[cig-commits] r5488 - mc/3D/CitcomS/trunk/doc/manual

[sue at geodynamics.org]

Author: sue
Date: 2006-12-06 16:12:17 -0800 (Wed, 06 Dec 2006)
New Revision: 5488

Modified:
   mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
small changes to chapt 6; standardized cross refference style; sstandardized code spacing

Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx	2006-12-06 23:51:21 UTC (rev 5487)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx	2006-12-07 00:12:17 UTC (rev 5488)
@@ -321,7 +321,7 @@
 CitComS is a finite element code designed to solve thermal convection problems
  relevant to earth's mantle released under the GNU General Public License
  (see Appendix 
-\begin_inset LatexCommand \ref{cha:License}
+\begin_inset LatexCommand \vref{cha:License}
 
 \end_inset
 
@@ -527,7 +527,7 @@
 l Data Format).
  The HDF5 format allows you to deal with the massive data output created
  for production runs (see Chapter 
-\begin_inset LatexCommand \ref{cha:Working-with-HDF5}
+\begin_inset LatexCommand \vref{cha:Working-with-HDF5}
 
 \end_inset
 
@@ -1408,7 +1408,7 @@
 \begin_layout Standard
 Optionally, CitComS can be configured to use a parallel HDF5 library.
  See Section 
-\begin_inset LatexCommand \ref{sec:HDF5-Configuration}
+\begin_inset LatexCommand \vref{sec:HDF5-Configuration}
 
 \end_inset
 
@@ -2221,7 +2221,7 @@
 C compiler command.
  This is usually set to the name of an MPI wrapper command.
  See Section 
-\begin_inset LatexCommand \ref{sec:MPI-Configuration}
+\begin_inset LatexCommand \vref{sec:MPI-Configuration}
 
 \end_inset
 
@@ -3080,7 +3080,7 @@
 Most of the properties you will set using CitComS.py have names which are
  identical to the parameters for the old CitComS, which are described in
  Appendix 
-\begin_inset LatexCommand \ref{cha:Appendix-A:-Input}
+\begin_inset LatexCommand \vref{cha:Appendix-A:-Input}
 
 \end_inset
 
@@ -4012,7 +4012,7 @@
 \family default
 .
  See Chapter 
-\begin_inset LatexCommand \ref{cha:Working-with-HDF5}
+\begin_inset LatexCommand \vref{cha:Working-with-HDF5}
 
 \end_inset
 
@@ -4472,7 +4472,7 @@
  files.
  This situation is inefficient since it requires an extra post-processing
  step for assembling the results from each processor (see Chapter 
-\begin_inset LatexCommand \ref{cha:Postprocessing-and-Graphics}
+\begin_inset LatexCommand \vref{cha:Postprocessing-and-Graphics}
 
 \end_inset
 
@@ -5833,7 +5833,7 @@
 \begin_layout Standard
 The former file is the data file containing simulation results and is referred
  to as the ``capfile''; its format can be found in Appendix 
-\begin_inset LatexCommand \ref{cha:Appendix-C:-CitComS,}
+\begin_inset LatexCommand \vref{cha:Appendix-C:-CitComS,}
 
 \end_inset
 
@@ -6793,8 +6793,8 @@
 \family default
 .
  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.
+ spherical version of the solver.
+ The default is to use the regional spherical version, so this must be set.
 \end_layout
 
 \begin_layout LyX-Code
@@ -7284,7 +7284,7 @@
 \family typewriter
 solver.visc
 \family default
- facility assign the viscosities.
+ facility assigns the viscosities.
  The parameters specify whether the viscosity should be updated at every
  time step (
 \family typewriter
@@ -7488,15 +7488,20 @@
 \end_layout
 
 \begin_layout Standard
-The parameter that controls if a mesh is to be uniform or refined is 
+The parameter that controls whether a mesh is to be uniform or refined is
+ 
 \family typewriter
 solver.mesher.coor
 \family default
 .
  Set it to 
 \family typewriter
-on (solver.mesher.coor=on)
+on
 \family default
+ 
+\family typewriter
+(solver.mesher.coor=on)
+\family default
  in order to read the uneven mesh point coordinates from an input file (specifie
 d by 
 \family typewriter
@@ -7550,8 +7555,6 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.controller]
 \newline
 mo
@@ -7559,8 +7562,6 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.solver]
 \newline
 rayleigh
@@ -7571,8 +7572,6 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.solver.ic]
 \newline
 num_perturbations = 1
@@ -7595,8 +7594,6 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.solver.mesher]
 \newline
 # Read uneven mesh
@@ -7636,8 +7633,6 @@
 \newline
 
 \newline
-
-\newline
 [CitcomS.solver.visc]
 \newline
 VISC_UPDATE
@@ -8087,25 +8082,25 @@
 \end_layout
 
 \begin_layout Enumerate
-On the nodes of the top surface, topography increment is computed by integrating
+On the nodes of the top surface, compute the topography increment by integrating
  normal velocity over time.
  
 \end_layout
 
 \begin_layout Enumerate
-The normal traction on the top surface is calculated based on the accumulated
- topography up to the current time step, and added to the forcing term in
- the matrix version of the momentum equation.
+Calculate the normal traction on the top surface based on the accumulated
+ topography up to the current time step, and add it to the forcing term
+ in the matrix version of the momentum equation.
  
 \end_layout
 
 \begin_layout Enumerate
-Update velocity field with the changed forcing term.
+Update the velocity field with the changed forcing term.
  
 \end_layout
 
 \begin_layout Enumerate
-If velocity field has not converged yet, reiterate steps 1 to 3.
+If the velocity field has not converged yet, repeat steps 1 to 3.
 \end_layout
 
 \begin_layout Subsection
@@ -8124,15 +8119,27 @@
 \end_layout
 
 \begin_layout Itemize
-Domain size: 45 deg 
+Domain size: 
+\begin_inset Formula $45{}^{\circ}$
+\end_inset
+
+ 
 \begin_inset Formula $\times$
 \end_inset
 
- 45 deg 
+ 
+\begin_inset Formula $45^{\circ}$
+\end_inset
+
+ 
 \begin_inset Formula $\times$
 \end_inset
 
- 1200 km
+ 
+\begin_inset Formula $1200\mathrm{\, km}$
+\end_inset
+
+
 \end_layout
 
 \begin_layout Itemize
@@ -8213,7 +8220,8 @@
 \align center
 \begin_inset Graphics
 	filename graphics/cookbook7.eps
-	scale 90
+	lyxscale 80
+	scale 80
 
 \end_inset
 
@@ -11359,7 +11367,7 @@
 \begin_layout Standard
 This section lists the facilities and properties in the Pyre version of
  CitComS.py.
- Most of the properties have identical names for the parameters as those
+ Most of the properties have names which are identical to the parameters
  used in the non-Pyre version of CitComS.py and are explained in the section
  above.
  This section highlights those which have changed and those which are entirely
@@ -11754,7 +11762,13 @@
 \end_layout
 
 \begin_layout Standard
-The job facility controls options for individual batch jobs.
+The 
+\family typewriter
+\size small
+job
+\family default
+\size default
+ facility controls options for individual batch jobs.
 \end_layout
 
 \begin_layout Standard