Recent Releases of ogs

Process' changes

New HMPhaseField process

!4809 Adds a hydromechanical phase-field process to address typically the hydraulic fracture problem using the phase-field fracture method.

Deprecated processes removed

!5329 Previously deprecated processes removed: SmallDeformationNonlocal, StokesFlow, TES, ThermoMechanicalPhasefield, and ThermalTwoPhaseFlowPrho.

Component transport process / reactive transport process with coupling of PHREEQC

!5243 Set the position function in the assembler, so that the retardation factor can be position dependent.

HeatTransportBHE

!5179 Improve weighting factor calculation used for Algebraic BC in the HEATTRANSPORTBHE process.

Richard's mechanics process

!5255 Bugfix; compute initial strain from displacement field, do not use strain integration point data.
!5316 Add parallel assembly.

SmallDeformation

!5220 Add parallel assembly.

ThermoHydroMechanics

!5288 Add parallel assembly.

Numerics

!5221 Reuse Jacobian once every n steps to accelerate non-linear solution.
!5187 Multithreading for CG solver can be enabled by setting matrix type (LowerUpper).
!5236 Time dependent deactivation in a domain bounded by a circle or a sphere.
!5237 Analytic block in the numerical Jacobian for CentralDifferences.
!5256 Improvements in ForwardDifferencesJacobian: eliminates one redundant local assembly and leverages the pre-computed analytical Jacobian block.
!5318 Multipliers of IterationBasedTimestepping can be linearly interpolated with <multiplier_interpolation_type>PiecewiseLinear</multiplier_interpolation_type>
!5262 Initial implementation of PETSc version of flux corrected transport - at the moment only for one MPI process
!4926 Introduce an iteration number based reduction of Newton-damping.

Tools

!5224 Remove tetgen dependency. We do not bundle tetgen anymore. Please install it with your package manager or Conda.
!5276 A tool mergeMeshToBulkMesh merges one mesh into a bulk mesh, which can be used in simulations of excavation, backfilling, and successive geo-engineering operations.

Python & Jupyter

!5216 Conda package includes MFront functionality, see also https://github.com/conda-forge/ogs-feedstock/pull/14.
!5222 Bump ogstools (used in benchmarks on the website) to 0.6.0.
!5238 New module ogs.mpl for MPL properties. Basic structure and for now only Constant and Linear properties bound, but more are coming.
!5304 PyVista 0.45, removes vtk-osmesa dependency and xvfb-run hacks

Testing

!5204 Adds a performance test verifying the functionality of !5194 in our CI. This MR can serve as a blueprint for other similar (performance) tests in the future. The MR contains a documentation section in the dev guide, too.

Logging

!5295 Introduces the command line option (--log-parallel). New default behaviour under MPI: Only rank 0 writes. With option: legacy behaviour.
!5295 Overhaul of log outputs. New log lines, more systematic, less redundancy.
!5295 Signal handling introduced: Terminate and interrupt signals are logged

Infrastructure

!5323 [web] Multi-site search on opengeosys.org, Doxygen and ogstools.

Material Property Library (MPL)

!5254 Add residual saturation in sigmoid function.
!5246 Add possibility to use time and spatial position in Curve, Linear, Exponential and Function property.
!5317 Add the possibility to use curves in Function property.

Bug fixes

!5227 Avoid dead-lock in MPI when AssemblyException is thrown.
!5325 Fix XDMF/HDF5 output on sub-meshes.

Documentation

!5244 Add a documentation page, showing how to establish a OGS mesh based on a PETREL structural model.
!5275 Liquid flow documentation.

Version info

!5281 Compiler updates and c++23 standard:
- Compiler: gcc-13.3, clang-16.0, msvc 17.0 Visual Studio 2022 toolchain 143
- Libraries: boost-1.84
!5314 Update spdlog to 1.15.3 (updates fmt to 11.2.0)
!5329 Sundials cvode solver dependency removed (used only by TES process, which is now deleted)

- C++
Published by bilke about 1 year ago

In this release the LargeDeformation process was extended to deal with nearly incompressible materials. Several usability and speed improvements in the HeatTransportBHE process were implemented. And for the material properties a "catch all" material ids option <medium id="*"> was added, simplifying input in the project files.

In the LargeDeformation process, the F-bar method for finite element (FE) analysis of large deformation of nearly incompressible materials is implemented to address volumetric locking phenomena that occur in standard FE analysis under these conditions. The algorithms of the F-bar method are derived for the total Lagrangian formulation of finite strain and implemented in the LargeDeformation process. This update introduces a new optional input tag, f_bar, to the LargeDeformation process. The tag accepts two values: element_center_value, which indicates that ${\mathbf F}0$ is computed at the element center, and `elementaverage`, which specifies that ${\mathbf F}_0$ is computed as an element average.

Process' changes

!5093 SmallDeformationNonlocal, StokesFlow, TES, ThermoMechanicalPhaseField, and TwoPhaseFlow-PRho processes were not extended for some time and are now marked as deprecated. They will be removed in the 6.5.5 release.

HeatTransportBHE

!5106 Add id-notation to <borehole_heat_exchanger> with the possibility to catch all BHE with id="*".
!5121 Add optional mass lumping.
!5194 Add assembly optimization for soil part in linear cases with <linear>.

LargeDeformation

!5045 F bar method for total Lagrangian formulation.

LIE

!5144 Replacing the parameter medium properties of HM#LIE with MPL ones. A Python script, convert_LIE_HM2MPL.py, to convert the project files to the present syntax is added to the input data directory: Tests/Data/LIE/HydroMechanics.

LiquidFlow process

!5112 Gas flow calculation in LiquidFLow. For this purpose, an optional input tag, equation_balance_type was introduced, which allows user to choose the volume-based or the mass-based PDE for this process.

Richard's mechanics process

!5120 Total initial stress input.

ThermoRichardsMechanics

- !5083 concludes a long series of developments making "extended" MFront material models usable with the TRM process: This MR finally adds a bunch of 0D and 1D test cases of a bentonite material behaviour implemented in GeneralMod and interfaced with OpenGeoSys via MFront. This is a joint work of BGETEC, CEA, TUBAF, Charles University, ČVUT and UFZ.

Numerics

!5182 Fixed parallel execution for Eigen linear solvers.

Generic features

!5150 Added LeastSquareCG solver and LeastSquareDIAGONAL preconditioner from Eigen

Python & Jupyter

!5118 ogs from wheel creates output directory too.
!5189 Build Python 3.13 wheels.

Testing

!5143 , !5148 Visual Studio 2022 is now tested too (MSVC 2019 still used for mkl job).

B-bar tests

Additional tests for the B-bar methods have been added to further evaluate their effectiveness:

!5105 A Jupyter Notebook benchmark for M for evaluating the B-bar method with simple tests and some others.
!5134 3D Cooks's Membrane test for M.

Code improvements

!5132 Reduce some redundancy in LiquidFlow and Hydromechanics.

CMake

!5146 [CMake] Split LIE to LIEM and LIEHM for optional compilation.

File I/O

!5127 Improve reading binary files with memory mapped I/O. Add the possibility to read curve definitions and fixed_output_times from binary files in the project directory.

Material Property Library (MPL)

!5111 Improved error reporting and added a "catch all" material ids option <medium id="*">.
!5126 Generalised SaturationVanGenuchten to independent pressure and saturation exponents. When single (pressure) exponent is used the saturation exponent is set to 1/(1-m) keeping the old behaviour.

Documentation

!5165 [web] Improvement of the document of the Theis' problem.

Version info

!5122 Boost 1.82.0
!5193 tclap 1.4.0

- C++
Published by bilke over 1 year ago

ogs - 6.5.3

Breaking changes

!5063 changes the handling of mesh file paths in the prj file: If such a path is a relative path with a directory separator (/ or \), this path will be resolved relative to the mesh directory (-m flag) or the prj file if the former is not passed. Before, such relative paths were resolved relative to the process's working directory. MR !5063 resolved that inconsistency.
!5030 Change time incrementing algorithm to use Kahan summation. This hopefully avoids any 1e-16 time steps near fixed output and end times.

New processes

!4481 adds the two-phase well-bore process.

Process' changes

!5050 Removed K and M matrices from assembleWithJacobian* interface as these are not needed.
!5054 Generalize openMP parallel assembly (Newton scheme) to staggered processes.

HeatTransportBHE

!5025 [BHE] Add Algebraic BC in the assemble of the HeatTransportBHE Process.

HydroMechanics

!5054 Use openMP parallel assembly for monolithic and staggered schemes.

LIE

!5078 Fix a memory leakage bug in LIE#HM when matrix is disabled for the flow process.
!5081 B bar method for HM#LIE.
!5084 B bar method for M#LIE.

Generic features

!5088 Consistent high-precision output using max_digits10 especially for time and time increments.

Tools

!5049 Generalised xyz interface to read any xyz raster file (was just complete rectangle images previously)

Data Explorer

!5049 Generalised xyz interface to read any xyz raster file (was just complete rectangle images previously)

Python & Jupyter

!5058 Refactored python bindings build structure and migrated Snakemake tests into pytests. Removed Snakemake dependency.

Testing

!4757 Reenabling TH2M process in the CI for Windows. Still takes long time to compile.

Infrastructure

!5023 [cmake,guix] Guix package (and container) includes OGSUSENETCDF=ON.
!5024 Container includes mpirun-executable.

- C++
Published by bilke almost 2 years ago

ogs - 6.5.2

Breaking changes

!4919 Removes the molar_flux secondary variable in favour of flux output for all chemical species.
!4971 THM and RM processes use current state for $C_{\text elastic}$ computation and no longer the "null"-state.
!4984 renames the cell averaged stress output from stress_avg to sigma_avg to be consistent with sigma and sigma_ip outputs.

Process' changes

!4982 Correct domain deactivation behaviour for multi-variable processes; Assembly is not run iff the element is deactivated for all variables.
!4984 introduces generic cell averaged output for all processes using reflections for IP data I/O (ATM these are TRM, LD, SD, TH2M). This enables cell average output of all IP data (except material models' internal state data) for these processes.

TH2M

!4980 finalizes at large the extraction of the constitutive relations into individual models, similar to how it is done in ThermoRichardsMechanics.

Component transport process / reactive transport process with coupling of Phreeqc

!4919 Adds flux output <c>Flux for all chemical species <c>.

SmallDeformation

!5007, !5016 B-bar method for linear deformation with Cook's-membrane test.

Generic features

!5009 Enables using Python and volumetric source terms as nodal source terms.

Testing

!5003 [ci] Fixes for win jupyter ctests

Bug fixes

!4919 Fixes the flux output computation in the ComponentTransport process. (The FEM assembly was/is correct.)

CMake

!4978 New CMake-preset sanitizer.
!4990 Refactored Eigen / MKL / OpenMP setup: Introduced new CMake option OGS_EIGEN_PARALLEL_BACKEND which is OpenMP by default. When using OGS_USE_MKL=ON then the backend is MKL. Also updated Eigen to a recent master.

Infrastructure

!4973 Removed ogs-container-maker dependency. OGS user container are now generated with GNU Guix. Due to improvements in dependency management (CPM) third-party developer container (e.g. C++ VSCode Devcontainer) are sufficient to use for OGS development.
!4974 Removed ThirdParty-folder.
!5011 Provide MKL container on https://www.opengeosys.org/releases/.

File I/O

!4989, !4996 ogs and partmesh create output directory when invoked with -o-parameter.
!4997 ogs -m-switch: fallback to reading gml from .prj-file directory.

Material Property Library (MPL)

!4992 Allow access of deformation_gradient, mechanical_strain, stress, total_strain, and total_stress in the exprtk expressions of the MPL Function property.

Documentation

Version info

!4974 VTK 9.3.0
!5014, !4992, https://gitlab.opengeosys.org/ogs/ogs/-/commit/5390a73f2475c3b55ae5eed95f5379790196cf15 ~gcc 11.4~ gcc 11.3

- C++
Published by bilke about 2 years ago

ogs - 6.5.1

This release introduces a suite of enhancements and new features across various processes within OpenGeoSys. Notably, the introduction of FCT numerical stabilization and optimization of the assembly process for HeatConduction, memory optimizations in LiquidFlow processes, and Newton implementation in the HeatTransportBHE implementation represent significant steps forward in improving the efficiency, stability, and flexibility of simulations. Additionally, the ability to input total stress as initial conditions in HydroMechanics and ThermoRichardsMechanics offer users greater control of their models. For the LIE mechanics and hydro-mechanics processes the strain and stress are now output as vectorial quantities, which should simplify post-processing.

For the future we also aim for more frequent releases (around every 3 months) and with this we discontinue the bugfix branches.

Process' changes

Component transport process / reactive transport process with coupling of Phreeqc

!4825 adds new numerical stabilization type "FCT" and apply it to the ComponentTransport process.
!4873 adds heat transport equation to enable non-isothermal component (HTC) process only in staggered way.

HeatConduction

!4867 adds the options <linear> and <linear_solver_compute_only_upon_timestep_change> that accelerate the assembly to the T process. These options are already present for the ComponentTransport process.

HeatTransportBHE

!4956 add the Newton nonlinear iteration feature to HeatTransportBHE process.

HydroMechanics

!4915 Enables to input total stress as the initial stress.

LargeDeformation

!4861 Add volume ratio to output

LIE

!4851 For HM process, improved output such as added output for nodal values of the secondary variables, and vectorized the output of the element-wise averaged multi-component secondary variables.
!4904 For M process, vectorized the output of the multi-component secondary variables.

LiquidFlow process

!4962 Use shape matrix cache in LiquidFlow process to reduce memory consumption of local assemblers

ThermoHydroMechanics

!4929 Enables to input total stress as the initial stress.

ThermoRichardsMechanics

!4908 Enables proper restart with material models such as PorosityFromMassBalance via the new setting <initialize_porosity_from_medium_property>.
!4923 Enables to input total stress as the initial stress.
!4942 Changes the flavour of TRM that uses the extended OGS-MFront interface such that this flavour uses the full stiffness matrix to compute solid compressibility instead of only the elastic tangent stiffness.

Constitutive relations (material models)

!4887 Linear elastic transverse isotropy model. Besides, this MR adds unit tests for LinearElasticOrthotropic too.

Parameters

!4882 Local coordinate system containing implicit bases.

Numerics

!4795 Class StaggeredCoupling.

Generic features

!4891 adds the possibility to read/write matrix-valued IP data (and extrapolated data thereof) for processes doing I/O via reflections (currently most notably TRM)

Python & Jupyter

!4866 All ruff issues fixed or silenced.

Testing

!4889 [cmake] Improvements to ctest (regex output checks with e.g. PASS_REGULAR_EXPRESSION).

Bug fixes

!4863 [cmake] Fix MKL dependency installation. Fixes Windows binary downloads.

CMake

!4814 Refactor netCDF library finding and removed everything Conan-related.
!4839 Simplify PETSc finding. pkg-config is now required for finding PETSc via CMake.

Infrastructure

!4858 [ci] Build container with netcdf (ogscm only, not in Guix container yet).
!4864 [ci] Docker Upgrade Ubuntu base image to 23.04 and gcc to 12.
!4898 Builds on cdash.opengeosys.org can be traced back to their GitLab CI job by an additional notes file which is added to the cdash build.
!4945 [ci] Remove linux docker jobs: test coverage is already in the other jobs and moved docker jobs to native linux jobs.
!4961 Added some helper scripts for release automation.

File I/O

!4872 Enable long paths in executables on Windows.

Material Property Library (MPL)

!4808 OGS distinguishes now between liquid_phase_pressure and gas_phase_pressure. This is required to for certain MPL properties such that they can be used across different processes. HM, as a single-phase process, sets both pressures equal to allow for gas and liquid phase properties.

Version info

!4849 Minimum PETSc version 3.18.6
!4864 Docker Ubuntu base image is now 23.04 which has gcc 12

- C++
Published by bilke over 2 years ago

ogs - 6.5.0

The release includes a new finite strain mechanics process, several run time performance optimizations, and new output options.

The LargeDeformation process for finite strain mechanical analysis was implemented. It is set up in a Total Lagrangian formulation. The process uses MFront/MGIS interface for the constitutive relations of the solid, which also takes care of the corresponding pull-back operations. The implementation will be the basis for simulations of large deformation processes, such as salt creep, crushed salt compaction, bentonite swelling or soil mechanics problems.

Optimizations include: - OpenMP assembly in TH2M/TRM/TRF, configurable OGS_ASM_THREADS=<n>.
Note that this might introduce race conditions, so better double-check simulation results when you use this feature. - CT linear case optimization with speedups of around 10 for certain linear setups.
Configurable via the <linear> and <linear_solver_compute_only_upon_timestep_change> prj file settings.
Note: these are expert options; OGS won't check if it's valid to use them, this is the sole responsibility of the user.

Output for the users and developers was extended. Finer-grained control options for result output (subdomains, variables) were implemented on the user's side. For developers possibility to output assembled local and global matrices is now available. It is configurable via the OGS_LOCAL_MAT_OUT_PREFIX="<some prefix>", OGS_LOCAL_MAT_OUT_ELEMENTS="0 1 5 16 123" and OGS_GLOBAL_MAT_OUT_PREFIX="some prefix>" environment variables. The local matrix output is available for all processes, and the global matrix output only for small deformation, TRF, TRM and TH2M at the moment. For better tests the vtkdiff was extended to compare integration point data. This new feature should be used in newly added CTests.

Other notable changes include, local coupling scheme for staggered processes, and thermo-mechanical part of a freezing liquid was implemented in ThermoHydroMechanics process; hydraulic part to come soon.

Breaking changes

This section lists changes in OGS that might make OGS terminate due to missing or unused configuration or might change OGS behaviour.

!4811 TRM/TRF vapour properties moved.
!4800 <media> used in two phase flow p-rho.
!4766 <dimension> configuration removed in HM, LIE/HM, LIE/M, RM, TH2M, THM, TRM.
!4699 x_dot renamed to x_prev in all assembly routines.
For new processes developed in private branches this change might entail a silent change of meaning, i.e., the code still compiles, but produces nonsensical simulation results.
!4403 The small deformation process now computes eps_prev instead of storing it. > The only problem appeared for the back-filling (subdomain deactivation) case where a different strain was stored. This is a not so simple issue to be dealt with in the future.
!4557 If some variables are specified for output, only those will be output, i.e., users might miss some outputs compared to before this MR. Please check/adapt your prj files if necessary.

New processes

!4821 Large deformations process.

Process' changes

ThermoRichardsFlow

!4811 additional gas phase added in the project file for vapour properties. This also includes property name changes. Compatibility script: movevapourpropertiestogas_phase.py

ThermalTwoPhaseFlowPrho

!4800 Use <media> in the two phase flow p-rho process reusing MPL implementations of constitutive relations.

Component transport process / reactive transport process with coupling of Phreeqc

!4713 and !4747 add an option <linear> that speeds up the simulation of linear problems.
!4730 adds an option <linear_solver_compute_only_upon_timestep_change> that speeds up simulations of linear problems further.

HT

!4613 enables use of lower dimensional fracture elements in HT process.

HydroMechanics

!4766 <dimension> keyword removed. Script to adapt all project files found recursively: removedimensionkeyword.py
!4578 Improvement of the fixed stress splitting approach in the staggered scheme

Richard's mechanics process

!4766 <dimension> keyword removed. Script to adapt all project files found recursively: removedimensionkeyword.py

SmallDeformation

!4403 Compute eps_prev instead of storing it.
!4643 Modified cam clay version with constant elasticity: clean-up, bug-fix and renaming (ModCamClaysemiExplconstE.mfront).
!4604 Modified cam clay version with pressure-dependent elasticity (original MCC model) added (ModCamClay_semiExpl.mfront).
!4739 SmallDeformation uses media for solid density evaluation.
!4763 Extract constitutive relations into graph-like structure.
!4766 <dimension> keyword removed. Script to adapt all project files found recursively: removedimensionkeyword.py

ThermoHydroMechanics

!4528 Extract constitutive relations update.
!4723 "Correct history variable update for freezing. Testing 9% volumetric strain expansion.
!4766 <dimension> keyword removed. Script to adapt all project files found recursively: removedimensionkeyword.py

ThermoRichardsMechanics

!4811 additional gas phase added in the project file for vapour properties. This also includes property name changes. Compatibility script: movevapourpropertiestogas_phase.py

Constitutive relations (material models)

Solids, multi-material internal states variable output and restart:
- !4535 SmallDeformation process,
- !4476 TH2M process,
- !4626 TRM process.
!4794 Add deformation gradient, second Piola-Kirchoff stress tensor, and Green-Lagrange strain to MFront interface and the MPL.
!4794 MFront uses gradients from latest iteration for the new behaviour data state from now on.

Generic features

!4507 adds a simple way to access blocks of finite element degrees of freedom: auto const [x1, x2, x3] = NumLib::localDOF<N1, NumLib::Vectorial<N2, 2>, N3>(x);.
!4522 adds a generic algorithm computing numerical derivatives.
!4546 adds the possibility to output local and global matrices for debugging purposes.
!4556 provides an OpenMP parallelized assembly for the Newton-Raphson solution scheme for TRM, TH2M and TRF that can be enabled via the environment variable OGS_ASM_THREADS=<NUMBER_OF_THREADS>. Solving the TH2M process with the Picard non-linear solver is not possible, anymore.
!4798 Neumann-type boundary condition: If possible evaluate parameter in Gauss points.
!4668 Reset integration point data by materialIDs.

Tools

!4560 New tool createTetgenSmeshFromRasters
!4773 partmesh is now build with the official METIS.
!4598 Use numerical element volume calculation in AddElementQuality.

Data Explorer

!4580 Raster data can now be saved to files
!4580 Raster files loaded into the Data Explorer can now be converted into *.asc format (same as via the Raster2ASC command line interface)

Python & Jupyter

!4575 Migrated wheel build backend to scikit-build-core
!4547 Relax Python requirements a bit, update PyVista to 0.39.
!4620 Python interface to access OGS mesh. Following properties of a MeshLib::Mesh can be accessed by the OGSMesh python wrapper:
- coordinates of the mesh nodes
- cell information (vtk cell types and the node ordering are used)
- properties assigned to MeshItemType::Node and MeshItemType::Cell can be read
- properties assigned to cells can be read and set
- properties assigned to nodes/points can be read and set
!4654 [wheel] Changes version scheme to guess-next-dev. Increments version number for development (master) wheels.
!4824 Fix most of the warnings issued by ruff in python code and notebooks.

Bug fixes

!4582 [MeL/IO] Increase time value output precision for xdmf.
!4666 Reset solution after rejected initial time step.
!4749 fixes a one time step lag of the output flow rates in ComponentTransport when used together with the <linear> optimization.
!4753 Suppress default output if fixed output time steps are given.
!4784 Simplifies the code and fixes a possible bug with dangling pointers in staggered coupled simulations
!4797 Frees some global matrices/vectors after use (bug introduced in !4749)
!4455 Fixed K_pT term of latent heat in TRM and TRF

CMake

!4525 [wheel,web] Use env var CMAKE_ARGS to override CMake preset for wheel.
!4538 Re-enable compilation on Eigen 3.4.0.
!4521 Removed option OGS_USE_PYTHON. OGS is now always built with Python (boundary conditions) support.
!4561 Better third-party license collection.
!4707 Refactored check header job.
!4750, !4473 Use bundled fmt from spdlog.
!4785 [cmake] Updated sanitizers logic. Changes CMake options OGS_ADDRESS_SANITIZER to ENABLE_ASAN and OGS_UNDEFINED_BEHAVIOR_SANITIZER to ENABLE_UBSAN.

Infrastructure

!4542 [ci] Introduced MR label ci::unit_tests which runs unit tests only (skips ctests).
!4550, !4685, !4820 Introducing reproducible builds with GNU Guix.
!4592 [eve] Updated to toolchain 2022b.
!4722 [ci] Deployed guix container to eve, see docs.
!4727 Added CI label ci::web only (fast) which skips notebook execution.
!4704 Notebooks can be placed in web/content as well.
!4762 [ci,nb] Refactored notebook testrunner, notebooks now use regular TOML frontmatter.
!4769 [ci] Limit max notebook runtime in MR pipelines to 10 minutes.
!4776 [cmake] Refactored coverage: simplified CMake logic, removed bilke/cmake-modules-dependency.
!4781 [guix] Include or package dependencies. This will allow building specific commits, e.g.: guix build [...] --with-commit=ogs=[some commit hash] ogs.
!4789 [cmake] Refactored MKL find logic to use CONFIG mode.
!4796 [guix] Build enhancements channel repo. Also added MFront support in !4810.

File I/O

!4557 Breaks default behaviour Updating prj files may be necessary
- Only the variables listed in the prj file output section are outputted
xml <output> ... <variables> <variable>X</variable> <variable>Z</variable> </variables> </output>

A possibly existing property Y will not be written! - In case of empty variables section all available variables are outputted

xml <output> ... <variables> </variables> </output> - OGS tools write all available properties to the result file
!4594 Output sub-mesh specified by material ids. Elements of the corresponding material IDs of the mesh will be extracted to a separate sub-mesh. The bulk-mesh properties are transferred to the sub-mesh. The file name of the sub-mesh in the example below will be bulkmesh_0_2_4.

xml <output> ... <meshes> <mesh>bulkmesh</mesh>  <mesh material_ids="0,2,4">bulkmesh</mesh>  </meshes> </output>

Material Property Library (MPL)

!4531 adds the water saturation temperature calculated according to the IAPWSIF97 in Region4.
!4543 adds the water liquid saturation density and enthalpy calculated from pressure based on the IAPWSIF97 in Region4.
!4562 adds the water temperature in IAPWSIF97 region1 calculated from pressure and enthalpy.
!4564 adds the water enthalpy in IAPWSIF97 region1 calculated from pressure and temperature.
!4524 adds the water vapour saturation density and enthalpy calculated from pressure based on the IAPWSIF97 in Region4.
!4636 initialization of internal state variables for solid models. New section in the project file:

xml <constitutive_relation> <initial_values> <state_variable name="InternalVariable" parameter="InitialValue"/> </initial_values> </constitutive_relation>

!4667 adds the cubic law permeability calculation method for fractures.
!4648 $\phi (1-S_L)$ is removed from vapour diffusion models, VapourDiffusionFEBEX and VapourDiffusionPMQ.

Numerics

!4387 Generalized numerical stabilizer and consequently applied full upwind stabilizer to HC.

Documentation

!4727 [web] Added possibility to directly convert a Notebook to webpage.
!4728 [web] Improved installation instructions and links.
!4704 Tutorial of creating mesh with BHEs.
!4804 [web] Better search.
!4783 Tutorial of creating mesh with inclined BHEs.

Version info

!4537 Boost 1.73.0
!4561 nlohmann/json 1.10.5
!4418 googletest 1.13.0
!4706 spdlog 1.12.0
!4801 Tested hdf5 version is 1.14.3 when built via ogs (minimum still at 1.10.7).

- C++
Published by bilke over 2 years ago

ogs - 6.4.4

Highlights

Some notable additions in this release include the output of residuum vectors on submeshes (now for the TRM and TH2M processes only), restart for parallel simulations were made possible as well as CI coverage for the PETSc configuration was increased and the infrastructure for Jupyter notebooks was extended.

There were also some substantial efforts to enhance the documentation especially for the project file, specific process configurations and tools.

Further CI improvements include the possibility to select subsets of test jobs via merge request labels to shorten feedback cycles and we added performance tracing of benchmarks via our CDash-platform.

Process' changes

LiquidFlow

!4203 Make process per default non-linear. One can enforce linear treatment in project file as follows:

xml <process>  <linear>true</linear> </process>

TH2M

!4362 Added a Jupyter notebook version of the Bourgeat test case
!4392 Function-type parameters can be used for MPL property and constituitive relation parameters. Fixes the "coordinates not set for spatial position"-error.
!4485 Enabled output of extrapolated node wise intrinsic permeability.

PhaseField

!4299 Added a variational phase-field hydraulic fracture model in toughness dominated regime (K-regime).

Component transport process / reactive transport process with coupling of Phreeqc

!4451 Added flow rates output for all components.
!4228 Use inclined elements in ComponentTransport.

ThermoHydroMechanics

!4386 Implemented freezing terms for the energy equation.

ThermoRichardsMechanics and ThermoHydroMechanics

!4363 Added a constitutive setting to the TRM process to make it possible to use either the existing mechanical material models or mechanical material models that use the new extended OGS-MFront interface.
!4410 Kelvin Vectors can now be formed from matrices, allowing the use of arbitrarily rotated anisotropic thermal expansivities if read in as a parameter property.

Constitutive relations (material models)

!4296 Extended the OGS-MFront interface beyond passing only stresses, strains and temperatures.
!4304 All saturation dependent thermal conductivity models have been merged into one (SaturationWeightedThermalConductivity) and can be accessed by specifying the mean type: arithmetic_linear, arithmetic_squareroot and geometric.
!4378 IAPWS density and viscosity as well as Vogels viscosity model were added to MPL.
!4391 Upgraded TFEL / MGIS to 4.0 branch.

Generic features

!4393 Added support to assemble and output residuum vectors on submeshes for the TRM and TH2M processes.

Tools

!4327 Added a tool writing integration point data from OGS output meshes to a new point cloud mesh whose nodes are the integration points of the input mesh.
!4360 Fixed issue where elevation information wasn't added for [OUTFALLS]- and [STORAGE]-entities.
!4452 Added a tool for converting any ascii raster formats OGS can read into *.asc-format.
!4264 Added integration point data partitioning in partmesh.
!4294 Added a new tool to convert pvtu-files to vtu-files: pvtu2vtu.
!4352 Added partitioning and reading of non-IP field data.
!4492 Extended checkMesh- and editMaterialID-tools to optionally output all existing MaterialIDs for a mesh (previously it was just displaying the range).
!4513 [partmesh] Renumbered the bulk node IDs of the bulk mesh.

Data Explorer

!4430 Reader for XYZ raster files added.

Python & Jupyter

!4285 Adds a simple wrapper around OGS CLI tools such that they can be easily used from Python. Available in the OGS wheels/via pip.
!4300 Enables Python BCs and STs in the OGS Python wheels.
!4502, !4512 Added support for markdown-based notebooks via jupytext.

Testing

!4408 Refactored PyVista in notebooks testing logic: no more special treatment for headless systems. User is responsible for providing a window environment, e.g. via xvfb-run, which is shortly documented. Added documentation on how to shorten pipeline run times by modifying the corresponding files. Added pipeline variable CTEST_INCLUDE_REGEX which corresponds to the -R ctest argument.
!4421 [ci] New job include-what-you-use.
!4437 Enabled large tests on PETSc configs in CI. Also added a CI variable CTEST_ARGS for temporarily selecting benchmarks in CI.

Bug fixes

!4281 Fixed IP data access to Kelvin vector valued data. The error was introduced in !4222.
!4302 Reimplement Robin-BCs which were incorrect for 2D and 3D setups.
!4369 Fixed the restart feature of the TRM process, which was broken since !4316.
!4397 Fixed PhaseField's BC for parallel simulations.
!4453 Corrected initial residuum computations when start time is negative.

CMake

!4306 Enabled MSVCs Multi-ToolTask scheduler for build parallelism and better multi-platform ccache setup.
!4408 Test properties can now directly be set. Simplifies CMake logic a bit and is potentially more powerful.
!4417 Don't include GKlibSystem.cmake (it defined NDEBUG on Debug configs!) from METIS and fixed some compile errors in asserts.
!4423 Moved VTK from CPM to external dependencies.
!4473 fmt-library is now used as a regular library. Before it was used as a spdlog-bundled library.
!4494, !4497 [cmake] Cache external dependencies in $CPM_SOURCE_CACHE.
!4365 Simplified CMake test infrastructure (replaced MeshTest() with regulard AddTest() and new TESTER vtkdiff-mesh).

Infrastructure

!4266 Enabled precompiled headers using CMake target_precompile_headers feature. Some improvement for release builds and around 30% improvement for debug builds.
!4329 Refactored notebook testing.
!4370 Added uploading OGS Python wheels to the GitLab registry.
!4401 Better web site and report previews on merge requests.
!4443 Run ctests serially on ubuntu1 for performance metrics collected via CDash.
!4464 [ci] Pipeline refactoring:
- Added scheduled pipeline for wheel build.
- ci::web only pipeline: just add this label to the MR to limit CI to Jupyter notebook runs and web site creation.
- Changed ci skip-label to ci::skip.
- !4465 ci::linux only and ci::mac only and ci::win only labels for running platform specific builds only.
!4491 [ci] Introduced MR label ci_large for enabling large tests.
!4502 Added a "Launch in BinderHub"-button to notebooks on the website: launches Jupyter Lab instance pre-configured with ogs via wheel, clones the current ogs repo in it and opens the respective notebook ready to run. Please note that startup times may be several minutes and the computing resource are limited (1 core, 2GB RAM). For improved performance we would need to setup own infrastructure. Also currently only works for serial ogs configs.
!4515 Updated Juwels modules for new 2023 stage.

File I/O

!4375 [ogs] Added -s parameter used for locating Python BC scripts.
!4430 Reader for XYZ raster files added.
!4431 Geometrical sets can be defined in the output section of the project file.

Material Property Library (MPL)

!4445 Added IAPWS thermal conductivity model for water.

Documentation

!4487,!4498,!4496 Added and extended documentation for many preprocessing- and mesh generation-tools.
!4442 Added a new ogs beginner user guide.
!4438, !4450 More process documentation.

Version info

!4473 fmt 8.1.1
!4473 spdlog 1.10.0

- C++
Published by bilke over 3 years ago

ogs - 6.4.3

See www.opengeosys.org/releases/6.4.3/ for binary downloads.

Highlights

We are happy to announce that the TH2M-process is now feature complete and has evaporation and dissolution implemented.

The two-component approach also enables the description of phase transition processes (evaporation, solution) under an equilibrium condition. The TH2M model is verified and validated on a benchmark suite which provides a hierarchical classification of different coupling combinations of the individual processes.

Stabilization is the numerical approach to eliminate the spatial oscillations produced by the Galerkin finite element method for the advection diffusion transport equation. There are two stabilization schemes, isotropic diffusion and full upwinding, are available now in HT and ThermoHydroMechanics.
Python bindings were extended in two ways: OGS got python wheels and can be now installed with pip, and has got a basic python interface to run a simulation from within python.
For developers the biggest improvement is the inclusion of the Eric Niebler's ranges library. Already used in few places in OGS it greatly improves code readability through easier composition.

Process' changes

!4087 Adding forward differences numerical Jacobian computation. It is less expensive then central differences, but not necessarily slower overall, and sometimes even faster.
!4161 Refactoring of domain deactivation.
!4204 Removes the IntegrationMethod template parameter from local assemblers that use Taylor-Hood elements.
!4217 Removes the IntegrationMethod template parameter from the remaining local assemblers (processes, STs, BCs).
!4233 Parameter type Function can be used for MPL property and constituitive relation parameters in THM, TRM and TR.
!4210 [PL/TH2M] Add/correct residuum output.
!4247 MPL: Reimplement VariableArray as own class. Less memory and a little faster. Easier usage.

TH2M

The TH2M process describes a two-phase, two-component approach, which is fully coupled with thermodynamic and geomechanical processes. Due to the complex process couplings, many different processes (e.g. in repository systems) can be investigated numerically, including media dry-out and resaturation, consolidation, stress- or deformation-dependent permeabilities, thermal expansion and heat-induced stresses, gas transport processes in fully or partially saturated media and others. The two-component approach also enables the description of phase transition processes (evaporation, solution) under an equilibrium condition. To validate the TH2M model, a benchmark suite was created that provides a hierarchical classification of different coupling combinations of the individual processes. This proves the validity and correct implementation of all terms of the model equations.

!4131 Dissolution of gas into the liquid phase, completing the phase transition feature in TH2M
!4131 Two tests validate the dissolution process and the diffusive transport of the dissolved gas in the water phase

PhaseField

Spectral decomposition for energy split has been added.

ThermoRichardsFlow

!4100 Adding thermo-osmotic and thermo-filtration effects

ThermalTwoPhaseFlowPP

!4136 Adding a third component with equilibrium partitioning between liquid and gas phases.
!4194 Correct the energy equation and heat pipe benchmark results.

Component transport process / reactive transport process with coupling of Phreeqc

!4106 Enable chemical speciation parallelization on CPU.
!4130 Update the description of governing equations in the documentation of the process.
!4207 Enable a new type of chemical solver "self-contained chemical solver".

HeatTransportBHE

!4102 Server Communication (Python Interface) pre and post timestep: Enabling the server communication (python interface) before (pre) and after (post) time step.
!4208 PowerCurveFlowCurve-function: Adding PowerCurveFlowCurve function to flowandtemperature_control options in HeatTransportBHE process.

LiquidFlow process

!4201 Aperture size for inclined element.

ThermoRichardsMechanics and ThermoHydroMechanics

!4100 Adding thermo-osmotic and thermo-filtration effects / fixing contributions in THM.
!4153 Separates the constitutive setting of the TRM process from computations involving shape matrices .
!4198 Splits the constitutive setting of the TRM process into modular pieces.
!4236 Re-enables pressure and temperature dependent density models in TRM.

Constitutive relations (material models)

Thermal models

!4162 Adding temperature-dependent thermal properties due to first order phase change of pore fluid making HeatConduction process nonlinear for capturing soil freezing phenomena

Numerics

!4178 Isotropic diffusion stabilization for solving the advection-diffusion equation.
!4185 Apply the isotropic diffusion stabilization to ThermoHydroMechanics process.
!4165 Full up winding scheme for HT.
!4196 Applied the full upwind stabilization to THM process.

Tools

!4176 Most of the tools should now also work when OGS was built with PETSc.
!4252 Allow the removal of point-elements from meshes via the removeMeshElements-tool.
!4270 Added "MeshMapping"-tool for handling all options for 2D mesh mapping, i.e. mapping based on a raster or another mesh, or to a static value.

Data Explorer

!4250 Adding support for *.2dm triangle meshes via GMS Import.
!4252 Allow the removal of point-elements from meshes.
!4265 Added resolution aware scaling for GUI elements

Python / Jupyter

!4135 Restored ipyvtklink and static PyVista rendering backend. Also added msh2vtu.
!4049 First basic implementation (init, exec, finalize) of a Python interface to drive OGS from Python.
!4263 Python wheels for module (see !4049) and ogs binaries.
!4242 A jupyter notebook for Theis solution is added.

Testing

!4086 Use VTK wheels from PyVista on Python 3.10 (when using the auto-generated Python virtual environment by setting OGS_USE_PIP=ON).
!4199 [ci] Trigger project-specific downstream pipeline.
!4221 [ci] Added new manual job 'advanced container' which builds and tests ogs with OGS_USE_INSITU=ON.

Bug fixes

!4089 checkMesh: Fixed -p parameter. Properties were always printed even if the -p-parameter was not given.
!4093 VerticalSliceFromLayers: Fixed mesh generation to be consistent with 3D mesh generation (i.e. meshes are built from bottom and top). This may require a fairly up-to-date GMSH version (GMSH 4.9.5 was working in our tests).
!4115:
- Fixes one wrongly oriented edge in Quad8 elements. Also affects Quad9 elements. Corrects the surface normal computation, in particular.
- Provides a corrected surface normal implementation for line elements.
- Corrects the determination whether a point is inside a line segment.
!4164 Fix pvtu output when VTK is build via CPM.
!4195 Excavation of neighbouring subdomains now produce expected results along the common boundary.
!4226 Fixes setting the previous temperature value in the OGS MFront interface.
!4243 Fixed a run time error when Python BC is used in the code built with PETSc.
!4246 Fixed a bug in Python source term with PETSc.

CMake

!4081, !4101 Some CMake cleanup and renovations. Better Python finding logic.
!4129 [cpm] Removed MPI dependencies in VTK.
!4132 Use only MKLs OpenMP implementation.
!4167 Some RPATH fixes for lib64-based systems. Also removed option OGS_INSTALL_EXTERNAL_DEPENDENCIES, use OGS_INSTALL_DEPENDENCIES instead!. Proper RPATH both for the build tree as well as the install tree.
!4221 Re-enabled insitu functionality. Renamed CMake variable OGS_INSITU to OGS_USE_INSITU.

Infrastructure

!4137 Refactored cpm offline cache handling.
!4145 Refactored MetisSetup.cmake and partmesh now uses 64 bit indices (was 32 bit before).
!4094 Introducing cdash.opengeosys.org, a test report dashboard.

File I/O

!4082 Copy bulk mesh node property values to sub-meshes specified for output.
!4126 [jupyter] Added gmsh and msh2vtu to Jupyter image.
!4121 PVD to XDMF (VTK to HDF5) conversion tool added.
!4176 Single threaded PETSc simulations now also writes .vtu instead of .pvtu files.
!4192 Added output of active/inactive elements for subdomain deactivation.
!4188 Refactoring / restructuring the Output class; enabled XDMF / HDF5 output for staggered scheme.

Documentation

!4193 Added docs on jupyter notebook generated web pages.
!4190 VS Code development container. See docs at https://www.opengeosys.org/docs/devguide/advanced/vscode-devcontainer/.
!4197 [web] Added mermaid diagrams.
!4205 Added a Citation File Format for citation metadata.
!4239 [web] Added a 1-D decay-chain benchmark in section Reactive Transport.
!4140 Added an instruction for how to conduct parallel computing with PETSc.

Version info

!4081, !4049 CMake ~~3.16~~ 3.22
!4108 GCC 10.2.0
!4108 VTK 9.1.0
!4108 Ubuntu 22.04
!4189 Apple clang 13.1.6
!4189 Clang 13
!4189 New range-v3 library version 0.12.0
!4227 spdlog 1.10.0

- C++
Published by bilke almost 4 years ago

ogs - 6.4.2

See www.opengeosys.org/releases/6.4.2/ for binary downloads.

Overview

Some of the highlights of this release are: the extension of the TH2M process to handle phase transitions, more processes can be run in parallel with PETSc and Taylor-Hood Elements, the new HDF5-based input/output routines, and the introduction of Jupyter Notebook based benchmarks (see an example).

Process' changes

!3963 Enabled equation wise flexibility in the use of compensatenonequilibriuminitialresiduum.

TH2M

!3839 Extend Jacobian with Laplacian's derivatives.
!3942 Thermal conductivity of the medium can now be defined in the input file.
!4034 Phase transition was revised and some errors were fixed. Energy transport now includes diffusion processes, diffusion in the mass balance is now dependent on capillary pressure. Tests have been added, including the revised heatpipe with analytical solution.

Component transport process / reactive transport process with coupling of Phreeqc

!3796 Extend the input of surface complexation sites in moles via the MaterialPropertyLib for HC-Phreeqc coupling.
!3903 Enable to use cation exchange and surface complexation models simultaneously for HC-Phreeqc coupling.
!3918 Add a "fixing pe" option.
!3931 Support the use of PETSc nonlinear solver.
!4004 Add Newton's method based linearization scheme for solving non-conservative formulation.
!4006 Output total mass flux and residual mass flux by node-wise.

Thermo-Richards-Mechanics

!3980 Added liquid density and viscosity output.
!3547 Implementation of the vapour diffusion and the latent heat terms of TRM.

HeatConduction

!3972 Assembly in inclined elements.

Hydro-Mechanics

!3848 Use permeability strain derivative in the jacobian for HM (for embedded fracture permeability model).

Heat Transport BHE

!4007 Changed python based Server Communication process (e.g. with SimulationX) from postTimestep to preTimestep.

ThermalTwoPhaseFlowPP

!3924, !4014 Employ MPL in ThermalTwoPhaseFlowWithPP process.

Material models

!3929 Add the Verma-Pruess porosity-permeability model.
!3941 Modify the "EffectiveThermalConductivityPorosityMixing" property to allow for two- and three phase media.
!3945 New property IdealGasLawBinaryMixture.
!3923 [MPL/RelPermNonWettingPhaseVanGenuchtenMualem] replace the Newton-Raphson method with the Regula–Falsi Method.
!3992 Enabled fracture normal rotation with the EmbeddedFracturePermeability model.

Numerics

!3871 Integration order 4 implemented for Tetrahedrals. For an overview over OGS's integration methods see also !4021.
!3907 Added new Eigen iterative solvers: BiCGSTABL, IDRS and IDRSTABL.
!3882 Adds support for Taylor-Hood elements to Python boundary conditions and Python source terms.
!3963 Enabled equation wise flexibility in the use of compensatenonequilibriuminitialresiduum.
!3991 Enable to use 13 node pyramid and 15 node prism.

Parallel computing

!3805 [partmesh] Removed the option of -q or --lh_elements for the implementation of parallel computing with Taylor Hood elements.
!3866 Parallel computing with Taylor-Hood elements: implementation and tests with HydroMechanics process.
!3920 Enable parallel computing in TRM with Taylor-Hood elements.
!3919 Enable node search function work under MPI.
!4047 Enable parallel computing in TH2M with Taylor-Hood elements.

File I/O

!3857 VTK mesh converter: safely convert all integer types.
!3915 HDF output option: Fast file I/O and data integrity
!4033 Rename HydraulicFlow and HeatFlux to VolumetricFlowRate (for volumetric formulations (mass balance divided by density) / MassFlowRate and HeatFlowRate.

Utility

!3863 Added the conversion of quadratic quadrilateral elements in GMSH2OGS

GeoLib

!3935 Change TemplateVec::getVector() return value from vector<T*> const* to vector<T*> const&

Project file syntax

!3962 Apply patches marked with after_includes="true"-attribute after <include>s are evaluatetd, docs.

ogs

!3976 Added parameter -m for specifying a mesh input directory.

Testing

!3930 Notebooks are now tested as part of ctest. See docs for more info.
!3901 [TRM] Added a benchmark of point heat source for TRM.
!4001 Added a simple MKL benchmark.
!4005 Run TaskCDECOVALEX2023 with parallel computing.
!4021 Adds extensive unit tests for OGS's quadrature schemes. Now for each supported integration method and integration on each mesh element type we test, which polynomial order we can integrate exactly.
!4012 Added parallel computing benchmarks for ThermoRichardsFlow.

Bug fixes

!3932 Fixed several memory leaks and access bugs.
!3956 THM: Fix temperature equation for case w/o thermal osmosis.
!3978 Fix access of transport porosity as medium property in TRM.
!3919 Enable node search function work under MPI.
!4021 Fixes pyramid integration for integration order 1. Note, the location of the single integration point was changed! If you have any restart data with integration order 1, the respective location will silently change. However, that seems acceptable since before the pyramid order 1 integration was just wrong.
!4051 Changes the input storage order of tensorial properties of MPL. Now it is row major, before it was column major. The new row major storage order is the storage order that naturally arises in prj files. The old behavior was not a bug per se, but could very likely lead to subtle errors with asymmetric tensorial properties.
!4055 Fixing a bug in Process::setInitialConditions under PETSc.

CMake

!3910 Updated Conan CMake integration.
!3940 Select lld over GNU gold over regular linker. Speeds up link times.
!3950, !4030 Added option ~~OGS_INSTALL_PETSC~~ OGS_INSTALL_EXTERNAL_DEPENDENCIES to install (locally build) PETSc or MFront / TFEL into CMAKE_INSTALL_PREFIX.
!3951 Removed std::filesystem hacks for older compilers.
!3983 [cmake] Refactored (and fixed) processes setup logic.
!3989, !3995 Offline build with cpm and external dependencies cache. See docs.
!3999 Added option OGS_DEPENDENCY_VERSIONS to overwrite entries in versions.json.
!4001, !4056 Use a better FindMKL.cmake which includes also linker flags.
!4027 Configure VTK modules and CMake options in versions.json.
!4041 Replaced poetry by simple python / pip calls:
- Poetry is not required anymore for automatic Python package installation. Only a Python interpreter is required (nowadays they already include venv and pip).
- Renamed CMake option OGS_USE_POETRY to OGS_USE_PIP (which now defaults to OFF!). Before poetry was used per default when it was found, now this behavior is reversed (needs to explicitly switched to ON).
!4059 Added --download-hypre to local CPM build.

Infrastructure

!3874 Allow utils build on PETSc config.
!3876 Added Jupyter image with PETSc support, image name: registry.opengeosys.org/ogs/ogs/ogs-petsc-jupyter.
!3597 Added CI linux build with debug checks, address and undefined behaviour sanitizers.
!3994 [ci] Added msvc-code-analysis.yml for GitHub Actions.
!4067 [web] Restructuring to use Hugo page bundles.
!4069 [ci] Deploy CLI on Windows GUI downloads.

Version info

!3844 Update gtest to version 1.11.0
!3910 Minimum Conan version 1.36.0
!3951 Minimum gcc version 9.1
!3968 Update exprtk to newest version Dec. 2021.
!4018 Update minimum PETSc version to 3.16.3.

- C++
Published by bilke over 4 years ago

ogs - 6.4.1

See www.opengeosys.org/releases/6.4.1/ for binary downloads.

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. 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 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 as well as the introduction of a first iteration of a Jupyter Notebook based user workflow. Stay tuned for more on interactive computing in future releases.

New processes

TH2M

A thermal two-phase flow in deformable solid media process.

!3588 Added an infrastructure for the TH2M Process that handles different models of phase transitions.
!3550 Monolithic scheme implementation using central differences Jacobian.
!3656 Collect all constitutive variables updates in single function.
!3684 HM flow-fully-saturated tests; liquid and gas formulations.
!3759 Restart; integration point data I/O.
!3763 Extract constitutive variables.
!3762 Excavation. Enable domain deactivation.
!3777 Switch to constant solid volume fraction
!3767 Implement partial analytical Jacobian, working for saturated media.
!3802 Gas and liquid phase density output directly from ip_data array.

Stokes flow

!3617 Monolithic scheme implementation.
!3658 Documentation
!3668 Extended to Stokes-Brinkman variant.

Process' changes

!3583 THM and TRM process need a thermal conductivity property on the medium level
!3561 Excavation support for coupled mechanics processes and Dirichlet boundary conditions on the excavated surfaces were added.
!3580 [THM] Replaced total thermal strain with incremental thermal strain
!3742 [THM] Adding integration point output for stress and strain and a restart test. !3706 Separate createLocalAssemblers respectively for BC/Source term and system of equations.

PhaseField

!3749 added constrained minimisation to the phase-field solution scheme.
!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 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 for details)

Component transport process / reactive transport process with coupling of Phreeqc

!3695 Enabled to input the amount of ion exchangers in subdomains via the MaterialPropertyLib
!3648 Added capability to model ion exchange reactions.
!3563 Added optional functionality for chemically induced porosity change.
!3567 Added optional functionality for irreversible equilibrium reactions to the ChemistryLib.
!3721 Provided a simple means of considering temperature effect on the diffusive transport process.
!3744 Allowed chemical calculations by means of the look-up table approach.
!3781 Solved the reaction equation in the reaction stage instead of doing extrapolation from integration points onto mesh nodes.
!3810 Incorporate the effect of change of storage capacity.

HeatTransportBHE

!3793 Add server communication feature after each time step

HydroMechanics

!3607 Simulation on a vertical slice of a 3D domain.

LIE

!3672 Use the existing class to compute the rotation matrix in LIE, which also corrects the orientation of the displacement jump.
!3676 Corrected the velocity and its orientation in the fracture.
!3834 Corrected matrix sizes in velocity computation.

LiquidFlow process

!3610 Use specific body force instead of darcy_gravity. Users LiquidFlow project files has to be adapted!
!3623 Use body force vector in the local assembler.
!3632 Add local assembly in inclined elements for simulating flow in fracture.

Richard's component transport process

!3606 !3614 Employ MPL in Richard's component transport process.

Richard's mechanics process

!3574 Extend integration point data output to solid material state internal variables used by e.g. MFront. This makes correct restart possible.
!3690 Local Newton-Raphson: add optional scaling for convergence tests, which is used in the computation of micro-porosity.

SmallDeformation

!3683 Use the element wise reference temperature.

ThermoMechanics

3738 Fixed integration point (IP) data IO for restart computation.

ThermoRichardsMechanics and ThermoHydroMechanics

!3583 THM and TRM process need a thermal conductivity property on the medium level
!3758 THM/TRM; Add heat flux output. Corrected HydraulicFlow.
!3611 TRM; Include the thermal strain into total mechanical strain.
!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 Enabled integration point data I/O in THM

Material models

!3572 IdealGasLaw now uses molar mass from VariableArray rather than from another MPL-Property.
!3579 New saturation-capillary pressure relation, SaturationExponential, mainly for testing and prototyping purposes.
!3546 Implementing medium level property to mix thermal conductivities from phases.
!3599 Added orthotropic embedded fracture permeability model
!3640 A Function type MPL property using exprtk, similar to the Function type parameter. All scalar variables from VariableArray can be used.
!3721 Added temperature dependent model for molecular diffusion.
!3745 New stationary creep model for rock salt.
!3747 The damage-free version of the Günther Salzer model for transient and stationary rock salt creep.

Numerics

!3676 Dropped the rotation of the shape function gradients. These changes also correct the velocity and its orientation in the fracture.

Data Explorer

!3578 Elevation of station data can be mapped based on meshes or rasters

Testing

!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 First implementation of a code coverage visualization.

Bug fixes

!3615 Bug fixing in EffectiveThermalConductivityPorosityMixing: Avoided the porosity calculation
!3566 Fixed a bug in NodalSourceTerm when the Taylor-Hood elements are used.
!3682 Fixed the output of phase compositions in TH2M process
!3585 Use correct saturatation for swelling stress update in output of the RichardsMechanics process.
!3652 Fixed a MFront related bug in HydroMechanics.
!3756 Speedup Dirichlet BCs for deactivated subdomains avoiding costly reallocations.
!3788 Use local topology information while removing global numbering dependencies in Mesh. Resolves base node id larger then higher order node id warning.
!3797 Refactored material ID list parser, prevents some (unlikely) bugs with malformed prj files.
!3816 Fix Brooks-Corey saturation derivative.
!3834 Fixed an Eigen matrix size related bug in LIE, which sporadically causes LIE benchmark failed on Mac OS.

CMake

!3592 Added build and test presets.
!3624 Job pools for Ninja: optimizes build parallelization (full cores for everything but processes, processes depend on available memory)
!3671 Integrate tfel with ExternalProject_Add() instead of Conan.
!3687 Qt is not handled by Conan anymore! Use aqt to install it on your system.
!3698 Moved LIS dependency from Conan to ExternalProject.
!3727 Added support for ccache on Windows, dropped clcache.
!3707 CMake test presets, requires CMake 3.21.

Infrastructure

!3555 and !3835 Clang-format all of the code base. Thriving for consistency.
!3562 Added threshold for Doxygen warnings (16).
!3570 Enabled compiler warnings for executables.
!3622 Correct naming of private data members using trailing underscore.
!3671 Enabled mfront on CI mac job.
!3712 Added library dependency reports to Doxygen documentation. Added Lizard code complexity report to Doxygen CI job as a build artifact.
!3720 Added clang-format check in pre-commit.
!3751 OGS binaries are now in the PATH in the container environment. Execution via --app ogs is not required anymore.
!3755, !3757 Initial Apple ARM (M1) support.
!3761 CI now runs with Pipelines for merged results. Also switched to git clang-format instead of clang-format.
!3776 Added predefined container with Jupyter Notebook, ogs and Python tools.

File I/O

!3598 Time is additional dimension HDF5 output data - allows slicing with h5py
!3604 HDF5 can now contain multiple meshes (boundary conditions) and an attribute "times" with time step values for each step
!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 MFront based on TFEL branch rliv-3.4
!3757 Conan 1.34.0 (optional)
!3707 CMake presets require CMake 3.21.

- C++
Published by bilke over 4 years ago

ogs - 6.4.0

See www.opengeosys.org/releases/6.4.0/ for binary downloads.

The current release forms the basis for the upcoming TH2M process and further extension of the newly implemented non-isothermal Richards mechanics. The highlights of this release are collected in the overview with details below.

Overview

The reactive transport process and its Phreeqc interface were enhanced: extended the porosity interface and provide two ways of calculating solid/liquid ratio. Many new material models were implemented including the Clausius-Clapeyron vapor pressure, the Somerton's thermal conductivity, the FEBEX and PMQ type vapour diffusion, a water vapour density property, and a linear latent heat of water property. A new process – the non-isothermal Richards mechanics – was implemented and extends our ability for complex thermo-hydro-mechanical interaction simulations further. The simpler Richards mechanics process was enhanced by a double structure porosity model, which has been used for simulations with Bentonite. And finally, modelling of the excavations got a fine-grained time control over the excavation progress.

The development and continuous integration environment was enhanced with automated spell-checking of code and documentation and a collection of code coverage metrics for the merge requests. Code has be become more consistent in formatting by using the clang-format and cmake-format tools. Most of the third-party libraries, which are required for certain OGS configurations, are now managed by a more integrated approach using CPM – the CMake Package Manager – instead of git submodules and Conan packages. We may phase out Conan for package management in the future but at the moment there are still Conan packages in use, most notably Qt and PETSc.

We implemented a release branch with bug fixes workflow, see #3093 and the Discourse announcement.

Features

!3549 Adapted license wording to fully conform to BSD 3-clause license.

New processes

!3166 Non-isothermal Richards mechanics (monolithic scheme).

Process' changes

Component transport process / reactive transport process with coupling of Phreeqc

!3326 Hide chemical solver interface inside the ComponentTransportProcess.
!3358 Utilize MPL for the setup of chemical system.
!3362 Update porosity accessing interface in support of incremental model type in ComponentTransportProcess.
!3467 Replaced molecular diffusion with pore diffusion in ComponentTransportProcess.
!3364 Rename reactant amount as molality.
!3372 !3490 !3507 Set solid/liquid ratio according to solid volume fraction, porosity and fluid density.

Common process' changes

!3325 Include swelling stress into total strain. Fixing effective stress usage.
!3355 Improve generic interface for setting initial conditions.
!3538 Time dependent excavation. Extending time intervals to time curves.

Hydro mechanical processes

!3405 !3441 Add double structure model to RichardsMechanics process using micro-saturation model and compatible with swelling.
!3429 Use MPL in ThermoMechanics.
!3459 Changed the strain and stress output in HydroMechanics.
!3477 !3503 Fix a bug in RichardsMechanics where the initial stress was ignored when using central differences Jacobian.
!3498 Permeability, porosity, storage, and transport porosity are now medium properties in RichardsMechanics.
!3114 Permeability, storage, Biot coefficient, and porosity are now medium properties in ThermoHydroMechanics, HydroMechanics and RichardsFlow.

Boundary condition

!3531 Separate time dependent Dirichlet boundary conditions and subdomain deactivation boundary conditions.

Numerics

!3422 Improving numerical stability in RM and TRM by using secant derivative of dSLdp_cap in local assembler.
!3431 Local Newton-Raphson methods supports increment tolerance additionally to the residuum tolerance now. Previously used error_tolerance tag is deprecated.
!3468 Update PETSc SNES solver and add interface for constraint variables.

Parameter

!3342 New parameter type "RandomFieldMeshElementParameter".

Time stepping

!3411 Fixed a bug in IterationNumberBasedTimeStepping.
!3416 Fixed a bug that skips output after a rejected time step followed by successful time step.

Material models

!3316 A vapour pressure model 'Clausius-Clapeyron'.
!3356 'Modified Cam clay' model for cohesion-less soil materials.
!3423 Split the relative permeability property by phase.
!3439 Gas pressure permeability model.
!3449 Added a function of formKelvinVectorFromThermalExpansivity.
!3450 Somerton's thermal conductivity model for soil.
!3498 PermeabilityOrthotropicPowerLaw, PorosityFromMassBalance and TransportPorosityFromMassBalance are now defined on the medium level.
!3491 Added vapour diffusion type and the FEBEX type vapour diffusion property.
!3527 A vapour diffusion property of VapourDiffusionPMQ .
!3489 A water vapour density property.
!3519 A linear latent heat of water property.
!3542 Add a notion of fluid phase to MPL allowing HM process to use Gas or AqueousLiquid for fluid phase.

Bug fixes

!3361 !3400 CMake fixes when using the MKL library.
!3397 Skip secondary variables evaluation if the nonlinear-solver failed, e.g. for MFront material model.

File I/O

!3383 Add iteration number output option to file names.
!3307 New HDF5 writer based on collective MPI IO
!3371 Node partitioned mesh reader handles all available element types.
!3532 Remove unused XmlNumInterface.
!3533 Sort and cleanup XML interfaces.

Code base changes

!3502 Using std::optional through all of the code base replacing boost::optional.
!3517 Using std::any replacing the boost::any.

Replacing the old implementations on small vectors and matrices with Eigen equivalents: - !3354 Change signatures of compute{2,3}DRotationMatrixToX - !3319 !3320 !3346 [GeoLib] Substitute Vector3 by Eigen - !3345 [GL] Change interface of computeRotationMatrixToXY. - !3359 Final removal of MaL::DenseMatrix and MaL::Vector3 - !3512 Replace scalarProduct() with Eigen::VectorXX::dot().

Testing and documentation

!3377 Added gmldiff tool.
!3351 xdmfdiff enabled for testing
!3446 Removed Parsl test. We will focus on Snakemake for workflow management instead.
!3448 Revived code coverage.
!3486 Doxygen will now generate full docs (suitable for all configurations).
!3505 [web] Updated development workflow and Conan usage.
!3552 Full-text search for Doxygen.

Tools and utilities

!3534 Adjusted reviseMesh command line utility to handle all mesh properties instead of just MaterialIDs

New tools

!3433 Creating a 3D voxel grid out of a list of 2D mesh layers
!3433 Marking all elements in a 3D voxel grid intersected by a 2D mesh (e.g. a fault)

Updates

!3482 GMSH2OGS can now extract boundary/subdomain meshes consisting of line elements.

CI & Infrastructure

!3343 Enable C++20 support.
!3381 Serial container is build with Python support.
!3385 Container have virtualenv installed to create custom Python environments.
!3401 Website provides binaries for release branch with bug fixes.
!3448 Code coverage reports for merge requests.
!3472 Automatic spell checker (codespell) as pre-commit check.
!3508 Serial container includes MFront support.
!3539 Fixed Doxygen warnings output.

CMake

!3428 Introduction of CMake presets for common build configurations.
!3435 Removed option OGS_USE_EIGEN. Eigen is used through all of the code for long time already.
!3437 Replaced git submodules with CPM. See docs.
!3466 Reverted back to out-of-source builds in presets.
!3494 More Conan packages moved to CPM. Renamed CMake option BUILD_TESTING to OGS_BUILD_TESTING.
!3496 Preparation of code formatting with clang-format and cmake-format.
!3504 Replaced Conan VTK module with CPM.
!3505 Enabled build configuration with sources from tar/zip archive (previously full git repo was required).
!3509 Added cmake-lint as a pre-commit check.
!3518 Added cmake-format as a pre-commit check and formatted all CMake files except of Third-party and Tests.cmake.
!3535 Simplified ccache setup, added third-party license info into installed ogs packages, simplified MSVC folder setup.

Version info

!3343 MSVC compiler 19.24
~~!3343 Boost 1.67.0~~
!3508 Boost 1.69.0
!3343 Eigen 3.3.9
~~!3374 Conan 1.32.1~~
!3473 Conan 1.33.0
!3428 CMake 3.19 (only when using CMake presets)
!3504 VTK 8.2.0

- C++
Published by bilke over 5 years ago

ogs - 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 HeatTransportBHE 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 square5500x5500staggeredschemeadaptive_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 targetlinklibraries(). !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)

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Published by bilke over 5 years ago

ogs - 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

- C++
Published by bilke almost 6 years ago

ogs - 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

- C++
Published by bilke about 6 years ago

ogs - 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

- C++
Published by endJunction over 6 years ago

ogs -

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 OGSBUILDPROCESSES=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

- C++
Published by endJunction over 6 years ago

ogs - 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

- C++
Published by bilke almost 7 years ago

ogs - 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 visualisation yet). #2110
Mesh element removal can now remove elements based on value ranges of arbitrary scalar arrays (currently only int- and double arrays are supported). #2115
added custom VTK filter to represent raster data as point clouds. #2121
geometrical points can now be converted into station points. #2369
fixed issue with geometrical surfaces not being loaded correctly. #2388
Replace deprecated QVTKWidget with QVTKOpenGLWidget #2432

Other notable code changes

C++17 standard is enabled and is allowed in the production code (given the compiler support). #2298
Separate monolithic ProcessLib into individual processes. Now it is possible to build ogs with selected processes only. This also improves linking times. #2017
Parameters are extracted in own library. #2413
Port secondary variable extrapolation and output for PETSc builds. #2082
Extend Kelvin mapping functions and move implementation to MathLib. #2060, #2075, #2044
Collect generic algorithms in single header file. #2161
Remove unused MeshSubsets class. #2135
Removed writing of xsd header in XML files, #2198

Infrastructure

Migrated LFS storage from GitLab to Artifactory. #2359
Optimized ctest runtime by starting long-running benchmarks first. #2310
Proper RPATH handling for shared library installations. #2208
Package OGS inside container with Singularity; more docs. #2193, #2356
Migrated opengeosys.org to a static site generator (Hugo) unifying documentation and general OGS info. #2088, #2095, #2123
Speed-up CMake run time. #2072, #2392

CMake options changes

OGS_USE_PYTHON enables Python BCs. #2170
OGS_BUILD_TESTS was renamed to BUILD_TESTING. #2350
Added OGS_USE_CVODE. #2344
Added OGS_BUILD_PROCESSES for ;-separated list of processes to build. #2233
OGS_USE_CONAN=ON is now the default when conan was found. #2207

Version info

CMake minimum version 3.10
Visual Studio minimum (and tested) version 2017
GCC minimum version 6.2 (tested: 6.4)
Clang minimum version 3.5 (tested: 7.0)
Boost minimum version 1.66.0
VTK minimum version 8.1. #2158
Qt tested version 5.11.2
Python tested version 3.7.2

- C++
Published by bilke over 7 years ago

ogs - 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 https://github.com/ufz/ogs/pull/1758
PhaseField https://github.com/ufz/ogs/pull/1813 and https://github.com/ufz/ogs/pull/1895
RichardsComponentTransport https://github.com/ufz/ogs/pull/1929
ThermoMechanics https://github.com/ufz/ogs/pull/1800
TwoPhaseFlow p-rho https://github.com/ufz/ogs/pull/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. https://github.com/ufz/ogs/pull/1970
Heterogeneous liquid flow properties (https://github.com/ufz/ogs/pull/1979, https://github.com/ufz/ogs/pull/2017)
New boundary conditions added: Nonuniform Dirichlet (https://github.com/ufz/ogs/pull/1952) and Neumann (https://github.com/ufz/ogs/pull/1891), and normal traction (https://github.com/ufz/ogs/pull/1896)
Framework for time stepping and a first application of adaptive time stepping, EvolutionaryPIDcontroller, and automatic time step control (https://github.com/ufz/ogs/pull/1803).
Nodal source terms (https://github.com/ufz/ogs/pull/1977)
Fix deformation processes to work correctly with PETSc parallelization (https://github.com/ufz/ogs/pull/1838).
Fix the access to local data of PETScVector (https://github.com/ufz/ogs/pull/1797).
Add damping factor to global Newton. https://github.com/ufz/ogs/pull/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 https://github.com/ufz/ogs/pull/1971
Add material forces as published in http://www.sciencedirect.com/science/article/pii/S0093641317303865 https://github.com/ufz/ogs/pull/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. https://github.com/ufz/ogs/pull/1917
Set default Eigen's cmake flag disabling vectorization since this lead to several problems in different environments. https://github.com/ufz/ogs/pull/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 (https://github.com/ufz/ogs/pull/1873).

- C++
Published by endJunction over 8 years ago

ogs - 2017

Features:

New processes:

ComponentTransport https://github.com/ufz/ogs/pull/1758
PhaseField https://github.com/ufz/ogs/pull/1813 and https://github.com/ufz/ogs/pull/1895
RichardsComponentTransport https://github.com/ufz/ogs/pull/1929
ThermoMechanics https://github.com/ufz/ogs/pull/1800
TwoPhaseFlow p-rho https://github.com/ufz/ogs/pull/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. https://github.com/ufz/ogs/pull/1970
- Heterogeneous liquid flow properties (https://github.com/ufz/ogs/pull/1979, https://github.com/ufz/ogs/pull/2017)
- New boundary conditions added: Nonuniform Dirichlet (https://github.com/ufz/ogs/pull/1952) and Neumann (https://github.com/ufz/ogs/pull/1891), and normal traction (https://github.com/ufz/ogs/pull/1896)
- Framework for time stepping and a first application of adaptive time stepping, EvolutionaryPIDcontroller, and automatic time step control (https://github.com/ufz/ogs/pull/1803).
- Nodal source terms (https://github.com/ufz/ogs/pull/1977)
- Fix deformation processes to work correctly with PETSc parallelization (https://github.com/ufz/ogs/pull/1838).
- Fix the access to local data of PETScVector (https://github.com/ufz/ogs/pull/1797).
- Add damping factor to global Newton. https://github.com/ufz/ogs/pull/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 https://github.com/ufz/ogs/pull/1971
Add material forces as published in http://www.sciencedirect.com/science/article/pii/S0093641317303865 https://github.com/ufz/ogs/pull/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. https://github.com/ufz/ogs/pull/1917
Set default Eigen's cmake flag disabling vectorization since this lead to several problems in different environments. https://github.com/ufz/ogs/pull/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 (https://github.com/ufz/ogs/pull/1873).

- C++
Published by endJunction over 8 years ago

ogs - 6.0.8 with insitu visualization capabilities

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

- C++
Published by bilke over 9 years ago

ogs - M and HM processes with Lower-Interface Elements.

The highlight of the release is the implementation of the Lower-Interface Elements for both the small deformation process (M) and hydro-mechanics process (HM) allowing fractures to be incorporated in the solution domain. For the liquid flow and two-phase flow processes several material models for the fluids pressure, density, permeability, and viscosity were added.

Features:

Implementation of hydro-mechanics (HM) with LIE. #1537-#1541
Implementation of small deformation (M) with LIE. #1452
Fracture constitutive models. #1434
Hydro-Mechanics process. #1508
First version of monolithic hydro-thermal process implementation with Boussinesq approximation using constant viscosity. #1534
Two phase flow process with pp model implementation. #1530
Richards flow process implementation. #1473
Liquid process. #1468
Classes for relative permeability models. #1531
Classes for capillary models. #1517, #1578
Ehlers single-surface yield function constitutive relation model. #1556
Support scaling, GMRES, and Pardiso in Eigen linear solvers. #1509 #1510
Piecewise linear Monotonic curve and a generic curve parser. #1529
Support searching boundary nodes in MeshLib::NodeSearch. #1459
Support specifying the shape function order in process variables. #1503
Command line option --unbuffered-std-out to deactivate buffer for standard output. #1514
CMake option OGSFATALABORT for debugging. #1432
Set the default OGSLOGLEVEL to debug in release builds. #1522
Add integration order in input files. #1464

Utilities

New utilities: - createQuadraticMesh #1500 - convertToLinearMesh #1554 - postLIE #1555

New features: - extend NodeReordering to correct ordering of nonlinear nodes #1519

Infrastructure:

Ctest now works on Windows too by removing time-wrappers. #1480
Moved to public Jenkins instance at jenkins.opengeosys.org. #1505
Doxygen warnings parser in Jenkins will mark a build as unstable if there are Doxygen warnings. #1585
Benchmarking on Jenkins now saves the standard output into a file for each test. #1528

Fixes:

Fix LocalToGlobalIndexMap with mutliple variables and with multiple componets. #1433 #1440
Fix PropertyVector for multi-component case. #1441
Fix checking IDs of nonlinear nodes. #1495
Fix incorrect use of getNumberOfBaseNodes(). #1515
Fix computing sparsity pattern for mixed shape function order cases. #1548
Fix that iterations and residuals were not printed when Eigen linear solver fails. #1499
Fix all of the Doxygen warnings in the code. #1569 #1573
Fix all of the input file/keyword documentation and its generation.

- C++
Published by endJunction over 9 years ago

ogs - Mechanics and heat conduction.

Features

The main features of this release is the implementation of two new processes, the small deformation, and the heat conduction. Some extensions were done to the DOF table to be able to manage multi-component/multi-variable processes. Also, during implementation of the Robin boundary conditions, the base classes for the boundary conditions were generalized. - Add small deformation process with linear elastic material model. The implementation is based on the Kelvin mapping. #1340 - Added B-Matrices and Kelvin mapping tools for deformation processes. #1359 - Heat conduction process implementation. #1328 - Finalize support for multicomponent boundary conditions adding configuration parser. #1343 - Added uniform Robin boundary condition. #1336 - Added a generic natural boundary condition class. #1337 - Added Robin boundary condition. #1336 - Reworked the Parameter class. It now serves as a basis for BCs and ICs. #1357, #1356 - Added time-dependent Dirichlet BCs. #1380 - Add calculation of surface flux, tests for groundwater flow. #1429 - Implemented numerical Jacobian assembly for Newton-Raphson solver. #1352 - Added the new parameter type "Group" which can be used for setting material ID dependent values. #1426 - Added fluid property class and several fluid density and viscosity models based on it. #1398, #1435 - Enabled solving of axially symmetric problems on 2D meshes for all currently implemented processes. #1443 - Added time measurement for assembly and solvers. #1322 - Added named functions, out of which expressions can be built up at run-time from the prj file, which can be used to output additional nodal quantities. #1314, #1315 - Added component-wise norms, and flexible convergence criteria for nonlinear solvers. #1349, #1342 - Restructured the time loop. #1364

Utilities

New utilities: - createNeumannBc: The tool integrates the given element property and writes the computed data as a PropertyVector with the name node_aggregated_gwn into the mesh. The tool also outputs an OGS-5 direct source term (Neumann boundary condition) data file. #1346 - scaleProperty for simple rescaling of mesh properties. #1347 - convertGEO for geometric file conversion, e.g. gli to glm. #1360 - swapNodeCoordinateAxes to swap node coordinate values, e.g. XY to XZ plane. #1361 New feature: - Support tetrahedra types in generateStructuredMesh. #1353

Infrastructure

Migrated all important Jenkins jobs to script-based Jenkins Pipeline functionality. For an introduction see docs.opengeosys.org - Continuous Integration. #1392, #1396, #1404, #1411, #1424, #1428, #1436
Moved CMake logic for packaging executable dependencies (such as shared libs) to the install and package targets instead of running after each executable gets build. #1458
Increase minimum clang compiler version to 3.5 in course of updating travis build enviroment to Ubuntu LTS 14.04. #1448
Added a script that generates crosslinked Doxygen pages out of ctest input files #1348

Fixes:

Fix an issue that a shape vector was defined as a column vector. Corrected to a row vector . #1288
Fix usage of boost::optional<T const&>, which has changed in version 1.61. #1385
Fix Grid (enlarge bounding box to fit all points). #1369
Fix mapping of geometries to mesh surfaces. #1327. #1368
Fix transmitting raster data to element properties. #1347
Fixed missing XSD files in packages. #1410
Fix a shape vector to a row vector. #1288
Fix FEFLOW import. #1397
Fix NodeReordering to check ordering of each element. #1425
Fix builds linking shared VTK library. #1431
Fix global Newton iteration counter. #1341
Correct few loops over mesh nodes, which should run over the mesh subsets. #1437
Fix shape function computation for 2D elements lying in the x-y-plane #1318
Fix AddTest, s.t. ctest now really checks results. #1325
Made Eigen preconditioner configurable. #1367

- C++
Published by endJunction almost 10 years ago

ogs -

Features:

Transferred the TES process, a monolithically coupled THC model for simulating thermochemical energy storag devices, from OGS5. #1181
Add external ode-solver interface with Sundials CVODE library. #1109
Introduced a general scheme for documenting OGS6 input file settings. #978
Add piecewise linear curves parser to the project files. The curves are specified by two vectors, the coordinates and values. They can be used for example to map temporal dependencies (time-dependent boundary conditions) or as approximations of coefficient dependencies (e.g. pressure-saturation curves). #1149
Extend the LocalAssemblerInterface by adding default implementations of pre/postTimestep and assembleJacobian functions. The current time and time step size are passed in the preTimestep call to the particular processes. #1214
Add support multi-variable/multi-component in the DOF table interface and extend the initial conditions to multi-components. #1224
Major rework of the general process interface. That also affects the interface of concrete processes and local assemblers. least squares optimization. #1145
Added functionality for the output of secondary variables. #1171
Added material properties for zeolite adsorption and Calcium oxide/hydroxide reactions. #1178
Added copy constructor for the class Surface, minor improvements in GeoLib. #1237
Added classes GeoLib::LineSegment and GeoLib::Polyline::SegmentIterator. #1139
GMSHInterface can handle stations as constraints. #1212
Added functionality to duplicate geometric data. #1229
Station names can be modified in Data Explorer #1273

Infrastructure

Fix circular dependencies on library level. This allows for dynamic linking which is faster than static and can be used in debug builds, where the compilation time is more important than the runtime.
- Enable shared linking of ogs libraries. #1133
- Break FileIO on ApplicationsLib dependency. #1138
- Remove MeshLib on FileIO dependency. #1143, #1153
- Cleanup some of AssemblerLib dependencies. #1166
- Split AssemblerLib and move to MathLib and NumLib #1208
- Move InsituLib to MeshLib #1208
- Remove MathLib depends on NumLib #1208
- Remove dependency of FileIO on Data Explorer #1302
Introduced Conan package manager for automatic fetching of build dependencies, #1141
Inconsistent formatting of tabs and spaces was finally resolved: now all formatting, indentation and alignment, are done with four spaces. #1201
Windows 32-bit builds are disallowed because they are not supported. Can be forced by setting OGS32BIT=ON. #1230
Simplified FindEigen.cmake, #1209
git diff --check is run in its own Travis job, #1207
Moved some IO implementations from FileIO to BaseLib/IO, GeoLib/IO, MeshLib/IO, #1182, #1235
Eigen is not optional anymore #1218
Removed OGSUSEEIGENLIS CMake option. Use OGSUSELIS instead #1251

Fixes:

Fix linking of Metis in MathLib. #1147
Fix memory leaks in GMSHInterface. #1212
Fix build with Lis #1267
Fixing several small issues with NetCDF import #1169
Restructure Applications related modules
- Move DataHolderLib and FileIO under Applications #1279
Remove calling std::abort within libraries. Exeptions are thrown instead. #1245
Fix finding Boost with BOOST_ROOT CMake argument #1287
Fix linking of Sundials CVODE library #1197
Fixed issue where geometry names would be missing after merging geometries #1295

- C++
Published by endJunction about 10 years ago

ogs - 6.0.5

Release notes

Implementation of several time integration methods and non-linear solver schemes is the major advance in this release. We have chosen to implement a first order implicit quasi-linear system solver for the equations in the form of $M\dot{x} + Kx + b = 0$, where M, K, and b depend on t and x.

The explicit and the implicit Euler, the Crank-Nicholson, and the BDF (second to sixth order) time integration methods are provided. For the non-linear systems, the Picard and Newton methods are available. See implementation details in the doxygen documentation.

Overall stability of the code was improved with recent usage of clang's address and undefined behaviour sanitizers.

Features:

Added an ODE solver library that can solve transient and nonlinear problems (see http://doxygen.opengeosys.org/df/d35/group__ODESolver.html).
Move up common Process parts from particular GroundwaterFlow process implementation. #951, #982
Separate Dirichlet boundary condition class implementation. #963
Split process output and post timestep. #998
Added pre- and postTimestep and -Iteration hooks to processes. #1094, #1100, #1101
Added a new configuration tree parser
- Checks configuration parameters more strictly, automatically prints error/warning messages.
- Requires Boost >= 1.56 because of boost::optional with move semantics.
- Command line argument --config-warnings-nonfatal that keeps OGS from terminating on warnings during configuration file parsing (errors still makes it terminate).
Improved axis aligned bounding box:
- Is now a from the right half-open interval.
- Removed template from class declaration.
Improved MeshLib: Class MeshElementGrid implements a grid data structure supporting search operations.
Added cmake option OGS_EIGEN_DYNAMIC_SHAPE_MATRICES that makes OGS use dynamically. allocated shape matrices.
Added several cmake options for selecting which element types, dimensions and orders to be built. Selecting only few element types speeds up compilation significantly. #1092
Added a command line argument of -l for OGS cli and testrunner to specify verbosity of logging. #1056
Added possibility to specify after which timesteps there shiuld be output.
Added possibility to specify timesteps of different size for use with transient processes.

DataExplorer and utilities

Added command line tool for creating layered meshes from raster files
Made OGSFileConverter as a separate library
Add a new functionality to the raster file to structured grid conversion, which can now convert pixel values in user-defined scalar arrays
Improved DataExplorer, which now enables the possibility to display all scalar arrays in mesh information window.
Added generation of structured meshes to DataExplorer
Restructured mesh creation access in DataExplorer
Added a new functionality to add mesh layers to existing meshes in DataExplorer
Reworked tools:
- CreateBoundaryConditionsAlongPolyline
- AddTopLayer
- ResetPropertyInPolygonalRegion
- removeMeshElements

Infrastructure

Minimum Boost version: 1.56.0. #943
Boost requirement is now header-only. #940
Optional support for VTK 7. #1083
Test data is now a git submodule. #1000
In-code defined Jenkins jobs. #970
Use clang's address and undefined behaviour sanitizers on Jenkins now. #958

Documentation

Speed up builds with ccache, #938
Overview of the new non-linear, transient solver in ODESolver source code documentation.

Fixes

Fix bugs in GeoLib:
- lineSegmentIntersects.
- Polygon::splitPolygonAtIntersection.
- Grid.
GeoMapper: Refactoring few methods, c++11. #977
Rework FileIO::GMSH interface
- Process geometries located other than in the x-y-plane.
- Respect the scaling factor for Stations.
- Fix memory leaks.
- Added/modified tests for GML-, GMS- and TetGen-files.

- C++
Published by endJunction about 10 years ago

ogs - 6.0.4

Release notes

| Released on 2015/01/05, GitHub Release Link

Features:

Parallel computing framework for FEM by using PETSc, which also includes
- Parallel input of partitioned mesh data.
- Parallel output of solutions by using pvtu data format.
New data structures for mesh properties are used everywhere replacing Element's value member.
The penalty method to impose first-type boundary conditions was substituted with a non-penalty method for LIS and Eigen linear solvers.
Support for multiple nodal variables is extended to the boundary conditions, the sparsity pattern.
Passing of linear solver options from the project files is now possible.
The global matrix and global vector type of indices is consistent with the linear solver library being used.

Infrastructure

Added CMake option OGS_CPU_ARCHITECTURE, #858, downloadable binaries build by Jenkins should now run on more CPUs
Added CMake options for Boost, VTK and Eigen (OGS_LIB_BOOST, ...) to specify if libs are searched on the system first, then build them locally (Default), or you can specify to just use system libs (System) or force a local build (Local)
Added CMake options for enabling Clang sanitizer:
- OGS_ADDRESS_SANITIZER
- OGS_UNDEFINED_BEHAVIOR_SANITIZER
The zlib library is removed from ThirdParty directory.
A LIS solver interface using Eigen's sparse matrices is now available through CMake option OGS_USE_EIGENLIS.
CMake configuration uses ccache if available.

Documentation

Added offline viewable Doxygen documentation

Fixes

Fix all ogs-internal warnings on all OS.
Move eigen solver compute call to solve(); different fix for 0237275

- C++
Published by bilke over 10 years ago

ogs - 6.0.3

| Released on 2015/09/21, GitHub Release Link

Release notes

Features:

Mesh properties are now used for:
- heterogeneous "initial conditions" (actually a start solution vector for the elliptic problem).
- spatially heterogeneous hydraulic conductivity values in the groundwater flow process.
First steps towards time dependent problems: Time loop integration for processes is provided.
Interpolation of nodal quantities on elements using shape functions.
Mesh generator can create surface meshes according to a given function

? - DataExplorer extensions: - Utilities: - MoveGeometry - The DOF table handles now all of the provided element types: Hex 8 and 20, Line 2 and 3, Prism 6 and 15, Pyramid 5 and 13, Quad 4, 8, and 9, Tet 4 and 10, Triangle 3 and 6. - Eigen linear solver library can be used for solution of the linear systems of equations. - Octree data structures for fast searches - Volumetric and surface grid - ElementSearcher NodeSearcher improvements - Generalized the computation of rotation matrix to xy

Fixes

FEFLOW interface supports element sets now.
Reduce compilation times by using forward declarations and removing unnecessary includes and using explicit template instantiation for often required classes.
GMSH2OGS: fixed bug in cases GMSH mesh does not contain line elements
CreateBoundaryConditionsAlongPolylines: fixed bug concerning the GeoLib and point ids.
PointVec corrected point id map
Shape interface creates polylines in a consistent state

Infrastructure

Replace quickcheck with autocheck. See https://github.com/thejohnfreeman/autocheck.git for more details on autocheck
Added support for cross-compiling with MXE: build native Windows binaries on Linux and Mac OS, see Cross-Compiling help page and #767
Migrated to new Travis infrastructure (faster build times), see #775
Simplified CMake library linking, see #769

Test examples

Test case: groundwater flow in the Unstrut catchment (model consists approximately of 9e6 hexahedral cells)
- Simulations using homogeneous and heterogeneous hydraulic conductivity
- Integrated rivers as Dirichlet type boundary conditions
- Integrated groundwater recharge (spatialy homogeneous) as Neumann boundary condition

unstrut_heterogeneous_rivers_top_layer_diff_recharge-no_recharge

Next steps

The next big step will be the implementation of a parallelization scheme using PETSc library

In development

OGS#PETSc interface for parallel computing
Solving of time dependent problems

Planned

Implementation of a linear parabolic pde solver
Extending the linear elliptic solver to non-linear problems

- C++
Published by bilke almost 11 years ago

ogs - 6.0.2 - Intermediate DOI release

| Released on 2015/06/15, GitHub Release Link

Release notes

The second release of ogs6 introduces Neumann boundary conditions and VTK result output.

Features:

Neumann boundary conditions
Implement mesh properties for storage of data fields. This also includes mapped values (e.g. based on material id) PR #542, PR #644,
Refactored mesh property classes to enable VTK output
Extended the available elements to quadratic (e.g. Quad8) based on generalized "element rules". #572, PR #656, PR #657,
Extend computation of shape matrices to lower dimensional elements embedded in higher dimensional space #655
Builds with MinGW (GCC) on Windows, see Developer Guide and the new MinGW platform instructions
Cross-compiling for Windows with MXE on Mac OS
Support for new cross-platform IDE CLion
Add gradual refinement to the structured mesh generator PR #539
Add a command line tool "queryMesh" to search mesh information PR #665
Add a command line tool "AddTopLayer" to add an additional top layer (for example a soil layer, see also the documentation) PR #649

Fixes

Performance optimizations in VTK mesh conversion, PR #695
Improve layered prism mesh construction
Fix a lot of warnings on gcc/clang/msvc compilers improving the code

Infrastructure

Test runtime is monitored at Jenkins for normal and nightly large tests
Utilities are build by separate Jenkins Jobs, e.g. Win_Utils

Test examples

Groundwater flow (Neumann):

Next steps

In development

Heterogeneous fields (for e.g. hydraulic conductivity parameters)
Octree data structures for fast searches
OGS#PETSc interface for parallel computing

Planned

Parallelization scheme using PETSc library
Extending the linear elliptic solver to non-linear problems

- C++
Published by bilke almost 11 years ago

ogs - 6.0.2

| Released on 2015/06/15, GitHub Release Link

Release notes

The second release of ogs6 introduces Neumann boundary conditions and VTK result output.

Features:

Neumann boundary conditions
Implement mesh properties for storage of data fields. This also includes mapped values (e.g. based on material id) PR #542, PR #644,
Refactored mesh property classes to enable VTK output
Extended the available elements to quadratic (e.g. Quad8) based on generalized "element rules". #572, PR #656, PR #657,
Extend computation of shape matrices to lower dimensional elements embedded in higher dimensional space #655
Builds with MinGW (GCC) on Windows, see Developer Guide and the new MinGW platform instructions
Cross-compiling for Windows with MXE on Mac OS
Support for new cross-platform IDE CLion
Add gradual refinement to the structured mesh generator PR #539
Add a command line tool "queryMesh" to search mesh information PR #665
Add a command line tool "AddTopLayer" to add an additional top layer (for example a soil layer, see also the documentation) PR #649

Fixes

Performance optimizations in VTK mesh conversion, PR #695
Improve layered prism mesh construction
Fix a lot of warnings on gcc/clang/msvc compilers improving the code

Infrastructure

Test runtime is monitored at Jenkins for normal and nightly large tests
Utilities are build by separate Jenkins Jobs, e.g. Win_Utils

Test examples

Groundwater flow (Neumann):

Next steps

In development

Heterogeneous fields (for e.g. hydraulic conductivity parameters)
Octree data structures for fast searches
OGS#PETSc interface for parallel computing

Planned

Parallelization scheme using PETSc library
Extending the linear elliptic solver to non-linear problems

- C++
Published by bilke about 11 years ago

ogs - 6.0.1

The 6th version of OpenGeoSys (OGS) is under way. After single and coupled FORTRAN modules in ROCKFLOW 1+2, the C version 3 with dynamic data structures, the object-oriented C++ parallelized version 4, completed with data integration and visualization tools by version 5; ogs6 - as an open source project - is aimed at performing on supercomputing platforms and providing complete workflows for solving of coupled multi-field problems in real world applications. The major paradigms of ogs6 are being developer-friendly, performing, and user-friendly.

Important links:

Getting started tutorial: http://docs.opengeosys.org/docs/quickstart
Descriptions of selected benchmarks: http://docs.opengeosys.org/docs/benchmarks
Source code access: https://github.com/ufz/ogs
Developer guide: http://docs.opengeosys.org/docs/devguide

Release notes

The first version ogs6 is dedicated for elliptic problems.

Features:

Basic structures of processes
Mathematical operations are based on Eigen3 library
Linear solvers: DenseMatrix with Gauss elimination, and LIS (http://www.ssisc.org/lis/)
XML based IO
Standard finite element method (FEM)
Available element types: lines, triangles, quads, hexahedra
Dirichlet boundary conditions
Linear elliptic solver (e.g. Groundwater flow) for scalar quantities in homogeneous media

Fixes

DenseMatrix Gauss algorithm pivoting

Test examples

- Example 1: Unit square (access) - Example 2: Unit cube (access): has 1000 hexahedra elements with Dirichlet boundary conditions (u=1|x=0) and (u=-1|x=1)

Next steps

In development

OGS#PETSc interface for parallel computing (02/2015*planned)
Neuman boundary conditions (03/2015*planned)

Planned

Parabolic solver

- C++
Published by bilke over 11 years ago

Recent Releases of ogs

ogs - 6.5.5

Process' changes

New HMPhaseField process

Deprecated processes removed

Component transport process / reactive transport process with coupling of PHREEQC

HeatTransportBHE

Richard's mechanics process

SmallDeformation

ThermoHydroMechanics

Numerics

Tools

Python & Jupyter

Testing

Logging

Infrastructure

Material Property Library (MPL)

Bug fixes

Documentation

Version info

ogs - 6.5.4

Process' changes

HeatTransportBHE

LargeDeformation

LIE

LiquidFlow process

Richard's mechanics process

ThermoRichardsMechanics

Numerics

Generic features

Python & Jupyter

Testing

B-bar tests

Code improvements

CMake

File I/O

Material Property Library (MPL)

Documentation

Version info

ogs - 6.5.3

Breaking changes

New processes

Process' changes

HeatTransportBHE

HydroMechanics

LIE

Generic features

Tools

Data Explorer

Python & Jupyter

Testing

Infrastructure

ogs - 6.5.2

Breaking changes

Process' changes

TH2M

Component transport process / reactive transport process with coupling of Phreeqc

SmallDeformation

Generic features

Testing

Bug fixes

CMake

Infrastructure

File I/O

Material Property Library (MPL)

Documentation

Version info

ogs - 6.5.1

Process' changes

Component transport process / reactive transport process with coupling of Phreeqc

HeatConduction

HeatTransportBHE

HydroMechanics

LargeDeformation

LIE

LiquidFlow process

ThermoHydroMechanics

ThermoRichardsMechanics

Constitutive relations (material models)

Parameters