# [cig-commits] r14439 - long/3D/Gale/trunk/documentation

sue at geodynamics.org sue at geodynamics.org
Tue Mar 24 16:31:29 PDT 2009

Author: sue
Date: 2009-03-24 16:31:28 -0700 (Tue, 24 Mar 2009)
New Revision: 14439

Modified:
long/3D/Gale/trunk/documentation/gale.lyx
Log:
various changes/fixes made until halfway through appendix a; more to come

Modified: long/3D/Gale/trunk/documentation/gale.lyx
===================================================================
--- long/3D/Gale/trunk/documentation/gale.lyx	2009-03-24 23:01:15 UTC (rev 14438)
+++ long/3D/Gale/trunk/documentation/gale.lyx	2009-03-24 23:31:28 UTC (rev 14439)
@@ -582,7 +582,7 @@
\end_layout

\begin_layout Standard
-Note that there is no explicit time dependency in the momentum equation
+Note that there is no explicit time dependency in the momentum Equation

\begin_inset LatexCommand ref
reference "eq:simple momentum conservation"
@@ -701,7 +701,7 @@
\end_layout

\begin_layout Standard
-You do this by adding a divergence term to the continuity equation (Eq.
+You do this by adding a divergence term to the continuity Equation (Eq.

\begin_inset LatexCommand ref
reference "eq:continuity"
@@ -726,7 +726,7 @@
However, since the velocity and pressure are not really independent, you
can also think of it as setting a condition on the pressure.
For example, consider a one dimensional isoviscous case with no gravity.
- You can write the momentum equation (Eq.
+ You can write the momentum Equation (Eq.

\begin_inset LatexCommand ref
reference "eq:simple momentum conservation"
@@ -742,7 +742,7 @@

\end_inset

- In one dimension, equation
+ In one dimension, Equation
\begin_inset LatexCommand ref
reference "eq:divergence"

@@ -780,7 +780,7 @@
\begin_layout Standard
Gale incorporates a number of different rheologies and allows you to create
- For more complicated, non-linear rheologies, Gale still solves equation
+ For more complicated, non-linear rheologies, Gale still solves Equation

\begin_inset LatexCommand ref
reference "eq:stress strain"
@@ -886,8 +886,9 @@
In Gale, the velocity and pressure are represented by linear (Q1) finite
elements (formally, this is called a Q1-Q1 scheme).
Normally, this formulation is unstable.
- To stabilize it, we follow Dohrmann & Bochev () and add a compressibility
- term to the divergence equation
+ To stabilize it, we follow Dohrmann & Bochev () [TODO: add bib item and
+ put ref.
+ here] and add a compressibility term to the divergence equation
\end_layout

\begin_layout Standard
@@ -926,10 +927,10 @@
\begin_layout Standard
Prior versions of Gale used constant elements for the pressure (a Q1-P0
scheme).
- That scheme admits solutions that have an arbitrarily sized checkboard
+ That scheme admits solutions that have an arbitrarily sized checkerboard
pressure term.
For simple viscous problems, the pressure is not used any further than
- getting the velocity solution, which the checkboard term does not affect.
+ getting the velocity solution, which the checkerboard term does not affect.
However, with a yielding rheology, pressure plays a critical role in determinin
g when materials yield.
We can moderate this checkerboard instability by averaging the pressure
@@ -1047,7 +1048,7 @@
The new scheme is not without its downsides.
First of all, the new code does not scale the physical quantities as well
as the old code.
- In particular, note that the units for equations
+ In particular, note that the units for Equations
\begin_inset LatexCommand ref
reference "eq:body force"

@@ -1060,7 +1061,7 @@
\end_inset

are different.
- In particular, equation
+ In particular, Equation
\begin_inset LatexCommand ref
reference "eq:stabilized"

@@ -1077,13 +1078,29 @@

, the compressibility pressure term will become too small and the code will
be unable to solve.
- One workaround is to scale the units of time and mass (e.g.
- seconds and kg) so that the viscosities are around 1.
+ One workaround is to scale the units of time and mass (e.g., seconds and
+ kg) so that the viscosities are around 1.
In particular, if the viscosities are around
\begin_inset Formula $10^{25}$
\end_inset

-, then scale time and mass as
+, then scale time and mass as [TODO: do you mean
+\begin_inset Quotes sld
+\end_inset
+
+is
+\begin_inset Quotes srd
+\end_inset
+
+\begin_inset Quotes sld
+\end_inset
+
+as
+\begin_inset Quotes srd
+\end_inset
+
+?]
\end_layout

\begin_layout Standard
@@ -1186,7 +1203,7 @@

\begin_layout Standard
To fix this, you can subtract out the hydrostatic term.
- You can write equation
+ You can write Equation
\begin_inset LatexCommand ref
reference "eq:body force"

@@ -1219,7 +1236,7 @@
\end_inset

are constructed to be hydrostatic, they cancel each other.
- You can then rewrite equations
+ You can then rewrite Equations
\begin_inset LatexCommand ref
reference "eq:body force"

@@ -1291,8 +1308,7 @@
\begin_inset Formula $f$
\end_inset

- is the body force (e.g.
- gravity), and
+ is the body force (e.g., gravity), and
\begin_inset Formula $d$
\end_inset

@@ -1348,7 +1364,7 @@
\end_inset

is known as a preconditioner.
- To actually solve equation
+ To actually solve Equation
\begin_inset LatexCommand ref
reference "eq:expanded matrix"

@@ -1369,7 +1385,7 @@
\begin_inset Formula $q_{0}$
\end_inset

-of the pressure-like variable.
+ of the pressure-like variable.
\end_layout

\begin_layout Enumerate
@@ -1377,7 +1393,7 @@
\begin_inset Formula $K\, u_{0}=f-Gq_{0}$
\end_inset

-for
+ for
\begin_inset Formula $u_{0}$
\end_inset

@@ -1393,7 +1409,23 @@
\end_layout

\begin_layout Enumerate
-do
+do [TODO: refers only to step 5 or also step 6?
+\begin_inset Quotes sld
+\end_inset
+
+Do
+\begin_inset Quotes srd
+\end_inset
+
+ doesn't match with
+\begin_inset Quotes sld
+\end_inset
+
+solve
+\begin_inset Quotes srd
+\end_inset
+
+ imho]
\end_layout

\begin_layout Enumerate
@@ -1425,7 +1457,8 @@
\InsetSpace ~
\InsetSpace ~
\InsetSpace ~
-if k==1
+if k==1 [TODO: you have 2 equals signs here.
+ Is that an error?]
\end_layout

\begin_layout Enumerate
@@ -1573,7 +1606,7 @@
\end_layout

\begin_layout Standard
-That will give us a single solution to equation
+That will give us a single solution to Equation
\begin_inset LatexCommand ref
reference "eq:expanded matrix"

@@ -1584,7 +1617,7 @@
will change and the solution will not be consistent.
To make it consistent, we need to recompute the viscosities with the new
solution for the pressure and velocity.
- Then we solve equation
+ Then we solve Equation
\begin_inset LatexCommand ref
reference "eq:expanded matrix"

@@ -1900,14 +1933,14 @@

\size small
Error in _AbstractContext_New: The dictionary is empty, meaning no input
- parameters have been feed
+ parameters have been fed
\end_layout

\begin_layout LyX-Code

\size small
- Perhaps you've forgot to pass any input files ( or command-line arguments
+ Perhaps you have forgotten to pass any input files ( or command-line arguments
) in.
\end_layout

@@ -2086,7 +2119,7 @@
\begin_layout Standard
You can also change the default values of the input file without modifying
that file by appending arguments.
- For example, to only change the number of time steps from the default value
+ For example, to change only the number of time steps from the default value
10 to value 20, use the following command
\end_layout

@@ -2369,8 +2402,6 @@
\end_inset

-\newpage
-
\end_layout

\end_deeper
@@ -2489,8 +2520,6 @@
\end_inset

-\newpage
-
\end_layout

\end_deeper
@@ -2545,8 +2574,6 @@
\end_inset

-\newpage
-
\end_layout

\end_deeper
@@ -2594,8 +2621,6 @@
\end_inset

-\newpage
-
\end_layout

\end_deeper
@@ -2633,8 +2658,6 @@
\end_inset

-\newpage
-
\end_layout

\end_deeper
@@ -2669,8 +2692,6 @@
\end_inset

-\newpage
-
\end_layout

\end_deeper
@@ -2722,9 +2743,6 @@
This displays the viscosity of the particles.
The red points represent the high viscosity ball, while the blue points
represent material that has yielded.
-
-\newpage
-
\end_layout

\end_deeper
@@ -3374,7 +3392,8 @@

\end_inset

- shows the velocity (see Section
+ [TODO: which figure? this label doesn't work now.] shows the velocity (see
+ Section
\begin_inset LatexCommand ref
reference "sub:Visualization-with-ParaView"

@@ -3542,7 +3561,7 @@
\begin_inset Graphics
filename images/Paraview_viscous_extension.png
lyxscale 75
-	scale 75
+	scale 70

\end_inset

@@ -3822,7 +3841,7 @@
\begin_inset Graphics
filename images/Paraview_viscous_split.png
lyxscale 75
-	scale 75
+	scale 70

\end_inset

@@ -4235,7 +4254,7 @@
\begin_inset Graphics
filename images/Paraview_viscous_inflow.png
lyxscale 75
-	scale 75
+	scale 70

\end_inset

@@ -4265,7 +4284,9 @@
\end_layout

\begin_layout Section
-Viscous Material with Inflow/Outflow and Fixed Internal Degrees of Freedom
+Viscous Material with Inflow/Outflow and Fixed Internal
+\newline
+ Degrees of Freedom
\end_layout

\begin_layout Standard
@@ -4493,7 +4514,7 @@
\align center
\begin_inset Graphics
filename images/Paraview_viscous_fixed.png
-	scale 45
+	scale 40

\end_inset

@@ -4895,7 +4916,7 @@
\begin_inset Graphics
filename images/Paraview_normal_stress.png
lyxscale 75
-	scale 75
+	scale 40

\end_inset

@@ -5094,7 +5115,7 @@
\begin_inset Graphics
filename images/Paraview_viscous_sinusoid.png
lyxscale 75
-	scale 75
+	scale 40

\end_inset

@@ -5403,7 +5424,7 @@
\begin_inset Graphics
filename images/Paraview_multi_material.png
lyxscale 75
-	scale 75
+	scale 40

\end_inset

@@ -5453,7 +5474,7 @@
\begin_inset Graphics
filename images/Paraview_multi_viscosity.png
lyxscale 75
-	scale 75
+	scale 40

\end_inset

@@ -5733,7 +5754,7 @@
\begin_inset Graphics
filename images/Paraview_yielding.png
lyxscale 75
-	scale 75
+	scale 40

\end_inset

@@ -5788,7 +5809,7 @@
\begin_inset Graphics
filename images/Paraview_yielding_viscosity.png
lyxscale 75
-	scale 75
+	scale 40

\end_inset

@@ -5843,7 +5864,7 @@
\begin_inset Graphics
filename images/Paraview_yielding_yielding.png
lyxscale 75
-	scale 75
+	scale 40

\end_inset

@@ -5877,7 +5898,7 @@
\end_layout

\begin_layout Standard
-Temperature can play a decisive role in geophyisical processes.
+Temperature can play a decisive role in geophysical processes.
This example takes the multiple viscous material example from Section
\begin_inset LatexCommand ref
reference "sec:Multiple-Viscous-Materials"
@@ -6427,7 +6448,7 @@
\end_layout

\begin_layout LyX-Code
-  <struct>
+  <struct>
\end_layout

\begin_layout LyX-Code
@@ -6485,7 +6506,7 @@
\begin_inset Graphics
filename images/Paraview_thermal.png
lyxscale 75
-	scale 75
+	scale 40

\end_inset

@@ -6745,7 +6766,7 @@

\end_inset

-Strain rate invariant for the 2D tibetan scale extension model after 30
+Strain rate invariant for the 2D Tibetan scale extension model after 30
km of extension.
\end_layout

@@ -6855,7 +6876,7 @@

\end_inset

-Strain rate invariant for the 3D tibetan scale extension model after 24
+Strain rate invariant for the 3D Tibetan scale extension model after 24
km of extension
\end_layout

@@ -8551,7 +8572,7 @@

\begin_layout Description
outputPath The directory to put output files in.
- Due to quirks in MPI, you may need to specify this as a full path (e.g.
+ Due to quirks in MPI, you may need to specify this as a full path (e.g.,

\family typewriter
/home/juser/simulatons/myoutput
@@ -15804,8 +15825,7 @@
\end_inset

, then it must be the textual name of one of the Standard Condition Functions
- (e.g.
- StepFunction).
+ (e.g., StepFunction).
\end_layout

\begin_layout Section