[cig-commits] r3847 - in
short/3D/PyLith/branches/pylith-0.8/doc/userguide: .
fileformats install intro runpylith tutorials/tutorialbm5
tutorials/tutorialbm5/figs
baagaard at geodynamics.org
baagaard at geodynamics.org
Wed Jun 21 21:12:00 PDT 2006
Author: baagaard
Date: 2006-06-21 21:12:00 -0700 (Wed, 21 Jun 2006)
New Revision: 3847
Modified:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/bc.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/keyval.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/prop.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/split.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/time.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/wink.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/makefile
short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.xml
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/figs/geometry.eps
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/figs/geometry.fig
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/figs/geometry.png
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/tutorialbm5.xml
Log:
User guide. Cleaned up text. Added explicit indication of commands in tutorial.
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 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/bc.xml 2006-06-22 04:12:00 UTC (rev 3847)
@@ -5,14 +5,14 @@
<title>xx.bc</title>
<para>
- The <filename>xx.bc</filename> file specifies the nodal boundary
- conditions (displacements, velocity, and forces).
+ The <filename>xx.bc</filename> file specifies the displacements,
+ velocity, and/or forces applied to vertices on the boundaries.
</para>
<figure>
<title>Format of <filename>xx.bc</filename> files</title>
<screen>
-# File containing nodal boundary conditions.
+# File containing boundary conditions at vertices.
#
# Comment lines begin with '#'
#
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/keyval.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/keyval.xml 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/keyval.xml 2006-06-22 04:12:00 UTC (rev 3847)
@@ -73,10 +73,10 @@
<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.
+ be set to uniform values independent of the parameters for 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>
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 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/prop.xml 2006-06-22 04:12:00 UTC (rev 3847)
@@ -26,8 +26,8 @@
#
# The material type and material property values are specified using a
# "keyword = value" syntax. The keywords for the different material
-# types are given below. The units for values with dimensions should
-# follow the value as shown in the examples below.
+# types are given below. Units for each of the values with dimensions
+# must follow the value as illustrated in the examples below.
#
# Materials and keywords:
# Isotropic linear elastic
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 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/split.xml 2006-06-22 04:12:00 UTC (rev 3847)
@@ -17,7 +17,6 @@
#
# Comment lines begin with '#'
#
-
# Displacements are specified for each vertex on the fault for each
# element containing the vertex. The displacements on each side of the
# fault or dike should have opposite signs. The displacements
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 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/time.xml 2006-06-22 04:12:00 UTC (rev 3847)
@@ -50,14 +50,14 @@
# step in each time step group.
# =0 Indicates that reformation should never occur.
# (7) Large deformation solution flag
-# =0 Linear strain
-# =1 Large strain but use only linear contribution to the
-# stiffness matrix (sometimes results in better convergence)
-# =2 Large strain and use nonlinear contribution to the
-# stiffness matrix
-# (8) Convergece tolerance for displacements (dimensionless value)
-# (9) Convergece tolerance for forces (dimensionless value)
-# (10) Convergece tolerance for energy (dimensionless value)
+# 0 = Linear strain
+# 1 = Large strain but use only linear contribution to the
+# stiffness matrix (sometimes results in better convergence)
+# 2 = Large strain and use nonlinear contribution to the
+# stiffness matrix
+# (8) Convergence tolerance for displacements (dimensionless value)
+# (9) Convergence tolerance for forces (dimensionless value)
+# (10) Convergence tolerance for energy (dimensionless value)
# (11) Maximum number of equilibrium iterations
#
0 1 0.0 5.0e-01 1001 4 0 1.0e+00 1.0e+0 1.0e+00 1
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/wink.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/wink.xml 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/wink.xml 2006-06-22 04:12:00 UTC (rev 3847)
@@ -20,7 +20,8 @@
# 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
+# -n = Winkler force applied according to load history n
+# (requires xx.hist file)
#
# Columns:
# (1) Vertex number
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.xml 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.xml 2006-06-22 04:12:00 UTC (rev 3847)
@@ -51,9 +51,9 @@
report to the <ulink
url="http://www.geodynamics.org/roundup">CIG
<application>Roundup</application> system</ulink>. Of course,
- it is helpful to first check to see if someone else has
- already submitted a report related to the issue; one of the
- CIG developers may have already posted a solution to the
+ it is helpful to first check to see if someone else already
+ submitted a report related to the issue; one of the CIG
+ developers may have already posted a solution to the
problem. You can reply to a current issue by clicking on the
issue title. To submit a new issue, click on <guibutton>Create
New</guibutton> under <guimenu>Issues</guimenu>.
@@ -90,10 +90,12 @@
</listitem>
<listitem>
<para>
- Unpack the tarball (i.e., <command>tar -zxvf
- pylith-0.8-linux-x86.tar.gz</command>) in a suitable
+ Unpack the tarball in a suitable
location.
</para>
+ <screen>
+<prompt>bash$ </prompt>tar -zxvf pylith-0.8-linux-x86.tar.gz
+ </screen>
</listitem>
<listitem>
<para>
@@ -101,7 +103,9 @@
class="directory">pylith-0.8-linux-x86/bin</filename> to
your <envar>PATH</envar>. You will likely want to add
something like
- <literal>PATH=${PATH}:replace_with_absolute_path/pylith-0.8-linux-x86/bin</literal>
+ <screen>
+PATH=${PATH}:<replaceable>replace_with_absolute_path</replaceable>/pylith-0.8-linux-x86/bin
+ </screen>
to your <filename>.bashrc</filename> file (if you are
using bash as your shell) or the equivalent to your
<filename>.cshrc</filename> file (if you are using tcsh as
@@ -154,7 +158,7 @@
<!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++ -->
<section>
- <title>Building the source code</title>
+ <title>Building from source</title>
<para>
Building PyLith from the source code is not a trivial task
@@ -186,10 +190,10 @@
the recommended way to build PyLith and the external packages
on which it depends. Some of the dependencies can be satisfied
using precompiled binaries (e.g., RedHat and Fink
- packages). When choosing whether to use a precompiled binary
- package to satisfy any of the dependencies remember that all
- of the compilers and settings used in building the code must
- be compatible.
+ packages). When considering whether to use a precompiled
+ binary package to satisfy any of the dependencies, remember
+ that all of the compilers and settings used in building the
+ code must be compatible.
</para>
<orderedlist>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.xml 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.xml 2006-06-22 04:12:00 UTC (rev 3847)
@@ -48,44 +48,34 @@
<!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
<section>
<title>Software Components</title>
+
<para>
- ADD STUFF HERE
+ PyLith is separated into modules to encapsulate behavior and
+ facilitate use across multiple applications. That way expert
+ users can replace functionality of a wide variety of components
+ without recompiling or polluting the main code. External
+ packages reduce development time and enhance computational
+ efficiency, for example, PyLith runs 2x faster by using the
+ PETSc linear solver.
</para>
+ <para>
+ PyLith is based on several programming languages. High-level
+ code is written in Python; this rich, expressive interpreted
+ language with dynamic typing reduces development
+ time. Low-level code is written in Fortran 77 for fast
+ execution. Bindings, written in C/C++, are used to allow the
+ low-level code (Fortran 77) to be called from high-level code
+ (Python).
+ </para>
+ <para>
+ PyLith makes extensive use of external software. Pyre is a
+ science neutral simulation framework being developed at
+ Caltech. PETSc is used to perform operations on matrices and
+ vectors in parallel.
+ </para>
<!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++ -->
<section>
- <title>PyLith</title>
-
- <para>
- In PyLith simulation software is separated into modules to
- encapsulate behavior and facilitate use across multiple
- applications. That way expert users can replace functionality
- of a wide variety of components without recompiling or
- polluting the main code. External packages reduce development
- time and enhance computational efficiency, for example, PyLith
- runs 2x faster by using the PETSc linear solver.
- </para>
- <para>
- PyLith is based on several programming languages. High-level
- code is written in Python; this rich, expressive interpreted
- language with dynamic typing reduces development
- time. Low-level code is written in Fortran 77 for fast
- execution. Bindings, written in C/C++, are used to allow the
- low-level code (Fortran 77)to be called from high-level code
- (Python).
- </para>
- <para>
- PyLith makes extensive use of external software. Pyre is a
- science neutral simulation framework being developed at
- Caltech. PETSc is used to perform operations on matrices and
- vectors in parallel. MPI is the Message Passing Interface
- which provides a standard interface for
- parallel-processing.
- </para>
- </section>
-
- <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++ -->
- <section>
<title>PETSc</title>
<para>
<ulink
@@ -98,7 +88,7 @@
subspace methods. It can also interface with many external
packages, including BlockSolve95, ESSL, Matlab, ParMeTis,
PVODE, and SPAI, thereby providing additional solvers and
- interfaces.
+ interaction with other software packages.
</para>
<para>
@@ -111,7 +101,7 @@
and other data structures for most parallel operations,
eliminating the need for explicit calls to Message Passing
Interface (MPI) routines. Many settings and options can be
- controlled with PETSc specific command line arguments,
+ controlled with PETSc specific command-line arguments,
including selection of preconditions, solvers, and generation
of performance logs.
</para>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/makefile
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/makefile 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/makefile 2006-06-22 04:12:00 UTC (rev 3847)
@@ -1,5 +1,5 @@
-XSLSTYLESHEET_DIR=/usr/share/sgml/docbook/xsl-stylesheets
-#XSLSTYLESHEET_DIR=/sw/share/xml/xsl/docbook-xsl
+#XSLSTYLESHEET_DIR=/usr/share/sgml/docbook/xsl-stylesheets
+XSLSTYLESHEET_DIR=/sw/share/xml/xsl/docbook-xsl
pylith_userguide.pdf pdf: pylith_userguide.fo
fop $< pylith_userguide.pdf
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.xml 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.xml 2006-06-22 04:12:00 UTC (rev 3847)
@@ -34,7 +34,7 @@
<para>
PyLith gets its input from a variety of files. Most of these are
associated with different kinds of boundary conditions. As a
- result only six are required. The remaining files are only used
+ result only six files are required. The remaining files are only used
when the associated boundary condition is used. See <xref
linkend="appendix_fileformats" /> for a detailed discussion of
the file formats.
@@ -45,17 +45,17 @@
the entire mesh and then writes out processor specific pieces
with one file for each processor. The filenames for these follow
the convention <filename>xx.PROC.ext</filename> where
- <filename>PROC</filename> refers to the processor number and the
- original filename was <filename>xx.ext</filename>. This
+ <filename>PROC</filename> refers to the processor number and
+ <filename>xx.ext</filename> was the original filename. This
procedure is applied to files with the following extensions:
<filename>coord</filename>, <filename>connect</filename>,
- <filename>split</filename>, <filename>bc</filename>.
+ <filename>split</filename>, and <filename>bc</filename>.
</para>
<para>
- The other files provide information common to all processors. As
- a result, the user must create copies of each one for each of
- the processors with filenames. By default PyLith expects the
- names of these files to follow the same form
+ The remaining files provide information common to all
+ processors. As a result, the user must create copies of each one
+ for each of the processors. By default PyLith expects the names
+ of these files to follow the same form,
<filename>xx.PROC.ext</filename>. Setting up this naming scheme
is most easily done using symbolic links or copying files to
local directories on each machine using a shell script that
@@ -87,7 +87,7 @@
<term><filename>xx.connect</filename></term>
<listitem>
<para>
- Topology of finite-element mesh.
+ Topology and material information for the finite-element mesh.
</para>
</listitem>
</varlistentry>
@@ -95,7 +95,7 @@
<term><filename>xx.bc</filename></term>
<listitem>
<para>
- Boundary conditions at nodes on external boundaries.
+ Boundary conditions at vertices on external boundaries.
</para>
</listitem>
</varlistentry>
@@ -131,10 +131,10 @@
<section>
<title>Optional Input Files</title>
<para>
- The optional input files are only read when they exist in the
- directory containing the rest of the input files. Explicit
- filenames (with alternate locations) can be specified using
- command-line arguments as discussed in <xref
+ The optional input files are only read when a file exists
+ matching the name of an input file PyLith expects to reaad.
+ Note that explicit filenames for each of the files can be
+ specified using command-line arguments as discussed in <xref
linkend="section_commandline_arguments" />.
</para>
<variablelist>
@@ -177,8 +177,8 @@
<term><filename>xx.wink</filename></term>
<listitem>
<para>
- Winkler sprint element boundary condition
- information. <emphasis>Not yest tested.</emphasis>
+ Winkler spring element boundary condition
+ information. <emphasis>Not yet tested.</emphasis>
</para>
</listitem>
</varlistentry>
@@ -186,8 +186,9 @@
<term><filename>xx.hist</filename></term>
<listitem>
<para>
- Time history split node and Winkler boundary
- conditions. <emphasis>Not yest tested.</emphasis>
+ Time histories for split node and Winkler boundary
+ conditions (if necessary). <emphasis>Not yet
+ tested.</emphasis>
</para>
</listitem>
</varlistentry>
@@ -199,12 +200,26 @@
<!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
<section id="section_commandline_arguments">
<title>Command-line Arguments</title>
+
<para>
- Command-line arguments associated with running PyLith fall into
- three categories: MPI settings, Pyre properties and facilities,
- and PETSc settings.
+ In general, PyLith's command-line arguments fall into three
+ categories: MPI settings, Pyre properties and facilities, and
+ PETSc settings.
</para>
+ <para>
+ If using the MPICH implementation of the Message Passing
+ Interface (MPI), as is done for the CIG distributed binaries,
+ the synopsis for running PyLith is:
+ </para>
+ <cmdsynopsis>
+ <command>mpirun</command>
+ <arg choice="req">-np <replaceable>NPROCS</replaceable></arg>
+ pylith3dapp.py
+ <arg choice="opt"><replaceable>PyLith settings</replaceable></arg>
+ <arg choice="opt"><replaceable>PETSc settings</replaceable></arg>
+ </cmdsynopsis>
+
<!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->
<section>
<title>MPI Settings</title>
@@ -243,9 +258,9 @@
</para>
<para>
In the current version of PyLith, all of the properties are
- associated with the "scanner" component. You can get a list of
- all of these properties along with a description of what they
- do by running PyLith with the
+ associated with the <literal>scanner</literal> component. You
+ can get a list of all of these properties along with a
+ description of what they do by running PyLith with the
<option>--scanner.help-properties</option> command-line
argument.
</para>
@@ -257,9 +272,9 @@
<command>mpirun</command>
<arg choice="plain">-np <replaceable>1</replaceable></arg>
<arg choice="plain">pylith3dapp.py</arg>
- <arg>--scanner.help-properties</arg><sbr/>
- <arg>--scanner.asciiOutput=<replaceable>none</replaceable></arg>
- <arg>--scanner.title=<replaceable>"My simulation"</replaceable></arg>
+ <arg choice="plain">--scanner.help-properties</arg><sbr/>
+ <arg choice="plain">--scanner.asciiOutput=<replaceable>none</replaceable></arg>
+ <arg choice="plain">--scanner.title=<replaceable>"My simulation"</replaceable></arg>
</cmdsynopsis>
</screen>
</example>
@@ -304,9 +319,13 @@
</row>
<row>
<entry><cmdsynopsis>
- <arg choice="plain">-ksp_monitor</arg>
+ <arg choice="plain">-ksp_monitor <replaceable>stdout</replaceable></arg>
</cmdsynopsis></entry>
- <entry>Dump preconditioned residual norm to stdout.</entry>
+ <entry>
+ Dump preconditioned residual norm to stdout. If only
+ <option>-ksp_monitor</option> is given, the default is
+ to use stdout.
+ </entry>
</row>
<row>
<entry><cmdsynopsis>
@@ -319,7 +338,7 @@
<arg choice="plain">-ksp_rtol
<replaceable>1.0e-09</replaceable></arg>
</cmdsynopsis></entry>
- <entry>Relative decrease in residual norm</entry>
+ <entry>Tolerance for relative decrease in residual norm</entry>
</row>
</tbody>
</tgroup>
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/figs/geometry.eps
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/figs/geometry.eps 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/figs/geometry.eps 2006-06-22 04:12:00 UTC (rev 3847)
@@ -1,8 +1,8 @@
%!PS-Adobe-2.0 EPSF-2.0
%%Title: geometry.fig
%%Creator: fig2dev Version 3.2 Patchlevel 4
-%%CreationDate: Wed Jun 21 08:15:43 2006
-%%For: brad at arling (Brad Aagaard)
+%%CreationDate: Wed Jun 21 20:08:00 2006
+%%For: brad at Brads-Computer.local (Brad Aagaard)
%%BoundingBox: 0 0 270 277
%%Magnification: 1.0000
%%EndComments
@@ -246,8 +246,11 @@
% here ends figure;
%
% here starts figure with depth 50
-% Arc
+% Polyline
7.500 slw
+n 4200 1950 m 2700 2625 l
+ 3900 5025 l gs col4 s gr
+% Arc
gs clippath
2956 3169 m 2997 3213 l 3082 3131 l 2997 3172 l 3041 3088 l cp
3152 2867 m 3092 2864 l 3088 2981 l 3122 2893 l 3148 2984 l cp
@@ -270,10 +273,6 @@
% Polyline
n 2400 2400 m 2400 4800 l 4200 6000 l 4200 3600 l
cp gs col0 s gr
-% Polyline
-7.500 slw
-n 4200 1950 m 2700 2625 l
- 3900 5025 l gs col4 s gr
/Helvetica-iso ff 180.00 scf sf
3088 3221 m
gs 1 -1 sc (45\260) col1 sh gr
@@ -287,18 +286,12 @@
% here ends figure;
%
% here starts figure with depth 42
+/Helvetica-iso ff 180.00 scf sf
+2625 2550 m
+gs 1 -1 sc (x) col1 sh gr
% Polyline
7.500 slw
gs clippath
-2430 2010 m 2370 2010 l 2370 2127 l 2400 2037 l 2430 2127 l cp
-eoclip
-n 2400 2400 m
- 2400 2025 l gs col1 s gr gr
-
-% arrowhead
-n 2430 2127 m 2400 2037 l 2370 2127 l 2430 2127 l cp gs col1 1.00 shd ef gr col1 s
-% Polyline
-gs clippath
2620 2583 m 2654 2533 l 2556 2468 l 2615 2543 l 2523 2518 l cp
2726 2270 m 2700 2216 l 2595 2269 l 2689 2256 l 2621 2323 l cp
eoclip
@@ -309,21 +302,42 @@
n 2621 2323 m 2689 2256 l 2595 2269 l 2621 2323 l cp gs col1 1.00 shd ef gr col1 s
% arrowhead
n 2523 2518 m 2615 2543 l 2556 2468 l 2523 2518 l cp gs col1 1.00 shd ef gr col1 s
+% Polyline
+gs clippath
+2430 2010 m 2370 2010 l 2370 2127 l 2400 2037 l 2430 2127 l cp
+eoclip
+n 2400 2400 m
+ 2400 2025 l gs col1 s gr gr
+
+% arrowhead
+n 2430 2127 m 2400 2037 l 2370 2127 l 2430 2127 l cp gs col1 1.00 shd ef gr col1 s
/Helvetica-iso ff 180.00 scf sf
2400 1950 m
gs 1 -1 sc (z) col1 sh gr
/Helvetica-iso ff 180.00 scf sf
2625 2175 m
gs 1 -1 sc (y) col1 sh gr
-/Helvetica-iso ff 180.00 scf sf
-2625 2550 m
-gs 1 -1 sc (x) col1 sh gr
% here ends figure;
%
% here starts figure with depth 40
% Polyline
7.500 slw
gs clippath
+6403 5203 m 6374 5134 l 6237 5192 l 6363 5180 l 6267 5261 l cp
+4246 6046 m 4275 6115 l 4412 6057 l 4287 6070 l 4382 5988 l cp
+eoclip
+n 4275 6075 m
+ 6375 5175 l gs col1 s gr gr
+
+% arrowhead
+n 4382 5988 m 4287 6070 l 4412 6057 l 4382 5988 l cp gs col1 1.00 shd ef gr col1 s
+% arrowhead
+n 6267 5261 m 6363 5180 l 6237 5192 l 6267 5261 l cp gs col1 1.00 shd ef gr col1 s
+/Helvetica-iso ff 180.00 scf sf
+3975 5400 m
+gs 1 -1 sc 327.0 rot (4 km) dup sw pop 2 div neg 0 rm col1 sh gr
+% Polyline
+gs clippath
4194 5358 m 4230 5310 l 4109 5219 l 4187 5315 l 4073 5267 l cp
3906 5067 m 3870 5115 l 3991 5206 l 3913 5110 l 4027 5158 l cp
eoclip
@@ -334,6 +348,24 @@
n 4027 5158 m 3913 5110 l 3991 5206 l 4027 5158 l cp gs col1 1.00 shd ef gr col1 s
% arrowhead
n 4073 5267 m 4187 5315 l 4109 5219 l 4073 5267 l cp gs col1 1.00 shd ef gr col1 s
+/Helvetica-iso ff 180.00 scf sf
+2250 4200 m
+gs 1 -1 sc 90.0 rot (12 km) dup sw pop 2 div neg 0 rm col1 sh gr
+/Helvetica-iso ff 180.00 scf sf
+3600 2175 m
+gs 1 -1 sc 22.0 rot (16 km) dup sw pop 2 div neg 0 rm col1 sh gr
+/Helvetica-iso ff 180.00 scf sf
+5434 5798 m
+gs 1 -1 sc 22.0 rot (24 km) dup sw pop 2 div neg 0 rm col1 sh gr
+/Helvetica-iso ff 180.00 scf sf
+6600 3900 m
+gs 1 -1 sc 90.0 rot (24 km) dup sw pop 2 div neg 0 rm col1 sh gr
+/Helvetica-iso ff 180.00 scf sf
+4258 1851 m
+gs 1 -1 sc 327.0 rot (4 km) dup sw pop 2 div neg 0 rm col1 sh gr
+/Helvetica-iso ff 180.00 scf sf
+3000 5550 m
+gs 1 -1 sc 327.0 rot (24 km) dup sw pop 2 div neg 0 rm col1 sh gr
% Polyline
gs clippath
2333 4835 m 2291 4897 l 2415 4979 l 2336 4882 l 2456 4917 l cp
@@ -394,39 +426,6 @@
n 6337 4967 m 6375 5087 l 6412 4967 l 6337 4967 l cp gs col1 1.00 shd ef gr col1 s
% arrowhead
n 6412 2833 m 6375 2713 l 6337 2833 l 6412 2833 l cp gs col1 1.00 shd ef gr col1 s
-% Polyline
-gs clippath
-6403 5203 m 6374 5134 l 6237 5192 l 6363 5180 l 6267 5261 l cp
-4246 6046 m 4275 6115 l 4412 6057 l 4287 6070 l 4382 5988 l cp
-eoclip
-n 4275 6075 m
- 6375 5175 l gs col1 s gr gr
-
-% arrowhead
-n 4382 5988 m 4287 6070 l 4412 6057 l 4382 5988 l cp gs col1 1.00 shd ef gr col1 s
-% arrowhead
-n 6267 5261 m 6363 5180 l 6237 5192 l 6267 5261 l cp gs col1 1.00 shd ef gr col1 s
-/Helvetica-iso ff 180.00 scf sf
-3975 5400 m
-gs 1 -1 sc 327.0 rot (4 km) dup sw pop 2 div neg 0 rm col1 sh gr
-/Helvetica-iso ff 180.00 scf sf
-3000 5550 m
-gs 1 -1 sc 327.0 rot (24 km) dup sw pop 2 div neg 0 rm col1 sh gr
-/Helvetica-iso ff 180.00 scf sf
-2250 4200 m
-gs 1 -1 sc 90.0 rot (12 km) dup sw pop 2 div neg 0 rm col1 sh gr
-/Helvetica-iso ff 180.00 scf sf
-3600 2175 m
-gs 1 -1 sc 22.0 rot (20 km) dup sw pop 2 div neg 0 rm col1 sh gr
-/Helvetica-iso ff 180.00 scf sf
-5434 5798 m
-gs 1 -1 sc 22.0 rot (24 km) dup sw pop 2 div neg 0 rm col1 sh gr
-/Helvetica-iso ff 180.00 scf sf
-6600 3900 m
-gs 1 -1 sc 90.0 rot (24 km) dup sw pop 2 div neg 0 rm col1 sh gr
-/Helvetica-iso ff 180.00 scf sf
-4258 1851 m
-gs 1 -1 sc 327.0 rot (4 km) dup sw pop 2 div neg 0 rm col1 sh gr
% here ends figure;
$F2psEnd
rs
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/figs/geometry.fig
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/figs/geometry.fig 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/figs/geometry.fig 2006-06-22 04:12:00 UTC (rev 3847)
@@ -164,7 +164,7 @@
4 0 1 42 -1 16 12 0.0000 4 105 90 2400 1950 z\001
4 0 1 42 -1 16 12 0.0000 4 150 105 2625 2175 y\001
4 0 1 42 -1 16 12 0.0000 4 105 90 2625 2550 x\001
-4 1 1 40 -1 16 12 0.3840 4 135 495 3600 2175 20 km\001
+4 1 1 40 -1 16 12 0.3840 4 135 495 3600 2175 16 km\001
4 1 1 40 -1 16 12 0.3840 4 135 495 5434 5798 24 km\001
4 1 1 40 -1 16 12 1.5708 4 135 495 6600 3900 24 km\001
4 1 1 40 -1 16 12 5.7072 4 135 390 4258 1851 4 km\001
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/figs/geometry.png
===================================================================
(Binary files differ)
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 2006-06-22 00:30:01 UTC (rev 3846)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorialbm5/tutorialbm5.xml 2006-06-22 04:12:00 UTC (rev 3847)
@@ -40,13 +40,15 @@
linear taper to 0 at z = -16 km.
</para>
<para>
- The boundary conditions on the lateral and bottom edges of the
- mesh are the displacements from the analytical elastic
- solution. These displacements are held fixed through time.
+ The plane y=0 is a plane of symmetry, so the y-DOF
+ displacements on this face are zero. The boundary conditions
+ on the other lateral faces and bottom of the mesh are the
+ displacements from the analytical elastic solution. These
+ displacements are held fixed through time.
</para>
<figure id="figure_bm5_geometry">
- <title>Geometry of model domain for SCEC benchmark 5.</title>
+ <title>Geometry of model domain for SCEC Benchmark 5.</title>
<mediaobject>
<imageobject role="fo">
<imagedata fileref="figs/geometry.eps" format="EPS" />
@@ -95,6 +97,9 @@
tarball</ulink> and unpack it in a location of your
choosing.
</para>
+ <screen>
+<prompt>bash$ </prompt>tar -zxvf pylith-0.8_tutorials.tgz
+ </screen>
</listitem>
<listitem>
<para>
@@ -106,10 +111,15 @@
tutorial. We will copy input files from this directory into
the <filename class="directory">workarea</filename>
directory. At each step, you can check to make sure your
- input and output agree with these files. These files also
- allow you to start at an intermediate step as described in
- the next section.
+ input and output agree with the files in the <filename
+ class="directory">archive</filename> directory. These files
+ also allow you to start at an intermediate step as described
+ in the next section.
</para>
+ <screen>
+<prompt>bash$ </prompt>cd tutorials/scecbm5
+ </screen>
+
</listitem>
</orderedlist>
@@ -133,12 +143,13 @@
</para>
<tip>
<para>
- When retrieving files from the archive,
+ When retrieving files from the <filename
+ classname="directory">archive</filename> directory,
<command>tutor.sh</command> will not overwrite files that
- already exist in <filename
- class="directory">workarea</filename>. This means that if
- you mangle files in the working area, you should remove them
- and let the tutor retrieve clean copies.
+ already exist in the <filename
+ class="directory">workarea</filename> directory. This means
+ that if you mangle files in the working area, you should
+ remove them and let the tutor retrieve clean copies.
</para>
</tip>
<tip>
@@ -148,6 +159,11 @@
"all" to clear out all old tutorial files.
</para>
</tip>
+ <screen>
+<prompt>bash$ </prompt>cd workarea
+<prompt>bash$ </prompt>cp ../archive/tutor.sh .
+<prompt>bash$ </prompt>./tutor.sh clean all
+ </screen>
</section>
</section>
@@ -163,13 +179,17 @@
<orderedlist numeration="arabic">
<listitem>
<para>
- Return to the <filename class="directory">scecbm5/workarea</filename>
- directory. Run <command>tutor.sh</command> for step "mesh"
+ In the <filename class="directory">scecbm5/workarea</filename>
+ directory, run <command>tutor.sh</command> for step "mesh"
with mode "retrieve" to fetch the geometry file for
<application>NetGen</application>. You may also want to run
<command>tutor.sh</command> for this step with mode "clean"
to clean out old files.
</para>
+ <screen>
+<prompt>bash$ </prompt>./tutor.sh retrieve mesh
+<prompt>bash$ </prompt>./tutor.sh clean mesh
+ </screen>
</listitem>
<listitem>
<para>
@@ -185,6 +205,9 @@
Start up <application>NetGen</application> by running
<command>ng</command>.
</para>
+ <screen>
+<prompt>bash$ </prompt>ng
+ </screen>
</listitem>
<listitem>
<para>
@@ -227,6 +250,9 @@
Run <command>tutor.sh</command> for step "setup" with mode
"retrieve" to fetch files from the archive.
</para>
+ <screen>
+<prompt>bash$ </prompt>./tutor.sh retrieve setup
+ </screen>
</listitem>
<listitem>
<para>
@@ -242,6 +268,9 @@
to the <filename class="directory">utils</filename>
sub-directory.
</para>
+ <screen>
+<prompt>bash$ </prompt>cd ../../utils
+ </screen>
</listitem>
<listitem>
<para>
@@ -276,14 +305,18 @@
</listitem>
</varlistentry>
</variablelist>
- </listitem>
- <listitem>
+ <screen>
+<prompt>bash$ </prompt>make
+ </screen>
+ <tip>
<para>
- Once you have built these utilities, move them to a
- location in your <envar>PATH</envar> or update your
- <envar>PATH</envar> to include the
- <filename class="directory">utils</filename> directory.
+ If you plan to use <application>NetGen</application> to
+ generate meshes, you may want to copy these utilities to
+ a location in your <envar>PATH</envar> or update your
+ <envar>PATH</envar> to include the <filename
+ class="directory">utils</filename> directory.
</para>
+ </tip>
</listitem>
</orderedlist>
</listitem>
@@ -301,6 +334,12 @@
<filename>bm5.1.fcoord</filename>,
<filename>bm5.1.fbc</filename>.
</para>
+ <screen>
+<prompt>bash$ </prompt>../../utils/readnetgen
+<prompt>ADD CORRECT PROMPT HERE</prompt>
+<prompt></prompt>
+<prompt></prompt>bm5
+ </screen>
</listitem>
<listitem>
<para>
@@ -314,12 +353,14 @@
in <filename>bm5.1.fbc</filename> and nodal coordinates in
<filename>bm5.coord</filename>. The file
<filename>bm5-fault.par</filename> contains the polynomial
- coefficients for this benchmark problem. Execute the command
- <userinput>faultcalc p=bm5-fault.par n=bm5.coord i=bm5.1.fbc
- o=bm5.split</userinput>. This will give you the
+ coefficients for this benchmark problem. Run
+ <command>faultcalc</command>to get the
<filename>bm5.split</filename> file that PyLith needs as
input.
</para>
+ <screen>
+<prompt>bash$ </prompt>../../utils/faultcalc p=bm5-fault.par n=bm5.coord i=bm5.1.fbc o=bm5.split
+ </screen>
</listitem>
<listitem>
<para>
@@ -361,10 +402,13 @@
Run <command>tutor.sh</command> for step "run1" with mode
"retrieve" to fetch some parameter files from the archive.
</para>
+ <screen>
+<prompt>bash$ </prompt>./tutor.sh retrieve run1
+ </screen>
</listitem>
<listitem>
<para>
- In the <filename>bm5.fuldat</filename>, we have specified
+ In <filename>bm5.fuldat</filename>, we have specified
that we want full output at time steps 10, 50, and 100. We
define six materials with both elastic and viscoelastic
behavior in <filename>bm5.prop</filename>. In
@@ -395,6 +439,9 @@
<option>--scanner.asciiOutput=full</option>.
</para>
</tip>
+ <screen>
+<prompt>bash$ </prompt>./runbm5.sh 1
+ </screen>
</listitem>
</orderedlist>
</section>
@@ -421,6 +468,9 @@
"viz1" with mode "retrieve" to fetch the simulation output
from the archive.
</para>
+ <screen>
+<prompt>bash$ </prompt>./tutor.sh retrieve viz1
+ </screen>
</listitem>
<listitem>
<para>
@@ -432,16 +482,20 @@
(<filename>bm5_1.0.mesh.inp</filename>) and the nodal
displacements at time step 10 file
(<filename>bm5_1.0.mesh.time.00010.inp</filename>) into
- <filename>bm5_1.0.mesh.t00010.inp</filename>, <userinput>cat
- bm5_1.0.mesh.inp bm5_1.0.mesh.time.00010.inp >
- bm5_1.0.mesh.t00010.inp</userinput>.
+ <filename>bm5_1.0.mesh.t00010.inp</filename>.
</para>
+ <screen>
+<prompt>bash$ </prompt>cat bm5_1.0.mesh.inp bm5_1.0.mesh.time.00010.inp > bm5_1.0.mesh.t00010.inp
+ </screen>
</listitem>
<listitem>
<para>
Start <application>ParaView</application> by executing
<command>paraview</command>.
</para>
+ <screen>
+<prompt>bash$ </prompt>paraview
+ </screen>
</listitem>
<listitem>
<para>
@@ -503,6 +557,9 @@
Run <command>tutor.sh</command> for step "run2" with mode
"retrieve" to make sure all parameter files are available.
</para>
+ <screen>
+<prompt>bash$ </prompt>./tutor.sh retrieve run2
+ </screen>
</listitem>
<listitem>
<para>
@@ -517,6 +574,9 @@
Run the simulation by executing <command>runbm5.sh
2</command>, where the 2 refers to the number of processors.
</para>
+ <screen>
+<prompt>bash$ </prompt>./runbm5.sh 2
+ </screen>
</listitem>
</orderedlist>
</section>
@@ -527,9 +587,9 @@
<para>
PyLith does not currently support parallel output, so each
- PyLith processor writes its <acronym>UCD</acronym> output to a
+ processor writes its <acronym>UCD</acronym> output to a
different file. This means that you need to form complete
- <acronym>UCD</acronym> files for each processor and then load in
+ <acronym>UCD</acronym> files for each processor and then load
each one into <application>ParaView</application>.
</para>
@@ -540,29 +600,33 @@
"viz2" with mode "retrieve" to fetch the simulation output
from the archive.
</para>
+ <screen>
+<prompt>bash$ </prompt>./tutor.sh retrieve viz2
+ </screen>
</listitem>
<listitem>
<para>
As in the case of the single processor run, the first step
is to combine the mesh topology information with the output
at a given time step into a complete <acronym>UCD</acronym>
- file. For example, use <command>cat</command> to merge the
- nodal coordinates file
- (<filename>bm5_1.0.mesh.inp</filename>) and the nodal
- displacements at time step 10 file
- (<filename>bm5_1.0.mesh.time.00010.inp</filename>) into
- <filename>bm5_1.0.mesh.t00010.inp</filename>, <userinput>cat
- bm5_1.0.mesh.inp bm5_1.0.mesh.time.00010.inp >
- bm5_1.0.mesh.t00010.inp</userinput>. Repeat this for processor
- 1, <userinput>cat bm5_1.1.mesh.inp bm5_1.1.mesh.time.00010.inp
- > bm5_1.1.mesh.t00010.inp</userinput>.
+ file. Because PyLith writes the output from each processor
+ into a different file, we must run <command>cat</command>
+ twice to create <acronym>UCD</acronym> files for each
+ processor.
</para>
+ <screen>
+<prompt>bash$ </prompt>cat bm5_1.0.mesh.inp bm5_1.0.mesh.time.00010.inp > bm5_1.0.mesh.t00010.inp
+<prompt>bash$ </prompt>cat bm5_1.1.mesh.inp bm5_1.1.mesh.time.00010.inp > bm5_1.1.mesh.t00010.inp
+ </screen>
</listitem>
<listitem>
<para>
Start <application>ParaView</application> by executing
<command>paraview</command>.
</para>
+ <screen>
+<prompt>bash$ </prompt>paraview
+ </screen>
</listitem>
<listitem>
<para>
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