[cig-commits] r7997 - doc/CitcomS/manual
tan2 at geodynamics.org
tan2 at geodynamics.org
Fri Sep 21 14:17:54 PDT 2007
Author: tan2
Date: 2007-09-21 14:17:53 -0700 (Fri, 21 Sep 2007)
New Revision: 7997
Modified:
doc/CitcomS/manual/citcoms.lyx
Log:
Renamed the eqn tags and add a section for configurating Exchanger
Modified: doc/CitcomS/manual/citcoms.lyx
===================================================================
--- doc/CitcomS/manual/citcoms.lyx 2007-09-21 16:40:59 UTC (rev 7996)
+++ doc/CitcomS/manual/citcoms.lyx 2007-09-21 21:17:53 UTC (rev 7997)
@@ -1,4 +1,4 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.2 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -593,7 +593,12 @@
s; (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; and (6) an exchanger package for solver
- coupling.
+ coupling; (7) fixed non-Newtonian solver.
+ Additional changes include: (1) the viscosity field at element level is
+ not smoothed; this might slow down the convergence but will represent the
+ viscosity field more accurately; (2) the Lenardic filter on temperature
+ is disable by default; (3) using a better pseudo-random number generator
+ to generate initial tracer; (4) monitoring maximum temperature
\end_layout
\begin_layout Section
@@ -675,7 +680,7 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Description
\begin_inset LatexCommand \label{Pyre-Architecture}
@@ -778,7 +783,7 @@
\shape italic
- is the density,
+ is the density,
\shape default
u
\emph default
@@ -931,7 +936,7 @@
\begin_layout Standard
\align right
\begin_inset Formula \begin{equation}
-\Gamma=\frac{1}{2}\left(1+\tanh\left(\frac{1-r-d_{ph}-s(T-T_{ph})}{w_{ph}}\right)\right)\label{eq:17}\end{equation}
+\Gamma=\frac{1}{2}\left(1+\tanh\left(\frac{1-r-d_{ph}-s(T-T_{ph})}{w_{ph}}\right)\right)\label{eq:phase function}\end{equation}
\end_inset
@@ -968,7 +973,7 @@
\begin_layout Standard
\align right
\begin_inset Formula \begin{equation}
-x_{i}=R_{0}x_{i}^{'}\label{eq:5}\end{equation}
+x_{i}=R_{0}x_{i}^{'}\label{eq:x dim}\end{equation}
\end_inset
@@ -977,7 +982,7 @@
\begin_layout Standard
\begin_inset Formula \begin{equation}
-u_{i}=\frac{\kappa}{R_{0}}u_{i}^{'}\label{eq:6}\end{equation}
+u_{i}=\frac{\kappa}{R_{0}}u_{i}^{'}\label{eq:u dim}\end{equation}
\end_inset
@@ -987,7 +992,7 @@
\begin_layout Standard
\align right
\begin_inset Formula \begin{equation}
-T=\Delta TT'+T_{0}\label{eq:7}\end{equation}
+T=\Delta TT'+T_{0}\label{eq:T dim}\end{equation}
\end_inset
@@ -997,7 +1002,7 @@
\begin_layout Standard
\align right
\begin_inset Formula \begin{equation}
-t=\frac{R_{0}^{2}}{\kappa}t^{'}\label{eq:8}\end{equation}
+t=\frac{R_{0}^{2}}{\kappa}t^{'}\label{eq:t dim}\end{equation}
\end_inset
@@ -1007,7 +1012,7 @@
\begin_layout Standard
\align right
\begin_inset Formula \begin{equation}
-H=c_{P0}\Delta TH^{'}\label{eq:9}\end{equation}
+H=c_{P0}\Delta TH^{'}\label{eq:H dim}\end{equation}
\end_inset
@@ -1017,7 +1022,7 @@
\begin_layout Standard
\align right
\begin_inset Formula \begin{equation}
-\eta=\eta_{0}\eta^{'}\label{eq:10}\end{equation}
+\eta=\eta_{0}\eta^{'}\label{eq:eta dim}\end{equation}
\end_inset
@@ -1027,7 +1032,7 @@
\begin_layout Standard
\align right
\begin_inset Formula \begin{equation}
-P=\frac{\eta_{0}\kappa}{R_{0}^{2}}P^{'}\label{eq:11}\end{equation}
+P=\frac{\eta_{0}\kappa}{R_{0}^{2}}P^{'}\label{eq:p dim}\end{equation}
\end_inset
@@ -1063,7 +1068,7 @@
\begin_layout Standard
\begin_inset Formula \begin{equation}
-u_{i,i}+\frac{d\ln\bar{\rho}}{dr}u_{r}=0\label{eq:12}\end{equation}
+u_{i,i}+\frac{d\ln\bar{\rho}}{dr}u_{r}=0\label{eq:non-dimensional continuity eqn}\end{equation}
\end_inset
@@ -1072,7 +1077,7 @@
\begin_layout Standard
\begin_inset Formula \begin{equation}
--P_{,i}+\left(\eta(u_{i,j}+u_{j,i}-\frac{2}{3}u_{k,k}\delta_{ij})\right)_{,i}+(Ra\bar{\rho}T+Rab\Gamma-RacC)\delta_{ir}=0\label{eq:13}\end{equation}
+-P_{,i}+\left(\eta(u_{i,j}+u_{j,i}-\frac{2}{3}u_{k,k}\delta_{ij})\right)_{,i}+(Ra\bar{\rho}T+Rab\Gamma-RacC)\delta_{ir}=0\label{eq:non-dimensional momentum eqn}\end{equation}
\end_inset
@@ -1082,7 +1087,7 @@
\begin_layout Standard
\align right
\begin_inset Formula \begin{equation}
-T_{,t}+u_{i}T_{,i}=T_{,ii}+H+(TODO)\label{eq:14}\end{equation}
+T_{,t}+u_{i}T_{,i}=T_{,ii}+H+(TODO)\label{eq:non-dimensional energy eqn}\end{equation}
\end_inset
@@ -1190,12 +1195,12 @@
.
The discrete form of Equations
-\begin_inset LatexCommand \ref{eq:12}
+\begin_inset LatexCommand \ref{eq:non-dimensional continuity eqn}
\end_inset
and
-\begin_inset LatexCommand \ref{eq:13}
+\begin_inset LatexCommand \ref{eq:non-dimensional momentum eqn}
\end_inset
@@ -1210,7 +1215,7 @@
\begin_layout Standard
\align right
\begin_inset Formula \begin{equation}
-\mathrm{\left(\mathbf{B}^{\mathit{T}}+\mathbf{C}\right)\mathit{u=0}}\label{eq:19}\end{equation}
+\mathrm{\left(\mathbf{B}^{\mathit{T}}+\mathbf{C}\right)\mathit{u=0}}\label{eq:discrete continuite eqn}\end{equation}
\end_inset
@@ -1220,7 +1225,7 @@
\begin_layout Standard
\align right
\begin_inset Formula \begin{equation}
-\mathbf{A\mathit{u+}}\mathbf{B\mathit{p=f}}\label{eq:20}\end{equation}
+\mathbf{A\mathit{u+}}\mathbf{B\mathit{p=f}}\label{eq:discrete momentum eqn}\end{equation}
\end_inset
@@ -1246,7 +1251,7 @@
\end_inset
is the second term in equation
-\begin_inset LatexCommand \ref{eq:12}
+\begin_inset LatexCommand \ref{eq:non-dimensional continuity eqn}
\end_inset
@@ -1291,7 +1296,7 @@
is zero.
Equation
-\begin_inset LatexCommand \ref{eq:20}
+\begin_inset LatexCommand \ref{eq:discrete momentum eqn}
\end_inset
@@ -1300,7 +1305,7 @@
\end_inset
and using equation
-\begin_inset LatexCommand \ref{eq:19}
+\begin_inset LatexCommand \ref{eq:discrete continuite eqn}
\end_inset
@@ -1310,7 +1315,7 @@
\begin_layout Standard
\align right
\begin_inset Formula \begin{equation}
-\mathbf{\mathbf{B}^{\mathit{T}}}\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p=\mathbf{\mathbf{B}^{\mathit{T}}A^{\mathit{-1}}\mathit{f}}}\label{eq:21}\end{equation}
+\mathbf{\mathbf{B}^{\mathit{T}}}\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p=\mathbf{\mathbf{B}^{\mathit{T}}A^{\mathit{-1}}\mathit{f}}}\label{eq:cg}\end{equation}
\end_inset
@@ -1336,20 +1341,21 @@
\end_layout
\begin_layout Standard
-In the incompressible case, there are two different strategies to solve
- Equation
-\begin_inset LatexCommand \ref{eq:19}
+In the compressible case, there are two different strategies to solve Equation
+
+\begin_inset LatexCommand \ref{eq:discrete continuite eqn}
\end_inset
and
-\begin_inset LatexCommand \ref{eq:20}
+\begin_inset LatexCommand \ref{eq:discrete momentum eqn}
\end_inset
.
- The first strategy is to add another iteration when solving Equation
-\begin_inset LatexCommand \ref{eq:21}
+ The first strategy is to add another layer of iterations when solving Equation
+
+\begin_inset LatexCommand \ref{eq:cg}
\end_inset
@@ -1360,7 +1366,7 @@
\begin_layout Standard
\begin_inset Formula \begin{equation}
-\mathbf{\mathbf{B}^{\mathit{T}}}\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p^{(i)}=\mathbf{\mathbf{B}^{\mathit{T}}A^{\mathit{-1}}\mathit{\left(f+\mathbf{C}u^{(i-1)}\right)}}}\label{eq:21}\end{equation}
+\mathbf{\mathbf{B}^{\mathit{T}}}\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p^{(i)}=\mathbf{\mathbf{B}^{\mathit{T}}A^{\mathit{-1}}\mathit{\left(f+\mathbf{C}u^{(i-1)}\right)}}}\label{eq:iter-cg}\end{equation}
\end_inset
@@ -1372,7 +1378,7 @@
This equation can be solved using the same conjugate gradient scheme as
the incompressible case.
The second strategy is to transform Equation
-\begin_inset LatexCommand \ref{eq:20}
+\begin_inset LatexCommand \ref{eq:discrete momentum eqn}
\end_inset
@@ -1381,13 +1387,13 @@
\end_inset
and using Equation
-\begin_inset LatexCommand \ref{eq:19}
+\begin_inset LatexCommand \ref{eq:discrete continuite eqn}
\end_inset
to eliminate the velocity unknowns:
\begin_inset Formula \begin{equation}
-\left(\mathbf{B}^{\mathit{T}}+\mathbf{C}\right)\mathit{\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p=\mathbf{\left(\mathbf{B}^{\mathit{T}}+\mathbf{C}\right)A^{\mathit{-1}}\mathit{f}}}}\label{eq:21}\end{equation}
+\left(\mathbf{B}^{\mathit{T}}+\mathbf{C}\right)\mathit{\mathbf{A}^{\mathbf{\mathit{-1}}}\mathbf{B}\mathit{p=\mathbf{\left(\mathbf{B}^{\mathit{T}}+\mathbf{C}\right)A^{\mathit{-1}}\mathit{f}}}}\label{eq:bicg}\end{equation}
\end_inset
@@ -1476,7 +1482,7 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Description
\begin_inset Graphics
@@ -1635,12 +1641,6 @@
\end_layout
-\begin_layout Standard
-\noindent
-\align center
-
-\end_layout
-
\begin_layout Chapter
Installation and Getting Help
\end_layout
@@ -1761,8 +1761,16 @@
\end_layout
\begin_layout Standard
-Optionally, CitComS can be configured to use a parallel HDF5 library.
+If you are going to use solver coupling, you will also need a decent C++
+ compiler (e.g., g++ 3.2 or newer) and the Exchanger package.
See Section
+\begin_inset LatexCommand \ref{sec:Exchanger-Configuration-(Optional)}
+
+\end_inset
+
+.
+ Optionally, CitComS can be configured to use a parallel HDF5 library.
+ See Section
\begin_inset LatexCommand \vref{sec:HDF5-Configuration}
\end_inset
@@ -2860,13 +2868,68 @@
\end_layout
\begin_layout Section
+\begin_inset LatexCommand \label{sec:Exchanger-Configuration-(Optional)}
+
+\end_inset
+
Exchanger Configuration (Optional)
\end_layout
\begin_layout Standard
-(TODO)
+This version of CitComS is capable of solver coupling.
+ Two or more instances of CitComS solvers can be coupled together to solve
+ a problem with different length and time scales
+\begin_inset LatexCommand \cite{Tan et al GeoFramework Part I}
+
+\end_inset
+
+.
+ An external Exchanger package is needed for solver coupling.
+ You can download Exchanger from CIG website (
+\family typewriter
+http://geodynamics.org/cig/software/packages/cs/exchanger/
+\family default
+).
+ After untar the package, you can configure and install Exchanger using
+ these commands:
\end_layout
+\begin_layout LyX-Code
+$ cd Exchanger-1.0.0/
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure --prefix=$HOME/cig
+\end_layout
+
+\begin_layout LyX-Code
+$ make
+\end_layout
+
+\begin_layout LyX-Code
+$ make install
+\end_layout
+
+\begin_layout Standard
+By default, CitComS will attempt to auto-detect your Exchanger installation,
+ and will disable HDF5 support if it is not found.
+ You may explicitly specify the location of your Exchanger installation
+ by setting the PYTHONPATH environment variable to the appropriate installation
+ prefix.
+\end_layout
+
+\begin_layout LyX-Code
+$ cd CitcomS-3.0.0/
+\end_layout
+
+\begin_layout LyX-Code
+$ export PYTHONPATH=$HOME/cig/lib/python-2.3/site-packages:$PYTHONPATH
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure --with-exchanger
+\end_layout
+
\begin_layout Section
\begin_inset LatexCommand \label{sec:HDF5-Configuration}
@@ -2916,7 +2979,7 @@
\end_layout
\begin_layout LyX-Code
-$ ./configure --with-hdf5 --prefix=$HOME/cig
+$ ./configure --with-hdf5
\end_layout
\begin_layout Subsection
@@ -7670,7 +7733,7 @@
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 Equation
-\begin_inset LatexCommand \vref{eq:6}
+\begin_inset LatexCommand \vref{eq:u dim}
\end_inset
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