[cig-commits] r4470 - in
short/3D/PyLith/branches/pylith-0.8/doc/userguide: .
fileformats install intro runpylith tutorials tutorials/splitcube
sue at geodynamics.org
sue at geodynamics.org
Tue Sep 5 11:54:23 PDT 2006
Author: sue
Date: 2006-09-05 11:54:22 -0700 (Tue, 05 Sep 2006)
New Revision: 4470
Modified:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.lyx
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/tutorials/tutorials.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.lyx
Log:
fixed typos found in readthru
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.lyx 2006-09-05 13:38:26 UTC (rev 4469)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.lyx 2006-09-05 18:54:22 UTC (rev 4470)
@@ -37,6 +37,10 @@
\begin_body
\begin_layout Chapter
+\begin_inset LatexCommand \label{cha:File-Formats}
+
+\end_inset
+
File Formats
\end_layout
@@ -66,7 +70,7 @@
\color black
xx.coord
\family default
-\color default
+\color none
file contains the coordinates of all of the vertices in the finite-element
mesh.
\end_layout
@@ -176,7 +180,7 @@
\color black
xx.coord
\family default
-\color default
+\color none
files.
\end_layout
@@ -199,7 +203,7 @@
\color black
xx.connect
\family default
-\color default
+\color none
file contains the finite-element mesh topology and material type information,
including the element type, material type, and the lists of vertices for
each element.
@@ -354,7 +358,7 @@
\color black
xx.connect
\family default
-\color default
+\color none
files.
\end_layout
@@ -377,7 +381,7 @@
\color black
xx.bc
\family default
-\color default
+\color none
file specifies the displacements, velocity, and/or forces applied to vertices
on the boundaries.
\end_layout
@@ -534,7 +538,7 @@
\color black
xx.bc
\family default
-\color default
+\color none
files.
\end_layout
@@ -557,7 +561,7 @@
\color black
xx.time
\family default
-\color default
+\color none
file specifies the time stepping parameters for the simulation.
\end_layout
@@ -567,7 +571,7 @@
\color red
Warning:
\series default
-\color default
+\color none
The convergence criteria depend on the type of solution and material models.
The time step for a linear elastic problem is much different than that
for a nonlinear or time-dependent problem.
@@ -759,7 +763,7 @@
\color black
xx.time
\family default
-\color default
+\color none
files.
\end_layout
@@ -789,7 +793,7 @@
\color red
Warning:
\series default
-\color default
+\color none
The materials must be listed in order according to the material number
assigned to the elements in
\family typewriter
@@ -1511,7 +1515,7 @@
\color red
Warning:
\series default
-\color default
+\color none
Use with caution as reduced quadrature can lead to numerical instabilities.
\end_layout
@@ -1798,7 +1802,7 @@
\color black
xx.keyval
\family default
-\color default
+\color none
files.
\end_layout
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.lyx 2006-09-05 13:38:26 UTC (rev 4469)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.lyx 2006-09-05 18:54:22 UTC (rev 4470)
@@ -37,6 +37,10 @@
\begin_body
\begin_layout Chapter
+\begin_inset LatexCommand \label{cha:Installation-and-Getting}
+
+\end_inset
+
Installation and Getting Help
\end_layout
@@ -48,7 +52,7 @@
Installation of PyLith on a desktop or laptop machine is, in most cases,
very easy.
Binary packages have been created for the most common platforms, including
- Linux, OSX, and Windows.
+ Linux, Mac OS X, and Windows.
Installation on machines that are not compatible with any of these operating
systems requires building the software from the source code, which can
be difficult for inexperienced users.
@@ -149,15 +153,14 @@
\begin_layout Enumerate
\noindent
-2.
- Unpack the tarball in a suitable location
+Unpack the tarball in a suitable location
\newline
\newline
\family typewriter
\color black
-tar -zxvf pylith-0.8-linux-x86.tar.gz
+$ tar -zxvf pylith-0.8-linux-x86.tar.gz
\end_layout
\begin_layout Enumerate
@@ -281,12 +284,12 @@
\family typewriter
PyLith
\family default
- folder to a suiteable location.
+ folder to a suitable location.
\end_layout
\begin_layout Enumerate
-To run PyLith, double click on the PyLith icon provided in the
+To run PyLith, double click on the PyLith icon found in the
\family typewriter
PyLith
\family default
@@ -299,7 +302,7 @@
\family typewriter
PyLith
\family default
- folder to the trash.
+ folder to the Trash.
\end_layout
@@ -329,7 +332,7 @@
\end_layout
\begin_layout Enumerate
-To run PyLith, double click on the PyLith icon on the desktop or select
+To run PyLith, double click on the PyLith icon on the Desktop or select
\family sans
Start
@@ -375,7 +378,7 @@
\end_layout
\begin_layout Section
-Building using source tarball
+Building Using Source Tarball
\end_layout
\begin_layout Standard
@@ -471,7 +474,7 @@
\end_deeper
\begin_layout Section
-Building using source repositories
+Building Using Source Repositories
\end_layout
\begin_layout Quote
@@ -575,7 +578,7 @@
If you have an architecture optimized version of BLAS/LAPACK you should
use those instead of asking PETSc to download and build one for you.
In some cases, PETSc will find known optimized implementations of BLAS/LAPACK
- (e.g., vecLib on Mac OSX).
+ (e.g., vecLib on Mac OS X).
\end_layout
\begin_layout Standard
@@ -603,7 +606,7 @@
\family default
\emph default
to
-\begin_inset LatexCommand \url[petsc-maint at mcs.anl.gov]{<petsc-maint at mcs.anl.gov>}
+\begin_inset LatexCommand \url{<petsc-maint at mcs.anl.gov>}
\end_inset
@@ -660,8 +663,11 @@
PETSC_ARCH
\family default
\emph default
- is a tag for this configuration of PETSc (e.g., linux_gcc-4.0_debug, darwin_gcc-3.4
-_opt, etc).
+ is a tag for this configuration of PETSc (e.g.,
+\family typewriter
+linux_gcc-4.0_debug, darwin_gcc-3.4_opt
+\family default
+, etc).
You will want to set these environment variables in your
\family typewriter
.bashrc
@@ -693,9 +699,16 @@
\begin_deeper
\begin_layout Standard
-Run config/configure.py with the appropriate arguments to configure PETSc
- for your computer.
- Run config/configure.py --help to see the long list of possible options.
+Run
+\family typewriter
+config/configure.py
+\family default
+ with the appropriate arguments to configure PETSc for your computer.
+ Run
+\family typewriter
+config/configure.py --help
+\family default
+ to see the long list of possible options.
Building PETSc for use with PyLith requires the following arguments:
\newline
@@ -720,7 +733,7 @@
Be sure to include flags indicating where MPI and BLAS/LAPACK are if you
want to use a preinstalled implementation.
If not, be sure to tell PETSc to download those packages.
- If you do not want build PETSc using the gnu compilers, be sure to let
+ If you do not want yo build PETSc using the gnu compilers, be sure to let
PETSc know which compilers you want to use instead.
\end_layout
@@ -769,7 +782,7 @@
\end_deeper
\begin_layout Enumerate
In the future, you will likely want to update the PETSc source tree to include
- bug fixes, new features etc.
+ bug fixes, new features, etc.
\end_layout
\begin_deeper
@@ -810,8 +823,11 @@
\series bold
TIP:
\series default
- If you run into problems configuring or building Pythia, send both the
-
+ If you run into problems configuring or building Pythia, send
+\emph on
+both
+\emph default
+ the
\family typewriter
config.log
\family default
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 2006-09-05 13:38:26 UTC (rev 4469)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.lyx 2006-09-05 18:54:22 UTC (rev 4470)
@@ -48,7 +48,7 @@
PyLith is a multi-scale simulation software package for earthquake physics.
It is portable, scalable software for simulation of crustal deformation
across spatial scales ranging from meters to hundreds of kilometers and
- temporal scales ranging from milliseconds to thousands of years
+ temporal scales ranging from milliseconds to thousands of years.
\end_layout
\begin_layout Section
@@ -139,7 +139,7 @@
\noindent
and the essential boundary conditions
\begin_inset Formula \begin{equation}
-u_{i}=u_{i}^{S_{u}}\, on\, S_{u}.\label{eq:3}\end{equation}
+u_{i}=u_{i}^{S_{u}}\,\mathrm{on}\, S_{u}.\label{eq:3}\end{equation}
\end_inset
@@ -212,7 +212,7 @@
\begin_inset Formula $t+\Delta t$
\end_inset
-, he stresses are therefore computed from the total elastic strain:
+, the stresses are therefore computed from the total elastic strain:
\end_layout
\begin_layout Standard
@@ -233,7 +233,7 @@
In our actual computations, we use a formulation that decomposes the stresses
into the deviatoric and volumetric parts, using ideas based on the "effective
stress function"
-\begin_inset LatexCommand \cite{Kojic:Bathe:1987}
+\begin_inset LatexCommand \cite{key-2}
\end_inset
@@ -297,9 +297,9 @@
\begin_layout Standard
PETSc includes interfaces for Fortran, C, and C++ for nearly all of the
routines, and PETSc can be installed on most Unix systems.
- PETSc can be built with user supplied highly optimized linear algebra routines
- (e.g., ATLAS and commercial versions of BLAS/LAPACK), thereby improving applicati
-on performance.
+ PETSc can be built with user-supplied, highly optimized linear algebra
+ routines (e.g., ATLAS and commercial versions of BLAS/LAPACK), thereby improving
+ application performance.
Users can use PETSc parallel matrices, vectors, and other data structures
for most parallel operations, eliminating the need for explicit calls to
Message Passing Interface (MPI) routines.
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 2006-09-05 13:38:26 UTC (rev 4469)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx 2006-09-05 18:54:22 UTC (rev 4470)
@@ -150,7 +150,7 @@
is used.
See Appendix\InsetSpace ~
-\begin_inset LatexCommand \ref{app:file:formats}
+\begin_inset LatexCommand \ref{cha:File-Formats}
\end_inset
@@ -174,7 +174,7 @@
\family typewriter
xx.ext
\family default
- was the original filename.
+ is the original filename.
This procedure is applied to files with the following extensions:
\family typewriter
coord, connect, split,
@@ -204,14 +204,14 @@
\family default
in section\InsetSpace ~
-\begin_inset LatexCommand \ref{sec:tutorial:reversenog}
+\begin_inset LatexCommand \ref{sec:Tutorial-Using-Reverse-Slip}
\end_inset
for a simple example.
You can also choose your own filename template by setting the appropriate
command-line argument.
- See \InsetSpace ~
+ See section\InsetSpace ~
\begin_inset LatexCommand \ref{sec:commandline:args}
@@ -226,7 +226,7 @@
\begin_layout Standard
The required input files define the finite-element mesh, boundary conditions,
- time step information, output, and material properties.
+ time-step information, output, and material properties.
\end_layout
\begin_layout Description
@@ -307,7 +307,7 @@
\color black
xx.fuldat
\family default
-\color default
+\color none
Time steps for which full output is requested.
\end_layout
@@ -318,7 +318,7 @@
\color black
xx.split
\family default
-\color default
+\color none
Dislocation boundary condition information (implemented using split nodes).
\end_layout
@@ -329,7 +329,7 @@
\color black
xx.skew
\family default
-\color default
+\color none
Local coordinate rotation information for boundary conditions.
\end_layout
@@ -340,7 +340,7 @@
\color black
xx.keyval
\family default
-\color default
+\color none
File for changing default parameters.
\end_layout
@@ -351,7 +351,7 @@
\color black
xx.wink
\family default
-\color default
+\color none
Winkler spring element boundary condition information.
\emph on
@@ -367,7 +367,7 @@
\color black
xx.hist
\family default
-\color default
+\color none
Time histories for split node and Winkler boundary conditions (if necessary).
\emph on
@@ -426,7 +426,7 @@
\color red
Warning:
\series default
-\color default
+\color none
This section applies only to PyLith compiled using the MPICH implementation
of the Message Passing Interface (MPI).
@@ -440,13 +440,13 @@
\color black
-np NPROCS
\family default
-\color default
+\color none
, where
\family typewriter
\color black
NPROCS
\family default
-\color default
+\color none
corresponds to the number of processors.
\end_layout
@@ -459,7 +459,7 @@
and facilities.
Properties correspond to simple settings in the form of strings, integers,
and real numbers.
- Facilities corresponds to software modules.
+ Facilities correspond to software modules.
Both facilities and properties have default values provided, so you only
need to set values when you want to deviate from the default behavior.
Unless you write a module that extends PyLith's functionality, you will
@@ -475,7 +475,7 @@
\color black
--scanner.help-properties
\family default
-\color default
+\color none
command-line argument.
\end_layout
@@ -525,7 +525,7 @@
\begin_layout Standard
PyLith relies on PETSc for the linear algebra computations.
- Many of PETSc options can be set using command-line arguments.
+ Many PETSc options can be set using command-line arguments.
The ones of primary interest in the case of PyLith are shown in table\InsetSpace ~
\begin_inset LatexCommand \ref{tab:Useful-command-line-arguments}
@@ -683,7 +683,7 @@
\color black
-ksp_monitor
\family default
-\color default
+\color none
is given, the default is to use stdout.
\end_layout
@@ -772,7 +772,7 @@
\color black
pml
\family default
-\color default
+\color none
files.
These are XML files that follow a special Pyre XML schema.
\end_layout
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 2006-09-05 13:38:26 UTC (rev 4469)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/splitcube.lyx 2006-09-05 18:54:22 UTC (rev 4470)
@@ -57,11 +57,31 @@
\end_layout
\begin_layout Standard
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+raggedbottom
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
The model domain is a cube with edges 1 km long (0 km
\begin_inset Formula $\leq$
\end_inset
- x
+
+\begin_inset Formula $x$
+\end_inset
+
+
\begin_inset Formula $\leq$
\end_inset
@@ -97,7 +117,11 @@
\begin_layout Standard
The strike-slip fault dips at an angle of 90 degrees.
The slip distribution is 1.0 m of uniform left-lateral motion.
- The face of the cube on the plane x=0 is held fixed.
+ The face of the cube on the plane
+\begin_inset Formula $x$
+\end_inset
+
+=0 is held fixed.
The other lateral faces and top and bottom of the mesh are traction-free.
The solution to this problem is zero stresses and strains with no displacements
for the region
@@ -175,7 +199,7 @@
\begin_layout Caption
Workflow for setting up input files for example with simple strike-slip
- faylt.
+ fault.
\end_layout
\begin_layout Standard
@@ -358,7 +382,7 @@
\end_layout
\begin_layout LyX-Code
-$./tutor.py -m clean -s mesh
+$ ./tutor.py -m clean -s mesh
\end_layout
\end_deeper
@@ -374,8 +398,11 @@
code.
This will be used to associate boundary conditions with the fault surface
and the associated nodes.
- We have not flagged the face on the plane x=0 because we generate this
- boundary condition by hand.
+ We have not flagged the face on the plane
+\begin_inset Formula $x$
+\end_inset
+
+=0 because we generate this boundary condition by hand.
We also do not have to flag the other faces because they are traction-free,
which is a natural boundary condition in the finite-element formulation.
@@ -556,7 +583,7 @@
\begin_layout LyX-Code
\series bold
-splitcube
+$ splitcube
\end_layout
\end_deeper
@@ -745,6 +772,22 @@
\end_layout
\end_deeper
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+
+\backslash
+raggedbottom
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsection
Visualize the single processor run
\end_layout
@@ -861,7 +904,7 @@
Open Data
\family default
.
- Select the file in the dialog box and the click the
+ Select the file in the dialog box and then click the
\family sans
Open
\family default
@@ -964,7 +1007,7 @@
\family sans
scalars
\family default
- button and the
+ button, and the
\family sans
iHat
\family default
@@ -1053,7 +1096,7 @@
\begin_layout Standard
In this step we will run the simulation on two processors.
- Even if your machine only has one processor, a "multprocessor" job will
+ Even if your machine only has one processor, a "multiprocessor" job will
run as multiple processes on the single processor.
In such cases, the job will run slower than the single processor run, but
the two processes will behave independently as if they are on different
@@ -1200,7 +1243,7 @@
Open Data.
\family default
- Select the file in the dialog box and the click the
+ Select the file in the dialog box and then click the
\family sans
Open
\family default
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorials.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorials.lyx 2006-09-05 13:38:26 UTC (rev 4469)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorials.lyx 2006-09-05 18:54:22 UTC (rev 4470)
@@ -55,9 +55,9 @@
\begin_layout Standard
Before you begin any of the tutorials, you will need to install PyLith following
- the instructions in section\InsetSpace ~
+ the instructions in chapter\InsetSpace ~
-\begin_inset LatexCommand \ref{sec:install}
+\begin_inset LatexCommand \ref{cha:Installation-and-Getting}
\end_inset
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.lyx 2006-09-05 13:38:26 UTC (rev 4469)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.lyx 2006-09-05 18:54:22 UTC (rev 4470)
@@ -200,5 +200,22 @@
\end_layout
+\begin_layout Bibliography
+
+\bibitem {key-2}
+Kojic, M.
+ and K.-J.
+ Bathe (1987), The 'Effective Stress-Function' Algorithm for Thermo-Elasto-Plast
+icity and Creep,
+\emph on
+Int.
+ J.
+ Num.
+ Meth.
+ Eng.
+\emph default
+, 24, 1509-1532.
+\end_layout
+
\end_body
\end_document
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