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ufz/ogs: 6.3.1

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


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<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>Dmitry Yu. Naumov</dc:creator>
  <dc:creator>Tom Fischer</dc:creator>
  <dc:creator>Lars Bilke</dc:creator>
  <dc:creator>Karsten Rink</dc:creator>
  <dc:creator>Norihiro Watanabe</dc:creator>
  <dc:creator>wenqing</dc:creator>
  <dc:creator>renchao.lu</dc:creator>
  <dc:creator>Norbert Grunwald</dc:creator>
  <dc:creator>FZill</dc:creator>
  <dc:creator>Yonghui56</dc:creator>
  <dc:creator>jbathmann</dc:creator>
  <dc:creator>Chaofan Chen</dc:creator>
  <dc:creator>HBShaoUFZ</dc:creator>
  <dc:creator>ShuangChen88</dc:creator>
  <dc:creator>xingyuanmiao</dc:creator>
  <dc:creator>boyanmeng</dc:creator>
  <dc:creator>Marc Walther</dc:creator>
  <dc:creator>skai95</dc:creator>
  <dc:creator>joergbuchwald</dc:creator>
  <dc:creator>joboog</dc:creator>
  <dc:creator>KeitaYoshioka</dc:creator>
  <dc:creator>Tianyuan Zheng</dc:creator>
  <dc:creator>ThieJan</dc:creator>
  <dc:creator>ZhangNing</dc:creator>
  <dc:creator>fparisio</dc:creator>
  <dc:creator>ogsbot</dc:creator>
  <dc:creator>nagelt</dc:creator>
  <dc:creator>carolinh</dc:creator>
  <dc:creator>Thomas</dc:creator>
  <dc:date>2020-06-19</dc:date>
  <dc:description>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
</dc:description>
  <dc:identifier>https://zenodo.org/record/3901385</dc:identifier>
  <dc:identifier>10.5281/zenodo.3901385</dc:identifier>
  <dc:identifier>oai:zenodo.org:3901385</dc:identifier>
  <dc:relation>url:https://github.com/ufz/ogs/tree/6.3.1</dc:relation>
  <dc:relation>doi:10.5281/zenodo.591265</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:title>ufz/ogs: 6.3.1</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>software</dc:type>
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