[cig-commits] r6391 - mc/3D/CitcomS/trunk/doc/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Sat Mar 24 16:05:03 PDT 2007
Author: tan2
Date: 2007-03-24 16:05:03 -0700 (Sat, 24 Mar 2007)
New Revision: 6391
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
Finished Cookbook7
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2007-03-24 23:03:00 UTC (rev 6390)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2007-03-24 23:05:03 UTC (rev 6391)
@@ -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
@@ -3450,7 +3450,7 @@
\begin_layout Enumerate
\family typewriter
-$HOME/.pyre/CitcomS.cfg
+$HOME/.pyre/CitcomS/CitcomS.cfg
\family default
, for user settings and preferences;
\end_layout
@@ -8500,10 +8500,10 @@
\begin_layout Itemize
Domain size:
-\begin_inset Formula $45{}^{\circ}$
+\begin_inset Formula $45^{\circ}$
\end_inset
-
+
\begin_inset Formula $\times$
\end_inset
@@ -8622,6 +8622,464 @@
\end_layout
+\begin_layout Section
+Cookbook 7: Thermo-chemical Convection
+\end_layout
+
+\begin_layout Subsection
+Problem
+\end_layout
+
+\begin_layout Standard
+You would like to solve 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.
+
+\end_layout
+
+\begin_layout Subsection
+Solution
+\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.
+
+\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 a subdirectory
+\family typewriter
+output/
+\family default
+.
+ This is done by specifying:
+\end_layout
+
+\begin_layout LyX-Code
+datadir = output
+\end_layout
+
+\begin_layout Standard
+You are interested in the composition field, so the compostion output is
+ enabled and some output files are disabled:
+\end_layout
+
+\begin_layout LyX-Code
+output_optional = tracer,comp_nd
+\end_layout
+
+\begin_layout Standard
+The most important parameters are in
+\family typewriter
+CitcomS.solver.tracer
+\family default
+ section.
+ You will turn on the tracer module by:
+\end_layout
+
+\begin_layout LyX-Code
+tracer = 1
+\end_layout
+
+\begin_layout Standard
+The number of tracers and their initial location must be set.
+ Here, you specify
+\family typewriter
+tracer_ic_method=0
+\family default
+.
+ The tracers will be generated pseudo-randomly automatically, with a total
+ number equal to
+\family typewriter
+tracers_per_element
+\family default
+
+\begin_inset Formula $\times$
+\end_inset
+
+(total number of finite elements).
+ If
+\family typewriter
+tracer_ic_method=1
+\family default
+, all processors will read the location (and flavors, see next paragraph)
+ of the tracers from the same file specified by
+\family typewriter
+tracer_file
+\family default
+.
+ If
+\family typewriter
+tracer_ic_method=2
+\family default
+ or
+\family typewriter
+restart=on
+\family default
+ (in
+\family typewriter
+CitcomS.solver.ic
+\family default
+ 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
+\family typewriter
+CitcomS.solver
+\family default
+ section) and
+\family typewriter
+solution_cycles_init
+\family default
+ (in
+\family typewriter
+CitcomS.solver.ic
+\family default
+ section).
+
+\end_layout
+
+\begin_layout LyX-Code
+tracer_ic_method = 0
+\newline
+tracers_per_element = 20
+\newline
+tracer_file = tracer.dat
+\end_layout
+
+\begin_layout Standard
+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 (
+\family typewriter
+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.
+ Because the tracers are automatically generated, you need to specify how
+ to assign the flavor to each tracer.
+ If
+\family typewriter
+ic_method_for_flavors=0
+\family default
+, tracers above
+\family typewriter
+z_interface
+\family default
+ are assigned to flavor 0, and tracers below
+\family typewriter
+z_interface
+\family default
+ to flavor 1.
+\end_layout
+
+\begin_layout LyX-Code
+tracer_flavors = 2
+\newline
+ic_method_for_flavors = 0
+\newline
+z_interface = 0.7
+\end_layout
+
+\begin_layout Standard
+The thermo-chemical convection module is turned on by:
+\end_layout
+
+\begin_layout LyX-Code
+chemical_buoyancy = 1
+\end_layout
+
+\begin_layout Standard
+The composition field is determined by the ratio method (
+\family typewriter
+buoy_type=1
+\family default
+)
+\begin_inset LatexCommand \cite{Tackely King tracer ratio method}
+
+\end_inset
+
+.
+ The density anomaly of the anomalous chemical composition is 0.4.
+
+\end_layout
+
+\begin_layout LyX-Code
+buoy_type = 1
+\newline
+buoyancy_ratio = 0.4
+\end_layout
+
+\begin_layout Standard
+The code keep the tracks 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.
+ If
+\family typewriter
+tracer_ic_method=2
+\family default
+ or
+\family typewriter
+restart=on
+\family default
+ (in
+\family typewriter
+CitcomS.solver.ic
+\family default
+ section), the code will read in the location of the tracers, as well as
+ the initial sum of the bulk composition, from the previous run.
+ One can reset the initial sum of the bulk composition with the current
+ sum by turning on this parameter:
+\end_layout
+
+\begin_layout LyX-Code
+reset_initial_composition = 0
+\end_layout
+
+\begin_layout Standard
+The regular grid is an auxillary grid to help locating 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.
+ A general rule of thumb is that the grid spacing of the regular grid should
+ be less than
+\begin_inset Formula $18/(nodex\times nprocx)$
+\end_inset
+
+.
+ These parameters are used only in the full spherical version.
+\end_layout
+
+\begin_layout LyX-Code
+regular_grid_deltheta = 1.0
+\newline
+regular_grid_delphi = 1.0
+\end_layout
+
+\begin_layout Standard
+If you encounter any error, look for the end of the tracer log files (
+\family typewriter
+cookbook7.tracer_log.*
+\family default
+) for error messages.
+ Note that this code does not work if
+\family typewriter
+nprocx
+\family default
+ or
+\family typewriter
+nprocy
+\family default
+ is greater than 1 in the full spherical version.
+ The regional spherical version does not have this constraint.
+\end_layout
+
+\begin_layout Subsubsection
+Example: Thermo-chemical Convection,
+\family typewriter
+cookbook7.cfg
+\end_layout
+
+\begin_layout LyX-Code
+[CitcomS]
+\newline
+solver = full
+\newline
+steps = 31 ; number of time steps
+\newline
+
+\newline
+
+\newline
+[CitcomS.c
+ontroller]
+\newline
+monitoringFrequency = 10 ; how often outputs are created
+\newline
+
+\newline
+
+\newline
+[CitcomS.solv
+er]
+\newline
+datadir = output ; path to output directory
+\newline
+datafile = cookbook7
+ ; prefix of output filenames
+\newline
+rayleigh = 1e7
+\newline
+
+\newline
+
+\newline
+[CitcomS.solver.ic]
+\newline
+num_perturbati
+ons = 1
+\newline
+perturbl = 3
+\newline
+perturbm = 2
+\newline
+perturblayer = 5
+\newline
+perturbmag = 0.05
+\newline
+
+\newline
+
+\newline
+[CitcomS.solver.out
+put]
+\newline
+output_optional = tracer,comp_nd
+\newline
+
+\newline
+
+\newline
+[CitcomS.solver.tracer]
+\newline
+tracer = 1
+\newline
+tracer_ic_met
+hod = 0
+\newline
+tracers_per_element = 20
+\newline
+tracer_file = tracer.dat
+\newline
+
+\newline
+tracer_flavors = 2
+\newline
+ic_metho
+d_for_flavors = 0
+\newline
+z_interface = 0.7
+\newline
+
+\newline
+chemical_buoyancy = 1
+\newline
+buoy_type = 1
+\newline
+buoyancy_rati
+o = 0.4
+\newline
+reset_initial_composition = 0
+\newline
+
+\newline
+regular_grid_deltheta = 1.0
+\newline
+regular_grid_delphi
+ = 1.0
+\newline
+
+\newline
+
+\newline
+# Assign the viscosities.
+\newline
+[CitcomS.solver.visc]
+\newline
+VISC_UPDATE = on
+\newline
+num_mat
+ = 4
+\newline
+visc0 = 1,1,1,1
+\newline
+TDEPV = on
+\newline
+viscE = 0.2,0.2,0.2,0.2
+\newline
+viscT = 0,0,0,0
+\newline
+VMIN = on
+\newline
+visc_min
+ = 1.0
+\newline
+VMAX = on
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Graphics
+ filename graphics/cookbook7.jpg
+ lyxscale 30
+ scale 30
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+\begin_inset LatexCommand \label{fig:Cookbook-7:-The}
+
+\end_inset
+
+Cookbook 7: The composition and velocity field at the 20th step.
+ The arrows are the velocity vectors.
+ The composition field is shown in an isosurface of 0.7 and in a cross section.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Discussion
+\end_layout
+
+\begin_layout Standard
+The results for this problem are presented in Figure
+\begin_inset LatexCommand \ref{fig:Cookbook-7:-The}
+
+\end_inset
+
+.
+ The buoyancy ratio in this model is too low to stablize 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 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.
+\end_layout
+
\begin_layout Part
Appendices
\end_layout
@@ -11962,7 +12420,7 @@
\begin_inset Text
\begin_layout Standard
-The grid space of the regular grid.
+The grid spacing of the regular grid.
The regular grid is an auxillary grid to help locating the tracers.
\end_layout
@@ -12015,7 +12473,12 @@
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.)
\end_layout
@@ -18952,5 +19415,15 @@
\end_layout
+\begin_layout Bibliography
+
+\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.
+ Geophys.
+ Geosyst., 4, 8302, doi:10.1029/2001GC000214.
+\end_layout
+
\end_body
\end_document
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