[cig-commits] r11349 - doc/cigma/manual

[luis at geodynamics.org]

Author: luis
Date: 2008-03-06 14:46:15 -0800 (Thu, 06 Mar 2008)
New Revision: 11349

Removed:
   doc/cigma/manual/scratch.lyx
Log:
Done with scratch file


Deleted: doc/cigma/manual/scratch.lyx
===================================================================
--- doc/cigma/manual/scratch.lyx	2008-03-06 22:38:11 UTC (rev 11348)
+++ doc/cigma/manual/scratch.lyx	2008-03-06 22:46:15 UTC (rev 11349)
@@ -1,624 +0,0 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
-\begin_document
-\begin_header
-\textclass book
-\begin_preamble
-\usepackage{hyperref}
-
-\let\myUrl\url
-\renewcommand{\url}[1]{(\myUrl{#1})}
-
-\newcommand{\note}[1]{}
-\end_preamble
-\language english
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-\tracking_changes false
-\output_changes false
-\author "" 
-\author "" 
-\end_header
-
-\begin_body
-
-\begin_layout Chapter
-Introduction
-\end_layout
-
-\begin_layout Section
-About Cigma
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status collapsed
-
-\begin_layout Standard
-
-
-\backslash
-note{here's a note}
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The CIG Model Analyzer (Cigma) consists of a suite of tools for comparing
- numerical models.
- CIG developed Cigma in response to demand from the short-term tectonics
- community for a tool that could perform rigorous error analysis on their
- FEM codes.
- [[XXX: additional notes here]]
-\end_layout
-
-\begin_layout Standard
-Cigma relies upon a number of software libraries.
- The 
-\begin_inset LatexCommand htmlurl
-name "FInite element Automatic Tabulator (FIAT)"
-target "www.fenics.org/wiki/FIAT"
-
-\end_inset
-
- Python Library supports generation of arbitrary order instances of the
- Lagrange elements on lines, triangles, and tetrahedra.
- It can also generate order instances of Jacobi-type quadrature rules on
- the same element shapes.
- The 
-\begin_inset LatexCommand htmlurl
-name "Approximate Nearest Neighbor (ANN)"
-target "www.cs.umd.edu/~mount/ANN/"
-
-\end_inset
-
- Library, written in C++, supports data structures and algorithms for both
- exact and nearest-neighbor searching in arbitrarily high dimensions.
- The Hierarchical Data Format (HDF5) library is used for organizing the
- input and output datasets.
- The Visualization Toolkit (VTK) library can be used to provide input datasets,
- as well as for visualization of output files.
- [[XXX]]
-\end_layout
-
-\begin_layout Section
-Citation
-\end_layout
-
-\begin_layout Standard
-Computational Infrastructure for Geodynamics (CIG) is making this source
- code available to you in the hope that the software will enhance your research
- in geophysics.
- This is a brand-new code and at present no papers are published or at press
- for use as citations other than this manual, which is cited as follows:
-\end_layout
-
-\begin_layout Itemize
-Armendariz, L., and S.
- Kientz.
- 
-\emph on
-Cigma User Manual.
-
-\emph default
- Pasadena, CA: Computational Infrastructure of Geodynamics, 2007.
- URL: geodynamics.org/cig/software/cs/cigma/cigma.pdf
-\end_layout
-
-\begin_layout Standard
-CIG requests that in your oral presentations and in your papers that you
- indicate your use of this code and acknowledge the author of the code and
- 
-\begin_inset LatexCommand htmlurl
-name "CIG"
-target "geodynamics.org"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Section
-Support
-\end_layout
-
-\begin_layout Standard
-Cigma development is supported by a grant from the National Science Foundation
- to CIG, managed by the California Institute of Technology.
- The code is being released under the GNU General Public License.
-\end_layout
-
-\begin_layout Chapter
-Error Analysis
-\end_layout
-
-\begin_layout Standard
-[[This chapter discusses error analysis, the basic components of cigma (discount
-ing I/O stuff), and the kinds of operations you'd perform with those components]
-]
-\end_layout
-
-\begin_layout Section
-Introduction
-\end_layout
-
-\begin_layout Standard
-XXX: Transfer most of this one
-\end_layout
-
-\begin_layout Standard
-[[move changes here]]
-\end_layout
-
-\begin_layout Standard
-[[move discussion of file formats to chapter 4]]
-\end_layout
-
-\begin_layout Chapter
-Installation and Getting Help
-\end_layout
-
-\begin_layout Standard
-[[In this chapter, give installation instructions for cigma.
- Give list of dependencies, plus instructions for Debian system.
- For each dependency, explain how to install from source if it's easy, otherwise
- refer the reader to the installation instructions on the appropriate web
- site]]
-\end_layout
-
-\begin_layout Section
-Getting Help
-\end_layout
-
-\begin_layout Standard
-For help, send an e-mail to the 
-\begin_inset LatexCommand url
-name "CIG Computational Science Mailing List"
-target "cig-cs at geodynamics.org"
-
-\end_inset
-
-.
- You can subscribe to the 
-\family typewriter
-cig-cs
-\family default
- mailing list and view archived discussions at the 
-\begin_inset LatexCommand htmlurl
-name "CIG Mail Lists web page"
-target "geodynamics.org/cig/lists"
-
-\end_inset
-
-.
- If you encounter any bugs or have problems installing Cigma, please submit
- a report to the 
-\begin_inset LatexCommand htmlurl
-name "CIG Bug Tracker"
-target "geodynamics.org/bugs"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Section
-Installation from Source
-\end_layout
-
-\begin_layout Standard
-To install Cigma, first download the source package from the 
-\begin_inset LatexCommand htmlurl
-name "CIG Cigma web page"
-target "geodynamics.org/cig/software/packages/cs/cigma"
-
-\end_inset
-
-.
- For this step, you will need the GNU C++ compiler and the HDF5 library.
- After unpacking the compressed tar file, issue the following commands
-\end_layout
-
-\begin_layout LyX-Code
-$ tar xvfz cigma-0.9.1
-\end_layout
-
-\begin_layout LyX-Code
-$ cd cigma-0.9.1
-\end_layout
-
-\begin_layout LyX-Code
-$ ./configure --with-hdf5=${HDF5_PREFIX}
-\end_layout
-
-\begin_layout LyX-Code
-$ make
-\end_layout
-
-\begin_layout LyX-Code
-$ sudo make install
-\end_layout
-
-\begin_layout Standard
-You should now be able to access the cigma executable.
- If your HDF5 library is installed with a default prefix location, then
- you can omit the configure flag --with-hdf5 in the commands listed above.
-\end_layout
-
-\begin_layout Section
-Software Dependencies
-\end_layout
-
-\begin_layout Standard
-While only the HDF5 library is required to be preinstalled, several other
- software packages are recommended to easily access the data in the output
- files, or to provide additional functionality.
-\end_layout
-
-\begin_layout Subsection
-HDF5
-\end_layout
-
-\begin_layout Standard
-HDF5 is available for download from 
-\begin_inset LatexCommand htmlurl
-name "The HDF Group"
-target "hdfgroup.org/HDF5"
-
-\end_inset
-
-.
- Binaries can be obtained at 
-\begin_inset LatexCommand htmlurl
-name "hdfgroup.org/HDF5/release/obtain5.html"
-target "hdfgroup.org/HDF5/release/obtain5.html"
-
-\end_inset
-
-.
- To install this library from source, download the latest stable version
- (currently 1.6.5) and issue the following commands
-\end_layout
-
-\begin_layout LyX-Code
-$ tar xvfz hdf5-1.6.5
-\end_layout
-
-\begin_layout LyX-Code
-$ cd hdf5-1.6.5
-\end_layout
-
-\begin_layout LyX-Code
-$ ./configure
-\end_layout
-
-\begin_layout LyX-Code
-$ make
-\end_layout
-
-\begin_layout LyX-Code
-$ sudo make install
-\end_layout
-
-\begin_layout Standard
-After running the above installation procedure, you should be able to access
- the h5ls and h5dump command line utilities.
-\end_layout
-
-\begin_layout Subsection
-VTK
-\end_layout
-
-\begin_layout Standard
-VTK is available from 
-\begin_inset LatexCommand htmlurl
-name "Kitware, Inc."
-target "www.vtk.org/get-software.php"
-
-\end_inset
-
-.
- We recommend that you install this library from a binary package by using
- your favorite package manager.
- However, make sure to install the associated development headers, which
- will typically be included inside a package suffixed with -dev or -devel.
- If you have installed VTK in a non-standard location, you will have to
- use the following additional flag when running configure in the installation
- procedure for Cigma.
-\end_layout
-
-\begin_layout LyX-Code
-$ ./configure [...] --with-vtk=${VTK_PREFIX}
-\end_layout
-
-\begin_layout Standard
-where you should substitute for your custom prefix path pointing to the
- VTK library.
-\end_layout
-
-\begin_layout Subsection
-NumPy
-\end_layout
-
-\begin_layout Standard
-NumPy is a Python module which adds support for large multi-dimensional
- arrays and matrices, and is available for download from the 
-\begin_inset LatexCommand htmlurl
-name "NumPy Home Page"
-target "numpy.scipy.org "
-
-\end_inset
-
-.
- To install this extension module from source, download it and issue the
- following command in the NumPy source directory
-\end_layout
-
-\begin_layout LyX-Code
-$ sudo python setup.py install
-\end_layout
-
-\begin_layout Standard
-You should now be able to successfully run 'import numpy' from within your
- standard Python interpreter shell.
-\end_layout
-
-\begin_layout Subsection
-FIAT
-\end_layout
-
-\begin_layout Standard
-The Finite Element Automatic Tabulator (FIAT) Python module supports generation
- of arbitrary order instances of the Lagrange elements, as well as arbitrary
- order instances of the Jacobi-type quadrature rules on the same element
- shapes.
- It is available from 
-\begin_inset LatexCommand htmlurl
-name "The FEniCS Project"
-target "www.fenics.org/wiki/FIAT"
-
-\end_inset
-
-.
- 
-\end_layout
-
-\begin_layout Standard
-To install this module, download it and issue the following command inside
- the FIAT source directory:
-\end_layout
-
-\begin_layout LyX-Code
-$ sudo python setup.py install
-\end_layout
-
-\begin_layout Standard
-You should now be able to successfully run 'import FIAT' from within your
- standard Python interpreter shell.
-\end_layout
-
-\begin_layout Subsection
-PyTables
-\end_layout
-
-\begin_layout Standard
-PyTables is a Python extension module that builds on top of the HDF5 library.
- It provides a convenient scripting interface to manipulate HDF5 files,
- which can be used to manipulate the input/output files created by Cigma.
- PyTables is available for download from 
-\begin_inset LatexCommand htmlurl
-name "PyTables"
-target "www.pytables.org"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-To install this extension from source, download the latest stable version
- (currently 2.0) and issue the following command in the PyTables source directory
-\end_layout
-
-\begin_layout LyX-Code
-$ sudo python setup.py install
-\end_layout
-
-\begin_layout Standard
-You should now be able to run 'import tables' from within your standard
- Python interpreter shell.
-\end_layout
-
-\begin_layout Subsection
-HDFView
-\end_layout
-
-\begin_layout Standard
-NCSA HDFView is a graphical user interface tool for accessing data in your
- HDF5 files.
- You can use it for viewing the internal file hierarchy in a tree structure,
- adding new datasets, and modifying or deleting existing datasets.
- You can download it from the 
-\begin_inset LatexCommand htmlurl
-name "HDFView home page"
-target "hdf.ncsa.uiuc.edu/hdf-java-html/hdfview"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Chapter
-Running Cigma
-\end_layout
-
-\begin_layout Standard
-[[This chapter explains the usage of every command in cigma, and any other
- information necessary for running the program (as such, the description
- of the file formats belongs here, not in chapter 2).
- The information given here should also be converted into the corresponding
- set of man pages and usage messages.]]
-\end_layout
-
-\begin_layout Section
-Design
-\end_layout
-
-\begin_layout Standard
-Cigma is designed to run from shell scripts, and thus all operations can
- be specifiead as command line arguments given to an executable program
- called cigma.
- This program understands a number of subcommands.
-\end_layout
-
-\begin_layout Standard
-Since cigma is used for obtaining error estimates between arbitrary fields,
- its primary operation revolves around the compare subcommand.
- When calling this subcommand, you will need to provide two dataset arguments
- (one for each field), a quadrature rule, and a mesh over which to integrate.
- 
-\end_layout
-
-\begin_layout Standard
-[[XXX: more notes here]]
-\end_layout
-
-\begin_layout Chapter
-Examples
-\end_layout
-
-\begin_layout Standard
-[[In this chapter offer various case studies as examples.
- Explain how to download the sample data, and provide the exact commands
- to run on that data.
- Show various visualization techniques for the output residuals.
- Some of these comparisons are targetted to be incorporated as examples
- for cigma-1.0 release.
- Preview images are to be included in a separtae lyx file.]]
-\end_layout
-
-\begin_layout Standard
-[[5.1 Sequence of meshes -- give 2d and 3d examples using a sequence of meshes
- with decreasing $h$ (or increasing $p$)]]
-\end_layout
-
-\begin_layout Standard
-[[5.2 Finite element vs.
- Finite element comparison -- pylith strikeslip benchmark for 3d example
- (hex vs tet)]]
-\end_layout
-
-\begin_layout Standard
-[[5.3 Finite element vs.
- Analytic -- gale vs analytic benchmark for 2d example, pylith vs disloc3d
- benchmark for 3d example]]
-\end_layout
-
-\begin_layout Standard
-[[5.4 Spectral vs.
- Finite element -- hc vs citcoms for 3d example]]
-\end_layout
-
-\begin_layout Standard
-[[5.5 Spectral vs.
- Analytic -- magma vs benchmarks]]
-\end_layout
-
-\begin_layout Standard
-[[5.6 Spectral vs.
- Analytic -- MAG vs analytic benchmark]]
-\end_layout
-
-\begin_layout Section
-Convergence of Global Residual
-\end_layout
-
-\begin_layout Standard
-XXX: Transfer more notes...
-\end_layout
-
-\begin_layout Standard
-[[Quick plot of h-sequence of meshes generated with gmsh]]
-\end_layout
-
-\begin_layout Standard
-[[Here, reproduce (similar?) convergence results as in Jasak H.'s Error analysis
- and estimation PhD thesis (chapter 4, pg 210)...XXX: add to refs!]]
-\end_layout
-
-\begin_layout Section
-Comparing two distinct finite element discretizations
-\end_layout
-
-\begin_layout Standard
-XXX: transfer notes
-\end_layout
-
-\begin_layout Standard
-[[Copy description of pylith from its manual]]
-\end_layout
-
-\begin_layout Standard
-[[Describing benchmark problem being solved...(only strikeslip benchmark, so
- cut discussion about the reverse slip benchmark]]
-\end_layout
-
-\begin_layout Section
-Comparing against analytic solution
-\end_layout
-
-\begin_layout Standard
-XXX: transfer notes...
-\end_layout
-
-\begin_layout Standard
-[[Describing okada disloc3d solution from paper (add okada paper to refs!)]]
-\end_layout
-
-\begin_layout Standard
-[[Describing (extract -> eval -> compare) command sequence]]
-\end_layout
-
-\begin_layout Standard
-[[Describing separate evaluation step using disloc3d executable]]
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-key "key-1"
-
-\end_inset
-
-[[XXX: Add new refs here]]
-\end_layout
-
-\end_body
-\end_document