From 80f50c45bf3e7ca804206500d51e23f78d26e7f4 Mon Sep 17 00:00:00 2001 From: Lars Bilke <lars.bilke@ufz.de> Date: Mon, 11 Oct 2021 13:52:34 +0200 Subject: [PATCH] OpenGeoSys 6.4.1 --- Documentation/mainpage.dox.in | 1 + README.md | 2 +- scripts/doc/_redirects | 2 + web/content/releases/6.4.1.md | 205 ++++++++++++++++++++++++++++++++++ 4 files changed, 209 insertions(+), 1 deletion(-) create mode 100644 web/content/releases/6.4.1.md diff --git a/Documentation/mainpage.dox.in b/Documentation/mainpage.dox.in index ef21f10b414..688842a9360 100644 --- a/Documentation/mainpage.dox.in +++ b/Documentation/mainpage.dox.in @@ -21,6 +21,7 @@ * * The documentation for OGS releases can be found here: * + * - https://doxygen.opengeosys.org/v6.4.1 * - https://doxygen.opengeosys.org/v6.4.0 * - https://doxygen.opengeosys.org/v6.3.3 * diff --git a/README.md b/README.md index b9ff0e34cc3..8dcf30d0aaa 100644 --- a/README.md +++ b/README.md @@ -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/v6.4.0 +[docs-release]: https://doxygen.opengeosys.org/v6.4.1 [license-source]: https://github.com/ufz/ogs/blob/master/LICENSE.txt diff --git a/scripts/doc/_redirects b/scripts/doc/_redirects index 04441deb8dd..7f5e57230fc 100644 --- a/scripts/doc/_redirects +++ b/scripts/doc/_redirects @@ -2,3 +2,5 @@ /v6.3.3/* https://ogs-doxygen-v6-3-3.netlify.app/:splat 200! /v6.4.0 https://doxygen.opengeosys.org/v6.4.0/index.html 301 /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! diff --git a/web/content/releases/6.4.1.md b/web/content/releases/6.4.1.md new file mode 100644 index 00000000000..7962831e098 --- /dev/null +++ b/web/content/releases/6.4.1.md @@ -0,0 +1,205 @@ ++++ +date = "2021-10-11T13:30:13+01:00" +title = "OpenGeoSys 6.4.1" +tag = "6.4.1" +author = "Lars Bilke" +release_date = "2021-10-11" + +[downloads] +binary = [ + "Windows-10.0.14393-python-3.7.2-de-utils.zip", + "Windows-10.0.14393-python-3.7.2-utils.zip", + "Windows-10.0.14393-de-utils.zip", + "Windows-10.0.14393-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 3.7.2](https://www.python.org/ftp/python/3.7.2/python-3.7.2-amd64-webinstall.exe) +""" ++++ + +## Overview + + This release features the implementation of the Thermo-Hydro-Hydro-Mechanical (`TH2M`) fully coupled process. The process is intended for modeling two-component two-phase flow in deformable porous media under non-isothermal conditions. Testing is in progress and development continues, so handle with care or wait a little longer until it got more refined. + +Another new process, the StokesFlow process, is mainly used for simulating the low-Reynolds-number [incompressible flow in fractures](https://www.opengeosys.org/docs/benchmarks/stokes-flow/parallel-plate-flow/). The Stokes equations are solved using the standard Taylor-Hood scheme. Additionally including the Darcy term in the momentum balance equations, the `StokesFlow` process module is capable of modeling the fluid flow in fractured porous media. + +The local assembly on inclined elements, which can be used to simulate the fluid low in fracture, are implemented. As a first application, [LiquidFlow](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3632) is enabled to use such local assembly. + +Also work continued on new material models, e.g. the Günther Salzer model for transient and stationary rock salt creep, an improved HDF5-based output file handling which allows for [parallel postprocessing](https://gitlab.opengeosys.org/ogs/ogs/-/wikis/Working-with-HDF-data-(examples-h5py)) as well as the introduction of a first iteration of a [Jupyter Notebook based user workflow](https://www.opengeosys.org/docs/userguide/basics/jupyter-notebooks/). Stay tuned for more on interactive computing in future releases. + +## New processes + +### TH2M + +A thermal two-phase flow in deformable solid media process. + +* [!3588](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3588) Added an infrastructure for the TH2M Process that handles different models of phase transitions. +* [!3550](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3550) Monolithic scheme implementation using central differences Jacobian. +* [!3656](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3656) Collect all constitutive variables updates in single function. +* [!3684](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3684) HM flow-fully-saturated tests; liquid and gas formulations. +* [!3759](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3759) Restart; integration point data I/O. +* [!3763](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3763) Extract constitutive variables. +* [!3762](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3762) Excavation. Enable domain deactivation. +* [!3777](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3777) Switch to constant solid volume fraction +* [!3767](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3767) Implement partial analytical Jacobian, working for saturated media. +* [!3802](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3802) Gas and liquid phase density output directly from ip_data array. + +### Stokes flow + +* [!3617](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3617) Monolithic scheme implementation. +* [!3658](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3658) Documentation +* [!3668](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3668) Extended to Stokes-Brinkman variant. + +## Process' changes + +* [!3583](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3583) THM and TRM process need a thermal conductivity property on the medium level +* [!3561](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3561) Excavation support for coupled mechanics processes and Dirichlet boundary conditions on the excavated surfaces were added. +* [!3580](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3580) \[THM\] Replaced total thermal strain with incremental thermal strain +* [!3742](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3742) \[THM\] Adding integration point output for stress and strain and a restart test. +[!3706](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3706) Separate createLocalAssemblers respectively for BC/Source term and system of equations. + +### PhaseField + +* [!3749](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3749) added constrained minimisation to the phase-field solution scheme. +* [!3779](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3779) added AT1 regularisation of the total energy (see (<https://link.springer.com/content/pdf/10.1007/s13137-019-0126-6.pdf>) for details). + +### ThermoRichardsFlow + +* [!3419](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3419) added ThermoRichardsFlow process with optional corrections for solid elasticity under simplified assumptions (see [Improved predictions of thermal fluid pressurization in hydro-thermal models based on consistent incorporation of thermo-mechanical effects in anisotropic porous media](https://www.sciencedirect.com/science/article/abs/pii/S0017931021002301) for details) + +### Component transport process / reactive transport process with coupling of Phreeqc + +* [!3695](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3695) Enabled to input the amount of ion exchangers in subdomains via the MaterialPropertyLib +* [!3648](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3648) Added capability to model ion exchange reactions. +* [!3563](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3563) Added optional functionality for chemically induced porosity change. +* [!3567](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3567) Added optional functionality for irreversible equilibrium reactions to the ChemistryLib. +* [!3721](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3721) Provided a simple means of considering temperature effect on the diffusive transport process. +* [!3744](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3744) Allowed chemical calculations by means of the look-up table approach. +* [!3781](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3781) Solved the reaction equation in the reaction stage instead of doing extrapolation from integration points onto mesh nodes. +* [!3810](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3810) Incorporate the effect of change of storage capacity. + +### HeatTransportBHE + +* [!3793](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3793) Add server communication feature after each time step + +### HydroMechanics + +* [!3607](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3607) Simulation on a vertical slice of a 3D domain. + +### LIE + +* [!3672](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3672) Use the existing class to compute the rotation matrix in LIE, which also corrects the orientation of the displacement jump. +* [!3676](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3676) Corrected the velocity and its orientation in the fracture. +* [!3834](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3834) Corrected matrix sizes in velocity computation. + +### LiquidFlow process + +* [!3610](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3610) Use specific body force instead of darcy_gravity. Users LiquidFlow project files has to be adapted! +* [!3623](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3623) Use body force vector in the local assembler. +* [!3632](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3632) Add local assembly in inclined elements for simulating flow in fracture. + +### Richard's component transport process + +* [!3606](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3606) [!3614](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3614) Employ MPL in Richard's component transport process. + +### Richard's mechanics process + +* [!3574](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3574) Extend integration point data output to solid material state internal variables used by _e.g._ MFront. This makes correct restart possible. +* [!3690](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3690) Local Newton-Raphson: add optional scaling for convergence tests, which is used in the computation of micro-porosity. + +### SmallDeformation + +* [!3683](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3683) Use the element wise reference temperature. + +### ThermoMechanics + +* [3738](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3738) Fixed integration point (IP) data IO for restart computation. + + +### ThermoRichardsMechanics and ThermoHydroMechanics + +* [!3583](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3583) THM and TRM process need a thermal conductivity property on the medium level +* [!3758](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3758) THM/TRM; Add heat flux output. Corrected HydraulicFlow. +* [!3611](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3611) TRM; Include the thermal strain into total mechanical strain. +* [!3714](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3714) Replaced the hard coded solid density model in THM with the MPL property. With changes, the input parameter of `reference_temperature` is removed. +* [!3718](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3718) +Enabled integration point data I/O in THM + +## Material models + +* [!3572](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3572) IdealGasLaw now uses molar mass from VariableArray rather than from another MPL-Property. +* [!3579](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3579) New saturation-capillary pressure relation, SaturationExponential, mainly for testing and prototyping purposes. +* [!3546](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3546) Implementing medium level property to mix thermal conductivities from phases. +* [!3599](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3599) Added orthotropic embedded fracture permeability model +* [!3640](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3640) A Function type MPL property using exprtk, similar to the Function type parameter. All scalar variables from VariableArray can be used. +* [!3721](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3721) Added temperature dependent model for molecular diffusion. +* [!3745](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3745) New stationary creep model for rock salt. +* [!3747](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3747) The damage-free version of the Günther Salzer model for transient and stationary rock salt creep. + +## Numerics + +* [!3676](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3676) Dropped the rotation of the shape function gradients. These changes also correct the velocity and its orientation in the fracture. + +## Data Explorer + +* [!3578](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3578) Elevation of station data can be mapped based on meshes or rasters + +## Testing + +* [!3586](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3586) Modular project files by patching a base project file with multiple patch files with syntax for adding, removing and modifying parts of the base. The selection is done via XPath expressions. +* [!3664](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3664) First implementation of a code coverage visualization. + +## Bug fixes + +* [!3615](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3615) Bug fixing in EffectiveThermalConductivityPorosityMixing: Avoided the porosity calculation +* [!3566](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3566) Fixed a bug in NodalSourceTerm when the Taylor-Hood elements are used. +* [!3682](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3682) Fixed the output of phase compositions in TH2M process +* [!3585](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3585) Use correct saturatation for swelling stress update in output of the RichardsMechanics process. +* [!3652](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3652) Fixed a MFront related bug in HydroMechanics. +* [!3756](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3756) Speedup Dirichlet BCs for deactivated subdomains avoiding costly reallocations. +* [!3788](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3788) Use local topology information while removing global numbering dependencies in Mesh. Resolves base node id larger then higher order node id warning. +* [!3797](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3797) Refactored material ID list parser, prevents some (unlikely) bugs with malformed prj files. +* [!3816](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3816) Fix Brooks-Corey saturation derivative. +* [!3834](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3834) Fixed an Eigen matrix size related bug in LIE, which sporadically causes LIE benchmark failed on Mac OS. + +## CMake + +* [!3592](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3592) Added build and test presets. +* [!3624](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3624) Job pools for Ninja: optimizes build parallelization (full cores for everything but processes, processes depend on available memory) +* [!3671](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3671) Integrate tfel with `ExternalProject_Add()` instead of Conan. +* [!3687](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3687) Qt is not handled by Conan anymore! Use [aqt](https://github.com/miurahr/aqtinstall) to install it on your system. +* [!3698](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3698) Moved LIS dependency from Conan to ExternalProject. +* [!3727](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3727) Added support for ccache on Windows, dropped clcache. +* [!3707](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3707) CMake test presets, requires CMake 3.21. + +## Infrastructure + +* [!3555](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3555) and [!3835](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3835) Clang-format all of the code base. Thriving for consistency. +* [!3562](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3562) Added threshold for Doxygen warnings (16). +* [!3570](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3570) Enabled compiler warnings for executables. +* [!3622](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3622) Correct naming of private data members using trailing underscore. +* [!3671](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3671) Enabled mfront on CI mac job. +* [!3712](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3712) Added library dependency reports to Doxygen documentation. Added Lizard code complexity report to Doxygen CI job as a build artifact. +* [!3720](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3720) Added clang-format check in pre-commit. +* [!3751](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3751) OGS binaries are now in the `PATH` in the container environment. Execution via `--app ogs` is not required anymore. +* [!3755](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3755), [!3757](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3757) Initial Apple ARM (M1) support. +* [!3761](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3761) CI now runs with [Pipelines for merged results](https://docs.gitlab.com/ee/ci/pipelines/pipelines_for_merged_results.html). Also switched to `git clang-format` instead of `clang-format`. +* [!3776](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3776) Added predefined container with Jupyter Notebook, ogs and Python tools. + +## File I/O + +* [!3598](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3598) Time is additional dimension HDF5 output data - allows slicing with h5py +* [!3604](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3604) HDF5 can now contain multiple meshes (boundary conditions) and an attribute "times" with time step values for each step +* [!3764](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3764) HDF5 can now be written to multiple files. The number of files can be adapted to allow different I/O-patterns (1-file-per-process, single-file, 1-file-per-node). + +## Version info + +* [!3647](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3647) MFront based on [TFEL branch rliv-3.4](https://github.com/thelfer/tfel/tree/rliv-3.4) +* [!3757](https://gitlab.opengeosys.org/ogs/ogs/-/merge_requests/3757) Conan 1.34.0 (optional) +* [!3707] [CMake presets](https://www.opengeosys.org/docs/devguide/getting-started/build-configuration/#available-cmake-presets) require CMake 3.21. -- GitLab