[cig-commits] r7453 - in short/3D/PyLith/trunk/doc/userguide: .
tutorials tutorials/twoquad4 tutorials/twotet4
tutorials/twotet4/figs tutorials/twotri3
willic3 at geodynamics.org
willic3 at geodynamics.org
Sun Jun 24 18:50:47 PDT 2007
Author: willic3
Date: 2007-06-24 18:50:46 -0700 (Sun, 24 Jun 2007)
New Revision: 7453
Added:
short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/
short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/twoquad4.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/
short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/
short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/axialdisp.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/dislocation.jpg
short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/twotet4-mesh.fig
short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/twotet4.lyx
Modified:
short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx
short/3D/PyLith/trunk/doc/userguide/userguide.lyx
Log:
More work on tutorials.
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx 2007-06-25 00:37:49 UTC (rev 7452)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx 2007-06-25 01:50:46 UTC (rev 7453)
@@ -124,13 +124,13 @@
\end_layout
\begin_layout Standard
-\begin_inset Include \input{splitcube/splitcube.lyx}
+\begin_inset Include \input{twotri3/twotri3.lyx}
preview false
\end_inset
-\begin_inset Include \input{reversenog/reversenog.lyx}
+\begin_inset Include \input{twoquad4/twoquad4.lyx}
preview false
\end_inset
Added: short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/twoquad4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/twoquad4.lyx 2007-06-25 00:37:49 UTC (rev 7452)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/twoquad4.lyx 2007-06-25 01:50:46 UTC (rev 7453)
@@ -0,0 +1,780 @@
+#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
+\lyxformat 245
+\begin_document
+\begin_header
+\textclass book
+\begin_preamble
+
+\end_preamble
+\language english
+\inputencoding latin1
+\fontscheme default
+\graphics default
+\paperfontsize default
+\spacing single
+\papersize default
+\use_geometry true
+\use_amsmath 0
+\cite_engine basic
+\use_bibtopic false
+\paperorientation portrait
+\leftmargin 1in
+\topmargin 1in
+\rightmargin 1in
+\bottommargin 2in
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\defskip medskip
+\quotes_language english
+\papercolumns 1
+\papersides 1
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\end_header
+
+\begin_body
+
+\begin_layout Section
+\begin_inset LatexCommand \label{sec:Tutorial-Two-triangle}
+
+\end_inset
+
+Tutorial Using Two Bilinear Quadrilaterals and PyLith Mesh ASCII Format
+\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
+ 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 three problems that use the same mesh.
+ In addition to this manual, each of the files for the example problem is
+ heavily documented to aid users in understanding the basic file formats.
+\end_layout
+
+\begin_layout Subsection
+Mesh Description
+\end_layout
+
+\begin_layout Standard
+The mesh consists of two square cells with edge lengths of one forming a
+ regular region (Figure
+\begin_inset LatexCommand \ref{fig:twoquad4-mesh}
+
+\end_inset
+
+).
+ The mesh geometry and topology is described in the file
+\family typewriter
+twoquad4.mesh
+\family default
+, which is in PyLith mesh ASCII format.
+ This file format is described in
+\begin_inset LatexCommand \ref{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 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
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename figs/twoquad4-mesh.eps
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Mesh used for the two triangle examples.
+\begin_inset LatexCommand \label{fig:twoquad4-mesh}
+
+\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 run directory, since this file is read automatically every time
+ PyLith is run.
+ Settings specific to a particular problem may be placed in other
+\family typewriter
+.cfg
+\family default
+ files, as described later, and placed on the command line.
+ The settings contained in pylithapp.cfg 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 ID's are to be associated with a particular material
+ type, and give the name of the spatial database containing material parameters
+ for the mesh.
+ The quadrature information is also given.
+\end_layout
+
+\begin_layout Description
+pylithapp.petsc PETSc settings to use for the problem, such as the preconditioner
+ type.
+\end_layout
+
+\begin_layout Standard
+All of the problems in this directory use the same material database, as
+ specified under
+\family typewriter
+pylithapp.timedependent.materials
+\family default
+ 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 parameters for the material model 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 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 settings are:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent We specify an implicit formulation for the problem
+ and specify a container for boundary conditions (
+\family typewriter
+pylith.bc.BC
+\family default
+FourSides) that allows them to be given along the edges of a rectangular
+ domain.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_neg We specify 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 we want, 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.x_pos We specify 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 we want, 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 We specify 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 we want, 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.problem.formulation.output.output We give the base filename for VTK
+ output (
+\family typewriter
+axialdisp.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The boundary conditions are described in the file
+\family typewriter
+axialdisp.spatialdb
+\family default
+, as specified in
+\family typewriter
+axialdisp.cfg
+\family default
+.
+ In this case, we give the desired displacement values at two points.
+ Since data is 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
+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
+Once the problem has run, there will be a file called
+\family typewriter
+axialdisp_t0.vtk
+\family default
+, which may be used with a number of visualization packages.
+ If the problem ran correctly, you should be able to generate a figure such
+ as
+\begin_inset LatexCommand \ref{fig:twoquad4-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 Standard
+\begin_inset Graphics
+ filename figs/axialdisp.jpg
+ lyxscale 50
+ scale 50
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Color contours and vectors of displacement for the axial displacement example.
+\begin_inset LatexCommand \label{fig:twoquad4-axial}
+
+\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 settings are:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent We specify an implicit formulation for the problem
+ and specify a container for boundary conditions (
+\family typewriter
+pylith.bc.BCFourSides
+\family default
+) that allows them to be given on four sides of a rectangular domain.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_neg We specify 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 we want, assigning a label to the boundary condition
+ set, and giving the name of the spatial database defining the boundary
+ conditions (
+\family typewriter
+sheardisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos We specify 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_
+\family default
+pos, defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) defining the points we want, assigning a label to the boundary condition
+ set, and giving the name of the spatial database defining the boundary
+ conditions (
+\family typewriter
+sheardisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.problem.formulation.output.output We give the base filename for VTK
+ output (
+\family typewriter
+sheardisp.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The 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, we give the desired displacement values at two points, correspond
+ing to the two edges we want to constrain.
+ Since data is 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
+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
+Once the problem has run, there will be a file called
+\family typewriter
+sheardisp_t0.vtk
+\family default
+, which may be used with a number of visualization packages.
+ If the problem ran correctly, you should be able to generate a figure such
+ as
+\begin_inset LatexCommand \ref{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 Standard
+\align center
+\begin_inset Graphics
+ filename figs/sheardispl.jpg
+ lyxscale 50
+ scale 50
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Color contours and vectors of displacement for the shear displacement example.
+\begin_inset LatexCommand \label{fig:twoquad4-shear}
+
+\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 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 are:
+\end_layout
+
+\begin_layout Description
+pylithapp.journal.info We turn on journaling for 1D quadrature (used for 2D
+ faults) and for cohesive kinematic faults.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent We specify an implicit formulation for the problem,
+ specify a container for boundary conditions (
+\family typewriter
+pylith.bc.BC
+\family default
+FourSides) that allows them to be given along the edges of a rectangular
+ domain, and specify a container for a single fault (
+\family typewriter
+pylith.faults.SingleFault
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_neg We specify 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 we want, assigning a label to the boundary condition
+ set, and giving the name of the spatial database defining the boundary
+ conditions (
+\family typewriter
+dislocation_disp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos We specify 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_
+\family default
+pos, defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) defining the points we want, assigning a label to the boundary condition
+ set, and giving the name of the spatial database defining the boundary
+ conditions (
+\family typewriter
+dislocation_disp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.interfaces We give the label (defined in
+\family typewriter
+twoquad4.mesh
+\family default
+) defining the points on the fault, provide quadrature information, and
+ then give database names for material properties (needed for conditioning),
+ fault slip, fault slip rate, and fault slip time.
+\end_layout
+
+\begin_layout Description
+pylithapp.problem.formulation.output.output We give the base filename for VTK
+ output (
+\family typewriter
+dislocation.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The boundary conditions are described in the file
+\family typewriter
+dislocation_disp.spatialdb
+\family default
+, as specified in
+\family typewriter
+dislocation.cfg
+\family default
+.
+ In this case, we give the desired displacement values for two points.
+ Since data is being specified at points, the data dimension is one.
+\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 is applied to all points
+ in the set.
+ It is also necessary to specify the slip rate, which is done in the file
+
+\family typewriter
+dislocation_sliprate.spatialdb
+\family default
+.
+ The slip rate of 1.0e6 m/s is essentially instantaneous.
+ Finally, we must provide the time at which slip begins.
+ The elastic solution begins at
+\begin_inset Formula $t=-dt$
+\end_inset
+
+, so this is the value given (
+\begin_inset Formula $t=-1\sec$
+\end_inset
+
+) in
+\family typewriter
+dislocation_sliptime.spatialdb
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+twoquad4.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
+\family default
+,
+\family typewriter
+dislocation_disp.spatialdb
+\family default
+,
+\family typewriter
+dislocation_slip.spatialdb
+\family default
+,
+\family typewriter
+dislocation_sliprate.spatialdb
+\family default
+,
+\family typewriter
+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
+Once the problem has run, there will be a file called
+\family typewriter
+dislocation_t0.vtk
+\family default
+, which may be used with a number of visualization packages.
+ If the problem ran correctly, you should be able to generate a figure such
+ as
+\begin_inset LatexCommand \ref{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 Standard
+\align center
+\begin_inset Graphics
+ filename figs/dislocation.jpg
+ lyxscale 50
+ scale 50
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Color contours and vectors of displacement for the kinematic fault example.
+\begin_inset LatexCommand \label{fig:twoquad4-disloc}
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document
Added: short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/axialdisp.jpg
===================================================================
(Binary files differ)
Property changes on: short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/axialdisp.jpg
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/dislocation.jpg
===================================================================
(Binary files differ)
Property changes on: short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/dislocation.jpg
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/twotet4-mesh.fig
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/twotet4-mesh.fig 2007-06-25 00:37:49 UTC (rev 7452)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/figs/twotet4-mesh.fig 2007-06-25 01:50:46 UTC (rev 7453)
@@ -0,0 +1,39 @@
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Added: short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/twotet4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/twotet4.lyx 2007-06-25 00:37:49 UTC (rev 7452)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/twotet4.lyx 2007-06-25 01:50:46 UTC (rev 7453)
@@ -0,0 +1,727 @@
+#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
+\lyxformat 245
+\begin_document
+\begin_header
+\textclass book
+\begin_preamble
+
+\end_preamble
+\language english
+\inputencoding latin1
+\fontscheme default
+\graphics default
+\paperfontsize default
+\spacing single
+\papersize default
+\use_geometry true
+\use_amsmath 0
+\cite_engine basic
+\use_bibtopic false
+\paperorientation portrait
+\leftmargin 1in
+\topmargin 1in
+\rightmargin 1in
+\bottommargin 2in
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\defskip medskip
+\quotes_language english
+\papercolumns 1
+\papersides 1
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\end_header
+
+\begin_body
+
+\begin_layout Section
+\begin_inset LatexCommand \label{sec:Tutorial-Two-triangle}
+
+\end_inset
+
+Tutorial Using Two Linear Tetrahedra and PyLith Mesh ASCII Format
+\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 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 problem is
+ heavily documented to aid users in understanding the basic file formats.
+\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 LatexCommand \ref{fig:twotri3-mesh}
+
+\end_inset
+
+).
+ The mesh geometry and topology is described in the file
+\family typewriter
+twotri3.mesh
+\family default
+, which is in PyLith Mesh ASCII format.
+ This file format is described in
+\begin_inset LatexCommand \ref{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 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
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename figs/twotri3-mesh.eps
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Mesh used for the two triangle examples.
+\begin_inset LatexCommand \label{fig:twotri3-mesh}
+
+\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 run directory, since this file is read automatically every time
+ PyLith is run.
+ Settings specific to a particular problem may be placed in other
+\family typewriter
+.cfg
+\family default
+ files, as described later, and placed on the command line.
+ The settings contained in pylithapp.cfg 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 ID's are to be associated with a particular material
+ type, and give the name of the spatial database containing material parameters
+ for the mesh.
+ The quadrature information is also given.
+\end_layout
+
+\begin_layout Description
+pylithapp.petsc PETSc settings to use for the problem, such as the preconditioner
+ type.
+\end_layout
+
+\begin_layout Standard
+All of the problems in this directory use the same material database, as
+ specified under
+\family typewriter
+pylithapp.timedependent.materials
+\family default
+ 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 parameters for the material model 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 override or 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 We specify an implicit formulation for the problem
+ and specify a container for boundary conditions (
+\family typewriter
+pylith.bc.BCSingle
+\family default
+) that allows them to be given at a point (or set of points).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.bc We define which degrees of freedom are being
+ constrained (x and y), we give the label (defined in
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points we want, we assign a label to the boundary condition
+ set, and we give the name of the spatial database defining the boundary
+ conditions (
+\family typewriter
+axialdisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.problem.formulation.output.output We give the base filename for VTK
+ output (
+\family typewriter
+axialdisp.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The boundary conditions are described 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, we give the desired displacement values at two points (lower
+ left and upper right).
+ Since data is 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, there will be a file called
+\family typewriter
+axialdisp_t0.vtk
+\family default
+, which may be used with a number of visualization packages.
+ If the problem ran correctly, you should be able to generate a figure such
+ as
+\begin_inset LatexCommand \ref{fig:twotri3-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 Standard
+\align center
+\begin_inset Graphics
+ filename figs/axialdisp.jpg
+ lyxscale 50
+ scale 50
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Color contours and vectors of displacement for the axial displacement example.
+\begin_inset LatexCommand \label{fig:twotri3-axial}
+
+\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 settings are:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent We specify an implicit formulation for the problem
+ and specify a container for boundary conditions (
+\family typewriter
+pylith.bc.BCFourSides
+\family default
+) that allows them to be given on four sides of a rectangular domain.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_neg We specify 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 we want, assigning a label to the boundary condition
+ set, and giving the name of the spatial database defining the boundary
+ conditions (
+\family typewriter
+sheardisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos We specify 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_
+\family default
+pos, defined in
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points we want, assigning a label to the boundary condition
+ set, and giving the name of the spatial database defining the boundary
+ conditions (
+\family typewriter
+sheardisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.problem.formulation.output.output We give the base filename for VTK
+ output (
+\family typewriter
+sheardisp.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The 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, we give the desired displacement values at two points, correspond
+ing to the two edges we want to constrain.
+ Since data is 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
+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, there will be a file called
+\family typewriter
+sheardisp_t0.vtk
+\family default
+, which may be used with a number of visualization packages.
+ If the problem ran correctly, you should be able to generate a figure such
+ as
+\begin_inset LatexCommand \ref{fig:twotri-shear}
+
+\end_inset
+
+, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename figs/sheardisp.jpg
+ lyxscale 50
+ scale 50
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Color contours and vectors of displacement for the shear displacement example.
+\begin_inset LatexCommand \label{fig:twotri-shear}
+
+\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 override or augment those in
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file
+\family typewriter
+dislocation.cfg
+\family default
+.
+ These settings are:
+\end_layout
+
+\begin_layout Description
+pylithapp.journal.info We turn on journaling for 1D quadrature (used for 2D
+ faults) and for cohesive kinematic faults.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent We specify an implicit formulation for the problem,
+ specify a container for boundary conditions (
+\family typewriter
+pylith.bc.BC
+\family default
+Single) that allows them to be given at a point (or set of points), and
+ specify a container for a single fault (
+\family typewriter
+pylith.faults.SingleFault
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.bc We define which degrees of freedom are being
+ constrained (x and y), we give the label (defined in
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points we want, we assign a label to the boundary condition
+ set, and we give the name of the spatial database defining the boundary
+ conditions (
+\family typewriter
+dislocation_disp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.interfaces We give the label (defined in
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points on the fault, provide quadrature information, and
+ then give database names for material properties (needed for conditioning),
+ fault slip, fault slip rate, and fault slip time.
+\end_layout
+
+\begin_layout Description
+pylithapp.problem.formulation.output.output We give the base filename for VTK
+ output (
+\family typewriter
+dislocation.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The boundary conditions are described in the file
+\family typewriter
+dislocation_disp.spatialdb
+\family default
+, as specified in
+\family typewriter
+dislocation.cfg
+\family default
+.
+ In this case, we give the desired displacement values at a single point.
+ Since data is being specified uniformly for all the labeled points, the
+ data dimension is 0.
+\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 is applied to all points
+ in the set.
+ It is also necessary to specify the slip rate, which is done in the file
+
+\family typewriter
+dislocation_sliprate.spatialdb
+\family default
+.
+ The slip rate of 1.0e6 m/s is essentially instantaneous.
+ Finally, we must provide the time at which slip begins.
+ The elastic solution begins at
+\begin_inset Formula $t=-dt$
+\end_inset
+
+, so this is the value given (
+\begin_inset Formula $t=-1\sec$
+\end_inset
+
+) in
+\family typewriter
+dislocation_sliptime.spatialdb
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+twotri3.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
+\family default
+,
+\family typewriter
+dislocation_disp.spatialdb
+\family default
+,
+\family typewriter
+dislocation_slip.spatialdb
+\family default
+,
+\family typewriter
+dislocation_sliprate.spatialdb
+\family default
+,
+\family typewriter
+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
+Once the problem has run, there will be a file called
+\family typewriter
+dislocation_t0.vtk
+\family default
+, which may be used with a number of visualization packages.
+ If the problem ran correctly, you should be able to generate a figure such
+ as
+\begin_inset LatexCommand \ref{fig:twotri-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 Standard
+\align center
+\begin_inset Graphics
+ filename figs/dislocation.jpg
+ lyxscale 50
+ scale 50
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Color contours and vectors of displacement for the kinematic fault example.
+\begin_inset LatexCommand \label{fig:twotri-disloc}
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx 2007-06-25 00:37:49 UTC (rev 7452)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx 2007-06-25 01:50:46 UTC (rev 7453)
@@ -583,7 +583,7 @@
pylithapp.problem.formulation.output.output We give the base filename for VTK
output (
\family typewriter
-sheardisp.vtk
+dislocation.vtk
\family default
).
\end_layout
Modified: short/3D/PyLith/trunk/doc/userguide/userguide.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/userguide.lyx 2007-06-25 00:37:49 UTC (rev 7452)
+++ short/3D/PyLith/trunk/doc/userguide/userguide.lyx 2007-06-25 01:50:46 UTC (rev 7453)
@@ -1,4 +1,4 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
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