[cig-commits] r6721 - in
short/3D/PyLith/branches/pylith-0.8/doc/userguide: . intro
materials runpylith tutorials/splitcube
sue at geodynamics.org
sue at geodynamics.org
Fri Apr 27 15:52:14 PDT 2007
Author: sue
Date: 2007-04-27 15:52:12 -0700 (Fri, 27 Apr 2007)
New Revision: 6721
Modified:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/preface.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/pylith_book.pdf
short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/splitcube.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.lyx
Log:
various edits, spacing fixes, image positioning, and long lines running off the page fixed
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.lyx 2007-04-27 21:47:33 UTC (rev 6720)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.lyx 2007-04-27 22:52:12 UTC (rev 6721)
@@ -365,6 +365,37 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status collapsed
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Graphics
+ filename figs/pyre_overview.eps
+ scale 75
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Pyre Architecture.
+ The integration framework is a set of cooperating abstract services.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
Pyre is a framework, a combination of software and design philosophy that
promotes the reuse of code.
In their canonical software design book,
@@ -409,38 +440,6 @@
development cycle, and good debugging support.
\end_layout
-\begin_layout Standard
-\begin_inset Float figure
-placement htbp
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-\align center
-\begin_inset Graphics
- filename figs/pyre_overview.eps
- scale 75
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Caption
-Pyre Architecture.
- The integration framework is a set of cooperating abstract services.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Section
PyLith Design
\end_layout
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.lyx 2007-04-27 21:47:33 UTC (rev 6720)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.lyx 2007-04-27 22:52:12 UTC (rev 6721)
@@ -1,4 +1,4 @@
-#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -42,12 +42,12 @@
\begin_layout Standard
There are six material models presently available in PyLith, as shown in
-
+ Table
\begin_inset LatexCommand \ref{tab:Material-models-available}
\end_inset
- and
+ and Figure
\begin_inset LatexCommand \ref{fig:Material-models}
\end_inset
@@ -71,7 +71,7 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\noindent
@@ -314,10 +314,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
+placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Caption
\begin_inset LatexCommand \label{fig:Material-models}
@@ -327,6 +330,11 @@
Spring-dashpot 1D representations of the material models available in PyLith.
The top model is a linear elastic model, the middle model is a Maxwell
model, and the bottom model is a generalized Maxwell model.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
\begin_inset Graphics
filename figs/pylith-materials.eps
@@ -346,7 +354,7 @@
\begin_layout Standard
In the following sections, we use a combination of vector and index notation,
- and our notation conventions are shown in
+ and our notation conventions are shown in Table
\begin_inset LatexCommand \ref{tab:Mathematical-notation}
\end_inset
@@ -418,8 +426,8 @@
\end_inset
-Due to the symmetry of the stress and strain tensors, it is somethimes convenien
-t to represent them as vectors:
+Due to the symmetry of the stress and strain tensors, it is sometimes convenient
+ to represent them as vectors:
\begin_inset Formula \begin{gather}
\overrightarrow{\sigma^{T}}=\left[\begin{array}{cccccc}
\sigma_{11} & \sigma_{22} & \sigma_{33} & \sigma_{12} & \sigma_{23} & \sigma_{31}\end{array}\right]\nonumber \\
@@ -432,7 +440,7 @@
\begin_inset Formula $\gamma_{ij}$
\end_inset
-) in
+) in equation
\begin_inset LatexCommand \ref{eq:5}
\end_inset
@@ -454,17 +462,17 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float table
+placement H
wide false
sideways false
status open
-\begin_layout Caption
-\begin_inset LatexCommand \label{tab:Mathematical-notation}
-
-\end_inset
-
-Mathematical notation used in this section.
+\begin_layout Standard
+\noindent
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="3">
<features>
@@ -577,9 +585,17 @@
\end_layout
+\begin_layout Caption
+\begin_inset LatexCommand \label{tab:Mathematical-notation}
+
\end_inset
+Mathematical notation used in this section.
+\end_layout
+\end_inset
+
+
\end_layout
\begin_layout Section
@@ -597,7 +613,7 @@
\end_inset
-due to symmetry considerations, however, the 81 components of the elasticity
+Due to symmetry considerations, however, the 81 components of the elasticity
matrix are reduced to 21 independent components for the most general case
of anisotropic elasticity.
For the case of isotropic elasticity, the number of independent components
@@ -672,7 +688,7 @@
\begin_inset Formula $^{t+\Delta t}\underline{e}^{C}$
\end_inset
- is the total viscous strain, is the initial deviatoric stress,
+ is the total viscous strain,
\begin_inset Formula $^{t+\Delta t}P$
\end_inset
@@ -694,7 +710,7 @@
\end_inset
, respectively.
- The topmost equation in
+ The topmost equation in equation
\begin_inset LatexCommand \ref{eq:9}
\end_inset
@@ -779,7 +795,7 @@
\end_inset
-Substituting
+Substituting equations
\begin_inset LatexCommand \ref{eq:13}
\end_inset
@@ -860,7 +876,7 @@
\end_inset
-From
+From equation
\begin_inset LatexCommand \ref{eq:11}
\end_inset
@@ -871,7 +887,7 @@
\end_inset
-and from
+and from equation
\begin_inset LatexCommand \ref{eq:3}
\end_inset
@@ -886,7 +902,7 @@
\end_inset
-Finally, from
+Finally, from equation
\begin_inset LatexCommand \ref{eq:19}
\end_inset
@@ -897,7 +913,7 @@
\end_inset
-From
+From equation
\begin_inset LatexCommand \ref{eq:24}
\end_inset
@@ -971,7 +987,7 @@
\end_layout
\begin_layout Subsection
-Power-law Maxwell viscoelastic material
+Power-law Maxwell Viscoelastic Material
\end_layout
\begin_layout Standard
@@ -984,11 +1000,11 @@
\begin_inset Formula $\nu$
\end_inset
-, the viscosity coefficient,
+, the viscosity coefficient
\begin_inset Formula $\eta$
\end_inset
-, and the power-law exponent,
+, and the power-law exponent
\begin_inset Formula $n$
\end_inset
@@ -1005,7 +1021,7 @@
\end_inset
-substituting
+substituting equations
\begin_inset LatexCommand \ref{eq:13}
\end_inset
@@ -1057,14 +1073,14 @@
\end_inset
- is a function of a single unknown - the second deviatoric stress invariant
+ is a function of a single unknown -- the second deviatoric stress invariant
at time
\begin_inset Formula $t+\Delta t$
\end_inset
- - and may be solved by bisection or by Newton's method.
+ -- and may be solved by bisection or by Newton's method.
Once this parameter has been found, the deviatoric stresses for the current
- time step may be found from
+ time step may be found from equations
\begin_inset LatexCommand \ref{eq:34}
\end_inset
@@ -1074,7 +1090,7 @@
\end_inset
-, and the total stresses may be found from
+, and the total stresses may be found from equation
\begin_inset LatexCommand \ref{eq:21}
\end_inset
@@ -1094,7 +1110,7 @@
\end_inset
is more complicated.
- We begin by rewriting
+ We begin by rewriting equation
\begin_inset LatexCommand \ref{eq:35}
\end_inset
@@ -1113,12 +1129,12 @@
The derivative is then
\begin_inset Formula \begin{gather}
-\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\frac{\partial{}^{t+\Delta t}S_{i}}{\partial{}^{t+\Delta t}e_{k}^{\prime\prime}}=\frac{1}{a_{E}+\alpha\Delta t^{\tau}\gamma}\nonumber \\
+\frac{\partial{}^{t+\Delta t}S_{i}}{\partial{}^{t+\Delta t}e_{k}^{\prime\prime}}=\frac{1}{a_{E}+\alpha\Delta t^{\tau}\gamma}\nonumber \\
\left\langle \delta_{ik}-\frac{\partial^{\tau}\gamma}{\partial{}^{t+\Delta t}e_{k}^{\prime\prime}}\left\{ \Delta t\left(1-\alpha\right)^{t}S_{i}+\frac{\alpha\Delta t}{a_{E}+\alpha\Delta t^{\tau}\gamma}\left[^{t+\Delta t}e_{i}^{\prime\prime}-\Delta t^{\tau}\gamma\left(1-\alpha\right)^{t}S_{i}+a_{E}\,^{I}S_{i}\right]\right\} \right\rangle \,.\label{eq:40}\end{gather}
\end_inset
-From
+From equation
\begin_inset LatexCommand \ref{eq:33}
\end_inset
@@ -1135,7 +1151,7 @@
\end_inset
- which allows us to rewrite
+ which allows us to rewrite equation
\begin_inset LatexCommand \ref{eq:36}
\end_inset
@@ -1170,7 +1186,7 @@
\end_inset
, this derivative is zero.
- This relation may be used in
+ This relation may be used in equation
\begin_inset LatexCommand \ref{eq:40}
\end_inset
@@ -1234,7 +1250,7 @@
\begin_layout Standard
To compute the zero of the effective stress function using Newton's method,
- we require the derivative of
+ we require the derivative of equation
\begin_inset LatexCommand \ref{eq:36}
\end_inset
@@ -1254,7 +1270,8 @@
\begin_layout Standard
The generalized Maxwell viscoelastic model consists of a number of Maxwell
- linear viscoelastic models in parallel with a spring, as shown in
+ linear viscoelastic models in parallel with a spring, as shown in Figure
+
\begin_inset LatexCommand \ref{fig:Material-models}
\end_inset
@@ -1264,12 +1281,13 @@
A number of common material models may be obtained from this model by setting
the shear moduli of various springs to zero, such as the Maxwell model,
the Kelvin model, and the standard linear solid.
- We follow formulations similar to those used by
+ We follow formulations similar to those used by Zienkiewicz and Taylor
+
\begin_inset LatexCommand \cite{Zienkiewicz:Taylor:2000}
\end_inset
- and
+ and Taylor
\begin_inset LatexCommand \cite{Taylor:2003}
\end_inset
@@ -1367,7 +1385,7 @@
\begin_inset Formula $\mu\left(t\right)$
\end_inset
-is the shear relaxation modulus function.
+ is the shear relaxation modulus function.
Using linearity and superposition for an arbitrary state of strain yields
an integral equation:
\end_layout
@@ -1396,7 +1414,7 @@
\end_inset
-With the form in
+With the form in equation
\begin_inset LatexCommand \ref{eq:54}
\end_inset
@@ -1439,7 +1457,7 @@
\end_inset
at time zero, and the last term covers the subsequent history of strain.
- Applying this separation to
+ Applying this separation to equation
\begin_inset LatexCommand \ref{eq:53}
\end_inset
@@ -1457,7 +1475,7 @@
\end_layout
\begin_layout Standard
-Substituting
+Substituting equation
\begin_inset LatexCommand \ref{eq:54}
\end_inset
@@ -1544,7 +1562,7 @@
\end_inset
The approximation is singular for zero time steps, but a series expansion
- may be used for small time step sizes:
+ may be used for small time-step sizes:
\end_layout
\begin_layout Standard
@@ -1581,7 +1599,8 @@
\end_inset
-where the second derivative on the right may be easily deduced from
+where the second derivative on the right may be easily deduced from equation
+
\begin_inset LatexCommand \ref{eq:3}
\end_inset
@@ -1601,7 +1620,7 @@
\end_inset
is the identity matrix.
- From
+ From equations
\begin_inset LatexCommand \ref{eq:64}
\end_inset
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/preface.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/preface.lyx 2007-04-27 21:47:33 UTC (rev 6720)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/preface.lyx 2007-04-27 22:52:12 UTC (rev 6721)
@@ -46,9 +46,8 @@
\begin_layout Standard
This document is organized into two parts.
- Part I begins with an introduction to PyLith and discusses how to run the
- software.
- Part II provides appendices and references.
+ The first part begins with an introduction to PyLith and discusses how
+ to run the software; the second part provides appendices and references.
\end_layout
\begin_layout Section
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/pylith_book.pdf
===================================================================
(Binary files differ)
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx 2007-04-27 21:47:33 UTC (rev 6720)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx 2007-04-27 22:52:12 UTC (rev 6721)
@@ -63,13 +63,16 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
-placement htbp
+placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
+\noindent
\align center
\begin_inset Graphics
filename figs/tet4.eps
@@ -97,11 +100,13 @@
\end_layout
\begin_layout Standard
+\noindent
+\align center
\begin_inset Float figure
-placement htbp
+placement t
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\align center
@@ -309,7 +314,6 @@
Time steps for which full output is requested.
\shape italic
-\color default
Required for time-dependent problems.
\end_layout
@@ -716,33 +720,11 @@
(1) overrides only the built-in defaults.
\end_layout
-\begin_layout Subsection
-PETSc Settings
-\end_layout
-
\begin_layout Standard
-PyLith relies on PETSc for the linear algebra computations.
- Many PETSc options can be set in
-\family typewriter
-.cfg
-\family default
- files.
- The ones of primary interest in the case of PyLith are shown in Table\InsetSpace ~
-
-\begin_inset LatexCommand \ref{tab:Useful-command-line-arguments}
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
+\noindent
+\align center
\begin_inset Float table
-placement htbp
+placement H
wide false
sideways false
status open
@@ -752,9 +734,9 @@
\begin_inset Tabular
<lyxtabular version="3" rows="7" columns="3">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1in">
-<column alignment="center" valignment="middle" leftline="true" width="1in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.1in">
+<column alignment="left" valignment="top" leftline="true" width="0.9in">
+<column alignment="center" valignment="middle" leftline="true" width="0.8in">
+<column alignment="left" valignment="top" leftline="true" rightline="true" width="4in">
<row topline="true" bottomline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
@@ -1012,9 +994,29 @@
\end_layout
+\begin_layout Subsection
+PETSc Settings
+\end_layout
+
\begin_layout Standard
+PyLith relies on PETSc for the linear algebra computations.
+ Many PETSc options can be set in
+\family typewriter
+.cfg
+\family default
+ files.
+ The ones of primary interest in the case of PyLith are shown in Table\InsetSpace ~
+\begin_inset LatexCommand \ref{tab:Useful-command-line-arguments}
+
+\end_inset
+
+.
\end_layout
+\begin_layout Standard
+
+\end_layout
+
\end_body
\end_document
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/splitcube.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/splitcube.lyx 2007-04-27 21:47:33 UTC (rev 6720)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/splitcube.lyx 2007-04-27 22:52:12 UTC (rev 6721)
@@ -237,13 +237,17 @@
\begin_layout Enumerate
Download the
-\begin_inset LatexCommand \htmlurl[tutorial tarball]{www.geodynamics.org/cig/Members/willic3/pylithusers/pylith0.8/pylith-0.8.1_tutorials.tgz}
+\begin_inset LatexCommand \htmlurl[tutorial tarball]{geodynamics.org/cig/Members/willic3/pylithusers/pylith0.8/pylith-0.8.1_tutorials.tgz}
\end_inset
- and unpack it in a location of your choosing.
+.
\end_layout
+\begin_layout Enumerate
+Unpack it in a location of your choosing.
+\end_layout
+
\begin_deeper
\begin_layout LyX-Code
$ tar -zxvf pylith-0.8.2_tutorials.tgz
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.lyx 2007-04-27 21:47:33 UTC (rev 6720)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.lyx 2007-04-27 22:52:12 UTC (rev 6721)
@@ -1,4 +1,4 @@
-#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -139,8 +139,21 @@
\end_inset
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+raggedbottom
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
\begin_inset Include \input{intro/intro.lyx}
preview false
@@ -269,9 +282,8 @@
\begin_layout Bibliography
\bibitem [5]{Taylor:2003}
-Taylor, R.
- L.
- (2003), 'FEAP--A Finite Element Analysis Program',
+Taylor, R.L.
+ (2003), `FEAP--A Finite Element Analysis Program',
\shape italic
Version 7.5 Theory Manual
\shape default
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