[cig-commits] r5400 - mc/3D/CitcomS/trunk/doc/manual

[tan2 at geodynamics.org]

Author: tan2
Date: 2006-11-30 15:08:42 -0800 (Thu, 30 Nov 2006)
New Revision: 5400

Modified:
   mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
Updated Chapter 6
* sync'd the manual with the cookbook scripts
* improving the resolution of cookbook5.2.eps is left until the next release

Also, fixed table borders in Appendix A.


Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx	2006-11-30 22:55:21 UTC (rev 5399)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx	2006-11-30 23:08:42 UTC (rev 5400)
@@ -1,4 +1,4 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.2 created this file. For more info see http://www.lyx.org/
 \lyxformat 245
 \begin_document
 \begin_header
@@ -5593,21 +5593,21 @@
  The output files are written in each node under the directory that you
  specified as the 
 \family typewriter
-datafile
-\family default
- property (and maybe 
-\family typewriter
 datadir
 \family default
- property) in the input file.
+ property in the input file.
  To examine those files, login to a node and change directories to the one
  you specified with a prefix.
- For example, if you selected your datafile to be called 
+ For example, if you set 
 \family typewriter
-datafile="/scratch/username/test-case"
+datadir=/scratch/username
 \family default
-, then your output file will be written to 
+ and 
 \family typewriter
+datafile=test-case
+\family default
+ in your input file, then your output files will be written to 
+\family typewriter
 /scratch/username
 \family default
  and will have the prefix 
@@ -6746,16 +6746,11 @@
 \newline
 
 \newline
-# In addition, to determine the temperature, the temperature field
+# In addition, set the initial temperature perturbation to zero.
 \newline
-#
- associated only with this imposed velocity, reset the initial
+[CitcomS.sol
+ver.ic]
 \newline
-# perturbation
- to zero.
-\newline
-[CitcomS.solver.ic]
-\newline
 num_perturbations = 1
 \newline
 perturbmag        = 0.0 
@@ -7178,6 +7173,8 @@
 \newline
 coor_file = coor.dat
 \newline
+
+\newline
 nprocx = 4
 \newline
 nprocy
@@ -7200,33 +7197,37 @@
 \newline
 fi_max = 1
 \newline
+radius_inner = 0.55
+\newline
+radius_outer = 1
+\newline
 
 \newline
 
 \newline
 [CitcomS.solver.visc]
 \newline
-VISC_UPDATE = on
+VISC_UPDATE
+ = on
 \newline
 num_mat = 4
 \newline
 visc0 = 1,1,1,1
 \newline
-TDEPV
- = on
+TDEPV = on
 \newline
 viscE = 0.2,0.2,0.2,0.2
 \newline
 viscT = 0,0,0,0
 \newline
-VMIN = on
+VMIN
+ = on
 \newline
 visc_min = 1.0
 \newline
 VMAX = on
 \newline
-visc_max
- = 100.0
+visc_max = 100.0
 \end_layout
 
 \begin_layout Standard
@@ -7372,8 +7373,12 @@
 \end_inset
 
 .
- The prefix of the file name is specified in 
+ The location and prefix of the file is specified in 
 \family typewriter
+datadir_old
+\family default
+ and 
+\family typewriter
 datafile_old
 \family default
 , and the time step of the velo file in 
@@ -7391,12 +7396,14 @@
 \end_layout
 
 \begin_layout LyX-Code
-datafile_old = ./restart_files/cookbook5
+datadir_old = ./restart_files
 \newline
+datafile_old = cookbook5
+\newline
 restart = on 
 \newline
-solution_cycles_init
- = 0
+solution_cycles
+_init = 0
 \end_layout
 
 \begin_layout Standard
@@ -7450,7 +7457,7 @@
 [CitcomS.controller]
 \newline
 mo
-nitoringFrequency = 10    ; how often outputs are 
+nitoringFrequency = 10    ; how often outputs are created
 \newline
 
 \newline
@@ -7459,14 +7466,16 @@
 datafile
  = cookbook5
 \newline
-datafile_old = ./restart_files/cookbook5
+datadir_old = ./restart_files
 \newline
-rayleigh = 4.07e+08
+datafile_old = cookbook5
 \newline
+rayleigh
+ = 4.07e+08
+\newline
 
 \newline
-[CitcomS.sol
-ver.bc]
+[CitcomS.solver.bc]
 \newline
 topvbc = 1
 \newline
@@ -7476,15 +7485,15 @@
 \newline
 file_vbcs = on
 \newline
-start_age = 55
+start_age
+ = 55
 \newline
 
 \newline
-# Since
- the starting age is set to 55 Ma, there will be 56 velocity
+# Since the starting age is set to 55 Ma, there will be 56 velocity
 \newline
-# files, one
- for each Ma (bvel.dat0, bvel.dat1, ...
+#
+ files, one for each Ma (bvel.dat0, bvel.dat1, ...
  bvel.dat56).
 \newline
 vel_bound_file = ./velocity/bvel.dat
@@ -7556,12 +7565,6 @@
 \end_layout
 
 \begin_layout Standard
-
-\series bold
-(TODO: Rerun cookbook 5 to  get better figure)
-\end_layout
-
-\begin_layout Standard
 \begin_inset Float figure
 placement h
 wide false
@@ -7725,7 +7728,7 @@
 \begin_layout Itemize
 
 \family typewriter
-solver.tsolver.fixed_timestep=7.770000e-10
+solver.tsolver.fixed_timestep = 7.770000e-10
 \family default
  (= ~1000 yrs)
 \end_layout
@@ -7733,7 +7736,7 @@
 \begin_layout Itemize
 
 \family typewriter
-solver.bc.pseudo_free_surf=on
+solver.bc.pseudo_free_surf = on
 \end_layout
 
 \begin_layout Subsection
@@ -7823,7 +7826,7 @@
 \begin_inset Tabular
 <lyxtabular version="3" rows="5" columns="2">
 <features islongtable="true">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="1.75in">
+<column alignment="left" valignment="top" leftline="true" width="1.75in">
 <column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
 <row topline="true">
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
@@ -7939,7 +7942,7 @@
 \end_inset
 </cell>
 </row>
-<row topline="true">
+<row>
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text