[cig-commits] r16971 - in short/3D/PyLith/trunk/doc/userguide: . boundaryconditions extending install intro materials runpylith tutorials/shearwave

brad at geodynamics.org brad at geodynamics.org
Wed Jun 9 21:42:34 PDT 2010 

Author: brad
Date: 2010-06-09 21:42:34 -0700 (Wed, 09 Jun 2010)
New Revision: 16971

Modified:
   short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx
   short/3D/PyLith/trunk/doc/userguide/extending/extending.lyx
   short/3D/PyLith/trunk/doc/userguide/install/install.lyx
   short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
   short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx
   short/3D/PyLith/trunk/doc/userguide/preface.lyx
   short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
   short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/hex8.lyx
   short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/quad4.lyx
   short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/tet4.lyx
Log:
Spell check.

Modified: short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx	2010-06-10 02:46:33 UTC (rev 16970)
+++ short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx	2010-06-10 04:42:34 UTC (rev 16971)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
 \lyxformat 345
 \begin_document
 \begin_header
@@ -2146,23 +2146,19 @@
 \end_layout
 
 \begin_layout Description
-up_dir Up-dir or up direction (only used in 3D simulations).
+up_dir Up-dir or up direction (used in 2D and 3D simulations).
+ In 2D the default in-plane slip is left-lateral, so we use the up-direction
+ to resolve the ambiguity in specifying reverse slip.
+ In 3D the up-direction is used to resolve the ambiguity in the along-strike
+ and dip-dir directions.
+ If the fault plane is horizontal, then the up-dir corresponds to the reverse-mo
+tion on the +z side of the fault.
  The only requirement for this direction is that it not be collinear with
  the fault normal direction.
- The default value of [0, 0, 1] can be used as long as the fault normal
- does not coincide with this direction.
+ The default value of [0, 0, 1] is appropriate for most 3D problems.
 \end_layout
 
 \begin_layout Description
-normal_dir General preferred direction for the fault normal (only used in
- 3D simulations).
- This direction is used to resolve the ambiguity as to which side of the
- fault to choose for the fault normal.
- This direction should point from the footwall to the hanging wall.
- The default value is [1, 0, 0].
-\end_layout
-
-\begin_layout Description
 quadrature Quadrature object used in integrating fault quantities.
 \end_layout
 
@@ -2237,10 +2233,6 @@
 \end_layout
 
 \begin_layout LyX-Code
-normal_dir = [1, 0, 0] ; default
-\end_layout
-
-\begin_layout LyX-Code
 quadrature.cell = pylith.feassemble.FIATLagrange
 \end_layout
 
@@ -2250,8 +2242,7 @@
 
 \begin_layout Standard
 The group of vertices has the label ``fault A.'' We replicate the default
- values for the fault ``up'' direction, and the desired general direction
- for the fault normal.
+ values for the fault ``up'' direction.
  These settings apply to a 2D fault surface embedded within a 3D mesh, so
  we use 2D Lagrange reference cells.
  The spatial database for elastic properties is used to determine the approximat
@@ -2348,7 +2339,7 @@
 \end_layout
 
 \begin_layout Paragraph
-Nondiagonal A
+Non-diagonal A
 \end_layout
 
 \begin_layout Standard
@@ -4436,9 +4427,9 @@
  their values just as they do in kinematic ruptures.
  In this case, the Lagrange multipliers correspond to the forces necessary
  to keep the slip zero.
- When the driving foces exceed those allowed by friction, we reduce the
+ When the driving forces exceed those allowed by friction, we reduce the
  values of the Lagrange multipliers to those consistent with friction from
- the fault constitutitive model.
+ the fault constitutive model.
  When we reduce the Lagrange multipliers, we must increment the slip accordingly
  to maintain consistency in the algebraic system of equations.
 \end_layout
@@ -4488,7 +4479,7 @@
 \end_layout
 
 \begin_layout Paragraph
-Nondiagonal A
+Non-diagonal A
 \end_layout
 
 \begin_layout Standard
@@ -4542,7 +4533,7 @@
 The solution of these two linear systems gives the increment in slip assuming
  all the degrees of freedom except those immediately adjacent to the fault
  remain fixed.
- In real appications where the deformation associated with fault slip is
+ In real applications where the deformation associated with fault slip is
  localized around the fault, this provides good enough approximations so
  that the nonlinear solver converges quickly.
  In problems where deformation associated with slip on the fault is not
@@ -4804,7 +4795,7 @@
 \begin_inset Text
 
 \begin_layout Plain Layout
-Left-lateral shear traction (including dipping faults)
+Left-lateral shear traction (reverse shear for dipping faults)
 \end_layout
 
 \end_inset

Modified: short/3D/PyLith/trunk/doc/userguide/extending/extending.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/extending/extending.lyx	2010-06-10 02:46:33 UTC (rev 16970)
+++ short/3D/PyLith/trunk/doc/userguide/extending/extending.lyx	2010-06-10 04:42:34 UTC (rev 16971)
@@ -357,7 +357,7 @@
  errors and create C++ tests as well as the Python tests included here.
  In our rather simple example, we simply test the overall functionality
  of the component.
- For examples of thorough testing, see the spatialdatabase and PyLith source
+ For examples of thorough testing, see the spatialdata and PyLith source
  code.
 \end_layout
 
@@ -477,7 +477,7 @@
 
 \begin_layout Standard
 The properties and state variables used in the bulk constitutive model are
- set using arguments to the constuctor of the C++ 
+ set using arguments to the constructor of the C++ 
 \family typewriter
 ElasticMaterial
 \family default
@@ -757,7 +757,7 @@
  In this example, we demonstrate how to extend PyLith by adding your own
  fault constitutive model.
  We implement a linear viscous fault constitutive model wherein the perturbation
- in the coeficient of friction is linearly proportional to the slip rate.
+ in the coefficient of friction is linearly proportional to the slip rate.
  This constitutive model, 
 \family typewriter
 ViscousFriction
@@ -792,7 +792,7 @@
 
 \begin_layout Standard
 The properties and state variables used in the fault constitutive model
- are set using arguments to the constuctor of the C++ 
+ are set using arguments to the constructor of the C++ 
 \family typewriter
 FrictionModel
 \family default

Modified: short/3D/PyLith/trunk/doc/userguide/install/install.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/install/install.lyx	2010-06-10 02:46:33 UTC (rev 16970)
+++ short/3D/PyLith/trunk/doc/userguide/install/install.lyx	2010-06-10 04:42:34 UTC (rev 16971)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
 \lyxformat 345
 \begin_document
 \begin_header
@@ -170,8 +170,8 @@
 \end_layout
 
 \begin_layout Standard
-Binary executables are available for Linux, Mac OS X (Power PC and Intel),
- and Windows from the PyLith web page 
+Binary executables are available for Linux, Mac OS X (Intel 10.5 and Intel
+ 10.6), and Windows from the PyLith web page 
 \begin_inset Flex URL
 status collapsed
 
@@ -282,7 +282,7 @@
 
 \end_deeper
 \begin_layout Enumerate
-Download the Darwin tarball from the PyLith web page 
+Download the appropriate Darwin tarball from the PyLith web page 
 \begin_inset Flex URL
 status collapsed
 
@@ -293,7 +293,8 @@
 
 \end_inset
 
- and save it to the desired location, e.g., 
+ based on your operating system and save it to the desired location, e.g.,
+ 
 \family typewriter
 $HOME/pylith
 \family default
@@ -302,12 +303,12 @@
 
 \begin_layout Enumerate
 Unpack the tarball.
- For the PowerPC architecture,
+ For 10.5.x operating system,
 \end_layout
 
 \begin_deeper
 \begin_layout LyX-Code
-$ tar -xzf pylith-1.5.0-darwin-powerpc.tgz
+$ tar -xzf pylith-1.5.0-darwin-i386.tgz
 \end_layout
 
 \end_deeper
@@ -434,7 +435,7 @@
 \end_layout
 
 \begin_layout Itemize
-A Fortran compiler (optional)
+A FORTRAN compiler (optional)
 \end_layout
 
 \begin_layout Itemize
@@ -490,17 +491,17 @@
 \end_inset
 
 .
- (Note that Xcode does not include a Fortran compiler.)
+ (Note that Xcode does not include a FORTRAN compiler.)
 \end_layout
 
 \begin_layout Subsubsection
-Fortran Compiler (optional)
+FORTRAN Compiler (optional)
 \end_layout
 
 \begin_layout Standard
-To build PETSc, you need either a Fortran-77 or Fortran-9x compiler.
- There are several free Fortran compilers available.
- GCC 4 contains a Fortran-95 compiler called 
+To build PETSc, you need either a FORTRAN-77 or FORTRAN-9x compiler.
+ There are several free FORTRAN compilers available.
+ GCC 4 contains a FORTRAN-95 compiler called 
 \family typewriter
 gfortran
 \family default
@@ -526,7 +527,7 @@
  projects offer pre-built binaries for a variety of systems, including Mac
  OS X.
  A number of optional PETSc packages that provide additional preconditioners
- and solvers require a Fortran compiler.
+ and solvers require a FORTRAN compiler.
 \end_layout
 
 \begin_layout Subsubsection
@@ -1223,7 +1224,7 @@
 
 \begin_layout Standard
 In our next example, we configure PETSc on a Mac OS X machine.
- We have installed Apple's Xcode and the G95 Fortran compiler.
+ We have installed Apple's Xcode and the G95 FORTRAN compiler.
  However, we don't have anything else preinstalled, so we instruct PETSc
  to download almost everything else, including MPICH.
  Intentionally, we don't specify anything about BLAS/LAPACK: PETSc automatically
@@ -1814,7 +1815,7 @@
 \end_layout
 
 \begin_layout LyX-Code
-$ cd proj-4.6.1/nad$ unzip proj-datumgrid-1.5.zip
+$ cd proj-4.7.0/nad$ unzip proj-datumgrid-1.5.zip
 \end_layout
 
 \begin_layout Standard
@@ -2226,7 +2227,7 @@
 \end_layout
 
 \begin_layout LyX-Code
-$ tar xzf spatialdata-0.5.2.tgz
+$ tar xzf spatialdata-0.6.0.tgz
 \end_layout
 
 \begin_layout Standard
@@ -2234,7 +2235,7 @@
 \end_layout
 
 \begin_layout LyX-Code
-$ gunzip -c spatialdata-0.5.2.tgz | tar xf -
+$ gunzip -c spatialdata-0.6.0.tgz | tar xf -
 \end_layout
 
 \begin_layout Subsubsection

Modified: short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx	2010-06-10 02:46:33 UTC (rev 16970)
+++ short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx	2010-06-10 04:42:34 UTC (rev 16971)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
 \lyxformat 345
 \begin_document
 \begin_header
@@ -509,7 +509,7 @@
 \end_layout
 
 \begin_layout Standard
-PETSc includes interfaces for Fortran 77/90, C, C++, and Python for nearly
+PETSc includes interfaces for FORTRAN 77/90, C, C++, and Python 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

Modified: short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx	2010-06-10 02:46:33 UTC (rev 16970)
+++ short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx	2010-06-10 04:42:34 UTC (rev 16971)
@@ -1,4 +1,4 @@
-#LyX 1.6.6 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
 \lyxformat 345
 \begin_document
 \begin_header
@@ -4498,7 +4498,7 @@
 \begin_inset Formula $\lambda$
 \end_inset
 
- is now known, we can substitue 
+ is now known, we can substitute 
 \begin_inset CommandInset ref
 LatexCommand ref
 reference "eq:112"

Modified: short/3D/PyLith/trunk/doc/userguide/preface.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/preface.lyx	2010-06-10 02:46:33 UTC (rev 16970)
+++ short/3D/PyLith/trunk/doc/userguide/preface.lyx	2010-06-10 04:42:34 UTC (rev 16971)
@@ -1,4 +1,4 @@
-#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
 \lyxformat 345
 \begin_document
 \begin_header
@@ -179,7 +179,7 @@
 \begin_inset Newline newline
 \end_inset
 
-short/pylith/pylith_book-1.4.pdf
+short/pylith/pylith_manual-1.5.pdf
 \end_layout
 
 \begin_layout Section
@@ -253,13 +253,14 @@
 
 \begin_layout Standard
 Your suggestions and corrections can only improve this documentation.
- Please report any errors, inaccuracies, or typos to Sue Kientz 
+ Please report any errors, inaccuracies, or typos to the CIG Short-Term
+ Tectonics email list 
 \begin_inset Flex URL
-status collapsed
+status open
 
 \begin_layout Plain Layout
 
-sue at geodynamics.org
+cig-short at geodynamics.org
 \end_layout
 
 \end_inset

Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx	2010-06-10 02:46:33 UTC (rev 16970)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx	2010-06-10 04:42:34 UTC (rev 16971)
@@ -1263,7 +1263,7 @@
 \end_layout
 
 \begin_layout Standard
-ParMetis is not included in the PyLith binaries due to licensing issues.
+ParMETIS is not included in the PyLith binaries due to licensing issues.
 \end_layout
 
 \begin_layout Subsection

Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/hex8.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/hex8.lyx	2010-06-10 02:46:33 UTC (rev 16970)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/hex8.lyx	2010-06-10 04:42:34 UTC (rev 16971)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
 \lyxformat 345
 \begin_document
 \begin_header
@@ -175,8 +175,8 @@
 
 \begin_layout Standard
 The simulation parameters match those in the tri3 and tet4 examples.
- As in the tet4 example, we both the longiudinal degree of freedom and the
- out-of-plane tranverse degree of freedom.
+ As in the tet4 example, we both the longitudinal degree of freedom and
+ the out-of-plane transverse degree of freedom.
  Using eight-point quadrature permits use of a time step of 1/20 s, which
  is slightly larger than the time step of 1/30 s used in the tri3 and tet4
  simulations.

Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/quad4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/quad4.lyx	2010-06-10 02:46:33 UTC (rev 16970)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/quad4.lyx	2010-06-10 04:42:34 UTC (rev 16971)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
 \lyxformat 345
 \begin_document
 \begin_header
@@ -567,7 +567,7 @@
 \begin_layout Standard
 and use a UniformDB to set the static friction parameters.
  We use a reference coefficient of friction of 0.6, reference slip rate of
- 1.0e-6 m/s, characterisitc slip distance of 0.037 m, coefficients a and b
+ 1.0e-6 m/s, characteristic slip distance of 0.037 m, coefficients a and b
  of 0.0125 and 0.0172, and no cohesion (0 MPa).
  The parameters specific to this example are in dynamic_
 \family typewriter

Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/tet4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/tet4.lyx	2010-06-10 02:46:33 UTC (rev 16970)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/tet4.lyx	2010-06-10 04:42:34 UTC (rev 16971)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
 \lyxformat 345
 \begin_document
 \begin_header
@@ -177,7 +177,7 @@
  of using the LaGriT mesh reader and switching the from a two-dimensional
  problem to a three-dimensional problem.
  In addition to fixing the longitudinal degree of freedom, we also fix the
- out-of-plane tranverse degree of freedom.
+ out-of-plane transverse degree of freedom.
  Because the fault separates two material regions in LaGriT, we use two
  materials in PyLith.
  All of the parameters are set in the pylithapp.cfg file.

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