[cig-commits] r11493 - in short/3D/PyLith/trunk/doc/userguide: . tutorials tutorials/3dhex8 tutorials/3dtet4 tutorials/3dtet4/figs

willic3 at geodynamics.org willic3 at geodynamics.org
Thu Mar 20 13:01:06 PDT 2008 

Author: willic3
Date: 2008-03-20 13:01:06 -0700 (Thu, 20 Mar 2008)
New Revision: 11493

Added:
   short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/
   short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx
   short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/figs/
   short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/figs/dislocation.jpg
   short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/figs/shear.jpg
   short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/figs/tet4-mesh.jpg
Modified:
   short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx
   short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx
   short/3D/PyLith/trunk/doc/userguide/userguide.lyx
Log:
Added tet4 example.



Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx	2008-03-20 19:29:56 UTC (rev 11492)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx	2008-03-20 20:01:06 UTC (rev 11493)
@@ -1,4 +1,4 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.3 created this file. For more info see http://www.lyx.org/
 \lyxformat 276
 \begin_document
 \begin_header
@@ -500,7 +500,7 @@
 \family default
  are contained in the file 
 \family typewriter
-axialdisp.cfg
+shearxy.cfg
 \family default
 .
  These settings are:

Added: short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx	                        (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx	2008-03-20 20:01:06 UTC (rev 11493)
@@ -0,0 +1,1361 @@
+#LyX 1.5.3 created this file. For more info see http://www.lyx.org/
+\lyxformat 276
+\begin_document
+\begin_header
+\textclass book
+\begin_preamble
+
+\end_preamble
+\language english
+\inputencoding latin1
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
+\graphics default
+\paperfontsize default
+\spacing single
+\papersize default
+\use_geometry true
+\use_amsmath 0
+\use_esint 0
+\cite_engine basic
+\use_bibtopic false
+\paperorientation portrait
+\leftmargin 1in
+\topmargin 1in
+\rightmargin 1in
+\bottommargin 2in
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\defskip medskip
+\quotes_language english
+\papercolumns 1
+\papersides 1
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\author "" 
+\author "" 
+\end_header
+
+\begin_body
+
+\begin_layout Section
+\begin_inset LatexCommand label
+name "sec:Tutorial-3d-tet4"
+
+\end_inset
+
+Tutorial Using Tetrahedral Mesh Created by LaGriT
+\end_layout
+
+\begin_layout Standard
+PyLith features discussed in this tutorial:
+\end_layout
+
+\begin_layout Itemize
+Quasi-static solution
+\end_layout
+
+\begin_layout Itemize
+LaGriT mesh format
+\end_layout
+
+\begin_layout Itemize
+Dirichlet boundary conditions
+\end_layout
+
+\begin_layout Itemize
+Kinematic fault interface conditions
+\end_layout
+
+\begin_layout Itemize
+Linearly elastic isotropic material
+\end_layout
+
+\begin_layout Itemize
+Specifying more than one material
+\end_layout
+
+\begin_layout Itemize
+VTK output
+\end_layout
+
+\begin_layout Itemize
+Linear tetrahedral cells
+\end_layout
+
+\begin_layout Itemize
+SimpleDB spatial database
+\end_layout
+
+\begin_layout Itemize
+FixedDOFDB spatial database
+\end_layout
+
+\begin_layout Subsection
+Overview
+\end_layout
+
+\begin_layout Standard
+This tutorial is a simple 3D example of a quasi-static finite element problem.
+ It is a mesh composed of 852 linear tetrahedra subject to displacement
+ boundary conditions.
+ This example demonstrates the usage of the 
+\begin_inset LatexCommand htmlurl
+name "LaGriT mesh generation package"
+target "lagrit.lanl.gov"
+
+\end_inset
+
+ to create a mesh, as well as describing how to use a LaGriT-generated mesh
+ in PyLith.
+ In this tutorial, we will walk through the steps necessary to construct,
+ run, and view two problems that use the same mesh.
+ In addition to this manual, each of the files for the example problems
+ includes extensive comments.
+\end_layout
+
+\begin_layout Subsection
+Mesh Generation and Description
+\end_layout
+
+\begin_layout Standard
+The mesh for these examples is a simple rectangular solid (Figure 
+\begin_inset LatexCommand ref
+reference "fig:3dtet4-mesh"
+
+\end_inset
+
+).
+ This mesh would be quite difficult to generate by hand, so we use the LaGriT
+ mesh generation package.
+ For this example, we provide a documented journal file in 
+\family typewriter
+examples/3d/tet4.
+
+\family default
+ Investigation of this journal file should provide some insight into how
+ to use LaGriT with PyLith.
+ For more detailed information on using LaGriT, refer to the 
+\begin_inset LatexCommand htmlurl
+name "LaGriT web site"
+target "lagrit.lanl..gov"
+
+\end_inset
+
+.
+ If you have LaGriT installed on your machine, you can use the journal file
+ to create your own mesh.
+ Otherwise, you can use the mesh that has already been created.
+\end_layout
+
+\begin_layout Standard
+If you are using LaGriT to generate your own mesh, there are two ways to
+ use the journal file.
+ The simplest method is to go to the
+\family sans
+ 
+\family default
+example directory (
+\family typewriter
+examples/3d/tet4
+\family default
+), start LaGriT, and then type:
+\end_layout
+
+\begin_layout LyX-Code
+input/mesh_tet4_1000m.lagrit
+\end_layout
+
+\begin_layout Standard
+This will run the commands in that file, which will produce the necessary
+ files to run the example.
+ This method will create the mesh, but you will gain very little insight
+ into what is being done.
+ A more informative approach is to input each command directly.
+ That way, you will see what each command does.
+ You can simply copy and paste the commands from 
+\family typewriter
+mesh_tet4_1000m.lagrit
+\family default
+.
+ For example, the first six commands, which define the block shape, are
+\end_layout
+
+\begin_layout LyX-Code
+define / domain_xm / -3.0e+3
+\end_layout
+
+\begin_layout LyX-Code
+define / domain_xp /  3.0e+3
+\end_layout
+
+\begin_layout LyX-Code
+define / domain_ym / -3.0e+3
+\end_layout
+
+\begin_layout LyX-Code
+define / domain_yp /  3.0e+3
+\end_layout
+
+\begin_layout LyX-Code
+define / domain_zm / -4.0e+3
+\end_layout
+
+\begin_layout LyX-Code
+define / domain_zp /  0.0e+3 
+\end_layout
+
+\begin_layout Standard
+Continuing through the remainder of the commands in 
+\family typewriter
+mesh_tet4_1000m.lagrit
+\family default
+, you will eventually end up with the files tet4_1000m_binary.gmv, 
+\family typewriter
+tet4_1000m_ascii.gmv
+\family default
+, 
+\family typewriter
+tet4_1000m_ascii.pset
+\family default
+, and 
+\family typewriter
+tet4_1000m_binary.pset
+\family default
+.
+ The ASCII files are not actually needed, but we create them so users can
+ see what is contained in the files.
+ These files may also be used instead of the binary versions, if desired.
+ The 
+\family typewriter
+.gmv
+\family default
+ files define the mesh information, and they may be read directly by the
+ 
+\begin_inset LatexCommand htmlurl
+name "GMV"
+target "laws.lanl.gov/XCM/gmv/GMVHome.html"
+
+\end_inset
+
+ mesh visualization package.
+ The 
+\family typewriter
+.pset
+\family default
+ files specify the vertices corresponding to each boundary used in the problem,
+ including the fault as well as external boundaries to with boundary conditions
+ are applied.
+ This mesh may then be used for the examples described below.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+	filename figs/tet4-mesh.jpg
+	lyxscale 50
+	scale 45
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
+Mesh used for the two tetrahedra examples.
+ The different colors represent the different material groups.
+\begin_inset LatexCommand label
+name "fig:3dtet4-mesh"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Additional Common Information
+\end_layout
+
+\begin_layout Standard
+In addition to the mesh, the two example problems share additional information.
+ For problems of this type, it is generally useful to create a file named
+ 
+\family typewriter
+pylithapp.cfg
+\family default
+ in the run directory, since this file is read automatically every time
+ PyLith is run.
+ Settings specific to a particular problem may be placed in other 
+\family typewriter
+.cfg
+\family default
+ files, as described later, and then those files are placed on the command
+ line.
+  The settings contained in 
+\family typewriter
+pylithapp.cfg
+\family default
+ for this problem consist of:
+\end_layout
+
+\begin_layout Description
+pylithapp.journal.info Settings that control the verbosity of the output for
+ the different components.
+\end_layout
+
+\begin_layout Description
+pylithapp.mesh_generator Settings that control mesh importing, such as the
+ importer type, the filenames, and the spatial dimension of the mesh.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent Settings that control the problem, such as the total
+ time, time step size, and number of entries in the material array.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials Settings that control the material type,
+ specify which material IDs are to be associated with a particular material
+ type, and give the name of the spatial database containing material parameters
+ for the mesh.
+ The quadrature information is also given.
+\end_layout
+
+\begin_layout Description
+pylithapp.petsc PETSc settings to use for the problem, such as the preconditioner
+ type.
+\end_layout
+
+\begin_layout Standard
+Since these examples use LaGriT format, we set the importer to 
+\family typewriter
+MeshIO
+\family default
+Lagrit:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.mesh_generator]
+\end_layout
+
+\begin_layout LyX-Code
+importer = pylith.meshio.MeshIOLagrit
+\end_layout
+
+\begin_layout LyX-Code
+ 
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.mesh_generator.importer]
+\end_layout
+
+\begin_layout LyX-Code
+filename_gmv = tet4_1000m_binary.gmv
+\end_layout
+
+\begin_layout LyX-Code
+filename_pset = tet4_1000m_binary.pset
+\end_layout
+
+\begin_layout LyX-Code
+flip_endian = True
+\end_layout
+
+\begin_layout LyX-Code
+# record_header_32bit = False
+\end_layout
+
+\begin_layout Standard
+Notice that there are a couple of settings pertinent to binary files.
+ The first flag (
+\family typewriter
+flip_endian
+\family default
+) is used if the binary files were produced on a machine with a different
+ endianness than the machine on which they are being read.
+ If you get an error when attempting to run an example, you may need to
+ change the setting of this flag.
+ The second flag (
+\family typewriter
+record_header_32bit
+\family default
+) may need to be set to 
+\family typewriter
+False
+\family default
+ if the version of LaGriT being used has 64-bit Fortran record headers.
+ 
+\end_layout
+
+\begin_layout Standard
+This example differs from most other examples, because we specify four material
+ groups:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent]
+\end_layout
+
+\begin_layout LyX-Code
+materials = elastic_neg1,elastic_neg2,elastic_pos1,elastic_pos2
+\end_layout
+
+\begin_layout LyX-Code
+ 
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.materials.elastic_pos1]
+\end_layout
+
+\begin_layout LyX-Code
+label = Elastic material +x (upper)
+\end_layout
+
+\begin_layout LyX-Code
+id = 1
+\end_layout
+
+\begin_layout LyX-Code
+db.iohandler.filename = mat_elastic.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+quadrature = pylith.feassemble.quadrature.Quadrature3D
+\end_layout
+
+\begin_layout LyX-Code
+quadrature.cell = pylith.feassemble.FIATSimplex
+\end_layout
+
+\begin_layout LyX-Code
+quadrature.cell.shape = tetrahedron
+\end_layout
+
+\begin_layout LyX-Code
+ 
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.materials.elastic_neg1]
+\end_layout
+
+\begin_layout LyX-Code
+label = Elastic material -x (upper)
+\end_layout
+
+\begin_layout LyX-Code
+id = 2
+\end_layout
+
+\begin_layout LyX-Code
+db.iohandler.filename = mat_elastic.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+quadrature = pylith.feassemble.quadrature.Quadrature3D
+\end_layout
+
+\begin_layout LyX-Code
+quadrature.cell = pylith.feassemble.FIATSimplex
+\end_layout
+
+\begin_layout LyX-Code
+quadrature.cell.shape = tetrahedron
+\end_layout
+
+\begin_layout LyX-Code
+ 
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.materials.elastic_pos2]
+\end_layout
+
+\begin_layout LyX-Code
+label = Elastic material +x (lower)
+\end_layout
+
+\begin_layout LyX-Code
+id = 3
+\end_layout
+
+\begin_layout LyX-Code
+db.iohandler.filename = mat_elastic.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+quadrature = pylith.feassemble.quadrature.Quadrature3D
+\end_layout
+
+\begin_layout LyX-Code
+quadrature.cell = pylith.feassemble.FIATSimplex
+\end_layout
+
+\begin_layout LyX-Code
+quadrature.cell.shape = tetrahedron
+\end_layout
+
+\begin_layout LyX-Code
+ 
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.materials.elastic_neg2]
+\end_layout
+
+\begin_layout LyX-Code
+label = Elastic material -x (lower)
+\end_layout
+
+\begin_layout LyX-Code
+id = 4
+\end_layout
+
+\begin_layout LyX-Code
+db.iohandler.filename = mat_elastic.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+quadrature = pylith.feassemble.quadrature.Quadrature3D
+\end_layout
+
+\begin_layout LyX-Code
+quadrature.cell = pylith.feassemble.FIATSimplex
+\end_layout
+
+\begin_layout LyX-Code
+quadrature.cell.shape = tetrahedron 
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout Standard
+The four material groups correspond to the four different colors in Figure
+ 
+\begin_inset LatexCommand ref
+reference "fig:3dtet4-mesh"
+
+\end_inset
+
+.
+ In a more realistic example, we would have used a different database for
+ each material; however, for this simple example, all material properties
+ are contained in the file 
+\family typewriter
+mat_elastic.spatialdb
+\family default
+.
+ One of the reasons that there are four material sets is because the boundary
+ between material sets is used to define the fault surface.
+ See the benchmarks for an example where these material sets are merged
+ back together.
+ Although the material groups are specified in 
+\family typewriter
+pylithapp.cfg
+\family default
+, the physical properties for the material model are given in 
+\family typewriter
+mat_elastic.spatialdb
+\family default
+.
+ For this example, values describing three-dimensional elastic material
+ properties are given at a single point, resulting in uniform material propertie
+s.
+\end_layout
+
+\begin_layout Subsection
+Shear Displacement Example
+\end_layout
+
+\begin_layout Standard
+The first example problem is shearing of the mesh along the y-direction,
+ with displacement boundary conditions applied on the planes corresponding
+ to the minimum and maximum x-values.
+ Parameter settings that override or augment those in 
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file 
+\family typewriter
+shearxy.cfg
+\family default
+.
+ These settings are:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent Specifies an implicit formulation for the problem
+ and specifies the array of boundary conditions.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.implicit Specifies an array of two output managers,
+ one for the full domain, and another for a subdomain corresponding to the
+ ground surface.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos Specifies the boundary conditions for the
+ right side of the mesh, defining which degrees of freedom are being constrained
+ (
+\family typewriter
+x
+\family default
+ and 
+\family typewriter
+y
+\family default
+), providing the label (defined in 
+\family typewriter
+tet4_1000m_binary.pset
+\family default
+) defining the points desired, assigning a label to the boundary condition
+ set, and giving the name of the spatial database defining the boundary
+ conditions (
+\family typewriter
+fixeddisp_shear.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_neg Specifies the boundary conditions for the
+ left side of the mesh, defining which degrees of freedom are being constrained
+ (
+\family typewriter
+x
+\family default
+ and 
+\family typewriter
+y
+\family default
+), providing the label (defined in 
+\family typewriter
+tet4_1000m_binary.
+\family default
+pset) defining the points desired, assigning a label to the boundary condition
+ set, and giving the name of the spatial database defining the boundary
+ conditions (
+\family typewriter
+fixeddisp_shear.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.z_neg Specifies the boundary conditions for the
+ bottom of the mesh, defining which degrees of freedom are being constrained
+ (
+\family typewriter
+x
+\family default
+ and 
+\family typewriter
+y
+\family default
+), providing the label (defined in 
+\family typewriter
+tet4_1000m_binary.
+\family default
+pset) defining the points desired, assigning a label to the boundary condition
+ set, and giving the name of the spatial database defining the boundary
+ conditions (
+\family typewriter
+fixeddisp_shear.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.problem.formulation.output.domain.writer Gives the base filename for
+ VTK output over the entire domain (
+\family typewriter
+shearxy.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.problem.formulation.output.subdomain Gives the label of the nodeset
+ defining the subdomain and gives the base filename for VTK output over
+ the subdomain corresponding to the ground surface (
+\family typewriter
+shearxy-groundsurf.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials.elastic_neg1.output Gives the base filename
+ for state variable output files for the 
+\family typewriter
+elastic_neg1
+\family default
+ material set (
+\family typewriter
+shearxy-statevars-neg1.vtk
+\family default
+), and causes state variables to be averaged over all quadrature points
+ in each cell.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials.elastic_pos1.output Gives the base filename
+ for state variable output files for the 
+\family typewriter
+elastic_pos1
+\family default
+ material set (
+\family typewriter
+shearxy-statevars-pos1.vtk
+\family default
+), and causes state variables to be averaged over all quadrature points
+ in each cell.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials.elastic_neg2.output Gives the base filename
+ for state variable output files for the 
+\family typewriter
+elastic_neg2
+\family default
+ material set (
+\family typewriter
+shearxy-statevars-neg2.vtk
+\family default
+), and causes state variables to be averaged over all quadrature points
+ in each cell.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials.elastic_pos2.output Gives the base filename
+ for state variable output files for the 
+\family typewriter
+elastic_pos2
+\family default
+ material set (
+\family typewriter
+shearxy-statevars-pos2.vtk
+\family default
+), and causes state variables to be averaged over all quadrature points
+ in each cell.
+\end_layout
+
+\begin_layout Standard
+The values for the Dirichlet boundary conditions are described in the file
+ 
+\family typewriter
+fixeddisp_shear.spatialdb
+\family default
+, as specified in 
+\family typewriter
+shearxy.cfg
+\family default
+.
+ The format of all spatial database files is similar.
+ Because data are being specified using two control points (rather than
+ being uniform over the mesh, for example), the data dimension is one.
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+tet4_1000m_binary.
+\family default
+gmv, 
+\family typewriter
+tet4_1000m_binary.pset
+\family default
+, 
+\family typewriter
+pylithapp.cfg
+\family default
+, 
+\family typewriter
+mat_elastic.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+shearxy.cfg
+\family default
+, 
+\family typewriter
+fixeddisp_shear.spatialdb
+\family default
+) provide a complete description of the problem, and we can then run this
+ example by typing
+\end_layout
+
+\begin_layout LyX-Code
+pylith shearxy.cfg
+\end_layout
+
+\begin_layout Standard
+Once the problem has run, ten files will be produced.
+ The first file is named 
+\family typewriter
+shearxy_t0000000.vtk
+\family default
+.
+ The 
+\family typewriter
+t0000000
+\family default
+ indicates that the output is for the first (and only) time step, corresponding
+ to an elastic solution.
+ This file contains mesh information as well as displacement values at the
+ mesh vertices.
+ The second file is named 
+\family typewriter
+shearxy-statevars-neg1_t0000000.vtk
+\family default
+.
+ This file contains the state variables for each cell in the material group
+ 
+\family typewriter
+elastic_neg1
+\family default
+.
+ The default fields are the total strain and stress fields.
+ These values are computed at each quadrature point in the cell.
+ We have requested that the values be averaged over all quadrature points
+ for each cell; however, since we only have a single quadrature point for
+ each linear tetrahedron, this will have no effect.
+ The third file (
+\family typewriter
+shearxy-statevars-neg1_info.vtk
+\family default
+) gives the material properties used for the 
+\family typewriter
+elastic_neg1
+\family default
+ material set.
+ Since we have not specified which properties to write, the default properties
+ (
+\family typewriter
+mu
+\family default
+, 
+\family typewriter
+lambda
+\family default
+, 
+\family typewriter
+density
+\family default
+) are written.
+ There are six additional files containing the state variables and material
+ properties for each of the three additional material sets.
+ The final file (
+\family typewriter
+shearxy-groundsurf_t0000000.vtk
+\family default
+) is analagous to 
+\family typewriter
+shearxy_t0000000.vtk
+\family default
+, but in this case the results are only given for a subset of the mesh correspon
+ding to the ground surface.
+ Also, the cells in this file are one dimension lower than the cells described
+ in 
+\family typewriter
+shearxy_t0000000.vtk
+\family default
+, so they are triangles rather than tetrahedra.
+ All of the 
+\family typewriter
+.vtk
+\family default
+ files may be used with a number of visualization packages.
+ If the problem ran correctly, you should be able to generate a figure such
+ as 
+\begin_inset LatexCommand ref
+reference "fig:3dtet4-shear"
+
+\end_inset
+
+, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+	filename figs/shear.jpg
+	lyxscale 50
+	scale 45
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
+Color contours and vectors of displacement for the axial displacement example.
+\begin_inset LatexCommand label
+name "fig:3dtet4-shear"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Kinematic Fault Slip Example
+\end_layout
+
+\begin_layout Standard
+The next example problem is a right-lateral fault slip applied on the vertical
+ fault defined by 
+\family typewriter
+x = 0
+\family default
+.
+ The left and right sides of the mesh are fixed in the 
+\family typewriter
+x
+\family default
+, 
+\family typewriter
+y
+\family default
+, and 
+\family typewriter
+z
+\family default
+ directions.
+ Parameter settings that override or augment those in 
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file 
+\family typewriter
+dislocation.cfg
+\family default
+.
+ These settings are:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent Specifies an implicit formulation for the problem,
+ the array of boundary conditions, and the array of interfaces.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.implicit Specifies an array of two output managers,
+ one for the full domain, and another for a subdomain corresponding to the
+ ground surface.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos Specifies the boundary conditions for the
+ right side of the mesh, defining which degrees of freedom are being constrained
+ (
+\family typewriter
+x
+\family default
+, 
+\family typewriter
+y
+\family default
+, and 
+\family typewriter
+z
+\family default
+), providing the label (defined in 
+\family typewriter
+tet4_1000m_binary.
+\family default
+pset) defining the points desired, and assigning a label to the boundary
+ condition set.
+ Rather than specifying a spatial database file to define the boundary condition
+s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+ condition, which sets the displacements to zero.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_neg Specifies the boundary conditions for the
+ left side of the mesh, defining which degrees of freedom are being constrained
+ (
+\family typewriter
+x
+\family default
+, 
+\family typewriter
+y
+\family default
+, and 
+\family typewriter
+z
+\family default
+), providing the label (defined in 
+\family typewriter
+tet4_1000m_binary.
+\family default
+pset) defining the points desired, and assigning a label to the boundary
+ condition set.
+ Rather than specifying a spatial database file to define the boundary condition
+s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+ condition, which sets the displacements to zero.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.interfaces Gives the label (defined in 
+\family typewriter
+tet4_1000m_binary.
+\family default
+pset) defining the points on the fault, provides quadrature information,
+ and then gives database names for material properties (needed for conditioning)
+, fault slip, peak fault slip rate, and fault slip time.
+\end_layout
+
+\begin_layout Description
+pylithapp.problem.formulation.output.output.writer Gives the base filename for
+ VTK output over the entire domain (
+\family typewriter
+dislocation.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.problem.formulation.output.subdomain Gives the label of the nodeset
+ defining the subdomain and gives the base filename for VTK output over
+ the subdomain corresponding to the ground surface (
+\family typewriter
+dislocation-groundsurf.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.interfaces.fault.output.writer Gives the base filename
+ for cohesive cell output files (
+\family typewriter
+dislocation-fault.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials.elastic_neg1.output Gives the base filename
+ for state variable output files for the 
+\family typewriter
+elastic_neg1
+\family default
+ material set (
+\family typewriter
+dislocation-statevars-neg1.vtk
+\family default
+), and causes state variables to be averaged over all quadrature points
+ in each cell.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials.elastic_pos1.output Gives the base filename
+ for state variable output files for the elastic_pos1 material set (
+\family typewriter
+dislocation-statevars-pos1.vtk
+\family default
+), and causes state variables to be averaged over all quadrature points
+ in each cell.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials.elastic_neg2.output Gives the base filename
+ for state variable output files for the 
+\family typewriter
+elastic_neg2
+\family default
+ material set (
+\family typewriter
+dislocation-statevars-neg2.vtk
+\family default
+), and causes state variables to be averaged over all quadrature points
+ in each cell.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials.elastic_pos2.output Gives the base filename
+ for state variable output files for the elastic_pos2 material set (
+\family typewriter
+dislocation-statevars-pos2.vtk
+\family default
+), and causes state variables to be averaged over all quadrature points
+ in each cell.
+\end_layout
+
+\begin_layout Standard
+The fault example requires three additional database files that were not
+ needed for the simple displacement example.
+ The first file (
+\family typewriter
+finalslip.spatialdb
+\family default
+) specifies a constant value of 2 m of right-lateral fault slip that then
+ tapers linearly to zero from 2 km to 4 km depth, and a linearly-varying
+ amount of reverse slip, with a maximum of 0.25 m at the surface, linearly
+ tapering to 0 m at 2 km depth.
+ The data dimension is one since the data vary linearly along a vertical
+ line.
+ It is also necessary to specify the peak slip rate, which is done in the
+ file 
+\family typewriter
+sliprate.spatialdb
+\family default
+.
+ The peak slip rate of 1.0e6 m/s creates a step function for the slip time
+ history.
+ Finally, we must provide the time at which slip begins.
+ The elastic solution begins at 
+\begin_inset Formula $t=-dt$
+\end_inset
+
+, so this is the value given (
+\begin_inset Formula $t=-1\sec$
+\end_inset
+
+) in 
+\family typewriter
+dislocation_sliptime.spatialdb
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+tet4_1000m_binary.gmv
+\family default
+, 
+\family typewriter
+tet4_1000m_binary.pset
+\family default
+, 
+\family typewriter
+pylithapp.cfg
+\family default
+, 
+\family typewriter
+mat_elastic.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+\size small
+dislocation.cfg
+\family default
+, 
+\family typewriter
+finalslip.spatialdb
+\family default
+, 
+\family typewriter
+sliprate.spatialdb
+\family default
+, 
+\family typewriter
+sliptime.spatialdb
+\family default
+\size default
+) provide a complete description of the problem, and we can then run this
+ example by typing
+\end_layout
+
+\begin_layout LyX-Code
+pylith dislocation.cfg
+\end_layout
+
+\begin_layout Standard
+Once the problem has run, 12 files will be produced.
+ The first file is named 
+\family typewriter
+dislocation_t0000000.vtk
+\family default
+.
+ The 
+\family typewriter
+t0000000
+\family default
+ indicates that the output is for the first (and only) time step, corresponding
+ to an elastic solution.
+ This file contains mesh information as well as displacement values at the
+ mesh vertices.
+ The second file is named 
+\family typewriter
+dislocation-statevars-neg1_t0000000.vtk
+\family default
+.
+ This file contains the state variables for each cell in the material group
+ 
+\family typewriter
+elastic_neg1
+\family default
+.
+ The default fields are the total strain and stress fields.
+ We have requested that the values be averaged over all quadrature points
+ for each cell; however, since we only have a single quadrature point for
+ each linear tetrahedron, this will have no effect.
+ The third file (
+\family typewriter
+dislocation-statevars-neg1_info.vtk
+\family default
+) gives the material properties used for the 
+\family typewriter
+elastic_neg1
+\family default
+ material set.
+ Since we have not specified which properties to write, the default properties
+ (
+\family typewriter
+mu
+\family default
+, 
+\family typewriter
+lambda
+\family default
+, 
+\family typewriter
+density
+\family default
+) are written.
+ There are six additional files containing the state variables and material
+ properties for each of the three additional material sets.
+ The tenth file (
+\family typewriter
+dislocation-groundsurf_t0000000.vtk
+\family default
+) is analagous to 
+\family typewriter
+dislocation_t0000000.vtk
+\family default
+, but in this case the results are only given for a subset of the mesh correspon
+ding to the ground surface.
+ Also, the cells in this file are one dimension lower than the cells described
+ in 
+\family typewriter
+dislocation_t0000000.vtk
+\family default
+, so they are triangles rather than tetrahedra.
+ The 11th file (
+\family typewriter
+dislocation-fault_t0000000.vtk
+\family default
+) gives the specified fault slip for each vertex on the fault, along with
+ the computed traction change for the cohesive cell.
+ The final file (
+\family typewriter
+dislocation-fault_info.vtk
+\family default
+) provides information such as the normal direction, final slip, and slip
+ time for each vertex on the fault.
+ All of the 
+\family typewriter
+.vtk
+\family default
+ files may be used with a number of visualization packages.
+ If the problem ran correctly, you should be able to generate a figure such
+ as
+\begin_inset LatexCommand vref
+reference "fig:3dtet-disloc"
+
+\end_inset
+
+, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+	filename figs/dislocation.jpg
+	lyxscale 50
+	scale 45
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
+Color contours and vectors of displacement for the kinematic fault example.
+\begin_inset LatexCommand label
+name "fig:3dtet-disloc"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document

Added: short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/figs/dislocation.jpg
===================================================================
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Property changes on: short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/figs/dislocation.jpg
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/figs/shear.jpg
===================================================================
(Binary files differ)


Property changes on: short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/figs/shear.jpg
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/figs/tet4-mesh.jpg
===================================================================
(Binary files differ)


Property changes on: short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/figs/tet4-mesh.jpg
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx	2008-03-20 19:29:56 UTC (rev 11492)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx	2008-03-20 20:01:06 UTC (rev 11493)
@@ -177,6 +177,12 @@
 \end_inset
 
 
+\begin_inset Include \input{3dtet4/3dtet4.lyx}
+preview false
+
+\end_inset
+
+
 \end_layout
 
 \end_body

Modified: short/3D/PyLith/trunk/doc/userguide/userguide.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/userguide.lyx	2008-03-20 19:29:56 UTC (rev 11492)
+++ short/3D/PyLith/trunk/doc/userguide/userguide.lyx	2008-03-20 20:01:06 UTC (rev 11493)
@@ -1,4 +1,4 @@
-#LyX 1.5.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.3 created this file. For more info see http://www.lyx.org/
 \lyxformat 276
 \begin_document
 \begin_header

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