[cig-commits] r22100 - in short/3D/PyLith/trunk/doc/userguide/tutorials: . twocells twocells/figs
brad at geodynamics.org
brad at geodynamics.org
Fri May 17 17:11:12 PDT 2013
Author: brad
Date: 2013-05-17 17:11:11 -0700 (Fri, 17 May 2013)
New Revision: 22100
Added:
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-axialdisp.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-dislocation.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-mesh.eps
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-mesh.fig
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-mesh.fig.bak
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-sheardisp.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-axialdisp.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-axialtract.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-dislocation.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-mesh.eps
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-mesh.fig
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-mesh.fig.bak
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-sheardisp.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotet4-axialdisp.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotet4-dislocation.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotet4-geoproj-dislocation.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotet4-mesh.eps
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotet4-mesh.fig
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotri3-axialdisp.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotri3-dislocation.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotri3-mesh.eps
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotri3-mesh.fig
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotri3-sheardisp.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twohex8.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twoquad4.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twotet4-geoproj.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twotet4.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twotri3.lyx
Removed:
short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/
short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/
short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4-geoproj/
short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/
short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/
Modified:
short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx
Log:
Cleanup of tutorials/twocells files.
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx 2013-05-17 21:14:54 UTC (rev 22099)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx 2013-05-18 00:11:11 UTC (rev 22100)
@@ -195,35 +195,35 @@
\begin_layout Standard
\begin_inset CommandInset include
LatexCommand input
-filename "twotri3/twotri3.lyx"
+filename "twocells/twotri3.lyx"
\end_inset
\begin_inset CommandInset include
LatexCommand input
-filename "twoquad4/twoquad4.lyx"
+filename "twocells/twoquad4.lyx"
\end_inset
\begin_inset CommandInset include
LatexCommand input
-filename "twotet4/twotet4.lyx"
+filename "twocells/twotet4.lyx"
\end_inset
\begin_inset CommandInset include
LatexCommand input
-filename "twohex8/twohex8.lyx"
+filename "twocells/twohex8.lyx"
\end_inset
\begin_inset CommandInset include
LatexCommand input
-filename "twotet4-geoproj/twotet4-geoproj.lyx"
+filename "twocells/twotet4-geoproj.lyx"
\end_inset
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-axialdisp.jpg (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/figs/axialdisp.jpg)
===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-dislocation.jpg (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/figs/dislocation.jpg)
===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-mesh.eps (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/figs/twohex8-mesh.eps)
===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-mesh.fig (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/figs/twohex8-mesh.fig)
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-mesh.fig (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-mesh.fig 2013-05-18 00:11:11 UTC (rev 22100)
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===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twohex8-sheardisp.jpg (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/figs/sheardisp.jpg)
===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-axialdisp.jpg (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/figs/axialdisp.jpg)
===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-axialtract.jpg (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/figs/axialtract.jpg)
===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-dislocation.jpg (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/figs/dislocation.jpg)
===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-mesh.eps (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/figs/twoquad4-mesh.eps)
===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-mesh.fig (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/figs/twoquad4-mesh.fig)
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-mesh.fig (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-mesh.fig 2013-05-18 00:11:11 UTC (rev 22100)
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===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-mesh.fig.bak (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-mesh.fig.bak 2013-05-18 00:11:11 UTC (rev 22100)
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Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twoquad4-sheardisp.jpg (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/figs/sheardispl.jpg)
===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotet4-axialdisp.jpg (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/axialdisp.jpg)
===================================================================
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Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotet4-dislocation.jpg (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/dislocation.jpg)
===================================================================
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Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotet4-geoproj-dislocation.jpg (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4-geoproj/figs/dislocation.jpg)
===================================================================
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Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotet4-mesh.eps (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/twotet4-mesh.eps)
===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotet4-mesh.fig (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/twotet4-mesh.fig)
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotet4-mesh.fig (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotet4-mesh.fig 2013-05-18 00:11:11 UTC (rev 22100)
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===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotri3-dislocation.jpg (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/figs/dislocation.jpg)
===================================================================
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===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotri3-mesh.fig (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/figs/twotri3-mesh.fig)
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotri3-mesh.fig (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotri3-mesh.fig 2013-05-18 00:11:11 UTC (rev 22100)
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Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/figs/twotri3-sheardisp.jpg (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/figs/sheardisp.jpg)
===================================================================
(Binary files differ)
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twohex8.lyx (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/twohex8.lyx)
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twohex8.lyx (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twohex8.lyx 2013-05-18 00:11:11 UTC (rev 22100)
@@ -0,0 +1,876 @@
+#LyX 2.0 created this file. For more info see http://www.lyx.org/
+\lyxformat 413
+\begin_document
+\begin_header
+\textclass book
+\begin_preamble
+
+\end_preamble
+\use_default_options false
+\maintain_unincluded_children false
+\language english
+\language_package default
+\inputencoding latin1
+\fontencoding global
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\use_non_tex_fonts false
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
+
+\graphics default
+\default_output_format default
+\output_sync 0
+\bibtex_command default
+\index_command default
+\paperfontsize default
+\spacing single
+\use_hyperref false
+\papersize default
+\use_geometry true
+\use_amsmath 0
+\use_esint 0
+\use_mhchem 1
+\use_mathdots 1
+\cite_engine basic
+\use_bibtopic false
+\use_indices false
+\paperorientation portrait
+\suppress_date false
+\use_refstyle 0
+\index Index
+\shortcut idx
+\color #008000
+\end_index
+\leftmargin 1in
+\topmargin 1in
+\rightmargin 1in
+\bottommargin 2in
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\paragraph_indentation default
+\quotes_language english
+\papercolumns 1
+\papersides 1
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\html_math_output 0
+\html_css_as_file 0
+\html_be_strict false
+\end_header
+
+\begin_body
+
+\begin_layout Section
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:Tutorial-Two-hexahedra"
+
+\end_inset
+
+Tutorial Using Two Hexahedra
+\end_layout
+
+\begin_layout Standard
+PyLith features discussed in this tutorial:
+\end_layout
+
+\begin_layout Itemize
+Quasi-static solution
+\end_layout
+
+\begin_layout Itemize
+Mesh ASCII format
+\end_layout
+
+\begin_layout Itemize
+Dirichlet boundary conditions
+\end_layout
+
+\begin_layout Itemize
+Kinematic fault interface conditions
+\end_layout
+
+\begin_layout Itemize
+Maxwell viscoelastic material
+\end_layout
+
+\begin_layout Itemize
+VTK output
+\end_layout
+
+\begin_layout Itemize
+Trilinear hexahedral cells
+\end_layout
+
+\begin_layout Itemize
+SimpleDB spatial database
+\end_layout
+
+\begin_layout Itemize
+ZeroDispDB spatial database
+\end_layout
+
+\begin_layout Itemize
+UniformDB spatial database
+\end_layout
+
+\begin_layout Itemize
+Filtering of cell output fields
+\end_layout
+
+\begin_layout Standard
+All of the files necessary to run the examples are contained in the directory
+
+\family typewriter
+examples/twocells/twohex8.
+\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 two trilinear hexahedra subject to displacement
+ boundary conditions.
+ One primary difference between this example and the example with two tetrahedra
+ is that we use a Maxwell viscoelastic material model, and run the model
+ for 10 time steps of 0.1 year each.
+ Due to the simple geometry of the problem, the mesh may be constructed
+ by hand, using PyLith mesh ASCII format to describe the mesh.
+ In this tutorial, we will walk through the steps necessary to construct,
+ run, and view three 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 Description
+\end_layout
+
+\begin_layout Standard
+The mesh consists of two hexahedra forming a rectangular prism (Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:twohex8-mesh"
+
+\end_inset
+
+).
+ The mesh geometry and topology are described in the file
+\family typewriter
+twohex8.mesh
+\family default
+, which is in PyLith mesh ASCII format.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twohex8-mesh.pdf
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Mesh composed of two trilinear hexahedral cells used for the example problems.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twohex8-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 three example problems share additional information
+, which we place in
+\family typewriter
+pylithapp.cfg
+\family default
+.
+ Note that in this example we make use of the UniformDB spatial database,
+ rather than the SimpleDB implementation used to specify the physical properties
+ in the other example problems.
+ For simple distributions of material properties (or boundary conditions),
+ this implementation is often easier to use.
+ Examining
+\family typewriter
+pylithapp.cfg
+\family default
+, we specify the material information with the following set of parameters:
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+[pylithapp.timedependent.materials]
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+material = pylith.materials.MaxwellIsotropic3D
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+[pylithapp.timedependent.materials.material]
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+label = viscoelastic material
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+id = 1
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+db = spatialdata.spatialdb.UniformDB
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+db.values = [vp,vs,density,viscosity]
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+db.data = [5773.502691896258*m/s, 3333.333333333333*m/s, 2700.0*kg/m**3, 1.0e18*Pa*s]
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+quadrature.cell = pylith.feassemble.FIATLagrange
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+quadrature.cell.dimension = 3
+\end_layout
+
+\begin_layout Subsection
+Axial Displacement Example
+\end_layout
+
+\begin_layout Standard
+The first example problem is extension of the mesh along the long axis of
+ the prism.
+ Parameter settings that override or augment those in
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file
+\family typewriter
+axialdisp.cfg
+\family default
+.
+ These settings include:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_neg Defines which degrees of freedom are being
+ constrained (x, y, and z), gives the label (
+\family typewriter
+x_neg
+\family default
+, defined in
+\family typewriter
+twohex8.mesh
+\family default
+) defining the points desired, assigns a label to the boundary condition
+ set, and gives the name of the spatial database with the values for the
+ Dirichlet boundary conditions (
+\family typewriter
+axialdisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos Defines which degrees of freedom are being
+ constrained (x, y, and z), gives the label (
+\family typewriter
+x_pos
+\family default
+, defined in
+\family typewriter
+twohex8.mesh
+\family default
+) defining the points desired, assigns a label to the boundary condition
+ set, and gives the name of the spatial database with the values for the
+ Dirichlet boundary conditions (
+\family typewriter
+axialdisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials.material.output Defines the filter to be used
+ when writing cell state variables (average over the quadrature points of
+ the cell), specifies which state variables and properties to output, gives
+ the base filename for state variable output files, and defines the format
+ to use when defining the output filenames for each time step.
+\end_layout
+
+\begin_layout Standard
+The values for the Dirichlet boundary conditions are given in the file
+\family typewriter
+axialdisp.spatialdb
+\family default
+, as specified in
+\family typewriter
+axialdisp.cfg
+\family default
+.
+ Since data are being specified using two control points (rather than being
+ uniform over the mesh, for example), the data dimension is one.
+ Note that since we are using a Maxwell viscoelastic model, we request that
+ additional state variables and properties be output:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.materials.material.output]
+\end_layout
+
+\begin_layout LyX-Code
+cell_data_fields = [total_strain,viscous_strain,stress]
+\end_layout
+
+\begin_layout LyX-Code
+cell_info_fields = [mu,lambda,density,maxwell_time]
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+twohex8.mesh
+\family default
+,
+\family typewriter
+pylithapp.cfg
+\family default
+) along with the problem-specific files (
+\family typewriter
+axialdisp.cfg
+\family default
+,
+\family typewriter
+axialdisp.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 axialdisp.cfg
+\end_layout
+
+\begin_layout Standard
+Once the problem has run, two sets of files will be produced, along with
+ one additional file.
+ The first set will have filenames such as
+\family typewriter
+axialdisp_txxxx.vtk
+\family default
+, where
+\family typewriter
+xxxx
+\family default
+ is the time for which output has been produced.
+ In
+\family typewriter
+axialdisp.cfg
+\family default
+ we specify that the time stamp should be normalized by a value of 1.0 years
+ and the time stamp should be of the form
+\family typewriter
+xxx.x
+\family default
+ (recall that the decimal point is removed in the filename).
+ As a result, the filenames contain the time in tenths of a year.
+ These files will contain mesh information as well as displacement values
+ for the mesh vertices at the given time.
+ The second set of files will have names such as
+\family typewriter
+axialdisp-statevars_txxxx.vtk
+\family default
+, where
+\family typewriter
+xxxx
+\family default
+ is the time in tenths of a year (as above) for which output has been produced.
+ These files contain the state variables for each cell at the given time.
+ The default fields are the total strain and stress fields; however, we
+ have also requested the viscous strains.
+ As specified in
+\family typewriter
+axialdisp.cfg
+\family default
+, these values are averaged over each cell.
+ The final file (
+\family typewriter
+axialdisp-statevars_info.vtk
+\family default
+) gives the material properties used for the problem.
+ We have requested all of the properties available for this material model
+ (
+\family typewriter
+mu
+\family default
+,
+\family typewriter
+lambda
+\family default
+,
+\family typewriter
+density
+\family default
+,
+\family typewriter
+maxwell_time
+\family default
+).
+ If the problem ran correctly, you should be able to produce a figure such
+ as Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:twohex8-axial"
+
+\end_inset
+
+, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twohex8-axialdisp.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the axial displacement example
+ using a mesh composed of two trilinear hexahedral cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twohex8-axial"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Shear Displacement Example
+\end_layout
+
+\begin_layout Standard
+The second example problem is shearing of the mesh in the y direction.
+ Parameter settings that override or augment those in
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file
+\family typewriter
+sheardisp.cfg
+\family default
+.
+ These settings include:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_neg Defines which degrees of freedom are being
+ constrained (x, y, and z), gives the label (
+\family typewriter
+x_neg
+\family default
+, defined in
+\family typewriter
+twohex8.mesh
+\family default
+) defining the points desired, assigns a label to the boundary condition
+ set, and gives the name of the spatial database with the values for the
+ Dirichlet boundary conditions (
+\family typewriter
+sheardisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos Defines which degrees of freedom are being
+ constrained (x, y, and z), gives the label (
+\family typewriter
+x_pos
+\family default
+, defined in
+\family typewriter
+twohex8.mesh
+\family default
+) defining the points desired, assigns a label to the boundary condition
+ set, and gives the name of the spatial database with the values for the
+ Dirichlet boundary conditions (
+\family typewriter
+sheardisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The values for the Dirichlet boundary conditions are given in the file
+\family typewriter
+sheardisp.spatialdb
+\family default
+, as specified in
+\family typewriter
+sheardisp.cfg
+\family default
+.
+ Data are being specified at two control points (rather than being uniform
+ over the mesh, for example), so the data dimension is one.
+ The files containing common information (
+\family typewriter
+twohex8.mesh
+\family default
+,
+\family typewriter
+pylithapp.cfg
+\family default
+) along with the problem-specific files (
+\family typewriter
+sheardisp.cfg
+\family default
+,
+\family typewriter
+sheardisp.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 sheardisp.cfg
+\end_layout
+
+\begin_layout Standard
+If the problem ran correctly, you should be able to generate a figure such
+ as Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:twohex8-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 Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twohex8-sheardisp.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the shear displacement example
+ using a mesh composed of two trilinear hexahedral cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twohex8-shear"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Kinematic Fault Slip Example
+\end_layout
+
+\begin_layout Standard
+The next example problem is left-lateral fault slip applied between the
+ two hexahedral cells using kinematic cohesive cells.
+ The vertices away from the fault are held fixed in the x, y, and z 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 include:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_neg Defines which degrees of freedom are being
+ constrained (x, y, and z), gives the label (
+\family typewriter
+x_neg
+\family default
+, defined in
+\family typewriter
+twohex8.mesh
+\family default
+) defining the points desired, and assigns a label to the boundary condition
+ set.
+ In this case, we use the default spatial database (ZeroDispDB) for the
+ Dirichlet boundary condition, which sets the displacements to zero.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos Defines which degrees of freedom are being
+ constrained (x, y, and z), gives the label (
+\family typewriter
+x_pos
+\family default
+, defined in
+\family typewriter
+twohex8.mesh
+\family default
+) defining the points desired, and assigns a label to the boundary condition
+ set.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.interfaces Gives the label (defined in
+\family typewriter
+twohex8.mesh
+\family default
+) 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 Standard
+The fault example requires three additional database files that were not
+ needed for the simple displacement examples.
+ The first file (
+\family typewriter
+dislocation_slip.spatialdb
+\family default
+) specifies 0.01 m of left-lateral fault slip for the entire fault.
+ The data dimension is zero since the same data are applied to all points
+ in the set.
+ The default slip time function is a step-function, so we also must provide
+ the time at which slip begins.
+ The elastic solution is associated with advancing from
+\begin_inset Formula $t=-dt$
+\end_inset
+
+ to
+\begin_inset Formula $t=0$
+\end_inset
+
+, so we set the slip initiation time for the step-function to 0 in
+\family typewriter
+dislocation_sliptime.spatialdb
+\family default
+.
+ The files containing common information (
+\family typewriter
+twohex8.mesh,
+\family default
+\size small
+
+\family typewriter
+
+\begin_inset Newline linebreak
+\end_inset
+
+
+\size default
+pylithapp.cfg
+\family default
+) along with the problem-specific files (
+\family typewriter
+dislocation.cfg, dislocation_slip.spatialdb, dislocation_sliptime.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 dislocation.cfg
+\end_layout
+
+\begin_layout Standard
+If the problem ran correctly, you should be able to generate a figure such
+ as Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:twohex8-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 Plain Layout
+\noindent
+\align center
+\begin_inset Graphics
+ filename figs/twohex8-dislocation.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the kinematic fault example
+ using a mesh composed of two trilinear hexahedral cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twohex8-disloc"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twoquad4.lyx (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/twoquad4.lyx)
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twoquad4.lyx (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twoquad4.lyx 2013-05-18 00:11:11 UTC (rev 22100)
@@ -0,0 +1,1009 @@
+#LyX 2.0 created this file. For more info see http://www.lyx.org/
+\lyxformat 413
+\begin_document
+\begin_header
+\textclass book
+\begin_preamble
+
+\end_preamble
+\use_default_options false
+\maintain_unincluded_children false
+\language english
+\language_package default
+\inputencoding latin1
+\fontencoding global
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\use_non_tex_fonts false
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
+
+\graphics default
+\default_output_format default
+\output_sync 0
+\bibtex_command default
+\index_command default
+\paperfontsize default
+\spacing single
+\use_hyperref false
+\papersize default
+\use_geometry true
+\use_amsmath 0
+\use_esint 0
+\use_mhchem 1
+\use_mathdots 1
+\cite_engine basic
+\use_bibtopic false
+\use_indices false
+\paperorientation portrait
+\suppress_date false
+\use_refstyle 0
+\index Index
+\shortcut idx
+\color #008000
+\end_index
+\leftmargin 1in
+\topmargin 1in
+\rightmargin 1in
+\bottommargin 1in
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\paragraph_indentation default
+\quotes_language english
+\papercolumns 1
+\papersides 1
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\html_math_output 0
+\html_css_as_file 0
+\html_be_strict false
+\end_header
+
+\begin_body
+
+\begin_layout Section
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:Tutorial-Two-quad4"
+
+\end_inset
+
+Tutorial Using Two Quadrilaterals
+\end_layout
+
+\begin_layout Standard
+PyLith features discussed in this tutorial:
+\end_layout
+
+\begin_layout Itemize
+Quasi-static solution
+\end_layout
+
+\begin_layout Itemize
+Mesh ASCII format
+\end_layout
+
+\begin_layout Itemize
+Dirichlet boundary conditions
+\end_layout
+
+\begin_layout Itemize
+Neumann boundary conditions
+\end_layout
+
+\begin_layout Itemize
+Kinematic fault interface conditions
+\end_layout
+
+\begin_layout Itemize
+Plane strain linearly elastic material
+\end_layout
+
+\begin_layout Itemize
+VTK output
+\end_layout
+
+\begin_layout Itemize
+Bilinear quadrilateral cells
+\end_layout
+
+\begin_layout Itemize
+SimpleDB spatial database
+\end_layout
+
+\begin_layout Itemize
+ZeroDispDB spatial database
+\end_layout
+
+\begin_layout Standard
+All of the files necessary to run the examples are contained in the directory
+
+\family typewriter
+examples/twocells/twoquad4.
+\end_layout
+
+\begin_layout Subsection
+Overview
+\end_layout
+
+\begin_layout Standard
+This tutorial is another simple 2D example of a quasi-static finite element
+ problem.
+ It is a mesh composed of two bilinear quadrilaterals subject to displacement
+ or traction boundary conditions, assuming plane-strain linear elastic behavior.
+ Due to the simple geometry of the problem, the mesh may be constructed
+ by hand, using PyLith mesh ASCII format to describe the mesh.
+ In this tutorial, we will walk through the steps necessary to construct,
+ run, and view four problems that use the same mesh.
+ In addition to this manual, each of the files for the example problem includes
+ extensive comments.
+\end_layout
+
+\begin_layout Subsection
+Mesh Description
+\end_layout
+
+\begin_layout Standard
+The mesh consists of two square cells with edge lengths of one unit forming
+ a regular region (Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:twoquad4-mesh"
+
+\end_inset
+
+).
+ The mesh geometry and topology are described in the file
+\family typewriter
+twoquad4.mesh
+\family default
+, which is in PyLith mesh ASCII format.
+ This file describes the dimensionality of the problem (in this case 2D),
+ the coordinates of the vertices (nodes), the vertices composing each cell
+ (element), the material ID to be associated with each cell, and then provides
+ groups of vertices that may be used to define faults or surfaces to which
+ boundary conditions may be applied.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twoquad4-mesh.pdf
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Mesh composed of two bilinear quadrilateral cells used for the example problems.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twoquad4-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 four example problems share additional information.
+ As in the previous examples, we place this information in
+\family typewriter
+pylithapp.cfg
+\family default
+, 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.
+\end_layout
+
+\begin_layout Subsection
+Axial Displacement Example
+\end_layout
+
+\begin_layout Standard
+The first example problem is extension of the mesh along the x axis.
+ Parameter settings that override or augment those in
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file
+\family typewriter
+axialdisp.cfg
+\family default
+.
+ These include:
+\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
+ (x), giving the label (defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) defining the points desired, assigning a label to the boundary condition
+ set, and giving the name of the spatial database with the values for the
+ Dirichlet boundary condition (
+\family typewriter
+axialdisp.spatialdb
+\family default
+).
+\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
+ (x), giving the label (defined in
+\family typewriter
+twoquad4.mesh
+\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
+axialdisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.y_neg Specifies the boundary conditions for the
+ bottom two corners of the mesh, defining which degrees of freedom are being
+ constrained (y), giving the label (defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) defining the points desired, assigning a label to the boundary condition
+ set, and giving the name of the spatial database with the values for the
+ Dirichlet boundary condition (
+\family typewriter
+axialdisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The values for the Dirichlet boundary condition are given in the file
+\family typewriter
+axialdisp.spatialdb
+\family default
+, as specified in
+\family typewriter
+axialdisp.cfg
+\family default
+.
+ Because the data are being specified using two control points with a linear
+ variation in the values between the two (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
+twoquad4.mesh
+\family default
+,
+\family typewriter
+pylithapp.cfg
+\family default
+,
+\family typewriter
+matprops.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+axialdisp.cfg
+\family default
+,
+\family typewriter
+axialdisp.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 axialdisp.cfg
+\end_layout
+
+\begin_layout Standard
+As in the two triangle axial displacement example, three files will be produced.
+ If the problem ran correctly, you should be able to produce a figure such
+ as Figure
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "fig:twoquad4-axial"
+
+\end_inset
+
+, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement t
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twoquad4-axialdisp.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the axial displacement example
+ using a mesh composed of two bilinear quadrilateral cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twoquad4-axial"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Shear Displacement Example
+\end_layout
+
+\begin_layout Standard
+The next example problem is shearing of the mesh in the y direction using
+ displacements applied along the positive and negative x boundaries.
+ Parameter settings that override or augment those in
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file
+\family typewriter
+sheardisp.cfg
+\family default
+.
+ These include:
+\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
+ (x and y), giving the label (
+\family typewriter
+x_neg
+\family default
+, defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) defining the points desired, assigning a label to the boundary condition
+ set, and giving the name of the spatial database with the values for the
+ Dirichlet boundary condition (
+\family typewriter
+sheardisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos Specifies the boundary conditions for the
+ left side of the mesh, defining which degrees of freedom are being constrained
+ (y only), giving the label (
+\family typewriter
+x_pos
+\family default
+, defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) defining the points desired, assigning a label to the boundary condition
+ set, and giving the name of the spatial database with the values for the
+ Dirichlet boundary condition (
+\family typewriter
+sheardisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The values for the Dirichlet boundary conditions are described in the file
+
+\family typewriter
+sheardisp.spatialdb
+\family default
+, as specified in
+\family typewriter
+sheardisp.cfg
+\family default
+.
+ In this case, the desired displacement values are given at two control
+ points, corresponding to the two edges we want to constrain.
+ Since data are being specified at two points with a linear variations in
+ the values between the 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
+twoquad4.mesh
+\family default
+,
+\family typewriter
+pylithapp.cfg
+\family default
+,
+\family typewriter
+matprops.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+sheardisp.cfg
+\family default
+,
+\family typewriter
+sheardisp.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 sheardisp.cfg
+\end_layout
+
+\begin_layout Standard
+As in the previous example, three files will be produced.
+ If the problem ran correctly, you should be able to produce a figure such
+ as Figure
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "fig:twoquad4-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 Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twoquad4-sheardisp.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the shear displacement example
+ using a mesh composed of two bilinear quadrilateral cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twoquad4-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 left-lateral fault slip applied between the
+ two square cells using kinematic cohesive cells.
+ The left and right boundaries are held fixed in the x and y 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 include:
+\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
+ (x and y), giving the label (
+\family typewriter
+x_neg
+\family default
+, defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) defining the points desired, and assigning a label to the boundary condition
+ set.
+ Instead of specifying a spatial database file for the values of the Dirichlet
+ boundary condition, we use the default spatial database (ZeroDispDB) for
+ the Dirichlet boundary condition, which sets the displacements to zero
+ for all time.
+\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
+ (x and y), giving the label (
+\family typewriter
+x_neg
+\family default
+, defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) defining the points desired, and assigning a label to the boundary condition
+ set.
+ We use the ZeroDispDB for this boundary condition as well, which sets the
+ displacements to zero for all time.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.interfaces Gives the label (defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) 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 Standard
+The fault example requires three additional database files that were not
+ needed for the simple displacement examples.
+ The first file (
+\family typewriter
+dislocation_slip.spatialdb
+\family default
+) specifies 0.01 m of left-lateral fault slip for the entire fault.
+ The data dimension is zero since the same data are applied to all points
+ in the set.
+ The default slip time function is a step-function, so we also must provide
+ the time at which slip begins.
+ The elastic solution is associated with advancing from
+\begin_inset Formula $t=-dt$
+\end_inset
+
+ to
+\begin_inset Formula $t=0$
+\end_inset
+
+, so we set the slip initiation time for the step-function to 0 in
+\family typewriter
+dislocation_sliptime.spatialdb
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+twoquad4.mesh
+\family default
+,
+\family typewriter
+pylithapp.cfg
+\family default
+,
+\family typewriter
+matprops.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+\size small
+dislocation.cfg
+\family default
+,
+\family typewriter
+dislocation_slip.spatialdb
+\family default
+,
+\family typewriter
+
+\begin_inset Newline linebreak
+\end_inset
+
+dislocation_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
+The addition of a fault results in two additional output files (as in the
+ two triangle fault example),
+\family typewriter
+
+\begin_inset Newline linebreak
+\end_inset
+
+dislocation-fault_t0000000.vtk
+\family default
+ and
+\family typewriter
+dislocation-fault_info.vtk
+\family default
+.
+ These files provide output of fault slip, change in tractions, and diagnostic
+ information such as the normal direction, final slip, and slip time for
+ each vertex on the fault.
+ If the problem ran correctly, you should be able to produce a figure such
+ as Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:twoquad4-disloc"
+
+\end_inset
+
+, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twoquad4-dislocation.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the kinematic fault example
+ using a mesh composed of two bilinear quadrilateral cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twoquad4-disloc"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+\begin_inset CommandInset label
+LatexCommand label
+name "sub:Tutorial-twoquad4-traction"
+
+\end_inset
+
+Axial Traction Example
+\end_layout
+
+\begin_layout Standard
+The fourth example demonstrates the use of Neumann (traction) boundary condition
+s.
+ Constant tractions are applied to the right edge of the mesh, while displacemen
+ts normal to the boundaries are held fixed along the left and bottom edges
+ of the mesh.
+ Parameter settings that override or augment those in
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file
+\family typewriter
+axialtract.cfg
+\family default
+.
+ These settings include:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent Specifies an implicit formulation for the problem
+ and specifies the array of boundary conditions.
+ The boundary condition type for
+\family typewriter
+x_pos
+\family default
+ is explicitly set to
+\family typewriter
+Neumann
+\family default
+, since the default boundary condition type is
+\family typewriter
+Dirichlet
+\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
+ (x) and giving the label (defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) defining the points desired.
+ In this case, rather than specifying a spatial database file with values
+ for the Dirichlet boundary conditions, we use the default spatial database
+ (ZeroDispDB) for the Dirichlet boundary condition, which sets the displacements
+ to zero for all time.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos Specifies the Neumann boundary conditions
+ for the right side of the mesh, giving the label (defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) defining the points desired, assigning a label to the boundary condition
+ set, and giving the name of the spatial database with the traction vectors
+ for the Neumann boundary condition (
+\family typewriter
+axialtract.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.y_neg Specifies the boundary conditions for the
+ bottom two corners of the mesh, defining which degrees of freedom are being
+ constrained (y) and giving the label (defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) defining the points desired.
+ In this case, we again use the ZeroDispDB, which sets the displacements
+ to zero for all time.
+\end_layout
+
+\begin_layout Description
+pylithapp.problem.formulation.output.output.writer Gives the base filename for
+ VTK output
+\begin_inset Newline newline
+\end_inset
+
+(
+\family typewriter
+axialtract.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos.output Gives the field to be output for the
+
+\family typewriter
+x_pos
+\family default
+ boundary (
+\family typewriter
+tractions
+\family default
+), and gives the base filename for
+\family typewriter
+x_pos
+\family default
+ boundary output (
+\family typewriter
+axialtract-tractions.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The traction vectors for the Neumann boundary conditions are given in the
+ file
+\family typewriter
+axialtract.spatialdb
+\family default
+, as specified in
+\family typewriter
+axialtract.cfg
+\family default
+.
+ The files containing common information (
+\family typewriter
+twoquad4.mesh
+\family default
+,
+\family typewriter
+pylithapp.cfg
+\family default
+,
+\family typewriter
+matprops.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+axialtract.cfg
+\family default
+,
+\family typewriter
+axialtract.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 axialtract.cfg
+\end_layout
+
+\begin_layout Standard
+Once the problem has run, six files will be produced.
+ This includes the five files as in the previous example plus
+\family typewriter
+axialtract-tractions_info.vtk
+\family default
+, which gives the
+\family typewriter
+x
+\family default
+ and
+\family typewriter
+y
+\family default
+ components of traction applied at each integration point.
+ If the problem ran correctly, you should be able to produce a figure such
+ as Figure
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "fig:twoquad4-axialtract"
+
+\end_inset
+
+, which was generated using ParaView.
+ The results may be compared against the analytical solution derived in
+ Section
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sub:Analytical-Constant-Traction"
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twoquad4-axialtract.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the axial traction example
+ using a mesh composed of two bilinear quadrilateral cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twoquad4-axialtract"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twotet4-geoproj.lyx (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4-geoproj/twotet4-geoproj.lyx)
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twotet4-geoproj.lyx (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twotet4-geoproj.lyx 2013-05-18 00:11:11 UTC (rev 22100)
@@ -0,0 +1,571 @@
+#LyX 2.0 created this file. For more info see http://www.lyx.org/
+\lyxformat 413
+\begin_document
+\begin_header
+\textclass book
+\begin_preamble
+
+\end_preamble
+\use_default_options false
+\maintain_unincluded_children false
+\language english
+\language_package default
+\inputencoding latin1
+\fontencoding global
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\use_non_tex_fonts false
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
+
+\graphics default
+\default_output_format default
+\output_sync 0
+\bibtex_command default
+\index_command default
+\paperfontsize default
+\spacing single
+\use_hyperref false
+\papersize default
+\use_geometry true
+\use_amsmath 0
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+\use_mhchem 1
+\use_mathdots 1
+\cite_engine basic
+\use_bibtopic false
+\use_indices false
+\paperorientation portrait
+\suppress_date false
+\use_refstyle 0
+\index Index
+\shortcut idx
+\color #008000
+\end_index
+\leftmargin 1in
+\topmargin 1in
+\rightmargin 1in
+\bottommargin 2in
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\paragraph_indentation default
+\quotes_language english
+\papercolumns 1
+\papersides 1
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\html_math_output 0
+\html_css_as_file 0
+\html_be_strict false
+\end_header
+
+\begin_body
+
+\begin_layout Section
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:Tutorial-Two-tet4-geoproj"
+
+\end_inset
+
+Tutorial Using Two Tetrahedra with Georeferenced Coordinate System Mesh
+\end_layout
+
+\begin_layout Standard
+PyLith features discussed in this tutorial:
+\end_layout
+
+\begin_layout Itemize
+Quasi-static solution
+\end_layout
+
+\begin_layout Itemize
+Mesh ASCII 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
+VTK output
+\end_layout
+
+\begin_layout Itemize
+Linear tetrahedral cells
+\end_layout
+
+\begin_layout Itemize
+SimpleDB spatial database with geographic coordinates
+\end_layout
+
+\begin_layout Itemize
+SCEC CVM-H spatial database
+\end_layout
+
+\begin_layout Itemize
+ZeroDispDB spatial database
+\end_layout
+
+\begin_layout Standard
+All of the files necessary to run the examples are contained in the directory
+
+\family typewriter
+examples/twocells/twotet4-geoproj.
+\end_layout
+
+\begin_layout Subsection
+Overview
+\end_layout
+
+\begin_layout Standard
+This tutorial is virtually identical to the other tutorial using two linear
+ tetrahedra (See Section
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sec:Tutorial-Two-tet4"
+
+\end_inset
+
+).
+ The primary difference is in how the material properties are assigned.
+ For this tutorial, the physical properties come from the SCEC CVM-H database
+ (described in Section
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sub:SCECCVMH-Impl"
+
+\end_inset
+
+).
+ Using the SCEC CVM-H database is straightforward, requiring only a few
+ modifications to
+\family typewriter
+pylithapp.cfg
+\family default
+.
+ Because the SCEC CVM-H database uses geographic coordinates, we must also
+ use geographic coordinates in the PyLith mesh ASCII file and other spatial
+ databases.
+ Note that all of these geographic coordinate systems do not need to be
+ the same.
+ PyLith will automatically transform from one geographic coordinate system
+ to another using the spatialdata package.
+ The spatial databases should all use a georeferenced Cartesian coordinate
+ system, such as a geographic projection to insure interpolation is performed
+ properly.
+ Since all aspects of this problem other than the material database and
+ the coordinate system are identical to the examples in Section
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sec:Tutorial-Two-tet4"
+
+\end_inset
+
+, we only describe the kinematic fault problem in this tutorial.
+\end_layout
+
+\begin_layout Subsection
+Mesh Description
+\end_layout
+
+\begin_layout Standard
+The mesh consists of two tetrahedra forming a pyramid shape (Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:twotet4-geoproj-mesh"
+
+\end_inset
+
+).
+ The mesh geometry and topology are described in the file
+\family typewriter
+twotet4.mesh
+\family default
+, which is in PyLith mesh ASCII format.
+ If you compare this mesh against the one used in
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sec:Tutorial-Two-tet4"
+
+\end_inset
+
+, you will notice that, although the mesh topology is the same, the vertex
+ coordinates are significantly different.
+ We use zone 11 UTM coordinates with the NAD27 datum for the mesh.
+ Although we used the same coordinate system as the SCEC CVM-H, we could
+ have also used any other geographic projection supported by spatialdata
+ and Proj.4.
+ See Appendix
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sec:Spatialdata:SimpleIOAscii"
+
+\end_inset
+
+ for other examples of using geographic coordinates.
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twotet4-mesh.pdf
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Mesh composed of two linear tetrahedral cells in a georeferenced coordinate
+ system used for the example problems.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotet4-geoproj-mesh"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Additional Common Information
+\end_layout
+
+\begin_layout Standard
+This problem has some unique aspects compared to the other tutorials.
+ First, all of the other tutorials use a Cartesian coordinate system, while
+ this one uses a geographic coordinate system.
+ In addition to using different vertex coordinates, we also define the coordinat
+e system for the mesh in
+\family typewriter
+pylithapp.cfg
+\family default
+:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.mesh_generator.importer]
+\end_layout
+
+\begin_layout LyX-Code
+coordsys = spatialdata.geocoords.CSGeoProj
+\end_layout
+
+\begin_layout LyX-Code
+filename = twotet4.mesh
+\end_layout
+
+\begin_layout LyX-Code
+coordsys.space_dim = 3
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.mesh_generator.importer.coordsys]
+\end_layout
+
+\begin_layout LyX-Code
+datum_horiz = NAD27
+\end_layout
+
+\begin_layout LyX-Code
+datum_vert = mean sea level
+\end_layout
+
+\begin_layout LyX-Code
+ellipsoid = clrk66
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.mesh_generator.importer.coordsys.projector]
+\end_layout
+
+\begin_layout LyX-Code
+projection = utm
+\end_layout
+
+\begin_layout LyX-Code
+proj-options = +zone=11
+\end_layout
+
+\begin_layout Standard
+At the top level, we define the type of coordinate system, give the file
+ describing the mesh, and give the number of spatial dimensions for the
+ coordinate system.
+ We then provide the horizontal datum and vertical datum for the coordinate
+ system, along with the ellipsoid to be used.
+ Finally, we specify a UTM projection, and specify zone 11 as the zone to
+ be used.
+\end_layout
+
+\begin_layout Standard
+In addition to the usual material information, we must specify that we want
+ to use the
+\family typewriter
+SCECCVMH
+\family default
+ database implementation:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.materials.material]
+\end_layout
+
+\begin_layout LyX-Code
+db = spatialdata.spatialdb.SCECCVMH
+\end_layout
+
+\begin_layout LyX-Code
+db.data_dir = /home/brad/data/sceccvm-h/vx53/bin
+\end_layout
+
+\begin_layout Standard
+The first
+\family typewriter
+db
+\family default
+ option defines
+\family typewriter
+SCECCVMH
+\family default
+ as the spatial database to be used.
+ The next line defines the location of the
+\family typewriter
+vx53
+\family default
+ data files, and must be changed to the location specified by the user when
+ the package is installed.
+ The package may be obtained from Harvard's Structural Geology and Tectonics
+
+\begin_inset Flex URL
+status collapsed
+
+\begin_layout Plain Layout
+
+structure.harvard.edu/cvm-h
+\end_layout
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Standard
+The final difference with the other examples is in the description of the
+ spatial databases.
+ They must also use geographic coordinates.
+ Examining
+\family typewriter
+dislocation_slip.spatialdb
+\family default
+, we find:
+\end_layout
+
+\begin_layout LyX-Code
+// We are specifying the data in a projected geographic coordinate system.
+\end_layout
+
+\begin_layout LyX-Code
+cs-data = geo-projected {
+\end_layout
+
+\begin_layout LyX-Code
+ to-meters = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+ ellipsoid = clrk66
+\end_layout
+
+\begin_layout LyX-Code
+ datum-horiz = NAD27
+\end_layout
+
+\begin_layout LyX-Code
+ datum-vert = mean sea level
+\end_layout
+
+\begin_layout LyX-Code
+ projector = projection {
+\end_layout
+
+\begin_layout LyX-Code
+ projection = utm
+\end_layout
+
+\begin_layout LyX-Code
+ units = m
+\end_layout
+
+\begin_layout LyX-Code
+ proj-options = +zone=11
+\end_layout
+
+\begin_layout LyX-Code
+ }
+\end_layout
+
+\begin_layout LyX-Code
+}
+\end_layout
+
+\begin_layout Subsection
+Kinematic Fault Slip Example
+\end_layout
+
+\begin_layout Standard
+This example problem is a left-lateral fault slip applied between the two
+ tetrahedral cells using kinematic cohesive cells.
+ Note that we vary the amount of fault slip for each vertex with this example,
+ as described in
+\family typewriter
+
+\begin_inset Newline linebreak
+\end_inset
+
+dislocation_slip.spatialdb
+\family default
+.
+ The vertices away from the fault are held fixed in the x, y, and z 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
+.
+\end_layout
+
+\begin_layout Standard
+Recall that we condition problems with the kinematic fault interface using
+ the material properties.
+ Since the material properties are being defined using the SCEC CVM-H database,
+ this same database should be used as the material database for the faults.
+ This also applies to the AbsorbingDampers boundary condition.
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+twotet4.mesh
+\family default
+,
+\family typewriter
+pylithapp.cfg
+\family default
+) along with the problem-specific files (
+\family typewriter
+dislocation.cfg, dislocation_slip.spatialdb, dislocation_sliptime.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 dislocation.cfg
+\end_layout
+
+\begin_layout Standard
+If the problem ran correctly, you should be able to generate a figure such
+ as Figure
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "fig:twotet4-geoproj-disloc"
+
+\end_inset
+
+, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twotet4-geoproj-dislocation.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the kinematic fault example
+ using a mesh composed of two linear tetrahedral cells in a georeferenced
+ coordinate system.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotet4-geoproj-disloc"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twotet4.lyx (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/twotet4.lyx)
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twotet4.lyx (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twotet4.lyx 2013-05-18 00:11:11 UTC (rev 22100)
@@ -0,0 +1,543 @@
+#LyX 2.0 created this file. For more info see http://www.lyx.org/
+\lyxformat 413
+\begin_document
+\begin_header
+\textclass book
+\begin_preamble
+
+\end_preamble
+\use_default_options false
+\maintain_unincluded_children false
+\language english
+\language_package default
+\inputencoding latin1
+\fontencoding global
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\use_non_tex_fonts false
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
+
+\graphics default
+\default_output_format default
+\output_sync 0
+\bibtex_command default
+\index_command default
+\paperfontsize default
+\spacing single
+\use_hyperref false
+\papersize default
+\use_geometry true
+\use_amsmath 0
+\use_esint 0
+\use_mhchem 1
+\use_mathdots 1
+\cite_engine basic
+\use_bibtopic false
+\use_indices false
+\paperorientation portrait
+\suppress_date false
+\use_refstyle 0
+\index Index
+\shortcut idx
+\color #008000
+\end_index
+\leftmargin 1in
+\topmargin 1in
+\rightmargin 1in
+\bottommargin 2in
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\paragraph_indentation default
+\quotes_language english
+\papercolumns 1
+\papersides 1
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\html_math_output 0
+\html_css_as_file 0
+\html_be_strict false
+\end_header
+
+\begin_body
+
+\begin_layout Section
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:Tutorial-Two-tet4"
+
+\end_inset
+
+Tutorial Using Two Tetrahedra
+\end_layout
+
+\begin_layout Standard
+PyLith features discussed in this tutorial:
+\end_layout
+
+\begin_layout Itemize
+Quasi-static solution
+\end_layout
+
+\begin_layout Itemize
+Mesh ASCII 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
+VTK output
+\end_layout
+
+\begin_layout Itemize
+Linear tetrahedral cells
+\end_layout
+
+\begin_layout Itemize
+SimpleDB spatial database
+\end_layout
+
+\begin_layout Itemize
+ZeroDispDB spatial database
+\end_layout
+
+\begin_layout Standard
+All of the files necessary to run the examples are contained in the directory
+
+\family typewriter
+examples/twocells/twotet4.
+\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 two linear tetrahedra subject to displacement
+ boundary conditions, and is probably the simplest example of a 3D elastic
+ problem.
+ Due to the simple geometry of the problem, the mesh may be constructed
+ by hand, using PyLith mesh ASCII format.
+ 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 problem includes
+ extensive comments.
+\end_layout
+
+\begin_layout Subsection
+Mesh Description
+\end_layout
+
+\begin_layout Standard
+The mesh consists of two tetrahedra forming a pyramid shape (Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:twotet4-mesh"
+
+\end_inset
+
+).
+ The mesh geometry and topology is described in the file
+\family typewriter
+twotet4.mesh
+\family default
+, which is in PyLith mesh ASCII format.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twotet4-mesh.pdf
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Mesh composed of two linear tetrahedral cells used for example problems.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotet4-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,
+ which we place in
+\family typewriter
+pylithapp.cfg
+\family default
+.
+\end_layout
+
+\begin_layout Subsection
+Axial Displacement Example
+\end_layout
+
+\begin_layout Standard
+The first example problem is extension of the mesh along the diagonal, extending
+ along the base of the pyramid between two opposing vertices.
+ Parameter settings that override or augment those in
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file
+\family typewriter
+axialdisp.cfg
+\family default
+.
+ These settings include:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.bc Defines which degrees of freedom are being constraine
+d (
+\family typewriter
+x
+\family default
+,
+\family typewriter
+y
+\family default
+, and
+\family typewriter
+z
+\family default
+), gives the label (defined in
+\family typewriter
+twotet4.mesh
+\family default
+) defining the points desired, assigns a label to the boundary condition
+ set, and gives the name of the spatial database defining the boundary condition
+s (
+\family typewriter
+axialdisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The values for the Dirichlet boundary conditions are described in the file
+
+\family typewriter
+axialdisp.spatialdb
+\family default
+, as specified in
+\family typewriter
+axialdisp.cfg
+\family default
+.
+ Because data are being specified using two control points (rather than
+ being uniform over the mesh), the data dimension is one.
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+twotet4.mesh
+\family default
+,
+\family typewriter
+pylithapp.cfg
+\family default
+,
+\family typewriter
+matprops.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+axialdisp.cfg
+\family default
+,
+\family typewriter
+axialdisp.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 axialdisp.cfg
+\end_layout
+
+\begin_layout Standard
+If the problem ran correctly, you should be able to produce a figure such
+ as Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:twotet4-axial"
+
+\end_inset
+
+, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twotet4-axialdisp.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the axial displacement example
+ using a mesh composed of two linear tetrahedral cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotet4-axial"
+
+\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 left-lateral fault slip applied between the
+ two tetrahedral cells using kinematic cohesive cells.
+ The vertices away from the fault are held 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 include:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.bc Defines which degrees of freedom are being constraine
+d (
+\family typewriter
+x
+\family default
+,
+\family typewriter
+y
+\family default
+, and
+\family typewriter
+z
+\family default
+), gives the label (defined in
+\family typewriter
+twotet4.mesh
+\family default
+) defining the points desired, and assigns 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 (ZeroDispDB) 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
+twotet4.mesh
+\family default
+) 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 Standard
+The fault example requires three additional database files that were not
+ needed for the simple displacement examples.
+ The first file (
+\family typewriter
+dislocation_slip.spatialdb
+\family default
+) specifies 0.01 m of left-lateral fault slip for the entire fault.
+ The data dimension is zero since the same data are applied to all points
+ in the set.
+ The default slip time function is a step-function, so we also must provide
+ the time at which slip begins.
+ The elastic solution is associated with advancing from
+\begin_inset Formula $t=-dt$
+\end_inset
+
+ to
+\begin_inset Formula $t=0$
+\end_inset
+
+, so we set the slip initiation time for the step-function to 0 in
+\family typewriter
+dislocation_sliptime.spatialdb
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+twotet4.mesh
+\family default
+,
+\family typewriter
+pylithapp.cfg
+\family default
+,
+\family typewriter
+matprops.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+dislocation.cfg, dislocation_slip.spatialdb,
+\begin_inset Newline linebreak
+\end_inset
+
+dislocation_sliptime.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 dislocation.cfg
+\end_layout
+
+\begin_layout Standard
+If the problem ran correctly, you should be able to generate a figure such
+ as Figure
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "fig:twotet4-disloc"
+
+\end_inset
+
+, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twotet4-dislocation.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the kinematic fault example
+ using a mesh composed of two linear tetrahedral cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotet4-disloc"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document
Copied: short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twotri3.lyx (from rev 22098, short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx)
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twotri3.lyx (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twocells/twotri3.lyx 2013-05-18 00:11:11 UTC (rev 22100)
@@ -0,0 +1,882 @@
+#LyX 2.0 created this file. For more info see http://www.lyx.org/
+\lyxformat 413
+\begin_document
+\begin_header
+\textclass book
+\begin_preamble
+
+\end_preamble
+\use_default_options false
+\maintain_unincluded_children false
+\language english
+\language_package default
+\inputencoding latin1
+\fontencoding global
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\use_non_tex_fonts false
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
+
+\graphics default
+\default_output_format default
+\output_sync 0
+\bibtex_command default
+\index_command default
+\paperfontsize default
+\spacing single
+\use_hyperref false
+\papersize default
+\use_geometry true
+\use_amsmath 0
+\use_esint 0
+\use_mhchem 1
+\use_mathdots 1
+\cite_engine basic
+\use_bibtopic false
+\use_indices false
+\paperorientation portrait
+\suppress_date false
+\use_refstyle 0
+\index Index
+\shortcut idx
+\color #008000
+\end_index
+\leftmargin 1in
+\topmargin 1in
+\rightmargin 1in
+\bottommargin 1in
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\paragraph_indentation default
+\quotes_language english
+\papercolumns 1
+\papersides 1
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\html_math_output 0
+\html_css_as_file 0
+\html_be_strict false
+\end_header
+
+\begin_body
+
+\begin_layout Section
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:Tutorial-Two-triangle"
+
+\end_inset
+
+Tutorial Using Two Triangles
+\end_layout
+
+\begin_layout Standard
+PyLith features discussed in this tutorial:
+\end_layout
+
+\begin_layout Itemize
+Quasi-static solution
+\end_layout
+
+\begin_layout Itemize
+Mesh ASCII format
+\end_layout
+
+\begin_layout Itemize
+Dirichlet boundary conditions
+\end_layout
+
+\begin_layout Itemize
+Kinematic fault interface conditions
+\end_layout
+
+\begin_layout Itemize
+Plane strain linearly elastic material
+\end_layout
+
+\begin_layout Itemize
+VTK output
+\end_layout
+
+\begin_layout Itemize
+Linear triangular cells
+\end_layout
+
+\begin_layout Itemize
+SimpleDB spatial database
+\end_layout
+
+\begin_layout Itemize
+ZeroDispDB spatial database
+\end_layout
+
+\begin_layout Standard
+All of the files necessary to run the examples are contained in the directory
+
+\family typewriter
+examples/twocells/twotri3.
+\end_layout
+
+\begin_layout Subsection
+Overview
+\end_layout
+
+\begin_layout Standard
+This tutorial is the simplest 2D example of a quasi-static finite element
+ problem (a simpler problem would consist of a 1D bar).
+ It is a mesh composed of two linear triangles subject to displacement boundary
+ conditions, assuming plane-strain linear elastic behavior.
+ Due to the simple geometry of the problem, the mesh may be constructed
+ by hand, using PyLith mesh ASCII format.
+ In this tutorial, we will walk through the steps necessary to construct,
+ run, and view three problems that use the same mesh.
+ In addition to this manual, each of the files for the example problem includes
+ extensive comments.
+\end_layout
+
+\begin_layout Subsection
+Mesh Description
+\end_layout
+
+\begin_layout Standard
+The mesh consists of two triangles forming a square with edge lengths of
+ one unit (Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:twotri3-mesh"
+
+\end_inset
+
+).
+ The mesh geometry and topology are described in the file
+\family typewriter
+twotri3.mesh
+\family default
+, which is in PyLith mesh ASCII format.
+ This file format is described in Appendix
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "cha:File-Formats"
+
+\end_inset
+
+.
+ This file describes the dimensionality of the problem (1D, 2D, or 3D),
+ the coordinates of the vertices (nodes), the vertices composing each cell
+ (element), the material ID to be associated with each cell, and groups
+ of vertices that may be used to define faults or surfaces to which boundary
+ conditions may be applied.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twotri3-mesh.pdf
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Mesh composed of two linear triangular cells used in the example problems.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotri3-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 three 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 working 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 filename, 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 spatial dimension.
+\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 the physical
+ properties for the material.
+ 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
+All of the problems in this directory use the same material database, as
+ specified under
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+pylithapp.timedependent.materials
+\family default
+
+\end_layout
+
+\begin_layout Standard
+in
+\family typewriter
+pylithapp.cfg
+\family default
+.
+ This information is contained in the file
+\family typewriter
+matprops.spatialdb
+\family default
+.
+ Although the material model is specified in
+\family typewriter
+pylithapp.cfg
+\family default
+, the values for the physical properties of the material are given in
+\family typewriter
+matprops.spatialdb
+\family default
+.
+ For this example, values describing elastic plane strain material properties
+ are given at a single point, resulting in uniform material properties.
+\end_layout
+
+\begin_layout Subsection
+Axial Displacement Example
+\end_layout
+
+\begin_layout Standard
+The first example problem is extension of the mesh along the diagonal extending
+ from the lower left to the upper right of the square mesh.
+ Parameter settings that augment those in
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file
+\family typewriter
+axialdisp.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.bc.bc Defines which degrees of freedom are being constraine
+d (x and y), gives the label (defined in
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points desired, assigns a label to the boundary condition
+ set, and gives the name of the spatial database with the values for the
+ Dirichlet boundary condition (
+\family typewriter
+axialdisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.problem.formulation.output.output.writer Gives the base filename for
+ VTK output
+\begin_inset Newline newline
+\end_inset
+
+(
+\family typewriter
+axialdisp.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials.material.output Gives the base filename for
+ state variable output files
+\begin_inset Newline linebreak
+\end_inset
+
+(
+\family typewriter
+axialdisp-statevars.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The values for the Dirichlet boundary condition are given in the file
+\family typewriter
+axialdisp.spatialdb
+\family default
+, as specified in
+\family typewriter
+axialdisp.cfg
+\family default
+.
+ The format of all spatial database files is similar.
+ In this case, the desired displacement values are given at two points (lower
+ left and upper right).
+ Since data are being specified at 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
+twotri3.mesh
+\family default
+,
+\family typewriter
+pylithapp.cfg
+\family default
+,
+\family typewriter
+matprops.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+axialdisp.cfg
+\family default
+,
+\family typewriter
+axialdisp.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 axialdisp.cfg
+\end_layout
+
+\begin_layout Standard
+Once the problem has run, three files will be produced.
+ The first file is named
+\family typewriter
+axialdisp_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
+axialdisp-statevars_t0000000.vtk
+\family default
+.
+ This file contains the state variables for each cell.
+ The default fields are the total strain and stress fields.
+ Since the cells are linear triangles, there is a single quadrature point
+ for each cell and thus a single set of stress and strain values for each
+ cell.
+ The final file (
+\family typewriter
+axialdisp-statevars_info.vtk
+\family default
+) gives the material properties used for the problem.
+ 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.
+ 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 Figure
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "fig:twotri3-axial"
+
+\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 Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twotri3-axialdisp.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the axial displacement example
+ using a mesh composed of two linear triangular cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotri3-axial"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Shear Displacement Example
+\end_layout
+
+\begin_layout Standard
+The next example problem is shearing of the mesh in the y direction using
+ displacements applied along the positive and negative x boundaries.
+ Parameter settings that augment those in
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file
+\family typewriter
+sheardisp.cfg
+\family default
+.
+ These settings include:
+\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
+ (x and y), giving the label (
+\family typewriter
+x_neg
+\family default
+, defined in
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points desired, assigning a label to the boundary condition
+ set, and giving the name of the spatial database with the values for the
+ Dirichlet boundary condition (
+\family typewriter
+sheardisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos Specifies the boundary conditions for the
+ left side of the mesh, defining which degrees of freedom are being constrained
+ (y only), giving the label (
+\family typewriter
+x_pos
+\family default
+, defined in
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points desired, assigning a label to the boundary condition
+ set, and giving the name of the spatial database with the values for the
+ Dirichlet boundary condition (
+\family typewriter
+sheardisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+twotri3.mesh
+\family default
+,
+\family typewriter
+pylithapp.cfg
+\family default
+,
+\family typewriter
+matprops.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+sheardisp.cfg
+\family default
+,
+\family typewriter
+sheardisp.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 sheardisp.cfg
+\end_layout
+
+\begin_layout Standard
+Once the problem has run, three files will be produced as in the previous
+ example.
+ If the problem ran correctly, you should be able to generate a figure such
+ as Figure
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "fig:twotri-shear"
+
+\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 Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twotri3-sheardisp.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the shear displacement example
+ using a mesh composed of two linear triangular cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotri-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 left-lateral fault slip applied between the
+ two triangular cells using kinematic cohesive cells.
+ The lower left and upper right boundaries are held fixed in the x and y
+ directions.
+ Parameter settings that augment those in
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file
+\family typewriter
+dislocation.cfg
+\family default
+.
+ The solution corresponds to rigid body rotation of each triangular cell.
+ As a result, the tractions on the fault are zero.
+ These settings include:
+\end_layout
+
+\begin_layout Description
+pylithapp.journal.info Turns on journaling for 1D quadrature (used for 2D
+ faults) and for cohesive kinematic faults.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.bc Defines which degrees of freedom are being constraine
+d (x and y), gives the label (defined in
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points desired, and assigns a label to the boundary condition
+ set.
+ In this case, rather than specifying a spatial database file with the values
+ for the Dirichlet boundary condition, the default database (ZeroDispDB)
+ for Dirichlet boundary conditions is used, which sets the displacements
+ to zero.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.interfaces Gives the label (defined in
+\family typewriter
+twotri3.mesh
+\family default
+) 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.timedependent.interfaces.fault.output.writer Gives the base filename
+ for cohesive cell output files
+\begin_inset Newline linebreak
+\end_inset
+
+(
+\family typewriter
+dislocation-fault.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+Rather than specifying the displacement boundary conditions in a spatial
+ database file, we use the default behavior for Dirichlet boundary conditions,
+ which is a uniform, constant displacement of zero.
+\end_layout
+
+\begin_layout Standard
+The fault example requires three additional database files that were not
+ needed for the simple displacement examples.
+ The first file (
+\family typewriter
+dislocation_slip.spatialdb
+\family default
+) specifies 0.01 m of left-lateral fault slip for the entire fault.
+ The data dimension is zero since the same data are applied to all points
+ in the set.
+ The default slip time function is a step-function, so we also must provide
+ the time at which slip begins.
+ The elastic solution is associated with advancing from
+\begin_inset Formula $t=-dt$
+\end_inset
+
+ to
+\begin_inset Formula $t=0$
+\end_inset
+
+, so we set the slip initiation time for the step-function to 0 in
+\family typewriter
+dislocation_sliptime.spatialdb
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+twotri3.mesh
+\family default
+,
+\family typewriter
+pylithapp.cfg
+\family default
+,
+\family typewriter
+matprops.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+\size small
+dislocation.cfg
+\family default
+,
+\family typewriter
+dislocation_slip.spatialdb
+\family default
+,
+\family typewriter
+
+\begin_inset Newline linebreak
+\end_inset
+
+dislocation_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, five files are produced.
+ In addition to the files produced in the previous two examples, this example
+ produces two files associated with the fault interface.
+ The file
+\family typewriter
+dislocation-fault_t0000000.vtk
+\family default
+ gives the fault slip for each vertex on the fault along with the computed
+ traction change for the cohesive cell.
+ The 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.
+ If the problem ran correctly, you should be able to generate a figure such
+ as Figure
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "fig:twotri-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 Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/twotri3-dislocation.jpg
+ lyxscale 50
+ scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the kinematic fault example
+ using a mesh composed of two linear triangular cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotri-disloc"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document
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