December 18, 2020 Software Open Access

ufz/ogs: 6.3.3

Dmitry Yu. Naumov; Lars Bilke; Tom Fischer; Karsten Rink; Norihiro Watanabe; wenqing; renchao.lu; Norbert Grunwald; FZill; Yonghui56; Chaofan Chen; jbathmann; joergbuchwald; ShuangChen88; HBShaoUFZ; xingyuanmiao; boyanmeng; KeitaYoshioka; Marc Walther; skai95; joboog; Tianyuan Zheng; ThieJan; ZhangNing; Dominik Kern; fparisio; ogsbot; Tobias Meisel; yezhigangzju

Overview

This release contains a lot of improvements in all processes and also new material properties. Mostly bug fixes and documentation and procedures improvements. Stay tuned for the next major release 6.4.0 featuring new processes implementations.

Features

• You can <include file="../path/to/file.xml"> other XML files into a .prj-file. !3081

Process' changes

• Reactive transport process:
  • allow to assign chemical formula alternative to a component when defining water composition. !3122
  • output equilibrium and kinetic reactants (immobile phase) in amount. !3138, !3141
• Heat Transport BHE process: allow to specify a flow and temperature control condition with the BHE inflow rate and temperature values both following the corresponding curves. !3125
• ThermoHydroMechanics:
  • The storage is now derived from the fluid density and the solid bulk modulus. !3159
  • Fix bug in temperature equation for non-zero velocity. !3193
• HydroMechanics: Allow linear shape functions for displacement. !3334
• Use MPL properties in HeatConduction process. !3062
• Fix bug in deactivation of subdomains !3065
• Exterior forces output in LiquidFlow and HeatConduction. !3068
• Allow thermal expansion to be anisotropic in ThermoHydroMechanics process. !3107
• Improve generic interface for updating medium property variables. !3262
• Improve generic interface for computing secondary variables. !3227
• Component transport process: output flow velocity averaged over integration points. !3254

Boundary condition and source terms

• Added a special Dirichlet boundary condition called "SolutionDependentDirichlet". The value assigned for the boundary condition is dependent on the process solution of last time step. !3085, !3123
• Cleanup of source term implementations (use volumetric source terms for line source terms). !3233

Numerics

• Changed the way to pass dot x for staggered scheme. !3082
• Add dotx to postNonLinearSolver. !3164
• The extrapolators now accept an empty integration point values vector, in which case these are ignored. For now relevant only for LIE/SD process. !3117
• LIE; Update Heaviside function to [-1/2,1/2] range. !3140

Parameter

• The "Function" type parameter becomes independent from a domain specification, i.e. it is not any longer possible and necessary to specify a domain via a mesh tag !3054
• Extend the "Function" type parameter to handle time in the expressions introducing the t variable, additionally to the currently available x, y, z. !3054
• Pass curves to the "Function" parameter, such that they can be used in expressions like curveA(sin(t)). !3058
• Increased the tolerance for |A|=1 test in coordinate system. !3203

Time stepping

• Fixed bugs in the fixed time output. !3026
• Removed the fixed output time data from time stepper classes. !3080
• Allow time stepping continue after nonlinear fails in the staggered coupling loop. !3106

Material models

• New material models:
  • strain dependent permeability !3236
  • relative permeability model 'RelativePermeabilityUdell'. !3290
  • saturation dependent thermal conductivity. !3298
  • permeability model 'Kozeny-Carman Model'. !3264
• Linear, saturation dependent swelling stress model. !3096
• Pass variables from previous time step to MPL Property::value() calls where increments are required. All *rate variables were removed in favor of the increments. !3102
• Use 2D coordinate system for LinearElasticOrthotropic solid material. A bugfix, now allowing 2D anisotropy and solid material orthotropy to be used simultaneously. !3165
• Unused MPL properties are shown as warnings after successful run in debug mode. !3197
• Error message now informs user of missing properties on the medium scale. !3337
• Bugfix of a 2D case in MFront's implementation of Mohr-Coulomb-Abbo-Sloan anisotropic model. !3260
• Update interface of the solid material models now accepting MPL Variables. !3261

File I/O

• New optional output format XDMF:
  • light data is written into .xdmf file and heavy data into .h5 file. !3184
  • reduced number of iNodes for HPC applications and removed redundancies in file output. !3246

Visualization

• Refactored insitu-functionality for VTK 9 / ParaView 5.8. The mpi container generated by the CI job now contains this functionality. !3092
• partmesh tool now exports "vtkGhostType" array indicating duplicate cells. !3111
• Fixed ghost element bug #3035. !3299

Documentation and webpages

• Update the Heat_Transport_BHE PipeNetwork Tutorial to TESPy version 0.3.x API. !3070
• Three-part video tutorial available on YouTube. !3278
• New benchmark based the Liakopoulos experiment for RichardsMechanics. !3175
• New test of heat transport in liquid flow with a constant velocity, HeatTransportInStationaryFlow. !3194, !3328
• Fixed a formula display in "BGRa creep model". !3329
• Switched from Pandoc to GoldMark Markdown parser. !3076
• Added troubleshooting web page for runtime issues. !3129
• Web site usage tracking with Plausible, No personal data is tracked. Fully GDPR-compliant. !3168
• Added web pages on how to get support and fill a bug report. Also enabled GitLabs Service Desk feature. !3270

Tests

• CTests now have labels based on their subdir in ProcessLib. !3079
• LARGE benchmarks are determined by their RUNTIME given in AddTest()/OgsTest(). Current threshold: 60 s. !3079
• Added DISABLED-paramter to AddTest()/`OgsTest(). !3079
• Run PETSc LARGE benchmarks in CI. !3079
• Add tests for mesh element quality criteria, fixing bug in AngleSkew criterion. !3279
• Updated to MathJax 3 for web formulas. !3300
• Better ctest dependencies and gui utils tests. !3323
• Changed the output name in square_5500x5500_staggered_scheme_adaptive_dt.prj. !3331

New tools

• Support for processing large meshes on envinf1. !3099
• Raster2PointCloud: Converts raster data into point clouds with an intensity-based density of randomised points per pixel for visualisation in ParaView/Unity. !3077
• Conversion of linear to quadratic mesh now supports Quad4 to Quad9 conversion. !3090
• Raster2Mesh: Converts an ASCII raster file into 2D mesh. Pixel values can be interpreted as elevation of mesh nodes or as scalar values for mesh elements. !3109
• AssignRasterDataToMesh: Adds raster information as a scalar array to an existing 2D mesh. !3174
• ExtractMaterials: Splits a mesh with n material groups into n meshes, each containing only the elements of the same material. !3116
• partmesh: Added optional -x-argument to specify metis input mesh. !3171
• IntegrateBoreholesIntoMesh: Integrates boreholes/BHEs as line elements into pre-existing mesh. !3188
• VerticalSliceExtraction: Constructs a vertical 2D slice out of a collection of horizontal 2D layers. !3273
• AddElementQuality: Adds evaluation of element quality criterion as data array to the mesh. !3283

CI & Infrastructure

• cppcheck-report. !3053.
• Package DataExplorer into container. !3105
• Unified and local (in the build-dir) Python environment with Poetry. !3133
• Python formatting check with black. !3158 and #3044
• Install dependencies for redistributable packages. !3226
• Publish to Docker container for serial configuration. !3271

CMake

• Reduced CMake runtime by 2-3 s. !3084
• Updated submodule MGIS for proper tfel finding. !3127
• Added option OGS_USE_XDMF (defaults to OFF) for enabling Xdmf output. !3295
• Use generator expressions for target_link_libraries(). !3297
• Move global preprocessor definitions to targets. !3330

Version info

• Pandoc requirement for web site removed! !3076
• PETSc 3.11.2. !3094
• Update exprtk submodule to the most recent master commit (d312ba9 ) dated 1 Jan. 2020. !3112
• Apple Clang (Xcode) 11.0 required. !3115
• New (optional) dependency: HDF5 1.10.5. (!3246, !3295)
• New (optional) dependency: Libxml2 2.9.10. (!3246, !3295)