[cig-commits] r11445 - in short/3D/PyLith/trunk/doc/userguide: . fileformats install intro runpylith
brad at geodynamics.org
brad at geodynamics.org
Fri Mar 14 12:41:48 PDT 2008
Author: brad
Date: 2008-03-14 12:41:48 -0700 (Fri, 14 Mar 2008)
New Revision: 11445
Modified:
short/3D/PyLith/trunk/doc/userguide/fileformats/fileformats.lyx
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/userguide.lyx
Log:
Worked on cleaning up intro, installation, and running chapters. Moved some stuff from file formats appendix to running chapter.
Modified: short/3D/PyLith/trunk/doc/userguide/fileformats/fileformats.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/fileformats/fileformats.lyx 2008-03-14 00:53:18 UTC (rev 11444)
+++ short/3D/PyLith/trunk/doc/userguide/fileformats/fileformats.lyx 2008-03-14 19:41:48 UTC (rev 11445)
@@ -1,5 +1,5 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 245
+#LyX 1.5.4 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:File-Formats}
+\begin_inset LatexCommand label
+name "cha:File-Formats"
\end_inset
@@ -45,7 +55,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand \label{sec:MeshIOAscii}
+\begin_inset LatexCommand label
+name "sec:MeshIOAscii"
\end_inset
@@ -79,14 +90,19 @@
\end_layout
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Diagram of mesh specified in Figure
-\begin_inset LatexCommand \ref{fig:meshioascii:format}
+\begin_inset LatexCommand ref
+reference "fig:meshioascii:format"
\end_inset
.
-\begin_inset LatexCommand \label{fig:meshioascii:diagram}
+\begin_inset LatexCommand label
+name "fig:meshioascii:diagram"
\end_inset
@@ -98,6 +114,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout LyX-Code
// This mesh file defines a finite-element mesh composed of two
\end_layout
@@ -395,13 +416,17 @@
sideways false
status open
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Format of
\family typewriter
PyLith
\family default
mesh ASCII files.
-\begin_inset LatexCommand \label{fig:meshioascii:format}
+\begin_inset LatexCommand label
+name "fig:meshioascii:format"
\end_inset
@@ -413,81 +438,25 @@
\end_layout
-\begin_layout Section
-\begin_inset LatexCommand \label{sec:Spatialdata:SimpleIOAscii}
-
\end_inset
-Spatial Database Files
-\end_layout
-\begin_layout Standard
-Spatial database files provide specification of a field over some set of
- points.
- There is no topology associated with the points.
- Spatial database files contain a header describing the set of points and
- then the data with each line listing the coordinates of a point followed
- by the values of the fields for that point.
- Although multiple values can be specified at each point with more than
- one value included in a search query, the interpolation of each value will
- be done independently.
- Time dependent variations of a field are not supported in these files.
- Alternative implementations of spatial databases using the same application
- programming interface (API) can provide other representations of spatial
- variations of parameters for material properties (for example, the USGS
- Bay Area Velocity Model), boundary conditions, and earthquake source parameters.
\end_layout
-\begin_layout Standard
-Spatial database files can specifiy spatial variations over zero, one, two,
- and three dimensions.
- Zero dimensional variations correspond to uniform values.
- One-dimensional spatial variations correspond to piecewise linear variations,
- which need not coincide with coordinate axes.
- Likewise, two-dimensional spatial variations correspond to variations on
- a planar surface (which need not coincide with the coordinate axes) and
- three-dimensional spatial variations correspond to variations over a volume.
- In one, two, or three dimensions, queries can use a
-\begin_inset Quotes eld
-\end_inset
+\begin_layout Section
+\begin_inset LatexCommand label
+name "sec:Spatialdata:SimpleIOAscii"
-nearest value
-\begin_inset Quotes erd
\end_inset
- search or linear interpolation.
+SimpleDB Spatial Database Files
\end_layout
\begin_layout Standard
-The spatial database files need not provide the data using the same coordinate
- system as the mesh coordinate system, provided the two coordinate systems
- are compatible.
- Examples of compatible coordinate systems include geographic coordinates
- (longitude/latitude/elevation), and projected coordiates (e.g., coordinates
- in a transverse Mercator projection).
- Spatial database queries use the
-\begin_inset LatexCommand \htmlurl[Proj.4 Cartographic Projections library]{proj.maptools.org}
-
-\end_inset
-
- to convert between coordinate systems, so a large number of geographic
- projections are available with support for converting between NAD27 and
- WGS84 horizontal datums as well as several other frequently used datums.
- Because the interpolation is done in the coordinate system of the spatial
- database, geographic coordinates should only be used for very simple datasets,
- or undesirable results will occur.
- This is especially true when the spatial database coordinate system combines
- latitude, longitude, and elevation in meters (longitude and latitude in
- degrees are often much smaller than elevations in meters leading to distorted
+SimplDB spatial database files contain a header describing the set of points
+ and then the data with each line listing the coordinates of a point followed
+ by the values of the fields for that point.
-\begin_inset Quotes eld
-\end_inset
-
-distance
-\begin_inset Quotes erd
-\end_inset
-
- between locations and interpolation).
\end_layout
\begin_layout LyX-Code
@@ -695,7 +664,10 @@
sideways false
status open
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Format of spatial database files.
\end_layout
@@ -704,6 +676,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Spatial Database Coordinate Systems
\end_layout
@@ -722,7 +699,9 @@
program in addition to the Proj.4 libraries, so that you can obtain a list
of support projections, datums, and ellipsoids.
Alternatively, refer to the documentation for the
-\begin_inset LatexCommand \htmlurl[Proj.4 Cartographic Projections library]{proj.maptools.org}
+\begin_inset LatexCommand htmlurl
+name "Proj.4 Cartographic Projections library"
+target "proj.maptools.org"
\end_inset
@@ -761,7 +740,10 @@
sideways false
status open
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Format for Cartesian coordinate systems in spatial database files.
\end_layout
@@ -770,6 +752,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsubsection
Geographic
\end_layout
@@ -905,7 +892,10 @@
sideways false
status open
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Format for geographic coordinate systems in spatial database files.
\end_layout
@@ -914,6 +904,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsubsection
Geographic Projection
\end_layout
@@ -1107,7 +1102,10 @@
sideways false
status open
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Format for geographic projection coordinate systems in spatial database
files.
\end_layout
@@ -1117,6 +1115,11 @@
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsubsection
Geographic Local Cartesian
\end_layout
@@ -1304,7 +1307,10 @@
sideways false
status open
-\begin_layout Caption
+\begin_layout Standard
+\begin_inset Caption
+
+\begin_layout Standard
Format for the geographic local Cartesian coordinate system in spatial database
files.
\end_layout
@@ -1314,65 +1320,10 @@
\end_layout
-\begin_layout Subsection
-Spatial Database Parameters
-\end_layout
+\end_inset
-\begin_layout Standard
-As in the other Pyre objects, spatial database objects contain parameters
- that can be set from the command line or using
-\family typewriter
-.cf
-\family default
-g or
-\family typewriter
-.pml
-\family default
- files.
- The parameters for a spatial database are:
-\end_layout
-\begin_layout Description
-label Label for the database, which is used in diagnostic messages.
\end_layout
-\begin_layout Description
-query_type Type of search query to perform.
- Values for this parameter are ``linear'' and ``nearest'' (default).
-\end_layout
-
-\begin_layout Description
-iohandler Database importer.
- Only one importer is implemented, so you do not need to change this setting.
-\end_layout
-
-\begin_layout Description
-iohandler.filename Filename for the spatial database.
-\end_layout
-
-\begin_layout Standard
-An example of setting these parameters in a
-\family typewriter
-.cfg
-\family default
- file is:
-\end_layout
-
-\begin_layout LyX-Code
-label = Material properties
-\end_layout
-
-\begin_layout LyX-Code
-query_type = linear
-\end_layout
-
-\begin_layout LyX-Code
-iohandler.filename = mydb.spatialdb
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
\end_body
\end_document
Modified: short/3D/PyLith/trunk/doc/userguide/install/install.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/install/install.lyx 2008-03-14 00:53:18 UTC (rev 11444)
+++ short/3D/PyLith/trunk/doc/userguide/install/install.lyx 2008-03-14 19:41:48 UTC (rev 11445)
@@ -1,4 +1,4 @@
-#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.4 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
@@ -261,9 +262,7 @@
\end_layout
\begin_layout Standard
-
-PyLith 1.1 depends on a number of other packages (see Figure
-pylith-dependencies).
+PyLith 1.1 depends on a number of other packages (see Figurepylith-dependencies).
This complicates building the software from the source code.
In many cases some of the packages required by PyLith are available as
binary packages.
@@ -280,21 +279,21 @@
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 the web interface
- to the source repository
- (http://www.geodynamics.org/wsvn/cig/short/3D/PyLith/trunk/doc/install/).
- Even though using the software repositories is recommended only for
- experienced users, less experienced users will find the platform
- specific instructions useful. For example, the platform specific
- instructions include a list of binary packages/distributions that
- can be used, eliminating the need to compile those packages from
- source. Thus, less experienced users should follow the platform
- specific instructions but replace checking out the source code from
- the repository (applies to PETSc and CIG code only) with downloading
- the prepackaged source code.
+\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 the web interface to the source
+ repository (http://www.geodynamics.org/wsvn/cig/short/3D/PyLith/trunk/doc/instal
+l/).
+ Even though using the software repositories is recommended only for experienc
+ed users, less experienced users will find the platform specific instructions
+ useful.
+ For example, the platform specific instructions include a list of binary
+ packages/distributions that can be used, eliminating the need to compile
+ those packages from source.
+ Thus, less experienced users should follow the platform specific instructions
+ but replace checking out the source code from the repository (applies
+ to PETSc and CIG code only) with downloading the prepackaged source code.
\end_layout
\begin_layout Subsection
@@ -637,11 +636,11 @@
\end_layout
\begin_layout Standard
-Dependencies marked with an asterisk (*) can be downloaded and
- installed automatically. The source code for Nemesis, Pyrexembed,
- spatialdata, and PyLith package can all be downloaded from the CIG
- PyLith web page
- (http://www.geodynamics.org/cig/software/packages/short/pylith/).
+Dependencies marked with an asterisk (*) can be downloaded and installed
+ automatically.
+ The source code for Nemesis, Pyrexembed, spatialdata, and PyLith package
+ can all be downloaded from the CIG PyLith web page (http://www.geodynamics.org/
+cig/software/packages/short/pylith/).
PyLith also has the following optional dependencies:
\end_layout
@@ -1368,14 +1367,18 @@
\end_layout
\begin_layout Standard
-As with many other packages, to install nemesis, first, download the source package available at the
+As with many other packages, to install nemesis, first, download the source
+ package available at the
\begin_inset LatexCommand htmlurl
name "Geodynamics Software Packages web page"
target "www.geodynamics.org/cig/software/packages/short/pylith"
\end_inset
-. After unpacking the source, run the prepackaged shell script to configure
- nemesis for your system. Finally, use the
+
+.
+ After unpacking the source, run the prepackaged shell script to configure
+ nemesis for your system.
+ Finally, use the
\family typewriter
make
\family default
@@ -1555,20 +1558,27 @@
PATH
\family default
.
+\end_layout
\begin_layout Subsection
Installing Proj.4
\end_layout
\begin_layout Standard
-As with many other packages, to install Proj.4, first, download the source package available at the
+As with many other packages, to install Proj.4, first, download the source
+ package available at the
\begin_inset LatexCommand htmlurl
name "PROJ.4 web page"
target "http://www.remotesensing.org/proj/"
\end_inset
-. You should download both the source code and the US, Canadian, and New Zealand datum shift grid. After unpacking the files, run the prepackaged shell script to configure
- Proj.4 for your system. Finally, use the
+
+.
+ You should download both the source code and the US, Canadian, and New
+ Zealand datum shift grid.
+ After unpacking the files, run the prepackaged shell script to configure
+ Proj.4 for your system.
+ Finally, use the
\family typewriter
make
\family default
@@ -1588,8 +1598,8 @@
\end_inset
-. Download the source archive and unpack
- it using the
+.
+ Download the source archive and unpack it using the
\family typewriter
tar
\family default
@@ -1609,8 +1619,8 @@
\end_layout
\begin_layout Standard
-Download the datum shift archive and unpack
- it in the proj-4.6.0/nad directory using the
+Download the datum shift archive and unpack it in the proj-4.6.0/nad directory
+ using the
\family typewriter
unzip
\family default
@@ -1618,8 +1628,7 @@
\end_layout
\begin_layout LyX-Code
-$ cd proj-4.6.0/nad
-$ unzip proj-datumgrid-1.3.zip
+$ cd proj-4.6.0/nad$ unzip proj-datumgrid-1.3.zip
\end_layout
\begin_layout Subsubsection
@@ -1705,19 +1714,25 @@
PATH
\family default
.
+\end_layout
\begin_layout Subsection
Installing numpy
\end_layout
\begin_layout Standard
-Numpy is written exclusively in Python, although it has some Python extension modules. As a result, its installation is relatively simple. First, download the source package available at the
+Numpy is written exclusively in Python, although it has some Python extension
+ modules.
+ As a result, its installation is relatively simple.
+ First, download the source package available at the
\begin_inset LatexCommand htmlurl
name "SciPy.org web page"
target "http://www.scipy.org/Download/"
\end_inset
-. Download the Numpy source code and install the package.
+
+.
+ Download the Numpy source code and install the package.
\end_layout
\begin_layout Subsubsection
@@ -1732,8 +1747,8 @@
\end_inset
-. Download the source archive and unpack
- it using the
+.
+ Download the source archive and unpack it using the
\family typewriter
tar
\family default
@@ -1807,19 +1822,24 @@
PATH
\family default
.
+\end_layout
\begin_layout Subsection
Installing FIAT
\end_layout
\begin_layout Standard
-FIAT is written exclusively in Python. As a result, its installation is very simple. First, download the source package available at the
+FIAT is written exclusively in Python.
+ As a result, its installation is very simple.
+ First, download the source package available at the
\begin_inset LatexCommand htmlurl
name "FENICS web page"
target "http://www.fenics.org/wiki/Download/"
\end_inset
-. Download the FIAT source code and install the package.
+
+.
+ Download the FIAT source code and install the package.
\end_layout
\begin_layout Subsubsection
@@ -1834,8 +1854,8 @@
\end_inset
-. Download the source archive and unpack
- it using the
+.
+ Download the source archive and unpack it using the
\family typewriter
tar
\family default
@@ -1909,19 +1929,25 @@
PATH
\family default
.
+\end_layout
\begin_layout Subsection
Installing Pyrex
\end_layout
\begin_layout Standard
-Pyrex is written exclusively in Python. As a result, its installation is very simple. First, download the source package available at the
+Pyrex is written exclusively in Python.
+ As a result, its installation is very simple.
+ First, download the source package available at the
\begin_inset LatexCommand htmlurl
name "Pyrex web page"
target "http://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/"
\end_inset
-. Some recent releases of Pyrex are incompatible with PyLith. Release 0.9.5.1 is known to work with PyLith.
+
+.
+ Some recent releases of Pyrex are incompatible with PyLith.
+ Release 0.9.5.1 is known to work with PyLith.
\end_layout
\begin_layout Subsubsection
@@ -1936,8 +1962,9 @@
\end_inset
-. Click on the Previous Releases link to retrieve release 0.9.5.1. Download the source archive and unpack
- it using the
+.
+ Click on the Previous Releases link to retrieve release 0.9.5.1.
+ Download the source archive and unpack it using the
\family typewriter
tar
\family default
@@ -2011,20 +2038,26 @@
PATH
\family default
.
+\end_layout
-
\begin_layout Subsection
Installing pyrexembed
\end_layout
\begin_layout Standard
-CIG distributes a customized version of Pyrexembed (http://www.freenet.org.nz/python/pyrexembed/) that handles C++ exceptions. Pyrexembed is written exclusively in Python and its installation is very simple. First, download the source package available at the
+CIG distributes a customized version of Pyrexembed (http://www.freenet.org.nz/pytho
+n/pyrexembed/) that handles C++ exceptions.
+ Pyrexembed is written exclusively in Python and its installation is very
+ simple.
+ First, download the source package available at the
\begin_inset LatexCommand htmlurl
name "Geodynamics Software Packages web page"
target "www.geodynamics.org/cig/software/packages/short/pylith"
\end_inset
-. Download the Pyrexembed source code and install the package.
+
+.
+ Download the Pyrexembed source code and install the package.
\end_layout
\begin_layout Subsubsection
@@ -2062,14 +2095,6 @@
command:
\end_layout
-. Download the source archive and unpack
- it using the
-\family typewriter
-tar
-\family default
- command:
-\end_layout
-
\begin_layout LyX-Code
$ tar xzf pyrexembed-1.0.tgz
\end_layout
@@ -2137,20 +2162,25 @@
PATH
\family default
.
+\end_layout
\begin_layout Subsection
Installing spatialdata
\end_layout
\begin_layout Standard
-As with many other packages, to install spatialdata, first, download the source package available at the
+As with many other packages, to install spatialdata, first, download the
+ source package available at the
\begin_inset LatexCommand htmlurl
name "Geodynamics Software Packages web page"
target "www.geodynamics.org/cig/software/packages/short/pylith"
\end_inset
-. After unpacking the source, run the prepackaged shell script to configure
- nemesis for your system. Finally, use the
+
+.
+ After unpacking the source, run the prepackaged shell script to configure
+ nemesis for your system.
+ Finally, use the
\family typewriter
make
\family default
@@ -2213,8 +2243,8 @@
\series bold
TIP:
\series default
- If you run into problems configuring or building spatialdata, send both the
-
+ If you run into problems configuring or building spatialdata, send both
+ the
\family typewriter
config.log
\family default
@@ -2275,8 +2305,9 @@
\family default
to configure the package for your system
\family typewriter
-. Note that PyLith requires spatialdata to be configured with the
---enable-pythia flag.
+.
+ Note that PyLith requires spatialdata to be configured with the--enable-pythia
+ flag.
\newline
\newline
@@ -2330,6 +2361,7 @@
PATH
\family default
.
+\end_layout
\begin_layout Subsection
\begin_inset LatexCommand label
@@ -3467,8 +3499,8 @@
\color none
Building PyLith using the source repositories is recommended only for expert
users who are willing to work with a moving target and rebuild on a frequent
- basis.
- The installation instructions cover the basic steps and assume the user
+ basis.
+ The installation instructions cover the basic steps and assume the user
has experience building and installing software.
\end_layout
Modified: short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2008-03-14 00:53:18 UTC (rev 11444)
+++ short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2008-03-14 19:41:48 UTC (rev 11445)
@@ -1,4 +1,4 @@
-#LyX 1.5.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.4 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -207,9 +207,14 @@
use across multiple applications.
This allows expert users to replace functionality of a wide variety of
components without recompiling or polluting the main code.
- PyLith employs external packages (ADD REFERENCE TO FIGURE) to reduce developmen
-t time and enhance computational efficiency; for example, PyLith 0.8 ran
- two times faster when the PETSc linear solver was used.
+ PyLith employs external packages (see Figure
+\begin_inset LatexCommand ref
+reference "fig:pylith-dependencies"
+
+\end_inset
+
+) to reduce development time and enhance computational efficiency; for example,
+ PyLith 0.8 ran two times faster when the PETSc linear solver was used.
\end_layout
\begin_layout Standard
@@ -222,6 +227,13 @@
status open
\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename figs/packages.eps
+ scale 75
+
+\end_inset
+
\begin_inset Caption
\begin_layout Standard
@@ -230,8 +242,9 @@
\end_inset
-PyLith dependencies. PyLith makes direct use of several other packages,
- some of which have their own dependencies.
+PyLith dependencies.
+ PyLith makes direct use of several other packages, some of which have
+ their own dependencies.
\end_layout
\end_inset
@@ -239,22 +252,11 @@
\end_layout
-\begin_layout Standard
-\align center
-\begin_inset Graphics
- filename figs/packages.eps
- scale 75
-
\end_inset
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Standard
PyLith is written in two programming languages.
High-level code is written in Python; this rich, expressive interpreted
@@ -346,6 +348,14 @@
status open
\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename figs/pyre_overview.png
+ scale 25
+
+\end_inset
+
+\begin_layout Standard
\begin_inset Caption
\begin_layout Standard
@@ -358,22 +368,12 @@
\end_layout
-\begin_layout Standard
-\align center
-\begin_inset Graphics
- filename figs/pyre_overview.png
- scale 75
\end_inset
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Standard
Pyre is a framework, a combination of software and design philosophy that
promotes the reuse of code.
Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2008-03-14 00:53:18 UTC (rev 11444)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2008-03-14 19:41:48 UTC (rev 11445)
@@ -1,4 +1,4 @@
-#LyX 1.5.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.4 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -1353,13 +1353,6 @@
or 3D variation).
This might be the case, for example, if the material properties are provided
by a database of seismic velocities and densities.
- See Section
-\begin_inset LatexCommand ref
-reference "sec:Spatialdata:SimpleIOAscii"
-
-\end_inset
-
- for the specification of the file format for the default spatial database.
For boundary conditions the simplest case would be where all vertices in
a given group have the same boundary condition parameters (
\begin_inset Quotes eld
@@ -1393,62 +1386,196 @@
\end_layout
\begin_layout Subsection
-SimpleDB Database Implementation
+SimpleDB Spatial Database
\end_layout
\begin_layout Standard
-In most cases the default type of spatial database for faults, boundary conditions, and materials
- is
+In most cases the default type of spatial database for faults, boundary
+ conditions, and materials is
\family typewriter
SimpleDB
\family default
.
- SimpleDB uses a simple ASCII file to specify the variation of values
- (e.g., displacement field, slip field, physical properties) in
- space. The file format is described in
+ Spatial database files provide specification of a field over some set of
+ points.
+ There is no topology associated with the points.
+ Although multiple values can be specified at each point with more than
+ one value included in a search query, the interpolation of each value will
+ be done independently.
+ Time dependent variations of a field are not supported in these files.
+ Spatial database files can specifiy spatial variations over zero, one,
+ two, and three dimensions.
+ Zero dimensional variations correspond to uniform values.
+ One-dimensional spatial variations correspond to piecewise linear variations,
+ which need not coincide with coordinate axes.
+ Likewise, two-dimensional spatial variations correspond to variations on
+ a planar surface (which need not coincide with the coordinate axes) and
+ three-dimensional spatial variations correspond to variations over a volume.
+ In one, two, or three dimensions, queries can use a
+\begin_inset Quotes eld
+\end_inset
+
+nearest value
+\begin_inset Quotes erd
+\end_inset
+
+ search or linear interpolation.
+\end_layout
+
+\begin_layout Standard
+The spatial database files need not provide the data using the same coordinate
+ system as the mesh coordinate system, provided the two coordinate systems
+ are compatible.
+ Examples of compatible coordinate systems include geographic coordinates
+ (longitude/latitude/elevation), and projected coordiates (e.g., coordinates
+ in a transverse Mercator projection).
+ Spatial database queries use the
+\begin_inset LatexCommand htmlurl
+name "Proj.4 Cartographic Projections library"
+target "proj.maptools.org"
+
+\end_inset
+
+ to convert between coordinate systems, so a large number of geographic
+ projections are available with support for converting between NAD27 and
+ WGS84 horizontal datums as well as several other frequently used datums.
+ Because the interpolation is done in the coordinate system of the spatial
+ database, geographic coordinates should only be used for very simple datasets,
+ or undesirable results will occur.
+ This is especially true when the spatial database coordinate system combines
+ latitude, longitude, and elevation in meters (longitude and latitude in
+ degrees are often much smaller than elevations in meters leading to distorted
+
+\begin_inset Quotes eld
+\end_inset
+
+distance
+\begin_inset Quotes erd
+\end_inset
+
+ between locations and interpolation).
+\end_layout
+
+\begin_layout Standard
+SimpleDB uses a simple ASCII file to specify the variation of values (e.g.,
+ displacement field, slip field, physical properties) in space.
+ The file format is described in Section
\begin_inset LatexCommand ref
- reference "sec:Spatialdata:SimpleIOAscii"
+reference "sec:Spatialdata:SimpleIOAscii"
\end_inset
-. The tutorials in (REFERENCE TUTORIALS CHAPTER) use SimpleDB files
-to specify the values for the boundary conditions, physical
-properties, and fault slip.
+.
+ The tutorials in Chapter
+\begin_inset LatexCommand ref
+reference "cha:Tutorials"
+\end_inset
+
+ use SimpleDB files to specify the values for the boundary conditions,
+ physical properties, and fault slip.
+\end_layout
+
+\begin_layout Standard
+As in the other Pyre objects, spatial database objects contain parameters
+ that can be set from the command line or using
+\family typewriter
+.cfg or
+\family typewriter
+.pml
+\family default
+ files.
+ The parameters for a spatial database are:
+\end_layout
+
+\begin_layout Description
+label Label for the database, which is used in diagnostic messages.
+\end_layout
+
+\begin_layout Description
+query_type Type of search query to perform.
+ Values for this parameter are ``linear'' and ``nearest'' (default).
+\end_layout
+
+\begin_layout Description
+iohandler Database importer.
+ Only one importer is implemented, so you do not need to change this setting.
+\end_layout
+
+\begin_layout Description
+iohandler.filename Filename for the spatial database.
+\end_layout
+
+\begin_layout Standard
+An example of setting these parameters in a
+\family typewriter
+.cfg
+\family default
+ file is:
+\end_layout
+
+\begin_layout LyX-Code
+label = Material properties
+\end_layout
+
+\begin_layout LyX-Code
+query_type = linear
+\end_layout
+
+\begin_layout LyX-Code
+iohandler.filename = mydb.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
\begin_layout Subsection
-UniformDB Database Implementation
+UniformDB Spatial Database
\end_layout
\begin_layout Standard
-The SimpleDB spatial database is quite general. When the values are
-uniform, it is often easier to use the UniformDB spatial database and
-specify the values directly (either on the command line or in a
-parameters settings file). However, if the values are used in more
-than one place, it is easier to place the values in a SimpleDB file,
-because they can then be referred to using the filename of the
-spatialdatabase rather than having to repeatedly list all of the
-values on the command line or in a parameter settings (.cfg) file.
+The SimpleDB spatial database is quite general.
+ When the values are uniform, it is often easier to use the UniformDB spatial
+ database and specify the values directly (either on the command line or
+ in aparameters settings file).
+ However, if the values are used in more than one place, it is easier to
+ place the values in a SimpleDB file, because they can then be referred
+ to using the filename of the spatial database rather than having to repeatedly
+ list all of the values on the command line or in a parameter settings (.cfg)
+ file.
+ The Pyre properties for a UniformDB are:
+\end_layout
-PYRE PROPERTIES
+\begin_layout Description
+values Array of names of values in spatial database
+\end_layout
-values Array of names of values in spatial database
+\begin_layout Description
data Array of values in spatial database
+\end_layout
-EXAMPLE
+\begin_layout Subsubsection
+Example
+\end_layout
-Specify the physical properties of a linearly elastic, isotropic
-material in a pylithapp.cfg file.
+\begin_layout Standard
+Specify the physical properties of a linearly elastic, isotropicmaterial
+ in a pylithapp.cfg file.
+\end_layout
-
\begin_layout LyX-Code
[pylithapp.timedependent.materials.material]
\end_layout
+
\begin_layout LyX-Code
db = spatialdata.spatialdb.UniformDB ; Set the db to a UniformDB
\end_layout
+
\begin_layout LyX-Code
db.values = [vp,vs,density] ; Set the names of the values in the database
\end_layout
+
\begin_layout LyX-Code
db.data = [5773.5, 3333.3, 2700.0] ; Set the values in the database
\end_layout
@@ -1459,99 +1586,157 @@
\end_inset
-SCECCVMH Implementation
+SCEC CVM-H Spatial Database
\end_layout
\begin_layout Standard
+Although the SimpleDB implementation is able to specify arbitrarily complex
+ spatial variations, there are existing databases for physical properties,
+ and when they are available, it is desirable to access these directly.
+ One such database is the SCEC CVM-H database, which provides seismic velocities
+ and density information for much of southern California.
+ Spatialdata provides a direct interface to this database.
+ See tutorial ?? for an example of using the SCEC CVM-H database for physical
+ properties of an elastic material.
+ The interface is known to work with versions 5.2 and 5.3 of the SCEC CVM-H.
+ The Pyre properties for the SCEC CVM-H are:
+\end_layout
-Although the SimpleDB implementation is able to specify arbitrarily
-complex spatial variations, there are existing databases for physical
-proeprties, and when they are available, it is desirable to access
-these directly. One such database is the SCEC CVM-H database, which
-provides seismic velocities and density information for much of
-southern California. Spatialdata provides a direct interface to this
-database. See tutorial ?? for an example of using the SCEC CVM-H
-database for physical properties of an elastic material. The interface
-for the SCEC CVM-H is known to work with versions 5.2 and 5.3.
+\begin_layout Description
+data_dir Directory containing the SCEC CVM-H data files
+\end_layout
-PYRE PROPERTIES
+\begin_layout Description
+squash Squash topography/bathymetry to sea level (make the Earth's surface
+ flat)
+\end_layout
-data_dir Directory containing the SCEC CVM-H data files (e.g., )
-squash Squash topography/bathymetry to sea level (make the Earth's surface flat).
-squash_limit Elevation above which topography is squashed (geometry below this elevation remains undistorted).
+\begin_layout Description
+squash_limit Elevation above which topography is squashed (geometry below
+ this elevation remains undistorted)
+\end_layout
-EXAMPLE
+\begin_layout Subsubsection
+Example
+\end_layout
-Specify the physical properties of a linearly elastic, isotropic
-material using the SCEC CVM-H in a pylithapp.cfg file.
+\begin_layout Standard
+Specify the physical properties of a linearly elastic, isotropicmaterial
+ using the SCEC CVM-H in a pylithapp.cfg file.
+\end_layout
\begin_layout LyX-Code
[pylithapp.timedependent.materials.material]
\end_layout
\begin_layout LyX-Code
-db = spatialdata.spatialdb.SCECCVMH
+db = spatialdata.spatialdb.SCECCVMH ; Set the database to the SCEC CVM-H
\end_layout
\begin_layout LyX-Code
-db.data_dir = /home/johndoe/data/sceccvm-h/vx53
+db.data_dir = /home/johndoe/data/sceccvm-h/vx53 ; Directory containing the
+ database data files
\end_layout
-.
+\begin_layout LyX-Code
+squash = True ; Turn on squashing
\end_layout
+\begin_layout LyX-Code
+squash_limit = -1000.0 ; Only distort the geometry above z = -1 km in flattening
+ the Earth
+\end_layout
+
\begin_layout Section
Labels and Identifiers for Materials, Boundary Conditions, and Faults
\end_layout
\begin_layout Standard
-For materials, the "label" is a string used only for error messages. The id is
-an integer that corresponds to the material identifier in LaGriT (imt1) and
-CUBIT (block id). The id also tags the cells in the mesh for associating
-cells with a specific material and quadrature rule.
+For materials, the "label" is a string used only for error messages.
+ The "id" is an integer that corresponds to the material identifier in LaGriT
+ (itetclr) and CUBIT (block id).
+ The id also tags the cells in the mesh for associating cells with a specific
+ material model and quadrature rule.
+ For boundary conditions the "label" is a string used to associate groups
+ of vertices (psets in LaGriT and nodesets in CUBIT) with aboundary condition.
+ PyLith 1.0 had an "id" for boundary conditions, but we removed it because
+ it was not used.
+ For faults the "label" is a string used to associated groups of vertices
+ (psets in LaGriT and nodesets in CUBIT) with vertices on the fault.
+ Note that some mesh generators use strings (LaGriT) to identify groups
+ of nodes while others use integers (CUBIT Exodus files).
+ Although CUBIT permits associated strings with nodesets, they are not included
+ in the Exodus files.
+ The fault "id" is a integer used to tag the cohesive cells in the mesh
+ with a specific fault and quadrature rule.
+ Because we use the fault "id" to tag the cohesive cells in the mesh, it
+ must be unique among the faults as well as the materials.
+\end_layout
-For BC, the "label" is a string used to associate groups of vertices (psets in
-LaGriT and nodesets in CUBIT) with vertices for a BC. I believe in 1.0.1 we
-had an "id", but we have since removed it because we were not using it.
+\begin_layout Section
+PyLith Output
+\end_layout
-For faults, the "label" is a string used to associated groups of vertices
-(psets in LaGriT and nodesets in CUBIT) with vertices on the fault. The "id"
-is a integer used to tag the cells in the mesh with a specific fault and
-quadrature rule. Because we use the "id" it to tag cohesive cells in the
-mesh, it must be unique among the faults as well as the materials.
+\begin_layout Standard
+ADD STUFF HERE
+\end_layout
-Fault "label"
+\begin_layout Section
+Troubleshooting Problems Running PyLith
+\end_layout
-In order to know which vertices are associated with the fault, we use
-the fault label (which is a string), because some mesh generators use
-strings (LaGriT) to identify groups of nodes while others use integers
-(CUBIT Exodus files).
+\begin_layout Itemize
+\family typewriter
+ImportError: liblapack.so.2: cannot open shared object file: No such file
+ or directory
+\end_layout
-Fault "id"
+\begin_layout Quote
+PyLith cannot find one of the libraries.
+ You need to setup your environment variables (e.g., PATH, PYTHONPATH, and
+ LD_LIBRARY_PATH) to match your installation.
+ If you are using the PyLith binary on Linux or Mac OS X, run the command
+
+\family typewriter
+source setup.sh
+\family default
+in the directory where you unpacked the distribution.
+ This will setup your environment variables for you.
+ If you are building PyLith from source, please consult the instructions
+ for building from source.
+\end_layout
-For each finite-element cell in the mesh, we set a "material-id" tag
-that corresponds to the material and quadrature scheme for that cell.
-The material-id is set based on the material id for bulk cells and the
-fault id for cohesive cells. When we want to operate on cells associated
-with a material, quadrature scheme, fault, etc., we ask Sieve for a list
-of all cells with material-id equal to some value.
+\begin_layout Itemize
+\paragraph_spacing single
+
+\family typewriter
+>> {command line}:: \newline
+-- pyre.inventory(error) \newline
+-- p4wd <- 'true' \newline
+-- unrecognized property 'p4wd' \newline
+>> {command line}:: \newline
+-- pyre.inventory(error) \newline
+-- p4pg <- 'true' \newline
+-- unrecognized property ' p4pg'
\end_layout
-\begin_layout Section
-PyLith Output
+\begin_layout Quote
+Verify that the 'mpirun' command included in the PyLith package is the first
+ one on your PATH:
\end_layout
-\begin_layout Section
-Troubleshooting Problems Running PyLith
+\begin_layout Quote
+
+\family typewriter
+$ which mpirun
\end_layout
-ImportError: liblapack.so.2: cannot open shared object file: No such file or directory
+\begin_layout Quote
+If it is not, adjust your PATH environment variable accordingly.
+\end_layout
-Need to set your environment variables.
-mpirun stuff
-nemesis (adding MPICH libraries)
\end_body
\end_document
Modified: short/3D/PyLith/trunk/doc/userguide/userguide.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/userguide.lyx 2008-03-14 00:53:18 UTC (rev 11444)
+++ short/3D/PyLith/trunk/doc/userguide/userguide.lyx 2008-03-14 19:41:48 UTC (rev 11445)
@@ -1,4 +1,4 @@
-#LyX 1.5.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.4 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
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