[cig-commits] r7656 - cs/cigma/branches/cigma-0.9b1/doc/manual
luis at geodynamics.org
luis at geodynamics.org
Thu Jul 12 19:04:04 PDT 2007
Author: luis
Date: 2007-07-12 19:04:04 -0700 (Thu, 12 Jul 2007)
New Revision: 7656
Modified:
cs/cigma/branches/cigma-0.9b1/doc/manual/cigma.lyx
Log:
Quick update
Modified: cs/cigma/branches/cigma-0.9b1/doc/manual/cigma.lyx
===================================================================
--- cs/cigma/branches/cigma-0.9b1/doc/manual/cigma.lyx 2007-07-13 02:00:42 UTC (rev 7655)
+++ cs/cigma/branches/cigma-0.9b1/doc/manual/cigma.lyx 2007-07-13 02:04:04 UTC (rev 7656)
@@ -1,4 +1,4 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -63,7 +63,7 @@
placement H
wide false
sideways false
-status collapsed
+status open
\begin_layout Standard
\begin_inset Graphics
@@ -268,7 +268,8 @@
\end_inset
.
- After unpacking the source, issue the following command
+ After unpacking the source and installing the dependencies, issue the following
+ command
\end_layout
\begin_layout LyX-Code
@@ -292,23 +293,45 @@
\end_layout
\begin_layout Standard
-The primary dependency for Cigma is the Hierarchical Data Format (HDF5)
- library, which can be obtained from [TODO: what did you wish here? URL
- that follows?].
- HDF5 is available for download from
-\begin_inset LatexCommand \htmlurl[The HDF Group]{hdf.ncsa.uiuc.edu/HDF5}
+HDF5 is available for download from
+\begin_inset LatexCommand \htmlurl[The HDF Group]{hdfgroup.org/HDF5}
\end_inset
.
+ Binaries can be obtained from http://hdfgroup.org/HDF5/release/obtain5.html
+ (TODO: linkify).
+ To install from source, download the latest stable version of this library
+ (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 --prefix=/usr/local
+\end_layout
+
+\begin_layout LyX-Code
+$ make
+\end_layout
+
+\begin_layout LyX-Code
+$ sudo make install
+\end_layout
+
\begin_layout Subsection
-PyTables (optional)
+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.
It is available from
\begin_inset LatexCommand \htmlurl[PyTables]{www.pytables.org}
@@ -318,18 +341,22 @@
\end_layout
\begin_layout Standard
-To compile and install this extension, download the latest stable version
+To install this extension from source, download the latest stable version
and issue the following commands
\end_layout
\begin_layout LyX-Code
-$ cd pytables-2.x.x
+$ tar xvfz pytables-2.x
\end_layout
\begin_layout LyX-Code
-$ python setup.py install --prefix=$HOME
+$ cd pytables-2.x
\end_layout
+\begin_layout LyX-Code
+$ sudo python setup.py install
+\end_layout
+
\begin_layout Subsection
HDFView (optional)
\end_layout
@@ -348,7 +375,7 @@
\end_layout
\begin_layout Standard
-(TODO: insert image of bmssnog.h5)
+(TODO: insert figures/hdfview-bmrsnog.png)
\end_layout
\begin_layout Section
@@ -422,20 +449,13 @@
\end_layout
\begin_layout Subsection
-Reference coordinates
-\end_layout
-
-\begin_layout Standard
-(TODO: insert vtk image here)
-\end_layout
-
-\begin_layout Subsection
Shape Functions
\end_layout
\begin_layout Standard
Note that the shape functions have been defined on the reference-coordinate
space.
+ [TODO: insert figures/reference-tet4.png]
\end_layout
\begin_layout Subparagraph*
@@ -456,6 +476,7 @@
\begin_layout Standard
For future reference, one can also evaluate the shape functions on a linear
hexahedral element.
+ [TODO: insert reference-hex8.png]
\end_layout
\begin_layout Subparagraph*
@@ -526,10 +547,6 @@
Support for metadata
\end_layout
-\begin_layout Standard
-(TODO: edit following part of intro-to-hdf5 chapter from CitcomS manual)
-\end_layout
-
\begin_layout Subsection
About HDF5
\end_layout
@@ -573,41 +590,6 @@
The storage layout specifies how the data arrays are arranged in the file.
\end_layout
-\begin_layout Standard
-The data array contains the values of the array elements and can be either
- stored together in a contiguous file space or split into smaller
-\shape italic
-chunks
-\shape default
- stored at any allocated location.
- Chunks are defined as equally-sized multi-dimensional subarrays (blocks)
- of the whole data array and each chunk is stored in a separate contiguous
- file space.
- Extensible datasets whose dimensions can grow are required to be stored
- in chunks.
- One dimension is increased by allocating new chunks at the end of the file
- to cover the extension.
-\end_layout
-
-\begin_layout Standard
-HDF5 also supports access to portions (or selections) of a dataset by
-\shape italic
-hyperslabs
-\shape default
-, which consist of a subarray or strided subarray of the multi-dimensional
- dataset.
- The selection is performed in the file dataspace for the dataset.
- HDF5 also supports parallel I/O.
- Parallel access is supported through MPI-IO.
- The file and datasets are collectively created/opened by all participating
- processes.
- Each process accesses part of a dataset by defining its own file dataspace
- for that dataset.
- When accessing data, the data transfer property specifies whether each
- process will perform independent I/O or all processes will perform collective
- I/O.
-\end_layout
-
\begin_layout Section
Field Metadata
\end_layout
@@ -631,17 +613,12 @@
inside the element.
\end_layout
-\begin_layout Standard
-(TODO: insert tree with all metadata definitions)
-\end_layout
-
\begin_layout Chapter
Running Cigma
\end_layout
\begin_layout Standard
-The data flow in Cigma is decoupled to the extent [TODO: more to this sentence?].
-
+As a command line utility, Cigma will
\end_layout
\begin_layout Section
@@ -651,7 +628,7 @@
\begin_layout LyX-Code
\series bold
-cigma compare --first=field1.h5:/path/to/displ/0
+cigma-compare --first=field1.h5:/path/to/displ/0
\backslash
\end_layout
@@ -677,7 +654,7 @@
\begin_layout LyX-Code
\series bold
-cigma import --coordinates=mesh.coord
+cigma-import.py --coordinates=mesh.coord
\backslash
\end_layout
@@ -685,7 +662,7 @@
\begin_layout LyX-Code
\series bold
- --connectivity=mesh.connect
+ --connectivity=mesh.connect
\backslash
\end_layout
@@ -693,7 +670,7 @@
\begin_layout LyX-Code
\series bold
- --variable=velocity
+ --variable=velocity
\backslash
\end_layout
@@ -701,7 +678,7 @@
\begin_layout LyX-Code
\series bold
- --variable-step=step00010
+ --variable-step=step00010
\backslash
\end_layout
@@ -709,7 +686,7 @@
\begin_layout LyX-Code
\series bold
- --variable-data=velo-field.10.time
+ --variable-data=velo-field.10.time
\backslash
\end_layout
@@ -717,7 +694,7 @@
\begin_layout LyX-Code
\series bold
- --output=model.h5
+ --output=model.h5
\end_layout
\begin_layout Standard
@@ -756,10 +733,6 @@
`-- step00010
\end_layout
-\begin_layout Standard
-
-\end_layout
-
\begin_layout Chapter
Numerical Results
\end_layout
@@ -773,17 +746,46 @@
\end_layout
\begin_layout Standard
-(TODO: insert vtk images for the t=0, 10, 50, 100 years)
+The following images depict isosurfaces of the residual field over a series
+ of time steps (0, 10, 50, 100 years)
\end_layout
+\begin_layout Standard
+For the displacement field,
+\end_layout
+
+\begin_layout Standard
+(insert: ssnog-p0250-g0500.velo-100.png)
+\end_layout
+
+\begin_layout Standard
+For the velocity field,
+\end_layout
+
+\begin_layout Standard
+(TODO: insert ssnog-p0500-g0500.velo-010.png)
+\end_layout
+
+\begin_layout Standard
+(insert: ssnog-p0500-g0500.velo-050.png)
+\end_layout
+
+\begin_layout Standard
+(insert: ssnog-p0500-g0500.velo-100.png)
+\end_layout
+
\begin_layout Subsection
Reverse-slip with no gravity
\end_layout
\begin_layout Standard
-(TODO: insert high res vtk image)
+(TODO: insert rsnog-p0250-g0500.disp-010.png)
\end_layout
+\begin_layout Standard
+(TODO: insert rsnog-p0250-analytic.disp-000.png)
+\end_layout
+
\begin_layout LyX-Code
\end_layout
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