[cig-commits] r5231 - mc/3D/CitcomS/trunk/doc/manual
sue at geodynamics.org
sue at geodynamics.org
Thu Nov 9 17:59:46 PST 2006
Author: sue
Date: 2006-11-09 17:59:45 -0800 (Thu, 09 Nov 2006)
New Revision: 5231
Modified:
mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
Log:
finished various typos and fixes after checking with Luis on questions
Modified: mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx
===================================================================
--- mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-11-10 01:49:48 UTC (rev 5230)
+++ mc/3D/CitcomS/trunk/doc/manual/citcoms.lyx 2006-11-10 01:59:45 UTC (rev 5231)
@@ -4,8 +4,6 @@
\begin_header
\textclass book
\begin_preamble
-\usepackage{natbib}
-
\usepackage{hyperref}
\let\myUrl\url
@@ -29,7 +27,7 @@
\topmargin 1in
\rightmargin 1in
\bottommargin 1in
-\secnumdepth 2
+\secnumdepth 3
\tocdepth 5
\paragraph_separation indent
\defskip medskip
@@ -630,7 +628,7 @@
The framework offers a way to add new solvers to CitComS.py and to fine-tune
CitComS.py simulations.
Future versions of this documentation will cover coupled simulations generated
- using via an "exchanger."
+ via an "exchanger" module.
\end_layout
\begin_layout Standard
@@ -1049,7 +1047,7 @@
\end_layout
\begin_layout Standard
-The governing equations are solved with the finite element method, see
+The governing equations are solved with the finite element method
\begin_inset LatexCommand \cite{Hughes The Finite Element Method}
\end_inset
@@ -1685,7 +1683,7 @@
\end_layout
\begin_layout Section
-Configuration (TODO: make the following sections to subsections)
+Configuration
\end_layout
\begin_layout Standard
@@ -1737,7 +1735,7 @@
\end_layout
-\begin_layout Section
+\begin_layout Subsection
Configure Usage
\end_layout
@@ -1767,7 +1765,7 @@
\end_layout
-\begin_layout Section
+\begin_layout Subsection
Environment Variables
\end_layout
@@ -1784,6 +1782,16 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float table
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\noindent
+\align left
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
<features>
@@ -1958,7 +1966,12 @@
\end_layout
-\begin_layout Section
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
\begin_inset LatexCommand \label{sec:MPI-Configuration}
\end_inset
@@ -1993,7 +2006,7 @@
source, and for linking shared libraries.
\end_layout
-\begin_layout Subsection
+\begin_layout Subsubsection
Manually Specifying MPI Wrappers
\end_layout
@@ -2038,7 +2051,7 @@
that the compiler can find the MPI header files and libraries.
\end_layout
-\begin_layout Subsection
+\begin_layout Subsubsection
Manually Specifying MPI
\family typewriter
include
@@ -2066,7 +2079,7 @@
MPILIBS="-L/opt/mpich-1.2.6/lib -lmpich"
\end_layout
-\begin_layout Subsection
+\begin_layout Subsubsection
Manually Specifying MPI
\family typewriter
include
@@ -2157,8 +2170,8 @@
\end_layout
\begin_layout Standard
-CitComS requires parallel HDF5 (PHDF5) for writing its output in binary
- format.
+For writing its output in binary format, CitComS requires parallel HDF5
+ (PHDF5).
In turn, PHDF5 requires an MPI compiler with MPI-IO support and a parallel
file system.
If an existing installation of the PHDF5 library is not available on your
@@ -2194,7 +2207,7 @@
$ ./configure --with-hdf5 --prefix=$HOME/cig
\end_layout
-\begin_layout Section
+\begin_layout Subsection
Additional Tools
\end_layout
@@ -2203,7 +2216,7 @@
CitComS, you may find it useful for accessing CitComS data in HDF5 files.
\end_layout
-\begin_layout Subsection
+\begin_layout Subsubsection
NumPy
\end_layout
@@ -2241,7 +2254,7 @@
ebuild.
\end_layout
-\begin_layout Subsection
+\begin_layout Subsubsection
PyTables
\end_layout
@@ -2282,7 +2295,7 @@
ebuild.
\end_layout
-\begin_layout Subsection
+\begin_layout Subsubsection
HDFView
\end_layout
@@ -2296,7 +2309,7 @@
.
\end_layout
-\begin_layout Subsection
+\begin_layout Subsubsection
\begin_inset LatexCommand \label{sub:OpenDXutils}
\end_inset
@@ -3234,7 +3247,7 @@
example0.cfg
\end_layout
-\begin_layout Paragraph
+\begin_layout Subsubsection
Example: Uniprocessor, example0.cfg
\end_layout
@@ -3291,7 +3304,7 @@
\end_layout
-\begin_layout Paragraph
+\begin_layout Subsubsection
Example: Multiprocessor,
\family typewriter
example1.cfg
@@ -4658,7 +4671,11 @@
As such we can use a variety of tools to inspect the structure of an HDF5
file, as well as for retrieving data in any order.
To quickly inspect the structure of an HDF5 file, you can use the command
- h5ls (TODO: font) from the HDF5 library
+
+\family typewriter
+h5ls
+\family default
+ from the HDF5 library
\end_layout
\begin_layout LyX-Code
@@ -4666,8 +4683,12 @@
\end_layout
\begin_layout Standard
-You can also recreate the ASCII combined cap format described in Chapter
- (TODO:insert reference here) for specific time steps by using the command:
+You can also recreate the ASCII combined cap format described in
+\begin_inset LatexCommand \ref{sec:ASCII-Output}
+
+\end_inset
+
+ for specific time steps by using the command included in CitComS:
\end_layout
\begin_layout LyX-Code
@@ -4717,6 +4738,21 @@
\end_layout
\begin_layout Standard
+
+\series bold
+(TODO
+\begin_inset Quotes sld
+\end_inset
+
+if this is a specific example in the distribution, it is important to return
+ a back or forward
+\begin_inset Quotes srd
+\end_inset
+
+)
+\end_layout
+
+\begin_layout Standard
In this case, the slice
\family typewriter
0:12
@@ -4749,8 +4785,17 @@
\end_layout
\begin_layout Standard
-For more details, refer to the documentation for PyTables (TODO:insert link
- here) and NumPy (TODO:insert link here).
+For more details, refer to the documentation for
+\begin_inset LatexCommand \htmlurl[PyTables]{www.pytables.org}
+
+\end_inset
+
+ and
+\begin_inset LatexCommand \htmlurl[NumPy]{numpy.scipy.org}
+
+\end_inset
+
+.
\end_layout
\begin_layout Subsection
@@ -4955,7 +5000,7 @@
\begin_layout Standard
If your Beowulf cluster uses ssh (rather than rsh) to access the computation
- nodes, you have to manually edit
+ nodes, you must manually edit
\family typewriter
PREFIX/bin/batchpaste.sh
\family default
@@ -4968,7 +5013,7 @@
\family typewriter
/scratch/username
\family default
-) on a parallel file system, you can postprocess your output files by following
+) on a parallel file system, postprocess your output files by following
the instructions in Section
\begin_inset LatexCommand \ref{sec:Postprocessing-in-a}
@@ -4983,8 +5028,8 @@
\family typewriter
autocombine.py
\family default
- has been run, you should end up with 2 files (or 24 files for the full
- spherical version of CitComS.py) that resemble these:
+ has run, you will have with 2 files (or 24 files for the full spherical
+ version of CitComS.py) formatted as follows:
\end_layout
\begin_layout LyX-Code
@@ -5015,8 +5060,8 @@
\end_layout
\begin_layout Standard
-If you have run CitComS.py in a non-cluster environment or all of your data
- resides in a single directory, you can still use
+If you run CitComS.py in a non-cluster environment or all of your data resides
+ in a single directory, you can still use
\family typewriter
autocombine.py
\family default
@@ -5048,11 +5093,14 @@
OpenDX modules designed for CitComS.py can be found in the directory called
\family typewriter
-PREFIX/share/CitcomS/visual
+PREFIX/visual
\family default
-, where PREFIX is the directory under which you installed CitComS.py (default
-
+, where
\family typewriter
+PREFIX
+\family default
+ is the directory under which you installed CitComS.py (default
+\family typewriter
/usr/local
\family default
).
@@ -5065,7 +5113,7 @@
visRegional.net
\family default
to visualize the result of regional CitComS.py.
- You should launch OpenDX by typing:
+ Launch OpenDX by typing:
\end_layout
\begin_layout LyX-Code
@@ -5075,56 +5123,38 @@
\begin_layout Standard
You will see an OpenDX
\family sans
-\series bold
Data Explorer
\family default
-\series default
window.
- Click
+ Click
+\series bold
+
\family sans
-\series bold
+\series default
Edit Visual Programs
\family default
-\series default
and select
-\family sans
-\series bold
+\family typewriter
visRegional.net
\family default
-\series default
from the file selector.
You will see a
\family sans
-\series bold
Visual Program Editor
\family default
-\series default
- window.
- Then select the
+ window and double-click on the
\family sans
-\series bold
-import
-\family default
-\series default
- tab in the main window and double-click on the
-\family sans
-\series bold
FileSelector
\family default
-\series default
block, which will open a
\family sans
-\series bold
Control Panel
\family default
-\series default
window.
In the
\family sans
-\series bold
CitcomSImport filename
\family default
-\series default
input box, select the header file of your postprocessed data, e.g.,
\end_layout
@@ -5139,21 +5169,17 @@
\family typewriter
\family sans
-\series bold
Execute\SpecialChar \menuseparator
Execute on Change
\family default
-\series default
.
A new window will appear with the image of the model.
If you want to zoom, rotate, change projection, and otherwise manipulate
the view of the model, experiment with the menu
\family sans
-\series bold
Options\SpecialChar \menuseparator
View Control
\family default
-\series default
.
\end_layout
@@ -5196,7 +5222,7 @@
CitcomSImport reduced
\family default
\series default
-, can increase or reduce the resolution of the velocity vectors and grids.
+ can increase or reduce the resolution of the velocity vectors and grids.
\end_layout
@@ -5230,7 +5256,7 @@
Slab cut dimension
\family default
\series default
- is the direction of the slab (an OpenDX term of cross-section).
+ is the direction of the slab (an OpenDX term for cross-section).
\end_layout
@@ -5258,58 +5284,52 @@
\end_layout
\begin_layout Standard
-After launched OpenDX, You will see an OpenDX
+After launching OpenDX, you will see an OpenDX
\family sans
-\series bold
Data Explorer
\family default
-\series default
window.
Click
\family sans
-\series bold
Edit Visual Programs
\family default
-\series default
and select
-\family sans
-\series bold
+\family typewriter
visFull.net
\family default
-\series default
from the file selector.
You will see a
\family sans
-\series bold
Visual Program Editor
\family default
+\series bold
+
\series default
- window.
- Then select the
+window.
+ Select the
\family sans
-\series bold
import
\family default
-\series default
- tab in the main window and double-click on the
+ tab in the
\family sans
-\series bold
+Visual Program Editor
+\family default
+'s main window and double-click on the
+\family sans
FileSelector
\family default
-\series default
block, which will open a
\family sans
+Control Panel
\series bold
-Control Panel
+
\family default
\series default
window.
In the
\family sans
-\series bold
Format String of CitcomSFullImport
\family default
-\series default
input box, select one of the 12 header files of your postprocessed data,
e.g.,
\end_layout
@@ -5341,26 +5361,22 @@
\family typewriter
\family sans
-\series bold
Execute\SpecialChar \menuseparator
Execute on Change
\family default
-\series default
.
A new window will appear with the image of the model.
If you want to zoom, rotate, change projection, and otherwise manipulate
the view of the model, experiment with the menu
\family sans
-\series bold
Options\SpecialChar \menuseparator
View Control
\family default
-\series default
.
\end_layout
\begin_layout Standard
-Additional options in the control panel window for the regional model include:
+Additional options in the control panel window for the spherical model include:
\end_layout
\begin_layout Itemize
@@ -5370,7 +5386,7 @@
CitcomSFullImport reduced
\family default
\series default
-, can increase or reduce the resolution of the velocity vectors and grids.
+ can increase or reduce the resolution of the velocity vectors and grids.
\end_layout
@@ -5423,7 +5439,7 @@
solver.output.output_format=hdf5
\family default
), you can directly visualize the data without postprocessing.
- First, you need to installl and setup OpenDXutils package (see Section
+ First, you need to install and set up the OpenDXutils package (see Section
\begin_inset LatexCommand \vref{sub:OpenDXutils}
@@ -5431,30 +5447,22 @@
).
Then, open either
-\family sans
-\series bold
+\family typewriter
visRegional.net
\family default
-\series default
or
-\family sans
-\series bold
+\family typewriter
visFull.net
\family default
-\series default
in OpenDX.
In the Tools panel of the main window, select the
\family sans
-\series bold
CitcomSImportHDF5
\family default
-\series default
module in the
\family sans
-\series bold
Macros
\family default
-\series default
category.
Place the module in the work space and rewire the network as shown in Figure
@@ -5467,11 +5475,14 @@
\begin_layout Standard
\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/CitcomSImportHDF5.net.gif
lyxscale 50
@@ -5488,13 +5499,11 @@
\end_inset
-Import CitComS.py HDF5 data.
+ How to import CitComS.py HDF5 data.
The
\family sans
-\series bold
CitcomSImportHDF5
\family default
-\series default
module is highlighted in the Tools panel.
\end_layout
@@ -5506,24 +5515,18 @@
\begin_layout Standard
There are four input tabs in the
\family sans
-\series bold
CitcomSImportHDF5
\family default
-\series default
module.
The first tab (connected to the
\family sans
-\series bold
FileSelector
\family default
-\series default
module) specifies the HDF5 filename.
The second tab (connected to the
\family sans
-\series bold
Integer
\family default
-\series default
module) specifies the resultion reduction factor.
The third tab (unconnected, default to 0) specifies which time frame to
import.
@@ -5549,12 +5552,12 @@
\family default
directory.
However, you might need to edit these example scripts slightly to launch
- the job on your cluster (see
+ the job on your cluster (see Section
\begin_inset LatexCommand \vref{sec:Multiprocessor-Example}
\end_inset
- for more information.)
+ for more information).
\end_layout
\begin_layout Section
@@ -5599,7 +5602,7 @@
\begin_layout Caption
Global Model "Caps": Left (A): Three-dimensional perspective image showing
- the 12 spherical caps used in a full CitComS.py run.
+ seven of the 12 spherical caps used in a full CitComS.py run.
Right (B): The temperature field at 1081 km depth from a Cookbook 1 run.
\end_layout
@@ -5649,10 +5652,10 @@
facility controls the temperature field for the initial conditions.
The last set of parameters includes the number of perturbations to the
initial temperature (1), the number of nodal lines of the perturbation
- in the longitudinal direction, e.g., spherical harmonic order (3), the number
- of nodal lines in the latitudinal direction, e.g., spherical harmonic degree
- (2), which layer the pertubation is on (5), and the amplitude of the perturbati
-on (0.05).
+ in the longitudinal direction, e.g., the spherical harmonic order (3), the
+ number of nodal lines in the latitudinal direction, e.g., the spherical harmonic
+ degree (2), which layer the pertubation is on (5), and the amplitude of
+ the perturbation (0.05).
Note that although the number of perturbations is assigned here as
\family typewriter
num_perturbations=1
@@ -5681,8 +5684,8 @@
$ citcoms cookbook1.cfg
\end_layout
-\begin_layout Paragraph*
-Example: Global Model, cookboo1.cfg
+\begin_layout Subsubsection
+Example: Global Model, cookbook1.cfg
\end_layout
\begin_layout LyX-Code
@@ -5726,7 +5729,7 @@
\begin_layout Standard
Once you have run the model, you can visualize the results using OpenDX,
described in the previous chapter.
- When you invoke "Edit Visual Program," you will need to select
+ When you invoke "Edit Visual Program," select
\family typewriter
visFull.net
\family default
@@ -5739,7 +5742,7 @@
placement H
wide false
sideways false
-status collapsed
+status open
\begin_layout Standard
\align center
@@ -5827,7 +5830,7 @@
\end_layout
\begin_layout Standard
-You will be using
+You will use
\family typewriter
cookbook2.cfg
\family default
@@ -5837,7 +5840,7 @@
\family typewriter
cookbook2
\family default
-), and how often the computation will be monitored (30).
+), and how often outputs will be created (30).
\end_layout
\begin_layout LyX-Code
@@ -5880,7 +5883,7 @@
\family default
facility allows you to impose a uniform velocity across the top surface.
You have a velocity which is purely in the colatitude direction with a
- non-dimensional velocity of 100 (see
+ non-dimensional velocity of 100 (see Section
\begin_inset LatexCommand \vref{eq:6}
\end_inset
@@ -5912,7 +5915,7 @@
perturbmag = 0.0
\end_layout
-\begin_layout Paragraph
+\begin_layout Subsubsection
Example: Velocity Boundary Conditions, cookbook2.cfg
\end_layout
@@ -5926,19 +5929,19 @@
[CitcomS.controller]
\newline
mo
-nitoringFrequency = 30 ; how often to monitor the computation
+nitoringFrequency = 30 ; how often outputs are created
\newline
\newline
[CitcomS.solver]
\newline
-d
-atafile = cookbook2 ; prefix of output filenames
+datafile
+ = cookbook2 ; prefix of output filenames
\newline
\newline
-# Modify the layout
- of the mesh.
+# Modify the layout of the
+ mesh.
\newline
[CitcomS.solver.mesher]
\newline
@@ -5948,19 +5951,19 @@
\newline
nodex = 17
\newline
-nodey
- = 17
+nodey = 17
\newline
-nodez = 9
+nodez
+ = 9
\newline
\newline
# Impose a uniform velocity across the top surface.
\newline
-[CitcomS.solve
-r.bc]
+[CitcomS.solver.bc]
\newline
-topvbc = 1
+topvbc
+ = 1
\newline
topvbxval = 100
\newline
@@ -5968,10 +5971,10 @@
\newline
# Modify the layout of the mesh.
\newline
-[CitcomS.solver.m
-esher]
+[CitcomS.solver.mesher]
\newline
-nprocx = 2
+npro
+cx = 2
\newline
nprocy = 2
\newline
@@ -5983,34 +5986,33 @@
\newline
\newline
-# Impose a
- uniform velocity across the top surface.
+# Impose a uniform velocity
+ across the top surface.
\newline
[CitcomS.solver.bc]
\newline
topvbc = 1
\newline
-topvbxva
-l = 100
+topvbxval = 100
\newline
-topvbyval = 0
+topvbyval
+ = 0
\newline
\newline
-# In addition, to determine the temperature, the temperatu
-re field
+# In addition, to determine the temperature, the temperature field
\newline
-# associated only with this imposed velocity, reset the initial
-\newline
#
- perturbation to zero.
+ associated only with this imposed velocity, reset the initial
\newline
+# perturbation
+ to zero.
+\newline
[CitcomS.solver.ic]
\newline
num_perturbations = 1
\newline
-perturbmag
- = 0.0
+perturbmag = 0.0
\end_layout
\begin_layout Subsection
@@ -6084,13 +6086,17 @@
\end_layout
\begin_layout Standard
-You will be using cookbook3.cfg.
- The parameters specify the number of time steps (200), how often the computatio
-n will be monitored (25), the prefix of the output filenames (
+You will use cookbook3.cfg.
+ The parameters specify the number of time steps (200), how often outputs
+ will be created (25), the prefix of the output filenames (
\family typewriter
cookbook3
\family default
-), and the Rayleigh number (10^6).
+), and the Rayleigh number (
+\begin_inset Formula $10^{6}$
+\end_inset
+
+).
\end_layout
\begin_layout LyX-Code
@@ -6129,7 +6135,7 @@
\family typewriter
on
\family default
-), at the value of the maximum cutoff (100.0).
+), and the value of the maximum cutoff (100.0).
\end_layout
@@ -6167,8 +6173,8 @@
\family typewriter
solver.const.z_410
\family default
- (default to 0.06435, or 410 km dimensionally); ayer 3 is below layer 2 and
- extends to a depth of
+ (default to 0.06435, or 410 km dimensionally); layer 3 is below layer 2
+ and extends to a depth of
\family typewriter
solver.const.z_lmantle
\family default
@@ -6180,14 +6186,14 @@
\begin_layout Standard
\begin_inset Formula \begin{equation}
-visc=visc0*exp\left(\frac{viscE}{T+viscT}-\frac{viscE}{1+viscT}\right)\label{eq:22}\end{equation}
+visc=visc0\times exp\left(\frac{viscE}{T+viscT}-\frac{viscE}{1+viscT}\right)\label{eq:22}\end{equation}
\end_inset
\end_layout
-\begin_layout Paragraph
+\begin_layout Subsubsection
Example: Temperature-Dependent Viscosity, cookbook3.cfg
\end_layout
@@ -6201,26 +6207,26 @@
[CitcomS.controller]
\newline
mo
-nitoringFrequency = 25 ; how often to monitor the computation
+nitoringFrequency = 25 ; how often outputs are created
\newline
\newline
[CitcomS.solver]
\newline
-d
-atafile = cookbook3 ; prefix of output filenames
+datafile
+ = cookbook3 ; prefix of output filenames
\newline
-rayleigh = 1e6
- ; Rayleigh number
+rayleigh = 1e6
+ ; Rayleigh number
\newline
\newline
# Modify the layout of the mesh.
\newline
-[CitcomS.solver.mesher
-]
+[CitcomS.solver.mesher]
\newline
-nprocx = 2
+nprocx
+ = 2
\newline
nprocy = 2
\newline
@@ -6234,8 +6240,8 @@
\newline
# Assign the viscosities.
\newline
-
-[CitcomS.solver.visc]
+[Citcom
+S.solver.visc]
\newline
VISC_UPDATE = on
\newline
@@ -6245,8 +6251,8 @@
\newline
TDEPV = on
\newline
-viscE
- = 0.2,0.2,0.2,0.2
+viscE =
+ 0.2,0.2,0.2,0.2
\newline
viscT = 0,0,0,0
\newline
@@ -6264,7 +6270,7 @@
placement H
wide false
sideways false
-status collapsed
+status open
\begin_layout Standard
\align center
@@ -6359,7 +6365,7 @@
= 1
\end_layout
-\begin_layout Paragraph
+\begin_layout Subsubsection
Example: Regionally Refined Meshes, cookbook4.cfg
\end_layout
@@ -6375,7 +6381,7 @@
[CitcomS.controller]
\newline
mo
-nitoringFrequency = 10 ; how often to monitor the computation
+nitoringFrequency = 10 ; how often outputs are created
\newline
\newline
@@ -6383,11 +6389,11 @@
\newline
[CitcomS.solver]
\newline
-r
-ayleigh = 1e6 ; Rayleigh number
+rayleigh
+ = 1e6 ; Rayleigh number
\newline
-datafile = cookbook4
- ; prefix of output filenames
+datafile = cookbook4 ; prefix
+ of output filenames
\newline
\newline
@@ -6397,17 +6403,17 @@
\newline
num_perturbations = 1
\newline
-perturbmag
- = 0.05
+perturbmag = 0.05
\newline
-perturblayer = 10
+pertur
+blayer = 10
\newline
\newline
-# Perturb the initial temperature gradient in the
- longitudinal
+# Perturb the initial temperature gradient in the longitudinal
\newline
-# direction.
+#
+ direction.
\newline
perturbl = 1
\newline
@@ -6419,17 +6425,17 @@
\newline
[CitcomS.solver.mesher]
\newline
-# Read
- uneven mesh point coordinates from 'coor.dat'.
+# Read uneven mesh
+ point coordinates from 'coor.dat'.
\newline
coor = on
\newline
coor_file = coor.dat
\newline
-nprocx
- = 4
+nprocx = 4
\newline
-nprocy = 2
+nprocy
+ = 2
\newline
nprocz = 2
\newline
@@ -6441,10 +6447,10 @@
\newline
theta_min = 1
\newline
-theta_max
- = 2
+theta_max = 2
\newline
-fi_min = 0
+fi_min
+ = 0
\newline
fi_max = 1
\newline
@@ -6458,10 +6464,10 @@
\newline
num_mat = 4
\newline
-visc0
- = 1,1,1,1
+visc0 = 1,1,1,1
\newline
-TDEPV = on
+TDEPV
+ = on
\newline
viscE = 0.2,0.2,0.2,0.2
\newline
@@ -6469,12 +6475,12 @@
\newline
VMIN = on
\newline
-visc_min
- = 1.0
+visc_min = 1.0
\newline
VMAX = on
\newline
-visc_max = 100.0
+visc_max
+ = 100.0
\end_layout
\begin_layout Standard
@@ -6482,7 +6488,7 @@
placement H
wide false
sideways false
-status collapsed
+status open
\begin_layout Standard
\align center
@@ -6563,7 +6569,7 @@
).
Initially, both plates have Euler poles situated far apart, so the velocities
- are approximately constants (about 5 cm/yr for the left plate and about
+ are approximately constant (about 5 cm/yr for the left plate and about
2 cm/yr for the right plate).
After 30 Ma, a pole jump occurred for the right slab only, so the Euler
pole moved closer.
@@ -6612,7 +6618,7 @@
\family typewriter
restart=on
\family default
- is set, the initial temperature field is read from files.
+ is set, the initial temperature field is read from setup files.
The files have the same naming scheme and format as the CitComS velo output,
as described in Appendix
\begin_inset LatexCommand \vref{sub:Velocity-and-Temperature}
@@ -6620,7 +6626,7 @@
\end_inset
.
- The prefix of the filename is specified in
+ The prefix of the file name is specified in
\family typewriter
datafile_old
\family default
@@ -6652,7 +6658,7 @@
placement H
wide false
sideways false
-status collapsed
+status open
\begin_layout Standard
\align center
@@ -6671,11 +6677,11 @@
\end_inset
-Cookbook 5: Left (A): initially, both plates have Euler poles (magenta and
+Cookbook 5: Left (A): Initially, both plates have Euler poles (magenta and
green dots) situated far apart from the plate, so the velocities are approximat
-e constants (about 5 cm/yr for the left plate and about 2 cm/yr for the
+ely constant (about 5 cm/yr for the left plate and about 2 cm/yr for the
right plate).
- Right (B): after 30 Ma a pole jump occurred for the right slab only, so
+ Right (B): After 30 Ma a pole jump occurred for the right slab only, so
the Euler pole moved closer.
\end_layout
@@ -6684,7 +6690,7 @@
\end_layout
-\begin_layout Paragraph
+\begin_layout Subsubsection
Example: Subduction Models with Trench Rollback, cookbook5.cfg
\end_layout
@@ -6698,14 +6704,14 @@
[CitcomS.controller]
\newline
mo
-nitoringFrequency = 10 ; how often to monitor the computation
+nitoringFrequency = 10 ; how often outputs are created
\newline
\newline
[CitcomS.solver]
\newline
-d
-atafile = cookbook5
+datafile
+ = cookbook5
\newline
datafile_old = ./restart_files/cookbook5
\newline
@@ -6713,8 +6719,8 @@
\newline
\newline
-[Cit
-comS.solver.bc]
+[CitcomS.sol
+ver.bc]
\newline
topvbc = 1
\newline
@@ -6728,11 +6734,11 @@
\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
@@ -6804,6 +6810,12 @@
\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
@@ -6914,9 +6926,9 @@
\begin_layout Standard
To verify that the above algorithm works, you will run two different CitComS.py
- models with each BC (free-slip and pseudo-free-surface) and compare the
- topography computed accordingly.
- The scripts
+ models with each boundary condition (BC) (free-slip and pseudo-free-surface)
+ and compare the topography computed accordingly.
+ The scripts in
\family typewriter
cookbook6.cfg
\family default
@@ -6924,21 +6936,40 @@
\end_layout
\begin_layout Itemize
-Domain size: 45 deg x 45 deg x 1200 km
+Domain size: 45 deg
+\begin_inset Formula $\times$
+\end_inset
+
+ 45 deg
+\begin_inset Formula $\times$
+\end_inset
+
+ 1200 km
\end_layout
\begin_layout Itemize
-Mesh size: 61 x 61 x 25 with mesh refinement (coord.dat)
+Mesh size: 61
+\begin_inset Formula $\times$
+\end_inset
+
+ 61
+\begin_inset Formula $\times$
+\end_inset
+
+ 25 with mesh refinement (coord.dat)
\end_layout
\begin_layout Itemize
-BC: free-slip/free-surface for top; free-slip for all the other surfaces
-
+Boundary Conditions (BC): free-slip/free-surface for top; free-slip for
+ all the other surfaces
\end_layout
\begin_layout Itemize
-IC: spherical hot blob with diameter of 1/4 of radial dimension is placed
- at the center of the domain
+Initial Conditions (IC): spherical hot blob with diameter of
+\begin_inset Formula $\frac{1}{4}$
+\end_inset
+
+ of radial dimension is placed at the center of the domain
\end_layout
\begin_layout Standard
@@ -6964,28 +6995,35 @@
\end_layout
\begin_layout Standard
-The plots of topography profile are consistent with results described in
-
+The plots of the topography profile are consistent with results described
+ in
\begin_inset LatexCommand \cite{Zhong et al Free-surface formulation}
\end_inset
.
- In the graphs below, the solid line indicates free-slip and the dashed
- line indicates free-surface.
+ In the graphs in Figure
+\begin_inset LatexCommand \ref{fig:Cookbook-6.-Graphs}
+
+\end_inset
+
+, the solid lines indicate free-slip and the dashed lines indicate free-surface.
\end_layout
\begin_layout Standard
\begin_inset Float figure
-placement h
+placement H
wide false
sideways false
status collapsed
\begin_layout Standard
+\noindent
+\align center
\begin_inset Graphics
filename graphics/cookbook7.eps
+ scale 90
\end_inset
@@ -6993,9 +7031,13 @@
\end_layout
\begin_layout Caption
+\begin_inset LatexCommand \label{fig:Cookbook-6.-Graphs}
+
+\end_inset
+
Cookbook 6.
Graphs of topography profiles.
- The unit of x axis is radians, not degrees.
+ The unit of the x axis is radians, not degrees.
\end_layout
@@ -7004,6 +7046,28 @@
\end_layout
+\begin_layout Standard
+
+\series bold
+(TODO: substitute
+\begin_inset Quotes sld
+\end_inset
+
+radians
+\begin_inset Quotes srd
+\end_inset
+
+ for
+\begin_inset Quotes sld
+\end_inset
+
+deg
+\begin_inset Quotes srd
+\end_inset
+
+ on image 6.8; remove second sentence of caption.)
+\end_layout
+
\begin_layout Part
Appendices
\end_layout
@@ -7022,7 +7086,7 @@
\end_layout
\begin_layout Standard
-This section explains the meaning the input parameters for CitComS.py.
+This section explains the meaning of the input parameters for CitComS.py.
These parameters are grouped by their functionality.
Parameters are given with their default values.
\end_layout
@@ -7044,15 +7108,7 @@
\begin_layout Standard
file_vbcs=off
\newline
-vel_bound_file=
-\begin_inset Quotes srd
-\end_inset
-
-bvel.dat
-\begin_inset Quotes srd
-\end_inset
-
-
+vel_bound_file="bvel.dat"
\end_layout
\end_inset
@@ -7095,15 +7151,7 @@
\begin_layout Standard
coor=off
\newline
-coor_file=
-\begin_inset Quotes srd
-\end_inset
-
-coor.dat
-\begin_inset Quotes srd
-\end_inset
-
-
+coor_file="coor.dat"
\end_layout
\end_inset
@@ -7140,15 +7188,7 @@
\begin_layout Standard
mat_control=off
\newline
-mat_file=
-\begin_inset Quotes srd
-\end_inset
-
-mat.dat
-\begin_inset Quotes srd
-\end_inset
-
-
+mat_file="mat.dat"
\end_layout
\end_inset
@@ -7161,7 +7201,7 @@
\family typewriter
mat_control
\family default
- is set to on, then the time- and positional- dependent viscosity factor
+ is set to on, then the time- and positional-dependent viscosity factor
is defined from the files specified by
\family typewriter
mat_file
@@ -7182,15 +7222,7 @@
\begin_layout Standard
lith_age=off
\newline
-lith_age_file=
-\begin_inset Quotes srd
-\end_inset
-
-age.dat
-\begin_inset Quotes srd
-\end_inset
-
-
+lith_age_file="age.dat"
\newline
lith_age_time=off
\end_layout
@@ -7270,15 +7302,7 @@
\begin_inset Text
\begin_layout Standard
-output_format=
-\begin_inset Quotes srd
-\end_inset
-
-ascii-local
-\begin_inset Quotes srd
-\end_inset
-
-
+output_format="ascii-local"
\end_layout
\end_inset
@@ -7288,14 +7312,10 @@
\begin_layout Standard
Choose the format and layout of the output files.
- Can either
+ Can be either "ascii-local
\begin_inset Quotes sld
\end_inset
-ascii-local
-\begin_inset Quotes srd
-\end_inset
-
,
\begin_inset Quotes sld
\end_inset
@@ -7323,15 +7343,7 @@
\begin_inset Text
\begin_layout Standard
-output_optional=
-\begin_inset Quotes srd
-\end_inset
-
-surf,botm
-\begin_inset Quotes srd
-\end_inset
-
-
+output_optional="surf,botm"
\end_layout
\end_inset
@@ -7353,7 +7365,7 @@
\end_inset
botm
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
,
@@ -7361,7 +7373,7 @@
\end_inset
stress
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
,
@@ -7369,7 +7381,7 @@
\end_inset
pressure
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
,
@@ -7377,7 +7389,7 @@
\end_inset
connectivity
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
, and
@@ -7385,7 +7397,7 @@
\end_inset
horiz_avg
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
.
@@ -7437,14 +7449,13 @@
\begin_inset Text
\begin_layout Standard
-Controls the prefix of output filenames.
- Files such as regtest.xxx.
+Controls the prefix of output file names such as regtest.xxx.
Cannot contain the
\begin_inset Quotes sld
\end_inset
/
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
character if
@@ -7464,13 +7475,13 @@
\begin_layout Standard
storage_spacing=10
\newline
-(in none-pyre version)
+(in non-Pyre version)
\newline
or
\newline
monitoringFrequency=10
\newline
-(in pyre
+(in Pyre
version)
\end_layout
@@ -7524,7 +7535,7 @@
\begin_inset Text
\begin_layout Standard
-This specifies the number of spherical caps of the mesh, must be 1 for regional
+This specifies the number of spherical caps of the mesh; must be 1 for regional
spherical model and 12 for full spherical model.
\end_layout
@@ -7558,7 +7569,7 @@
\family typewriter
nprocx
\family default
- must equal to
+ must be equal to
\family typewriter
nprocy
\end_layout
@@ -7593,7 +7604,7 @@
\family typewriter
nodex
\family default
- must equal to
+ must be equal to
\family typewriter
nodey
\end_layout
@@ -7621,23 +7632,30 @@
\begin_inset Text
\begin_layout Standard
-These specify the nested level of multigrid unit.
+These specify the nested level of multigrid units.
Used by multigrid solver only.
These parameters are not completely independent to each other.
- Following constraints must be satisfied:
+ The following constraints must be satisfied:
\newline
\newline
-\family typewriter
-nodex = 1 + nprocx * mgunitx * 2**(levels-1)
+\begin_inset Formula $\mathrm{nodex}=1+\mathrm{nprocx}\times\mathrm{mgunitx}\times2^{levels-1}$
+\end_inset
+
+
\newline
-nodey = 1 + nprocy * mgunity
- * 2**(levels-1)
+
+\begin_inset Formula $\mathrm{nodey}=1+\mathrm{nprocy}\times\mathrm{mgunity}\times2^{levels-1}$
+\end_inset
+
+
\newline
-nodez = 1 + nprocz * mgunitz * 2**(levels-1)
-\family default
+\begin_inset Formula $\mathrm{nodez}=1+\mathrm{nprocz}\times\mathrm{mgunitz}\times2^{levels-1}$
+\end_inset
+
+
\newline
\newline
@@ -7645,7 +7663,7 @@
\family typewriter
mgunitx
\family default
- must equal to
+ must be equal to
\family typewriter
mgunity
\end_layout
@@ -7692,7 +7710,7 @@
\begin_inset Text
\begin_layout Standard
-These parameters specify the horizontal extent of the computation domain.
+These parameters specify the horizontal extent of the computational domain.
\family typewriter
theta_min
@@ -7733,7 +7751,7 @@
\begin_inset Text
\begin_layout Standard
-These parameters specify the radial extent of the computation domain.
+These parameters specify the radial extent of the computational domain.
\family typewriter
radius_inner
@@ -7742,8 +7760,8 @@
\family typewriter
radius_outer
\family default
- are the inner and outer radius in non-dimensional units.
- It is probably most convenient to normalize lengths by the radius of the
+ are the inner and outer radii in non-dimensional units.
+ It is probably more convenient to normalize lengths by the radius of the
Earth.
If you do this, then the Rayleigh number, given below, must be calculated
with the radius of the Earth, not the thickness of the mantle.
@@ -7790,7 +7808,7 @@
\family typewriter
restart
\family default
- is on, eacho processor will read its initial temperature field from a velo
+ is on, each processor will read its initial temperature field from a velo
file.
\end_layout
@@ -7828,11 +7846,11 @@
\begin_layout Standard
datadir_old=
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
.
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
@@ -7928,14 +7946,14 @@
\newline
maxtotstep=1000000
\newline
-(only in none-pyre version)
+(only in non-Pyre version)
\newline
or
\newline
steps=1
\newline
-(only in
- pyre version)
+(only in Pyre
+ version)
\end_layout
\end_inset
@@ -7970,8 +7988,8 @@
\begin_inset Text
\begin_layout Standard
-Control the termination of the code based on total wall clock time used.
- Available only in none-pyre version.
+Controls the termination of the code based on total wall clock time used.
+ Available only in non-Pyre version.
\end_layout
\end_inset
@@ -8056,7 +8074,7 @@
perturbmag
\family default
.
- In full spherical model,
+ In a full spherical model,
\family typewriter
perturbl
\family default
@@ -8066,7 +8084,7 @@
\family default
specify the shape of the perturbations in spherical harmonic degree and
order.
- In region model,
+ In a regional model,
\family typewriter
perturbl
\family default
@@ -8085,7 +8103,7 @@
\family typewriter
num_perturbations
\family default
- in a comma-separated list .
+ in a comma-separated list.
\end_layout
@@ -8119,12 +8137,12 @@
tic_method
\family default
=2 and in the regional model.
- This create a top thermal boundary with a half-space cooling age specified
+ This creates a top thermal boundary with a half-space cooling age specified
by
\family typewriter
half_space_age
\family default
- in million years and a warm spherical blob
+ in millions of years and a warm spherical blob
\family roman
\series medium
\shape up
@@ -8137,7 +8155,8 @@
These parameters specify the temperature of the ambient mantle, the location
and radius of the blob, and also the amplitude of temperature change in
the blob relative to the ambient mantle temperautre.
- The location of the blob is default to the center of the computation domain.
+ The location of the blob is default to the center of the computational
+ domain.
\end_layout
\end_inset
@@ -8362,7 +8381,7 @@
\begin_inset Text
\begin_layout Standard
-Additional parameters for temperature boundary condition when
+Additional parameters for temperature boundary conditions when
\family typewriter
lith_age
\family default
@@ -8380,7 +8399,7 @@
\end_layout
\begin_layout Subsection
-Non-dimensional Numbers
+Non-Dimensional Numbers
\end_layout
\begin_layout Standard
@@ -8469,8 +8488,8 @@
\begin_inset Text
\begin_layout Standard
-Specify the non-dimensional depth of the Moho, 410km discontinuity, 660km
- discontinuity and D".
+These specify the non-dimensional depth of the Moho, 410km discontinuity,
+ 660km discontinuity and D".
These parameters are used to determine the depth of viscosity layers and
phase changes (see next two sections).
The names are only suggestive.
@@ -8690,6 +8709,8 @@
\size footnotesize
\newline
+
+\newline
visc = visc0 * exp( viscE/(T+viscT) - viscE/(1+viscT) )
\family default
\size default
@@ -9002,7 +9023,7 @@
\begin_layout Standard
If you wish only to solve for the velocity once (e.g., Stokes flow) then make
this parameter on.
- However, if you want to do a convection problem then this should be off.
+ However, if you want to do a convection problem, this should be off.
\end_layout
\end_inset
@@ -9027,7 +9048,7 @@
\end_inset
cgrad
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
for conjugate gradient solver or
@@ -9035,7 +9056,7 @@
\end_inset
multigrid
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
for multigrid solver for the outer loop of the momentum solver.
@@ -9129,7 +9150,7 @@
\begin_inset Text
\begin_layout Standard
-Maximum iterations of the outer loop for momentum solver.
+Maximum iterations of the outer loop for the momentum solver.
\end_layout
\end_inset
@@ -9151,7 +9172,7 @@
\begin_inset Text
\begin_layout Standard
-Convergence criterion for momentum solver.
+Convergence criterion for the momentum solver.
\end_layout
@@ -9230,7 +9251,7 @@
\begin_inset Text
\begin_layout Standard
-If on, solve the energy equation.
+If on, solves the energy equation.
\end_layout
\end_inset
@@ -9250,9 +9271,9 @@
\begin_inset Text
\begin_layout Standard
-If it is equal to 0, the size of time step is variable and is determined
+If it is equal to 0, the size of the time step is variable and is determined
dynamically.
- Otherwise, the size of time step is fixed at the specified value.
+ Otherwise, the size of the time step is fixed at the specified value.
\end_layout
\end_inset
@@ -9272,7 +9293,7 @@
\begin_inset Text
\begin_layout Standard
-Set the size of the time step to the specified fraction of maximum stable
+Set the size of the time step to the specified fraction of a maximum stable
advection time step.
Must be between 0 and 1.
\end_layout
@@ -9294,7 +9315,7 @@
\begin_inset Text
\begin_layout Standard
-The number of iterations for energy solver.
+The number of iterations for the energy solver.
\end_layout
\end_inset
@@ -9334,7 +9355,7 @@
\begin_inset Text
\begin_layout Standard
-At this point, don't change the parameter.
+Currently, don't change this parameter.
It is used only in problems which are integrated backward in time.
\end_layout
@@ -9451,7 +9472,7 @@
\begin_layout Standard
These parameters affect the echo behavior of the CitComS parser.
- Only in none-pyre version.
+ Only in non-Pyre version.
\end_layout
\end_inset
@@ -9768,10 +9789,10 @@
\end_layout
\begin_layout Standard
-This section lists the facilities and properties in the pyre version of
+This section lists the facilities and properties in the Pyre version of
CitComS.py.
Most of the properties have identical names for the parameters as those
- used in the none-pyre version of CitComS.py and is explained in the section
+ used in the non-Pyre version of CitComS.py and aare explained in the section
above.
This section highlights those which have changed and those which are entirely
new.
@@ -9804,7 +9825,7 @@
\begin_inset Text
\begin_layout Standard
-How many time steps to run, including the 0-th time step.
+How many time steps to run, including the 0th time step.
\end_layout
\end_inset
@@ -9830,7 +9851,7 @@
\end_inset
mpich
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
,
@@ -9838,7 +9859,7 @@
\end_inset
lam-mpi
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
,
@@ -9846,7 +9867,7 @@
\end_inset
lsf
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
,
@@ -9854,7 +9875,7 @@
\end_inset
pbs
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
, and
@@ -9862,7 +9883,7 @@
\end_inset
globus
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
.
@@ -9912,7 +9933,7 @@
\end_inset
regional
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
or
@@ -9920,7 +9941,7 @@
\end_inset
full
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
.
@@ -10002,7 +10023,7 @@
\end_inset
n%03d
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
@@ -10048,7 +10069,7 @@
\begin_inset Text
\begin_layout Standard
-Filename of machine file.
+File name of machine file.
Available only if
\family typewriter
launcher=mpich
@@ -10136,7 +10157,7 @@
\end_inset
full-sphere
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
or
@@ -10144,7 +10165,7 @@
\end_inset
regional-sphere
-\begin_inset Quotes srd
+\begin_inset Quotes sld
\end_inset
.
@@ -12465,7 +12486,15 @@
\begin_inset Text
\begin_layout Standard
-vel_bound_file="bvel.dat"
+vel_bound_file=
+\begin_inset Quotes srd
+\end_inset
+
+bvel.dat
+\begin_inset Quotes srd
+\end_inset
+
+
\end_layout
\end_inset
@@ -12505,7 +12534,15 @@
\begin_inset Text
\begin_layout Standard
-mat_file="mat.dat"
+mat_file=
+\begin_inset Quotes srd
+\end_inset
+
+mat.dat
+\begin_inset Quotes srd
+\end_inset
+
+
\end_layout
\end_inset
@@ -12545,7 +12582,15 @@
\begin_inset Text
\begin_layout Standard
-lith_age_file="age.dat"
+lith_age_file=
+\begin_inset Quotes srd
+\end_inset
+
+age.dat
+\begin_inset Quotes srd
+\end_inset
+
+
\end_layout
\end_inset
@@ -12961,7 +13006,15 @@
\begin_inset Text
\begin_layout Standard
-tracer_file="tracer.dat"
+tracer_file=
+\begin_inset Quotes srd
+\end_inset
+
+tracer.dat
+\begin_inset Quotes srd
+\end_inset
+
+
\end_layout
\end_inset
@@ -12999,7 +13052,15 @@
\begin_inset Text
\begin_layout Standard
-Viscosity="system"
+Viscosity=
+\begin_inset Quotes srd
+\end_inset
+
+system
+\begin_inset Quotes srd
+\end_inset
+
+
\end_layout
\end_inset
@@ -13329,10 +13390,8 @@
\begin_layout Standard
The Pyre facility
\family typewriter
-\size footnotesize
journal
\family default
-\size default
provides five types of debugging output for conceptually different types
of information.
The journal output stream can be instantiated as separated channels multiple
@@ -13517,7 +13576,7 @@
\end_inset
-Coordinate files
+Coordinate Files
\end_layout
\begin_layout Standard
@@ -13602,7 +13661,7 @@
\begin_layout Standard
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
+ Only the vertical dimension is specified by
\family typewriter
coor_file
\family default
@@ -13642,7 +13701,7 @@
\end_inset
-Velocity boundary condition files
+Velocity Boundary Condition Files
\end_layout
\begin_layout Standard
@@ -13658,7 +13717,7 @@
\family typewriter
bvel.dat
\family default
- file per cap for each million year interval.
+ file per cap for each million-year interval.
For example, if
\family typewriter
start_age=83
@@ -13696,9 +13755,9 @@
\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:
+For the global mesh, each of the 12 caps requires one file for each million-year
+ interval.
+ For example, these files are needed for an 82-million-year age:
\end_layout
\begin_layout LyX-Code
@@ -13724,7 +13783,7 @@
\end_layout
\begin_layout Section
-Material files
+Material Files
\end_layout
\begin_layout Standard
@@ -13739,7 +13798,7 @@
\family typewriter
mat.dat
\family default
-, then it is necessary to have one mat.dat file for each million year interval.
+, then it is necessary to have one mat.dat file for each million-year interval.
For example, if
\family typewriter
start_age=83
@@ -13764,7 +13823,12 @@
\family typewriter
vel_bound_file
\family default
- (see above) applies.
+ (see Section
+\begin_inset LatexCommand \ref{sec:Velocity-boundary-condition}
+
+\end_inset
+
+ above) applies.
The format of
\family typewriter
mat_file
@@ -13795,7 +13859,7 @@
\family typewriter
bvel.dat
\family default
- file for each million year interval.
+ file for each million-year interval.
For example, if
\family typewriter
start_age=83
@@ -13820,11 +13884,16 @@
\family typewriter
vel_bound_file
\family default
- (see above) still applies.
+ (see Section
+\begin_inset LatexCommand \ref{sec:Velocity-boundary-condition}
+
+\end_inset
+
+ above) still applies.
The input age is in millions of years.
- 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:
+ For the global mesh, each of the 12 caps requires one file for each million-yea
+r interval.
+ For example, these files are needed for and 82-million-year age:
\end_layout
\begin_layout LyX-Code
@@ -13951,8 +14020,8 @@
\end_layout
\begin_layout Standard
-It reports non-dimensional elapsed model time and spent CPU time (in seconds).
- Only outputted on computer node 0.
+This file reports non-dimensional elapsed model time and spent CPU time
+ (in seconds), and it is only outputted on computer node 0.
The meaning of each column is:
\end_layout
@@ -13961,6 +14030,10 @@
\end_layout
\begin_layout Section
+\begin_inset LatexCommand \label{sec:ASCII-Output}
+
+\end_inset
+
ASCII Output
\end_layout
@@ -13969,7 +14042,7 @@
\end_layout
\begin_layout Standard
-Only outputted at 0th time step.
+This file is only outputted at the 0th time step.
The first line is a header.
The rest of the file is column-based, where the meaning of each column
is:
@@ -13988,7 +14061,7 @@
\end_layout
\begin_layout Standard
-The two lines are headers.
+The first two lines of this file are headers.
The rest of the file is column-based, where the meaning of each column
is:
\end_layout
@@ -14002,8 +14075,8 @@
\end_layout
\begin_layout Standard
-The first line is a header.
- The rest of the file is column-based, where the meaning of each column
+The first line of this file is a header.
+ The rest of the file is column-based, where the meaning of the only column
is:
\end_layout
@@ -14019,7 +14092,7 @@
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.
- Only output at 0th time step.
+ This file is only output at the 0th time step.
There is no header.
The meaning of each column is:
\end_layout
@@ -14033,8 +14106,8 @@
\end_layout
\begin_layout Standard
-The first line is a header.
- The rest of the file is column-based, where the meaning of each column
+The first line of each file is a header.
+ The rest of each file is column-based, where the meaning of each column
is:
\end_layout
@@ -14047,7 +14120,7 @@
\end_layout
\begin_layout Standard
-The first two lines are headers.
+The first two lines of the file are headers.
The rest of the file is column-based, where the meaning of each column
is:
\end_layout
@@ -14056,13 +14129,29 @@
Sxx Syy Szz Sxy Sxz Syz
\end_layout
+\begin_layout Standard
+You can use the above values to form the following symmetric stress tensor:
+\end_layout
+
+\begin_layout Standard
+\begin_inset Formula \begin{equation}
+\left[\begin{array}{ccc}
+Sxx & Sxy & Sxz\\
+Syx & Syy & Syz\\
+Szx & Szy & Szz\end{array}\right]\label{eq:symmetric stress tensor}\end{equation}
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Pressure Output (test-case.pressure.0.10)
\end_layout
\begin_layout Standard
-The first line is a header.
- The rest of the file is column-based, where the meaning of each column
+The first line of the file is a header.
+ The rest of the file is column-based, where the meaning of the only column
is:
\end_layout
@@ -14075,7 +14164,7 @@
\end_layout
\begin_layout Standard
-The first line is a header.
+The first line of the file is a header.
The rest of the file is column-based, where the meaning of each column
is:
\end_layout
@@ -14088,6 +14177,12 @@
HDF5 Output (test-case.h5)
\end_layout
+\begin_layout Standard
+
+\series bold
+(TODO: Insert Data Output table in section 4.3, Luis)
+\end_layout
+
\begin_layout Chapter
License
\end_layout
@@ -14188,21 +14283,49 @@
\end_layout
\begin_layout Standard
-0.
- This License applies to any program or other work which contains a notice
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+begin{itemize}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+item[0.]
+\end_layout
+
+\end_inset
+
+This License applies to any program or other work which contains a notice
placed by the copyright holder saying it may be distributed under the terms
of this General Public License.
- The "Program,",below, refers to any such program or work, and a "work based
+ The "Program" below refers to any such program or work, and a "work based
on the Program" means either the Program or any derivative work under copyright
law: that is to say, a work containing the Program or a portion of it,
either verbatim or with modifications and/or translated into another language.
(Hereinafter, translation is included without limitation in the term "modificat
ion.") Each licensee is addressed as "you."
-\end_layout
+\newline
-\begin_layout Standard
-Activities other than copying, distribution and modification are not covered
- by this License; they are outside its scope.
+\newline
+Activities other than copying,
+ distribution and modification are not covered by this License; they are
+ outside its scope.
The act of running the Program is not restricted, and the output from the
Program is covered only if its contents constitute a work based on the
Program (independent of having been made by running the Program).
@@ -14211,8 +14334,23 @@
\end_layout
\begin_layout Standard
-1.
- You may copy and distribute verbatim copies of the Program's source code
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+end{itemize}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Enumerate
+You may copy and distribute verbatim copies of the Program's source code
as you receive it, in any medium, provided that you conspicuously and appropria
tely publish on each copy an appropriate copyright notice and disclaimer
of warranty; keep intact all the notices that refer to this License and
@@ -14221,36 +14359,38 @@
\end_layout
+\begin_deeper
\begin_layout Standard
You may charge a fee for the physical act of transferring a copy, and you
may at your option offer warranty protection in exchange for a fee.
\end_layout
-\begin_layout Standard
-2.
- You may modify your copy or copies of the Program or any portion of it,
+\end_deeper
+\begin_layout Enumerate
+You may modify your copy or copies of the Program or any portion of it,
thus forming a work based on the Program, and copy and distribute such
modifications or work under the terms of Section 1 above, provided that
you also meet all of these conditions:
\end_layout
-\begin_layout Standard
-a) You must cause the modified files to carry prominent notices stating
- that you changed the files and the date of any change.
+\begin_deeper
+\begin_layout Enumerate
+You must cause the modified files to carry prominent notices stating that
+ you changed the files and the date of any change.
\end_layout
-\begin_layout Standard
-b) You must cause any work that you distribute or publish, that in whole
- or in part contains or is derived from the Program or any part thereof,
- to be licensed as a whole at no charge to all third parties under the terms
+\begin_layout Enumerate
+You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to
+ be licensed as a whole at no charge to all third parties under the terms
of this License.
\end_layout
-\begin_layout Standard
-c) If the modified program normally reads commands interactively when run,
+\begin_layout Enumerate
+If the modified program normally reads commands interactively when run,
you must cause it, when started running for such interactive use in the
most ordinary way, to print or display an announcement including an appropriate
copyright notice and a notice that there is no warranty (or else, saying
@@ -14292,30 +14432,30 @@
\end_layout
-\begin_layout Standard
-3.
- You may copy and distribute the Program (or a work based on it, under Section
+\end_deeper
+\begin_layout Enumerate
+You may copy and distribute the Program (or a work based on it, under Section
2) in object code or executable form under the terms of Sections 1 and
2 above provided that you also do one of the following:
\end_layout
-\begin_layout Standard
-a) Accompany it with the complete corresponding machine-readable source
- code, which must be distributed under the terms of Sections 1 and 2 above
- on a medium customarily used for software interchange; or,
+\begin_deeper
+\begin_layout Enumerate
+Accompany it with the complete corresponding machine-readable source code,
+ which must be distributed under the terms of Sections 1 and 2 above on
+ a medium customarily used for software interchange; or,
\end_layout
-\begin_layout Standard
-b) Accompany it with a written offer, valid for at least three years, to
- give any third party, for a charge no more than your cost of physically
- performing source distribution, a complete machine-readable copy of the
- corresponding source code, to be distributed under the terms of Sections
- 1 and 2 above on a medium customarily used for software interchange; or,
-
+\begin_layout Enumerate
+Accompany it with a written offer, valid for at least three years, to give
+ any third party, for a charge no more than your cost of physically performing
+ source distribution, a complete machine-readable copy of the corresponding
+ source code, to be distributed under the terms of Sections 1 and 2 above
+ on a medium customarily used for software interchange; or,
\end_layout
-\begin_layout Standard
-c) Accompany it with the information you received as to the offer to distribute
+\begin_layout Enumerate
+Accompany it with the information you received as to the offer to distribute
corresponding source code.
(This alternative is allowed only for noncommercial distribution and only
if you received the program in object code or executable form with such
@@ -14344,10 +14484,10 @@
\end_layout
-\begin_layout Standard
-4.
- You may not copy, modify, sublicense, or distribute the Program except
- as expressly provided under this License.
+\end_deeper
+\begin_layout Enumerate
+You may not copy, modify, sublicense, or distribute the Program except as
+ expressly provided under this License.
Any attempt otherwise to copy, modify, sublicense or distribute the Program
is void, and will automatically terminate your rights under this License.
However, parties who have received copies, or rights, from you under this
@@ -14356,10 +14496,8 @@
\end_layout
-\begin_layout Standard
-5.
- You are not required to accept this License, since you have not signed
- it.
+\begin_layout Enumerate
+You are not required to accept this License, since you have not signed it.
However, nothing else grants you permission to modify or distribute the
Program or its derivative works.
These actions are prohibited by law if you do not accept this License.
@@ -14370,9 +14508,8 @@
\end_layout
-\begin_layout Standard
-6.
- Each time you redistribute the Program (or any work based on the Program),
+\begin_layout Enumerate
+Each time you redistribute the Program (or any work based on the Program),
the recipient automatically receives a license from the original licensor
to copy, distribute or modify the Program subject to these terms and conditions.
You may not impose any further restrictions on the recipients' exercise
@@ -14382,9 +14519,8 @@
\end_layout
-\begin_layout Standard
-7.
- If, as a consequence of a court judgment or allegation of patent infringement
+\begin_layout Enumerate
+If, as a consequence of a court judgment or allegation of patent infringement
or for any other reason (not limited to patent issues), conditions are
imposed on you (whether by court order, agreement or otherwise) that contradict
the conditions of this License, they do not excuse you from the conditions
@@ -14398,6 +14534,7 @@
be to refrain entirely from distribution of the Program.
\end_layout
+\begin_deeper
\begin_layout Standard
If any portion of this section is held invalid or unenforceable under any
particular circumstance, the balance of the section is intended to apply
@@ -14423,27 +14560,27 @@
\end_layout
-\begin_layout Standard
-8.
- If the distribution and/or use of the Program is restricted in certain
- countries either by patents or by copyrighted interfaces, the original
- copyright holder who places the Program under this License may add an explicit
- geographical distribution limitation excluding those countries, so that
- distribution is permitted only in or among countries not thus excluded.
+\end_deeper
+\begin_layout Enumerate
+If the distribution and/or use of the Program is restricted in certain countries
+ either by patents or by copyrighted interfaces, the original copyright
+ holder who places the Program under this License may add an explicit geographic
+al distribution limitation excluding those countries, so that distribution
+ is permitted only in or among countries not thus excluded.
In such case, this License incorporates the limitation as if written in
the body of this License.
\end_layout
-\begin_layout Standard
-9.
- The Free Software Foundation may publish revised and/or new versions of
+\begin_layout Enumerate
+The Free Software Foundation may publish revised and/or new versions of
the General Public License from time to time.
Such new versions will be similar in spirit to the present version, but
may differ in detail to address new problems or concerns.
\end_layout
+\begin_deeper
\begin_layout Standard
Each version is given a distinguishing version number.
If the Program specifies a version number of this License which applies
@@ -14454,9 +14591,9 @@
choose any version ever published by the Free Software Foundation.
\end_layout
-\begin_layout Standard
-10.
- If you wish to incorporate parts of the Program into other free programs
+\end_deeper
+\begin_layout Enumerate
+If you wish to incorporate parts of the Program into other free programs
whose distribution conditions are different, write to the author to ask
for permission.
For software which is copyrighted by the Free Software Foundation, write
@@ -14472,8 +14609,35 @@
\end_layout
\begin_layout Standard
-11.
- BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+begin{itemize}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+item[11.]
+\end_layout
+
+\end_inset
+
+BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER
PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER
@@ -14487,8 +14651,19 @@
\end_layout
\begin_layout Standard
-12.
- IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+item[12.]
+\end_layout
+
+\end_inset
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING
ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF
@@ -14499,6 +14674,22 @@
OF SUCH DAMAGES.
\end_layout
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+end{itemize}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Section*
END OF TERMS AND CONDITIONS
\end_layout
@@ -14523,12 +14714,12 @@
\end_layout
\begin_layout Quote
-one line to give the program's name and a brief idea of what it does.
+One line to give the program's name and a brief idea of what it does.
Copyright
\size footnotesize
-(C)
+© (
\size default
- (year) (name of author)
+year) (name of author)
\end_layout
\begin_layout Quote
@@ -14564,12 +14755,8 @@
\end_layout
\begin_layout Quote
-Gnomovision version 69, Copyright
-\size footnotesize
-(C)
-\size default
- year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for
- details type `show w'.
+Gnomovision version 69, Copyright © year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it under certain
conditions; type `show c' for details.
@@ -14623,9 +14810,9 @@
\emph on
Comp.
Sci.
- Engin.,
+ Engin., 2
\emph default
-2, 22-33.
+, 22-33.
\end_layout
\begin_layout Bibliography
@@ -14640,7 +14827,11 @@
Phys.
Fluid,
\emph default
- 7, 2,154-2,162.
+
+\emph on
+7
+\emph default
+, 2,154-2,162.
\end_layout
\begin_layout Bibliography
@@ -14655,7 +14846,11 @@
Sci.
Lett.,
\emph default
- 138, 15-28.
+
+\emph on
+138
+\emph default
+, 15-28.
\end_layout
\begin_layout Bibliography
@@ -14670,7 +14865,11 @@
Geophys.
Res.,
\emph default
- 103, 15,255-15,268.
+
+\emph on
+103
+\emph default
+, 15,255-15,268.
\end_layout
\begin_layout Bibliography
@@ -14686,9 +14885,9 @@
\emph on
J.
Geophys.
- Res.,
+ Res., 105
\emph default
-105, 11,063-11,082.
+, 11,063-11,082.
\end_layout
\begin_layout Bibliography
@@ -14703,7 +14902,11 @@
Geophys.
Geosys.,
\emph default
- 3, 1067.
+
+\emph on
+3
+\emph default
+, 1067.
\end_layout
\begin_layout Bibliography
@@ -14718,7 +14921,11 @@
Geophys.
Geosys.,
\emph default
- 4(3), 1031, doi:10.1029/2001GC000299.
+
+\emph on
+4(3)
+\emph default
+, 1031, doi:10.1029/2001GC000299.
\end_layout
\begin_layout Bibliography
@@ -14750,7 +14957,11 @@
Methods.
Fluids,
\emph default
- 19, 67-83.
+
+\emph on
+19
+\emph default
+, 67-83.
\end_layout
\begin_layout Bibliography
@@ -14780,7 +14991,11 @@
Methods.
Fluids,
\emph default
- 8, 869-895.
+
+\emph on
+8
+\emph default
+, 869-895.
\end_layout
\begin_layout Bibliography
@@ -14796,7 +15011,11 @@
Methods.
Fluids,
\emph default
- 14, 71-81.
+
+\emph on
+14
+\emph default
+, 71-81.
\end_layout
\begin_layout Bibliography
@@ -14812,7 +15031,11 @@
Geophys.
Res.,
\emph default
- 86, 4,843-4,867.
+
+\emph on
+86
+\emph default
+, 4,843-4,867.
\end_layout
\begin_layout Bibliography
@@ -14847,7 +15070,11 @@
J.
Int.
\emph default
-, 127, 708-718.
+,
+\emph on
+127
+\emph default
+, 708-718.
\end_layout
\begin_layout Bibliography
@@ -14862,8 +15089,12 @@
J.
Int.,
\emph default
- 155, 679-695.
+\emph on
+155
+\emph default
+, 679-695.
+
\end_layout
\end_body
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