From b3560256b2f64d5726e91e51793e0ebabe66ba6f Mon Sep 17 00:00:00 2001 From: Lars Bilke <lars.bilke@ufz.de> Date: Wed, 13 Mar 2019 20:20:30 +0100 Subject: [PATCH] Replaced PR ids with full links. Find and Replace in VS Code: -> [#$1](https://github.com/ufz/ogs/pull/$1) --- CHANGELOG.md | 440 +++++++++++++++++++++++++-------------------------- 1 file changed, 220 insertions(+), 220 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0a44e58d5d3..739ea185178 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,181 +4,181 @@ ### 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 +- HeatTransportBHE process supporting 1U, CXA, and CXC BHE types. [#2221](https://github.com/ufz/ogs/pull/2221), [#2332](https://github.com/ufz/ogs/pull/2332), + [#2271](https://github.com/ufz/ogs/pull/2271), [#2275](https://github.com/ufz/ogs/pull/2275) +- Staggered implementation of a thermo-mechanical with phasefield process. [#2102](https://github.com/ufz/ogs/pull/2102) +- Richards mechanics process. [#2189](https://github.com/ufz/ogs/pull/2189) +- Small deformation process with non-local integration of damage. [#2294](https://github.com/ufz/ogs/pull/2294) +- Staggered implementation of phasefield process. [#2052](https://github.com/ufz/ogs/pull/2052) +- ComponentTransport process in revised formulation. [#2200](https://github.com/ufz/ogs/pull/2200) +- Multi-component transport process. [#2304](https://github.com/ufz/ogs/pull/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 + numerical Jacobian (mostly for development. [#2238](https://github.com/ufz/ogs/pull/2238) +- Add `setInitialConditions()` call to processes and local assemblers. [#2334](https://github.com/ufz/ogs/pull/2334) - Several bug fixes for LIE/HM process including "fracture into matrix - leak-off", Darcy velocity output in the fracture. #2129 + leak-off", Darcy velocity output in the fracture. [#2129](https://github.com/ufz/ogs/pull/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 + process. [#2235](https://github.com/ufz/ogs/pull/2235), [#2293](https://github.com/ufz/ogs/pull/2293) +- Fixed the calculation of the Darcy velocity in staggered TH. [#2127](https://github.com/ufz/ogs/pull/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 + [#2016](https://github.com/ufz/ogs/pull/2016) +- Subdomain deactivation within time intervals. [#2297](https://github.com/ufz/ogs/pull/2297) +- Add a driver for an iteration based time stepping algorithm. [#2318](https://github.com/ufz/ogs/pull/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 +- Implementation of Python boundary conditions. [#2170](https://github.com/ufz/ogs/pull/2170) +- Implementation of constraint boundary conditions. [#2145](https://github.com/ufz/ogs/pull/2145) +- Dirichlet boundary condition within a time interval. [#2272](https://github.com/ufz/ogs/pull/2272) +- BoundaryElementSearch: Return bulk element id and bulk element face id. [#2125](https://github.com/ufz/ogs/pull/2125) - Removed Neumann boundary condition for displacement jumps in LIE processes. - #2153 + [#2153](https://github.com/ufz/ogs/pull/2153) #### Source term -- Use parameter for source terms. #2061 -- Volumetric source terms implementation. #2220, #2234, #2241, #2261 +- Use parameter for source terms. [#2061](https://github.com/ufz/ogs/pull/2061) +- Volumetric source terms implementation. [#2220](https://github.com/ufz/ogs/pull/2220), [#2234](https://github.com/ufz/ogs/pull/2234), [#2241](https://github.com/ufz/ogs/pull/2241), [#2261](https://github.com/ufz/ogs/pull/2261) #### Input and output - Writing and reading of integration point data. Implemented sigma and epsilon - output for some processes. #2071, #2203, #2324 + output for some processes. [#2071](https://github.com/ufz/ogs/pull/2071), [#2203](https://github.com/ufz/ogs/pull/2203), [#2324](https://github.com/ufz/ogs/pull/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 + This is later used by the heterogeneous parameters and source terms. [#2140](https://github.com/ufz/ogs/pull/2140), + [#2141](https://github.com/ufz/ogs/pull/2141), [#2156](https://github.com/ufz/ogs/pull/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 + previously only homogeneous, counterparts. [#2376](https://github.com/ufz/ogs/pull/2376) - Parameters now support space-dependent function input via exprtk library. - #2325, #2339 -- Output of primary variables on arbitrary subdomains. #2372, #2299 + [#2325](https://github.com/ufz/ogs/pull/2325), [#2339](https://github.com/ufz/ogs/pull/2339) +- Output of primary variables on arbitrary subdomains. [#2372](https://github.com/ufz/ogs/pull/2372), [#2299](https://github.com/ufz/ogs/pull/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 + evolutionaryPIDController. [#2079](https://github.com/ufz/ogs/pull/2079) +- Calculate and output specific flux. [#2411](https://github.com/ufz/ogs/pull/2411) +- Enable surface flux calculation for component transport process. [#2168](https://github.com/ufz/ogs/pull/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 + Richards-mechanics and hydro-mechanics processes. [#2228](https://github.com/ufz/ogs/pull/2228) +- Improve output of nodal aperture and aperture vector in LIE/HM. [#2050](https://github.com/ufz/ogs/pull/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 + mechanics processes, SD, HM, LIE/SD, LIE/HM. [#2118](https://github.com/ufz/ogs/pull/2118) +- Enable surface flux calculation for HT process. [#2132](https://github.com/ufz/ogs/pull/2132) +- Fixed pvd output. [#2036](https://github.com/ufz/ogs/pull/2036) ### Material models -- BGRa creep model. #2167 -- New cohesive zone mode I fracture model for LIE processes. #2142, #2157 +- BGRa creep model. [#2167](https://github.com/ufz/ogs/pull/2167) +- New cohesive zone mode I fracture model for LIE processes. [#2142](https://github.com/ufz/ogs/pull/2142), [#2157](https://github.com/ufz/ogs/pull/2157) - Add MFront/TFEL solid constitutive relation support via. - MFrontGenericInterfaceSupport library. CMake option `OGS_USE_MFRONT`. #2259 + MFrontGenericInterfaceSupport library. CMake option `OGS_USE_MFRONT`. [#2259](https://github.com/ufz/ogs/pull/2259) - Infrastructure for multi-phase, multi-component material properties library. - #2303 -- 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 + [#2303](https://github.com/ufz/ogs/pull/2303) +- Anisotropic tensors may now be given in given local coordinate system. [#2370](https://github.com/ufz/ogs/pull/2370) +- Non-constant density model implementation in HC process. [#2200](https://github.com/ufz/ogs/pull/2200) +- Add second derivatives of permeability functions in Richards flow. [#2188](https://github.com/ufz/ogs/pull/2188) - Different solid material models can now be defined on different materialIDs. - #2216, #2262, #2270 -- Move solid constitutive relation creation in single place. #2160 + [#2216](https://github.com/ufz/ogs/pull/2216), [#2262](https://github.com/ufz/ogs/pull/2262), [#2270](https://github.com/ufz/ogs/pull/2270) +- Move solid constitutive relation creation in single place. [#2160](https://github.com/ufz/ogs/pull/2160) ### Testing and documentation - Migrated Appveyor tests to [Azure - Pipelines](https://dev.azure.com/ogsci/ogs/_build). #2342 -- Added cppcheck, clang-tidy and include-what-you-use. #2078, #2328, #2377 + Pipelines](https://dev.azure.com/ogsci/ogs/_build). [#2342](https://github.com/ufz/ogs/pull/2342) +- Added cppcheck, clang-tidy and include-what-you-use. [#2078](https://github.com/ufz/ogs/pull/2078), [#2328](https://github.com/ufz/ogs/pull/2328), [#2377](https://github.com/ufz/ogs/pull/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 + 'OGS_CHECK_HEADER_COMPILATION=ON'. [#2043](https://github.com/ufz/ogs/pull/2043) +- Jenkins shows nice summaries of compiler warnings. [#2206](https://github.com/ufz/ogs/pull/2206) +- Large tests are fixed and run on Jenkins upon master merge. [#2056](https://github.com/ufz/ogs/pull/2056), [#2155](https://github.com/ufz/ogs/pull/2155) - Re-enabled code coverage reports (for the testrunner only) with - [Codecov](http://codecov.io/gh/ufz/ogs). #2333, #2336 + [Codecov](http://codecov.io/gh/ufz/ogs). [#2333](https://github.com/ufz/ogs/pull/2333), [#2336](https://github.com/ufz/ogs/pull/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 + alternative to the `AddTest`. [#2255](https://github.com/ufz/ogs/pull/2255), [#2257](https://github.com/ufz/ogs/pull/2257) ### New tools - `TecPlotTools`: splitting files containing multiple zones into seperate - TecPlot files. #2114 + TecPlot files. [#2114](https://github.com/ufz/ogs/pull/2114) - `TecPlot-Reader`: converting TecPlot rasters into OGS meshes (one file per - zone, containing all variables as scalar arrays). #2114 + zone, containing all variables as scalar arrays). [#2114](https://github.com/ufz/ogs/pull/2114) - [`constructMeshesFromGeometry`](https://www.opengeosys.org/docs/tools/model-preparation/constructmeshesfromgeometry/): - Construction of boundary meshes from bulk mesh and gml files. #2144 + Construction of boundary meshes from bulk mesh and gml files. [#2144](https://github.com/ufz/ogs/pull/2144) - [`identifySubdomains`](https://www.opengeosys.org/docs/tools/model-preparation/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 + `bulk_node_ids` and `bulk_element_ids` maps. [#2227](https://github.com/ufz/ogs/pull/2227), [#2252](https://github.com/ufz/ogs/pull/2252) - `Mesh2Raster`: converts 2D OGS meshes into raster files of arbitrary pixel - size, where node elevation is represented by pixel value. #2367 + size, where node elevation is represented by pixel value. [#2367](https://github.com/ufz/ogs/pull/2367) - `GocadSGridReader` tool reading the Gocad/SKUA stratigraphic grid format and - writing the data in the vtu format. #2316 + writing the data in the vtu format. [#2316](https://github.com/ufz/ogs/pull/2316) ### New tools and CLI usage -- `ogs --help` shows the given CMake options. #2210 -- Unify command line version info output. #2194 +- `ogs --help` shows the given CMake options. [#2210](https://github.com/ufz/ogs/pull/2210) +- Unify command line version info output. [#2194](https://github.com/ufz/ogs/pull/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 + in general) according to the partition of the bulk mesh. [#2159](https://github.com/ufz/ogs/pull/2159), [#2178](https://github.com/ufz/ogs/pull/2178), [#2195](https://github.com/ufz/ogs/pull/2195) +- Add new features to `ExtractSurface` tool. [#2387](https://github.com/ufz/ogs/pull/2387), [#2401](https://github.com/ufz/ogs/pull/2401) - updated utility `moveMeshNodes`: algorithm for mesh on mesh mapping now - calculates exact node elevation instead of using interpolation. #2390 + calculates exact node elevation instead of using interpolation. [#2390](https://github.com/ufz/ogs/pull/2390) ### Data Explorer - Listing of source terms and boundary conditions in Data Explorer DataView (no - visualisation yet). #2110 + visualisation yet). [#2110](https://github.com/ufz/ogs/pull/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 + [#2115](https://github.com/ufz/ogs/pull/2115) +- added custom VTK filter to represent raster data as point clouds. [#2121](https://github.com/ufz/ogs/pull/2121) +- geometrical points can now be converted into station points. [#2369](https://github.com/ufz/ogs/pull/2369) +- fixed issue with geometrical surfaces not being loaded correctly. [#2388](https://github.com/ufz/ogs/pull/2388) ### Other notable code changes - C++17 standard is enabled and is allowed in the production code (given the - compiler support). #2298 + compiler support). [#2298](https://github.com/ufz/ogs/pull/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 + [#2017](https://github.com/ufz/ogs/pull/2017) +- Parameters are extracted in own library. [#2413](https://github.com/ufz/ogs/pull/2413) +- Port secondary variable extrapolation and output for PETSc builds. [#2082](https://github.com/ufz/ogs/pull/2082) +- Extend Kelvin mapping functions and move implementation to MathLib. [#2060](https://github.com/ufz/ogs/pull/2060), + [#2075](https://github.com/ufz/ogs/pull/2075), [#2044](https://github.com/ufz/ogs/pull/2044) +- Collect generic algorithms in single header file. [#2161](https://github.com/ufz/ogs/pull/2161) +- Remove unused MeshSubsets class. [#2135](https://github.com/ufz/ogs/pull/2135) +- Removed writing of xsd header in XML files, [#2198](https://github.com/ufz/ogs/pull/2198) ## Infrastructure - Migrated LFS storage from GitLab to [Artifactory](https://ogs.jfrog.io/ogs). - #2359 -- Optimized ctest runtime by starting long-running benchmarks first. #2310 -- Proper RPATH handling for shared library installations. #2208 + [#2359](https://github.com/ufz/ogs/pull/2359) +- Optimized ctest runtime by starting long-running benchmarks first. [#2310](https://github.com/ufz/ogs/pull/2310) +- Proper RPATH handling for shared library installations. [#2208](https://github.com/ufz/ogs/pull/2208) - [Package OGS inside container](https://www.opengeosys.org/docs/userguide/basics/container/) with [Singularity](https://www.sylabs.io/singularity/); [more - docs](https://www.opengeosys.org/docs/devguide/advanced/singularity/). #2193, - #2356 + docs](https://www.opengeosys.org/docs/devguide/advanced/singularity/). [#2193](https://github.com/ufz/ogs/pull/2193), + [#2356](https://github.com/ufz/ogs/pull/2356) - Migrated opengeosys.org to a static site generator ([Hugo](https://gohugo.io)) - unifying documentation and general OGS info. #2088, #2095, #2123 -- Speed-up CMake run time. #2072, #2392 + unifying documentation and general OGS info. [#2088](https://github.com/ufz/ogs/pull/2088), [#2095](https://github.com/ufz/ogs/pull/2095), [#2123](https://github.com/ufz/ogs/pull/2123) +- Speed-up CMake run time. [#2072](https://github.com/ufz/ogs/pull/2072), [#2392](https://github.com/ufz/ogs/pull/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 +- `OGS_USE_PYTHON` enables Python BCs. [#2170](https://github.com/ufz/ogs/pull/2170) +- `OGS_BUILD_TESTS` was renamed to `BUILD_TESTING`. [#2350](https://github.com/ufz/ogs/pull/2350) +- Added `OGS_USE_CVODE`. [#2344](https://github.com/ufz/ogs/pull/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 + [#2233](https://github.com/ufz/ogs/pull/2233) +- `OGS_USE_CONAN=ON` is now the default when `conan` was found. [#2207](https://github.com/ufz/ogs/pull/2207) ### Version info @@ -187,7 +187,7 @@ - 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 +- VTK minimum version 8.1. [#2158](https://github.com/ufz/ogs/pull/2158) - Qt tested version 5.11.2 - Python tested version 3.7.2 @@ -242,14 +242,14 @@ improvements of the CI. #### Testing and documentation: - Insitu visualization with ParaView Catalyst. See [presentation](https://github.com/ufz/ogs/files/867280/Insitu-Department.pdf). - #1744, #1732. As a consequence VTK 7.1 is now required. + [#1744](https://github.com/ufz/ogs/pull/1744), [#1732](https://github.com/ufz/ogs/pull/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](https://dev.opengeosys.org/docs/benchmarks/elliptic/groundwater-flow-neumann/#results-and-evaluation) - via [vtk.js](https://kitware.github.io/vtk-js/). #1706, #1714, #1723, #1729. + via [vtk.js](https://kitware.github.io/vtk-js/). [#1706](https://github.com/ufz/ogs/pull/1706), [#1714](https://github.com/ufz/ogs/pull/1714), [#1723](https://github.com/ufz/ogs/pull/1723), [#1729](https://github.com/ufz/ogs/pull/1729). - Migrated handling of test data files from *git-submodule* to *git-lfs*, see - [docs](https://docs.opengeosys.org/docs/devguide/testing/test-data). #1964, - #1982, #1984, #2010, #2012. Now [git-lfs](https://git-lfs.github.com/) is + [docs](https://docs.opengeosys.org/docs/devguide/testing/test-data). [#1964](https://github.com/ufz/ogs/pull/1964), + [#1982](https://github.com/ufz/ogs/pull/1982), [#1984](https://github.com/ufz/ogs/pull/1984), [#2010](https://github.com/ufz/ogs/pull/2010), [#2012](https://github.com/ufz/ogs/pull/2012). Now [git-lfs](https://git-lfs.github.com/) is required. Check the [installation](https://docs.opengeosys.org/docs/devguide/getting-started/prerequisites) instructions. @@ -258,14 +258,14 @@ improvements of the CI. - Fully moved to Conan for automatic third-party library handling. Can be enabled with `OGS_USE_CONAN=ON`, see [docs](https://docs.opengeosys.org/docs/devguide/advanced/conan-package-manager). - #1907 + [#1907](https://github.com/ufz/ogs/pull/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 + config, ON otherwise. Can be overridden by explicitly setting the option. [#1673](https://github.com/ufz/ogs/pull/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. @@ -279,8 +279,8 @@ improvements of the CI. - PETSc config is tested on Jenkins (envinf1) - OGS binaries are provided as eve / envinf1 modules. See [docs](https://docs.opengeosys.org/docs/quickstart/basics/envinf1) for - details. #1753 -- Migrated Data Explorer to Qt5. #1622, #1625 + details. [#1753](https://github.com/ufz/ogs/pull/1753) +- Migrated Data Explorer to Qt5. [#1622](https://github.com/ufz/ogs/pull/1622), [#1625](https://github.com/ufz/ogs/pull/1625) - Windows builds are tested on MSVC 2017 on own hardware and on MS @@ -294,57 +294,57 @@ 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 + - Implementation of hydro-mechanics (HM) with LIE. [#1537](https://github.com/ufz/ogs/pull/1537)-[#1541](https://github.com/ufz/ogs/pull/1541) + - Implementation of small deformation (M) with LIE. [#1452](https://github.com/ufz/ogs/pull/1452) + - Fracture constitutive models. [#1434](https://github.com/ufz/ogs/pull/1434) + - Hydro-Mechanics process. [#1508](https://github.com/ufz/ogs/pull/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 OGS_FATAL_ABORT for debugging. #1432 - - Set the default OGS_LOG_LEVEL to debug in release builds. #1522 - - Add integration order in input files. #1464 - - Migrated Data Explorer to Qt5. #1622, #1625 + Boussinesq approximation using constant viscosity. [#1534](https://github.com/ufz/ogs/pull/1534) + - Two phase flow process with pp model implementation. [#1530](https://github.com/ufz/ogs/pull/1530) + - Richards flow process implementation. [#1473](https://github.com/ufz/ogs/pull/1473) + - Liquid process. [#1468](https://github.com/ufz/ogs/pull/1468) + - Classes for relative permeability models. [#1531](https://github.com/ufz/ogs/pull/1531) + - Classes for capillary models. [#1517](https://github.com/ufz/ogs/pull/1517), [#1578](https://github.com/ufz/ogs/pull/1578) + - Ehlers single-surface yield function constitutive relation model. [#1556](https://github.com/ufz/ogs/pull/1556) + - Support scaling, GMRES, and Pardiso in Eigen linear solvers. [#1509](https://github.com/ufz/ogs/pull/1509) [#1510](https://github.com/ufz/ogs/pull/1510) + - Piecewise linear Monotonic curve and a generic curve parser. [#1529](https://github.com/ufz/ogs/pull/1529) + - Support searching boundary nodes in MeshLib::NodeSearch. [#1459](https://github.com/ufz/ogs/pull/1459) + - Support specifying the shape function order in process variables. [#1503](https://github.com/ufz/ogs/pull/1503) + - Command line option --unbuffered-std-out to deactivate buffer for standard output. [#1514](https://github.com/ufz/ogs/pull/1514) + - CMake option OGS_FATAL_ABORT for debugging. [#1432](https://github.com/ufz/ogs/pull/1432) + - Set the default OGS_LOG_LEVEL to debug in release builds. [#1522](https://github.com/ufz/ogs/pull/1522) + - Add integration order in input files. [#1464](https://github.com/ufz/ogs/pull/1464) + - Migrated Data Explorer to Qt5. [#1622](https://github.com/ufz/ogs/pull/1622), [#1625](https://github.com/ufz/ogs/pull/1625) - Benchmarks can be run on specific configurations only by using the new parameter - `REQUIREMENTS` in `AddTest()` (in CMake). #1610 + `REQUIREMENTS` in `AddTest()` (in CMake). [#1610](https://github.com/ufz/ogs/pull/1610) ### Utilities New utilities: - - createQuadraticMesh #1500 - - convertToLinearMesh #1554 - - postLIE #1555 + - createQuadraticMesh [#1500](https://github.com/ufz/ogs/pull/1500) + - convertToLinearMesh [#1554](https://github.com/ufz/ogs/pull/1554) + - postLIE [#1555](https://github.com/ufz/ogs/pull/1555) New features: - - extend NodeReordering to correct ordering of nonlinear nodes #1519 + - extend NodeReordering to correct ordering of nonlinear nodes [#1519](https://github.com/ufz/ogs/pull/1519) ### Infrastructure: - - Ctest now works on Windows too by removing time-wrappers. #1480 - - Moved to public Jenkins instance at jenkins.opengeosys.org. #1505 + - Ctest now works on Windows too by removing time-wrappers. [#1480](https://github.com/ufz/ogs/pull/1480) + - Moved to public Jenkins instance at jenkins.opengeosys.org. [#1505](https://github.com/ufz/ogs/pull/1505) - Doxygen warnings parser in Jenkins will mark a build as unstable - if there are Doxygen warnings. #1585 + if there are Doxygen warnings. [#1585](https://github.com/ufz/ogs/pull/1585) - Benchmarking on Jenkins now saves the standard output into a file for each - test. #1528 + test. [#1528](https://github.com/ufz/ogs/pull/1528) ### Fixes: - - Fix LocalToGlobalIndexMap with mutliple variables and with multiple componets. #1433 #1440 - - Fix PropertyVector<T*> 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 LocalToGlobalIndexMap with mutliple variables and with multiple componets. [#1433](https://github.com/ufz/ogs/pull/1433) [#1440](https://github.com/ufz/ogs/pull/1440) + - Fix PropertyVector<T*> for multi-component case. [#1441](https://github.com/ufz/ogs/pull/1441) + - Fix checking IDs of nonlinear nodes. [#1495](https://github.com/ufz/ogs/pull/1495) + - Fix incorrect use of getNumberOfBaseNodes(). [#1515](https://github.com/ufz/ogs/pull/1515) + - Fix computing sparsity pattern for mixed shape function order cases. [#1548](https://github.com/ufz/ogs/pull/1548) + - Fix that iterations and residuals were not printed when Eigen linear solver fails. [#1499](https://github.com/ufz/ogs/pull/1499) + - Fix all of the Doxygen warnings in the code. [#1569](https://github.com/ufz/ogs/pull/1569) [#1573](https://github.com/ufz/ogs/pull/1573) - Fix all of the input file/keyword documentation and its generation. @@ -359,145 +359,145 @@ 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 - - Added B-Matrices and Kelvin mapping tools for deformation processes. #1359 - - Heat conduction process implementation. #1328 + 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 - - Added uniform Robin boundary condition. #1336 - - Added a generic natural boundary condition class. #1337 - - Added Robin boundary condition. #1336 + 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, #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 + [#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 + 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, #1435 + 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 - - Added time measurement for assembly and solvers. #1322 + 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, #1315 + [#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, #1342 - - Restructured the time loop. #1364 + 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 - - scaleProperty for simple rescaling of mesh properties. #1347 - - convertGEO for geometric file conversion, e.g. gli to glm. #1360 + 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 + [#1361](https://github.com/ufz/ogs/pull/1361) New feature: - - Support tetrahedra types in generateStructuredMesh. #1353 + - 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, #1396, #1404, #1411, #1424, #1428, #1436 + [#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 + gets build. [#1458](https://github.com/ufz/ogs/pull/1458) - Increase minimum clang compiler version to 3.5 in course of updating travis - build enviroment to Ubuntu LTS 14.04. #1448 + build enviroment 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 + 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 + 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 - - 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 + [#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 - - 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 + [#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) # 6.0.6 ### Features: - Add external ode-solver interface with [Sundials CVODE - library](http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/cvode). #1109 + 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 + 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 + 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 + 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 - - Added functionality for the output of secondary variables. #1171 + 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 + reactions. [#1178](https://github.com/ufz/ogs/pull/1178) - Transferred the TES process, a monolithically coupled THC model for simulating - thermochemical energy storag devices, from OGS5. #1181 + thermochemical energy storag 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 - - 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 + - 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 - - 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 + - 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 + 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 - - Simplified FindEigen.cmake, #1209 - - git diff --check is run in its own Travis job, #1207 + 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, #1235 - - Eigen is not optional anymore #1218 - - Removed OGS_USE_EIGENLIS CMake option. Use OGS_USE_LIS instead #1251 + - 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 - - Fix memory leaks in GMSHInterface. #1212 - - Fix build with Lis #1267 - - Fixing several small issues with NetCDF import #1169 + - 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 - - 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 + - Move DataHolderLib and FileIO under Applications [#1279](https://github.com/ufz/ogs/pull/1279) + - Remove calling std::abort within libraries. Exeptions 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) # 6.0.5 @@ -508,7 +508,7 @@ New feature: 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 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. @@ -522,8 +522,8 @@ New feature: 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 - - Command line argument `-l` for OGS cli and testrunner to specify verbosity of logging. #1056 + 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. @@ -546,8 +546,8 @@ New feature: - 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 +- 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 -- GitLab