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ufz/ogs: 6.4.1

Dmitry Yu. Naumov

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    <subfield code="u">Helmholtz Centre for Environmental Research -- UFZ</subfield>
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    <subfield code="a">ufz/ogs: 6.4.1</subfield>
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    <subfield code="a">Other (Open)</subfield>
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    <subfield code="a">&lt;p&gt;See for binary downloads.&lt;/p&gt;
&lt;p&gt;This release features the implementation of the Thermo-Hydro-Hydro-Mechanical (&lt;code&gt;TH2M&lt;/code&gt;) 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.&lt;/p&gt;
&lt;p&gt;Another new process, the StokesFlow process, is mainly used for simulating the low-Reynolds-number &lt;a href=""&gt;incompressible flow in fractures&lt;/a&gt;. The Stokes equations are solved using the standard Taylor-Hood scheme. Additionally including the Darcy term in the momentum balance equations, the &lt;code&gt;StokesFlow&lt;/code&gt; process module is capable of modeling the fluid flow in fractured porous media.&lt;/p&gt;
&lt;p&gt;The local assembly on inclined elements, which can be used to simulate the fluid low in fracture, are implemented. As a first application, &lt;a href=""&gt;LiquidFlow&lt;/a&gt; is enabled to use  such local assembly.&lt;/p&gt;
&lt;p&gt;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 &lt;a href=""&gt;parallel postprocessing&lt;/a&gt;) as well as the introduction of a first iteration of a &lt;a href=""&gt;Jupyter Notebook based user workflow&lt;/a&gt;. Stay tuned for more on interactive computing in future releases.&lt;/p&gt;
New processes
&lt;p&gt;A thermal two-phase flow in deformable solid media process.&lt;/p&gt;
&lt;li&gt;&lt;a href=""&gt;!3588&lt;/a&gt; Added an infrastructure for the TH2M Process that handles different models of phase transitions.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3550&lt;/a&gt; Monolithic scheme implementation using central differences Jacobian.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3656&lt;/a&gt; Collect all constitutive variables updates in single function.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3684&lt;/a&gt; HM flow-fully-saturated tests; liquid and gas formulations.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3759&lt;/a&gt; Restart; integration point data I/O.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3763&lt;/a&gt; Extract constitutive variables.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3762&lt;/a&gt; Excavation. Enable domain deactivation.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3777&lt;/a&gt; Switch to constant solid volume fraction&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3767&lt;/a&gt; Implement partial analytical Jacobian, working for saturated media.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3802&lt;/a&gt; Gas and liquid phase density output directly from ip_data array.&lt;/li&gt;
Stokes flow
&lt;li&gt;&lt;a href=""&gt;!3617&lt;/a&gt; Monolithic scheme implementation.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3658&lt;/a&gt; Documentation&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3668&lt;/a&gt; Extended to Stokes-Brinkman variant.&lt;/li&gt;
Process' changes
&lt;li&gt;&lt;a href=""&gt;!3583&lt;/a&gt; THM and TRM process need a thermal conductivity property on the medium level&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3561&lt;/a&gt; Excavation support for coupled mechanics processes and Dirichlet boundary conditions on the excavated surfaces were added.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3580&lt;/a&gt; [THM] Replaced total thermal strain with incremental thermal strain&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3742&lt;/a&gt; [THM] Adding integration point output for stress and strain and a restart test.
&lt;a href=""&gt;!3706&lt;/a&gt; Separate createLocalAssemblers respectively for BC/Source term and system of equations.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3749&lt;/a&gt; added constrained minimisation to the phase-field solution scheme.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3779&lt;/a&gt; added AT1 regularisation of the total energy (see (&lt;a href=""&gt;;/a&gt;) for details).&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3419&lt;/a&gt; added ThermoRichardsFlow process with optional corrections for solid elasticity under simplified assumptions (see &lt;a href=""&gt;Improved predictions of thermal fluid pressurization in hydro-thermal models based on consistent incorporation of thermo-mechanical effects in anisotropic porous media&lt;/a&gt; for details)&lt;/li&gt;
Component transport process / reactive transport process with coupling of Phreeqc
&lt;li&gt;&lt;a href=""&gt;!3695&lt;/a&gt; Enabled to input the amount of ion exchangers in subdomains via the MaterialPropertyLib&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3648&lt;/a&gt; Added capability to model ion exchange reactions.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3563&lt;/a&gt; Added optional functionality for chemically induced porosity change.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3567&lt;/a&gt; Added optional functionality for irreversible equilibrium reactions to the ChemistryLib.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3721&lt;/a&gt; Provided a simple means of considering temperature effect on the diffusive transport process.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3744&lt;/a&gt; Allowed chemical calculations by means of the look-up table approach.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3781&lt;/a&gt; Solved the reaction equation in the reaction stage instead of doing extrapolation from integration points onto mesh nodes.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3810&lt;/a&gt; Incorporate the effect of change of storage capacity.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3793&lt;/a&gt; Add server communication feature after each time step&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3607&lt;/a&gt; Simulation on a vertical slice of a 3D domain.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3672&lt;/a&gt; Use the existing class to compute the rotation matrix in LIE, which also corrects the orientation of the displacement jump.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3676&lt;/a&gt; Corrected the velocity and its orientation in the fracture.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3834&lt;/a&gt; Corrected matrix sizes in velocity computation.&lt;/li&gt;
LiquidFlow process
&lt;li&gt;&lt;a href=""&gt;!3610&lt;/a&gt; Use specific body force instead of darcy_gravity. Users LiquidFlow project files has to be adapted!&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3623&lt;/a&gt; Use body force vector in the local assembler.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3632&lt;/a&gt; Add local assembly in inclined elements for simulating flow in fracture.&lt;/li&gt;
Richard's component transport process
&lt;li&gt;&lt;a href=""&gt;!3606&lt;/a&gt; &lt;a href=""&gt;!3614&lt;/a&gt; Employ MPL in Richard's component transport process.&lt;/li&gt;
Richard's mechanics process
&lt;li&gt;&lt;a href=""&gt;!3574&lt;/a&gt; Extend integration point data output to solid material state internal variables used by &lt;em&gt;e.g.&lt;/em&gt; MFront. This makes correct restart possible.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3690&lt;/a&gt; Local Newton-Raphson: add optional scaling for convergence tests, which is used in the computation of micro-porosity.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3683&lt;/a&gt; Use the element wise reference temperature.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;3738&lt;/a&gt; Fixed integration point (IP) data IO for restart computation.&lt;/li&gt;
ThermoRichardsMechanics and ThermoHydroMechanics
&lt;li&gt;&lt;a href=""&gt;!3583&lt;/a&gt; THM and TRM process need a thermal conductivity property on the medium level&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3758&lt;/a&gt; THM/TRM; Add heat flux output. Corrected HydraulicFlow.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3611&lt;/a&gt; TRM; Include the thermal strain into total mechanical strain.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3714&lt;/a&gt; Replaced the hard coded solid density model in THM with the MPL property. With changes, the input parameter of &lt;code&gt;reference_temperature&lt;/code&gt; is removed.&lt;/li&gt;
&lt;li&gt;&lt;p&gt;&lt;a href=""&gt;!3718&lt;/a&gt; 
Enabled integration point data I/O in THM
# Material models&lt;/p&gt;
&lt;li&gt;&lt;p&gt;&lt;a href=""&gt;!3572&lt;/a&gt; IdealGasLaw now uses molar mass from VariableArray rather than from another MPL-Property.&lt;/p&gt;
&lt;li&gt;&lt;a href=""&gt;!3579&lt;/a&gt; New saturation-capillary pressure relation, SaturationExponential, mainly for testing and prototyping purposes.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3546&lt;/a&gt; Implementing medium level property to mix thermal conductivities from phases.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3599&lt;/a&gt; Added orthotropic embedded fracture permeability model&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3640&lt;/a&gt; A Function type MPL property using exprtk, similar to the Function type parameter. All scalar variables from VariableArray can be used.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3721&lt;/a&gt; Added temperature dependent model for molecular diffusion.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3745&lt;/a&gt; New stationary creep model for rock salt.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3747&lt;/a&gt; The damage-free version of the Günther Salzer model for transient and stationary rock salt creep.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3676&lt;/a&gt; Dropped the rotation of the shape function gradients. These changes also correct the velocity and its orientation in the fracture.&lt;/li&gt;
Data Explorer
&lt;li&gt;&lt;a href=""&gt;!3578&lt;/a&gt; Elevation of station data can be mapped based on meshes or rasters&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3586&lt;/a&gt; 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.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3664&lt;/a&gt; First implementation of a code coverage visualization.&lt;/li&gt;
Bug fixes
&lt;li&gt;&lt;a href=""&gt;!3615&lt;/a&gt; Bug fixing in EffectiveThermalConductivityPorosityMixing: Avoided the porosity calculation&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3566&lt;/a&gt; Fixed a bug in NodalSourceTerm when the Taylor-Hood elements are used.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3682&lt;/a&gt; Fixed the output of phase compositions in TH2M process&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3585&lt;/a&gt; Use correct saturatation for swelling stress update in output of the RichardsMechanics process.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3652&lt;/a&gt; Fixed a MFront related bug in HydroMechanics.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3756&lt;/a&gt; Speedup Dirichlet BCs for deactivated subdomains avoiding costly reallocations.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3788&lt;/a&gt; Use local topology information while removing global numbering dependencies in Mesh. Resolves base node id larger then higher order node id warning.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3797&lt;/a&gt; Refactored material ID list parser, prevents some (unlikely) bugs with malformed prj files.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3816&lt;/a&gt; Fix Brooks-Corey saturation derivative.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3834&lt;/a&gt; Fixed an Eigen matrix  size related bug in LIE, which sporadically causes LIE benchmark failed on Mac OS.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3592&lt;/a&gt; Added build and test presets.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3624&lt;/a&gt; Job pools for Ninja: optimizes build parallelization (full cores for everything but processes, processes depend on available memory)&lt;/li&gt;
&lt;li&gt;&lt;a href="/ogs/ogs/-/merge_requests/3671"&gt;!3671&lt;/a&gt; Integrate tfel with &lt;code&gt;ExternalProject_Add()&lt;/code&gt; instead of Conan.&lt;/li&gt;
&lt;li&gt;&lt;a href="/ogs/ogs/-/merge_requests/3687"&gt;!3687&lt;/a&gt; Qt is not handled by Conan anymore! Use &lt;a href=""&gt;aqt&lt;/a&gt; to install it on your system.&lt;/li&gt;
&lt;li&gt;&lt;a href="/ogs/ogs/-/merge_requests/3698"&gt;!3698&lt;/a&gt; Moved LIS dependency from Conan to ExternalProject.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3727&lt;/a&gt; Added support for ccache on Windows, dropped clcache.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3707&lt;/a&gt; CMake test presets, requires CMake 3.21.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3555&lt;/a&gt; and &lt;a href=""&gt;!3835&lt;/a&gt; Clang-format all of the code base. Thriving for consistency.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3562&lt;/a&gt; Added threshold for Doxygen warnings (16).&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3570&lt;/a&gt; Enabled compiler warnings for executables.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3622&lt;/a&gt; Correct naming of private data members using trailing underscore.&lt;/li&gt;
&lt;li&gt;&lt;a href="/ogs/ogs/-/merge_requests/3671"&gt;!3671&lt;/a&gt; Enabled mfront on CI mac job.&lt;/li&gt;
&lt;li&gt;&lt;a href="/ogs/ogs/-/merge_requests/3712"&gt;!3712&lt;/a&gt; Added library dependency reports to Doxygen documentation. Added Lizard code complexity report to Doxygen CI job as a build artifact.&lt;/li&gt;
&lt;li&gt;&lt;a href="/ogs/ogs/-/merge_requests/3720"&gt;!3720&lt;/a&gt; Added clang-format check in pre-commit.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3751&lt;/a&gt; OGS binaries are now in the &lt;code&gt;PATH&lt;/code&gt; in the container environment. Execution via &lt;code&gt;--app ogs&lt;/code&gt; is not required anymore.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3755&lt;/a&gt;, &lt;a href=""&gt;!3757&lt;/a&gt; Initial Apple ARM (M1) support.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3761&lt;/a&gt; CI now runs with &lt;a href=""&gt;Pipelines for merged results&lt;/a&gt;. Also switched to &lt;code&gt;git clang-format&lt;/code&gt; instead of &lt;code&gt;clang-format&lt;/code&gt;.&lt;/li&gt;
&lt;li&gt;&lt;a href=""&gt;!3776&lt;/a&gt; Added predefined container with Jupyter Notebook, ogs and Python tools.&lt;/li&gt;
File I/O
&lt;li&gt;&lt;a href="/ogs/ogs/-/merge_requests/3598"&gt;!3598&lt;/a&gt; Time is additional dimension HDF5 output data - allows slicing with h5py&lt;/li&gt;
&lt;li&gt;&lt;a href="/ogs/ogs/-/merge_requests/3604"&gt;!3604&lt;/a&gt; HDF5 can now contain multiple meshes (boundary conditions) and an attribute "times" with time step values for each step&lt;/li&gt;
&lt;li&gt;&lt;a href="/ogs/ogs/-/merge_requests/3764"&gt;!3764&lt;/a&gt; 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).&lt;/li&gt;
Version info
&lt;li&gt;&lt;a href="/ogs/ogs/-/merge_requests/3647"&gt;!3647&lt;/a&gt; MFront based on &lt;a href=""&gt;TFEL branch rliv-3.4&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;&lt;a href="/ogs/ogs/-/merge_requests/3757"&gt;!3757&lt;/a&gt; Conan 1.34.0 (optional)&lt;/li&gt;
&lt;li&gt;[!3707] &lt;a href=""&gt;CMake presets&lt;/a&gt; require CMake 3.21.&lt;/li&gt;
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