[cig-commits] r5193 - mc/3D/CitcomS/trunk/doc/manual

[tan2 at geodynamics.org]

Author: tan2
Date: 2006-11-07 11:33:31 -0800 (Tue, 07 Nov 2006)
New Revision: 5193

Modified:
   mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
* Fixed a few typos
* Added "TODO" in front of all unfinished text.


Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx	2006-11-07 04:47:48 UTC (rev 5192)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx	2006-11-07 19:33:31 UTC (rev 5193)
@@ -537,7 +537,7 @@
  the most important being the use of HDF5 (a parallel version of the Hierarchica
 l Data Format).
  The HDF5 format allows you to deal with the massive number of files that
- were created for production runs with the del system (see Chapter ???).
+ were created for production runs with the del system (see Chapter (TODO: xref)).
  The new version incorporates 
 \family typewriter
 .cfg
@@ -554,7 +554,7 @@
 
 \end_inset
 
- (in addition to VMT and 
+ (in addition to GMT (TODO: url) and 
 \begin_inset LatexCommand \htmlurl[OpenDX]{www.opendx.org}
 
 \end_inset
@@ -1367,7 +1367,7 @@
 
 \begin_layout Standard
 Users familiar with older versions of CitComS may prefer to install only
- the legacy CitComS tools, CitcomSFull and CitcomSRegional, and forgo use
+ the legacy CitComS tools, CitcomSFull and CitcomSRegional (TODO: fixed font), and forgo use
  of the Pyre framework.
  This process requires only a C compiler.
 \end_layout
@@ -1386,6 +1386,7 @@
 
 \begin_layout Itemize
 (Optional) the Parallel HDF5 library
+(TODO: move this bullet after MPI)
 \end_layout
 
 \begin_layout Itemize
@@ -1456,6 +1457,7 @@
 \begin_layout Quote
 
 \series bold
+(TODO: move this section after MPI)
 Note for Mac OS X Users
 \series default
 : You will need Xcode, which is freely available from 
@@ -1683,7 +1685,7 @@
 \end_layout
 
 \begin_layout Section
-Configuration
+Configuration (TODO: make the following sections to subsections)
 \end_layout
 
 \begin_layout Standard
@@ -2617,6 +2619,7 @@
 \end_layout
 
 \begin_layout LyX-Code
+(TODO: update this description)
 $ svn checkout svn://geodynamics.org/cig/vendor/pythia/v0.8 pythia-0.8 
 \end_layout
 
@@ -3747,6 +3750,7 @@
 \begin_layout Standard
 CitComS.py has already been tested on several NSF TeraGrid platforms.
  Accounts for small allocations are available directly from CIG.
+ (TODO: description of CSA)
 \end_layout
 
 \begin_layout Chapter
@@ -4611,8 +4615,8 @@
 \end_layout
 
 \begin_layout Standard
-For more details, refer to (insert reference to chapter) in the HDF5 documentati
-on, the (insert reference to chapter) in the MPI-2 reference book, and the
+For more details, refer to (TODO:insert reference to chapter) in the HDF5 documentati
+on, the (TODO:insert reference to chapter) in the MPI-2 reference book, and the
  documentation for your parallel file system.
 \end_layout
 
@@ -4625,6 +4629,7 @@
  As such we can use a variety of tools to inspect the structure of an HDF5
  file, as well as for retrieving data in any order.
  To quickly inspect the structure of an HDF5 file, you can use the command
+ h5ls (TODO: font) from the HDF5 library
 \end_layout
 
 \begin_layout LyX-Code
@@ -4633,13 +4638,15 @@
 
 \begin_layout Standard
 You can also recreate the ASCII combined cap format described in Chapter
- (insert reference here) for specific time steps by using the command:
+ (TODO:insert reference here) for specific time steps by using the command:
 \end_layout
 
 \begin_layout LyX-Code
-$ h5tocap file.h5 [step1 [step2 [...]]]
+$ h5tocap file.h5 [frame1 [frame2 [...]]]
 \end_layout
 
+(TODO: output of h5tocap)
+
 \begin_layout Subsection
 Python
 \end_layout
@@ -4707,8 +4714,8 @@
 \end_layout
 
 \begin_layout Standard
-For more details, refer to the documentation for PyTables (insert link here)
- and NumPy (insert link here).
+For more details, refer to the documentation for PyTables (TODO:insert link here)
+ and NumPy (TODO:insert link here).
 \end_layout
 
 \begin_layout Subsection
@@ -4720,11 +4727,11 @@
  You can use it for viewing the internal file hierarchy in a tree structure,
  creating new files, adding or deleting groups and datasets, modifying existing
  datasets.
- (insert image 1 here).
+ (TODO:insert image 1 here).
  HDFView is capable of displaying 2D slices of multi-dimensional datasets,
  with an additional slider that can range over the entire extent of a third
  dimension.
- (insert image 2) here.
+ (TODO:insert image 2) here.
 \end_layout
 
 \begin_layout Chapter
@@ -5479,6 +5486,8 @@
  The fourth tab (unconnected, default to 0) specifies which cap(s) to import.
 \end_layout
 
+(TODO: GMT scripts)
+
 \begin_layout Chapter
 Cookbooks
 \end_layout
@@ -5569,6 +5578,7 @@
 .
  The first set of parameters specifies that you are going to use the full
  spherical version of solver.
+ The default is to use the regional sphercal version, so this must be set.
 \end_layout
 
 \begin_layout LyX-Code
@@ -5576,8 +5586,7 @@
 \end_layout
 
 \begin_layout Standard
-The default is a res?? run, so this must be set.
- The second set of parameters specifies the number of time steps (101),
+The second set of parameters specifies the number of time steps (101),
  how often full outputs of the computation are created (25), and the prefix
  of output filenames (cookbook1).
 \end_layout