Commit 58a45518 authored by Lars Bilke's avatar Lars Bilke
Browse files

Merge branch 'release-6.4.2' into 'master'

Release procedure 6.4.2.

See merge request !4075
parents 43fc3fb9 ead9370d
Pipeline #9600 passed with stages
in 92 minutes and 29 seconds
# Unreleased
[Please see the wiki-page](https://gitlab.opengeosys.org/ogs/ogs/-/wikis/Release-notes-6.4.2)
[Please see the wiki-page](https://gitlab.opengeosys.org/ogs/ogs/-/wikis/Release-notes-6.4.3)
----
# 6.4.2
[Changelog for OpenGeoSys 6.4.2](https://gitlab.opengeosys.org/ogs/ogs/-/wikis/Release-notes-6.4.2)
# 6.4.1
......
......@@ -21,6 +21,7 @@
*
* The documentation for OGS releases can be found here:
*
* - https://doxygen.opengeosys.org/v6.4.2
* - https://doxygen.opengeosys.org/v6.4.1
* - https://doxygen.opengeosys.org/v6.4.0
* - https://doxygen.opengeosys.org/v6.3.3
......
......@@ -29,5 +29,5 @@ OpenGeoSys is distributed under the Modified BSD License. See the
[ogs]: https://www.opengeosys.org
[documentation]: https://www.opengeosys.org/docs/
[docs-master]: https://doxygen.opengeosys.org/
[docs-release]: https://doxygen.opengeosys.org/v6.4.1
[docs-release]: https://doxygen.opengeosys.org/v6.4.2
[license-source]: https://github.com/ufz/ogs/blob/master/LICENSE.txt
......@@ -4,3 +4,4 @@
/v6.4.0/* https://ogs-doxygen-v6-4-0.netlify.app/:splat 200!
/v6.4.1 https://doxygen.opengeosys.org/v6.4.1/index.html 301
/v6.4.1/* https://ogs-doxygen-v6-4-1.netlify.app/:splat 200!
/v6.4.2/* https://ogs-doxygen-v6-4-2.netlify.app/:splat 200!
+++
date = "2022-04-01T11:10:13+01:00"
title = "OpenGeoSys 6.4.2"
tag = "6.4.2"
author = "Lars Bilke"
release_date = "2022-04-01"
[downloads]
binary = [
"Windows-10.0.19043-python-3.9.10-de-utils.zip",
"Windows-10.0.19043-python-3.9.10-utils.zip",
"Windows-10.0.19043-de-utils.zip",
"Windows-10.0.19043-utils.zip"
]
container = [
"serial.sif",
"openmpi-4.0.5.sif",
]
note = """
**Note:** When using Python bindings make sure to have Python installed on your system:
- Windows: [Python 3.9.10](https://www.python.org/ftp/python/3.9.10/python-3.9.10-amd64-webinstall.exe)
"""
+++
## Overview
Some of the highlights of this release are: the extension of the TH2M process to handle phase transitions, more processes can be run in parallel with PETSc and Taylor-Hood Elements, the new HDF5-based input/output routines, and the introduction of Jupyter Notebook based benchmarks (see an [example](https://www.opengeosys.org/docs/benchmarks/notebooks/diffusionsorptiondecay/)).
### Process' changes
* [!3963](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3963) Enabled equation wise flexibility in the use of compensate_non_equilibrium_initial_residuum.
#### TH2M
* [!3839](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3839) Extend Jacobian with Laplacian's derivatives.
* [!3942](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3942) Thermal conductivity of the medium can now be defined in the input file.
* [!4034](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4034) Phase transition was revised and some errors were fixed. Energy transport now includes diffusion processes, diffusion in the mass balance is now dependent on capillary pressure. Tests have been added, including the revised heatpipe with analytical solution.
#### Component transport process / reactive transport process with coupling of Phreeqc
* [!3796](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3796) Extend the input of surface complexation sites in moles via the MaterialPropertyLib for HC-Phreeqc coupling.
* [!3903](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3903) Enable to use cation exchange and surface complexation models simultaneously for HC-Phreeqc coupling.
* [!3918](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3918) Add a "fixing pe" option.
* [!3931](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3931) Support the use of PETSc nonlinear solver.
* [!4004](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4004) Add Newton's method based linearization scheme for solving non-conservative formulation.
* [!4006](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4006) Output total mass flux and residual mass flux by node-wise.
#### Thermo-Richards-Mechanics
* [!3980](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3980) Added liquid density and viscosity output.
* [!3547](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3547)
Implementation of the vapour diffusion and the latent heat terms of TRM.
#### HeatConduction
* [!3972](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3972) Assembly in inclined elements.
#### Hydro-Mechanics
* [!3848](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3848) Use permeability strain derivative in the jacobian for HM (for embedded fracture permeability model).
#### Heat Transport BHE
* [!4007](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4007) Changed python based Server Communication process (e.g. with SimulationX) from postTimestep to preTimestep.
#### ThermalTwoPhaseFlowPP
* [!3924](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3924), [!4014](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4014) Employ MPL in ThermalTwoPhaseFlowWithPP process.
### Material models
* [!3929](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3929) Add the Verma-Pruess porosity-permeability model.
* [!3941](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3941) Modify the "EffectiveThermalConductivityPorosityMixing" property to allow for two- and three phase media.
* [!3945](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3945) New property IdealGasLawBinaryMixture.
* [!3923](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3923)
[MPL/RelPermNonWettingPhaseVanGenuchtenMualem] replace the Newton-Raphson method with the Regula–Falsi Method.
* [!3992](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3992) Enabled fracture normal rotation with the EmbeddedFracturePermeability model.
### Numerics
* [!3871](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3871) Integration order 4 implemented for Tetrahedrals. For an overview over OGS's integration methods see also !4021.
* [!3907](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3907) Added new Eigen iterative solvers: BiCGSTABL, IDRS and IDRSTABL.
* [!3882](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3882) Adds support for Taylor-Hood elements to Python boundary conditions and Python source terms.
* [!3963](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3963) Enabled equation wise flexibility in the use of compensate_non_equilibrium_initial_residuum.
* [!3991](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3991) Enable to use 13 node pyramid and 15 node prism.
### Parallel computing
* [!3805](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3805) [partmesh] Removed the option of `-q` or `--lh_elements` for the implementation of parallel computing with Taylor Hood elements.
* [!3866](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3866) Parallel computing with Taylor-Hood elements: implementation and tests with HydroMechanics process.
* [!3920](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3920) Enable parallel computing in TRM with Taylor-Hood elements.
* [!3919](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3919)
Enable node search function work under MPI.
* [!4047](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4047) Enable parallel computing in TH2M with Taylor-Hood elements.
### File I/O
* [!3857](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3857) VTK mesh converter: safely convert all integer types.
* [!3915](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3915) HDF output option: Fast file I/O and data integrity
* [!4033](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4033) Rename HydraulicFlow and HeatFlux to VolumetricFlowRate (for volumetric formulations (mass balance divided by density) / MassFlowRate and HeatFlowRate.
### Utility
* [!3863](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3863) Added the conversion of quadratic quadrilateral elements in GMSH2OGS
### GeoLib
* [!3935](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3935) Change TemplateVec::getVector() return value from `vector<T*> const*` to `vector<T*> const&`
### Project file syntax
* [!3962](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3962) Apply patches marked with `after_includes="true"`-attribute after `<include>`s are evaluatetd, [docs](https://www.opengeosys.org/docs/userguide/basics/project-file#combination_of_include_and_patch_method).
### ogs
* [!3976](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3976) Added parameter `-m` for specifying a mesh input directory.
### Testing
* [!3930](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3930) Notebooks are now tested as part of `ctest`. See [docs](https://www.opengeosys.org/docs/devguide/testing/test-data/#notebook-testing) for more info.
* [!3901](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3901) [TRM] Added a benchmark of point heat source for TRM.
* [!4001](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4001) Added a simple MKL benchmark.
* [!4005](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4005) Run TaskCDECOVALEX2023 with parallel computing.
* [!4021](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4021) Adds extensive unit tests for OGS's quadrature schemes. Now for each supported integration method and integration on each mesh element type we test, which polynomial order we can integrate exactly.
### Bug fixes
* [!3932](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3932) Fixed several memory leaks and access bugs.
* [!3956](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3956) THM: Fix temperature equation for case w/o thermal osmosis.
* [!3978](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3978) Fix access of transport porosity as medium property in TRM.
* [!3919](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3919)
Enable node search function work under MPI.
* [!4021](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4021) Fixes pyramid integration for integration order 1. Note, the location of the single integration point was changed! If you have any restart data with integration order 1, the respective location will silently change. However, that seems acceptable since before the pyramid order 1 integration was just wrong.
* [!4051](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4051) Changes the input storage order of tensorial properties of MPL. Now it is row major, before it was column major. The new row major storage order is the storage order that naturally arises in prj files. The old behavior was not a bug per se, but could very likely lead to subtle errors with asymmetric tensorial properties.
* [!4055](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4055) Fixing a bug in Process::setInitialConditions under PETSc.
### CMake
* [!3910](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3910) Updated Conan CMake integration.
* [!3940](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3940) Select lld over GNU gold over regular linker. Speeds up link times.
* [!3950](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3950), [!4030](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4030) Added option ~~`OGS_INSTALL_PETSC`~~ `OGS_INSTALL_EXTERNAL_DEPENDENCIES` to install (locally build) PETSc or MFront / TFEL into `CMAKE_INSTALL_PREFIX`.
* [!3951](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3951) Removed `std::filesystem` hacks for older compilers.
* [!3983](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3983) [cmake] Refactored (and fixed) processes setup logic.
* [!3989](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3989), [!3995](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3995) Offline build with cpm and external dependencies cache. See [docs](https://www.opengeosys.org/docs/devguide/advanced/offline-build).
* [!3999](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3999) Added option `OGS_DEPENDENCY_VERSIONS` to overwrite entries in versions.json.
* [!4001](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4001), [!4056](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4056) Use a better FindMKL.cmake which includes also linker flags.
* [!4027](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4027) Configure VTK modules and CMake options in versions.json.
* [!4041](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4041) Replaced poetry by simple python / pip calls:
- Poetry is not required anymore for automatic Python package installation. Only a Python interpreter is required (nowadays they already include `venv` and `pip`).
- Renamed CMake option `OGS_USE_POETRY` to `OGS_USE_PIP` (which now defaults to `OFF`!). Before poetry was used per default when it was found, now this behavior is reversed (needs to explicitly switched to `ON`).
* [!4059](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4059) Added --download-hypre to local CPM build.
### Infrastructure
* [!3874](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3874) Allow utils build on PETSc config.
* [!3876](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3876) Added Jupyter image with PETSc support, image name: `registry.opengeosys.org/ogs/ogs/ogs-petsc-jupyter`.
* [!3597](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3597) Added CI linux build with debug checks, address and undefined behaviour sanitizers.
* [!3994](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3994) [ci] Added msvc-code-analysis.yml for GitHub Actions.
* [!4067](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4067) [web] Restructuring to use [Hugo page bundles](https://gohugo.io/content-management/page-bundles/).
* [!4069](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4069) [ci] Deploy CLI on Windows GUI downloads.
### Version info
* [!3844](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3844) Update gtest to version 1.11.0
* [!3910](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3910) Minimum Conan version 1.36.0
* [!3951](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3951) Minimum gcc version 9.1
* [!3968](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3968) Update exprtk to newest version Dec. 2021.
* [!4018](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/4018) Update minimum PETSc version to 3.16.3.
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