Ogs

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 boundary conditions were generalized.

- Add small deformation process with linear elastic material model. The
implementation is based on the Kelvin mapping. [1340](https://github.com/ufz/ogs/pull/1340)
- Added B-Matrices and Kelvin mapping tools for deformation processes. [1359](https://github.com/ufz/ogs/pull/1359)
- Heat conduction process implementation. [1328](https://github.com/ufz/ogs/pull/1328)
- Finalize support for multicomponent boundary conditions adding configuration
parser. [1343](https://github.com/ufz/ogs/pull/1343)
- Added uniform Robin boundary condition. [1336](https://github.com/ufz/ogs/pull/1336)
- Added a generic natural boundary condition class. [1337](https://github.com/ufz/ogs/pull/1337)
- Added Robin boundary condition. [1336](https://github.com/ufz/ogs/pull/1336)
- Reworked the Parameter class. It now serves as a basis for BCs and ICs.
[1357](https://github.com/ufz/ogs/pull/1357), [#1356](https://github.com/ufz/ogs/pull/1356)
- Added time-dependent Dirichlet BCs. [1380](https://github.com/ufz/ogs/pull/1380)
- Add calculation of surface flux, tests for groundwater flow. [1429](https://github.com/ufz/ogs/pull/1429)
- Implemented numerical Jacobian assembly for Newton-Raphson solver. [1352](https://github.com/ufz/ogs/pull/1352)
- Added the new parameter type "Group" which can be used for setting material
ID dependent values. [1426](https://github.com/ufz/ogs/pull/1426)
- Added fluid property class and several fluid density and viscosity models
based on it. [1398](https://github.com/ufz/ogs/pull/1398), [#1435](https://github.com/ufz/ogs/pull/1435)
- Enabled solving of axially symmetric problems on 2D meshes for all currently
implemented processes. [1443](https://github.com/ufz/ogs/pull/1443)
- Added time measurement for assembly and solvers. [1322](https://github.com/ufz/ogs/pull/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](https://github.com/ufz/ogs/pull/1314), [#1315](https://github.com/ufz/ogs/pull/1315)
- Added component-wise norms, and flexible convergence criteria for nonlinear
solvers. [1349](https://github.com/ufz/ogs/pull/1349), [#1342](https://github.com/ufz/ogs/pull/1342)
- Restructured the time loop. [1364](https://github.com/ufz/ogs/pull/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](https://github.com/ufz/ogs/pull/1346)
- scaleProperty for simple rescaling of mesh properties. [1347](https://github.com/ufz/ogs/pull/1347)
- convertGEO for geometric file conversion, e.g. gli to glm. [1360](https://github.com/ufz/ogs/pull/1360)
- swapNodeCoordinateAxes to swap node coordinate values, e.g. XY to XZ plane.
[1361](https://github.com/ufz/ogs/pull/1361)
New feature:
- Support tetrahedra types in generateStructuredMesh. [1353](https://github.com/ufz/ogs/pull/1353)

Infrastructure

- Migrated all important Jenkins jobs to script-based
[Jenkins Pipeline](https://jenkins.io/doc/pipeline/)
functionality. For an introduction see
[docs.opengeosys.org - Continuous Integration](https://docs.opengeosys.org/docs/devguide/development-workflows/continuous-integration).
[1392](https://github.com/ufz/ogs/pull/1392), [#1396](https://github.com/ufz/ogs/pull/1396), [#1404](https://github.com/ufz/ogs/pull/1404), [#1411](https://github.com/ufz/ogs/pull/1411), [#1424](https://github.com/ufz/ogs/pull/1424), [#1428](https://github.com/ufz/ogs/pull/1428), [#1436](https://github.com/ufz/ogs/pull/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](https://github.com/ufz/ogs/pull/1458)
- Increase minimum clang compiler version to 3.5 in course of updating travis
build environment to Ubuntu LTS 14.04. [1448](https://github.com/ufz/ogs/pull/1448)
- Added a script that generates crosslinked Doxygen pages out of ctest input
files [1348](https://github.com/ufz/ogs/pull/1348)

Fixes

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

Features

- Add external ode-solver interface with [Sundials CVODE
library](http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/cvode). [#1109](https://github.com/ufz/ogs/pull/1109)
- 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](https://github.com/ufz/ogs/pull/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](https://github.com/ufz/ogs/pull/1214)
- Add support multi-variable/multi-component in the DOF table interface and
extend the initial conditions to multi-components. [1224](https://github.com/ufz/ogs/pull/1224)
- Major rework of the general process interface. That also affects the
interface of concrete processes and local assemblers.
least squares optimization. [1145](https://github.com/ufz/ogs/pull/1145)
- Added functionality for the output of secondary variables. [1171](https://github.com/ufz/ogs/pull/1171)
- Added material properties for zeolite adsorption and Calcium oxide/hydroxide
reactions. [1178](https://github.com/ufz/ogs/pull/1178)
- Transferred the TES process, a monolithically coupled THC model for simulating
thermochemical energy storage devices, from OGS5. [1181](https://github.com/ufz/ogs/pull/1181)
- Introduced a general scheme for documenting OGS6 input file settings. 978
- Added copy constructor for the class Surface, minor improvements in GeoLib. [1237](https://github.com/ufz/ogs/pull/1237)
- Added classes GeoLib::LineSegment and GeoLib::Polyline::SegmentIterator. [1139](https://github.com/ufz/ogs/pull/1139)
- GMSHInterface can handle stations as constraints. [1212](https://github.com/ufz/ogs/pull/1212)
- Added functionality to duplicate geometric data. [1229](https://github.com/ufz/ogs/pull/1229)
- Station names can be modified in Data Explorer [1273](https://github.com/ufz/ogs/pull/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](https://github.com/ufz/ogs/pull/1133)
- Break FileIO on ApplicationsLib dependency. [1138](https://github.com/ufz/ogs/pull/1138)
- Remove MeshLib on FileIO dependency. [1143](https://github.com/ufz/ogs/pull/1143), [#1153](https://github.com/ufz/ogs/pull/1153)
- Cleanup some of AssemblerLib dependencies. [1166](https://github.com/ufz/ogs/pull/1166)
- Split AssemblerLib and move to MathLib and NumLib [1208](https://github.com/ufz/ogs/pull/1208)
- Move InsituLib to MeshLib [1208](https://github.com/ufz/ogs/pull/1208)
- Remove MathLib depends on NumLib [1208](https://github.com/ufz/ogs/pull/1208)
- Remove dependency of FileIO on Data Explorer [1302](https://github.com/ufz/ogs/pull/1302)
- Introduced Conan package manager for automatic fetching of build dependencies, [1141](https://github.com/ufz/ogs/pull/1141)
- Inconsistent formatting of tabs and spaces was finally resolved: now all
formatting, indentation and alignment, are done with four spaces. [1201](https://github.com/ufz/ogs/pull/1201)
- Windows 32-bit builds are disallowed because they are not supported.
Can be forced by setting OGS_32_BIT=ON. [1230](https://github.com/ufz/ogs/pull/1230)
- Simplified FindEigen.cmake, [1209](https://github.com/ufz/ogs/pull/1209)
- git diff --check is run in its own Travis job, [1207](https://github.com/ufz/ogs/pull/1207)

- Moved some IO implementations from FileIO to BaseLib/IO, GeoLib/IO, MeshLib/IO, [1182](https://github.com/ufz/ogs/pull/1182), [#1235](https://github.com/ufz/ogs/pull/1235)
- Eigen is not optional anymore [1218](https://github.com/ufz/ogs/pull/1218)
- Removed OGS_USE_EIGENLIS CMake option. Use OGS_USE_LIS instead [1251](https://github.com/ufz/ogs/pull/1251)

Fixes

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

Features

- Added an ODE solver library that can solve transient and nonlinear processes
(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](https://github.com/ufz/ogs/pull/1094), [#1100](https://github.com/ufz/ogs/pull/1100), [#1101](https://github.com/ufz/ogs/pull/1101)
- 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).
- Axis aligned bounding box:
- Is now a from the right half-open interval.
- Removed template from class declaration.
- 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](https://github.com/ufz/ogs/pull/1092)
- Command line argument `-l` for OGS cli and testrunner to specify verbosity of logging. [1056](https://github.com/ufz/ogs/pull/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
- OGSFileConverter is now a separate library
- Raster file to structured grid conversion can now convert pixel values in user-defined scalar arrays
- All scalar arrays will be displayed in mesh information window in DataExplorer
- Added generation of structured meshes to DataExplorer
- Restructured mesh creation access in DataExplorer
- Mesh layers can be added to existing meshes in DataExplorer
- Rework 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](https://github.com/ufz/ogs/pull/1083)
- Test data is now a git submodule. [1000](https://github.com/ufz/ogs/pull/1000)
- In-code defined Jenkins jobs. 970
- Use [clang's address and undefined behaviour sanitizers](https://svn.ufz.de:8443/job/OGS-6/job/Docker/job/clang-sanitizer/) on Jenkins now. #958

Documentation

- Speed up builds with [ccache](http://docs.opengeosys.org/docs/devguide/advanced/using-ccache), #938
- Overview of the new non-linear, transient solver in [ODESolver](see
<http://doxygen.opengeosys.org/df/d35/group__ODESolver.html>) 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.

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](http://docs.opengeosys.org/download) 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](https://ccache.dev/) if available.

Documentation

- Added [offline viewable Doxygen documentation](http://docs.opengeosys.org/docs/devguide/documentation/offline-documentation-viewer)

Fixes

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

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

- 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.

- Implemented [OctTree](https://github.com/ufz/ogs/pull/714) for fast searching
points and nodes
- 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](http://mxe.cc/): build native Windows binaries on Linux and Mac OS, see [Cross-Compiling help page](http://docs.opengeosys.org/docs/devguide/advanced/cross-compiling) 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


Next steps

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

In development

- OGSPETSc 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

| Released on 2015/06/15, [GitHub Release Link](https://github.com/ufz/ogs/releases/tag/6.0.2)

Release notes

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

Features

- [Neumann boundary conditions](http://docs.opengeosys.org/docs/benchmarks/elliptic/groundwater-flow-neumann)
- Implement mesh properties for storage of data fields. This also includes mapped values (e.g. based on material id) [PR 542](https://github.com/ufz/ogs/pull/542), [PR #644](https://github.com/ufz/ogs/pull/644),
- Refactored mesh property classes to [enable VTK output](https://github.com/ufz/ogs/pull/692)
- Extended the available elements to quadratic (e.g. Quad8) based on generalized "element rules". [572](https://github.com/ufz/ogs/pull/572), [PR #656](https://github.com/ufz/ogs/pull/656), [PR #657](https://github.com/ufz/ogs/pull/657),
- Extend computation of shape matrices to lower dimensional elements embedded in higher dimensional space [655](https://github.com/ufz/ogs/pull/655)
- Builds with MinGW (GCC) on Windows, see [Developer Guide](http://docs.opengeosys.org/docs/devguide/getting-started/prerequisites) and the new MinGW platform instructions
- [Cross-compiling for Windows with MXE on Mac OS](http://docs.opengeosys.org/docs/devguide/advanced/cross-compiling)
- [Support for new cross-platform IDE CLion](http://docs.opengeosys.org/docs/devguide/development-workflows/development-ides#clion)
- Add gradual refinement to the structured mesh generator [PR 539](https://github.com/ufz/ogs/pull/539)
- Add a command line tool "queryMesh" to search mesh information [PR 665](https://github.com/ufz/ogs/pull/665)
- Add a command line tool "AddTopLayer" to add an additional top layer (for example a soil layer, see also the [documentation](http://docs.opengeosys.org/docs/tools/meshing/addtoplayer)) [PR #649](https://github.com/ufz/ogs/pull/649)

Fixes

- Performance optimizations in VTK mesh conversion, [PR 695](https://github.com/ufz/ogs/pull/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](https://svn.ufz.de:8443/job/OGS-6/job/Tests_Linux/) and [nightly large tests](https://svn.ufz.de:8443/job/OGS-6/job/Tests_Linux_Large/)
- Utilities are build by separate Jenkins Jobs, e.g. [Win_Utils](https://svn.ufz.de:8443/job/OGS-6/job/Win_Utils/)

Test examples

- [Groundwater flow (Neumann)](http://docs.opengeosys.org/docs/benchmarks/elliptic/groundwater-flow-neumann)

Next steps

In development

- Heterogeneous fields (for e.g. hydraulic conductivity parameters)
- Octree data structures for fast searches
- OGSPETSc interface for parallel computing

Planned

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