[cig-commits] r5459 - mc/3D/CitcomS/trunk/doc/manual

[sue at geodynamics.org]

Author: sue
Date: 2006-12-05 11:19:02 -0800 (Tue, 05 Dec 2006)
New Revision: 5459

Modified:
   mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
small fixes to chap 4, text and table placement

Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx	2006-12-05 18:04:11 UTC (rev 5458)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx	2006-12-05 19:19:02 UTC (rev 5459)
@@ -4741,18 +4741,20 @@
  improve your parallel I/O performance.
 \end_layout
 
-\begin_layout LyX-Code
+\begin_layout Standard
 
 \family roman
 Finally, here is an example section that would appear in a typical CitComS
  input file:
+\end_layout
+
+\begin_layout LyX-Code
+
 \family typewriter
-
-\newline
 [CitcomS.solver.output]
-\family default
+\end_layout
 
-\newline
+\begin_layout LyX-Code
 cb_block_size = 1048576              # 1 MiB
 \newline
 cb_buffer_size = 4194304   
@@ -4783,14 +4785,18 @@
 Time independent data (e.g., node coordinates, grid connectivity) are saved
  in a file (for example, 
 \family typewriter
+\size small
 test-case.h5
 \family default
+\size default
 ) at the first output stage.
  Subsequently, each output stage will save time dependent data (e.g., velocity,
  and temperature) in a separated file (for example, 
 \family typewriter
+\size small
 test-case.100.h5
 \family default
+\size default
  contains data of time step 10).
  Most of the output data from CitComS is specified at the nodes of a logically
  cartesian grid and is therefore well represented by multi-dimensional arrays.
@@ -4811,26 +4817,41 @@
  An additional dimension is provided for storing the components of vector
  and tensor data.
  These data arrays are stored in different groups.
- Each group has a decriptive name.
+ Each group has a descriptive name.
  In addition, there is an 
 \family typewriter
+\size small
 /input
 \family default
+\size default
  group archiving the input parameters of the model.
- Two sample h5 files are provided in 
+ Two sample 
 \family typewriter
+\size small
+.h5
+\family default
+\size default
+ files are provided in 
+\family typewriter
+\size small
 visual/samples/
 \family default
+\size default
  directory.
 \end_layout
 
 \begin_layout Standard
+\noindent
+\align center
 \begin_inset Float table
+placement H
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Standard
+\noindent
+\align center
 \begin_inset Tabular
 <lyxtabular version="3" rows="4" columns="2">
 <features>
@@ -4949,12 +4970,17 @@
 \end_layout
 
 \begin_layout Standard
+\noindent
+\align center
 \begin_inset Float table
+placement H
 wide false
 sideways false
-status open
+status collapsed
 
 \begin_layout Standard
+\noindent
+\align center
 \begin_inset Tabular
 <lyxtabular version="3" rows="16" columns="2">
 <features>
@@ -5392,7 +5418,11 @@
 \end_layout
 
 \begin_layout LyX-Code
-$ h5ls -r file.h5
+$ h5ls -r 
+\emph on
+file
+\emph default
+.h5
 \end_layout
 
 \begin_layout Subsection
@@ -5438,8 +5468,8 @@
  provides a good example for using the PyTables extension module to access
  the data contained in the CitComS HDF5 files.
  In PyTables, datasets can be retrieved from disk as NumPy arrays.
- The retrieval can avoids unnecessary copying of data by using hyperslabs,
- which takes advantage of Python's powerful array slice-indexing.
+ The retrieval avoids unnecessary copying of data by using hyperslabs, which
+ take advantage of Python's powerful array slice-indexing.
 \end_layout
 
 \begin_layout Standard
@@ -5453,29 +5483,22 @@
 
 \begin_layout LyX-Code
 import tables
-\end_layout
+\newline
 
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
+\newline
 h5file = tables.openFile('samples/cookbook1.h5', 'r')
 \end_layout
 
 \begin_layout LyX-Code
 surface_coords = h5file.root.coord[0:12,:,:,-1,:]
-\end_layout
+\newline
 
-\begin_layout LyX-Code
-
+\newline
+data100 = tables.openFile('samples
+/cookbook1.100.h5', 'r')
 \end_layout
 
 \begin_layout LyX-Code
-data100 = tables.openFile('samples/cookbook1.100.h5', 'r')
-\end_layout
-
-\begin_layout LyX-Code
 surface_temperature = data100.root.temperature[0:12,:,:,-1]
 \end_layout