Merge branch 'develop' into primal_contact

.gitignore

@@ -31,3 +31,4 @@ bin/*
 *.ipynb_checkpoints*
 *.eps
 *.pdf
+.eggs/

Readme.md

@@ -63,7 +63,7 @@ For the moment, Docker support should be considered experimental.
 To function optimally, PorePy should have access to the pypi packages:
 *  `pymetis` (for mesh partitioning). Will be installed on Linux (not so on Windows, to avoid installation issues for the core package in the case where no C compiler is available).
 * Some computationally expensive methods can be accelerated with `Cython` or `Numba`. Cython is automatically installed on many Linux systems, if not, use pip or conda. Numba can be installed using `conda`.
-* Visualization by either matplotlib or (preferrable for larger problems) vtk/paraview. To dump data to paraview, a vtk filter must be available; the only solution we have found is from the 'conda' repositories, e.g. 'conda install -c clinicalgraphics vtk=7.1.0' (note that vtk should be version 7.0.0 or later, hence not the official channel)
+* Visualization by either matplotlib or (preferrable for larger problems) vtk/paraview. To dump data to paraview, a vtk filter must be available; the only solution we have found is from the 'conda' repositories, e.g. 'RUN conda install -c conda-forge vtk'
 * We use `shapely` for certain geometry-operations.
 * Meshing: currently by [gmsh](http://gmsh.info/doc/texinfo/gmsh.html). For its configuration see [Install](https://github.com/pmgbergen/porepy/blob/develop/Install.md).
 

dockerfiles/Dockerfile

@@ -72,7 +72,9 @@ RUN git clone https://github.com/pmgbergen/porepy.git pp
 #    python setup.py install 
 
 WORKDIR /home/porepy/pp
-RUN conda install numpy=1.16.3 scipy=1.2.1 networkx=2.3 sympy=1.4 cython=0.29.7 numba=0.43.1 matplotlib=3.0.3 pytest=4.5.0 pytest-cov=2.6.1 pytest-runner=4.4 vtk=8.2.0 jupyter=1.0.0
+RUN conda install numpy=1.16.3 scipy=1.2.1 networkx=2.3 sympy=1.4 cython=0.29.7 numba=0.43.1 matplotlib=3.0.3 pytest=4.5.0 pytest-cov=2.6.1 pytest-runner=4.4 jupyter=1.0.0
+# Vtk should be install from conda-forged (not all dependencies are installed otherwise):
+RUN conda install -c conda-forge vtk
 RUN pip install meshio==2.3.8 shapely==1.6.4.post2 shapely[vectorized]==1.6.4.post2
 
 RUN python setup.py install

examples/papers/Readme.md

@@ -13,5 +13,8 @@ We try to keep the examples updated as the code changes, but may not always succ
 * [arXiv_1803_01732](./arXiv_1803_01732) paper "*Conforming, non-conforming and non-matching discretization couplings in discrete fracture network simulations*" by Alessio Fumagalli, Eirik Keilegavlen, and Stefano Scialo'. See [arXiv pre-print](https://arxiv.org/abs/1803.01732) or [journal article](https://www.sciencedirect.com/science/article/pii/S0021999118306508).
 * [arXiv_1802_05961](./arXiv_1802_05961) paper "*Unified approach to discretization of flow in fractured porous media*" by Jan M. Nordbotten, Wietse M. Boon, Alessio Fumagalli, and  Eirik Keilegavlen. See [arXiv pre-print](https://arxiv.org/abs/1802.05961) or [journal article](https://link.springer.com/article/10.1007/s10596-018-9778-9).
 * [arXiv_1809_06926](./arXiv_1809_06926) paper "*Call for participation: Verification benchmarks for single-phase flow in three-dimensional fractured porous media*" by Inga Berre, Wietse Boon, Bernd Flemisch, Alessio Fumagalli, Dennis Glaser, Eirik Keilegavlen, Anna Scotti, Ivar Stefansson, Alexandru Tatomir. See [arXiv pre-print](https://arxiv.org/abs/1809.06926).
-* [arXiv_1810_12761](./arXiv_1810_12761) paper "*A multiscale flux basis for mortar mixed discretizations of reduced Darcy-Forchheimer fracture models*" by Elyes Ahmed, Alessio Fumagalli, Ana Budisa. See [arXiv pre-print](https://arxiv.org/abs/1810.12761).
+* [arXiv_1810_12761](./arXiv_1810_12761) paper "*A multiscale flux basis for mortar mixed discretizations of reduced Darcy-Forchheimer fracture models*" by Elyes Ahmed, Alessio Fumagalli, Ana Budiša. See [arXiv pre-print](https://arxiv.org/abs/1810.12761) or [journal article](https://www.sciencedirect.com/science/article/pii/S0045782519303044).
 * [arXiv_1903_01117](./arXiv_1903_01117) paper "*A multi-layer reduced model for flow in porous media with a fault and surrounding damage zones*" by Alessio Fumagalli, Anna Scotti. See [arXiv pre-print](https://arxiv.org/abs/1903.01117).
+
+# Separate repository
+* [repo](https://github.com/alessiofumagalli/multiscale_timedependent) paper "*Robust linear domain decomposition schemes for reduced non-linear fracture flow models*" by Elyes Ahmed, Alessio Fumagalli, Ana Budiša, Eirik Keilegavlen, Jan M. Nordbotten, A. Radu Florin. See [arXiv pre-print](https://arxiv.org/abs/1906.05831).