[cig-commits] r13663 - doc/snac
sue at geodynamics.org
sue at geodynamics.org
Fri Dec 12 11:21:54 PST 2008
Author: sue
Date: 2008-12-12 11:21:54 -0800 (Fri, 12 Dec 2008)
New Revision: 13663
Modified:
doc/snac/snac.lyx
Log:
some typos, format fixes
Modified: doc/snac/snac.lyx
===================================================================
--- doc/snac/snac.lyx 2008-12-12 15:20:18 UTC (rev 13662)
+++ doc/snac/snac.lyx 2008-12-12 19:21:54 UTC (rev 13663)
@@ -1,4 +1,4 @@
-#LyX 1.5.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -134,7 +134,7 @@
\begin_inset Formula $Ra=10^{6},$
\end_inset
-and longer 4
+ and longer 4
\begin_inset Formula $\times$
\end_inset
@@ -142,7 +142,7 @@
\begin_inset Formula $\times$
\end_inset
-64 elements).
+ 64 elements).
\end_layout
@@ -323,8 +323,9 @@
\begin_layout Standard
SNAC (StGermaiN Analysis of Continua) is an updated Lagrangian explicit
- finite difference code for modeling a finitely deforming viscoplastic solid
- in 3D, released under the GNU General Public License (see Appendix
+ finite difference code for modeling a finitely deforming elasto-visco-plastic
+ solid in 3D, released under the GNU General Public License (see Appendix
+
\begin_inset LatexCommand vref
reference "cha:License"
@@ -412,7 +413,7 @@
\end_layout
\begin_layout Standard
-A 3-D domain is discretized into hexahedral elements, each of which is filled
+A 3D domain is discretized into hexahedral elements, each of which is filled
with two sets of 5 tetrahedra (Fig.
\begin_inset LatexCommand ref
@@ -1690,7 +1691,7 @@
A tree-like diagram showing the hierarchy of entry points set up in SNAC
together with hooked-up functions in each entry point.
The functions defined by StGermain are marked in blue while those defined
- in SNAC in red.
+ in SNAC are in red.
\end_layout
\end_inset
@@ -2077,16 +2078,23 @@
\end_layout
\begin_layout Standard
-The Libxml2 library and toolkit are required for Snac to handle the input
+The Libxml2 library and toolkit are required for SNAC to handle the input
files.
Although already included in most of the recent linux systems, it can be
- obtained from http://xmlsoft.org and installed manually.
+ obtained from
+\begin_inset LatexCommand htmlurl
+name "The XML C parser and toolkit of Gnome"
+target "xmlsoft.org"
+
+\end_inset
+
+ and installed manually.
Precompiled packages for various linux distributions and OS X are available
through their own package management softwares, too.
\end_layout
\begin_layout Subsection
-Other environment variables
+Other Environment Variables
\end_layout
\begin_layout Standard
@@ -2095,7 +2103,11 @@
\end_layout
\begin_layout Standard
-In bash,
+In
+\family typewriter
+bash
+\family default
+,
\end_layout
\begin_layout LyX-Code
@@ -2123,7 +2135,11 @@
\end_layout
\begin_layout Standard
-In tsch,
+In
+\family typewriter
+tsch
+\family default
+,
\end_layout
\begin_layout LyX-Code
@@ -2938,9 +2954,9 @@
determines how many elements in one local domain are made to transfer variables
to neighbor domains.
- It takes a non-negative inger value corresponding to the number of layers
+ It takes a non-negative integer value corresponding to the number of layers
of elements.
- To run Snac in parallel, this parameter should be 1 or larger.
+ To run SNAC in parallel, this parameter should be 1 or larger.
``
\family typewriter
decompDims
@@ -5013,7 +5029,7 @@
One is for the open source Open Visualization Data Explorer, better known
as OpenDX.
The other generates Visualization Tool Kit (VTK) files.
- OpenDX with documentations are available from the
+ OpenDX with documentation is available from the
\begin_inset LatexCommand htmlurl
name "OpenDX website"
target "www.opendx.org"
@@ -5024,7 +5040,7 @@
There are several programs that can visualization VTK files:
\begin_inset LatexCommand htmlurl
name "ParaView"
-target "http://www.paraview.org"
+target "www.paraview.org"
\end_inset
@@ -5047,7 +5063,7 @@
\end_layout
\begin_layout Subsection
-Outputs from Snac
+Outputs from SNAC
\end_layout
\begin_layout Standard
@@ -5087,28 +5103,38 @@
\begin_layout Standard
To convert binary files into ascii OpenDX files, you need to run a program
-\begin_inset Quotes sld
-\end_inset
-
+\family typewriter
snac2dx
-\begin_inset Quotes srd
-\end_inset
-
+\family default
.
- The source code is Snac/snac2dx/snac2dx.c and compiled during the Snac's
- building procedure and placed in ${SNAC_BINDIR} together with other executables.
+ The source code is
+\family typewriter
+Snac/snac2dx/snac2dx.c
+\family default
+ and compiled during the SNAC's building procedure and placed in
+\family typewriter
+${SNAC_BINDIR}
+\family default
+ together with other executables.
\end_layout
\begin_layout Standard
-Running snac2dx without any arguments converts data for all the time steps
- recorded in
+Running
\family typewriter
+snac2dx
+\family default
+ without any arguments converts data for all the time steps recorded in
+
+\family typewriter
timeStep.0
\family default
.
Optionally, a range of time steps can be set if two positive integers are
given as arguments.
- The converted output files are always written in the directory where snac2dx
+ The converted output files are always written in the directory where
+\family typewriter
+snac2dx
+\family default
is run.
The naming convention for the ascii dx files is
\family typewriter
@@ -5118,11 +5144,22 @@
\end_layout
\begin_layout Standard
-When visualize outputs from a parallel run, one more step is needed to combine
+To visualize outputs from a parallel run, one more step is needed to combine
the .dx files into a single dx file for each time step.
- A Python script, snac_combine.py, is provided for this purpose.
- This script is under Snac/snac2dx, but not automatically installed in ${SNAC_BI
-NDIR}.
+ A Python script,
+\family typewriter
+snac_combine.py
+\family default
+, is provided for this purpose.
+ This script is under
+\family typewriter
+Snac/snac2dx
+\family default
+, but not automatically installed in
+\family typewriter
+${SNAC_BINDIR}
+\family default
+.
The following 8 arguments are required:
\end_layout
@@ -5133,18 +5170,10 @@
\series default
: Suffix for the combined data files.
-\begin_inset Quotes sld
-\end_inset
-
-
\family typewriter
-snac
+``snac
\family default
-
-\begin_inset Quotes srd
-\end_inset
-
- unless snac2dx.c is modified.
+'' unless snac2dx.c is modified.
\end_layout
\begin_layout Itemize
@@ -5174,7 +5203,7 @@
\end_layout
\begin_layout Paragraph*
-Example list of Snac output files in the OpenDX format: 8 processors and
+Example list of SNAC output files in the OpenDX format: 8 processors and
51 outputs per processor.
\end_layout
@@ -5194,7 +5223,6 @@
\end_layout
\begin_layout LyX-Code
-\SpecialChar \ldots{}
\end_layout
@@ -5210,11 +5238,7 @@
decompDims
\family default
=3) by 8 processors.
- Also, we assume that the contents of sim.0 is ``25 15 20
-\begin_inset Quotes srd
-\end_inset
-
-.
+ Also, we assume that the contents of sim.0 is ``25 15 20''.
Then, we can infer that 2 processors were assigned in each dimension.
\end_layout
@@ -5227,12 +5251,20 @@
\end_layout
\begin_layout Standard
-The name of a combined file has the format of ``snac.{time step in 6 digits}.dx
+The name of a combined file has the format of ``
+\family typewriter
+snac.{time step in 6 digits}.dx
+\family default
+
\begin_inset Quotes srd
\end_inset
.
- ``snac.000035.dx
+ ``
+\family typewriter
+snac.000035.dx
+\family default
+
\begin_inset Quotes srd
\end_inset
@@ -5244,10 +5276,17 @@
\end_layout
\begin_layout Standard
-snac_visualize.net, an OpenDX visual program, is provided for convenience
- and is placed in Snac/snac2dx.
+An OpenDX visual program,
+\family typewriter
+snac_visualize.net
+\family default
+, is provided for convenience and is placed in
+\family typewriter
+Snac/snac2dx
+\family default
+.
It can be opened in OpenDX to read data, map node- and element-based variables
- on the domain, visualize vector quantities as 3-D glyphs, create isosurfaces,
+ on the domain, visualize vector quantities as 3D glyphs, create isosurfaces,
and make cross-sections.
\end_layout
@@ -5256,10 +5295,21 @@
\end_layout
\begin_layout Standard
-A program called snac2vtk is provided to convert the binary outputs from
- Snac to ascii files in the XML VTK Structured Grid format (.vts).
- snac2vtk is compiled during the building procedure and installed in ${SNAC_BIND
-IR}.
+A program called
+\family typewriter
+snac2vtk
+\family default
+ is provided to convert the binary outputs from SNAC to ascii files in the
+ XML VTK Structured Grid format (.vts).
+
+\family typewriter
+snac2vtk
+\family default
+ is compiled during the building procedure and installed in
+\family typewriter
+${SNAC_BINDIR}
+\family default
+.
The usage is
\end_layout
@@ -5268,22 +5318,29 @@
\end_layout
\begin_layout Standard
-where the meaning of arguments are the same with those for snac2dx described
- in the previous section.
+where the meaning of arguments is the same as those for
+\family typewriter
+snac2dx
+\family default
+ described in the previous section.
The last two optional arguments are used to set the range of time steps
for data conversion.
\end_layout
\begin_layout Standard
-snac2vtk automatically generates Parallel VTK Structures Grid files (.pvts)
- for each time step so that there is no need for an extra step to combine
- data even for the parallel cases.
+
+\family typewriter
+snac2vtk
+\family default
+ automatically generates Parallel VTK Structures Grid files (.pvts) for each
+ time step so that there is no need for an extra step to combine data even
+ for the parallel cases.
However, .vts files should not be removed because .pvts files only refer
to .vts files rather than contain actual data.
\end_layout
\begin_layout Paragraph*
-Example list of Snac output files in the VTK format: 8 processors and 51
+Example list of SNAC output files in the VTK format: 8 processors and 51
outputs per processor.
\end_layout
@@ -5352,7 +5409,7 @@
\end_layout
\begin_layout Chapter
-Benchmark problems
+Benchmark Problems
\end_layout
\begin_layout Section
@@ -6149,7 +6206,7 @@
\end_layout
\begin_layout Section
-Parallel-plate viscometer problem
+Parallel-Plate Viscometer Problem
\end_layout
\begin_layout Standard
@@ -6270,7 +6327,7 @@
\begin_layout Standard
Color field represents stress.
- Colored arrows for Snac's velocity; black arrows for analytic solution.
+ Colored arrows for SNAC's velocity; black arrows for analytic solution.
Over the most part of the domain, two sets of arrows show good agreement.
\end_layout
@@ -6308,7 +6365,7 @@
\begin_layout Standard
The second invariant of stress and velocities plotted on the deformed mesh.
- Colored arrows for the Snac's solution and black ones for the analytic
+ Colored arrows for the SNAC's solution and black ones for the analytic
solution.
\end_layout
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