Merge branch 'develop' into make_examples_working

Conflicts:
    src/porepy/fracs/fractures.py
    src/porepy/fracs/simplex.py
    src/porepy/grids/gmsh/gmsh_interface.py
    src/porepy/grids/grid.py
    src/porepy/utils/comp_geom.py

.gitignore

@@ -25,3 +25,6 @@
 *.coverage
 .cache/*
 bin/*
+*.pvd
+*.so
+*.png

Install.md

@@ -18,10 +18,12 @@ The expectation is that it should work out nicely. If you try this, please let u
 # Setting up GMSH
 PorePy currently depends on `GMSH` for meshing of fractured domains. 
 To make this work, you need gmsh installed on your system, and PorePy needs to know where to look for it.
-First, visit the [GMSH webpage](http://gmsh.info) and download a suitable version. 
+First, visit the [Gmsh webpage](http://gmsh.info) and download a suitable version. 
 Extract, and move the binary (probably located in the subfolder gmsh-x.x.x-Linux/bin or similar) to whereever you prefer.
 
-Note to Linux users: Although GMSH is available through the standard packaging tools, it tends to be hopelessly outdated, 
+NOTE: We have experienced that some fracture geometries are best handled by somewhat older versions of Gmsh (2.11 seems to be a good version) - newer versions are often result in error messages. Until this is resolved, we therefore recommend to use Gmsh 2.11 with PorePy.
+
+Note to Linux users: Although Gmsh is available through the standard packaging tools, it tends to be hopelessly outdated, 
 and resulted in severe issues for the fracture meshing last time we checked. Use the GMSH web page instead.
 
 

examples/example3/test_simple_networks.py

@@ -199,7 +199,12 @@ def test_T_intersection_within_plane(**kwargs):
 
     domain = {'xmin':-1, 'xmax': 2, 'ymin': -2, 'ymax': 2, 'zmin': -1,
               'zmax':2}
-    grids = meshing.simplex_grid([p1, p2], domain)
+    # This test, when used with certain versions of gmsh (<2.15?) gives a
+    # a mismatch between 2d cells and 3d faces on fracture surfaces. The bug
+    # can be located in the .msh-file. To function as a test, we disband the
+    # test of cell-face relations.
+    grids = meshing.simplex_grid([p1, p2], domain,
+                                 ensure_matching_face_cell=False)
 
 def test_T_intersection_one_outside_plane(**kwargs):
     p1 = np.array([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0]]).T
@@ -216,3 +221,45 @@ def test_T_intersection_both_outside_plane(**kwargs):
     domain = {'xmin':-1, 'xmax': 2, 'ymin': -2, 'ymax': 2, 'zmin': -1,
               'zmax':2}
     grids = meshing.simplex_grid([p1, p2], domain)
+
+def test_T_intersection_both_on_boundary(**kwargs):
+    p1 = np.array([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0]]).T
+    p2 = np.array([[0., 0.5, 0], [1, 0.5, 0], [0.5, 0.5, 1.]]).T
+
+    domain = {'xmin':-1, 'xmax': 2, 'ymin': -2, 'ymax': 2, 'zmin': -1,
+              'zmax':2}
+    grids = meshing.simplex_grid([p1, p2], domain)
+
+def test_T_intersection_one_boundary_one_outside(**kwargs):
+    p1 = np.array([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0]]).T
+    p2 = np.array([[-0.2, 0.5, 0], [1, 0.5, 0], [0.5, 0.5, 1.]]).T
+
+    domain = {'xmin':-1, 'xmax': 2, 'ymin': -2, 'ymax': 2, 'zmin': -1,
+              'zmax':2}
+    grids = meshing.simplex_grid([p1, p2], domain)
+
+def test_T_intersection_one_boundary_one_inside(**kwargs):
+    p1 = np.array([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0]]).T
+    p2 = np.array([[0.2, 0.5, 0], [1, 0.5, 0], [0.5, 0.5, 1.]]).T
+
+    domain = {'xmin':-1, 'xmax': 2, 'ymin': -2, 'ymax': 2, 'zmin': -1,
+              'zmax':2}
+    grids = meshing.simplex_grid([p1, p2], domain)
+
+def test_issue_54():
+    mesh_kwargs = {}
+    mesh_size = 5e-1
+    mesh_kwargs['mesh_size'] = {'mode': 'constant',
+    'value': mesh_size, 'bound_value': 1.2*mesh_size}
+    mesh_kwargs['file_name'] = 'bounding_box_test'
+    domain = {'xmin': -1, 'xmax': 1,
+              'ymin': 0, 'ymax': 1,
+              'zmin': 0, 'zmax': 1}
+    f_1 = np.array([[.5,.5,.5,.5],
+                    [.4,.5,.5,.4],
+                    [0.2,0.2,.8,.8]])
+    f_2 = np.array([[0,.8,.8,0],
+                    [.5,.5,.5,.5],
+                    [0.2,0.2,.8,.8]])
+    grids = meshing.simplex_grid([f_1, f_2], domain,
+                                 ensure_matching_face_cell=False)