add domain and mesh generation document for layered soil.

.gitignore

@@ -31,7 +31,7 @@
 
 # Ignoriere temp files von gaengigen Texteditoren
 *~
-
+.Rhistory
 
 # MATLAB Numerische Experimente
 *.mat
@@ -77,4 +77,4 @@
 
 
 # Directories
-
+demo/

domain_layered_soil.py

+"""This demo program demonstrates how to mark sub domains of a mesh
+and store the sub domain markers as a mesh function to a DOLFIN XML
+file.
+
+The sub domain markers produced by this demo program are the ones used
+for the Stokes demo programs.
+"""
+
+# Copyright (C) 2007 Kristian B. Oelgaard
+#
+# This file is part of DOLFIN.
+#
+# DOLFIN is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# DOLFIN is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with DOLFIN. If not, see <http://www.gnu.org/licenses/>.
+#
+# Modified by Anders Logg, 2008.
+#
+# First added:  2007-11-15
+# Last changed: 2011-01-25
+# Begin demo
+
+from dolfin import *
+
+set_log_level(1)
+
+# Sub domain for no-slip (mark whole boundary, inflow and outflow will overwrite)
+class Noslip(SubDomain):
+    def inside(self, x, on_boundary):
+        return on_boundary
+
+# Sub domain for inflow (right)
+class Inflow(SubDomain):
+    def inside(self, x, on_boundary):
+        return x[0] > 1.0 - DOLFIN_EPS and on_boundary
+
+# Sub domain for outflow (left)
+class Outflow(SubDomain):
+    def inside(self, x, on_boundary):
+        return x[0] < DOLFIN_EPS and on_boundary
+
+# Read mesh
+mesh = Mesh("../dolfin_fine.xml.gz")
+
+# Create mesh functions over the cell facets
+sub_domains = MeshFunction("size_t", mesh, mesh.topology().dim() - 1)
+sub_domains_bool = MeshFunction("bool", mesh, mesh.topology().dim() - 1)
+sub_domains_double = MeshFunction("double", mesh, mesh.topology().dim() - 1)
+
+# Mark all facets as sub domain 3
+sub_domains.set_all(3)
+sub_domains_bool.set_all(False)
+sub_domains_double.set_all(0.3)
+
+# Mark no-slip facets as sub domain 0, 0.0
+noslip = Noslip()
+noslip.mark(sub_domains, 0)
+noslip.mark(sub_domains_double, 0.0)
+
+# Mark inflow as sub domain 1, 01
+inflow = Inflow()
+inflow.mark(sub_domains, 1)
+inflow.mark(sub_domains_double, 0.1)
+
+# Mark outflow as sub domain 2, 0.2, True
+outflow = Outflow()
+outflow.mark(sub_domains, 2)
+outflow.mark(sub_domains_double, 0.2)
+outflow.mark(sub_domains_bool, True)
+
+# Save sub domains to file
+file = File("subdomains.xml")
+file << sub_domains
+
+# FIXME: Not implemented
+#file_bool = File("subdomains_bool.xml")
+#file_bool << sub_domains_bool
+
+file_double = File("subdomains_double.xml")
+file_double << sub_domains_double
+
+# Save sub domains to VTK files
+file = File("subdomains.pvd")
+file << sub_domains
+
+file = File("subdomains_double.pvd")
+file << sub_domains_double