[cig-commits] r7923 - doc/CitcomS/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Fri Aug 31 15:50:36 PDT 2007
Author: tan2
Date: 2007-08-31 15:50:35 -0700 (Fri, 31 Aug 2007)
New Revision: 7923
Modified:
doc/CitcomS/manual/citcoms.lyx
Log:
Update the manual up to chapter 5
Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx 2007-08-31 21:30:26 UTC (rev 7922)
+++ doc/CitcomS/manual/citcoms.lyx 2007-08-31 22:50:35 UTC (rev 7923)
@@ -595,7 +595,7 @@
other by Eh Tan; 2) the ability to resume computation from previous checkpoints
; 3) multi-component chemical convection; 4) compressed ASCII output by
Thorsten Becker; 5) reading in initial temperature and tracer location
- from GRD files by Thorsten Becker; 6)solver coupling.
+ from GRD files by Thorsten Becker; 6) exchanger package for solver coupling.
\end_layout
\begin_layout Section
@@ -736,8 +736,8 @@
\begin_layout Standard
With CitComS, the mantle is treated as an anelastic, compressible, viscous
spherical shell under Truncated Anelastic Liquid Approximation.
- With these assumptions, thermal convection is governed by the non-dimensionaliz
-ed equations for conservation of mass, momentum, and energy:
+ With these assumptions, thermal convection is governed by the equations
+ for conservation of mass, momentum, and energy:
\end_layout
\begin_layout Standard
@@ -1335,17 +1335,170 @@
There are two forms of meshes and geometries for CitComS.
By default CitComS will produce a mesh within a regional geometry that
is bound by lines of constant latitude and longitude.
- For a regional mesh there is an option for mesh refinement in which the
- mesh is refined as a function of latitude, longitude, or radius.
+ There is an option to general a global mesh of a spherical shell.
+\end_layout
+
+\begin_layout Standard
+For a regional mesh, CitComS uses meshes that are regular, although considerable
+ flexibility exists for grid refinement in the regional models.
+ There is an option for mesh refinement in which the mesh is refined as
+ a function of latitude, longitude, or radius.
Such refinement is suitable for higher resolutions near boundary layers
or within the center of the map domain, but is incapable of increasing
the resolution near a curvilinear feature, as a plate boundary, unless
that plate boundary is orientated north-south or east-west.
- CitComS is also capable of generating a mesh for an entire spherical shell
- in which elements in map view are approximately equal in area.
- In the full spherical mode, CitComS has 12 caps numbered 0 to 11.
- The caps are approximately square in map view so that the edges of the
- square are orientated diagonally with respect to latitude and longitude.
+\end_layout
+
+\begin_layout Standard
+In regional meshes,
+\emph on
+theta
+\emph default
+ (or
+\begin_inset Formula $x$
+\end_inset
+
+) is the colatitude measured from the north pole,
+\emph on
+fi
+\emph default
+ (or
+\begin_inset Formula $y$
+\end_inset
+
+) is the east longitude, and
+\begin_inset Formula $z$
+\end_inset
+
+ is the radius.
+
+\emph on
+theta
+\emph default
+ and
+\emph on
+fi
+\emph default
+ are in units of radians.
+ Figure
+\begin_inset LatexCommand \ref{fig:Global-Node-Numbering.}
+
+\end_inset
+
+ shows the organization of the mesh in a regional problem.
+ The numbering of the nodes is
+\begin_inset Formula $z$
+\end_inset
+
+-direction first, then
+\begin_inset Formula $x$
+\end_inset
+
+-direction, then
+\begin_inset Formula $y$
+\end_inset
+
+-direction.
+ This numbering convention is used for the input and output data.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Description
+\begin_inset Graphics
+ filename graphics/c_fig3.jpg
+ lyxscale 75
+ width 75page%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+\begin_inset LatexCommand \label{fig:Global-Node-Numbering.}
+
+\end_inset
+
+Global Node Numbering.
+ Left: Global node numbering starts at the base of arrow A (theta_min, fi_min,
+ radius_inner), and advances from 1 at the base to
+\emph on
+nodez
+\emph default
+ at the tip.
+ Upon reaching the tip, numbering continues from the base of arrow B (
+\emph on
+nodez
+\emph default
++1) to its tip (2
+\emph on
+nodez
+\emph default
+), and so on for all nodes on the plane fi = fi_min.
+ Right: After completing each theta radius plane, the fi index is incremented
+ and numbering commences from (theta_min, radius_inner) as on the left.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+For a global mesh, CitComS is also capable of generating a mesh for an entire
+ spherical shell in which elements in map view are approximately equal in
+ area.
+ In the full spherical mode, CitComS has 12 caps numbered 0 to 11 (Figure
+
+\begin_inset LatexCommand \ref{fig:Topological-connectivity-of}
+
+\end_inset
+
+).
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename graphics/cap_order.eps
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+\begin_inset LatexCommand \label{fig:Topological-connectivity-of}
+
+\end_inset
+
+Topological connectivity of the 12 caps.
+ N is the north pole and S is the south pole.
+ The red line marks the 0 degree meridian.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+The caps are approximately square in map view so that the edges of the square
+ are orientated diagonally with respect to latitude and longitude.
The four corners of the domain are connected by great circles (Figure
\begin_inset LatexCommand \ref{fig:Orthographic-projection-of}
@@ -1411,6 +1564,12 @@
\end_layout
+\begin_layout Standard
+\noindent
+\align center
+
+\end_layout
+
\begin_layout Chapter
Installation and Getting Help
\end_layout
@@ -2174,7 +2333,7 @@
\end_layout
\begin_layout Standard
-CitComS v2.1 requires Pythia v0.8.1.x, which
+CitComS 3.0.0 requires Pythia v0.8.1.x, which
\family typewriter
configure
\family default
@@ -2198,7 +2357,15 @@
\family typewriter
.egg
\family default
- packages, in addition to Pythia.
+ packages, in addition to Pythia and store them under
+\family typewriter
+\shape italic
+\emph on
+deps/
+\family default
+\shape default
+\emph default
+.
These are Python packages which are required (either directly or indirectly)
by CitComS.py.
\end_layout
@@ -2622,6 +2789,14 @@
\end_layout
\begin_layout Section
+Exchanger Configuration (Optional)
+\end_layout
+
+\begin_layout Standard
+(TODO)
+\end_layout
+
+\begin_layout Section
\begin_inset LatexCommand \label{sec:HDF5-Configuration}
\end_inset
@@ -3550,115 +3725,12 @@
(1) overrides only the built-in defaults.
\end_layout
-\begin_layout Section
-Coordinate System and Mesh
-\end_layout
-
\begin_layout Standard
-In general, CitComS uses meshes that are regular, although considerable
- flexibility exists for grid refinement in the regional models.
- In regional meshes,
-\emph on
-theta
-\emph default
- (or
-\begin_inset Formula $x$
-\end_inset
-
-) is the colatitude measured from the north pole,
-\emph on
-fi
-\emph default
- (or
-\begin_inset Formula $y$
-\end_inset
-
-) is the east longitude, and
-\begin_inset Formula $z$
-\end_inset
-
- is the radius.
-
-\emph on
-theta
-\emph default
- and
-\emph on
-fi
-\emph default
- are in units of radians.
- Figure
-\begin_inset LatexCommand \ref{fig:Global-Node-Numbering.}
-
-\end_inset
-
- shows the organization of the mesh in a regional problem.
- The numbering of the nodes is
-\begin_inset Formula $z$
-\end_inset
-
--direction first, then
-\begin_inset Formula $x$
-\end_inset
-
--direction, then
-\begin_inset Formula $y$
-\end_inset
-
--direction.
- This numbering convention is used for the input and output data.
-\end_layout
-
-\begin_layout Standard
\noindent
\align center
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status collapsed
-\begin_layout Description
-\begin_inset Graphics
- filename graphics/c_fig3.jpg
- lyxscale 75
- width 75page%
-
-\end_inset
-
-
\end_layout
-\begin_layout Caption
-\begin_inset LatexCommand \label{fig:Global-Node-Numbering.}
-
-\end_inset
-
-Global Node Numbering.
- Left: Global node numbering starts at the base of arrow A (theta_min, fi_min,
- radius_inner), and advances from 1 at the base to
-\emph on
-nodez
-\emph default
- at the tip.
- Upon reaching the tip, numbering continues from the base of arrow B (
-\emph on
-nodez
-\emph default
-+1) to its tip (2
-\emph on
-nodez
-\emph default
-), and so on for all nodes on the plane fi = fi_min.
- Right: After completing each theta radius plane, the fi index is incremented
- and numbering commences from (theta_min, radius_inner) as on the left.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Section
Uniprocessor Example
\end_layout
@@ -4200,6 +4272,11 @@
\end_layout
\begin_layout Standard
+(TODO: ascii-gz output) Be warned that the post-process scripts do not understan
+d this output format.
+\end_layout
+
+\begin_layout Standard
The last choice is the most powerful one.
Instead of writing many ASCII files, CitComS.py can write its results into
a single HDF5 (Hierarchical Data Format) file per timestep.
@@ -4715,7 +4792,7 @@
\end_inset
).
- The CitComS.py 2.1 release solves this problem when running the software
+ Since v2.1 release, CitComS.py solves this problem when running the software
on computers that have parallel file systems by assembling a binary HDF5
file in parallel I/O mode.
@@ -6000,6 +6077,16 @@
\end_layout
\begin_layout Standard
+If you select compressed ASCII
+\family typewriter
+(ascii-gz)
+\family default
+ for the output format, there is no post-processing script for it.
+ You need to decompress and rename the output files before you can use the
+ post-processing script described below.
+\end_layout
+
+\begin_layout Standard
If you select ASCII for the output format, you will have many output files.
An example of a filename for the velocity output is
\family typewriter
@@ -6151,6 +6238,10 @@
The latter file is the OpenDX header for the data.
\end_layout
+\begin_layout Standard
+(TODO: optional output)
+\end_layout
+
\begin_layout Section
Postprocessing in a Non-Cluster Environment
\end_layout
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