# [cig-commits] r18631 - in short/3D/PyLith/trunk/doc/userguide: materials runpylith tutorials/3dhex8 tutorials/3dhex8/quasistatic tutorials/3dtet4 tutorials/subduction

willic3 at geodynamics.org willic3 at geodynamics.org
Tue Jun 14 19:17:18 PDT 2011

Author: willic3
Date: 2011-06-14 19:17:17 -0700 (Tue, 14 Jun 2011)
New Revision: 18631

Modified:
short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx
short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/quasistatic/quasistatic.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/subduction.lyx
Log:
Made some last minute changes, including spell checking, fixing some
descriptions, and fixing a few typos.

Modified: short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx	2011-06-15 00:37:04 UTC (rev 18630)
+++ short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx	2011-06-15 02:17:17 UTC (rev 18631)
@@ -2250,8 +2250,8 @@
models.
As described in the previous paragraph, 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.
+ springs to zero or infinity (or a large number), such as the Maxwell model,
+ the Kelvin model, and the standard linear solid.
We follow formulations similar to those used by Zienkiewicz and Taylor

\begin_inset CommandInset citation

Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx	2011-06-15 00:37:04 UTC (rev 18630)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx	2011-06-15 02:17:17 UTC (rev 18631)
@@ -1352,7 +1352,7 @@

\begin_layout Plain Layout
Global uniform mesh refinement of 2-D and 3-D linear cells.
- The blue lines and orange curcles identify the edges and vertices in the
+ The blue lines and orange circles identify the edges and vertices in the
original cells.
The purple lines and green circles identify the new edges and vertices
added to the original cells to refine the mesh by a factor of two.
@@ -1377,7 +1377,7 @@

\begin_layout Standard
Refinement occurs after distribution of the mesh among processors.
- This allows one to run much large simulations by (1) permitting the mesh
+ This allows one to run much larger simulations by (1) permitting the mesh
generator to construct a mesh with a node spacing twice as large as that
needed in the simulation and (2) operations performed in serial during
the simulation setup phase, such as, adjusting the topology to insert cohesive
@@ -1628,7 +1628,7 @@
[pylithapp.petsc]
\family default
.
- The ones of primary interest in the case of PyLith are shown in Table
+ The options of primary interest in the case of PyLith are shown in Table
\begin_inset space ~
\end_inset

@@ -1674,8 +1674,9 @@
\end_inset

.
- These settings are limited to a nonsymmetric sparse matrix and require
- additional settings for the formulation,
+ These settings are limited to problems where we store the stiffness matrix
+ as a nonsymmetric sparse matrix and require additional settings for the
+ formulation,
\end_layout

\begin_layout LyX-Code
@@ -2007,7 +2008,7 @@
\begin_inset Text

\begin_layout Plain Layout
-Print nonlinear solver paremeters.
+Print nonlinear solver parameters.
\end_layout

\end_inset
@@ -2040,7 +2041,7 @@
\begin_inset Text

\begin_layout Plain Layout
-Convergence tolerance for releative decrease in residual norm.
+Convergence tolerance for relative decrease in residual norm.
\end_layout

\end_inset
@@ -3130,7 +3131,8 @@
ve models and kinematic fault ruptures.
The nonlinear solver, SolverNonlinear, corresponds to the PETSc SNES solver
and is used in nonlinear problems with nonlinear viscoelastic or elastoplastic
- bulk constitutive models or dynamic fault ruptures.
+ bulk constitutive models, dynamic fault ruptures, or problems involving
+ finite strain (small strain formulation).
The lumped solver (SolverLumped) is a specialized solver used with the
lumped system Jacobian matrix.
The options for the PETSc KSP and SNES solvers are set via the top-level
@@ -4430,7 +4432,7 @@

.
In order for visualization tools, such as ParaView, to determine which
- datasets to read and where to find them in the hiearchy of groups within
+ datasets to read and where to find them in the hierarchy of groups within
the HDF5 file, we create an Xdmf (eXtensible Data Model and Format,
\begin_inset Flex URL
status open
@@ -4452,7 +4454,7 @@
\family default
) in ParaView or Visit.
The Xdmf file contains the relative path to the HDF5 file so the files
- can be moved but must be located together in the same direstory.
+ can be moved but must be located together in the same directory.

\end_layout

@@ -4512,7 +4514,7 @@
Layout of PyLith HDF5 file.
The orange rectangles with rounded corners identify the groups and the
blue rectangles with sharp corners identify the datasets.
- The dimensions of the data sets are shown in parantheses.
+ The dimensions of the data sets are shown in parentheses.
Most HDF5 files will contain either
\family typewriter
vertex_fields
@@ -4545,7 +4547,7 @@
\begin_layout Standard
HDF5 files do not contain self-correcting features that allow a file to
be read if part of a dataset is corrupted.
- This type of error can occur if a job terminates abnornally in the middle
+ This type of error can occur if a job terminates abnormally in the middle
or at the end of a simulation on a large cluster or other parallel machine.
Fortunately, HDF5 also offers the ability to store datasets in external
binary files with the locations specified by links in the HDF5 file.
@@ -4598,7 +4600,7 @@
\end_layout

\begin_layout Standard
-Accessing the datasets for additional analysis or visualiation is identical
+Accessing the datasets for additional analysis or visualization is identical
in the two methods because the use of external data files is completely
transparent to the user except for the presence of the additional files.
\end_layout

Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx	2011-06-15 00:37:04 UTC (rev 18630)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx	2011-06-15 02:17:17 UTC (rev 18631)
@@ -549,7 +549,7 @@
ElasticIsotropic3D
\family default
material type for both materials.
- This behavior will be overriden by example-specific
+ This behavior will be overridden by example-specific
\family typewriter
.cfg
\family default

Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/quasistatic/quasistatic.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/quasistatic/quasistatic.lyx	2011-06-15 00:37:04 UTC (rev 18630)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/quasistatic/quasistatic.lyx	2011-06-15 02:17:17 UTC (rev 18631)
@@ -924,7 +924,7 @@
The upper (locked) portion of the fault has 4 m of left-lateral slip every
200 years, while the lower (creeping) portion of the fault slips at a steady
rate of 2 cm/year.
- The problem bears some similarity to the strike-slip fault model of Savange
+ The problem bears some similarity to the strike-slip fault model of Savage
and Prescott
\begin_inset CommandInset citation
LatexCommand cite

Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx	2011-06-15 00:37:04 UTC (rev 18630)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx	2011-06-15 02:17:17 UTC (rev 18631)
@@ -156,7 +156,7 @@
to create a mesh, as well as describing how to use a LaGriT-generated mesh
in PyLith.
In this tutorial, we will walk through the steps necessary to construct,
- run, and visualzie the results for two problems that use the same mesh.
+ run, and visualize the results for two problems that use the same mesh.
For each of these problems we also consider a simulation using a custom
algebraic multigrid preconditioner with a globally uniformly refined mesh
that reduces the node spacing by a factor of two.
@@ -978,7 +978,7 @@

Number of iterations in linear solve for the Shear Displacement and Kinematic
Fault Slip problems discussed in this section.
- The preconditioner using split fields and an algebriac multigrid algorithm
+ The preconditioner using split fields and an algebraic multigrid algorithm
solves the linear system with fewer iterations with only a small to moderate
increase as the problem size grows.
\end_layout

Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/subduction.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/subduction.lyx	2011-06-15 00:37:04 UTC (rev 18630)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/subduction.lyx	2011-06-15 02:17:17 UTC (rev 18631)
@@ -103,7 +103,7 @@
\end_layout

\begin_layout Itemize
-AREPRO programming language
+APREPRO programming language
\end_layout

\end_deeper
@@ -369,10 +369,10 @@

\begin_layout Standard
We construct the mesh in CUBIT by constructing the geometry, prescribing
- the discretization, runnig the mesher, and then grouping cells and vertices
+ the discretization, running the mesher, and then grouping cells and vertices
for boundary conditions and materials.
We use the APREPRO programming language within the journal files to enable
- use of units and setting variables for values used many times.
+ use of units and to set variables for values used many times.
An appendix in the CUBIT documentation discusses the features available
with APREPRO in CUBIT.
The CUBIT commands are in three separate journal files.
@@ -486,7 +486,7 @@

\begin_layout Standard
As in the examples discussed in previous sections of these tutorials, we
- place parameters common to among the three steps in the
+ place parameters common to the three steps in the
\family typewriter
pylithapp.cfg
\family default
@@ -522,7 +522,7 @@
\end_layout

\begin_layout Description
-pylithapp.problem.formuation.output Settings related output of the solution
+pylithapp.problem.formulation.output Settings related output of the solution
over the domain and subdomain (ground surface).
\end_layout

@@ -562,7 +562,7 @@
The first example problem is earthquake rupture involving coseismic slip
along the interface between the subducting slab and the continental crust
and upper most portion of the mantle below the continental crust.
- The spatial variation of slip comes from a cross-section of Gavin Hayes
+ The spatial variation of slip comes from a cross-section of Gavin Hayes'
finite-source model
\begin_inset Flex URL
status collapsed
@@ -583,7 +583,8 @@

\end_inset

-.Parameter settings that augment those in
+.
+ Parameter settings that augment those in
\family typewriter
pylithapp.cfg
\family default
@@ -733,7 +734,7 @@

\begin_layout Standard
In this example we simulate the interseismic deformation associated with
- the oceanic crust subducting beneath the contiental crust and into the
+ the oceanic crust subducting beneath the continental crust and into the
mantle.
We prescribe steady aseismic slip of 8 cm/yr along the interfaces between
the oceanic crust and mantle with the interface between the oceanic crust
@@ -918,7 +919,7 @@
On the interface along the top of the subducting oceanic crust and the
continental crust and mantle we create two earthquake ruptures, The first
rupture applies the coseismic slip form Step 1 at 150 years, while the
- second rupture prescribes the same steady, asismic slip as in Step 2.
+ second rupture prescribes the same steady, aseismic slip as in Step 2.
\end_layout

\begin_layout Description
@@ -1003,7 +1004,7 @@
\end_layout

\begin_layout Subsection
-Suggestions Variations
+Suggested Variations
\end_layout

\begin_layout Standard