List of Changes for Multiphase Code Repository by HZDR

[Latest Release]

Bugfix

Make potential force insensitive against phase order
Fix name of linked addon fvModel library
Make oversizedToContinuous robust against phase order

Deployment

Restructure stages to get user environment also in dev image
Enforce use of Python virtual environment to install additional pip packages in Docker & Apptainer containers
Make image compatible with Singularity

Documentation

Fix sprint cycle version in INSTALLATION.md
Fix sprint cycle version in hemera sample sbatch scripts
Point to installation instructions of multiphasepy rather than repeating the commands here
update INSTALLATION.md
Move files to copier template in infrastructure project

Misc

Correct spaces in test case according to pre-commit rules
Enable code style checks with pre-commit hooks
Add heuristic to reference update script

MultiMorph Model

Volume fraction filtering procedure for over-resolved scenarios
remove deprecated detrainment phase transfer model

OpenFOAM

Sprint Cycle Upgrade 12-s.1

Physical Modelling

Implementation of turbulent dispersion force revised

Test

Added single-cell test case for simulating desorption with a population balance model
add shockTube case for addonMultiphaseEuler with compressibilty

[11-s.1-hzdr.1] - 2024-08-22

Bugfix

Suppress warning for not declared variables from hadolint
Separate docker build for current sprint cycle release and dev release
Specify positional dummy argument for runCommand

Deployment

Remove env files and update sprint cycle instructions
Rename docker images according to docker naming conventions
Update release procedure
Use a default python venv to install multiphasepy

Documentation

Fix image path in section on using Apptainer
Update release template and docker build arguments
Source tutorial run functions -> Source run functions
Fix wrong order for applying patches
Fix sprint cycle version in INSTALLATION.md
Add information on installing and using Apptainer

MultiMorph Model

Raise compactness requirements for cluster tracking

OpenFOAM

foamDictionary is now able to edit files in-place with new output option
Sprint Cycle Upgrade 11-s.1

Post-Processing

Generally turn on ./createGraphs in all tutorials and test cases to test post-processing also in single timestep mode
remove whitespace from variable in phaseStucture functionObjects
Generally use Gnuplot terminal pngcairo for proper handling of postscript symbols and enhanced text
remove converToCSV and reformatHeader, use mpyconv from multiphasepy package instead
Move tool to multiphasepy package

[multiphase-code-repository-by-hzdr-10-s.2-hzdr.3] - 2024-07-16

Baseline

Introduce upper limiter for EoH in Hessenkemper lift model

Bugfix

Remove conflicting python packages installed via pip

Deployment

Update to Ubuntu 24.04 and backport of configuration file changes from OpenFOAM-dev
Fix unbound variable error in runParallel.sh
Refactor runParallel RunFunction w.r.t. handling of option array
Add all tests and tutorials to release

Misc

add instant and refresh options to progressBar

Post-Processing

Move foamTimeAverageData to multiphasepy python package

Test

Added test for assessing performance of containerized MPI on foreign HPC systems

[multiphase-code-repository-by-hzdr-10-s.2-hzdr.2] - 2024-06-14

Baseline

Optional clipping of lift coefficient for Hessenkemper

Bugfix

Remove chown for files in home directory from entrypoint
Fix log file output logic with respect to cluster tracking
Ensure correct configuration and for home directory in docker image
Restore .env-dev for OpenFOAM-dev builds
fix wrong results due to optimisation level with g++11
make constantAttachment work independent from phase order
make disintegrationToDisperse work independent from phase order
funcName --> name

Deployment

Use PMI2 interface only for multi-node simulations
Remove UCX communication middleware
Rely on UCX as communication middleware for Open MPI
Make runParallel RunFunction compatible with Singularity
Make the sprint cycle version the default in Dockerfile instead of dev
Avoid unbound variable warnings when using new runParallel function for Apptainer in bash strict mode, e.g. within a workflow
Fix unbound variable error when running Snakemake workflow with Apptainer containers
Adjusted RunFunctions to allow for running distributed MPI Jobs with Apptainer and Slurm on the basis of a fully containerized MPI implementation using the runParallel function
Merge NVIDIAGL image into our docker image
Remove docker compose and user management in docker images
Force pseudo-termional allocation in runParallelApptainer function
Added specialized run function for starting OpenFOAM MPI jobs with Apptainer
Merge Nvidia and Linux Docker images
Add bsdmainutils package to Debian package dependencies
Revise handling for ccache in docker image
Enable caching and slim down dockerfile
Moved Python dependencies to new Python repository which provides a the multiphasepy package that is installed in the final stage of the Docker build process
Fix application of sprint patches for Hemera cluster installation
Lift scipy version 1.9.0 required by testAddon/postProcessing/foamFourierTransform
Snakemake 7.25 requires toposort>=1.10
Upgrade Docker images to Ubuntu 22.04 LTS Jammy Jellyfish
Add new stage for multiphase python module and add compile options to scotch library
Remove ThirdParty from docker images
Fix bug for kaniko with major version detection
Fix Paraview variables and build args for linuxArm64
Use hard-coded environment variables for OpenFOAM in docker image
Update numpy and scipy version
Fix bug in path to foamExec
Use foamExec as entry point for docker image
Remove arm64 from codemeta as it crashed debian build

Documentation

Improved documentation on setting Apptainer as default module upon login on HPC cluster
Mark OpenFOAM directories for git as safe directories
Add image specification examples to hemeraApptainer template batch script
Add mpy prefix to tools from multiphasepy package
Minor follow-up for generalized source code header
Introduce FILES.md to specify new, modified and copied files from OpenFOAM Foundation Software
Introduce new generalized source code header
Sorting command with duplicates removal for configuration files
Revise some minor left overs from renaming of the repository

Misc

Use RunFunctions from $WM_PROJECT_SITE for compatibility with Apptainer
Add docker as recommended VS Code extension
Add live-server as recommended VS Code extension
Add model to control integral mass of selected phases
Fix etc/vscode/settings.json with respect to error squiggles
Create a default user in docker image
Add option to launch jupyter lab server in docker image with foamDockerRun.sh
Backport OpenFOAM-dev commit eb8e221f
Singularity is now Apptainer
Remove setCaseNumberOrDefault from casesFunctions.sh following new convention that default case should be set in a case-level caseSettings.orig file
Update VS Code tasks to absolute path
Allow foamDockerRun.sh to mount single files
Addon code is now compiled into $WM_PROJECT_SITE/$WM_PROJECT_VERSION for all installation options
Fix ending of patch file enabling the HZDR header
Add helper scripts to reformat dat files and update reference data
setCaseNumberOrDefault for templated cases
Fix ssh setting in docker-compose for Mac OS
Add writeAtFile FO to allow result writing during running simulations
use writeTime() rather than deprecated outputTime()

MultiMorph Model

Optimize oversizedToContinuous logic for serial processing of multiple cluster tracking pairs
Number-conservative conversion of large disperse fluid particles to resolved state
Allow continuous phase with actual diameter model

OpenFOAM

Fix HZDR banner for case files

Physical Modelling

add phaseTransferModel BhutaniBritoParada

Population Balance

There is no need for the phaseChange driftModel to read the specie-specific mass transfer rate from the InterfaceCompositionPhaseChangePhaseSystem as the entire mass transfer rate is what drives drift
Allow for specie-specific mass transfer between velocity groups triggered e.g. by absorption or desorption processes

Post-Processing

add filmThickness functionObject
Plot script for Courant number and time step size
Introduce new collection for bash functions in cases repository

Test

Add test for new runParallel RunFunction to use OpenFOAM with Apptainer in distributed parallel runs
tutorials/Allrun now checks success of Gnuplot scripts executed as part of OpenFOAM job scripts
Add another heuristic to reference data update script
Remove redundant fieldAverage caseDict from repo which was only used to allow single time-step tests of cases with field-averaging, but is not necessary anymore due to improvements of the Alltest script in commit 2042998044aa1e78cd07e739b0b545f79e429c70
Remove naming of temporary controlDict file within Alltest script
Temporarily deactivate selected LES model tests (wrong results if addon is compiled with g++-11, which is the default in Ubuntu 22.04)
Use mktemp instead of tempfile for creating temporary controlDict file, since tempfile is deprecated
Enhance robustness of Alltest
Expand controlDict and set timeStart to zero

[Multiphase-Code-Repository-10-s.2-hzdr.1] - 2023-06-02

Bugfix

Remove unneccessary char

Deployment

Remove arm64 from codemeta as it crashed debian build
Fix a issue with OpenMPI and shared memory
Enable ARM64 images and separate Paraview into own docker stage
Build customized OpenMPI and libfabric
Enable ccache for clang compiler
Update REGISTRY variable in .env
Merge cuda and nvidia images

Documentation

Rename to Multiphase Code Repository by HZDR for OpenFOAM Foundation Software
Minor fix to INSTALLATION.md
More straigtforward commands for release management

Misc

Further generalization to facilitate maintenance of other addon code repositories
Adjust Alltest for cases with time-averaging starting later than time zero
Add debugging options to pvserver SLURM script
Update list of partitions in SLURM script templates
Several modifications and bugfixes

OpenFOAM

Sprint Cycle Upgrade 10-s.2

Post-Processing

write blending fields, fG, fS, f1D2 and f2D1, on debug
Update ParaView server SLURM script
ParaView server SLURM script
Use pngcairo instead of png terminal for plotting with Gnuplot to enable dashed lines
Made profiling functionality use standard C++ such that it can be used outside of OpenFOAM

[HZDR-Multiphase-Addon-10-s.1-hzdr.3] - 2023-03-21

Bugfix

Sort out QT dependencies for addon and Paraview
fix post processing of dropletEntrainmentByShear test case
Fix path to online repository for Doxygen
alphaMax moved to phaseProperties for flotation tutorials
Allow control dict update when using HZDRCourantNo

Deployment

Fix GitLab instance URL in docker-compose.override.yml sample
Simplify some header and descriptions for easier sync with RCS
Install rsync in Docker container images
Simplify dockerfile and reduce layers
Make ssh for container deployment optional
Free deploy job for OpenFOAM installations on hemera from deploying site directory
Fix application of sprint patches to cluster installation for OpenFOAM-versions > 9

Documentation

Update QT dependencies
More descriptive merge request template for releases
Installation instructions for Mac OS
Modify command for running megalinter locally such that container is removed upon exit
Update domain to GitLab instance
beautify shortcut table

Misc

Remove configuration files for flotation cases and switch to SchillerNaumann drag model
Replaced prefix "HZDR" for libraries and exucutables by the more general "addon"
Make display support for docker images optional
Correct sprint cycle bash script to make linter happy
Fixed formatting of blockMeshDictCylinder template
Update Snakemake version for new workflow design
Adapt VS Code instructions
Provide VS Code settings as files and add instructions to CONTRIBUTING.md
Remove checkbox for template repository

MultiMorph Model

Rename OpenFOAM-Hybrid to MultiMorph Model

OpenFOAM

Remove foamyHexMesh

OpenFOAM-Hybrid

add description of addon specific changes to header of ...
write shear based under-resolution indicator at start time

Physical Modelling

Added drag models of Tomiyama et al. (1998) for pure and slightly contaminated systems
Entrainment model revision
Remove not working freeSurface mesh motion solver
Make degassingPhases fvModel compatible with blending framework

Population Balance

Added GPU-accelerated version of the coalescence model of Lehr et al. (2002) that works with the GPU-accelerated source term assembly
Enabled runtime selection of GPU-accelerated binary breakup models in combination with CUDApopulationBalance
Enabled runtime selection of GPU-accelerated coalescence models in combination with CUDApopulationBalance
Introduced automatic assignment of MPI ranks to one or more GPU devices
Added GPU-accelerated source term assembly for breakup, binary breakup and drift
Some improvements to GPU-accelerated coalescence source term assembly
Add test cases for (binary)Breakup and drift for testing the GPU-accelerated source term assembly
First working GPU-accelerated coalescence source term assembly
Added basic code structure for implementing the GPU-acceleration of the source term assembly using NVIDIA CUDA

Post-Processing

add caseDict volAverage

Test

revise Ma entrainment test case to be more standard OF-Hybrid
Added HZDR header to Alltest script to mark it as an extension of the original script supplied by OpenFOAM
Add -configure option to Alltest that only prepares setups to run a single time step but skips execution

Tutorial

sync hybrid cases among repositories

[HZDR-Multiphase-Addon-10-s.1-hzdr.2] - 2022-10-19

Documentation

Clarify that Debian, Docker and compiling from sources are exclusive installation options
Add references to README.md

[HZDR-Multiphase-Addon-10-s.1-hzdr.1] - 2022-10-14

Bugfix

use unquoted value to allow for proper command line argumens generation
functionObject deviation now properly writes out deviation as field as well as in log file
wrong apt command in dockerfile
define arguments of foamShellRunner with '--' preventing abbreviations
for degassingPhases fvModel add sink terms for transported variables
qt5-default package is not available in Ubuntu 21 and newer

Deployment

remove unnecessary patch tgz files from OpenFOAM directory
Do not commit changes to etc/bashrc or etc/cshrc if there aren't any
Adjust regular expressions for detecting sprint cycles to match also beyond one digit, i.e. 10-s.10
Check for existence of patch files before applying them
Changes to WM_PROJECT_VERSION, _COMPILER and _COMPILE_OPTION in basic are now committed to git
Fix updateSprintCycle.sh to also consider the WM_PROJECT_VERSION entry in codemeta.json
Add patches for OpenFOAM installation to code publication
bin directory in WM_PROJECT_USER_DIR has highest priority in docker images
Add Paraview to debian package

Documentation

Make sure to remove all hyphens from docker compose commands
Source OpenFOAM environment before applying sprint cycle patches
Fix typo in installation instructions
Re-structure file headers with better information about copyright
Modified header with improved copyright
Refer to nightly build addon Debian package in installation instructions
correct latex formulas and remove problematic extra package to fix Doxygen formula rendering
Automatically generate changelog file based on git commits
align keywords in Gitlab, Rodare, codemeta.json and HIFIS Software Spotlight
Correct Email address of Mazen Draw in codemeta.json
add position information to contact details
Add milestone information to support request issue template
New issue template for internal and external support requests
Fix broken links in doxygen
correct typo in installation instruction
add information to installation instructions that adding the local ssh key to the gitlab account is required for cloning the repository
Correct non-compliant file headers
Correct statement on supported Ubuntu versions
Add Tingting Zhang as contributor

Misc

Add words to spell checker list
Refine gitignore rules with respect to postProcessing folders
Refine gitignore rules related to postProcessing folders
Enable various models and utilities for release
Adapt VS Code configuration script to meet linter requirements
Include recommended VS Code extensions in configuration script
Fix typo in VS Code settings
Let VS Code classify C and H files as C++ independently from any extension
update VS Code settings to disable recommendations and clean-up
Do not hide .git* in VS Code file explorer (.git folder is hidden anyway)
Remove tar.gz and tgz from gitignore
minor corrections in createVSCodeProject.sh
writeCellCoords functionObject to print the cell-centre coodinates for a given cell id
Removed duplicate category from .gitignore
allow tracking of folders with leading digits, only ignore names consisting exclusively of digits and decimal points

OpenFOAM

Sprint Cycle Upgrade 10-s.1

OpenFOAM-Hybrid

protect dominant continuous phase from disintegration
simplify user access to curvature
prevent disintegration of dominant continuous phase

Physical Modelling

add kOmegaSSTSatoIt turbulence model
Implement droplet entrainment model
Add low-Re correction to Shi wallLubrication model
Write mass rate only once for master

Post-Processing

Added multiphaseEulerFoam-specific functionObject for extracting dimensionless numbers

Test

Counter-current test for resolved interface drag
Correct exit code of foamShellRunner.py upon failure
add test and demo case for disintegrationToDisperse morphology transfer
Simplified commands for obtaining directory basename in Allrun scripts
Refactor functionObject deviation

[HZDR-Multiphase-Addon-9-s.1-hzdr.2] - 2022-06-21

Bugfix

Add output to doxygen to check sprint version detection
correct path for cleaning bot
Fix wrong variable name in gitlab deploy job for debian package
fix deployment pipeline for openfoam debian packages

Deployment

add bot for cleaning up package files
enhance fabric for deployment of debian packages on local machines
remove custom aliases for FOAM_USER_DIR from docker images
create a latest release badge based on releases
Add QT dependencies for graphical functionObjects
remove cleanup for nightly packages
minor fixes due to wrong variable names
fix bug in version numbering
remove dublicated job for release pipeline
Enhance documentation and bug fixes for debian packaging
Ensure that sprint related patches of OpenFOAM release are applied for Hemera
Enable packaging for Debian nightly and stable packages

Documentation

Substituted remaining apt-get in installation instructions
added missing QtCharts package to installation instructions
fix headers of HZDR dictionary files

Misc

replaced m4-based template blockMesh dictionaries using #calc and #codeStream
update and unify gitignore

OpenFOAM-Hybrid

Write mass transfer rates for all morphology transfer phaseTransfer models
re-formulation of turbulent dispersion force to make it consistent and more stable
unify default hybrid setups with caseDicts

Physical Modelling

Updated SaffmanMei lift model implementation following its contribution to OpenFOAM-dev
Updated Kusters breakup model implementation following its contribution to OpenFOAM-dev
Updated AdachiStuartFokkink agglomeration model implementation following its contribution to OpenFOAM-dev
Added basic infrastructure for an iterative drag and non-drag force correction

Post-Processing

generally use CSV as output format

Test

added -from and -to options to Alltest
Fix and simplify some cases regarding post-processing and plotting

Tutorial

Added case simulating solid particle agglomeration and breakage

HZDR-Multiphase-Addon-9-s.1-hzdr.1 - 2022-04-26

Baseline

swarm correction model to blend out drag and lift model
breakup and coalescence case dictionaries and degassing boundary condition for bubble columns

Bugfix

Update sizeDistribution caseDict to British English
Cross-project pipeline is now allowed to fail
patch does not contain any data

Deployment

fix missing environment variable for username
add templates from WM_PROJECT_USER_DIR to ~/.OpenFOAM
Enable profiling images for docker-compose

Documentation

update license information to GPL v3 or later
add information about clone for docker compose
correct sprint cycle commit sha for OpenFOAM-dev and ThirdParty-dev
add links for further information about syntax of Compose files
add missing docker login registry.hzdr.de
Correct installation instructions with respect to WM_PROJECT_SITE_DIR
Added information on git-lfs to installation instructions
Add doi to codemeta and openfoam website link to Readme.md
Split command line commands into blocks for efficient use of "copy" button from the browser
reference to OpenFOAM code quality guide
New checklist for merge requests containing a possible release contribution
Modify cite us as for processing with pandoc to pdf
New installation instructions
Centred the Class Declaration comment

OpenFOAM

Rationalized the naming of scalar limits

Physical Modelling

Shi et al (2021) wall lubrication model for rigid spheres

Population Balance

functionObject for computing integral and mean properties of a size distribution
Cleanup of unnecessary includes files
Prepare coalescence and breakup models of Liao et al. (2015) for contribution
Correct Ceff coefficient in Liao coalescence model implementation
CUDA CoulaloglouTavlarides kernel
Configurable number of CUDA streams
add reference solution to test cases
Cuda Test for LehrMilliesMewes kernel
CUDA LehrMilliesMewes binary breakup model

Post-Processing

Python script for calculating time derivative of time series

Test

set terminal to color in createGraph scripts of population balance tests

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