[cig-commits] r6392 - mc/3D/CitcomS/trunk/doc/manual
sue at geodynamics.org
sue at geodynamics.org
Sun Mar 25 15:56:46 PDT 2007
Author: sue
Date: 2007-03-25 15:55:42 -0700 (Sun, 25 Mar 2007)
New Revision: 6392
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
mc/3D/CitcomS/trunk/doc/manual/citcoms.pdf
Log:
edits of new copy; attempt to fix an image that is not displaying, still unresolved
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2007-03-24 23:05:03 UTC (rev 6391)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2007-03-25 22:55:42 UTC (rev 6392)
@@ -1,4 +1,4 @@
-#LyX 1.4.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -6258,15 +6258,16 @@
\noindent
\align center
\begin_inset Float figure
-placement H
wide false
sideways false
-status collapsed
+status open
\begin_layout Standard
+\noindent
\align center
\begin_inset Graphics
filename graphics/c_fig5.eps
+ scale 85
\end_inset
@@ -7120,7 +7121,7 @@
\end_layout
\begin_layout Standard
-You would like to solve for thermal convection within a full spherical shell
+This example solves for thermal convection within a full spherical shell
domain.
The full spherical version of CitComS.py is designed to run on a cluster
that decomposes the spherical shell into 12 equal ``caps'' and then distributes
@@ -7333,8 +7334,8 @@
\end_layout
\begin_layout Standard
-As a note, it is not required that 12 processors, with one spherical cap
- per processor, be used.
+As a side note, it is not required that 12 processors, with one spherical
+ cap per processor, be used.
As an end-member possibility, for example, 12 different jobs could be run
on a single computer (
\family typewriter
@@ -7369,9 +7370,9 @@
\end_layout
\begin_layout Standard
-You would like to solve for thermal convection with velocity boundary conditions
+This example solves for thermal convection with velocity boundary conditions
imposed on the top surface within a given region of a sphere.
- You will need to use the regional version of CitComS.py.
+ This requires using the regional version of CitComS.py.
\end_layout
@@ -7587,7 +7588,7 @@
placement h
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\align center
@@ -7634,7 +7635,11 @@
\end_layout
\begin_layout Standard
-You will use cookbook3.cfg.
+You will use
+\family typewriter
+cookbook3.cfg
+\family default
+.
The parameters specify the number of time steps (200), how often outputs
will be created (25), the prefix of the output filenames (
\family typewriter
@@ -7820,7 +7825,7 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\align center
@@ -8623,7 +8628,7 @@
\end_layout
\begin_layout Section
-Cookbook 7: Thermo-chemical Convection
+Cookbook 7: Thermo-Chemical Convection
\end_layout
\begin_layout Subsection
@@ -8631,11 +8636,11 @@
\end_layout
\begin_layout Standard
-You would like to solve for thermo-chemical convection within a full spherical
+This example solves for thermo-chemical convection within a full spherical
shell domain.
Composition heterogenity exists in the Earth mantle.
- The density anomalies due to the composition heterogenity, as well as due
- to the thermal heterogeneity, drives the convection flow.
+ The density anomalies due to composition heterogenity, as well as due to
+ thermal heterogeneity, drive the convection flow.
\end_layout
@@ -8644,22 +8649,25 @@
\end_layout
\begin_layout Standard
-You will use cookbook7.cfg.
- You have encountered most of the parameters in previous cookbooks.
- The initial condition is the same as that in Cookbook 1.
- The viscosity law is the same as that in Cookbook 3.
+You will use
+\family typewriter
+cookbook7.cfg
+\family default
+.
+ Most of the parameters you have encountered in previous cookbooks.
+ The initial condition is the same as in Cookbook 1, and the viscosity law
+ is the same as in Cookbook 3.
\end_layout
\begin_layout Standard
A large number of ASCII files will be output.
- In order to keep the current directory tidy, the output files will be put
+ In order to keep the current directory tidy, the output files can be put
in a subdirectory
\family typewriter
output/
\family default
-.
- This is done by specifying:
+ by specifying
\end_layout
\begin_layout LyX-Code
@@ -8667,8 +8675,8 @@
\end_layout
\begin_layout Standard
-You are interested in the composition field, so the compostion output is
- enabled and some output files are disabled:
+Since you are interested in the composition field, the composition output
+ should be enabled and some output files disabled:
\end_layout
\begin_layout LyX-Code
@@ -8676,12 +8684,12 @@
\end_layout
\begin_layout Standard
-The most important parameters are in
+The most important parameters are in the
\family typewriter
CitcomS.solver.tracer
\family default
section.
- You will turn on the tracer module by:
+ Turn on the tracer module:
\end_layout
\begin_layout LyX-Code
@@ -8709,7 +8717,7 @@
\family typewriter
tracer_ic_method=1
\family default
-, all processors will read the location (and flavors, see next paragraph)
+, all processors will read the location (and flavors; see next paragraph)
of the tracers from the same file specified by
\family typewriter
tracer_file
@@ -8723,16 +8731,16 @@
\family typewriter
restart=on
\family default
- (in
+ (in the
\family typewriter
CitcomS.solver.ic
\family default
- section), each processor will read the location (and flavors, see next
+ section), each processor will read the location (and flavors; see next
paragraph) of the tracers from the file specified by
\family typewriter
datafile_old
\family default
- (in
+ (in the
\family typewriter
CitcomS.solver
\family default
@@ -8740,7 +8748,7 @@
\family typewriter
solution_cycles_init
\family default
- (in
+ (in the
\family typewriter
CitcomS.solver.ic
\family default
@@ -8757,7 +8765,7 @@
\end_layout
\begin_layout Standard
-Each tracer can have a "flavor" attached to it.
+Each tracer can have a ``flavor'' attached to it.
The meaning of the flavor depends on the application.
Here, the flavor indicates the chemical species of the tracer.
There are two flavors of tracers (
@@ -8765,8 +8773,8 @@
tracer_flavors=2
\family default
).
- A tracer of flavor 0 is of the "normal", or ambient, chemical composition,
- while a tracer of flavor 1 is of the "anomalous" chemical composition.
+ A tracer of flavor 0 is of the ``normal,'' or ambient, chemical composition,
+ while a tracer of flavor 1 is of the ``anomalous'' chemical composition.
Because the tracers are automatically generated, you need to specify how
to assign the flavor to each tracer.
If
@@ -8793,7 +8801,7 @@
\end_layout
\begin_layout Standard
-The thermo-chemical convection module is turned on by:
+The thermo-chemical convection module is turned on by
\end_layout
\begin_layout LyX-Code
@@ -8805,7 +8813,7 @@
\family typewriter
buoy_type=1
\family default
-)
+)
\begin_inset LatexCommand \cite{Tackely King tracer ratio method}
\end_inset
@@ -8822,11 +8830,11 @@
\end_layout
\begin_layout Standard
-The code keep the tracks of the sum of the bulk composition.
+The code keeps track of the sum of the bulk composition.
In a perfect world, the sum of the bulk composition would not change with
time.
- However, due to numerical issues, the sum of the bulk composition tends
- to decrease with time.
+ But due to numerical issues, the sum of the bulk composition tends to decrease
+ with time.
If
\family typewriter
tracer_ic_method=2
@@ -8835,7 +8843,7 @@
\family typewriter
restart=on
\family default
- (in
+ (in the
\family typewriter
CitcomS.solver.ic
\family default
@@ -8850,14 +8858,14 @@
\end_layout
\begin_layout Standard
-The regular grid is an auxillary grid to help locating the tracers
+The regular grid is an auxillary grid that helps locate the tracers
\begin_inset LatexCommand \cite{McNamara Zhong Thermochemical}
\end_inset
.
- The optimal grid spacing of the regular grid depends on the size of CitComS
- mesh.
+ The optimal grid spacing of the regular grid depends on the size of the
+ CitComS mesh.
A general rule of thumb is that the grid spacing of the regular grid should
be less than
\begin_inset Formula $18/(nodex\times nprocx)$
@@ -8874,7 +8882,7 @@
\end_layout
\begin_layout Standard
-If you encounter any error, look for the end of the tracer log files (
+If you encounter any error, look at the end of the tracer log files (
\family typewriter
cookbook7.tracer_log.*
\family default
@@ -8892,7 +8900,7 @@
\end_layout
\begin_layout Subsubsection
-Example: Thermo-chemical Convection,
+Example: Thermo-Chemical Convection,
\family typewriter
cookbook7.cfg
\end_layout
@@ -9031,7 +9039,7 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\noindent
@@ -9072,12 +9080,12 @@
\end_inset
.
- The buoyancy ratio in this model is too low to stablize the chemical layer.
+ The buoyancy ratio in this model is too low to stabilize the chemical layer.
A few thermo-chemical plumes are rising from the lower mantle, especially
- the ones at 4, 11, and 12 o'clock directions.
+ the ones at the 4, 11, and 12 o'clock directions.
The resolution of this model is fairly low.
The composition isosurface is slightly discontinuous across the cap boundary.
- A model of higher resultion will not have this kind of artifacts.
+ A model of higher resolution will not have this kind of artifact.
\end_layout
\begin_layout Part
@@ -10360,7 +10368,7 @@
perturblayer
\family default
is ignored in this case.
- The perturbatio is given by:
+ The perturbation is given by:
\begin_inset Formula \[
mag\times\sin\left(\frac{(r-r_{in})\pi}{r_{out}-r_{in}}\right)\left(\sin(m\phi)+\cos(m\phi)\right)P_{lm}(\cos\theta)\]
@@ -11221,7 +11229,7 @@
\begin_layout Standard
Used in conjunction with tracers.
- The tracers define the upper boundary of subducted slab.
+ The tracers define the upper boundary of the subducted slab.
\end_layout
@@ -11266,11 +11274,11 @@
or
\family typewriter
\size small
- low_visc_channel
+ low_visc_wedge
\family default
\size default
- is on, these parameters specify the radial extents of the low viscosity
- zones and the viscosity reduction factor.
+ is on, this specifies the radial extent of the low viscosity zones and
+ the viscosity reduction factor, respectively.
\end_layout
\end_inset
@@ -12255,7 +12263,7 @@
\begin_inset Text
\begin_layout Standard
-If on, enable the tracers.
+If on, enables the tracers.
\end_layout
@@ -12291,7 +12299,7 @@
\family default
\size default
, the tracers are generated randomly, with the number of tracers per element
- speicified by
+ specified by
\family typewriter
\size small
tracers_per_element
@@ -12304,7 +12312,7 @@
tracer_ic_method=1
\family default
\size default
-, the location of the tracers are read from a file specified in
+, the location of the tracers is read from a file specified in
\family typewriter
\size small
tracer_file
@@ -12317,7 +12325,7 @@
tracer_ic_method=
\family default
\size default
-2, the location of the tracers are read from the old tracer output, similar
+2, the location of the tracers is read from the old tracer output, similar
to
\family typewriter
\size small
@@ -12348,7 +12356,7 @@
\begin_layout Standard
The number of flavors among the tracers.
- If it is 0, flavor counting is turned off.
+ If set to 0, flavor counting is turned off.
\end_layout
\end_inset
@@ -12395,7 +12403,7 @@
z_interface
\family default
\size default
- is of flavor 0, otherwise, of flavor 1.
+ are of flavor 0; otherwise, of flavor 1.
\end_layout
\end_inset
@@ -12421,7 +12429,7 @@
\begin_layout Standard
The grid spacing of the regular grid.
- The regular grid is an auxillary grid to help locating the tracers.
+ The regular grid is an auxiliary grid to help locate the tracers.
\end_layout
\end_inset
@@ -12444,7 +12452,7 @@
\begin_inset Text
\begin_layout Standard
-If on, enable thermo-chemical convection.
+If on, enables thermo-chemical convection.
\end_layout
\end_inset
@@ -12473,13 +12481,13 @@
buoy_type=1
\family default
\size default
-, the composition field is determined by the ratio method
+, the composition field is determined by the ratio method
\begin_inset LatexCommand \cite{Tackely King tracer ratio method}
\end_inset
.
- (Other method is not implemented yet.)
+ (No other methods are implemented yet.)
\end_layout
\end_inset
@@ -12502,7 +12510,7 @@
\begin_inset Text
\begin_layout Standard
-The ratio of chemical density anomaly to the reference density
+The ratio of chemical density anomaly to the reference density.
\end_layout
\end_inset
@@ -18428,7 +18436,7 @@
The second field in the header is the number of tracers in the file.
The third field in the header is the number of columns in the file.
The rest of the file is column-based, where the meaning of the columns
- are:
+ is:
\end_layout
\begin_layout LyX-Code
@@ -18461,7 +18469,7 @@
comp_nd
\family default
).
- The format of the files are the same.
+ The format of the files is the same.
The first line of the file is a header.
The fourth field in the header is the bulk sum of the current composition.
The fifth field in the header is the bulk sum of the initial composition.
@@ -18497,7 +18505,7 @@
\end_inset
-License
+License
\end_layout
\begin_layout Standard
@@ -19420,9 +19428,13 @@
\bibitem {Tackely King tracer ratio method}
Tackley, P.J., and S.D.
King (2003), Testing the tracer ratio method for modeling active compositional
- fields in mantle convection simulations, Geochem.
+ fields in mantle convection simulations,
+\emph on
+Geochem.
Geophys.
- Geosyst., 4, 8302, doi:10.1029/2001GC000214.
+ Geosyst., 4,
+\emph default
+8302, doi:10.1029/2001GC000214.
\end_layout
\end_body
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.pdf
===================================================================
(Binary files differ)
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