6.3.3

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)

6.3.2

Overview

We have migrated to GitLab (issue 2947 on GitHub)! See GitLab migration guide.

The source code license was slightly modified, PR 2977 on GitHub!

Features

Process' changes

• Reactive transport process: perform chemical calculation on the integration points !3017, !3018, !3019
• HeatConduction; Add Newton assembly and mass lumping. Results of the mass-lumping are discussed on the benchmarks web page. !3045

Numerics

• Implementation of primary variable constraint Dirichlet-type boundary condition !3014
• Add the PETSc-SNES non-linear solver to possible list of solvers. This is still experimental feature. !3049

New tools

• Rename AddTopLayer to AddLayer (tool can also add bottom layer) !3015

Infrastructure

• Git LFS files were converted to plain git, issue 2961 on GitHub, see GitLab migration guide.
• Migrated from Jenkins to GitLab CI.
• Update MGIS to latest release following tfel version 3.3.0 !3028

Version info

• tfel-3.3.0

6.3.1

Overview

This is the last release before the announced license change (see #2973 pull request), and we are moving to GitLab! GitHub has served us well in the past years but we would like to employ the more powerful feature set of GitLab. See the announcement for more details.

Features

Process' changes

• LiquidFlow move porosity/storage from MPL solid phase to medium scale. #2872
• Reactive transport process: enrich Phreeqc interface using direct memory access approach for equilibrium-controlled reactions. #2883
• Rename Groundwater flow to SteadyStateDiffusion. #2860
• ThermoHydroMechanics now accepts linear shape functions for displacement. #2885
• Output intgration point data in RichardsMechanics process for proper restart option. #2911
• RichardsMechanics now uses the alternative mass balance formulation. #2914, #2921
• Computation of all secondary variables for output and restart in RichardsMechanics process is now consistent with the latest solution. #2936
• RichardsMechanics now relies on the solid's bulk modulus and Biot coefficient to compute grain compressibility. #2955

Numerics

• Add bulk element mappings for triangles. #2901
• Add mapping from points of a pyramid face to points in the pyramid element. #2913
• Remove unused time discretization schemes. Only backward Euler is being used now. This simplifies certain upcoming refactorings. #2908

Input and output

• Fixed bug of fixed time output not being written in case of repeated time step. #3000

Material models

• New MPL property:

  • CurveProperty. #2857
  • van Genuchten capillary pressure model. #2919
  • Regularized van Genuchten capillary pressure model. #2959
  • PermeabilityMohrCoulombFailureIndexModel. #2989

• Added back names of properties for better error messages. #2958

• Store properties' definition scale for each property. #2958

• Improve error handling in MPL when accessing a property of wrong type. #2941

• Add computation of bulk modulus for MFront solid material models. #2955

• Add solid pressure. Used by RichardsMechanics for solid density update. #2999

• Generalize exponential property, which now has an additive offset. #3008

File I/O

• Write PVD files for each subdomain output. #2949.

Testing and documentation

• Refactored FileTools.cpp to use std::filesystem. #2918
• Added documentation on how to use windows subsystem for linux (WSL). #2946
• Test definitions in the project files now support regular expressions. #2945

New tools

• Tool to convert PVTU-meshes into regular, non-partishioned meshes and remove ghost information. #2876
• Add prism element type to structured mesh generator tool. #2903
• Create regular mesh consisting of pyramid elements. #2909
• Correct reordering for pyramid elements in NodeReorder tool. #2937

Data Explorer

• Adding an array to a 2D mesh based on a raster file is now possible. #2984

Infrastructure

• Serial container image is built with Python enabled. #2765
• Added CMake-function ogs_add_library() as a drop-in replacement for the add_library()-function. #2881
• Bumped minimum compiler and use std::filesystem for temporary file creation. #2827
• Replace logog logger with a modern and type safe spdlog logger. It also includes the formatting library fmt, which is a great alternative to the iostreams. #2875, #2873, #2891, #2882
• Add GMRES restart to linear solver options. #2910
• More flexible algorithm to specify the file names of the output in the project file. #2927
• Now x_dot and dt are being passed to the computeSecondaryVariables() function allowing rate dependent secondary variable evaluation. #2935
• The order of postTimeStep() and computeSecondaryVariables() has been changed, s.t. all quantities computed in the secondary variables computation are available before the post time-step call. #2936
• Added GitLab CI config. #2968

CMake options changes

• Removed option OGS_USE_PCH, added option OGS_USE_UNITY_BUILDS to speed up compilation by using Unity builds. #2906

Version info

New compiler minima (#2827):

• gcc: 9.0, see also #3006
• clang: 9
• msvc: 2019

6.3.0

In this release the Material Property Library is significantly enriched with new constitutive relations and gets wide use in the processes.

Other significant changes are:

Features

Process' changes

• Richards mechanics process now correctly computes porosity changes in presence of swelling. #2825
• HydroMechanics process has now the option to use mass lumping. #2826
• HydroMechanics process now uses permeability in tensor form with corresponding output. #2848
• Reactive transport process has a mesh tag for restricting the place where chemical reactions take place within a specified subdomain. #2851

Numerics

• Pass x_dot to processes' assemble functions. Used by rate-dependent material models. #2795
• triangular elements with 7 integration points (order 4). #2798

Input and output

• Output of surface fluxes (for 2D and 3D bulk domains) for balance computations is now available for LiquidFlow process. #2760
• Compute and output element-average porosity in RichardsMechanics process. #2803
• Output of fixed time when using IterationBasedTimeStepping is now available. #2831

Material models

• Enable orthotropy in MFront solid material model interface. #2774
• Enable shared medium definition for multiple materials. #2786
• Implement van Genuchten saturation and relative permeability models in MPL. #2788
• Convert processes to use MPL for the fluid and porous media models:
  • Hydro-mechanics. #2779
  • Richards-mechanics. #2787
  • LiquidFlow. #2807
  • GroundwaterFlow. #2820
• Pass time increment dt to the material models. #2801
• Add initialValue(x, t) for material properties. #2804
• Implement mass balance porosity, used in RichardsMechanics. #2804, #2829
• Orthotropic permeability power law, used in RichardsMechanics. #2813
• Implement saturation dependent swelling, used in RichardsMechanics. #2819, #2832
• Bishop's effective stress models; power law and saturation cutoff, used in RichardsMechanics. #2823

File I/O

Testing and documentation

• A new test verifies the correct conversion from PropertyType enum to string and back. #2770

New tools

• ExtractEntireSurface: The tool extracts either lines in case of a 2D bulk mesh as input or quads/triangles in case of a 3D bulk mesh as input. #2764

Infrastructure

• Added a Code of Conduct. #2834

Fixes

• Fixed bugs in the element deactivation #2753, #2789.

CMake options changes

• Added version requirements file in json-format to have a single source used by CMake and the web site generator. #2783

Version info

• See versions.json

6.2.2

Features

Other process' changes

• Surface sorption / desorption process implemented. #2658
• Tag to fix amount of a KineticReactant in ChemistryLib. #2638
• Replaced the material parameters of ThermoHydroMechanicsProcess with MPL. #2614
• Explicit tag to set initial stresses in SmallDeformation, ThermoMechancis, HydroMechanics, and RichardsMechanics processes. #2635
• Invoke material parameters that are associated with component transport process from MPL. #2646
• Integrated another Phreeqc interface using direct memory access approach for reactive transport modeling. #2640
• Replaced the specific material properties of TwoPhaseFlowWithPP with generalized MPL. #2644
• Pass dt through interfaces instead of storage in process' data or coupled solutions. #2673

Numerics

• Generalized implementation for specification of the non-equilibrium initial states. #2633
• Bulk element point mapping for tetrahedrons added. #2662
• Repeat time step if assembly failed. Specifically for MFront material models if the integration fails, the time step will be repeated given adaptive time stepping scheme. #2730

Boundary condition

• Add possibility to specify 'lower' dimensional Robin/Neumann boundary conditions. #2710

Source term

• Line source terms are available. #2685

Input and output

• [HT] Test if all the needed material properties read from project file. #2727
• Extend internal state variables (MFront) output to TM, RM, and HM. #2732

Material models

• New ParameterProperty can be used for heterogeneous spatial distributed MPL properties. #2616, #2683
• Include MFrontGenericInterface as submodule and update to version tfel-3.2.1. #2631
• Add Mohr-Coulomb-Abbo-Sloan (and its orthotropic version) to MFront material models. #2634
• Extend LinearProperty for linear dependency upon multiple dependent variables. #2649
• New IdealGasLaw MPL property for pure phases consisting of ideal gases. #2651
• New MPL property Saturation based on the Brooks and Corey material model. #2652
• New MPL property Relative Permeability based on the Brooks and Corey material model. #2656
• New MPL properties Saturation and Relative Permeability according to the original Liakopoulos multiphase flow experiment. #2657

File I/O

• A no longer used RapidStnInterface for stn files is dropped. The used XmlStnInterface remains. #2609

New tools

• command line utility to interpolate equidistant raster files between two boundary rasters (for vertical refinement of subsurface layers). #2621
• command line utility to convert 2D meshes into ESRI shape files. #2627
• command line utility to conver netCDF-files into OGS meshes. #2654
• command line utility for for 3D mesh to grid conversion. #2704

Other notable code changes

• Split BuildInfo from BaseLib into separate libs to reduce re-linking after changes in the info variables. #2625
• Remove almost unused "named functions". #2708

Infrastructure

• Update tetgen to version 1.5.1 released on 18. of August 2018. #2618
• Add options to enable gcc sanitizer flags. #2706

Jenkins

• Builds Singularity container with OGS compiled for different MPI versions on master, #2628
• Run benchmarks in Singularity container, #2648

CMake options changes

• Added option to set OGS_BUILD_PROCESSES=OFF to disable building of all processes. #2752

Web / Docs

• Added links to latest benchmark pages to homepage, added sticky navigation. #2620
• Website is now fully built (including generation of CSS and JS files) by Netlify, #2731

Version info

• Hugo 0.60.1 (for website generation). #2731
• Conan 1.21.0, #2654, #2756

6.2.1

Features

New processes

• A thermo-hydro-mechanical (THM) process, monolithic implementation for Newton non-linear solver. #2446

Other process' changes

• Non-equilibrium initial state in the small deformation, HM, and TM processes. #2501, #2561, and #2544
• A reactive transport process, integrated IPhreeqc Module 3.5.0 for reactive transport modeling. #2494, #2512
• Fix velocity output in HM. #2507
• Store process' names in the Process class instead of an outside map. #2534
• Generalize permeability models for the fracture flow in LIE/HM:
  • CubicLaw (just generalization). #2542
  • ConstantPermeability. #2543
• Add simple mass lumping to the RichardsMechanics. #2590

Numerics

Parameter

• new TimeDependentHeterogeneousParameter. #2588
  Feature can be used for time dependent heterogeneous boundary condition or source term specification.

Boundary condition

Source term

Input and output

• HT process: Use MaterialPropertyLibrary for solid phase properties, too. This makes it necessary to changed the project files. #2487
• Reactive transport process: Output time-series amounts of kinetic reactants and equilibrium phases defined under the subtree of chemical system. #2564

Material models

• Orthotropic elasticity model. #2428
• Dupuit permeability relation. #2330

File I/O

• Gocad TSurface reader has been added #2547
• Gocad PLine reader has been added #2586

Testing and documentation

New tools

• GocadTSurfaceReader command line utility #2547/#2586

New tools and CLI usage

• Add switch multiple-nodes-allowed to tool constructMeshesFromGeometry, #2459
• Add option to vtkdiff tool to compare meshes using absolute tolerances and connectivity, #2485
• Scalar arrays are copied when using the ExtractSurface-tool, #2492

Data Explorer

• Mesh to shape export is now writing all cell-based scalar arrays to the DBF-file, #2436
• Added support of world files to georeference arbitrary raster files, #2460
• Scalar arrays are copied when extracting mesh surfaces, #2492
• Gocad TSurfaces can be imported into Data Explorer #2547
• Gocad PLines can be imported into Data Explorer #2586

Other notable code changes

• Conversion to linear mesh is now independent of node numbering. #2519

Development workflows

• Added git hooks via pre-commit. See docs/devguide/getting-started/get-the-source-code/ for installation instructions, #2599

Infrastructure

Jenkins

• Added web link checker, #2572
• Reordered Jenkins pipeline for better concurrency, #2560
• Updated Docker base images to Ubuntu 18.04, #2493
• Migrated from envinf1 to frontend2, #2440
• Conan: Use lower-case package names for qt, vtk and shapelib, #2450, #2573

CMake options changes

• Bumbed miniumum CMake version to 3.12, #2597
• Added option OGS_CONAN_BUILD_TYPE to overwrite Conan build type, #2577

Web / Docs

• Added embedded screen recordings with https://asciinema.org, #2510

Version info

• CMake minimum 3.12
• VTK minimum 8.2

6.2.0

Changelog

Features

New processes

• HeatTransportBHE process supporting 1U, CXA, and CXC BHE types. #2221, #2332,
  #2271, #2275
• Staggered implementation of a thermo-mechanical with phasefield process. #2102
• Richards mechanics process. #2189
• Small deformation process with non-local integration of damage. #2294
• Staggered implementation of phasefield process. #2052
• ComponentTransport process in revised formulation. #2200
• Multi-component transport process. #2304

Other process' changes

• A Jacobian tester: a process's Jacobian assembly can be compared to a
  numerical Jacobian (mostly for development. #2238
• Add setInitialConditions() call to processes and local assemblers. #2334
• Several bug fixes for LIE/HM process including "fracture into matrix
  leak-off", Darcy velocity output in the fracture. #2129
• Support for intersecting fractures (x-crossing and t-junction) in LIE/SD
  process. #2235, #2293
• Fixed the calculation of the Darcy velocity in staggered TH. #2127

Numerics

• Staggered scheme for coupled processes with different orders of elements.
  #2016
• Subdomain deactivation within time intervals. #2297
• Add a driver for an iteration based time stepping algorithm. #2318

Boundary condition

• Implementation of Python boundary conditions. #2170
• Implementation of constraint boundary conditions. #2145
• Dirichlet boundary condition within a time interval. #2272
• BoundaryElementSearch: Return bulk element id and bulk element face id. #2125
• Removed Neumann boundary condition for displacement jumps in LIE processes.
  #2153

Source term

• Use parameter for source terms. #2061
• Volumetric source terms implementation. #2220, #2234, #2241, #2261

Input and output

• Writing and reading of integration point data. Implemented sigma and epsilon
  output for some processes. #2071, #2203, #2324
• Add input of vtu-meshes for boundary conditions additionally to the gml input.
  This is later used by the heterogeneous parameters and source terms. #2140,
  #2141, #2156
• Parameters may now be explicitly defined on arbitrary subdomains. This merges
  the Heterogeneous Dirichlet and Neumann boundary conditions with their,
  previously only homogeneous, counterparts. #2376
• Parameters now support space-dependent function input via exprtk library.
  #2325, #2339
• Output of primary variables on arbitrary subdomains. #2372, #2299
• Output is possible at specific times for adaptive time stepping and
  evolutionaryPIDController. #2079
• Calculate and output specific flux. #2411
• Enable surface flux calculation for component transport process. #2168
• Interpolated pressure (on higher order elements' nodes) output for
  Richards-mechanics and hydro-mechanics processes. #2228
• Improve output of nodal aperture and aperture vector in LIE/HM. #2050
• Add output of nodal forces and hydraulic flow in mechanics and coupled
  mechanics processes, SD, HM, LIE/SD, LIE/HM. #2118
• Enable surface flux calculation for HT process. #2132
• Fixed pvd output. #2036

Material models

• BGRa creep model. #2167
• New cohesive zone mode I fracture model for LIE processes. #2142, #2157
• Add MFront/TFEL solid constitutive relation support via.
  MFrontGenericInterfaceSupport library. CMake option OGS_USE_MFRONT. #2259
• Infrastructure for multi-phase, multi-component material properties library.
  #2303,
  #2415
• Anisotropic tensors may now be given in given local coordinate system. #2370
• Non-constant density model implementation in HC process. #2200
• Add second derivatives of permeability functions in Richards flow. #2188
• Different solid material models can now be defined on different materialIDs.
  #2216, #2262, #2270
• Move solid constitutive relation creation in single place. #2160

Testing and documentation

• Migrated Appveyor tests to Azure
  Pipelines. #2342
• Added cppcheck, clang-tidy and include-what-you-use. #2078, #2328, #2377
• Added check for header standalone compilation, can be enabled with
  OGS_CHECK_HEADER_COMPILATION=ON. #2043
• Jenkins shows nice summaries of compiler warnings. #2206
• Large tests are fixed and run on Jenkins upon master merge. #2056, #2155
• Re-enabled code coverage reports (for the testrunner only) with
  Codecov. #2333, #2336
• Commits containing [ci skip] in the commit message do not trigger a Jenkins
  build.
• Add vtkdiff test configuration to project files, s.t. the vtkdiff tests are
  performed after successful run comparing output to reference files. This
  possibility is also reflected in a new CMake function OgsTest as an
  alternative to the AddTest. #2255, #2257

New tools

• TecPlotTools: splitting files containing multiple zones into seperate
  TecPlot files. #2114
• TecPlot-Reader: converting TecPlot rasters into OGS meshes (one file per
  zone, containing all variables as scalar arrays). #2114
• constructMeshesFromGeometry:
  Construction of boundary meshes from bulk mesh and gml files. #2144
• identifySubdomains:
  Identification of boundary meshes (or any subdomains in general) in the bulk
  mesh. Performs geometrical tests and creates and verifies necessary
  bulk_node_ids and bulk_element_ids maps. #2227, #2252
• Mesh2Raster: converts 2D OGS meshes into raster files of arbitrary pixel
  size, where node elevation is represented by pixel value. #2367
• GocadSGridReader tool reading the Gocad/SKUA stratigraphic grid format and
  writing the data in the vtu format. #2316

New tools and CLI usage

• ogs --help shows the given CMake options. #2210
• Unify command line version info output. #2194
• Rewrite partmesh tool and add partitioning of boundary meshes (or subdomains
  in general) according to the partition of the bulk mesh. #2159, #2178, #2195
• Add new features to ExtractSurface tool. #2387, #2401
• updated utility moveMeshNodes: algorithm for mesh on mesh mapping now
  calculates exact node elevation instead of using interpolation. #2390

Data Explorer

• Listing of source terms and boundary conditions in Data Explorer DataView (no
  visua...

6.1.0

Overview of changes since 6.0.8 release.

The changes since the prerelease 6.1.0-rc1 contain few bug fixes and improvements of the CI.

Features:

New processes:

• ComponentTransport #1758
• PhaseField #1813 and #1895
• RichardsComponentTransport #1929
• ThermoMechanics #1800
• TwoPhaseFlow p-rho #1613

Other process' changes:

• New equation assembly approach for the staggered scheme. With that, the coupling assembly computations are changed from performing assembly across the different Process classes for a coupling to a single Process class for coupled processes, which was assumed only for the monolithic before. With the changes, the original Process class that for monolithic scheme originally can now handle both of the monolithic and staggered schemes. So far, HT classes get the staggered scheme based on this new framework of assembly. #1970
• Heterogeneous liquid flow properties (#1979, #2017)
• New boundary conditions added: Nonuniform Dirichlet (#1952) and Neumann (#1891), and normal traction (#1896)
• Framework for time stepping and a first application of adaptive time stepping, EvolutionaryPIDcontroller, and automatic time step control (#1803).
• Nodal source terms (#1977)
• Fix deformation processes to work correctly with PETSc parallelization (#1838).
• Fix the access to local data of PETScVector (#1797).
• Add damping factor to global Newton. #2004
• Extend extrapolator to vectorial quantities and replace the component-wise output of Darcy velocity and the stress/strain in mechanical processes with single vectorial output.

Material model changes

• Separate FractureModels in LIE #1971
• Add material forces as published in http://www.sciencedirect.com/science/article/pii/S0093641317303865 #1936

Testing and documentation:

• Insitu visualization with ParaView Catalyst. See presentation. #1744, #1732. As a consequence VTK 7.1 is now required.
• Benchmark docs are now part of the code (in web/content) and can contain
  interactive 3D visualizations via vtk.js. #1706, #1714, #1723, #1729.
• Migrated handling of test data files from git-submodule to git-lfs, see docs. #1964, #1982, #1984, #2010, #2012.
  Now git-lfs is required. Check the installation instructions.

Infrastructure:

• Fully moved to Conan for automatic third-party library handling. Can be enabled with OGS_USE_CONAN=ON, see docs. #1907
• Conan version 1.0 is now required.
• Dropped travis CI environment and added few new tests on Jenkins because of simpler maintenance.

CMake options changes:

• OGS_EIGEN_DYNAMIC_SHAPE_MATRICES defaults to OFF on Release
  config, ON otherwise. Can be overridden by explicitly setting the option. #1673
• New OGS_EIGEN_INITIALIZE_MATRICES_BY_NAN defaults to ON for easier spotting of non-initialized matrices. When OFF, the Eigen's default initialization to 0 is skipped resulting in slightly faster execution. #1917
• Set default Eigen's cmake flag disabling vectorization since this lead to several problems in different environments. #1919 and the issue linked there https://github.com/ufz/ogs/issues/1881

Other

• PETSc config is tested on Jenkins (envinf1)
• OGS binaries are provided as eve / envinf1 modules. See docs for details. #1753
• Migrated Data Explorer to Qt5. #1622, #1625
• Windows builds are tested on MSVC 2017 on own hardware and on MSVC 2015 on AppVeyor. #1802
• Minimum GCC version is 4.9 (tested on Travis and Docker builds), 6.2 is tested on UFZ cluster system (envinf1). #1810
• Removed Windows 32-bit builds from testing --> no Windows XP binaries are provided anymore. #1988
• Migrated Jenkins Pipeline scripts to new syntax called Declarative Pipeline. #1976
• Tests to check the gradient of shape function by comparing the given and the computed element volumes (#1873).

2017

Features:

New processes:

• ComponentTransport #1758
• PhaseField #1813 and #1895
• RichardsComponentTransport #1929
• ThermoMechanics #1800
• TwoPhaseFlow p-rho #1613

Other process' changes:

• New equation assembly approach for the staggered scheme. With that, the coupling assembly computations are changed from performing assembly across the different Process classes for a coupling to a single Process class for coupled processes, which was assumed only for the monolithic before. With the changes, the original Process class that for monolithic scheme originally can now handle both of the monolithic and staggered schemes. So far, HT classes get the staggered scheme based on this new framework of assembly. #1970
• Heterogeneous liquid flow properties (#1979, #2017)
• New boundary conditions added: Nonuniform Dirichlet (#1952) and Neumann (#1891), and normal traction (#1896)
• Framework for time stepping and a first application of adaptive time stepping, EvolutionaryPIDcontroller, and automatic time step control (#1803).
• Nodal source terms (#1977)
• Fix deformation processes to work correctly with PETSc parallelization (#1838).
• Fix the access to local data of PETScVector (#1797).
• Add damping factor to global Newton. #2004
• Extend extrapolator to vectorial quantities and replace the component-wise output of Darcy velocity and the stress/strain in mechanical processes with single vectorial output.

Material model changes

• Separate FractureModels in LIE #1971
• Add material forces as published in http://www.sciencedirect.com/science/article/pii/S0093641317303865 #1936

Testing and documentation:

• Insitu visualization with ParaView Catalyst. See presentation. #1744, #1732. As a consequence VTK 7.1 is now required.
• Benchmark docs are now part of the code (in web/content) and can contain
  interactive 3D visualizations via vtk.js. #1706, #1714, #1723, #1729.
• Migrated handling of test data files from git-submodule to git-lfs, see docs. #1964, #1982, #1984, #2010, #2012.
  Now git-lfs is required. Check the installation instructions.

Infrastructure:

• Fully moved to Conan for automatic third-party library handling. Can be enabled with OGS_USE_CONAN=ON, see docs. #1907

CMake options changes:

• OGS_EIGEN_DYNAMIC_SHAPE_MATRICES defaults to OFF on Release
  config, ON otherwise. Can be overridden by explicitly setting the option. #1673
• New OGS_EIGEN_INITIALIZE_MATRICES_BY_NAN defaults to ON for easier spotting of non-initialized matrices. When OFF, the Eigen's default initialization to 0 is skipped resulting in slightly faster execution. #1917
• Set default Eigen's cmake flag disabling vectorization since this lead to several problems in different environments. #1919 and the issue linked there https://github.com/ufz/ogs/issues/1881

Other

• PETSc config is tested on Jenkins (envinf1)
• OGS binaries are provided as eve / envinf1 modules. See docs for details. #1753
• Migrated Data Explorer to Qt5. #1622, #1625
• Windows builds are tested on MSVC 2017 on own hardware and on MSVC 2015 on AppVeyor. #1802
• Minimum GCC version is 4.9 (tested on Travis and Docker builds), 6.2 is tested on UFZ cluster system (envinf1). #1810
• Removed Windows 32-bit builds from testing --> no Windows XP binaries are provided anymore. #1988
• Migrated Jenkins Pipeline scripts to new syntax called Declarative Pipeline. #1976
• Tests to check the gradient of shape function by comparing the given and the computed element volumes (#1873).

6.0.8 with insitu visualization capabilities

See #1744. Just used this release for DOI generation.