[cig-commits] r3843 - in
short/3D/PyLith/branches/pylith-0.8/doc/userguide:
fileformats tutorials/tutorialbm5
baagaard at geodynamics.org
baagaard at geodynamics.org
Wed Jun 21 16:12:56 PDT 2006
Author: baagaard
Date: 2006-06-21 16:12:55 -0700 (Wed, 21 Jun 2006)
New Revision: 3843
Added:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/hist.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/keyval.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/wink.xml
Modified:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/bc.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/connect.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/coord.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fuldat.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/prop.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/skew.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/split.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/statevar.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/time.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/tutorialbm5.xml
Log:
User guide. Added documentation for final types of input files.
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/bc.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/bc.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/bc.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
-<section id="section_bc">
+<section id="file_bc">
<title>xx.bc</title>
<para>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/connect.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/connect.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/connect.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
-<section id="section_connect">
+<section id="file_connect">
<title>xx.connect</title>
<para>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/coord.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/coord.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/coord.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
-<section id="section_coord">
+<section id="file_coord">
<title>xx.coord</title>
<para>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -4,11 +4,20 @@
<chapter id="appendix_fileformats">
<title>File Formats</title>
- <para>
- CHARLES- DO ALL FILES PERMIT COMMENT LINES?
- </para>
+ <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
+ <section>
+ <title>Input Files</title>
- <!-- REQUIRED INPUT FILES -->
+ <para>
+ PyLith gathers its input from several different types of
+ files. All of these area ASCII files and can include comment
+ lines that begin with '#'. Note that the placement of comments
+ is restricted to certain locations in some files (see the
+ discussion of each file format for more information).
+ </para>
+ </section>
+
+ <!-- REQUIRED INPUT FILES ++++++++++++++++++++++++++++++++++++++ -->
<xi:include
xmlns:xi="http://www.w3.org/2001/XInclude" href="coord.xml" />
<xi:include
@@ -18,15 +27,21 @@
<xi:include
xmlns:xi="http://www.w3.org/2001/XInclude" href="time.xml" />
<xi:include
+ xmlns:xi="http://www.w3.org/2001/XInclude" href="prop.xml" />
+ <xi:include
xmlns:xi="http://www.w3.org/2001/XInclude" href="statevar.xml" />
- <xi:include
- xmlns:xi="http://www.w3.org/2001/XInclude" href="prop.xml" />
- <!-- OPTIONAL INPUT FILES -->
+ <!-- OPTIONAL INPUT FILES ++++++++++++++++++++++++++++++++++++++ -->
<xi:include
xmlns:xi="http://www.w3.org/2001/XInclude" href="split.xml" />
<xi:include
xmlns:xi="http://www.w3.org/2001/XInclude" href="fuldat.xml" />
<xi:include
xmlns:xi="http://www.w3.org/2001/XInclude" href="skew.xml" />
+ <xi:include
+ xmlns:xi="http://www.w3.org/2001/XInclude" href="keyval.xml" />
+ <xi:include
+ xmlns:xi="http://www.w3.org/2001/XInclude" href="hist.xml" />
+ <xi:include
+ xmlns:xi="http://www.w3.org/2001/XInclude" href="wink.xml" />
</chapter>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fuldat.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fuldat.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fuldat.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
-<section id="section_fuldat">
+<section id="file_fuldat">
<title>xx.fuldat</title>
<para>
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/hist.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/hist.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/hist.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -0,0 +1,35 @@
+<?xml version="1.0"?>
+<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
+<section id="file_hist">
+ <title>xx.hist</title>
+
+ <para>
+ The <filename>xx.hist</filename> files provide time histories for
+ use in boundary conditions.
+ </para>
+
+ <figure>
+ <title>Format of <filename>xx.hist</filename> files</title>
+ <screen>
+# File specifying time variation of boundary conditions.
+#
+# Comment lines begin with '#'
+#
+# Each time history consists of two or more lines. The first line
+# indicates the number of points in the history and the default load
+# value for the history. Subsequent lines define time/load pairs.
+#
+# Line 1, column 1: The number of points in the time history
+# Line 1, column 2: The value assigned to every point by default
+# (overrided by values in time history)
+# Line 2+, column 1: Time (in seconds) for a given load value
+# Line 2+, column 2: Load value at given time
+#
+ 2 1.0
+2.84014e+08 0.1
+3.15576e+08 0.5
+ </screen>
+ </figure>
+
+</section>
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/keyval.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/keyval.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/keyval.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -0,0 +1,152 @@
+<?xml version="1.0"?>
+<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
+<section id="file_keyval">
+ <title>xx.keyval</title>
+
+ <para>
+ The <filename>xx.keyval</filename> file specifies some simple
+ parameters settings.
+ </para>
+
+ <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
+ <section>
+ <title>Winkler forces</title>
+
+ <para>
+ Scaling factors can be applied to Windkler forces, permitting a
+ quick and easy way to change the density or gravitational
+ acceleration when Winkler forces are used to simulate
+ gravity. Scaling factors for differential Winkler forces are
+ applied across a slippery node interface. These factors provide
+ a simple way of scaling the forces so that the fault remains
+ sufficiently locked.
+ </para>
+ </section>
+
+ <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
+ <section>
+ <title>Quadrature order</title>
+
+ <variablelist>
+ <varlistentry>
+ <term><literal>Full</literal></term>
+ <listitem>
+ <para>
+ Quadrature order that should give the exact element
+ matrices when the elements are geometrically
+ undistorted.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><literal>Reduced</literal></term>
+ <listitem>
+ <para>
+ Quadrature order that is one order less than full
+ quadrature.
+ </para>
+ <warning>
+ <para>Use with caution as reduced quadrature can lead to
+ numerical instabilities.</para>
+ </warning>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><literal>Reduced</literal></term>
+ <listitem>
+ <para>
+ Uses Hughes' b-bar formulation to perform reduced
+ quadrature on the dilatational parts of the
+ strain-displacement matrix. This can be useful in
+ nearly-incompressible problems.
+ </para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </section>
+
+ <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
+ <section>
+ <title>Prestresses</title>
+
+ <para>
+ Gravitational prestresses can be computed automatically. In such
+ cases, the elastic properties in the prestress calculation can
+ be set to uniform values independent of any of the material
+ models. When gravity is being used and prestresses are not
+ computed automatically, each prestress component can be scaled
+ independently.
+ </para>
+ </section>
+
+ <figure>
+ <title>Format of <filename>xx.keyval</filename> files</title>
+ <screen>
+# Simple parameter values for various PyLith settings. Defaults are
+# listed.
+#
+# Scaling factors applied to Winkler forces.
+#
+winklerScaleX = 1.0
+winklerScaleY = 1.0
+winklerScaleZ = 1.0
+#
+# Scaling factors applied to differential Winkler forces.
+#
+winklerSlipScaleX = 1.0
+winklerSlipScaleY = 1.0
+winklerSlipScaleZ = 1.0
+#
+# Stress integration and numerical computation of the tangent
+# material matrix. Default values should be reasonable for most cases.
+#
+stressTolerance = 1.0e-12*Pa
+minimumStrainPerturbation = 1.0e-7
+initialStrainPerturbation = 1.0e-1
+#
+# Specify whether to use the solution from the previous time step as
+# the starting guess for the elastic solution in the current time step.
+#
+usePreviousDisplacementFlag = 0
+</screen>
+ </figure>
+<figure>
+ <title>Format of <filename>xx.keyval</filename> files (cont.)</title>
+<screen>
+# Quadrature order for the problem.
+#
+quadratureOrder = "Full"
+#
+# Gravitational acceleration in each direction.
+#
+gravityX = 0.0*m/(s*s)
+gravityY = 0.0*m/(s*s)
+gravityZ = 0.0*m/(s*s)
+#
+# Factors controlling computation of prestresses.
+#
+prestressAutoCompute = False
+prestressAutoChangeElasticProperties = False
+prestressAutoComputePoisson = 0.49
+prestressAutoComputeYoungs = 1.0e30*Pa
+#
+prestressScaleXx = 1.0
+prestressScaleYy = 1.0
+prestressScaleZz = 1.0
+prestressScaleXy = 1.0
+prestressScaleXz = 1.0
+prestressScaleYz = 1.0
+#
+# Unit numbers used in Fortran code.
+#
+f77StandardInput = 5
+f77StandardOutput = 6
+f77FileInput = 10
+f77AsciiOutput = 11
+f77PlotOutput = 12
+f77UcdOutput = 13
+ </screen>
+ </figure>
+
+</section>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/prop.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/prop.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/prop.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
-<section id="section_prop">
+<section id="file_prop">
<title>xx.prop</title>
<para>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/skew.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/skew.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/skew.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
-<section id="section_skew">
+<section id="file_skew">
<title>xx.skew</title>
<para>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/split.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/split.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/split.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
-<section id="section_split">
+<section id="file_split">
<title>xx.split</title>
<para>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/statevar.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/statevar.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/statevar.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
-<section id="section_statevar">
+<section id="file_statevar">
<title>xx.statevar</title>
<para>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/time.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/time.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/time.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
-<section id="section_time">
+<section id="file_time">
<title>xx.time</title>
<para>
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/wink.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/wink.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/wink.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -0,0 +1,40 @@
+<?xml version="1.0"?>
+<!DOCTYPE section PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
+<section id="file_wink">
+ <title>xx.wink</title>
+
+ <para>
+ The <filename>xx.wink</filename> file specifies Winkler elements,
+ which may be used as spring foundations in the simulation of
+ gravity.
+ </para>
+
+ <figure>
+ <title>Format of <filename>xx.wink</filename> files</title>
+ <screen>
+# File containing Winkler elements.
+#
+# Comment lines begin with '#'
+#
+# Flags for the degrees of freedom can have the following values:
+# 0 = no Winkler force
+# 1 = Winkler force applied at all times
+# -n = Winkler force applied according to loead history n
+#
+# Columns:
+# (1) Vertex number
+# (2) Flag for DOF in x-direction
+# (3) Flag for DOF in y-direction
+# (4) Flag for DOF in z-direction
+# (5) Magnitude of restoring force for x-direction
+# (6) Magnitude of restoring force for x-direction
+# (7) Magnitude of restoring force for x-direction
+#
+14 0 -1 0 0.0e+00 1.0e+25 0.0e+00
+18 0 1 0 1.0e+20 0.0e+00 0.0e+00
+...
+ </screen>
+ </figure>
+
+</section>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/tutorialbm5.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/tutorialbm5.xml 2006-06-21 21:30:31 UTC (rev 3842)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/tutorialbm5.xml 2006-06-21 23:12:55 UTC (rev 3843)
@@ -404,11 +404,12 @@
<title>Visualize the single processor run</title>
<para>
Now it is time to visualize the results of the simulation. By
- default, PyLith writes simulation output using
+ default, PyLith writes simulation output using <ulink
+ url="http://help.avs.com/Express/doc/help/reference/dvmac/UCD_Form.htm">
<application>AVS</application> <acronym>UCD</acronym>
- files. These can also be read by several other visualization
- tools besides <application>AVS</application>, e.g.,
- <application>ParaView</application> and <application>Iris
+ files</ulink>. These can also be read by several other
+ visualization tools besides <application>AVS</application>,
+ e.g., <application>ParaView</application> and <application>Iris
Explorer</application>. We will use the open-source application
<application>ParaView</application> to visualize the results.
</para>
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