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ufz/ogs: 6.1.0

Tom Fischer; Dmitry Yu. Naumov; Lars Bilke; Karsten Rink; Christoph Lehmann; Norihiro Watanabe; wenqing; Yonghui56; xingyuanmiao; Marc Walther; Tianyuan Zheng; ogsbot; fparisio; carolinh; mylese


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  <dc:creator>Tom Fischer</dc:creator>
  <dc:creator>Dmitry Yu. Naumov</dc:creator>
  <dc:creator>Lars Bilke</dc:creator>
  <dc:creator>Karsten Rink</dc:creator>
  <dc:creator>Christoph Lehmann</dc:creator>
  <dc:creator>Norihiro Watanabe</dc:creator>
  <dc:creator>wenqing</dc:creator>
  <dc:creator>Yonghui56</dc:creator>
  <dc:creator>xingyuanmiao</dc:creator>
  <dc:creator>Marc Walther</dc:creator>
  <dc:creator>Tianyuan Zheng</dc:creator>
  <dc:creator>ogsbot</dc:creator>
  <dc:creator>fparisio</dc:creator>
  <dc:creator>carolinh</dc:creator>
  <dc:creator>mylese</dc:creator>
  <dc:date>2018-01-11</dc:date>
  <dc:description>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 --&gt; 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).
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  <dc:identifier>https://zenodo.org/record/1145843</dc:identifier>
  <dc:identifier>10.5281/zenodo.1145843</dc:identifier>
  <dc:identifier>oai:zenodo.org:1145843</dc:identifier>
  <dc:relation>url:https://github.com/ufz/ogs/tree/6.1.0</dc:relation>
  <dc:relation>doi:10.5281/zenodo.591265</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:title>ufz/ogs: 6.1.0</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>software</dc:type>
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