[cig-commits] r4782 - mc/3D/CitcomS/trunk/doc/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Tue Oct 10 16:48:38 PDT 2006
Author: tan2
Date: 2006-10-10 16:48:38 -0700 (Tue, 10 Oct 2006)
New Revision: 4782
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
* Added subsection on installing OpenDXutils package
* Aligned figures to the center
* Changed the layout of the Appendices
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-10-10 23:26:19 UTC (rev 4781)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-10-10 23:48:38 UTC (rev 4782)
@@ -2016,7 +2016,7 @@
NumPy is an extension to Python which adds support for multi-dimensional
arrays for use in scientific computing.
You may download NumPy at the
-\begin_inset LatexCommand \htmlurl[Numby home page]{http://numpy.scipy.org/}
+\begin_inset LatexCommand \htmlurl[NumPy home page]{http://numpy.scipy.org/}
\end_inset
@@ -2085,6 +2085,34 @@
.
\end_layout
+\begin_layout Subsection
+\begin_inset LatexCommand \label{sub:OpenDXutils}
+
+\end_inset
+
+OpenDXutils
+\end_layout
+
+\begin_layout Standard
+In order to import HDF5 file into OpenDX, you will need the OpenDXutils
+ package from the Cactus project.
+ Go to the
+\begin_inset LatexCommand \url[OpenDXutils package website]{http://www.cactuscode.org/Visualization/openDX}
+
+\end_inset
+
+ and follow the instuction in the webpage to download and install the package.
+ Note that you will need to set both
+\family typewriter
+DXMODULES
+\family default
+ and
+\family typewriter
+DXMDF
+\family default
+ environment variables before running OpenDX to load the package.
+\end_layout
+
\begin_layout Section
\begin_inset LatexCommand \label{sec:Batch-System-Configuration}
@@ -2724,7 +2752,7 @@
\begin_layout Enumerate
In
\family typewriter
-~username/.pyre/CitcomS
+$HOME/.pyre/CitcomS
\family default
directory, meant to override variables for just one user.
\end_layout
@@ -3061,8 +3089,11 @@
status collapsed
\begin_layout Standard
+\align center
\begin_inset Graphics
filename graphics/cookbook2.eps
+ width 50page%
+ keepAspectRatio
\end_inset
@@ -3326,7 +3357,7 @@
\end_layout
\begin_layout Standard
-If you are using LAM/MPI, there is no machinefile genrated.
+If you are using LAM/MPI, there is no machinefile generated.
In addition, you can pass additional environment variables to LAM/MPI via:
\end_layout
@@ -3809,6 +3840,7 @@
status collapsed
\begin_layout Standard
+\align center
\begin_inset Graphics
filename graphics/c_fig5.eps
@@ -4066,8 +4098,14 @@
solver.output.output_format=hdf5
\family default
), you can directly visualize the data without postprocessing.
- First, you need to installl and setup OpenDXutils package.
- (TODO: link to installation) Then, open either
+ First, you need to installl and setup OpenDXutils package (see Section
+
+\begin_inset LatexCommand \vref{sub:OpenDXutils}
+
+\end_inset
+
+).
+ Then, open either
\family sans
\series bold
visRegional.net
@@ -4106,7 +4144,7 @@
\begin_inset Float figure
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -4165,7 +4203,6 @@
The third tab (unconnected, default to 0) specifies which time frame to
import.
The fourth tab (unconnected, default to 0) specifies which cap(s) to import.
-
\end_layout
\begin_layout Chapter
@@ -4223,9 +4260,10 @@
placement h
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
+\align center
\begin_inset Graphics
filename graphics/cookbook1.eps
@@ -4375,9 +4413,10 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
+\align center
\begin_inset Graphics
filename graphics/cookbook1.2.jpg
lyxscale 50
@@ -4673,9 +4712,10 @@
placement h
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
+\align center
\begin_inset Graphics
filename graphics/cookbook2.2.eps
@@ -4898,9 +4938,10 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
+\align center
\begin_inset Graphics
filename graphics/cookbook3.eps
@@ -5115,9 +5156,10 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
+\align center
\begin_inset Graphics
filename graphics/cookbook4.eps
@@ -5284,9 +5326,10 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
+\align center
\begin_inset Graphics
filename graphics/cookbook5.eps
lyxscale 65
@@ -5439,9 +5482,10 @@
placement h
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
+\align center
\begin_inset Graphics
filename graphics/cookbook5.2.eps
@@ -5611,7 +5655,7 @@
placement h
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -5647,7 +5691,7 @@
Facilities, Properties, and Parameters
\end_layout
-\begin_layout Section*
+\begin_layout Section
Introduction
\end_layout
@@ -5662,7 +5706,11 @@
\end_layout
-\begin_layout Section*
+\begin_layout Section
+Input parameters
+\end_layout
+
+\begin_layout Subsection
Parameters that Control Input Files
\end_layout
@@ -5954,7 +6002,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Mesh Set-up and Processors
\end_layout
@@ -6111,7 +6159,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
\noindent
Domain Size
\end_layout
@@ -6195,7 +6243,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Restarting the Code
\end_layout
@@ -6277,7 +6325,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Run Length, Output Interval
\end_layout
@@ -6347,7 +6395,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Initial Conditions
\end_layout
@@ -6406,7 +6454,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Boundary Conditions
\end_layout
@@ -6547,7 +6595,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Miscellaneous
\end_layout
@@ -6619,7 +6667,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Required Information
\end_layout
@@ -6667,7 +6715,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Depth Information
\end_layout
@@ -6715,7 +6763,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Viscosity
\end_layout
@@ -6911,7 +6959,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Phase Change Information
\end_layout
@@ -7010,7 +7058,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Dimensional Information
\end_layout
@@ -7063,7 +7111,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Data input and program debugging
\end_layout
@@ -7146,7 +7194,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Solver Related Parameters
\end_layout
@@ -7376,7 +7424,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Age Information
\end_layout
@@ -7438,7 +7486,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
Spherical Harmonics Information
\end_layout
@@ -7483,7 +7531,11 @@
\end_layout
-\begin_layout Section*
+\begin_layout Section
+CitComS.py Components
+\end_layout
+
+\begin_layout Subsection
launcher
\end_layout
@@ -7604,7 +7656,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
journal
\end_layout
@@ -7764,7 +7816,7 @@
--journal.debug.Exchanger=on --journal.debug.CitComSExchanger=on
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
controller
\end_layout
@@ -7802,7 +7854,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
solver
\end_layout
@@ -8143,7 +8195,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
solver.mesher
\end_layout
@@ -8565,7 +8617,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
solver.tsolver
\end_layout
@@ -8747,7 +8799,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
solver.vsolver
\end_layout
@@ -8969,7 +9021,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
solver.bc
\end_layout
@@ -9272,7 +9324,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
solver.const
\end_layout
@@ -9554,7 +9606,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
solver.ic
\end_layout
@@ -9756,7 +9808,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
solver.param
\end_layout
@@ -10038,7 +10090,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
solver.phase
\end_layout
@@ -10300,7 +10352,7 @@
\end_layout
-\begin_layout Section*
+\begin_layout Subsection
solver.visc
\end_layout
@@ -10646,7 +10698,7 @@
CitComS.py Input File Format
\end_layout
-\begin_layout Section*
+\begin_layout Section
Introduction
\end_layout
@@ -10660,15 +10712,17 @@
courier
\family default
must be input exactly as shown, while
+\family typewriter
\series bold
bold
+\family default
\series default
words should be substituted by your values.
All parameters are in non-dimensional units unless specified.
\end_layout
-\begin_layout Section*
+\begin_layout Section
\begin_inset LatexCommand \label{sec:Coordinate-files}
\end_inset
@@ -10677,11 +10731,8 @@
\end_layout
\begin_layout Standard
-For regional version of
-\family typewriter
-CitComS
-\family default
-.py, the mesh must be regular, but the mesh spacing may be unequal.
+For regional version of CitComS.py, the mesh must be regular, but the mesh
+ spacing may be unequal.
The
\family typewriter
coor_file
@@ -10690,110 +10741,77 @@
\end_layout
\begin_layout LyX-Code
-nsd=1
-\end_layout
-
-\begin_layout LyX-Code
+nsd=1
+\newline
1
\series bold
theta1
\series default
-
-\end_layout
-\begin_layout LyX-Code
+\newline
2
\series bold
theta2
-\end_layout
+\series default
-\begin_layout LyX-Code
+\newline
...
...
-
-\end_layout
+\series bold
-\begin_layout LyX-Code
-
-\series bold
+\newline
nodex theta_nodex
\series default
-
-\end_layout
-\begin_layout LyX-Code
-nsd=2
-\end_layout
-
-\begin_layout LyX-Code
+\newline
+nsd=2
+\newline
1
\series bold
phi1
\series default
-
-\end_layout
-\begin_layout LyX-Code
+\newline
2
\series bold
phi2
\series default
-
-\end_layout
-\begin_layout LyX-Code
+\newline
...
...
-
-\end_layout
+\series bold
-\begin_layout LyX-Code
-
-\series bold
+\newline
nodey phi_nodey
\series default
-
-\end_layout
-\begin_layout LyX-Code
-nsd=3
-\end_layout
-
-\begin_layout LyX-Code
+\newline
+nsd=3
+\newline
1
\series bold
r1
\series default
-
-\end_layout
-\begin_layout LyX-Code
+\newline
2
\series bold
r2
\series default
-
-\end_layout
-\begin_layout LyX-Code
+\newline
...
...
-
-\end_layout
+\series bold
-\begin_layout LyX-Code
-
-\series bold
+\newline
nodez r_nodez
\end_layout
\begin_layout Standard
-For full spherical version of
-\family typewriter
-CitComS
-\family default
-.py, the mesh of each cap must be regular and equidistant in the horizontal
- dimension.
+For full spherical version of CitComS.py, the mesh of each cap must be regular
+ and equidistant in the horizontal dimension.
Only vertical dimension is specified by
\family typewriter
coor_file
@@ -10807,38 +10825,29 @@
\end_layout
\begin_layout LyX-Code
-nsd=3
-\end_layout
-
-\begin_layout LyX-Code
+nsd=3
+\newline
1
\series bold
r1
\series default
-
-\end_layout
-\begin_layout LyX-Code
+\newline
2
\series bold
r2
\series default
-
-\end_layout
-\begin_layout LyX-Code
+\newline
...
...
-
-\end_layout
+\series bold
-\begin_layout LyX-Code
-
-\series bold
+\newline
nodez r_nodez
\end_layout
-\begin_layout Section*
+\begin_layout Section
\begin_inset LatexCommand \label{sec:Velocity-boundary-condition}
\end_inset
@@ -10859,32 +10868,23 @@
\family typewriter
bvel.dat
\family default
- file for each million year interval.
+ file per cap for each million year interval.
For example, if
\family typewriter
start_age=83
\family default
-, then the following files are needed:
+, then the following files are needed for the regional mesh:
\end_layout
\begin_layout LyX-Code
-bvel.dat84
-\end_layout
-
-\begin_layout LyX-Code
-bvel.dat83
-\end_layout
-
-\begin_layout LyX-Code
-bvel.dat82
-\end_layout
-
-\begin_layout LyX-Code
+bvel.dat84
+\newline
+bvel.dat83
+\newline
+bvel.dat82
+\newline
...
-
-\end_layout
-
-\begin_layout LyX-Code
+\newline
bvel.dat0
\end_layout
@@ -10902,23 +10902,46 @@
\family default
and call it
\family typewriter
-bvel.d
-\family default
-
+bvel.dat84
\end_layout
+\begin_layout Standard
+For the global mesh, each of the 12 caps requires one file for each million
+ year interval.
+ For example, these files are needed for 82 million year age:
+\end_layout
+
\begin_layout LyX-Code
+bvel.dat82.0
+\newline
+bvel.dat82.1
+\newline
+bvel.dat82.2
+\newline
+...
+\newline
+bvel.dat82.11
+\end_layout
+\begin_layout Standard
+Each velocity boundary condition file has the format:
+\end_layout
+
+\begin_layout LyX-Code
+
\series bold
Vx Vy
\end_layout
-\begin_layout Section*
+\begin_layout Section
Material files
\end_layout
\begin_layout Standard
-If
+In this version of CitComS.py, the implementation of material support is
+ not working.
+ The material output has been disabled and is documented here for completion.
+ If
\family typewriter
mat_file
\family default
@@ -10935,23 +10958,14 @@
\end_layout
\begin_layout LyX-Code
-mat.dat84
-\end_layout
-
-\begin_layout LyX-Code
-mat.dat83
-\end_layout
-
-\begin_layout LyX-Code
-mat.dat82
-\end_layout
-
-\begin_layout LyX-Code
+mat.dat84
+\newline
+mat.dat83
+\newline
+mat.dat82
+\newline
...
-
-\end_layout
-
-\begin_layout LyX-Code
+\newline
mat.dat0
\end_layout
@@ -10974,7 +10988,7 @@
n viscosity_factor
\end_layout
-\begin_layout Section*
+\begin_layout Section
Lithosphere Age Files
\end_layout
@@ -10996,27 +11010,18 @@
\family typewriter
start_age=83
\family default
-, then the following files are needed:
+, then the following files are needed for the regional mesh:
\end_layout
\begin_layout LyX-Code
lith.dat84
-\end_layout
-
-\begin_layout LyX-Code
-lith.dat83
-\end_layout
-
-\begin_layout LyX-Code
-lith.dat82
-\end_layout
-
-\begin_layout LyX-Code
+\newline
+lith.dat83
+\newline
+lith.dat82
+\newline
...
-
-\end_layout
-
-\begin_layout LyX-Code
+\newline
lith.dat0
\end_layout
@@ -11027,7 +11032,25 @@
\family default
(see above) still applies.
The input age is in millions of years.
- The format of
+ For the global mesh, each of the 12 caps requires one file for each million
+ year interval.
+ For example, these files are needed for 82 million year age:
+\end_layout
+
+\begin_layout LyX-Code
+lith.dat82.0
+\newline
+lith.dat82.1
+\newline
+lith.dat82.2
+\newline
+...
+\newline
+lith.dat82.11
+\end_layout
+
+\begin_layout Standard
+The format of
\family typewriter
lith_age_file
\family default
@@ -11040,7 +11063,7 @@
n age
\end_layout
-\begin_layout Section*
+\begin_layout Section
Tracer Files
\end_layout
@@ -11061,12 +11084,8 @@
\begin_layout LyX-Code
\series bold
-num_tracers
-\end_layout
-
-\begin_layout LyX-Code
-
-\series bold
+num_tracers
+\newline
type x y z
\end_layout
@@ -11078,15 +11097,21 @@
CitComS.py Output File Format
\end_layout
-\begin_layout Section*
+\begin_layout Section
Introduction
\end_layout
\begin_layout Standard
-All outputs are in non-dimensional units unless specified.
+The format of the output files of CitComS.py is described here.
+ In the following sections, the model prefix is assumed as
+\family typewriter
+test-case
+\family default
+, the processor number as 0, and the time step as 10.
+ All outputs are in non-dimensional units unless specified.
\end_layout
-\begin_layout Section*
+\begin_layout Section
Postprocessed Cap Output
\end_layout
@@ -11131,21 +11156,7 @@
colatitude longitude radius vel_colat vel_lon vel_r temperature viscosity
\end_layout
-\begin_layout Section*
-CitComS Output
-\end_layout
-
-\begin_layout Standard
-The format of the raw output of CitComS.py is described here.
- In the following sections, the model prefix is assumed as
-\family typewriter
-test-case
-\family default
-, the processor number as 0, and the time step as 10.
-
-\end_layout
-
-\begin_layout Subsection*
+\begin_layout Section
Time Output (test-case.time)
\end_layout
@@ -11159,7 +11170,11 @@
step total_t delta_t total_cpu_time step_cpu_time
\end_layout
-\begin_layout Subsection*
+\begin_layout Section
+ASCII Output
+\end_layout
+
+\begin_layout Subsection
Coordinate Output (test-case.coord.0)
\end_layout
@@ -11174,7 +11189,7 @@
colatitude longitude radius
\end_layout
-\begin_layout Subsection*
+\begin_layout Subsection
\begin_inset LatexCommand \label{sub:Velocity-and-Temperature}
\end_inset
@@ -11192,7 +11207,7 @@
vel_colat vel_lon vel_r temperature
\end_layout
-\begin_layout Subsection*
+\begin_layout Subsection
Viscosity Output (test-case.visc.0.10)
\end_layout
@@ -11206,7 +11221,7 @@
viscosity
\end_layout
-\begin_layout Subsection*
+\begin_layout Subsection
Material Output (test-case.mat.0)
\end_layout
@@ -11223,10 +11238,8 @@
element_number layer material
\end_layout
-\begin_layout Subsection*
-Surface Variables Output (test-case.surf.0.10 and
-\newline
-test-case.botm.0.10)
+\begin_layout Subsection
+Surface Variables Output (test-case.surf.0.10 and test-case.botm.0.10)
\end_layout
\begin_layout Standard
@@ -11239,6 +11252,10 @@
topography heatflux vel_colat vel_lon
\end_layout
+\begin_layout Section
+HDF5 Output (test-case.h5)
+\end_layout
+
\begin_layout Chapter
License
\end_layout
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