[cig-commits] r6657 - in
short/3D/PyLith/branches/pylith-0.8/doc/userguide: . intro
materials runpylith tutorials
sue at geodynamics.org
sue at geodynamics.org
Tue Apr 24 13:16:06 PDT 2007
Author: sue
Date: 2007-04-24 13:16:06 -0700 (Tue, 24 Apr 2007)
New Revision: 6657
Modified:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/license.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/preface.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorials.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.lyx
Log:
various edits, incl. resized table in Materials and changed quotes to match other manuals
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.lyx 2007-04-24 19:55:01 UTC (rev 6656)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.lyx 2007-04-24 20:16:06 UTC (rev 6657)
@@ -1,4 +1,4 @@
-#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -68,9 +68,12 @@
This release of PyLith offers both tetrahedral and hexahedral linear elements,
the use of traction boundary conditions, load histories for split nodes,
a number of new material models, including power-law Maxwell and generalized
- Maxwell (3 Maxwell models in parallel), the use of .cfg files for setting
- simulation parameters, much simpler top-level code structure, and several
- bug fixes.
+ Maxwell (3 Maxwell models in parallel), the use of
+\family typewriter
+.cfg
+\family default
+ files for setting simulation parameters, much simpler top-level code structure,
+ and several bug fixes.
\end_layout
\begin_layout Standard
@@ -78,7 +81,7 @@
powerful simulation package.
This new code will include earthquake dynamics (both rupture propagation
and seismic wave propagation).
- A beta release is expected in early 2007.
+ A beta release is expected in Spring 2007.
\end_layout
\begin_layout Section
@@ -92,7 +95,7 @@
only formulation available at present.
If a large deformation solution is desired, interested users may contact
-\begin_inset LatexCommand \htmlurl[Charles Williams]{willic3 at rpi.edu}
+\begin_inset LatexCommand \url[Charles Williams]{willic3 at rpi.edu}
\end_inset
@@ -181,7 +184,7 @@
\begin_inset Formula $f_{i}^{S_{f}}$
\end_inset
-are the components of the surface tractions, and the
+ are the components of the surface tractions, and the
\begin_inset Formula $u_{i}^{S_{u}}$
\end_inset
@@ -241,7 +244,7 @@
In our actual computations, we use several different formulations, depending
on the constitutive relation.
One such formulation decomposes the stresses into the deviatoric and volumetric
- parts, using ideas based on the "effective stress function"
+ parts, using ideas based on the ``effective stress function''
\begin_inset LatexCommand \cite{Kojic:Bathe:1987}
\end_inset
@@ -249,7 +252,8 @@
.
This allows the time integration of stresses to be performed in terms of
a single parameter related to the second deviatoric stress invariant.
- We also use viscoelastic formulations based on those of
+ We also use viscoelastic formulations based on those of Zienkiewicz and
+ Taylor
\begin_inset LatexCommand \cite{Zienkiewicz:Taylor:2000}
\end_inset
@@ -341,9 +345,9 @@
Sieve
\family default
also provides a number of other useful features, such as the ability to
- grab 'sections' of a mesh that share common characteristics, such as elements
- of the same material type or nodes to which boundary conditions have been
- applied.
+ grab ``sections'' of a mesh that share common characteristics, such as
+ elements of the same material type or nodes to which boundary conditions
+ have been applied.
\end_layout
\begin_layout Subsection
@@ -372,8 +376,8 @@
et al
\shape default
.
- condense the concept of a framework concept down to, "When you use a framework,
- you reuse the main body and write the code it calls." In the context of
+ condense the concept of a framework concept down to, ``When you use a framework
+, you reuse the main body and write the code it calls.'' In the context of
frameworks and object-oriented programming, Pyre can be thought of as a
collection of classes and the way their instances interact.
Programming applications based on Pyre will look similar to those written
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/license.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/license.lyx 2007-04-24 19:55:01 UTC (rev 6656)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/license.lyx 2007-04-24 20:16:06 UTC (rev 6657)
@@ -1,4 +1,4 @@
-#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -46,7 +46,7 @@
\begin_layout Standard
Permission is hereby granted, free of charge, to any person obtaining a
- copy of this software and associated documentation files (the "Software"),
+ copy of this software and associated documentation files (the ``Software''),
to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the Software
@@ -59,7 +59,7 @@
\end_layout
\begin_layout Standard
-THE SOFTWARE IS PROVIDED "AS IS," WITHOUT WARRANTY OF ANY KIND, EXPRESS
+THE SOFTWARE IS PROVIDED ``AS IS,'' WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.lyx 2007-04-24 19:55:01 UTC (rev 6656)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.lyx 2007-04-24 20:16:06 UTC (rev 6657)
@@ -1,4 +1,4 @@
-#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -45,16 +45,29 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float table
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\noindent
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="7" columns="2">
<features>
-<column alignment="center" valignment="top" leftline="true" width="0">
-<column alignment="center" valignment="top" leftline="true" rightline="true" width="0">
+<column alignment="left" valignment="top" leftline="true" width="0">
+<column alignment="center" valignment="top" leftline="true" rightline="true" width="3.5in">
<row topline="true" bottomline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Standard
+
+\series bold
Model Name
\end_layout
@@ -64,6 +77,8 @@
\begin_inset Text
\begin_layout Standard
+
+\series bold
Description
\end_layout
@@ -199,6 +214,15 @@
\end_layout
+\begin_layout Caption
+Material models available in PyLith.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
Note that there are two formulations for two of the material models (linear
and power-law Maxwell viscoelastic).
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/preface.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/preface.lyx 2007-04-24 19:55:01 UTC (rev 6656)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/preface.lyx 2007-04-24 20:16:06 UTC (rev 6657)
@@ -1,4 +1,4 @@
-#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -81,12 +81,34 @@
acknowledgements in talks and publications.
At this time there are no refereed journal articles discussing the design
and implementation of PyLith, so we request that you cite two AGU meeting
- abstracts associated with PyLith,
-\begin_inset LatexCommand \cite{Williams:etal:2005,Williams:2006}
+ abstracts associated with PyLith:
+\end_layout
-\end_inset
+\begin_layout Itemize
+Williams, C.A., B.
+ Aagaard, M.G.
+ Knepley (2005), Development of software for studying earthquakes across
+ multiple spatial and temporal scales by coupling quasi-static and dynamic
+ simulations,
+\emph on
+Eos Trans.
+ AGU
+\emph default
+, 86(52), Fall Meet.
+ Suppl., Abstract S53A-1072.
+\end_layout
-.
+\begin_layout Itemize
+Williams, C.A.
+ (2006), Development of a package for modeling stress in the lithosphere,
+
+\emph on
+Eos Trans.
+ AGU
+\emph default
+, 87(36), Jt.
+ Assem.
+ Suppl., Abstract T24A-01 Invited.
\end_layout
\begin_layout Section
@@ -117,7 +139,7 @@
\begin_layout Standard
Your suggestions and corrections can only improve this documentation.
Please report any errors, inaccuracies, or typos to
-\begin_inset LatexCommand \htmlurl[Sue Kientz]{sue at geodynamics.org}
+\begin_inset LatexCommand \url[Sue Kientz]{sue at geodynamics.org}
\end_inset
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx 2007-04-24 19:55:01 UTC (rev 6656)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx 2007-04-24 20:16:06 UTC (rev 6657)
@@ -1,4 +1,4 @@
-#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -152,9 +152,9 @@
\begin_layout Standard
The first step in the simulation process involves partitioning the mesh
among the processors.
- In this phase, PyLith reads in the entire mesh and then writes out processor
- specific pieces with one file for each processor.
- The filenames for these follow the convention
+ In this phase, PyLith reads in the entire mesh and then writes out processor-sp
+ecific pieces with one file for each processor.
+ The file names for these follow the convention
\family typewriter
xx.PROC.ext
\family default
@@ -166,7 +166,7 @@
\family typewriter
xx.ext
\family default
- is the original filename.
+ is the original file name.
This procedure is applied to files with the following extensions:
\family typewriter
coord, connect, split, bc
@@ -183,8 +183,8 @@
\begin_layout Standard
In some cases, a user may want to run the same simulation using different
numbers of processors.
- In this case, users may wish to provide distinctive sets of filenames to
- distinguish between the different runs.
+ In this case, users may wish to provide distinctive sets of file names
+ to distinguish between the different runs.
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 starts a simulation.
@@ -192,16 +192,16 @@
\family typewriter
mklinks.py
\family default
- in section\InsetSpace ~
+ in Section\InsetSpace ~
\begin_inset LatexCommand \ref{sec:Tutorial-Using-Reverse-Slip}
\end_inset
for a simple example.
- You can also choose your own filename template by setting the appropriate
+ You can also choose your own file-name template by setting the appropriate
parameters.
- See section\InsetSpace ~
+ See Section\InsetSpace ~
\begin_inset LatexCommand \ref{sec:setting:parameters}
@@ -281,7 +281,7 @@
\begin_layout Standard
The optional input files are only read when a file exists matching the name
of an input file PyLith expects to read.
- Note that explicit filenames for each of the files can be specified using
+ Note that explicit file names for each of the files can be specified using
command-line arguments, with
\family typewriter
.cfg
@@ -290,7 +290,7 @@
\family typewriter
.pml
\family default
- files, as discussed in section\InsetSpace ~
+ files, as discussed in Section\InsetSpace ~
\begin_inset LatexCommand \ref{sec:setting:parameters}
@@ -341,7 +341,7 @@
Local coordinate rotation information for boundary conditions.
\shape italic
-\color inherit
+\color default
Not yet implemented.
\end_layout
@@ -355,9 +355,13 @@
File for changing default parameters.
\shape italic
-\color inherit
+\color default
Now considered obsolete.
- Use .cfg file instead.
+ Use
+\family typewriter
+.cfg
+\family default
+ file instead.
\end_layout
\begin_layout Description
@@ -405,9 +409,12 @@
\end_layout
\begin_layout Standard
-There are several methods for setting input parameters for pylith3dapp.py:
- via the command line, or by using a configuration file in
+There are several methods for setting input parameters for
\family typewriter
+pylith3dapp.py
+\family default
+: via the command line, or by using a configuration file in
+\family typewriter
.cfg
\family default
or
@@ -490,14 +497,16 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
placement H
wide false
sideways false
status open
-\begin_layout Standard
-\align left
+\begin_layout Quote
+\noindent
\family typewriter
\color black
@@ -706,14 +715,14 @@
(1) overrides only the built-in defaults.
\end_layout
-\begin_layout Standard
+\begin_layout Subsection
PETSc Settings
\end_layout
\begin_layout Standard
PyLith relies on PETSc for the linear algebra computations.
Many PETSc options can be set using command-line arguments.
- The ones of primary interest in the case of PyLith are shown in table\InsetSpace ~
+ The ones of primary interest in the case of PyLith are shown in Table\InsetSpace ~
\begin_inset LatexCommand \ref{tab:Useful-command-line-arguments}
@@ -734,9 +743,9 @@
\begin_inset Tabular
<lyxtabular version="3" rows="7" columns="2">
<features>
-<column alignment="left" valignment="top" width="1.75in">
-<column alignment="left" valignment="top" width="4in">
-<row>
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="4in">
+<row topline="true" bottomline="true">
<cell alignment="left" valignment="top" usebox="none">
\begin_inset Text
@@ -760,7 +769,7 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row topline="true" bottomline="true">
<cell alignment="left" valignment="top" topline="true" usebox="none">
\begin_inset Text
@@ -783,7 +792,7 @@
\end_inset
</cell>
</row>
-<row>
+<row bottomline="true">
<cell alignment="left" valignment="top" usebox="none">
\begin_inset Text
@@ -810,7 +819,7 @@
\end_inset
</cell>
</row>
-<row>
+<row bottomline="true">
<cell alignment="left" valignment="top" usebox="none">
\begin_inset Text
@@ -839,7 +848,7 @@
\end_inset
</cell>
</row>
-<row>
+<row bottomline="true">
<cell alignment="left" valignment="top" usebox="none">
\begin_inset Text
@@ -874,7 +883,7 @@
\end_inset
</cell>
</row>
-<row>
+<row bottomline="true">
<cell alignment="left" valignment="top" usebox="none">
\begin_inset Text
@@ -898,7 +907,7 @@
\end_inset
</cell>
</row>
-<row>
+<row bottomline="true">
<cell alignment="left" valignment="top" usebox="none">
\begin_inset Text
@@ -946,14 +955,18 @@
\end_layout
\begin_layout Section
-Setting Pyre properties using pml files
+Setting Pyre properties using
+\family typewriter
+.pml
+\family default
+ files
\end_layout
\begin_layout Standard
PyLith's Pyre properties can also be set using
\family typewriter
\color black
-pml
+.pml
\family default
\color none
files.
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorials.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorials.lyx 2007-04-24 19:55:01 UTC (rev 6656)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorials.lyx 2007-04-24 20:16:06 UTC (rev 6657)
@@ -55,7 +55,7 @@
\begin_layout Standard
Before you begin any of the tutorials, you will need to install PyLith following
- the instructions in chapter\InsetSpace ~
+ the instructions in Chapter\InsetSpace ~
\begin_inset LatexCommand \ref{cha:Installation-and-Getting}
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.lyx 2007-04-24 19:55:01 UTC (rev 6656)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.lyx 2007-04-24 20:16:06 UTC (rev 6657)
@@ -1,4 +1,4 @@
-#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -207,25 +207,30 @@
\begin_layout Bibliography
\bibitem {Williams:etal:2005}
-Williams, C.
- A., B.
- Aagaard, M.
- G.
+Williams, C.A., B.
+ Aagaard, M.G.
Knepley (2005), Development of software for studying earthquakes across
multiple spatial and temporal scales by coupling quasi-static and dynamic
- simulations, Eos Trans.
- AGU, 86 (52), Fall Meet.
+ simulations,
+\emph on
+Eos Trans.
+ AGU
+\emph default
+, 86(52), Fall Meet.
Suppl., Abstract S53A-1072.
\end_layout
\begin_layout Bibliography
\bibitem {Williams:2006}
-Williams, C.
- A.
+Williams, C.A.
(2006), Development of a package for modeling stress in the lithosphere,
- Eos Trans.
- AGU, 87(36), Jt.
+
+\emph on
+Eos Trans.
+ AGU,
+\emph default
+ 87(36), Jt.
Assem.
Suppl., Abstract T24A-01 Invited.
\end_layout
@@ -250,10 +255,8 @@
\begin_layout Bibliography
\bibitem [4]{Zienkiewicz:Taylor:2000}
-Zienkiewicz, O.
- C.
- and R.
- L.
+Zienkiewicz, O.C.
+ and R.L.
Taylor (2000),
\shape italic
The Finite Element Method, Fifth Edition, Volume 2: Solid Mechanics
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