[cig-commits] r11264 - in short/3D/PyLith/trunk: . doc/userguide doc/userguide/install doc/userguide/intro doc/userguide/runpylith doc/userguide/tutorials doc/userguide/tutorials/twotri3
brad at geodynamics.org
brad at geodynamics.org
Tue Feb 26 21:42:49 PST 2008
Author: brad
Date: 2008-02-26 21:42:49 -0800 (Tue, 26 Feb 2008)
New Revision: 11264
Modified:
short/3D/PyLith/trunk/TODO
short/3D/PyLith/trunk/doc/userguide/install/install.lyx
short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
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:
Added more comments on where we need to update manual.
Modified: short/3D/PyLith/trunk/TODO
===================================================================
--- short/3D/PyLith/trunk/TODO 2008-02-27 02:52:26 UTC (rev 11263)
+++ short/3D/PyLith/trunk/TODO 2008-02-27 05:42:49 UTC (rev 11264)
@@ -65,6 +65,11 @@
5. Install cases
+ 3 kinds of spatial databases
+ UniformDB
+ SimpleDB
+ SCECCVMHDB
+
Release 1.2
1. Dynamic fault interface conditions.
Modified: short/3D/PyLith/trunk/doc/userguide/install/install.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/install/install.lyx 2008-02-27 02:52:26 UTC (rev 11263)
+++ short/3D/PyLith/trunk/doc/userguide/install/install.lyx 2008-02-27 05:42:49 UTC (rev 11264)
@@ -1,5 +1,5 @@
-#LyX 1.4.3-5 created this file. For more info see http://www.lyx.org/
-\lyxformat 245
+#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 276
\begin_document
\begin_header
\textclass book
@@ -8,13 +8,21 @@
\end_preamble
\language english
\inputencoding latin1
-\fontscheme default
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
\graphics default
\paperfontsize default
\spacing single
\papersize default
\use_geometry true
\use_amsmath 1
+\use_esint 0
\cite_engine basic
\use_bibtopic false
\paperorientation portrait
@@ -32,12 +40,14 @@
\paperpagestyle default
\tracking_changes false
\output_changes false
+\author ""
\end_header
\begin_body
\begin_layout Chapter
-\begin_inset LatexCommand \label{cha:Installation-and-Getting}
+\begin_inset LatexCommand label
+name "cha:Installation-and-Getting"
\end_inset
@@ -62,14 +72,18 @@
\begin_layout Standard
The
-\begin_inset LatexCommand \url[CIG Short-Term Crustal Dynamics Mailing List]{cig-short at geodynamics.org}
+\begin_inset LatexCommand url
+name "CIG Short-Term Crustal Dynamics Mailing List"
+target "cig-short at geodynamics.org"
\end_inset
is dedicated to CIG issues associated with short-term crustal dynamics,
including the use of PyLith.
You can subscribe to the mailing list and view messages at
-\begin_inset LatexCommand \htmlurl[cig-short Mailing List]{geodynamics.org/cig/lists/cig-short}
+\begin_inset LatexCommand htmlurl
+name "cig-short Mailing List"
+target "geodynamics.org/cig/lists/cig-short"
\end_inset
@@ -84,7 +98,9 @@
\family default
for bug tracking.
If you find a bug in PyLith, please submit a bug report to the
-\begin_inset LatexCommand \htmlurl[CIG Roundup System]{geodynamics.org/roundup/}
+\begin_inset LatexCommand htmlurl
+name "CIG Roundup System"
+target "geodynamics.org/roundup/"
\end_inset
@@ -109,9 +125,11 @@
\end_layout
\begin_layout Standard
-Binary executables are available for Linux, Mac OS X (Power PC), and Windows
- from the
-\begin_inset LatexCommand \htmlurl[CIG website]{geodynamics.org/cig/software/packages/short/pylith/}
+Binary executables are available for Linux, Mac OS X (Power PC and Intel),
+ and Windows from the
+\begin_inset LatexCommand htmlurl
+name "CIG website"
+target "geodynamics.org/cig/software/packages/short/pylith/"
\end_inset
@@ -141,7 +159,9 @@
\begin_layout Itemize
Download the
-\begin_inset LatexCommand \htmlurl[Linux tarball]{geodynamics.org/cig/software/packages/short/pylith/}
+\begin_inset LatexCommand htmlurl
+name "Linux tarball"
+target "geodynamics.org/cig/software/packages/short/pylith/"
\end_inset
@@ -157,7 +177,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar -xzf pylith-1.0.0-linux-i686.tar.gz
+$ tar -xzf pylith-1.1.0-linux-i686.tar.gz
\end_layout
\begin_layout Itemize
@@ -165,9 +185,13 @@
\end_layout
\begin_layout LyX-Code
-$ PATH=${PATH}:${HOME}/pylith/pylith-1.0.0-linux-i686/bin
+$ PATH=${PATH}:${HOME}/pylith/pylith-1.1.0-linux-i686/bin
\end_layout
+\begin_layout LyX-Code
+ADD setup.sh for Linux
+\end_layout
+
\begin_layout Subsection
Mac OS X
\end_layout
@@ -191,7 +215,9 @@
\begin_layout Itemize
Download the
-\begin_inset LatexCommand \htmlurl[Darwin tarball]{geodynamics.org/cig/software/packages/short/pylith/}
+\begin_inset LatexCommand htmlurl
+name "Darwin tarball"
+target "geodynamics.org/cig/software/packages/short/pylith/"
\end_inset
@@ -204,10 +230,11 @@
\begin_layout Itemize
Unpack the tarball.
+ For the PowerPC architecture,
\end_layout
\begin_layout LyX-Code
-$ tar -xzf pylith-1.0.0-darwin-powerpc.tar.gz
+$ tar -xzf pylith-1.1.0-darwin-powerpc.tar.gz
\end_layout
\begin_layout Itemize
@@ -224,7 +251,9 @@
\begin_layout Itemize
Download the
-\begin_inset LatexCommand \htmlurl[Windows installer]{geodynamics.org/cig/software/packages/short/pylith/}
+\begin_inset LatexCommand htmlurl
+name "Windows installer"
+target "geodynamics.org/cig/software/packages/short/pylith/"
\end_inset
@@ -236,7 +265,7 @@
\end_layout
\begin_layout Standard
-PyLith 1.0 depends on a number of other packages.
+PyLith 1.1 depends on a number of other packages.
This complicates building the software from the source code.
In many cases some of the packages required by PyLith are available as
binary packages.
@@ -253,8 +282,15 @@
PyLith is developed and tested on Linux and Mac OS X.
\end_layout
+\begin_layout Standard
+Detailed installation instructions for building PyLith using the SVN source
+ repository are available for several platforms.
+ The instructions can be accessed via ADD URL HERE.
+\end_layout
+
\begin_layout Subsection
-\begin_inset LatexCommand \label{sec:System-Requirements}
+\begin_inset LatexCommand label
+name "sec:System-Requirements"
\end_inset
@@ -274,7 +310,7 @@
\end_layout
\begin_layout Itemize
-A Fortran compiler
+A Fortran compiler (optional)
\end_layout
\begin_layout Itemize
@@ -296,10 +332,7 @@
are already installed.
Check with your system administrator if you are unsure of the name of your
C and C++ compiler commands.
-\end_layout
-
-\begin_layout Standard
-On Linux, the standard C and C++ compilers are
+ On Linux, the standard C and C++ compilers are
\family typewriter
gcc
\family default
@@ -318,13 +351,12 @@
\family default
commands are not available, install the corresponding GCC packages using
the package manager for your distribution.
-\end_layout
-
-\begin_layout Standard
-The Mac OS X version of GCC is included in a software development suite
+ The Mac OS X version of GCC is included in a software development suite
called Xcode.
Xcode is available as a free download at the
-\begin_inset LatexCommand \htmlurl[Apple Developer Connection]{developer.apple.com}
+\begin_inset LatexCommand htmlurl
+name "Apple Developer Connection"
+target "developer.apple.com"
\end_inset
@@ -333,15 +365,12 @@
\end_layout
\begin_layout Subsubsection
-Fortran Compiler
+Fortran Compiler (optional)
\end_layout
\begin_layout Standard
To build PETSc, you need either a Fortran-77 or Fortran-9x compiler.
-\end_layout
-
-\begin_layout Standard
-There are several free Fortran compilers available.
+ There are several free Fortran compilers available.
GCC 4 contains a Fortran-95 compiler called
\family typewriter
gfortran
@@ -356,8 +385,17 @@
\family typewriter
g95
\family default
-; the G95 project offers pre-built binaries for a variety of systems, which
- makes it an attractive option for Mac OS X users.
+.
+ Both the
+\family typewriter
+gfortran
+\family default
+ and
+\family typewriter
+g95
+\family default
+ projects offer pre-built binaries for a variety of systems, including Mac
+ OS X.
\end_layout
\begin_layout Subsubsection
@@ -410,7 +448,9 @@
Mac OS X 10.3 and later ships with a suitable version of Python preinstalled.
If you're using an older version of Mac OS X, or for more information in
general, see
-\begin_inset LatexCommand \htmlurl[Python on the Mac]{www.python.org/download/mac}
+\begin_inset LatexCommand htmlurl
+name "Python on the Mac"
+target "www.python.org/download/mac"
\end_inset
@@ -518,7 +558,9 @@
If absolutely necessary, one can easily build Python from source using a
C compiler.
You can download Python from the
-\begin_inset LatexCommand \htmlurl[Python website]{www.python.org}
+\begin_inset LatexCommand htmlurl
+name "Python website"
+target "www.python.org"
\end_inset
@@ -558,6 +600,14 @@
\end_layout
\begin_layout Itemize
+Pyrex (v0.9.5.1)
+\end_layout
+
+\begin_layout Itemize
+pyrexembed (CIG version)
+\end_layout
+
+\begin_layout Itemize
Pythia* (v0.8.1.4 or later)
\end_layout
@@ -580,12 +630,9 @@
\begin_layout Standard
Dependencies marked with an asterisk (*) can be downloaded and installed
automatically.
+ In addition, PyLith has the following optional dependencies:
\end_layout
-\begin_layout Standard
-In addition, PyLith has the following optional dependencies:
-\end_layout
-
\begin_layout Itemize
netcdf (v3.6)
\end_layout
@@ -597,24 +644,24 @@
\begin_layout Standard
After successfully building and installing PyLith from source, you will
need to configure Pyre to launch parallel runs of PyLith (see Section
-\begin_inset LatexCommand \vref{sec:Pyre-Configuration}
+\begin_inset LatexCommand vref
+reference "sec:Pyre-Configuration"
\end_inset
).
-\end_layout
+ We strongly recommend downloading the latest PyLith and PETSc source code
+ directly from the source code repositories, instead of using the source
+ packages; see Section
+\begin_inset LatexCommand ref
+reference "sec:Software-Repository"
-\begin_layout Standard
-Advanced users and software developers may be interested in downloading
- the latest PyLith and PETSc source code directly from the source code repositor
-ies, instead of using the prepared source packages; see Section
-\begin_inset LatexCommand \ref{sec:Software-Repository}
-
\end_inset
later in this chapter.
Note that this requires additional tools; see Section
-\begin_inset LatexCommand \ref{sub:Additional-Tools}
+\begin_inset LatexCommand ref
+reference "sub:Additional-Tools"
\end_inset
@@ -622,7 +669,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand \label{sec:Installing-PETSc}
+\begin_inset LatexCommand label
+name "sec:Installing-PETSc"
\end_inset
@@ -643,7 +691,9 @@
\begin_layout Standard
For general information about the development version of PETSc, visit
-\begin_inset LatexCommand \htmlurl[the PETSc Developers Site]{http://www-unix.mcs.anl.gov/petsc/petsc-as/developers/}
+\begin_inset LatexCommand htmlurl
+name "the PETSc Developers Site"
+target "http://www-unix.mcs.anl.gov/petsc/petsc-as/developers/"
\end_inset
@@ -670,14 +720,15 @@
\begin_layout Quote
\series bold
-TIP:
+TIP:
\series default
-If you run into problems configuring or building PETSc, send
+ If you run into problems configuring or building PETSc, send
\emph on
both
+\emph default
+
\family typewriter
-\emph default
- configure.log
+configure.log
\family default
and
\family typewriter
@@ -687,7 +738,9 @@
\family default
\emph default
to
-\begin_inset LatexCommand \url[PETSc Maintenance Mailing List]{petsc-maint at mcs.anl.gov}
+\begin_inset LatexCommand url
+name "PETSc Maintenance Mailing List"
+target "petsc-maint at mcs.anl.gov"
\end_inset
@@ -696,7 +749,9 @@
\begin_layout Standard
For detailed information on installing PETSc, see
-\begin_inset LatexCommand \htmlurl[the PETSc Installation Docs]{http://www-unix.mcs.anl.gov/petsc/petsc-as/documentation/installation.html}
+\begin_inset LatexCommand htmlurl
+name "the PETSc Installation Docs"
+target "http://www-unix.mcs.anl.gov/petsc/petsc-as/documentation/installation.html"
\end_inset
@@ -720,7 +775,9 @@
petsc-dev
\family default
from the
-\begin_inset LatexCommand \htmlurl[the PETSc Developers Site]{http://www-unix.mcs.anl.gov/petsc/petsc-as/developers/}
+\begin_inset LatexCommand htmlurl
+name "the PETSc Developers Site"
+target "http://www-unix.mcs.anl.gov/petsc/petsc-as/developers/"
\end_inset
@@ -802,10 +859,6 @@
--with-shared=1
\end_layout
-\begin_layout LyX-Code
---CXXFLAGS=-DNEW_SECTION
-\end_layout
-
\begin_layout Standard
You will need to specify additional options; the specific set of options
you will use depends upon the libraries and compilers you have available.
@@ -866,16 +919,12 @@
is available.
PyLith will not work correctly with a static MPI library (e.g.,
\family typewriter
-\color default
libmpi.a
\family default
-\color none
or
\family typewriter
-\color default
libmpich.a
\family default
-\color none
).
\end_layout
@@ -963,17 +1012,17 @@
\end_layout
\begin_layout LyX-Code
-
+
\family typewriter
- --with-sieve=1
+ --with-sieve=1
\backslash
\end_layout
\begin_layout LyX-Code
-
+
\family typewriter
- --with-clanguage=C++
+ --with-clanguage=C++
\backslash
\end_layout
@@ -985,23 +1034,17 @@
\end_layout
\begin_layout LyX-Code
- --CXXFLAGS=-DNEW_SECTION
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
+
\family typewriter
- --with-boost=1 --download-boost=1
+ --with-boost=1 --download-boost=1
\backslash
\end_layout
\begin_layout LyX-Code
-
+
\family typewriter
- --with-chaco=1 --download-chaco=1
+ --with-chaco=1 --download-chaco=1
\end_layout
\begin_layout Standard
@@ -1044,12 +1087,6 @@
\end_layout
\begin_layout LyX-Code
- --CXXFLAGS=-DNEW_SECTION
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
--with-boost=1 --download-boost=1
\backslash
@@ -1087,17 +1124,17 @@
\end_layout
\begin_layout LyX-Code
-
+
\family typewriter
- --with-sieve=1
+ --with-sieve=1
\backslash
\end_layout
\begin_layout LyX-Code
-
+
\family typewriter
- --with-clanguage=C++
+ --with-clanguage=C++
\backslash
\end_layout
@@ -1109,23 +1146,17 @@
\end_layout
\begin_layout LyX-Code
- --CXXFLAGS=-DNEW_SECTION
-\backslash
-
-\end_layout
-
-\begin_layout LyX-Code
-
+
\family typewriter
- --with-mpi-dir=/opt/mpich/myrinet_mx2g/intel
+ --with-mpi-dir=/opt/mpich/myrinet_mx2g/intel
\backslash
\end_layout
\begin_layout LyX-Code
-
+
\family typewriter
- --download-f-blas-lapack=1
+ --download-f-blas-lapack=1
\family default
\family typewriter
@@ -1135,17 +1166,17 @@
\end_layout
\begin_layout LyX-Code
-
+
\family typewriter
- --with-boost=1 --download-boost=1
+ --with-boost=1 --download-boost=1
\backslash
\end_layout
\begin_layout LyX-Code
-
+
\family typewriter
- --with-chaco=1 --download-chaco=1
+ --with-chaco=1 --download-chaco=1
\end_layout
\begin_layout Subsubsection
@@ -1321,8 +1352,65 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand \label{sec:Installing-PyLith}
+Installing nemesis
+\end_layout
+\begin_layout Standard
+ADD STUFF HERE
+\end_layout
+
+\begin_layout Subsection
+Installing proj
+\end_layout
+
+\begin_layout Standard
+ADD STUFF HERE
+\end_layout
+
+\begin_layout Subsection
+Installing FIAT
+\end_layout
+
+\begin_layout Standard
+ADD STUFF HERE
+\end_layout
+
+\begin_layout Subsection
+Installing numpy
+\end_layout
+
+\begin_layout Standard
+ADD STUFF HERE
+\end_layout
+
+\begin_layout Subsection
+Installing Pyrex
+\end_layout
+
+\begin_layout Standard
+ADD STUFF HERE
+\end_layout
+
+\begin_layout Subsection
+Installing pyrexembed
+\end_layout
+
+\begin_layout Standard
+ADD STUFF HERE
+\end_layout
+
+\begin_layout Subsection
+Installing spatialdata
+\end_layout
+
+\begin_layout Standard
+ADD STUFF HERE
+\end_layout
+
+\begin_layout Subsection
+\begin_inset LatexCommand label
+name "sec:Installing-PyLith"
+
\end_inset
Installing PyLith
@@ -1332,7 +1420,9 @@
To install PyLith, you follow the procedure that is commonly used with other
open source software packages.
First, download the source package available at the
-\begin_inset LatexCommand \htmlurl[Geodynamics Software Packages web page]{www.geodynamics.org/cig/software/packages}
+\begin_inset LatexCommand htmlurl
+name "Geodynamics Software Packages web page"
+target "www.geodynamics.org/cig/software/packages"
\end_inset
@@ -1353,7 +1443,9 @@
\begin_layout Standard
Download PyLith from the
-\begin_inset LatexCommand \htmlurl[Geodynamics website]{www.geodynamics.org}
+\begin_inset LatexCommand htmlurl
+name "Geodynamics website"
+target "www.geodynamics.org"
\end_inset
@@ -1411,7 +1503,9 @@
make.log
\family default
files to the
-\begin_inset LatexCommand \url[CIG Short-Term Crustal Dynamics Mailing List]{cig-short at geodynamics.org}
+\begin_inset LatexCommand url
+name "CIG Short-Term Crustal Dynamics Mailing List"
+target "cig-short at geodynamics.org"
\end_inset
@@ -1451,7 +1545,7 @@
\newline
\newline
-$ cd pylith-1.0.1
+$ cd pylith-1.1.0
\end_layout
\begin_layout Enumerate
@@ -1465,7 +1559,7 @@
\newline
\newline
-$ ./configure CXXFLAGS=-DNEW_SECTION --prefix=$HOME/cig
+$ ./configure --prefix=$HOME/cig
\end_layout
\begin_layout Enumerate
@@ -1536,7 +1630,8 @@
configure
\family default
, see Section
-\begin_inset LatexCommand \ref{sec:Configuration}
+\begin_inset LatexCommand ref
+reference "sec:Configuration"
\end_inset
@@ -1556,7 +1651,8 @@
\end_layout
\begin_layout Subsubsection
-\begin_inset LatexCommand \label{sec:Configuration}
+\begin_inset LatexCommand label
+name "sec:Configuration"
\end_inset
@@ -1629,7 +1725,9 @@
configure
\family default
failures on the
-\begin_inset LatexCommand \url[CIG Short-Term Crustal Dynamics Mailing List]{cig-short at geodynamics.org}
+\begin_inset LatexCommand url
+name "CIG Short-Term Crustal Dynamics Mailing List"
+target "cig-short at geodynamics.org"
\end_inset
@@ -1655,7 +1753,7 @@
\end_layout
\begin_layout Standard
-PyLith v0.8.2 requires Pythia v0.8.1.4 or later, which
+PyLith 1.1 requires Pythia v0.8.1.4 or later, which
\family typewriter
configure
\family default
@@ -1920,7 +2018,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand \label{sec:Pyre-Configuration}
+\begin_inset LatexCommand label
+name "sec:Pyre-Configuration"
\end_inset
@@ -2036,7 +2135,8 @@
\end_layout
\begin_layout Subsubsection
-\begin_inset LatexCommand \label{sub:Launchers-and-Schedulers}
+\begin_inset LatexCommand label
+name "sub:Launchers-and-Schedulers"
\end_inset
@@ -2298,9 +2398,9 @@
\begin_layout Quote
\color red
-Warning:
+Warning:
\color none
-This assumes your machine list has enough nodes for the simulation in question.
+ This assumes your machine list has enough nodes for the simulation in question.
\end_layout
\begin_layout Standard
@@ -2402,7 +2502,9 @@
\begin_layout Standard
For more information on configuring Pyre for your batch system, see CIG's
-\begin_inset LatexCommand \htmlurl[Pythia page]{www.geodynamics.org/cig/software/packages/cs/pythia}
+\begin_inset LatexCommand htmlurl
+name "Pythia page"
+target "www.geodynamics.org/cig/software/packages/cs/pythia"
\end_inset
@@ -2410,7 +2512,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Software-Repository}
+\begin_inset LatexCommand label
+name "sec:Software-Repository"
\end_inset
@@ -2419,7 +2522,9 @@
\begin_layout Standard
The PyLith source code is available via the
-\begin_inset LatexCommand \htmlurl[Geodynamics Subversion Repository]{www.geodynamics.org/cig/software/Repository/}
+\begin_inset LatexCommand htmlurl
+name "Geodynamics Subversion Repository"
+target "www.geodynamics.org/cig/software/Repository/"
\end_inset
@@ -2449,7 +2554,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand \label{sub:Additional-Tools}
+\begin_inset LatexCommand label
+name "sub:Additional-Tools"
\end_inset
@@ -2510,7 +2616,9 @@
\begin_layout Standard
For more information on Subversion, visit the
-\begin_inset LatexCommand \htmlurl[Subversion website]{subversion.tigris.org}
+\begin_inset LatexCommand htmlurl
+name "Subversion website"
+target "subversion.tigris.org"
\end_inset
@@ -2526,7 +2634,9 @@
You will likely have to build Mercurial from source, but this is a very
easy task that takes only a couple of minutes.
To learn how to download and install Mercurial, visit
-\begin_inset LatexCommand \htmlurl[the Mercurial web site]{http://www.selenic.com/mercurial/}
+\begin_inset LatexCommand htmlurl
+name "the Mercurial web site"
+target "http://www.selenic.com/mercurial/"
\end_inset
@@ -2546,7 +2656,9 @@
.
Pyrex is a Python-like language for writing native Python extension modules.
To download Pyrex, visit
-\begin_inset LatexCommand \htmlurl[the Pyrex web site]{http://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/}
+\begin_inset LatexCommand htmlurl
+name "the Pyrex web site"
+target "http://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/"
\end_inset
@@ -2588,7 +2700,9 @@
\begin_layout Standard
For more information about these GNU tools, see the
-\begin_inset LatexCommand \htmlurl[GNU website]{www.gnu.org/software}
+\begin_inset LatexCommand htmlurl
+name "GNU website"
+target "www.gnu.org/software"
\end_inset
@@ -2752,7 +2866,8 @@
\begin_layout Standard
You are now ready to install PETSc as described in Section
-\begin_inset LatexCommand \ref{sec:Installing-PETSc}
+\begin_inset LatexCommand ref
+reference "sec:Installing-PETSc"
\end_inset
@@ -2824,7 +2939,8 @@
autoreconf
\family default
, install PyLith as described in Section
-\begin_inset LatexCommand \ref{sec:Installing-PyLith}
+\begin_inset LatexCommand ref
+reference "sec:Installing-PyLith"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2008-02-27 02:52:26 UTC (rev 11263)
+++ short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2008-02-27 05:42:49 UTC (rev 11264)
@@ -1,4 +1,4 @@
-#LyX 1.5.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -41,6 +41,7 @@
\tracking_changes false
\output_changes false
\author ""
+\author ""
\end_header
\begin_body
@@ -118,11 +119,12 @@
\begin_layout Standard
PyLith is under active development and we expect a number of additions and
improvements in the near future.
- Likely enhancements will include additional constitutive models for both
- volume elements and cohesive (fault) elements, automatic generation of
- higher-order elements from linear elements, and the generation of Green's
- functions to be used in inversions.
- Many of these features should be available in Fall 2008.
+ Likely enhancements will include fault constitutive models with cohesive
+ (fault) cells, integration with PETSc's nonlinear solvers, additional bulk
+ constitutive models, automatic generation of higher-order elements from
+ linear elements, and the generation of Green's functions to be used in
+ inversions.
+ Many of these features should be available by Fall 2008.
\end_layout
\begin_layout Section
Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2008-02-27 02:52:26 UTC (rev 11263)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2008-02-27 05:42:49 UTC (rev 11264)
@@ -1,4 +1,4 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -51,13 +51,13 @@
\end_layout
\begin_layout Standard
-There are essentially three major pieces needed to run a problem with PyLith:
+There are essentially three major inputs needed to run a problem with PyLith:
\end_layout
\begin_layout Enumerate
A set of parameters describing the problem.
These parameters describe the type of problem to be run, solver information,
- time-stepping information, etc.
+ time-stepping information, boundary conditions, materials, etc.
This information can be provided from the command-line or by using a
\family typewriter
.cfg
@@ -72,9 +72,9 @@
\begin_layout Enumerate
Mesh information.
This includes the topology of the finite-element mesh (coordinates of vertices
- and how the vertices are connected into cells), the material identifier
- for each cell, and sets of vertices associated with boundary conditions,
- faults, and output (for subsets of the mesh).
+ and how the vertices are connected into cells), a material identifier for
+ each cell, and sets of vertices associated with boundary conditions, faults,
+ and output (for subsets of the mesh).
This information can be provided using the PyLith mesh ASCII format (See
Chapter
\begin_inset LatexCommand ref
@@ -89,7 +89,7 @@
\end_inset
for the format specification) or by importing the information from the
- LaGriT or CUBIT meshing packages (See
+ LaGriT or CUBIT meshing packages (see
\family typewriter
examples/3d/hex8
\family default
@@ -101,10 +101,10 @@
\end_layout
\begin_layout Enumerate
-Databases specifying the material properties and boundary conditions to
- be used.
+Databases specifying the material property values and boundary condition
+ values to be used.
Arbitrarily complex spatial variations in boundary and fault conditions
- and material properties may be given in the spatial database (See Chapter
+ and material properties may be given in the spatial database (see Chapter
\begin_inset LatexCommand ref
reference "cha:Tutorials"
@@ -121,16 +121,12 @@
\end_layout
\begin_layout Section
-Setting Parameters for PyLith
-\end_layout
-
-\begin_layout Standard
\begin_inset LatexCommand label
name "sec:setting:parameters"
\end_inset
-
+Setting Parameters for PyLith
\end_layout
\begin_layout Standard
@@ -141,7 +137,7 @@
\family typewriter
pylith
\family default
- executable: via the command line, or by using a configuration file in
+ executable: via the command line, or by using a text file in
\family typewriter
.cfg
\family default
@@ -150,7 +146,7 @@
.pml
\family default
format.
- PyLith gathers many simulation parameters and settings using Pyre properties
+ PyLith gathers most simulation parameters and settings using Pyre properties
and facilities.
Properties correspond to simple settings in the form of strings, integers,
and real numbers.
@@ -214,8 +210,8 @@
pylithapp
\family default
component.
- You can get a list of all of these properties along with a description
- of what they do by running PyLith with the
+ You can get a list of all of these top-level properties along with a descriptio
+n of what they do by running PyLith with the
\family typewriter
--help-properties
\family default
@@ -238,6 +234,10 @@
$ pylith --problem.help-properties
\end_layout
+\begin_layout LyX-Code
+DISCUSS SUBCOMPONENTS AND EXAMPLES
+\end_layout
+
\begin_layout Subsection
Using a
\family typewriter
@@ -259,7 +259,7 @@
\end_layout
\begin_layout LyX-Code
-[pylithapp.component1.component2]
+[pylithapp.subcomponent1.subcomponent2]
\end_layout
\begin_layout LyX-Code
@@ -280,7 +280,7 @@
.cfg
\family default
files for your work.
- The files are syntax-colored by the vim editor.
+ The files are syntax-colored in the vim editor.
\end_layout
\begin_layout Subsection
@@ -442,9 +442,9 @@
\end_inset
.
- In many quasi-static simulations, runtime can be reduced by replacing the
- Jacobi preconditioner with Additive Schwarz with Gram-Schmidt orthogonalization
- (see Table\InsetSpace ~
+ In many quasi-static or dynamic elasticity simulations, runtime can be
+ reduced by replacing the Jacobi preconditioner with Additive Schwartz with
+ Gram-Schmidt orthogonalization (see Table\InsetSpace ~
\begin_inset LatexCommand ref
reference "tab:petsc:options:quasistatic"
@@ -893,7 +893,7 @@
\end_inset
PETSc options that often result in improved performance in quasi-static
- problems.
+ and dynamic elasticity problems.
\end_layout
\end_inset
@@ -964,7 +964,7 @@
\end_layout
\begin_layout Standard
-The mesh information defines the nodal coordinates as well as specifying
+The mesh information defines the vertex coordinates as well as specifying
the vertices composing each cell in the mesh.
The mesh information must also define at least one set of vertices for
which displacement (Dirichlet) boundary conditions will be provided.
@@ -973,7 +973,7 @@
For example, one group might define a surface of the mesh where displacement
(Dirichlet) boundary conditions will be applied, another might define a
surface where traction (Neumann) boundary conditions will be applied, while
- a third might specify a surface that will define a fault.
+ a third might specify a surface that defines a fault.
Similarly, the mesh information contains cell labels that define the material
type for each cell in the mesh.
For a mesh with a single material type, there will only be a single label
@@ -1291,8 +1291,12 @@
spatial database files.
\end_layout
+\begin_layout Section
+Labels and Identifiers for Materials, Boundary Conditions, and Faults
+\end_layout
+
\begin_layout Standard
-
+ADD STUFF HERE
\end_layout
\end_body
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx 2008-02-27 02:52:26 UTC (rev 11263)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx 2008-02-27 05:42:49 UTC (rev 11264)
@@ -1,5 +1,5 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 245
+#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 276
\begin_document
\begin_header
\textclass book
@@ -8,13 +8,21 @@
\end_preamble
\language english
\inputencoding latin1
-\fontscheme default
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
\graphics default
\paperfontsize default
\spacing single
\papersize default
\use_geometry true
\use_amsmath 1
+\use_esint 0
\cite_engine basic
\use_bibtopic false
\paperorientation portrait
@@ -32,12 +40,14 @@
\paperpagestyle default
\tracking_changes false
\output_changes false
+\author ""
\end_header
\begin_body
\begin_layout Chapter
-\begin_inset LatexCommand \label{cha:Tutorials}
+\begin_inset LatexCommand label
+name "cha:Tutorials"
\end_inset
@@ -61,20 +71,25 @@
Before you begin any of the tutorials, you will need to install PyLith following
the instructions in Chapter\InsetSpace ~
-\begin_inset LatexCommand \ref{cha:Installation-and-Getting}
+\begin_inset LatexCommand ref
+reference "cha:Installation-and-Getting"
\end_inset
.
-
+
\color none
-For more complex tutorials, you will also need either the
-\begin_inset LatexCommand \htmlurl[CUBIT]{cubit.sandia.gov}
+ For more complex tutorials, you will also need either the
+\begin_inset LatexCommand htmlurl
+name "CUBIT"
+target "cubit.sandia.gov"
\end_inset
or
-\begin_inset LatexCommand \htmlurl[LaGriT]{meshing.lanl.gov}
+\begin_inset LatexCommand htmlurl
+name "LaGriT"
+target "meshing.lanl.gov"
\end_inset
@@ -82,7 +97,9 @@
If you do not wish to create your own mesh at this time, the meshes are
also provided as part of the tutorial.
The
-\begin_inset LatexCommand \htmlurl[ParaView]{www.paraview.org}
+\begin_inset LatexCommand htmlurl
+name "ParaView"
+target "www.paraview.org"
\end_inset
@@ -105,7 +122,7 @@
examples/twocells
\family default
, each consisting of just two cells (elements).
- These very simple examples make use of PyLith mesh ASCII format to describe
+ These very simple examples make use of PyLith mesh ASCII format to define
the mesh.
This format is useful for understanding the basics of how PyLith works,
since it is easy to create these files by hand.
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx 2008-02-27 02:52:26 UTC (rev 11263)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx 2008-02-27 05:42:49 UTC (rev 11264)
@@ -1,5 +1,5 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 245
+#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 276
\begin_document
\begin_header
\textclass book
@@ -8,13 +8,21 @@
\end_preamble
\language english
\inputencoding latin1
-\fontscheme default
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
\graphics default
\paperfontsize default
\spacing single
\papersize default
\use_geometry true
\use_amsmath 0
+\use_esint 0
\cite_engine basic
\use_bibtopic false
\paperorientation portrait
@@ -32,12 +40,14 @@
\paperpagestyle default
\tracking_changes false
\output_changes false
+\author ""
\end_header
\begin_body
\begin_layout Section
-\begin_inset LatexCommand \label{sec:Tutorial-Two-triangle}
+\begin_inset LatexCommand label
+name "sec:Tutorial-Two-triangle"
\end_inset
@@ -54,7 +64,7 @@
It is a mesh composed of two linear triangles subject to displacement boundary
conditions, assuming plane-strain linear elastic behavior.
Due to the simple geometry of the problem, the mesh may be constructed
- by hand, using PyLith mesh ASCII format to describe the mesh.
+ by hand, using PyLith mesh ASCII format.
In this tutorial, we will walk through the steps necessary to construct,
run, and view three problems that use the same mesh.
In addition to this manual, each of the files for the example problem is
@@ -68,7 +78,8 @@
\begin_layout Standard
The mesh consists of two triangles forming a square with edge lengths of
one unit (Figure
-\begin_inset LatexCommand \ref{fig:twotri3-mesh}
+\begin_inset LatexCommand ref
+reference "fig:twotri3-mesh"
\end_inset
@@ -79,16 +90,17 @@
\family default
, which is in PyLith mesh ASCII format.
This file format is described in Appendix
-\begin_inset LatexCommand \ref{cha:File-Formats}
+\begin_inset LatexCommand ref
+reference "cha:File-Formats"
\end_inset
.
This file describes the dimensionality of the problem (1D, 2D, or 3D),
the coordinates of the vertices (nodes), the vertices composing each cell
- (element), the material ID to be associated with each cell, and then provides
- groups of vertices that may be used to define faults or surfaces to which
- boundary conditions may be applied.
+ (element), the material ID to be associated with each cell, and groups
+ of vertices that may be used to define faults or surfaces to which boundary
+ conditions may be applied.
\end_layout
\begin_layout Standard
@@ -107,10 +119,14 @@
\end_layout
-\begin_layout Caption
-Mesh used for the two triangle examples.
-\begin_inset LatexCommand \label{fig:twotri3-mesh}
+\begin_layout Standard
+\begin_inset Caption
+\begin_layout Standard
+Mesh used in the two triangle examples.
+\begin_inset LatexCommand label
+name "fig:twotri3-mesh"
+
\end_inset
@@ -121,6 +137,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Additional Common Information
\end_layout
@@ -132,7 +153,7 @@
\family typewriter
pylithapp.cfg
\family default
- in the run directory, since this file is read automatically every time
+ in the working directory, since this file is read automatically every time
PyLith is run.
Settings specific to a particular problem may be placed in other
\family typewriter
@@ -190,16 +211,16 @@
pylithapp.cfg
\family default
.
- This information is contained in the file
+ This information is contained in the file
\family typewriter
- matprops.spatialdb
+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
+, the values for the physical properties of the material are given in
\family typewriter
matprops.spatialdb
\family default
@@ -215,7 +236,7 @@
\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
+ Parameter settings that augment those in
\family typewriter
pylithapp.cfg
\family default
@@ -229,11 +250,7 @@
\begin_layout Description
pylithapp.timedependent Specifies an implicit formulation for the problem
- and specifies 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).
+ and specifies the array of boundary conditions.
\end_layout
\begin_layout Description
@@ -261,6 +278,10 @@
\end_layout
\begin_layout Standard
+ADD MORE STUFF ON OUTPUT HERE
+\end_layout
+
+\begin_layout Standard
The boundary conditions are described in the file
\family typewriter
axialdisp.spatialdb
@@ -314,7 +335,8 @@
is produced 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 \vref{fig:twotri3-axial}
+\begin_inset LatexCommand vref
+reference "fig:twotri3-axial"
\end_inset
@@ -341,9 +363,13 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Color contours and vectors of displacement for the axial displacement example.
-\begin_inset LatexCommand \label{fig:twotri3-axial}
+\begin_inset LatexCommand label
+name "fig:twotri3-axial"
\end_inset
@@ -355,6 +381,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Shear Displacement Example
\end_layout
@@ -362,7 +393,7 @@
\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
+ Parameter settings that augment those in
\family typewriter
pylithapp.cfg
\family default
@@ -376,11 +407,7 @@
\begin_layout Description
pylithapp.timedependent Specifies an implicit formulation for the problem
- and specifies 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.
+ and specifies the array of boundary conditions.
\end_layout
\begin_layout Description
@@ -433,6 +460,10 @@
\end_layout
\begin_layout Standard
+ADD MORE ABOUT OUTPUT HERE
+\end_layout
+
+\begin_layout Standard
The boundary conditions are described in the file
\family typewriter
sheardisp.spatialdb
@@ -485,7 +516,8 @@
is produced 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 \vref{fig:twotri-shear}
+\begin_inset LatexCommand vref
+reference "fig:twotri-shear"
\end_inset
@@ -512,9 +544,13 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Color contours and vectors of displacement for the shear displacement example.
-\begin_inset LatexCommand \label{fig:twotri-shear}
+\begin_inset LatexCommand label
+name "fig:twotri-shear"
\end_inset
@@ -526,6 +562,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Kinematic Fault Slip Example
\end_layout
@@ -535,7 +576,7 @@
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
+ Parameter settings that augment those in
\family typewriter
pylithapp.cfg
\family default
@@ -554,16 +595,7 @@
\begin_layout Description
pylithapp.timedependent Specifies an implicit formulation for the problem,
- specifies 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
- specifies a container for a single fault (
-\family typewriter
-pylith.faults.SingleFault
-\family default
-).
+ the array of boundary conditions, and the array of interfaces.
\end_layout
\begin_layout Description
@@ -605,15 +637,17 @@
\end_layout
\begin_layout Standard
+ADD MORE ABOUT OUTPUT HERE
+\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
-\newline
-.cfg
+dislocation.cfg
\family default
.
In this case, the desired displacement values are given at a single point.
@@ -705,7 +739,8 @@
is produced 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 \vref{fig:twotri-disloc}
+\begin_inset LatexCommand vref
+reference "fig:twotri-disloc"
\end_inset
@@ -732,9 +767,13 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Color contours and vectors of displacement for the kinematic fault example.
-\begin_inset LatexCommand \label{fig:twotri-disloc}
+\begin_inset LatexCommand label
+name "fig:twotri-disloc"
\end_inset
@@ -746,5 +785,10 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\end_body
\end_document
Modified: short/3D/PyLith/trunk/doc/userguide/userguide.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/userguide.lyx 2008-02-27 02:52:26 UTC (rev 11263)
+++ short/3D/PyLith/trunk/doc/userguide/userguide.lyx 2008-02-27 05:42:49 UTC (rev 11264)
@@ -1,4 +1,4 @@
-#LyX 1.5.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
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