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An example of reaction diffusion in 1D with no source

This is a simple example of reaction diffusion with zero source for testing.
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1 parent 90745e3 commit e2f47cb5f9870b706f4c352f21262d1fe53f860c Vijay Rajagopal committed Apr 14, 2012
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+ Group name: Region 2
+ Shape. Dimension=1
+ #Scale factor sets= 1
+ l.Lagrange, #Scale factors=2
+ #Nodes= 2
+ #Fields=5
+ 1) Coordinate, coordinate, rectangular cartesian, #Components=1
+ x. l.Lagrange, no modify, standard node based.
+ #Nodes= 2
+ 1. #Values=1
+ Value indices: 1
+ Scale factor indices: 1
+ 2. #Values=1
+ Value indices: 1
+ Scale factor indices: 2
+ 2) Coordinate, field, rectangular cartesian, #Components=1
+ 1. l.Lagrange, no modify, standard node based.
+ #Nodes= 2
+ 1. #Values=1
+ Value indices: 1
+ Scale factor indices: 1
+ 2. #Values=1
+ Value indices: 1
+ Scale factor indices: 2
+ 3) del U/del n, field, rectangular cartesian, #Components=1
+ 1. l.Lagrange, no modify, standard node based.
+ #Nodes= 2
+ 1. #Values=1
+ Value indices: 1
+ Scale factor indices: 1
+ 2. #Values=1
+ Value indices: 1
+ Scale factor indices: 2
+ 4) Coordinate, field, rectangular cartesian, #Components=2
+ 1. l.Lagrange, no modify, grid based.
+ #xi1=1
+ 2. l.Lagrange, no modify, standard node based.
+ #Nodes= 2
+ 1. #Values=1
+ Value indices: 1
+ Scale factor indices: 1
+ 2. #Values=1
+ Value indices: 1
+ Scale factor indices: 2
+ 5) Coordinate, field, rectangular cartesian, #Components=1
+ 1. l.Lagrange, no modify, standard node based.
+ #Nodes= 2
+ 1. #Values=1
+ Value indices: 1
+ Scale factor indices: 1
+ 2. #Values=1
+ Value indices: 1
+ Scale factor indices: 2
+ Element: 1 0 0
+ Values:
+ 5.0000000000000000E-01 5.0000000000000000E-01
+ Nodes:
+ 1 2
+ Scale factors:
+ 1.0000000000000000E+00 1.0000000000000000E+00
+ Element: 2 0 0
+ Values:
+ 5.0000000000000000E-01 5.0000000000000000E-01
+ Nodes:
+ 2 3
+ Scale factors:
+ 1.0000000000000000E+00 1.0000000000000000E+00
@@ -0,0 +1,34 @@
+ Group name: Region 2
+ #Fields=5
+ 1) Coordinate, coordinate, rectangular cartesian, #Components=1
+ x. Value index= 1, #Derivatives= 0
+ 2) Coordinate, field, rectangular cartesian, #Components=1
+ 1. Value index= 2, #Derivatives= 0
+ 3) del U/del n, field, rectangular cartesian, #Components=1
+ 1. Value index= 3, #Derivatives= 0
+ 4) Coordinate, field, rectangular cartesian, #Components=2
+ 1. Value index= 4, #Derivatives= 0
+ 2. Value index= 5, #Derivatives= 0
+ 5) Coordinate, field, rectangular cartesian, #Components=1
+ 1. Value index= 6, #Derivatives= 0
+ Node: 1
+ 0.0000000000000000E+00
+ 1.5000000000000000E+00
+ 0.0000000000000000E+00
+ 1.2345678806304932E+00
+ 1.0000000000000000E+00
+ 0.0000000000000000E+00
+ Node: 2
+ 2.5000000000000000E+00
+ 1.6623468967852575E-01
+ 0.0000000000000000E+00
+ 1.2345678806304932E+00
+ 1.0000000000000000E+00
+ 0.0000000000000000E+00
+ Node: 3
+ 5.0000000000000000E+00
+ 1.5000000000000000E+00
+ 0.0000000000000000E+00
+ 1.2345678806304932E+00
+ 1.0000000000000000E+00
+ 0.0000000000000000E+00
@@ -0,0 +1,70 @@
+# -*- makefile -*-
+#
+# For use with GNU make.
+#
+#
+#----------------------------------------------------------------------------------------------------------------------------------
+# Makefile for compiling openCMISS examples
+#
+# Original by Chris Bradley adapted from the CMISS Makefile by Karl Tomlinson
+# Changes:
+#
+#----------------------------------------------------------------------------------------------------------------------------------
+#
+# LICENSE
+#
+# Version: MPL 1.1/GPL 2.0/LGPL 2.1
+#
+# The contents of this file are subject to the Mozilla Public License
+# Version 1.1 (the "License"); you may not use this file except in
+# compliance with the License. You may obtain a copy of the License at
+# http://www.mozilla.org/MPL/
+#
+# Software distributed under the License is distributed on an "AS IS"
+# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
+# License for the specific language governing rights and limitations
+# under the License.
+#
+# The Original Code is openCMISS
+#
+# The Initial Developer of the Original Code is University of Auckland,
+# Auckland, New Zealand and University of Oxford, Oxford, United
+# Kingdom. Portions created by the University of Auckland and University
+# of Oxford are Copyright (C) 2007 by the University of Auckland and
+# the University of Oxford. All Rights Reserved.
+#
+# Contributor(s):
+#
+# Alternatively, the contents of this file may be used under the terms of
+# either the GNU General Public License Version 2 or later (the "GPL"), or
+# the GNU Lesser General Public License Version 2.1 or later (the "LGPL"),
+# in which case the provisions of the GPL or the LGPL are applicable instead
+# of those above. If you wish to allow use of your version of this file only
+# under the terms of either the GPL or the LGPL, and not to allow others to
+# use your version of this file under the terms of the MPL, indicate your
+# decision by deleting the provisions above and replace them with the notice
+# and other provisions required by the GPL or the LGPL. If you do not delete
+# the provisions above, a recipient may use your version of this file under
+# the terms of any one of the MPL, the GPL or the LGPL.
+#
+#----------------------------------------------------------------------------------------------------------------------------------
+
+MAKEFLAGS = --no-builtin-rules --warn-undefined-variables
+
+#----------------------------------------------------------------------------------------------------------------------------------
+
+ifndef OPENCMISS_ROOT
+ OPENCMISS_ROOT := ../../..
+ GLOBAL_ROOT := $(CURDIR)/../../..
+else
+ GLOBAL_ROOT := ${OPENCMISS_ROOT}/cm
+endif
+
+#----------------------------------------------------------------------------------------------------------------------------------
+
+EXAMPLE_PATH=ClassicalField/Diffusion/
+
+EXAMPLE_NAME = ReactionDiffusionNoSource1D
+
+include $(GLOBAL_ROOT)/ExampleMakefile
+
@@ -0,0 +1,67 @@
+ Group name: Region 2
+ Shape. Dimension=1
+ #Scale factor sets= 1
+ l.Lagrange, #Scale factors=2
+ #Nodes= 2
+ #Fields=5
+ 1) Coordinate, coordinate, rectangular cartesian, #Components=1
+ x. l.Lagrange, no modify, standard node based.
+ #Nodes= 2
+ 1. #Values=1
+ Value indices: 1
+ Scale factor indices: 1
+ 2. #Values=1
+ Value indices: 1
+ Scale factor indices: 2
+ 2) Coordinate, field, rectangular cartesian, #Components=1
+ 1. l.Lagrange, no modify, standard node based.
+ #Nodes= 2
+ 1. #Values=1
+ Value indices: 1
+ Scale factor indices: 1
+ 2. #Values=1
+ Value indices: 1
+ Scale factor indices: 2
+ 3) del U/del n, field, rectangular cartesian, #Components=1
+ 1. l.Lagrange, no modify, standard node based.
+ #Nodes= 2
+ 1. #Values=1
+ Value indices: 1
+ Scale factor indices: 1
+ 2. #Values=1
+ Value indices: 1
+ Scale factor indices: 2
+ 4) Coordinate, field, rectangular cartesian, #Components=2
+ 1. l.Lagrange, no modify, grid based.
+ #xi1=1
+ 2. l.Lagrange, no modify, standard node based.
+ #Nodes= 2
+ 1. #Values=1
+ Value indices: 1
+ Scale factor indices: 1
+ 2. #Values=1
+ Value indices: 1
+ Scale factor indices: 2
+ 5) Coordinate, field, rectangular cartesian, #Components=1
+ 1. l.Lagrange, no modify, standard node based.
+ #Nodes= 2
+ 1. #Values=1
+ Value indices: 1
+ Scale factor indices: 1
+ 2. #Values=1
+ Value indices: 1
+ Scale factor indices: 2
+ Element: 1 0 0
+ Values:
+ 5.0000000000000000E-01 5.0000000000000000E-01
+ Nodes:
+ 1 2
+ Scale factors:
+ 1.0000000000000000E+00 1.0000000000000000E+00
+ Element: 2 0 0
+ Values:
+ 5.0000000000000000E-01 5.0000000000000000E-01
+ Nodes:
+ 2 3
+ Scale factors:
+ 1.0000000000000000E+00 1.0000000000000000E+00
@@ -0,0 +1,34 @@
+ Group name: Region 2
+ #Fields=5
+ 1) Coordinate, coordinate, rectangular cartesian, #Components=1
+ x. Value index= 1, #Derivatives= 0
+ 2) Coordinate, field, rectangular cartesian, #Components=1
+ 1. Value index= 2, #Derivatives= 0
+ 3) del U/del n, field, rectangular cartesian, #Components=1
+ 1. Value index= 3, #Derivatives= 0
+ 4) Coordinate, field, rectangular cartesian, #Components=2
+ 1. Value index= 4, #Derivatives= 0
+ 2. Value index= 5, #Derivatives= 0
+ 5) Coordinate, field, rectangular cartesian, #Components=1
+ 1. Value index= 6, #Derivatives= 0
+ Node: 1
+ 0.0000000000000000E+00
+ 1.5000000000000000E+00
+ 0.0000000000000000E+00
+ 1.2345678806304932E+00
+ 1.0000000000000000E+00
+ 0.0000000000000000E+00
+ Node: 2
+ 2.5000000000000000E+00
+ 1.6623468967852575E-01
+ 0.0000000000000000E+00
+ 1.2345678806304932E+00
+ 1.0000000000000000E+00
+ 0.0000000000000000E+00
+ Node: 3
+ 5.0000000000000000E+00
+ 1.5000000000000000E+00
+ 0.0000000000000000E+00
+ 1.2345678806304932E+00
+ 1.0000000000000000E+00
+ 0.0000000000000000E+00
@@ -0,0 +1,13 @@
+{"example": {
+ "globalTestDir" : the global test directory, e.g. "42testingPoints", the default is ""
+ "test": [
+ {
+ "id": 1,
+ "args": arguments passed into the test, e.g. "4 4 0 1", the default is "",
+ "path": the path to the directory the test is executing from the globalTestDir, the default is the examplePath
+ "processors": number of computational nodes running, the default is 1,
+ "expectedPath": the path to the expected files from test.path, the default is unset,
+ "outputPath": the path to the output directory from test.path, the default is unset,
+ "tolerance": the tolerance allowed to compare the output with expected values, the default is "1e-7"}]
+}}
+
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