - name: Run Lethe tests (Release-deal.ii:${{ matrix.dealii_version }})
+        if: ${{ matrix.dealii_version == 'master'}}
         run: |
           #Allow OMPI to run as root
           export OMPI_ALLOW_RUN_AS_ROOT=1
@@ -73,9 +76,13 @@ jobs:
           ctest -N --exclude-regex ${{ env.MULTI_CORE_TESTS_REGEX }}
           # Run in parallel
           ctest --output-on-failure -j${{ env.COMPILE_JOBS }} --exclude-regex ${{ env.MULTI_CORE_TESTS_REGEX }}
-      
+
+
       # These tests require two cores each so we will run them sequencially
+      # Only run tests on deal.ii master version
+      # Restart files are not compatible with deal.ii v9.5.0
       - name: Run multi-core Lethe tests (Release-deal.ii:${{ matrix.dealii_version }})
+        if: ${{ matrix.dealii_version == 'master'}}
         run: |
           #Allow OMPI to run as root
           export OMPI_ALLOW_RUN_AS_ROOT=1
@@ -84,4 +91,4 @@ jobs:
           # Print the tests to be executed
           ctest -N --tests-regex ${{ env.MULTI_CORE_TESTS_REGEX }}
           # Run sequencially
-          ctest --output-on-failure --tests-regex ${{ env.MULTI_CORE_TESTS_REGEX }}
+          ctest --output-on-failure --tests-regex ${{ env.MULTI_CORE_TESTS_REGEX }}

CHANGELOG.md

@@ -3,6 +3,13 @@
 All notable changes to the Lethe project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/).
 
+## [Master] - 2024-06-16
+
+### Changed
+
+- MINOR Some application-test restart files have been updated using p4est 2.3.6. Some test results have changed for lethe-fluid-particles and lethe-fluid-vans, since the DEM solver has slightly changed since the previous restart files generation, and it is now impossible to regenerate the exact same initial condition. [#1181](https://github.com/chaos-polymtl/lethe/pull/1181)
+
+
 ## [Master] - 2024-06-16
 
 ### Changed

applications_tests/lethe-fluid-particles/CMakeLists.txt

@@ -10,13 +10,6 @@ file(COPY particle_sedimentation_files/dem.triangulation.info DESTINATION "${CMA
 file(COPY particle_sedimentation_files/dem.triangulation_fixed.data DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/particle_sedimentation.${_build_type}/mpirun=1/")
 file(COPY particle_sedimentation_files/dem.triangulation_variable.data DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/particle_sedimentation.${_build_type}/mpirun=1/")
 
-file(COPY restart_particle_sedimentation_files/dem.particles DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/restart_particle_sedimentation.${_build_type}/mpirun=1/")
-file(COPY restart_particle_sedimentation_files/dem.pvdhandler DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/restart_particle_sedimentation.${_build_type}/mpirun=1/")
-file(COPY restart_particle_sedimentation_files/dem.simulationcontrol DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/restart_particle_sedimentation.${_build_type}/mpirun=1/")
-file(COPY restart_particle_sedimentation_files/dem.triangulation DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/restart_particle_sedimentation.${_build_type}/mpirun=1/")
-file(COPY restart_particle_sedimentation_files/dem.triangulation.info DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/restart_particle_sedimentation.${_build_type}/mpirun=1/")
-file(COPY restart_particle_sedimentation_files/dem.triangulation_fixed.data DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/restart_particle_sedimentation.${_build_type}/mpirun=1/")
-file(COPY restart_particle_sedimentation_files/dem.triangulation_variable.data DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/restart_particle_sedimentation.${_build_type}/mpirun=1/")
 file(COPY restart_particle_sedimentation_files/case.particles DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/restart_particle_sedimentation.${_build_type}/mpirun=1/")
 file(COPY restart_particle_sedimentation_files/case.pvdhandler DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/restart_particle_sedimentation.${_build_type}/mpirun=1/")
 file(COPY restart_particle_sedimentation_files/case_particles.pvdhandler DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/restart_particle_sedimentation.${_build_type}/mpirun=1/")

applications_tests/lethe-fluid-particles/adaptive_sparse_contacts.mpirun=1.output

@@ -32,11 +32,11 @@ DEM contact search at dem step 0
 DEM contact search at dem step 1
 Finished 50 DEM iterations
 ---------------------------------------------------------------
-Global continuity equation error: 3.13678e-09 s^-1
-Max local continuity error: 6.13917e-08 s^-1
+Global continuity equation error: 2.803e-09 s^-1
+Max local continuity error: 7.07295e-08 s^-1
 
 **********************************************************************************
-Transient iteration: 2        Time: 0.002    Time step: 0.001    CFL: 7.47157e-05
+Transient iteration: 2        Time: 0.002    Time step: 0.001    CFL: 7.48857e-05
 **********************************************************************************
 --------------
 Void Fraction
@@ -50,11 +50,11 @@ DEM
 DEM contact search at dem step 1
 Finished 50 DEM iterations
 ---------------------------------------------------------------
-Global continuity equation error: -7.56756e-09 s^-1
-Max local continuity error: 3.10857e-06 s^-1
+Global continuity equation error: -1.26904e-09 s^-1
+Max local continuity error: 7.28588e-07 s^-1
 
 **********************************************************************************
-Transient iteration: 3        Time: 0.003    Time step: 0.001    CFL: 0.000162479
+Transient iteration: 3        Time: 0.003    Time step: 0.001    CFL: 0.000149645
 **********************************************************************************
 --------------
 Void Fraction
@@ -68,11 +68,11 @@ DEM
 DEM contact search at dem step 1
 Finished 50 DEM iterations
 ---------------------------------------------------------------
-Global continuity equation error: 1.94709e-09 s^-1
-Max local continuity error: 5.08953e-07 s^-1
+Global continuity equation error: 3.9841e-09 s^-1
+Max local continuity error: 1.05602e-06 s^-1
 
 **********************************************************************************
-Transient iteration: 4        Time: 0.004    Time step: 0.001    CFL: 0.000224045
+Transient iteration: 4        Time: 0.004    Time step: 0.001    CFL: 0.000224447
 **********************************************************************************
 --------------
 Void Fraction
@@ -86,12 +86,12 @@ DEM
 DEM contact search at dem step 1
 Finished 50 DEM iterations
 ---------------------------------------------------------------
-Global continuity equation error: 7.6613e-09 s^-1
-Max local continuity error: 5.17523e-07 s^-1
+Global continuity equation error: 1.16336e-09 s^-1
+Max local continuity error: 1.41713e-06 s^-1
 
-*********************************************************************************
-Transient iteration: 5        Time: 0.005    Time step: 0.001    CFL: 0.00029829
-*********************************************************************************
+**********************************************************************************
+Transient iteration: 5        Time: 0.005    Time step: 0.001    CFL: 0.000299344
+**********************************************************************************
 --------------
 Void Fraction
 --------------
@@ -107,7 +107,7 @@ print_from_processor_0
 0 1
 0
 1 8
-3 3 3 3 3 3 3 3
+4 4 4 4 4 4 4 4
 
 
 [deal.II intermediate Patch<3,3>]
@@ -117,7 +117,7 @@ print_from_processor_0
 1 1
 0
 1 8
-2 2 2 2 2 2 2 2
+4 4 4 4 4 4 4 4
 
 
 [deal.II intermediate Patch<3,3>]
@@ -127,7 +127,7 @@ print_from_processor_0
 2 1
 0
 1 8
-2 2 2 2 2 2 2 2
+4 4 4 4 4 4 4 4
 
 
 [deal.II intermediate Patch<3,3>]
@@ -137,7 +137,7 @@ print_from_processor_0
 3 1
 0
 1 8
-2 2 2 2 2 2 2 2
+4 4 4 4 4 4 4 4
 
 
 [deal.II intermediate Patch<3,3>]
@@ -147,7 +147,7 @@ print_from_processor_0
 4 1
 0
 1 8
-3 3 3 3 3 3 3 3
+4 4 4 4 4 4 4 4
 
 
 [deal.II intermediate Patch<3,3>]
@@ -188,5 +188,5 @@ DEM
 DEM contact search at dem step 1
 Finished 50 DEM iterations
 ---------------------------------------------------------------
-Global continuity equation error: 6.76463e-10 s^-1
-Max local continuity error: 6.79928e-07 s^-1
+Global continuity equation error: -8.07686e-10 s^-1
+Max local continuity error: 1.81029e-06 s^-1

applications_tests/lethe-fluid-particles/adaptive_sparse_contacts_files/dem.particles

@@ -1 +1 @@
-0 0 350 74 350
+0 0 350 78 350

applications_tests/lethe-fluid-particles/adaptive_sparse_contacts_files/dem.pvdhandler

@@ -1,2 +1,2 @@
 0
-Time File
+Time File