Software Open Access

ufz/ogs: 6.4.1

Dmitry Yu. Naumov

JSON Export

  "files": [
      "links": {
        "self": ""
      "checksum": "md5:4502ea90769ce125c3714c2dc6c1e3ca", 
      "bucket": "62743101-8cda-4ac5-a0e2-3dc6efa57f74", 
      "key": "ufz/", 
      "type": "zip", 
      "size": 447015556
  "owners": [
  "doi": "10.5281/zenodo.5562297", 
  "stats": {
    "version_unique_downloads": 101.0, 
    "unique_views": 38.0, 
    "views": 52.0, 
    "version_views": 933.0, 
    "unique_downloads": 4.0, 
    "version_unique_views": 787.0, 
    "volume": 1788062224.0, 
    "version_downloads": 294.0, 
    "downloads": 4.0, 
    "version_volume": 75706445749.0
  "links": {
    "doi": "", 
    "conceptdoi": "", 
    "bucket": "", 
    "conceptbadge": "", 
    "html": "", 
    "latest_html": "", 
    "badge": "", 
    "latest": ""
  "conceptdoi": "10.5281/zenodo.591265", 
  "created": "2021-10-11T13:44:14.574673+00:00", 
  "updated": "2021-10-11T13:48:35.373280+00:00", 
  "conceptrecid": "591265", 
  "revision": 3, 
  "id": 5562297, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.5562297", 
    "description": "<p>See for binary downloads.</p>\nOverview\n<p>This release features the implementation of the Thermo-Hydro-Hydro-Mechanical (<code>TH2M</code>) 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.</p>\n<p>Another new process, the StokesFlow process, is mainly used for simulating the low-Reynolds-number <a href=\"\">incompressible flow in fractures</a>. The Stokes equations are solved using the standard Taylor-Hood scheme. Additionally including the Darcy term in the momentum balance equations, the <code>StokesFlow</code> process module is capable of modeling the fluid flow in fractured porous media.</p>\n<p>The local assembly on inclined elements, which can be used to simulate the fluid low in fracture, are implemented. As a first application, <a href=\"\">LiquidFlow</a> is enabled to use  such local assembly.</p>\n<p>Also work continued on new material models, e.g. the G\u00fcnther Salzer model for transient and stationary rock salt creep, an improved HDF5-based output file handling which allows for <a href=\"\">parallel postprocessing</a>) as well as the introduction of a first iteration of a <a href=\"\">Jupyter Notebook based user workflow</a>. Stay tuned for more on interactive computing in future releases.</p>\nNew processes\nTH2M\n<p>A thermal two-phase flow in deformable solid media process.</p>\n<ul>\n<li><a href=\"\">!3588</a> Added an infrastructure for the TH2M Process that handles different models of phase transitions.</li>\n<li><a href=\"\">!3550</a> Monolithic scheme implementation using central differences Jacobian.</li>\n<li><a href=\"\">!3656</a> Collect all constitutive variables updates in single function.</li>\n<li><a href=\"\">!3684</a> HM flow-fully-saturated tests; liquid and gas formulations.</li>\n<li><a href=\"\">!3759</a> Restart; integration point data I/O.</li>\n<li><a href=\"\">!3763</a> Extract constitutive variables.</li>\n<li><a href=\"\">!3762</a> Excavation. Enable domain deactivation.</li>\n<li><a href=\"\">!3777</a> Switch to constant solid volume fraction</li>\n<li><a href=\"\">!3767</a> Implement partial analytical Jacobian, working for saturated media.</li>\n<li><a href=\"\">!3802</a> Gas and liquid phase density output directly from ip_data array.</li>\n</ul>\nStokes flow\n<ul>\n<li><a href=\"\">!3617</a> Monolithic scheme implementation.</li>\n<li><a href=\"\">!3658</a> Documentation</li>\n<li><a href=\"\">!3668</a> Extended to Stokes-Brinkman variant.</li>\n</ul>\nProcess' changes\n<ul>\n<li><a href=\"\">!3583</a> THM and TRM process need a thermal conductivity property on the medium level</li>\n<li><a href=\"\">!3561</a> Excavation support for coupled mechanics processes and Dirichlet boundary conditions on the excavated surfaces were added.</li>\n<li><a href=\"\">!3580</a> [THM] Replaced total thermal strain with incremental thermal strain</li>\n<li><a href=\"\">!3742</a> [THM] Adding integration point output for stress and strain and a restart test.\n<a href=\"\">!3706</a> Separate createLocalAssemblers respectively for BC/Source term and system of equations.</li>\n</ul>\nPhaseField\n<ul>\n<li><a href=\"\">!3749</a> added constrained minimisation to the phase-field solution scheme.</li>\n<li><a href=\"\">!3779</a> added AT1 regularisation of the total energy (see (<a href=\"\"></a>) for details).</li>\n</ul>\nThermoRichardsFlow\n<ul>\n<li><a href=\"\">!3419</a> added ThermoRichardsFlow process with optional corrections for solid elasticity under simplified assumptions (see <a href=\"\">Improved predictions of thermal fluid pressurization in hydro-thermal models based on consistent incorporation of thermo-mechanical effects in anisotropic porous media</a> for details)</li>\n</ul>\nComponent transport process / reactive transport process with coupling of Phreeqc\n<ul>\n<li><a href=\"\">!3695</a> Enabled to input the amount of ion exchangers in subdomains via the MaterialPropertyLib</li>\n<li><a href=\"\">!3648</a> Added capability to model ion exchange reactions.</li>\n<li><a href=\"\">!3563</a> Added optional functionality for chemically induced porosity change.</li>\n<li><a href=\"\">!3567</a> Added optional functionality for irreversible equilibrium reactions to the ChemistryLib.</li>\n<li><a href=\"\">!3721</a> Provided a simple means of considering temperature effect on the diffusive transport process.</li>\n<li><a href=\"\">!3744</a> Allowed chemical calculations by means of the look-up table approach.</li>\n<li><a href=\"\">!3781</a> Solved the reaction equation in the reaction stage instead of doing extrapolation from integration points onto mesh nodes.</li>\n<li><a href=\"\">!3810</a> Incorporate the effect of change of storage capacity.</li>\n</ul>\nHeatTransportBHE\n<ul>\n<li><a href=\"\">!3793</a> Add server communication feature after each time step</li>\n</ul>\nHydroMechanics\n<ul>\n<li><a href=\"\">!3607</a> Simulation on a vertical slice of a 3D domain.</li>\n</ul>\nLIE\n<ul>\n<li><a href=\"\">!3672</a> Use the existing class to compute the rotation matrix in LIE, which also corrects the orientation of the displacement jump.</li>\n<li><a href=\"\">!3676</a> Corrected the velocity and its orientation in the fracture.</li>\n<li><a href=\"\">!3834</a> Corrected matrix sizes in velocity computation.</li>\n</ul>\nLiquidFlow process\n<ul>\n<li><a href=\"\">!3610</a> Use specific body force instead of darcy_gravity. Users LiquidFlow project files has to be adapted!</li>\n<li><a href=\"\">!3623</a> Use body force vector in the local assembler.</li>\n<li><a href=\"\">!3632</a> Add local assembly in inclined elements for simulating flow in fracture.</li>\n</ul>\nRichard's component transport process\n<ul>\n<li><a href=\"\">!3606</a> <a href=\"\">!3614</a> Employ MPL in Richard's component transport process.</li>\n</ul>\nRichard's mechanics process\n<ul>\n<li><a href=\"\">!3574</a> Extend integration point data output to solid material state internal variables used by <em>e.g.</em> MFront. This makes correct restart possible.</li>\n<li><a href=\"\">!3690</a> Local Newton-Raphson: add optional scaling for convergence tests, which is used in the computation of micro-porosity.</li>\n</ul>\nSmallDeformation\n<ul>\n<li><a href=\"\">!3683</a> Use the element wise reference temperature.</li>\n</ul>\nThermoMechanics\n<ul>\n<li><a href=\"\">3738</a> Fixed integration point (IP) data IO for restart computation.</li>\n</ul>\nThermoRichardsMechanics and ThermoHydroMechanics\n<ul>\n<li><a href=\"\">!3583</a> THM and TRM process need a thermal conductivity property on the medium level</li>\n<li><a href=\"\">!3758</a> THM/TRM; Add heat flux output. Corrected HydraulicFlow.</li>\n<li><a href=\"\">!3611</a> TRM; Include the thermal strain into total mechanical strain.</li>\n<li><a href=\"\">!3714</a> Replaced the hard coded solid density model in THM with the MPL property. With changes, the input parameter of <code>reference_temperature</code> is removed.</li>\n<li><p><a href=\"\">!3718</a> \nEnabled integration point data I/O in THM\n# Material models</p>\n</li>\n<li><p><a href=\"\">!3572</a> IdealGasLaw now uses molar mass from VariableArray rather than from another MPL-Property.</p>\n</li>\n<li><a href=\"\">!3579</a> New saturation-capillary pressure relation, SaturationExponential, mainly for testing and prototyping purposes.</li>\n<li><a href=\"\">!3546</a> Implementing medium level property to mix thermal conductivities from phases.</li>\n<li><a href=\"\">!3599</a> Added orthotropic embedded fracture permeability model</li>\n<li><a href=\"\">!3640</a> A Function type MPL property using exprtk, similar to the Function type parameter. All scalar variables from VariableArray can be used.</li>\n<li><a href=\"\">!3721</a> Added temperature dependent model for molecular diffusion.</li>\n<li><a href=\"\">!3745</a> New stationary creep model for rock salt.</li>\n<li><a href=\"\">!3747</a> The damage-free version of the G\u00fcnther Salzer model for transient and stationary rock salt creep.</li>\n</ul>\nNumerics\n<ul>\n<li><a href=\"\">!3676</a> Dropped the rotation of the shape function gradients. These changes also correct the velocity and its orientation in the fracture.</li>\n</ul>\nData Explorer\n<ul>\n<li><a href=\"\">!3578</a> Elevation of station data can be mapped based on meshes or rasters</li>\n</ul>\nTesting\n<ul>\n<li><a href=\"\">!3586</a> 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.</li>\n<li><a href=\"\">!3664</a> First implementation of a code coverage visualization.</li>\n</ul>\nBug fixes\n<ul>\n<li><a href=\"\">!3615</a> Bug fixing in EffectiveThermalConductivityPorosityMixing: Avoided the porosity calculation</li>\n<li><a href=\"\">!3566</a> Fixed a bug in NodalSourceTerm when the Taylor-Hood elements are used.</li>\n<li><a href=\"\">!3682</a> Fixed the output of phase compositions in TH2M process</li>\n<li><a href=\"\">!3585</a> Use correct saturatation for swelling stress update in output of the RichardsMechanics process.</li>\n<li><a href=\"\">!3652</a> Fixed a MFront related bug in HydroMechanics.</li>\n<li><a href=\"\">!3756</a> Speedup Dirichlet BCs for deactivated subdomains avoiding costly reallocations.</li>\n<li><a href=\"\">!3788</a> Use local topology information while removing global numbering dependencies in Mesh. Resolves base node id larger then higher order node id warning.</li>\n<li><a href=\"\">!3797</a> Refactored material ID list parser, prevents some (unlikely) bugs with malformed prj files.</li>\n<li><a href=\"\">!3816</a> Fix Brooks-Corey saturation derivative.</li>\n<li><a href=\"\">!3834</a> Fixed an Eigen matrix  size related bug in LIE, which sporadically causes LIE benchmark failed on Mac OS.</li>\n</ul>\nCMake\n<ul>\n<li><a href=\"\">!3592</a> Added build and test presets.</li>\n<li><a href=\"\">!3624</a> Job pools for Ninja: optimizes build parallelization (full cores for everything but processes, processes depend on available memory)</li>\n<li><a href=\"/ogs/ogs/-/merge_requests/3671\">!3671</a> Integrate tfel with <code>ExternalProject_Add()</code> instead of Conan.</li>\n<li><a href=\"/ogs/ogs/-/merge_requests/3687\">!3687</a> Qt is not handled by Conan anymore! Use <a href=\"\">aqt</a> to install it on your system.</li>\n<li><a href=\"/ogs/ogs/-/merge_requests/3698\">!3698</a> Moved LIS dependency from Conan to ExternalProject.</li>\n<li><a href=\"\">!3727</a> Added support for ccache on Windows, dropped clcache.</li>\n<li><a href=\"\">!3707</a> CMake test presets, requires CMake 3.21.</li>\n</ul>\nInfrastructure\n<ul>\n<li><a href=\"\">!3555</a> and <a href=\"\">!3835</a> Clang-format all of the code base. Thriving for consistency.</li>\n<li><a href=\"\">!3562</a> Added threshold for Doxygen warnings (16).</li>\n<li><a href=\"\">!3570</a> Enabled compiler warnings for executables.</li>\n<li><a href=\"\">!3622</a> Correct naming of private data members using trailing underscore.</li>\n<li><a href=\"/ogs/ogs/-/merge_requests/3671\">!3671</a> Enabled mfront on CI mac job.</li>\n<li><a href=\"/ogs/ogs/-/merge_requests/3712\">!3712</a> Added library dependency reports to Doxygen documentation. Added Lizard code complexity report to Doxygen CI job as a build artifact.</li>\n<li><a href=\"/ogs/ogs/-/merge_requests/3720\">!3720</a> Added clang-format check in pre-commit.</li>\n<li><a href=\"\">!3751</a> OGS binaries are now in the <code>PATH</code> in the container environment. Execution via <code>--app ogs</code> is not required anymore.</li>\n<li><a href=\"\">!3755</a>, <a href=\"\">!3757</a> Initial Apple ARM (M1) support.</li>\n<li><a href=\"\">!3761</a> CI now runs with <a href=\"\">Pipelines for merged results</a>. Also switched to <code>git clang-format</code> instead of <code>clang-format</code>.</li>\n<li><a href=\"\">!3776</a> Added predefined container with Jupyter Notebook, ogs and Python tools.</li>\n</ul>\nFile I/O\n<ul>\n<li><a href=\"/ogs/ogs/-/merge_requests/3598\">!3598</a> Time is additional dimension HDF5 output data - allows slicing with h5py</li>\n<li><a href=\"/ogs/ogs/-/merge_requests/3604\">!3604</a> HDF5 can now contain multiple meshes (boundary conditions) and an attribute \"times\" with time step values for each step</li>\n<li><a href=\"/ogs/ogs/-/merge_requests/3764\">!3764</a> 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).</li>\n</ul>\nVersion info\n<ul>\n<li><a href=\"/ogs/ogs/-/merge_requests/3647\">!3647</a> MFront based on <a href=\"\">TFEL branch rliv-3.4</a></li>\n<li><a href=\"/ogs/ogs/-/merge_requests/3757\">!3757</a> Conan 1.34.0 (optional)</li>\n<li>[!3707] <a href=\"\">CMake presets</a> require CMake 3.21.</li>\n</ul>", 
    "license": {
      "id": "other-open"
    "title": "ufz/ogs: 6.4.1", 
    "relations": {
      "version": [
          "count": 21, 
          "index": 20, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "591265"
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "5562297"
    "version": "6.4.1", 
    "publication_date": "2021-10-11", 
    "creators": [
        "affiliation": "Helmholtz Centre for Environmental Research -- UFZ", 
        "name": "Dmitry Yu. Naumov"
    "access_right": "open", 
    "resource_type": {
      "type": "software", 
      "title": "Software"
    "related_identifiers": [
        "scheme": "url", 
        "identifier": "", 
        "relation": "isSupplementTo"
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.591265", 
        "relation": "isVersionOf"
All versions This version
Views 93352
Downloads 2944
Data volume 75.7 GB1.8 GB
Unique views 78738
Unique downloads 1014


Cite as