[cig-commits] r15172 - in short/3D/PyLith/trunk/doc/userguide: . benchmarks boundaryconditions fileformats install intro materials runpylith tutorials tutorials/3dhex8 tutorials/3dtet4 tutorials/twohex8 tutorials/twoquad4 tutorials/twotet4 tutorials/twotet4-geoproj tutorials/twotri3
brad at geodynamics.org
brad at geodynamics.org
Wed Jun 10 11:19:16 PDT 2009
Author: brad
Date: 2009-06-10 11:19:15 -0700 (Wed, 10 Jun 2009)
New Revision: 15172
Modified:
short/3D/PyLith/trunk/doc/userguide/benchmarks/benchmarks.lyx
short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx
short/3D/PyLith/trunk/doc/userguide/fileformats/fileformats.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/3dhex8/3dhex8.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/twohex8.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/twoquad4.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4-geoproj/twotet4-geoproj.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/twotet4.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx
short/3D/PyLith/trunk/doc/userguide/userguide.lyx
Log:
Initial pass. Added sections needing updates to top-level TODO.
Modified: short/3D/PyLith/trunk/doc/userguide/benchmarks/benchmarks.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/benchmarks/benchmarks.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/benchmarks/benchmarks.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 1
@@ -47,7 +50,8 @@
\begin_body
\begin_layout Chapter
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "cha:Benchmarks"
\end_inset
@@ -64,22 +68,31 @@
Earthquake Center and the Short-Term Tectonics Working Group within CIG
developed a suite of benchmarks to test the accuracy and performance of
3D numerical codes.
- The benchmark definitions are posted on the CIG website at
-\begin_inset LatexCommand htmlurl
-name "Short-Term Tectonics Benchmarks"
-target "geodynamics.org/cig/workinggroups/short/workarea/benchmarks/"
+ The benchmark definitions are posted on the CIG website at Short-Term Tectonics
+ Benchmarks
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/workinggroups/short/workarea/benchmarks/
+\end_layout
+
\end_inset
.
These benchmarks permit evaluating the relative performance of different
types of basis functions, quadrature schemes, and discretizations for geophysic
al applications.
- The files needed to run the benchmarks are in the
-\begin_inset LatexCommand htmlurl
-name "CIG SVN Repository"
-target "geodynamics.org/svn/cig/short/3D/PyLith/benchmarks"
+ The files needed to run the benchmarks are in the CIG SVN Repository
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/svn/cig/short/3D/PyLith/benchmarks
+\end_layout
+
\end_inset
.
@@ -94,8 +107,9 @@
\end_layout
\begin_layout Standard
-\begin_inset Include \input{strikeslip/strikeslip.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "strikeslip/strikeslip.lyx"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,8 +1,9 @@
-#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
+\use_default_options false
\language english
\inputencoding auto
\font_roman default
@@ -13,9 +14,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 1
@@ -44,7 +47,8 @@
\begin_body
\begin_layout Chapter
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "cha:boundary:interface:conditions"
\end_inset
@@ -96,7 +100,8 @@
generator.
For meshes specified using the PyLith mesh ASCII format, the sets of vertices
are specified using groups (see Appendix
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:MeshIOAscii"
\end_inset
@@ -357,7 +362,8 @@
case of the UniformDB) and specify the velocity in the z-direction to be
1.0e-06 m/s.
See Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:spatial:databases"
\end_inset
@@ -374,13 +380,14 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "tab:dirichlet:output"
\end_inset
@@ -394,14 +401,14 @@
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="3">
<features>
-<column alignment="center" valignment="top" leftline="true" width="0">
-<column alignment="center" valignment="top" leftline="true" rightline="true" width="0">
-<column alignment="center" valignment="top" rightline="true" width="0">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="0">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Field Type
@@ -409,10 +416,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Field
@@ -420,10 +427,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Description
@@ -432,11 +439,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
vertex_info_fields
@@ -447,7 +454,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
initial
@@ -455,30 +462,30 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Displacement vector at reference time in global coordinate system
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
rate_of_change
@@ -486,10 +493,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Rate of change of displacement field in global coordinate system
\end_layout
@@ -540,12 +547,12 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Values in spatial database used for Dirichlet boundary conditions.
\end_layout
@@ -555,13 +562,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
<features>
-<column alignment="center" valignment="top" leftline="true" width="0">
-<column alignment="center" valignment="top" leftline="true" rightline="true" width="0">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="0">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Value in
@@ -574,10 +581,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Name in Spatial Database
@@ -586,11 +593,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
0
\end_layout
@@ -599,7 +606,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
dof-0
@@ -608,11 +615,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
1
\end_layout
@@ -621,7 +628,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
dof-1
@@ -630,20 +637,20 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
2
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
dof-2
@@ -680,7 +687,8 @@
The tractions are integrated over each cell and assembled to obtain the
forces applied at the vertices.
See Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sub:Tutorial-twoquad4-traction"
\end_inset
@@ -811,7 +819,8 @@
\begin_layout Standard
These settings correspond to the example problem described in Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sub:Tutorial-twoquad4-traction"
\end_inset
@@ -845,13 +854,14 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "tab:neumann:output"
\end_inset
@@ -865,14 +875,14 @@
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="3">
<features>
-<column alignment="center" valignment="top" leftline="true" width="0">
-<column alignment="center" valignment="top" leftline="true" rightline="true" width="0">
-<column alignment="center" valignment="top" rightline="true" width="0">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="0">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Field Type
@@ -880,10 +890,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Field
@@ -891,10 +901,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Description
@@ -903,11 +913,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
cell_info_fields
@@ -915,10 +925,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
tractions
@@ -926,10 +936,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Traction vector in global coordinate system
\end_layout
@@ -1314,7 +1324,8 @@
\begin_layout Standard
Slip corresponds to relative motion across a fault surface.
Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:fault:orientation"
\end_inset
@@ -1326,7 +1337,8 @@
angles over potentially complex, nonplanar fault surfaces.
Instead, the user specifies fault parameters in terms of lateral motion,
reverse motion, and fault opening as shown in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:fault:slip:motions"
\end_inset
@@ -1343,7 +1355,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/faultOrientation.eps
@@ -1353,10 +1365,10 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Orientation of a fault surface in 3D, where
\begin_inset Formula $\phi$
\end_inset
@@ -1371,7 +1383,8 @@
the rake angle.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:fault:orientation"
\end_inset
@@ -1398,7 +1411,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/slipmotions.eps
@@ -1408,14 +1421,15 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Sign conventions associated with fault slip.
Positive values are associated with left-lateral, reverse, and fault opening
motions.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:fault:slip:motions"
\end_inset
@@ -1446,7 +1460,8 @@
on the two sides of the fault.
PyLith automatically adds cohesive cells for each fault surface.
Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:fault:cohesive:quad4"
\end_inset
@@ -1464,7 +1479,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/quad4cohesive.eps
@@ -1474,15 +1489,16 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Example of cohesive cell inserted into a mesh of two quadrilateral cells.
The zero thickness cohesive cell (shown with dashed lines) controls slip
on the fault via the relative motion between vertices 3 and 7 and 2 and
6.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:fault:cohesive:quad4"
\end_inset
@@ -1509,7 +1525,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/quad4cohesivekin.eps
@@ -1519,10 +1535,10 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Example of cohesive cell using Lagrange multipliers inserted into a mesh
of two quadrilateral cells.
The zero thickness cohesive cell (shown with dashed lines) controls slip
@@ -1533,7 +1549,8 @@
vertices 2 and 6, and the constraint associated with vertex 9 controls
the relative motion between vertices 3 and 7.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:fault:cohesive:quad4:kin"
\end_inset
@@ -1598,11 +1615,6 @@
\end_layout
\begin_layout Description
-mat_db Spatial database for bulk material properties (used in improving
- the conditioning of the system).
-\end_layout
-
-\begin_layout Description
output Manager for output of diagnostic and data fields for the fault.
\end_layout
@@ -1611,7 +1623,8 @@
normal direction, final slip, and slip initiation time) and the slip at
each time step.
Table
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "tab:fault:kin:output"
\end_inset
@@ -1619,7 +1632,8 @@
lists the fields available for output for a fault with kinematic (prescribed)
earthquake rupture.
The fault coordinate system is shown in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:fault:slip:motions"
\end_inset
@@ -1676,10 +1690,6 @@
\end_layout
\begin_layout LyX-Code
-quadrature = pylith.feassemble.Quadrature2Din3D
-\end_layout
-
-\begin_layout LyX-Code
quadrature.cell = pylith.feassemble.FIATLagrange
\end_layout
@@ -1687,17 +1697,12 @@
quadrature.cell.dimension = 2
\end_layout
-\begin_layout LyX-Code
-mat_db.iohandler.filename = elastic_materials.spatialdb
-\end_layout
-
\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.
These settings apply to a 2D fault surface embedded within a 3D mesh, so
- we use 2D quadrature in a 3D spatial coordinate system with 2D Lagrange
- reference cells.
+ we use 2D Lagrange reference cells.
The spatial database for elastic properties is used to determine the approximat
e shear modulus and condition the equations for faster convergence rates.
\end_layout
@@ -1731,7 +1736,8 @@
provides for an easy implementation; we simply add the additional degrees
of freedom associated with the Lagrange multipliers to the cohesive cells
as shown in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:fault:cohesive:quad4:kin"
\end_inset
@@ -1778,34 +1784,7 @@
across the fault, the slip vector and Lagrange multipliers (forces required
to impose the slip) are in the local fault coordinate system (lateral motion,
reverse motion, and fault opening).
- Because the solution vector now mixes displacements,
-\begin_inset Formula $\overrightarrow{u}$
-\end_inset
-
-, and forces,
-\begin_inset Formula $\overrightarrow{L}$
-\end_inset
-
-, the matrix on the left-hand side is ill-conditioned.
- In order to improve the conditioning, we scale the direction cosines in
- the upper right portion of the matrix by an amount necessary to reduce
- the forces in the solution vector to within a few orders of magnitude of
- the displacements, resulting in
-\begin_inset Formula \begin{equation}
-\left[\begin{array}{cc}
-A & a\underline{C}^{T}\\
-\underline{C} & 0\end{array}\right]\left[\begin{array}{c}
-\overrightarrow{u}\\
-\frac{1}{a}\overrightarrow{L}\end{array}\right]=\left[\begin{array}{c}
-\overrightarrow{b}\\
-\overrightarrow{D}\end{array}\right]\,.\end{equation}
-
-\end_inset
-
-While the matrix on the left-hand side is now nonsymmetric, the solution
- converges very quickly.
- Future releases of PyLith may use alternative conditioning algorithms to
- retain the symmetry of the matrix, thereby reducing storage requirements.
+
\end_layout
\begin_layout Subsubsection
@@ -1877,13 +1856,14 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "tab:fault:kin:output"
\end_inset
@@ -1897,14 +1877,14 @@
\begin_inset Tabular
<lyxtabular version="3" rows="8" columns="3">
<features>
-<column alignment="center" valignment="top" leftline="true" width="0">
-<column alignment="center" valignment="top" leftline="true" rightline="true" width="0">
-<column alignment="center" valignment="top" rightline="true" width="0">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="0">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Field Type
@@ -1912,10 +1892,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Field
@@ -1923,10 +1903,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Description
@@ -1935,11 +1915,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
vertex_info_fields
@@ -1950,7 +1930,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
normal_dir
@@ -1958,10 +1938,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Direction of fault normal in global coordinate system
\end_layout
@@ -1969,19 +1949,19 @@
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
strike_dir
@@ -1989,10 +1969,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Direction of fault strike in global coordinate system
\end_layout
@@ -2000,19 +1980,19 @@
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
dip_dir
@@ -2020,10 +2000,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Up-dip direction on hanging wall in global coordinate system
\end_layout
@@ -2031,19 +2011,19 @@
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
final_slip_NAME
@@ -2051,30 +2031,30 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Vector of final slip (in fault coordinate system) in meters
\end_layout
\end_inset
</cell>
</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
slip_time
@@ -2087,10 +2067,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Time at which slip begins in seconds
\end_layout
@@ -2098,10 +2078,10 @@
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
vertex_data_fields
@@ -2109,10 +2089,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
slip
@@ -2120,30 +2100,30 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Slip vector at time step (in fault coordinate system) in meters
\end_layout
\end_inset
</cell>
</row>
-<row bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
tractions_change
@@ -2151,10 +2131,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Change in fault tractions (in fault coordinate system) in Pa
\end_layout
@@ -2238,7 +2218,8 @@
for quasi-static modeling of earthquake rupture, (2) a constant slip rate
time function for modeling steady aseismic slip, and (3) the integral of
Brune's far-field time function
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Brune:1970"
\end_inset
@@ -2334,7 +2315,8 @@
The spatial database files for the slip time function specify the spatial
variation in the parameters for the slip time function, as shown in Table
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "tab:step-function-db-params"
\end_inset
@@ -2351,13 +2333,14 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "tab:step-function-db-params"
\end_inset
@@ -2372,14 +2355,14 @@
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="3">
<features>
-<column alignment="left" valignment="top" leftline="true" width="0">
-<column alignment="left" valignment="top" leftline="true" width="0">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="2.5in">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="0">
+<column alignment="left" valignment="top" width="0">
+<column alignment="left" valignment="top" width="2.5in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Database
@@ -2387,10 +2370,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Value
@@ -2398,10 +2381,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Description
@@ -2410,11 +2393,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
final_slip
@@ -2425,7 +2408,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
left-lateral-slip
@@ -2436,7 +2419,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Amount of left-lateral final slip in meters.
Use negative values for right-lateral slip.
Applies to faults in 2D and 3D only.
@@ -2446,19 +2429,19 @@
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
reverse-slip
@@ -2466,10 +2449,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Amount of reverse slip in meters.
Use negative values for normal slip.
Applies to faults in 3D only.
@@ -2479,19 +2462,19 @@
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
fault-opening
@@ -2499,10 +2482,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Amount of fault opening in meters.
Negative values imply penetration.
\end_layout
@@ -2510,11 +2493,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
slip_time
@@ -2522,10 +2505,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
slip_time
@@ -2533,10 +2516,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Slip initiation time (
\begin_inset Formula $t_{t})$
\end_inset
@@ -2646,7 +2629,8 @@
The spatial database files for the slip time function specify the spatial
variation in the parameters for the slip time function, as shown in Table
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "tab:const-slip-rate-db-params"
\end_inset
@@ -2663,13 +2647,14 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "tab:const-slip-rate-db-params"
\end_inset
@@ -2684,14 +2669,14 @@
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="3">
<features>
-<column alignment="left" valignment="top" leftline="true" width="0">
-<column alignment="left" valignment="top" leftline="true" width="0">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="2.5in">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="0">
+<column alignment="left" valignment="top" width="0">
+<column alignment="left" valignment="top" width="2.5in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Database
@@ -2699,10 +2684,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Value
@@ -2710,10 +2695,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Description
@@ -2722,11 +2707,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
slip_rate
@@ -2737,7 +2722,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
left-lateral-slip
@@ -2748,7 +2733,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Slip rate for left-lateral final slip in meters per second.
Use negative values for right-lateral slip.
Applies to faults in 2D and 3D only.
@@ -2758,19 +2743,19 @@
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
reverse-slip
@@ -2778,10 +2763,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Slip rate for reverse slip in meters per second.
Use negative values for normal slip.
Applies to faults in 3D only.
@@ -2791,19 +2776,19 @@
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
fault-opening
@@ -2811,10 +2796,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Slip rate for fault opening in meters per second.
Negative values imply penetration.
\end_layout
@@ -2822,11 +2807,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
slip_time
@@ -2834,10 +2819,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
slip_time
@@ -2845,10 +2830,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Slip initiation time (
\begin_inset Formula $t_{t})$
\end_inset
@@ -2877,7 +2862,8 @@
\begin_layout Standard
We use an integral of Brune's far-field time function
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Brune:1970"
\end_inset
@@ -2978,7 +2964,8 @@
The spatial database files for the slip time function specify the spatial
variation in the parameters for the slip time function, as shown in Table
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "tab:Brune-slip-db-params"
\end_inset
@@ -2995,13 +2982,14 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "tab:Brune-slip-db-params"
\end_inset
@@ -3015,14 +3003,14 @@
\begin_inset Tabular
<lyxtabular version="3" rows="6" columns="3">
<features>
-<column alignment="left" valignment="top" leftline="true" width="0">
-<column alignment="left" valignment="top" leftline="true" width="0">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="2.5in">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="left" valignment="top" width="0">
+<column alignment="left" valignment="top" width="0">
+<column alignment="left" valignment="top" width="2.5in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Database
@@ -3030,10 +3018,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Value
@@ -3041,10 +3029,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Description
@@ -3053,11 +3041,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
slip
@@ -3068,7 +3056,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
left-lateral-slip
@@ -3079,7 +3067,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Amount of left-lateral final slip in meters.
Use negative values for right-lateral slip.
Applies to faults in 2D and 3D only.
@@ -3089,19 +3077,19 @@
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
reverse-slip
@@ -3109,10 +3097,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Amount of reverse slip in meters.
Use negative values for normal slip.
Applies to faults in 3D only.
@@ -3122,19 +3110,19 @@
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
fault-opening
@@ -3142,10 +3130,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Amount of fault opening in meters.
Negative values imply penetration.
\end_layout
@@ -3153,11 +3141,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
slip_rate
@@ -3168,7 +3156,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
slip_rate
@@ -3179,7 +3167,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Peak slip rate (
\begin_inset Formula $V_{max})$
\end_inset
@@ -3190,11 +3178,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
slip_time
@@ -3202,10 +3190,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
slip_time
@@ -3213,10 +3201,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Slip initiation time (
\begin_inset Formula $t_{t})$
\end_inset
@@ -3252,7 +3240,8 @@
forces will affect plastic yield criteria and the deformation field for
large deformation/finite strain problems.
As described in Chapter
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Governing-Equations"
\end_inset
@@ -3354,7 +3343,8 @@
\begin_layout Standard
An example problem using gravity is described in Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Tutorial-3d-hex8"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/fileformats/fileformats.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/fileformats/fileformats.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/fileformats/fileformats.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 1
@@ -47,7 +50,8 @@
\begin_body
\begin_layout Chapter
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "cha:File-Formats"
\end_inset
@@ -56,7 +60,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:MeshIOAscii"
\end_inset
@@ -80,7 +85,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -91,18 +96,20 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Diagram of mesh specified in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:meshioascii:format"
\end_inset
.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:meshioascii:diagram"
\end_inset
@@ -417,16 +424,17 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Format of
\family typewriter
PyLith
\family default
mesh ASCII files.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:meshioascii:format"
\end_inset
@@ -445,7 +453,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Spatialdata:SimpleIOAscii"
\end_inset
@@ -549,20 +558,10 @@
\end_layout
\begin_layout LyX-Code
- // Specify the units of the values.
- Currently, these are read
+ // Specify the units of the values in Python syntax (e.g., kg/m**3).
\end_layout
\begin_layout LyX-Code
- // and stored but not parsed for meaning.
- Unit conversions will
-\end_layout
-
-\begin_layout LyX-Code
- // likely be implemented in a future PyLith release.
-\end_layout
-
-\begin_layout LyX-Code
value-units = m m m
\end_layout
@@ -665,10 +664,10 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Format of spatial database files.
\end_layout
@@ -699,11 +698,16 @@
\family default
program in addition to the Proj.4 libraries, so that you can obtain a list
of support projections, datums, and ellipsoids.
- Alternatively, refer to the documentation for the
-\begin_inset LatexCommand htmlurl
-name "Proj.4 Cartographic Projections library"
-target "trac.osgeo.org/proj"
+ Alternatively, refer to the documentation for the Proj.4 Cartographic Projection
+s library
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+trac.osgeo.org/proj
+\end_layout
+
\end_inset
.
@@ -741,10 +745,10 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Format for Cartesian coordinate systems in spatial database files.
\end_layout
@@ -893,10 +897,10 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Format for geographic coordinate systems in spatial database files.
\end_layout
@@ -1103,10 +1107,10 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Format for geographic projection coordinate systems in spatial database
files.
\end_layout
@@ -1308,10 +1312,10 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Format for the geographic local Cartesian coordinate system in spatial database
files.
\end_layout
@@ -1327,7 +1331,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:FileFormat:TimeStepUser"
\end_inset
@@ -1407,10 +1412,10 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Format of user-specified time step files.
\end_layout
Modified: short/3D/PyLith/trunk/doc/userguide/install/install.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/install/install.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/install/install.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 1
@@ -47,7 +50,8 @@
\begin_body
\begin_layout Chapter
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "cha:Installation-and-Getting"
\end_inset
@@ -63,18 +67,24 @@
Installation of PyLith on other operating systems -- or installation on
a cluster -- requires building the software from the source code, which
can be difficult for inexperienced users.
- Help is available from both a CIG mailing list and
-\begin_inset LatexCommand htmlurl
-name "CIG Roundup Bug Tracking System"
-target "geodynamics.org/roundup/"
+ Help is available from both a CIG mailing list and CIG Roundup Bug Tracking
+ System
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/roundup/
+\end_layout
+
\end_inset
.
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Getting-Help-and"
\end_inset
@@ -83,20 +93,29 @@
\end_layout
\begin_layout Standard
-The
-\begin_inset LatexCommand url
-name "CIG Short-Term Crustal Dynamics Mailing List"
-target "cig-short at geodynamics.org"
+The CIG Short-Term Crustal Dynamics Mailing List
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cig-short at geodynamics.org
+\end_layout
+
\end_inset
is dedicated to CIG issues associated with short-term crustal dynamics,
including the use of PyLith.
- You can subscribe to the mailing list and view messages at
-\begin_inset LatexCommand htmlurl
-name "cig-short Mailing List"
-target "geodynamics.org/cig/lists/cig-short"
+ You can subscribe to the mailing list and view messages at cig-short Mailing
+ List
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/lists/cig-short
+\end_layout
+
\end_inset
.
@@ -109,11 +128,16 @@
Roundup
\family default
for bug tracking.
- If you find a bug in PyLith, please submit a bug report to the
-\begin_inset LatexCommand htmlurl
-name "CIG Roundup System"
-target "geodynamics.org/roundup/"
+ If you find a bug in PyLith, please submit a bug report to the CIG Roundup
+ System
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/roundup/
+\end_layout
+
\end_inset
.
@@ -138,11 +162,15 @@
\begin_layout Standard
Binary executables are available for Linux, Mac OS X (Power PC and Intel),
- and Windows from the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith/"
+ and Windows from the PyLith web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/short/pylith/
+\end_layout
+
\end_inset
.
@@ -172,11 +200,15 @@
\end_deeper
\begin_layout Enumerate
-Download the Linux tarball from the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith/"
+Download the Linux tarball from the PyLith web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/short/pylith/
+\end_layout
+
\end_inset
, and save it to the desired location, e.g.,
@@ -192,7 +224,7 @@
\begin_deeper
\begin_layout LyX-Code
-$ tar -xzf pylith-1.3.1-linux-i686.tgz
+$ tar -xzf pylith-1.4.0-linux-i686.tgz
\end_layout
\end_deeper
@@ -241,11 +273,15 @@
\end_deeper
\begin_layout Enumerate
-Download the Darwin tarball from the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith/"
+Download the Darwin tarball from the PyLith web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/short/pylith/
+\end_layout
+
\end_inset
and save it to the desired location, e.g.,
@@ -262,7 +298,7 @@
\begin_deeper
\begin_layout LyX-Code
-$ tar -xzf pylith-1.3.1-darwin-powerpc.tgz
+$ tar -xzf pylith-1.4.0-darwin-powerpc.tgz
\end_layout
\end_deeper
@@ -292,11 +328,15 @@
\end_layout
\begin_layout Enumerate
-Download the Windows installer from the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith/"
+Download the Windows installer from the PyLith web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/short/pylith/
+\end_layout
+
\end_inset
and save it to your desktop.
@@ -312,7 +352,8 @@
\begin_layout Standard
PyLith depends on a number of other packages (see Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:pylith-dependencies"
\end_inset
@@ -337,11 +378,16 @@
\begin_layout Standard
Detailed installation instructions for building PyLith using the SVN source
repository are available for several platforms.
- The instructions can be accessed via the
-\begin_inset LatexCommand htmlurl
-name "web interface into the PyLith source repository"
-target "geodynamics.org/wsvn/cig/short/3D/PyLith/trunk/doc/install/"
+ The instructions can be accessed via the web interface into the PyLith
+ source repository
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/wsvn/cig/short/3D/PyLith/trunk/doc/install/
+\end_layout
+
\end_inset
.
@@ -357,7 +403,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:System-Requirements"
\end_inset
@@ -421,11 +468,16 @@
the package manager for your distribution.
The Mac OS X version of GCC is included in a software development suite
called Xcode.
- Xcode is available as a free download at the
-\begin_inset LatexCommand htmlurl
-name "Apple Developer Connection"
-target "developer.apple.com"
+ Xcode is available as a free download at the Apple Developer Connection
+
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+developer.apple.com
+\end_layout
+
\end_inset
.
@@ -517,11 +569,15 @@
\begin_layout Standard
Mac OS X 10.3 and later ships with a suitable version of Python preinstalled.
If you're using an older version of Mac OS X, or for more information in
- general, see
-\begin_inset LatexCommand htmlurl
-name "Python on the Mac"
-target "www.python.org/download/mac"
+ general, see Python on the Mac
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.python.org/download/mac
+\end_layout
+
\end_inset
at the Python web site.
@@ -627,11 +683,15 @@
\begin_layout Standard
If absolutely necessary, one can easily build Python from source using a
C compiler.
- You can download Python from the
-\begin_inset LatexCommand htmlurl
-name "Python website"
-target "www.python.org"
+ You can download Python from the Python website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.python.org
+\end_layout
+
\end_inset
.
@@ -670,14 +730,6 @@
\end_layout
\begin_layout Itemize
-Pyrex (v0.9.5.1)
-\end_layout
-
-\begin_layout Itemize
-pyrexembed (CIG version)
-\end_layout
-
-\begin_layout Itemize
Pythia* (v0.8.1.6 or later)
\end_layout
@@ -700,16 +752,23 @@
\begin_layout Standard
Dependencies marked with an asterisk (*) can be downloaded and installed
automatically.
- The source code for Nemesis, Pyrexembed, spatialdata, and PyLith package
- can all be downloaded from the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith/"
+ The source code for Nemesis, spatialdata, and PyLith package can all be
+ downloaded from the PyLith web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/short/pylith/
+\end_layout
+
\end_inset
.
- PyLith also has the following optional dependencies:
+ Whereas the SWIG generated Python and C++ sources files are included in
+ the source distribution, they are not in the PyLith repository, so building
+ from the source repository also requires SWIG.
+ PyLith also has the following optional dependencies:
\end_layout
\begin_layout Itemize
@@ -723,7 +782,8 @@
\begin_layout Standard
After successfully building and installing PyLith from source, you will
need to configure Pyre to launch parallel runs of PyLith (see Section
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "sec:Pyre-Configuration"
\end_inset
@@ -732,14 +792,16 @@
We strongly recommend downloading the latest PyLith and PETSc source code
directly from the source code repositories, instead of using the source
packages; see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Software-Repository"
\end_inset
later in this chapter.
Note that this requires additional tools; see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sub:Additional-Tools"
\end_inset
@@ -748,7 +810,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Installing-PETSc"
\end_inset
@@ -770,11 +833,15 @@
\begin_layout Standard
For general information about the development version of PETSc, visit the
-
-\begin_inset LatexCommand htmlurl
-name "PETSc Developers Site"
-target "www-unix.mcs.anl.gov/petsc/petsc-as/developers"
+ PETSc Developers Site
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www-unix.mcs.anl.gov/petsc/petsc-as/developers
+\end_layout
+
\end_inset
.
@@ -820,22 +887,31 @@
\shape default
/conf/make.log
\family default
-to
-\begin_inset LatexCommand url
-name "PETSc Maintenance Mailing List"
-target "petsc-maint at mcs.anl.gov"
+to PETSc Maintenance Mailing List
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+petsc-maint at mcs.anl.gov
+\end_layout
+
\end_inset
.
\end_layout
\begin_layout Standard
-For detailed information on installing PETSc, see the
-\begin_inset LatexCommand htmlurl
-name "PETSc Installation Docs"
-target "www-unix.mcs.anl.gov/petsc/petsc-as/documentation/installation.html"
+For detailed information on installing PETSc, see the PETSc Installation
+ Docs
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www-unix.mcs.anl.gov/petsc/petsc-as/documentation/installation.html
+\end_layout
+
\end_inset
.
@@ -857,11 +933,15 @@
\family typewriter
petsc-dev
\family default
- for PyLith from
-\begin_inset LatexCommand htmlurl
-name "PyLith PETSc tarball"
-target "geodynamics.org/cig/software/packages/short/pylith/petsc-dev-pylith-1_1_0.tgz"
+ for PyLith from PyLith PETSc tarball
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/short/pylith/petsc-dev-pylith-1_1_0.tgz
+\end_layout
+
\end_inset
.
@@ -873,7 +953,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf petsc-dev-pylith-1.3.1.tgz
+$ tar xzf petsc-dev-pylith-1.4.0.tgz
\end_layout
\begin_layout Standard
@@ -881,7 +961,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c petsc-dev-pylith-1.3.1.tgz | tar xf -
+$ gunzip -c petsc-dev-pylith-1.4.0.tgz | tar xf -
\end_layout
\begin_layout Standard
@@ -1444,11 +1524,15 @@
\begin_layout Standard
As with many other packages, to install nemesis, first download the source
- package available at the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith"
+ package available at the PyLith web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/short/pylith
+\end_layout
+
\end_inset
.
@@ -1467,11 +1551,15 @@
\end_layout
\begin_layout Standard
-Download Nemesis from the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith"
+Download Nemesis from the PyLith web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/short/pylith
+\end_layout
+
\end_inset
and unpack it using the
@@ -1511,11 +1599,15 @@
\family typewriter
make.log
\family default
- files to the
-\begin_inset LatexCommand url
-name "CIG Short-Term Crustal Dynamics Mailing List"
-target "cig-short at geodynamics.org"
+ files to the CIG Short-Term Crustal Dynamics Mailing List
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cig-short at geodynamics.org
+\end_layout
+
\end_inset
.
@@ -1551,9 +1643,13 @@
) to the directory containing the Nemesis source
\family typewriter
.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ cd nemesis-1.0
\end_layout
@@ -1565,9 +1661,13 @@
to configure the package for your system
\family typewriter
.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ ./configure --prefix=$HOME/cig
\end_layout
@@ -1579,9 +1679,13 @@
to build the package.
\family typewriter
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ make
\end_layout
@@ -1593,9 +1697,13 @@
to install the package.
\family typewriter
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ make install
\end_layout
@@ -1626,11 +1734,15 @@
\begin_layout Standard
As with many other packages, to install Proj.4, first download the source
- package available at the
-\begin_inset LatexCommand htmlurl
-name "PROJ.4 web page"
-target "trac.osgeo.org/proj"
+ package available at the PROJ.4 web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+trac.osgeo.org/proj
+\end_layout
+
\end_inset
.
@@ -1651,11 +1763,15 @@
\end_layout
\begin_layout Standard
-Download Proj.4 from the
-\begin_inset LatexCommand htmlurl
-name "Proj.4 website"
-target "trac.osgeo.org/proj"
+Download Proj.4 from the Proj.4 website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+trac.osgeo.org/proj
+\end_layout
+
\end_inset
.
@@ -1667,7 +1783,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf proj-4.6.0.tar.gz
+$ tar xzf proj-4.6.1.tar.gz
\end_layout
\begin_layout Standard
@@ -1675,7 +1791,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c proj-4.6.0.tar.gz | tar xf -
+$ gunzip -c proj-4.6.1.tar.gz | tar xf -
\end_layout
\begin_layout Standard
@@ -1691,9 +1807,16 @@
\end_layout
\begin_layout LyX-Code
-$ cd proj-4.6.0/nad$ unzip proj-datumgrid-1.4.zip
+$ cd proj-4.6.1/nad$ unzip proj-datumgrid-1.4.zip
\end_layout
+\begin_layout Standard
+Note: The Ubuntu Proj.4 package does not include the datum shifts due to
+ licensing issues.
+ Consequently, if you are using Ubuntu, we recommend that you build from
+ source with the datum shifts.
+\end_layout
+
\begin_layout Subsubsection
Proj.4 Installation Procedure
\end_layout
@@ -1710,10 +1833,14 @@
) to the directory containing the Proj.4 source
\family typewriter
.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-$ cd proj-4.6.0
+
+\begin_inset Newline newline
+\end_inset
+
+$ cd proj-4.6.1
\end_layout
\begin_layout Enumerate
@@ -1724,9 +1851,13 @@
to configure the package for your system
\family typewriter
.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ ./configure --prefix=$HOME/cig
\end_layout
@@ -1738,9 +1869,13 @@
to build the package.
\family typewriter
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ make
\end_layout
@@ -1752,9 +1887,13 @@
to install the package.
\family typewriter
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ make install
\end_layout
@@ -1787,11 +1926,15 @@
Numpy is written exclusively in Python, although it has some Python extension
modules.
As a result, its installation is relatively simple.
- First, download the source package available at the
-\begin_inset LatexCommand htmlurl
-name "SciPy.org web page"
-target "www.scipy.org/Download"
+ First, download the source package available at the SciPy.org web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.scipy.org/Download
+\end_layout
+
\end_inset
.
@@ -1803,11 +1946,15 @@
\end_layout
\begin_layout Standard
-Download Numpy from the
-\begin_inset LatexCommand htmlurl
-name "SciPy website"
-target "www.scipy.org"
+Download Numpy from the SciPy website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.scipy.org
+\end_layout
+
\end_inset
.
@@ -1819,7 +1966,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf numpy-1.0.4.tar.gz
+$ tar xzf numpy-1.3.0.tar.gz
\end_layout
\begin_layout Standard
@@ -1827,7 +1974,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c numpy-1.0.4.tar.gz | tar xf -
+$ gunzip -c numpy-1.3.0.tar.gz | tar xf -
\end_layout
\begin_layout Subsubsection
@@ -1846,10 +1993,14 @@
) to the directory containing the Numpy source
\family typewriter
.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-$ cd numpy-1.0.4
+
+\begin_inset Newline newline
+\end_inset
+
+$ cd numpy-1.3.0
\end_layout
\begin_layout Enumerate
@@ -1860,9 +2011,13 @@
to configure the package for your system
\family typewriter
.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ python setup.py install --prefix=$HOME/cig
\end_layout
@@ -1894,11 +2049,15 @@
\begin_layout Standard
FIAT is written exclusively in Python.
As a result, its installation is very simple.
- First, download the source package available at the
-\begin_inset LatexCommand htmlurl
-name "FENICS web page"
-target "www.fenics.org/wiki/Download"
+ First, download the source package available at the FENICS web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.fenics.org/wiki/Download
+\end_layout
+
\end_inset
.
@@ -1910,11 +2069,15 @@
\end_layout
\begin_layout Standard
-Download FIAT from the
-\begin_inset LatexCommand htmlurl
-name "FENICS website"
-target "www.fenics.org"
+Download FIAT from the FENICS website
+\begin_inset Flex URL
+status open
+\begin_layout Plain Layout
+
+www.fenics.org
+\end_layout
+
\end_inset
.
@@ -1953,122 +2116,17 @@
) to the directory containing the FIAT source
\family typewriter
.
-\newline
-
-\newline
-$ cd FIAT-0.3.4
-\end_layout
-
-\begin_layout Enumerate
-Run
-\family typewriter
-python setup.py install
-\family default
- to configure the package for your system
-\family typewriter
-.
-\newline
-
-\newline
-$ python setup.py install --prefix=$HOME/cig
-\end_layout
-
-\begin_layout Standard
-The above commands will install FIAT under
-\family typewriter
-$HOME/cig
-\family default
-.
- Afterwards, you may wish to add
-\family typewriter
-PREFIX/bin
-\family default
- (
-\family typewriter
-$HOME/cig/bin
-\family default
-, in this example) to your
-\family typewriter
-PATH
-\family default
-.
-\end_layout
-
-\begin_layout Subsection
-Installing Pyrex
-\end_layout
-
-\begin_layout Standard
-Pyrex is written exclusively in Python.
- As a result, its installation is very simple.
- First, download the source package available at the
-\begin_inset LatexCommand htmlurl
-name "Pyrex web page"
-target "www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex"
-
+\begin_inset Newline newline
\end_inset
-.
- Some recent releases of Pyrex are incompatible with PyLith.
- Release 0.9.5.1 is known to work with PyLith.
-\end_layout
-\begin_layout Subsubsection
-Downloading and Unpacking the Pyrex Source
-\end_layout
-
-\begin_layout Standard
-Download Pyrex 0.9.5.1 from the
-\begin_inset LatexCommand htmlurl
-name "Pyrex website"
-target "www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex"
-
+\begin_inset Newline newline
\end_inset
-.
- Click on the Previous Releases link to retrieve release 0.9.5.1.
- Download the source archive and unpack it using the
-\family typewriter
-tar
-\family default
- command:
+$ cd FIAT-0.3.4
\end_layout
-\begin_layout LyX-Code
-$ tar xzf Pyrex-0.9.5.1.1.tar.gz
-\end_layout
-
-\begin_layout Standard
-If you don't have GNU Tar, try the following command instead:
-\end_layout
-
-\begin_layout LyX-Code
-$ gunzip -c Pyrex-0.9.5.1.1.tar.gz | tar xf -
-\end_layout
-
-\begin_layout Subsubsection
-Pyrex Installation Procedure
-\end_layout
-
-\begin_layout Standard
-After unpacking the source, use the following procedure to install Pyrex:
-\end_layout
-
\begin_layout Enumerate
-Navigate (i.e.,
-\family typewriter
-cd
-\family default
-) to the directory containing the Pyrex source
-\family typewriter
-.
-\newline
-
-\newline
-$ cd Pyrex-0.9.5.1a
-\end_layout
-
-\begin_layout Enumerate
Run
\family typewriter
python setup.py install
@@ -2076,127 +2134,18 @@
to configure the package for your system
\family typewriter
.
-\newline
-
-\newline
-$ python setup.py install --prefix=$HOME/cig
-\end_layout
-
-\begin_layout Standard
-The above commands will install Pyrex under
-\family typewriter
-$HOME/cig
-\family default
-.
- Afterwards, you may wish to add
-\family typewriter
-PREFIX/bin
-\family default
- (
-\family typewriter
-$HOME/cig/bin
-\family default
-, in this example) to your
-\family typewriter
-PATH
-\family default
-.
-\end_layout
-
-\begin_layout Subsection
-Installing pyrexembed
-\end_layout
-
-\begin_layout Standard
-CIG distributes a customized version of
-\begin_inset LatexCommand htmlurl
-name "Pyrexembed"
-target "www.freenet.org.nz/python/pyrexembed"
-
+\begin_inset Newline newline
\end_inset
- that handles C++ exceptions.
- Pyrexembed is written exclusively in Python and its installation is very
- simple.
- First, download the source package available at the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith"
+\begin_inset Newline newline
\end_inset
-, unpack the source, and install the package.
-\end_layout
-
-\begin_layout Subsubsection
-Downloading and Unpacking the Pyrexembed Source
-\end_layout
-
-\begin_layout Standard
-Download Pyrexembed from the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith"
-
-\end_inset
-
- and unpack it using the
-\family typewriter
-tar
-\family default
- command:
-\end_layout
-
-\begin_layout LyX-Code
-$ tar xzf pyrexembed-1.0.tgz
-\end_layout
-
-\begin_layout Standard
-If you don't have GNU Tar, try the following command instead:
-\end_layout
-
-\begin_layout LyX-Code
-$ gunzip -c pyrexembed-1.0.tgz | tar xf -
-\end_layout
-
-\begin_layout Subsubsection
-Pyrexembed Installation Procedure
-\end_layout
-
-\begin_layout Standard
-After unpacking the source, use the following procedure to install Pyrexembed:
-\end_layout
-
-\begin_layout Enumerate
-Navigate (i.e.,
-\family typewriter
-cd
-\family default
-) to the directory containing the Pyrexembed source
-\family typewriter
-.
-\newline
-
-\newline
-$ cd pyrexembed-1.0
-\end_layout
-
-\begin_layout Enumerate
-Run
-\family typewriter
-python setup.py install
-\family default
- to configure the package for your system
-\family typewriter
-.
-\newline
-
-\newline
$ python setup.py install --prefix=$HOME/cig
\end_layout
\begin_layout Standard
-The above commands will install Pyrexembed under
+The above commands will install FIAT under
\family typewriter
$HOME/cig
\family default
@@ -2222,11 +2171,15 @@
\begin_layout Standard
As with many other packages, to install Spatialdata, first download the
- source package available at the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith"
+ source package available at the PyLith web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/short/pylith
+\end_layout
+
\end_inset
.
@@ -2244,11 +2197,15 @@
\end_layout
\begin_layout Standard
-Download Spatialdata from the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith"
+Download Spatialdata from the PyLith web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/short/pylith
+\end_layout
+
\end_inset
and unpack it using the
@@ -2259,7 +2216,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf spatialdata-0.4.tgz
+$ tar xzf spatialdata-0.5.tgz
\end_layout
\begin_layout Standard
@@ -2267,7 +2224,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c spatialdata-0.4.tgz | tar xf -
+$ gunzip -c spatialdata-0.5.tgz | tar xf -
\end_layout
\begin_layout Subsubsection
@@ -2288,11 +2245,15 @@
\family typewriter
make.log
\family default
- files to the
-\begin_inset LatexCommand url
-name "CIG Short-Term Crustal Dynamics Mailing List"
-target "cig-short at geodynamics.org"
+ files to the CIG Short-Term Crustal Dynamics Mailing List
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cig-short at geodynamics.org
+\end_layout
+
\end_inset
.
@@ -2328,9 +2289,13 @@
) to the directory containing the Spatialdata source
\family typewriter
.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ cd spatialdata
\end_layout
@@ -2342,19 +2307,14 @@
to configure the package for your system
\family typewriter
.
-
-\family default
-Note that PyLith requires Spatialdata to be configured with the
-\family typewriter
---enable-pythia
-\family default
- flag
-\family typewriter
-.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-$ ./configure --enable-pythia --prefix=$HOME/cig
+
+\begin_inset Newline newline
+\end_inset
+
+$ ./configure --prefix=$HOME/cig
\end_layout
\begin_layout Enumerate
@@ -2365,9 +2325,13 @@
to build the package.
\family typewriter
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ make
\end_layout
@@ -2379,9 +2343,13 @@
to install the package.
\family typewriter
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ make install
\end_layout
@@ -2407,7 +2375,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Installing-PyLith"
\end_inset
@@ -2416,11 +2385,16 @@
\end_layout
\begin_layout Standard
-To install PyLith, download the source package available at the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith"
+To install PyLith, download the source package available at the PyLith web
+ page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/short/pylith
+\end_layout
+
\end_inset
.
@@ -2439,11 +2413,15 @@
\end_layout
\begin_layout Standard
-Download PyLith from the
-\begin_inset LatexCommand htmlurl
-name "PyLith web page"
-target "geodynamics.org/cig/software/packages/short/pylith"
+Download PyLith from the PyLith web page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/short/pylith
+\end_layout
+
\end_inset
and unpack it using the
@@ -2454,7 +2432,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf pylith-1.3.1.tgz
+$ tar xzf pylith-1.4.0.tgz
\end_layout
\begin_layout Standard
@@ -2462,7 +2440,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c pylith-1.3.1.tgz | tar xf -
+$ gunzip -c pylith-1.4.0.tgz | tar xf -
\end_layout
\begin_layout Subsubsection
@@ -2483,11 +2461,15 @@
\family typewriter
make.log
\family default
- files to the
-\begin_inset LatexCommand url
-name "CIG Short-Term Crustal Dynamics Mailing List"
-target "cig-short at geodynamics.org"
+ files to the CIG Short-Term Crustal Dynamics Mailing List
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cig-short at geodynamics.org
+\end_layout
+
\end_inset
.
@@ -2523,10 +2505,14 @@
) to the directory containing the PyLith source
\family typewriter
.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
-$ cd pylith-1.3.1
+
+\begin_inset Newline newline
+\end_inset
+
+$ cd pylith-1.4.0
\end_layout
\begin_layout Enumerate
@@ -2537,9 +2523,13 @@
to configure the package for your system
\family typewriter
.
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ ./configure --prefix=$HOME/cig
\end_layout
@@ -2551,9 +2541,13 @@
to build the package.
\family typewriter
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ make
\end_layout
@@ -2565,9 +2559,13 @@
to install the package.
\family typewriter
-\newline
+\begin_inset Newline newline
+\end_inset
-\newline
+
+\begin_inset Newline newline
+\end_inset
+
$ make install
\end_layout
@@ -2611,7 +2609,8 @@
configure
\family default
, see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Configuration"
\end_inset
@@ -2632,7 +2631,8 @@
\end_layout
\begin_layout Subsubsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Configuration"
\end_inset
@@ -2705,11 +2705,15 @@
\family typewriter
configure
\family default
- failures on the
-\begin_inset LatexCommand url
-name "CIG Short-Term Crustal Dynamics Mailing List"
-target "cig-short at geodynamics.org"
+ failures on the CIG Short-Term Crustal Dynamics Mailing List
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cig-short at geodynamics.org
+\end_layout
+
\end_inset
, please send
@@ -2818,19 +2822,19 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
<features>
-<column alignment="center" valignment="top" leftline="true" width="1in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="3.5in">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="center" valignment="top" width="1in">
+<column alignment="left" valignment="top" width="3.5in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Variable
@@ -2838,10 +2842,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Description
@@ -2850,11 +2854,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
CXX
\end_layout
@@ -2863,18 +2867,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
C++ compiler
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
PYTHON
\end_layout
@@ -2883,37 +2887,59 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Python interpreter.
This is useful if you have Python installed in a non-standard location,
e.g.,
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
-\InsetSpace ~
-\InsetSpace ~
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
./configure
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
PYTHON=/opt/python2.3/bin/python
\family default
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
By default,
\family typewriter
configure
@@ -2928,11 +2954,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
PETSC_DIR
\end_layout
@@ -2941,27 +2967,27 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
PETSc installation/build directory.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
PETSC_ARCH
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
(optional) PETSc configuration tag.
If not specified,
\family typewriter
@@ -2999,7 +3025,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Pyre-Configuration"
\end_inset
@@ -3116,7 +3143,8 @@
\end_layout
\begin_layout Subsubsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sub:Launchers-and-Schedulers"
\end_inset
@@ -3486,18 +3514,23 @@
\begin_layout Standard
For more information on configuring Pyre for your batch system, see CIG's
-
-\begin_inset LatexCommand htmlurl
-name "Pythia page"
-target "geodynamics.org/cig/software/packages/cs/pythia"
+ Pythia page
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/packages/cs/pythia
+\end_layout
+
\end_inset
.
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Software-Repository"
\end_inset
@@ -3506,11 +3539,15 @@
\end_layout
\begin_layout Standard
-The PyLith source code is available via the
-\begin_inset LatexCommand htmlurl
-name "CIG Subversion Repository"
-target "geodynamics.org/cig/software/Repository/"
+The PyLith source code is available via the CIG Subversion Repository
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+geodynamics.org/cig/software/Repository/
+\end_layout
+
\end_inset
.
@@ -3534,7 +3571,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sub:Additional-Tools"
\end_inset
@@ -3560,6 +3598,10 @@
GNU Autotools (Autoconf, Automake, and Libtool)
\end_layout
+\begin_layout Itemize
+SWIG (1.3.33 or later)
+\end_layout
+
\begin_layout Subsubsection
Subversion
\end_layout
@@ -3587,11 +3629,15 @@
\end_layout
\begin_layout Standard
-For more information on Subversion, visit the
-\begin_inset LatexCommand htmlurl
-name "Subversion website"
-target "subversion.tigris.org"
+For more information on Subversion, visit the Subversion website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+subversion.tigris.org
+\end_layout
+
\end_inset
.
@@ -3605,11 +3651,16 @@
To check out the PETSc source, you must have Mercurial 0.9 or later installed.
You will likely have to build Mercurial from source, but this is a very
easy task that takes only a couple of minutes.
- To learn how to download and install Mercurial, visit the
-\begin_inset LatexCommand htmlurl
-name "Mercurial web site"
-target "www.selenic.com/mercurial"
+ To learn how to download and install Mercurial, visit the Mercurial web
+ site
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.selenic.com/mercurial
+\end_layout
+
\end_inset
.
@@ -3638,11 +3689,15 @@
\end_layout
\begin_layout Standard
-For more information about these GNU tools, see the
-\begin_inset LatexCommand htmlurl
-name "GNU website"
-target "www.gnu.org/software"
+For more information about these GNU tools, see the GNU website
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.gnu.org/software
+\end_layout
+
\end_inset
.
@@ -3805,7 +3860,8 @@
\begin_layout Standard
You are now ready to install PETSc as described in Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Installing-PETSc"
\end_inset
@@ -3878,7 +3934,8 @@
autoreconf
\family default
, install PyLith as described in Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Installing-PyLith"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 1
@@ -70,7 +73,8 @@
atic) and explicit (dynamic) problems and was a complete rewrite of the
original PyLith.
PyLith 1.0 combines the functionality of EqSim
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Aagaard:etal:2001a,Aagaard:etal:2001b"
\end_inset
@@ -92,8 +96,8 @@
the number of features as well as improve performance.
The PyLith 1.x series of releases allows the solution of both quasi-static
and dynamic problems in one, two, or three dimensions.
- The code runs in either serial or parallel mode, and the design allows
- for relatively easy scripting using the Python programming language.
+ The code runs in either serial or parallel, and the design allows for relativel
+y easy scripting using the Python programming language.
Material properties and values for boundary and fault conditions are specified
using spatial databases, which permit easy prescription of complex spatial
variations of properties and parameters.
@@ -108,9 +112,10 @@
possible to create a quadratic mesh from the linear meshes provided by
most meshing packages.
Materials presently available include isotropic elastic, linear Maxwell
- viscoelastic (3D only), and generalized Maxwell viscoelastic (3D only).
+ viscoelastic (3D only), generalized Maxwell viscoelastic (3D only), and
+ power-law viscoelastic (3D only).
Boundary conditions include Dirichlet (prescribed displacements and velocities)
-, Neumann (traction), and absorbing boundaries.
+, Neumann (traction), point forces, and absorbing boundaries.
Cohesive elements are used to implement slip across interior surfaces (faults).
At present, only kinematically-specified fault slip is available.
In the near future, we will provide several constitutive models for cohesive
@@ -122,11 +127,10 @@
PyLith is under active development and we expect a number of additions and
improvements in the near future.
Likely enhancements will include fault constitutive models with cohesive
- (fault) cells, integration with PETSc's nonlinear solvers, additional bulk
- constitutive models, automatic generation of higher-order elements from
- linear elements, and the generation of Green's functions to be used in
- inversions.
- Several of these features should be available by Jan 2009.
+ (fault) cells, additional bulk constitutive models, automatic generation
+ of higher-order elements from linear elements, and the generation of Green's
+ functions to be used in inversions.
+ Several of these features should be available by Jan 2010.
\end_layout
\begin_layout Section
@@ -136,7 +140,8 @@
\begin_layout Standard
PyLith is one component in the process of investigating problems in tectonics
(Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Workflow-summary"
\end_inset
@@ -162,7 +167,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/workflow.eps
@@ -174,11 +179,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Workflow-summary"
\end_inset
@@ -206,7 +212,8 @@
This allows expert users to replace functionality of a wide variety of
components without recompiling or polluting the main code.
PyLith employs external packages (see Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:pylith-dependencies"
\end_inset
@@ -224,7 +231,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/packages.eps
@@ -235,8 +242,9 @@
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:pylith-dependencies"
\end_inset
@@ -269,8 +277,9 @@
This low-level code relies on PETSc to perform operations on matrices and
vectors in parallel.
We also make extensive use of two Python packages.
- Pyrex is a package that simplifies the task of adding C extensions to Python
- code, and pyrexembed extends Pyrex to handle C++ code.
+ SWIG is a package that simplifies the task of adding C++ extensions to
+ Python code, and FIAT provides tabulated basis functions and numerical
+ quadrature points.
\end_layout
\begin_layout Standard
@@ -289,7 +298,7 @@
The new code design leverages Pyre, Sieve, and PETSc much more extensively
than the previous version.
Pyre is used to glue together the various modules used to construct a
- simulation and specify the parameters.
+ simulation and specify the parameters.
Sieve is used for all finite-element storage and manipulation and handles
the creation of the PETSc matrices and vectors.
As a result, most of the PyLith source code pertains to implementing the
@@ -303,14 +312,14 @@
Nemesis allows PyLith to run Python using the Message Passing Interface
(MPI) for parallel processing.
Additional, indirect dependencies (see Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:pylith-dependencies"
\end_inset
) include numpy (efficient operations on numerical arrays in Python), Proj.4
- (geographic projections), and Pyrex/Pyrexembed (calling C and C++ functions
- from Python).
+ (geographic projections), and SWIG (calling C++ functions from Python).
\end_layout
\begin_layout Standard
@@ -326,7 +335,8 @@
Additionally, we have run the Southern California Earthquake Center crustal
deformation benchmarks for strike-slip and reverse-slip to determine the
relative local and global error (see Chapter
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Benchmarks"
\end_inset
@@ -357,7 +367,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/pyre_overview.png
@@ -368,10 +378,10 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Pyre Architecture.
The integration framework is a set of cooperating abstract services.
\end_layout
@@ -473,10 +483,15 @@
\end_layout
\begin_layout Standard
-\begin_inset LatexCommand htmlurl
-name "PETSc"
-target "www-unix.mcs.anl.gov/petsc/petsc-as"
+PETSc
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www-unix.mcs.anl.gov/petsc/petsc-as
+\end_layout
+
\end_inset
, the Portable, Extensible Toolkit for Scientific computation, provides
Modified: short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\newcommand\Prefix[3]{\vphantom{#3}#1#2#3}
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 1
@@ -47,7 +50,8 @@
\begin_body
\begin_layout Chapter
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "cha:material:models"
\end_inset
@@ -59,7 +63,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
\backslash
@@ -156,13 +160,15 @@
If a set of material groups is not specified, a single material model is
used for the entire problem.
See Sections
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Tutorial-3d-hex8"
\end_inset
and
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Tutorial-3d-tet4"
\end_inset
@@ -190,11 +196,16 @@
\end_layout
\begin_layout Description
-db Spatial database specifying the spatial variation in the parameters of
- the bulk constitutive model (default is a SimpleDB).
+db_properties Spatial database specifying the spatial variation in the parameter
+s of the bulk constitutive model (default is a SimpleDB).
\end_layout
\begin_layout Description
+db_initial_state Spatial database specifying the spatial variation in the
+ initial variables (default is none).
+\end_layout
+
+\begin_layout Description
output The output manager used for outputting material information.
\end_layout
@@ -250,14 +261,10 @@
\end_layout
\begin_layout LyX-Code
-db.iohandler.filename = mat_elastic.spatialdb
+db_properties.iohandler.filename = mat_elastic.spatialdb
\end_layout
\begin_layout LyX-Code
-quadrature = pylith.feassemble.quadrature.Quadrature3D
-\end_layout
-
-\begin_layout LyX-Code
quadrature.cell = pylith.feassemble.FIATLagrange
\end_layout
@@ -282,14 +289,10 @@
\end_layout
\begin_layout LyX-Code
-db.iohandler.filename = mat_viscoelastic.spatialdb
+db_properties.iohandler.filename = mat_viscoelastic.spatialdb
\end_layout
\begin_layout LyX-Code
-quadrature = pylith.feassemble.quadrature.Quadrature3D
-\end_layout
-
-\begin_layout LyX-Code
quadrature.cell = pylith.feassemble.FIATLagrange
\end_layout
@@ -303,7 +306,8 @@
Section
\family default
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Tutorial-3d-hex8"
\end_inset
@@ -322,7 +326,8 @@
Refer to the discussion of each material model to find the parameters that
must be specified in the spatial database.
Appendix
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Spatialdata:SimpleIOAscii"
\end_inset
@@ -343,11 +348,11 @@
\end_layout
\begin_layout LyX-Code
-cell_filter = pylith.meshio.CellFilterAvg
+cell_filter = pylith.meshio.CellFilterAvgMesh
\end_layout
\begin_layout LyX-Code
-writer.filename = dislocation-statevars-upper.vtk
+writer.filename = dislocation-elastic.vtk
\end_layout
\begin_layout LyX-Code
@@ -359,11 +364,11 @@
\end_layout
\begin_layout LyX-Code
-cell_filter = pylith.meshio.CellFilterAvg
+cell_filter = pylith.meshio.CellFilterAvgMesh
\end_layout
\begin_layout LyX-Code
-writer.filename = dislocation-statevars-lower.vtk
+writer.filename = dislocation-viscoelastic.vtk
\end_layout
\begin_layout Standard
@@ -372,7 +377,8 @@
Section
\family default
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Tutorial-3d-hex8"
\end_inset
@@ -415,7 +421,8 @@
see Section
\family default
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Tutorial-Two-hexahedra"
\end_inset
@@ -438,7 +445,8 @@
\begin_layout Standard
The properties and state variable available for output in each material
model are listed in Table
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "tab:material-model-output"
\end_inset
@@ -446,7 +454,8 @@
.
The order of the state variables in the output arrays is given in Table
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "tab:material-model-statevars"
\end_inset
@@ -468,12 +477,13 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "tab:material-model-output"
\end_inset
@@ -495,16 +505,16 @@
\begin_inset Tabular
-<lyxtabular version="3" rows="4" columns="3">
+<lyxtabular version="3" rows="5" columns="3">
<features>
-<column alignment="center" valignment="top" leftline="true" width="1.5in">
-<column alignment="center" valignment="top" leftline="true" width="1.5in">
-<column alignment="center" valignment="top" leftline="true" rightline="true" width="1.5in">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="center" valignment="top" width="1.5in">
+<column alignment="center" valignment="top" width="1.5in">
+<column alignment="center" valignment="top" width="1.5in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Model
@@ -512,10 +522,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Physical Properties
@@ -523,10 +533,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
State Variables
@@ -535,11 +545,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Elastic
\end_layout
@@ -548,7 +558,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
mu, lambda, density
\end_layout
@@ -557,18 +567,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
total_strain, stress
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Maxwell Viscoelastic
\end_layout
@@ -577,7 +587,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
mu, lambda, density, maxwell_time
\end_layout
@@ -586,18 +596,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
total_strain, viscous_strain, stress
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Generalized Maxwell Viscoelastic
\end_layout
@@ -606,7 +616,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
mu, lambda, density, shear_ratio, maxwell_time
\end_layout
@@ -615,13 +625,42 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
total_strain, viscous_strain, stress
\end_layout
\end_inset
</cell>
</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Power-law
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
</lyxtabular>
\end_inset
@@ -638,12 +677,13 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "tab:material-model-statevars"
\end_inset
@@ -657,15 +697,15 @@
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="4">
<features>
-<column alignment="center" valignment="top" leftline="true" width="1.25in">
-<column alignment="center" valignment="top" leftline="true" width="0.5in">
-<column alignment="center" valignment="top" leftline="true" rightline="true" width="1.25in">
-<column alignment="center" valignment="top" rightline="true" width="2.25in">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="center" valignment="top" width="1.25in">
+<column alignment="center" valignment="top" width="0.5in">
+<column alignment="center" valignment="top" width="1.25in">
+<column alignment="center" valignment="top" width="2.25in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
State Variable
@@ -673,10 +713,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
1D
@@ -684,10 +724,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
2D
@@ -695,10 +735,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
3D
@@ -707,11 +747,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
total_strain, viscous_strain
\end_layout
@@ -720,8 +760,8 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
-\begin_inset Formula $\epsilon_{11}$
+\begin_layout Plain Layout
+\begin_inset Formula $\epsilon_{xx}$
\end_inset
@@ -732,16 +772,16 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
-\begin_inset Formula $\epsilon_{11}$
+\begin_layout Plain Layout
+\begin_inset Formula $\epsilon_{xx}$
\end_inset
,
-\begin_inset Formula $\epsilon_{22}$
+\begin_inset Formula $\epsilon_{yy}$
\end_inset
,
-\begin_inset Formula $\epsilon_{12}$
+\begin_inset Formula $\epsilon_{xy}$
\end_inset
@@ -749,31 +789,31 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
-\begin_inset Formula $\epsilon_{11}$
+\begin_layout Plain Layout
+\begin_inset Formula $\epsilon_{xx}$
\end_inset
,
-\begin_inset Formula $\epsilon_{22}$
+\begin_inset Formula $\epsilon_{yy}$
\end_inset
,
-\begin_inset Formula $\epsilon_{33}$
+\begin_inset Formula $\epsilon_{zz}$
\end_inset
,
-\begin_inset Formula $\epsilon_{12}$
+\begin_inset Formula $\epsilon_{xy}$
\end_inset
,
-\begin_inset Formula $\epsilon_{23}$
+\begin_inset Formula $\epsilon_{yz}$
\end_inset
,
-\begin_inset Formula $\epsilon_{13}$
+\begin_inset Formula $\epsilon_{xz}$
\end_inset
@@ -782,21 +822,21 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
stress
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
-\begin_inset Formula $\sigma_{11}$
+\begin_layout Plain Layout
+\begin_inset Formula $\sigma_{xx}$
\end_inset
@@ -804,19 +844,19 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
-\begin_inset Formula $\sigma_{11}$
+\begin_layout Plain Layout
+\begin_inset Formula $\sigma_{xx}$
\end_inset
,
-\begin_inset Formula $\sigma_{22}$
+\begin_inset Formula $\sigma_{yy}$
\end_inset
,
-\begin_inset Formula $\sigma_{12}$
+\begin_inset Formula $\sigma_{xy}$
\end_inset
@@ -824,31 +864,31 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
-\begin_inset Formula $\sigma_{11}$
+\begin_layout Plain Layout
+\begin_inset Formula $\sigma_{xx}$
\end_inset
,
-\begin_inset Formula $\sigma_{22}$
+\begin_inset Formula $\sigma_{yy}$
\end_inset
,
-\begin_inset Formula $\sigma_{33}$
+\begin_inset Formula $\sigma_{zz}$
\end_inset
,
-\begin_inset Formula $\sigma_{12}$
+\begin_inset Formula $\sigma_{xy}$
\end_inset
,
-\begin_inset Formula $\sigma_{23}$
+\begin_inset Formula $\sigma_{yz}$
\end_inset
,
-\begin_inset Formula $\sigma_{13}$
+\begin_inset Formula $\sigma_{xz}$
\end_inset
@@ -961,12 +1001,12 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Values in spatial database used as parameters in the elastic material constituti
ve models.
\end_layout
@@ -977,13 +1017,13 @@
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
<features>
-<column alignment="center" valignment="middle" leftline="true" rightline="true" width="0.85in">
-<column alignment="center" valignment="middle" leftline="true" rightline="true" width="2.47in">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="center" valignment="middle" width="0.85in">
+<column alignment="center" valignment="middle" width="2.47in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Parameter
@@ -991,10 +1031,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\series bold
@@ -1004,11 +1044,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Formula $v_{p}$
\end_inset
@@ -1020,7 +1060,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
Vp
@@ -1029,11 +1069,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Formula $v_{s}$
\end_inset
@@ -1045,7 +1085,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
Vs
@@ -1054,11 +1094,11 @@
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Formula $\rho$
\end_inset
@@ -1067,10 +1107,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
density
@@ -1310,13 +1350,15 @@
\begin_layout Standard
At present, there are two viscoelastic material models available in PyLith,
with at least one additional model planned for the near future (Table
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "tab:Material-models-available"
\end_inset
and Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Material-models"
\end_inset
@@ -1337,13 +1379,14 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "tab:Material-models-available"
\end_inset
@@ -1357,14 +1400,14 @@
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="3">
<features>
-<column alignment="center" valignment="top" leftline="true" rightline="true" width="0.68in">
-<column alignment="left" valignment="top" leftline="true" rightline="true" width="2.85in">
-<column alignment="center" valignment="top" leftline="true" rightline="true" width="2.47in">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="center" valignment="top" width="0.68in">
+<column alignment="left" valignment="top" width="2.85in">
+<column alignment="center" valignment="top" width="2.47in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Available?
@@ -1372,10 +1415,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Model Name
@@ -1383,10 +1426,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Description
@@ -1395,20 +1438,20 @@
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Yes
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
MaxwellIsotropic3D
\end_layout
@@ -1417,27 +1460,27 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Isotropic Maxwell material with linear viscous rheology
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Yes
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
GenMaxwellIsotropic3D
\end_layout
@@ -1446,36 +1489,36 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Generalized model consisting of 3 Maxwell models in parallel
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
-No
+\begin_layout Plain Layout
+Yes
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
-PowerLawMaxwellIsotropic3D
+\begin_layout Plain Layout
+PowerLaw3D
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Isotropic Maxwell material with power-law viscous rheology
\end_layout
@@ -1503,7 +1546,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/pylith-materials.ai
@@ -1514,9 +1557,10 @@
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:Material-models"
\end_inset
@@ -1557,7 +1601,8 @@
\begin_layout Standard
In the following sections, we use a combination of vector and index notation
(our notation conventions are shown in Table
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "tab:Mathematical-notation"
\end_inset
@@ -1644,7 +1689,8 @@
\end_inset
) in Equation
-\begin_inset LatexCommand vpageref
+\begin_inset CommandInset ref
+LatexCommand vpageref
reference "eq:5"
\end_inset
@@ -1674,13 +1720,14 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "tab:Mathematical-notation"
\end_inset
@@ -1694,43 +1741,43 @@
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="3">
<features>
-<column alignment="center" valignment="top" leftline="true" width="0">
-<column alignment="center" valignment="top" leftline="true" width="0">
-<column alignment="center" valignment="top" leftline="true" rightline="true" width="0">
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="0">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Index notation
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Vector notation
\end_layout
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Description
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Formula $a_{i}$
\end_inset
@@ -1742,7 +1789,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Formula $\overrightarrow{a}$
\end_inset
@@ -1754,18 +1801,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Vector field a
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Formula $a_{ij}$
\end_inset
@@ -1774,10 +1821,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Formula $\underline{a}$
\end_inset
@@ -1786,10 +1833,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Second order tensor field a
\end_layout
@@ -1816,7 +1863,8 @@
The generalized Maxwell viscoelastic model consists of a number of Maxwell
linear viscoelastic models in parallel with a spring, as shown in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Material-models"
\end_inset
@@ -1830,13 +1878,15 @@
the Kelvin model, and the standard linear solid.
We follow formulations similar to those used by Zienkiewicz and Taylor
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Zienkiewicz:Taylor:2000"
\end_inset
and Taylor
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Taylor:2003"
\end_inset
@@ -1950,7 +2000,8 @@
\end_inset
With the form in Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:23"
\end_inset
@@ -1985,7 +2036,8 @@
at time zero, and the last term covers the subsequent history of strain.
Applying this separation to Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:22"
\end_inset
@@ -2001,13 +2053,15 @@
\begin_layout Standard
Substituting Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:25"
\end_inset
into
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:28"
\end_inset
@@ -2096,7 +2150,8 @@
where the second derivative on the right may be easily deduced from Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:16"
\end_inset
@@ -2114,13 +2169,15 @@
is the identity matrix.
From Equations
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:33"
\end_inset
through
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:35"
\end_inset
@@ -2153,15 +2210,16 @@
\begin_layout Standard
As an alternative to the approach outlined above, an effective stress function
formulation
-\begin_inset LatexCommand cite
+\begin_inset CommandInset citation
+LatexCommand cite
key "Kojic:Bathe:1987"
\end_inset
may be employed for both a linear Maxwell model and a power-law Maxwell
model.
- Note that this formulation is not presently employed for either linear
- or power-law models in PyLith 1.3, but it may be employed in future versions.
+ Note that this formulation is not presently employed for linear
+ viscoelastic models, but it may be employed in future versions.
For the viscoelastic materials considered here, the viscous volumetric
strains are zero (incompressible flow), and it is convenient to separate
the general stress-strain relationship at time
@@ -2214,7 +2272,8 @@
, respectively.
The topmost equation in Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:42"
\end_inset
@@ -2300,25 +2359,29 @@
\end_inset
Substituting Equations
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:46"
\end_inset
,
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:50"
\end_inset
, and
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:51"
\end_inset
into
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:43"
\end_inset
@@ -2381,7 +2444,8 @@
\end_inset
From Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:44"
\end_inset
@@ -2393,7 +2457,8 @@
\end_inset
and from Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:16"
\end_inset
@@ -2409,7 +2474,8 @@
\end_inset
Finally, from Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:53"
\end_inset
@@ -2421,7 +2487,8 @@
\end_inset
From Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:57"
\end_inset
@@ -2486,7 +2553,8 @@
\end_inset
This is consistent with the regular elasticity matrix, and Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:63"
\end_inset
@@ -2532,25 +2600,29 @@
\end_inset
substituting Equations
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:46"
\end_inset
,
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:65"
\end_inset
, and
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:66"
\end_inset
into
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:43"
\end_inset
@@ -2583,7 +2655,8 @@
\end_inset
Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:69"
\end_inset
@@ -2596,19 +2669,22 @@
-- 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 Equations
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:65"
\end_inset
and
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:66"
\end_inset
, and the total stresses may be found from Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:54"
\end_inset
@@ -2619,14 +2695,16 @@
\begin_layout Standard
To compute the tangent stress-strain relation, we proceed as for the linear
case, but the evaluation of the first derivative in Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:58"
\end_inset
is more complicated.
We begin by rewriting Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:68"
\end_inset
@@ -2651,7 +2729,8 @@
\end_inset
From Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:66"
\end_inset
@@ -2669,7 +2748,8 @@
\end_inset
which allows us to rewrite Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:69"
\end_inset
@@ -2705,20 +2785,23 @@
, this derivative is zero.
This relation may be used in Equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:73"
\end_inset
.
Then, using Equations
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:57"
\end_inset
through
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:60"
\end_inset
@@ -2768,7 +2851,8 @@
\begin_layout Standard
To compute the zero of the effective stress function using Newton's method,
we require the derivative of equation
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "eq:69"
\end_inset
@@ -2833,7 +2917,8 @@
flag must be set to true and a spatial database with values the initial
stress tensor provided as in this example from the tutorial in Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Tutorial-3d-hex8"
\end_inset
@@ -2846,10 +2931,6 @@
\end_layout
\begin_layout LyX-Code
-use_initial_state = True
-\end_layout
-
-\begin_layout LyX-Code
initial_state_db.iohandler.filename = initial_state.spatialdb
\end_layout
Modified: short/3D/PyLith/trunk/doc/userguide/preface.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/preface.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/preface.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -152,13 +152,13 @@
Williams.
\emph on
-PyLith User Manual, Version 1.3.
+PyLith User Manual, Version 1.4.
\emph default
Pasadena, CA: Computational Infrastructure of Geodynamics, 2008.
URL: geodynamics.org/cig/software/
\newline
-short/pylith/pylith_book-1.3.pdf
+short/pylith/pylith_book-1.4.pdf
\end_layout
\begin_layout Section
Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 1
@@ -77,20 +80,23 @@
and output (for subsets of the mesh).
This information can be provided using the PyLith mesh ASCII format (see
Chapter
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Tutorials"
\end_inset
for examples and Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:MeshIOAscii"
\end_inset
for the format specification) or by importing the information from the
LaGriT or CUBIT meshing packages (see Chapter
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Tutorials"
\end_inset
@@ -104,13 +110,15 @@
Arbitrarily complex spatial variations in boundary and fault conditions
and material properties may be given in the spatial database (see Chapter
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Tutorials"
\end_inset
for examples and Appendix
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Spatialdata:SimpleIOAscii"
\end_inset
@@ -119,7 +127,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:setting:parameters"
\end_inset
@@ -533,9 +542,13 @@
[pylithapp.petsc]
\family default
.
- The ones of primary interest in the case of PyLith are shown in Table\InsetSpace ~
+ The ones of primary interest in the case of PyLith are shown in Table
+\begin_inset space ~
+\end_inset
-\begin_inset LatexCommand ref
+
+\begin_inset CommandInset ref
+LatexCommand ref
reference "tab:petsc:options:defaults"
\end_inset
@@ -543,11 +556,15 @@
.
In many quasi-static or dynamic elasticity simulations, runtime can be
reduced by replacing the Jacobi preconditioner with Additive Schwartz with
- Gram-Schmidt orthogonalization (see Table\InsetSpace ~
+ Gram-Schmidt orthogonalization (see Table
+\begin_inset space ~
+\end_inset
-\begin_inset LatexCommand ref
-reference "tab:petsc:options:quasistatic"
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "tab:petsc:options:recommended"
+
\end_inset
).
@@ -562,12 +579,13 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "tab:petsc:options:defaults"
\end_inset
@@ -581,14 +599,14 @@
\begin_inset Tabular
<lyxtabular version="3" rows="6" columns="3">
<features>
-<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">
+<column alignment="left" valignment="top" width="0.9in">
+<column alignment="center" valignment="middle" width="0.8in">
+<column alignment="left" valignment="top" width="4in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Property
@@ -596,10 +614,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Default Value
@@ -607,10 +625,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Description
@@ -619,11 +637,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
log_summary
@@ -634,7 +652,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\shape italic
false
@@ -645,18 +663,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Print logging objects and events.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
ksp_monitor
@@ -667,7 +685,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
false
\end_layout
@@ -676,18 +694,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Dump preconditioned residual norm to stdout.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
ksp_view
@@ -698,7 +716,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
false
\end_layout
@@ -707,7 +725,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Print linear solver parameters.
\end_layout
@@ -715,11 +733,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
ksp_rtol
@@ -730,7 +748,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\shape italic
1.0e-05
@@ -741,18 +759,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Convergence tolerance for relative decrease in residual norm.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
pc_type
@@ -760,10 +778,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\shape italic
jacobi
@@ -771,10 +789,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Set preconditioner type to block Jacobi.
See PETSc documentation for a list of all preconditioner types.
@@ -799,13 +817,14 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "tab:petsc:options:quasistatic"
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
+name "tab:petsc:options:recommended"
\end_inset
@@ -817,16 +836,16 @@
\begin_inset Tabular
-<lyxtabular version="3" rows="5" columns="3">
+<lyxtabular version="3" rows="7" columns="3">
<features>
-<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">
+<column alignment="left" valignment="top" width="0.9in">
+<column alignment="center" valignment="middle" width="0.8in">
+<column alignment="left" valignment="top" width="4in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Property
@@ -834,10 +853,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Value
@@ -845,10 +864,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Description
@@ -857,11 +876,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
pc_type
@@ -872,7 +891,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\shape italic
asm
@@ -883,20 +902,84 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
-Additive Schwarz method
+\begin_layout Plain Layout
+Additive Schwarz method.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
+sub_pc_factor_shift_positive_definite
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\shape italic
+0
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Turn off positive definite shifting.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+sub_pc_factor_shift_nonzero
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+n/a
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Turn on nonzero shifting.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
ksp_max_it
\end_layout
@@ -905,7 +988,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\emph on
100
@@ -916,18 +999,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Maximum number of iterations.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
ksp_gmres_restart
@@ -938,7 +1021,7 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
50
\end_layout
@@ -947,18 +1030,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
-Number of iterations after which Gram-Schmidt orthogonalization is restarted
+\begin_layout Plain Layout
+Number of iterations after which Gram-Schmidt orthogonalization is restarted.
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
ksp_rtol
@@ -966,10 +1049,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\shape italic
1.0e-08
@@ -977,10 +1060,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Convergence tolerance for relative decrease in residual norm.
\end_layout
@@ -1009,7 +1092,8 @@
a GMV file and an accompanying Pset file from LaGriT, or by specifying
the information in PyLith mesh ASCII format.
See Chapter
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Tutorials"
\end_inset
@@ -1019,32 +1103,37 @@
\begin_layout Standard
PyLith supports linear cells in 1D (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:1D-linear-elements"
\end_inset
), 2D (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:2D-linear-elements"
\end_inset
), and 3D (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:3D-linear-elements"
\end_inset
).
The vertex ordering must follow the convention shown in Figures
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:1D-linear-elements"
\end_inset
-
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:3D-linear-elements"
\end_inset
@@ -1072,13 +1161,15 @@
For a mesh with a single material type, there will only be a single label
for every cell in the mesh.
See Chapters
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:material:models"
\end_inset
and
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:boundary:interface:conditions"
\end_inset
@@ -1095,7 +1186,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -1106,10 +1197,10 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Linear bar cell available for 1D problems.
\end_layout
@@ -1118,8 +1209,9 @@
\end_layout
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:1D-linear-elements"
\end_inset
@@ -1141,7 +1233,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -1149,25 +1241,82 @@
\end_inset
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
\begin_inset Graphics
filename figs/quad4.eps
@@ -1177,10 +1326,10 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Linear cells available for 2D problems are the triangle (left) and the quadrilat
eral (right).
\end_layout
@@ -1190,8 +1339,9 @@
\end_layout
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "fig:2D-linear-elements"
\end_inset
@@ -1213,7 +1363,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -1221,25 +1371,82 @@
\end_inset
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
-\InsetSpace ~
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset space ~
+\end_inset
+
\begin_inset Graphics
filename figs/hex8.eps
@@ -1249,13 +1456,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Linear cells available for 3D problems are the tetrahedron (left) and the
hexahedron (right).
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:3D-linear-elements"
\end_inset
@@ -1274,7 +1482,8 @@
\end_layout
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:spatial:databases"
\end_inset
@@ -1295,7 +1504,8 @@
\family default
file is used to associate boundary condition types and spatial databases
with each vertex group (see Chapter
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:boundary:interface:conditions"
\end_inset
@@ -1307,7 +1517,8 @@
\family default
file is used to associate material types and spatial databases with cells
identified by the material identifier (see Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:Material-models"
\end_inset
@@ -1373,7 +1584,8 @@
This sort of condition might be used, for example, to specify the variation
of slip on a fault plane.
The examples discussed in Chapter
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Tutorials"
\end_inset
@@ -1426,11 +1638,16 @@
Examples of compatible coordinate systems include geographic coordinates
(longitude/latitude/elevation), and projected coordinates (e.g., coordinates
in a transverse Mercator projection).
- Spatial database queries use the
-\begin_inset LatexCommand htmlurl
-name "Proj.4 Cartographic Projections library"
-target "proj.maptools.org"
+ Spatial database queries use the Proj.4 Cartographic Projections library
+
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+proj.maptools.org
+\end_layout
+
\end_inset
to convert between coordinate systems, so a large number of geographic
@@ -1457,14 +1674,16 @@
SimpleDB uses a simple ASCII file to specify the variation of values (e.g.,
displacement field, slip field, physical properties) in space.
The file format is described in Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Spatialdata:SimpleIOAscii"
\end_inset
.
The tutorials in Chapter
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Tutorials"
\end_inset
@@ -1569,6 +1788,8 @@
pylithapp.cfg
\family default
file.
+ The data values are dimensioned with the appropriate units using Python
+ syntax.
\end_layout
\begin_layout LyX-Code
@@ -1584,33 +1805,34 @@
\end_layout
\begin_layout LyX-Code
-db.data = [5773.5, 3333.3, 2700.0] ; Set the values in the database
+db.data = [5773.5*m/s, 3333.3*m/s, 2700.0*kg/m**3] ; Set the values in the database
\end_layout
\begin_layout Subsubsection
-FixedDOFDB
+ZeroDispDB
\end_layout
\begin_layout Standard
-The FixedDOFDB is a a special case of the UniformDB for the Dirichlet boundary
+The ZeroDispDB is a a special case of the UniformDB for the Dirichlet boundary
conditions.
The values in the database are the ones requested by the Dirichlet boundary
conditions,
\family typewriter
-dof-0
+displacement-x
\family default
,
\family typewriter
-dof-1
+displacement-y
\family default
, and
\family typewriter
-dof-2
+displacement-z
\family default
, and are all set to zero.
This makes it trivial to set displacements to zero on a boundary.
The examples discussed in Chapter
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Tutorials"
\end_inset
@@ -1619,7 +1841,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sub:SCECCVMH-Impl"
\end_inset
@@ -1635,7 +1858,8 @@
and density information for much of southern California.
Spatialdata provides a direct interface to this database.
See Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Tutorial-Two-tet4-geoproj"
\end_inset
@@ -1694,7 +1918,9 @@
\begin_layout LyX-Code
db.data_dir = /home/johndoe/data/sceccvm-h/vx53 ; Directory containing the
database
-\newline
+\begin_inset Newline newline
+\end_inset
+
data files
\end_layout
@@ -1709,7 +1935,9 @@
\begin_layout LyX-Code
squash_limit = -1000.0 ; Only distort the geometry above z = -1 km in flattening
the
-\newline
+\begin_inset Newline newline
+\end_inset
+
earth
\end_layout
@@ -1984,7 +2212,8 @@
\begin_layout Standard
The nonuniform, user-specified time step implementation allows the user
to specify the time steps in an ASCII file (see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:FileFormat:TimeStepUser"
\end_inset
@@ -2142,13 +2371,15 @@
Additional diagnostic information can be included by setting the appropriate
output parameters.
See Chapters
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:material:models"
\end_inset
and
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:boundary:interface:conditions"
\end_inset
@@ -2222,7 +2453,8 @@
\begin_layout Description
vertex_filter Filter to apply to all vertex fields (see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sub:vertex:field:filters"
\end_inset
@@ -2232,7 +2464,8 @@
\begin_layout Description
cell_filter Filter to apply to all cell fields (see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sub:cell:field:filters"
\end_inset
@@ -2261,7 +2494,7 @@
\end_layout
\begin_layout LyX-Code
-cell_filter = pylith.meshio.CellFilterAvg
+cell_filter = pylith.meshio.CellFilterAvgMesh
\end_layout
\begin_layout LyX-Code
@@ -2273,7 +2506,7 @@
\end_layout
\begin_layout LyX-Code
-writer.filename = dislocation-statevars-elastic.vtk
+writer.filename = dislocation-elastic.vtk
\end_layout
\begin_layout Subsubsection
@@ -2324,7 +2557,8 @@
\end_layout
\begin_layout Subsubsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sub:vertex:field:filters"
\end_inset
@@ -2344,7 +2578,8 @@
\end_layout
\begin_layout Subsubsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sub:cell:field:filters"
\end_inset
@@ -2358,10 +2593,17 @@
\end_layout
\begin_layout Description
-CellFilterAvg Compute the weighted average of the values within a cell.
+CellFilterAvgMesh Compute the weighted average of the values within a bulk
+ cell.
The weights are determined from the quadrature associated with the cells.
\end_layout
+\begin_layout Description
+CellFilterAvgSubMesh Compute the weighted average of the values for a boundary
+ cell.
+ The weights are determined from the quadrature associated with the cells.
+\end_layout
+
\begin_layout Subsection
VTK Output
\end_layout
@@ -2505,21 +2747,33 @@
\family typewriter
>> {command line}::
-\newline
+\begin_inset Newline newline
+\end_inset
+
-- pyre.inventory(error)
-\newline
+\begin_inset Newline newline
+\end_inset
+
-- p4wd <- 'true'
-\newline
--- unrecognized
- property 'p4wd'
-\newline
+\begin_inset Newline newline
+\end_inset
+
+-- unrecognized property 'p4wd'
+\begin_inset Newline newline
+\end_inset
+
>> {command line}::
-\newline
+\begin_inset Newline newline
+\end_inset
+
-- pyre.inventory(error)
-\newline
--- p4pg <-
- 'true'
-\newline
+\begin_inset Newline newline
+\end_inset
+
+-- p4pg <- 'true'
+\begin_inset Newline newline
+\end_inset
+
-- unrecognized property ' p4pg'
\end_layout
@@ -2601,7 +2855,8 @@
the bug).
If this occurs with any of the problems distributed with PyLith, simply
submit a bug report (see Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Getting-Help-and"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 0
@@ -47,7 +50,8 @@
\begin_body
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Tutorial-3d-hex8"
\end_inset
@@ -108,7 +112,7 @@
\end_layout
\begin_layout Itemize
-FixedDOFDB spatial database
+ZeroDispDB spatial database
\end_layout
\begin_layout Subsection
@@ -119,11 +123,16 @@
This tutorial is a simple 3D example of a quasi-static finite element problem.
It is a mesh composed of 144 trilinear hexahedra subject to displacement
boundary conditions.
- This example demonstrates the usage of the
-\begin_inset LatexCommand htmlurl
-name "CUBIT mesh generation package"
-target "cubit.sandia.gov"
+ This example demonstrates the usage of the CUBIT mesh generation package
+
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cubit.sandia.gov
+\end_layout
+
\end_inset
to create a mesh, as well as describing how to use a CUBIT-generated mesh
@@ -140,7 +149,8 @@
\begin_layout Standard
The mesh for these examples is a simple rectangular solid (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:3dhex8-mesh"
\end_inset
@@ -156,11 +166,16 @@
\family default
Investigation of these journal files should provide some insight into how
to use CUBIT with PyLith.
- For more detailed information on using CUBIT, refer to the
-\begin_inset LatexCommand htmlurl
-name "CUBIT web site"
-target "cubit.sandia.gov"
+ For more detailed information on using CUBIT, refer to the CUBIT web site
+
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cubit.sandia.gov
+\end_layout
+
\end_inset
.
@@ -273,7 +288,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/hex8-mesh.jpg
@@ -285,14 +300,15 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Mesh composed of trilinear hexahedral cells generated by CUBIT used for
the example problems.
The different colors represent the two different material groups.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:3dhex8-mesh"
\end_inset
@@ -334,7 +350,7 @@
\end_layout
\begin_layout LyX-Code
-importer = pylith.meshio.MeshIOCubit
+reader = pylith.meshio.MeshIOCubit
\end_layout
\begin_layout LyX-Code
@@ -342,7 +358,7 @@
\end_layout
\begin_layout LyX-Code
-[pylithapp.mesh_generator.importer]
+[pylithapp.mesh_generator.reader]
\end_layout
\begin_layout LyX-Code
@@ -387,10 +403,6 @@
\end_layout
\begin_layout LyX-Code
-quadrature = pylith.feassemble.quadrature.Quadrature3D
-\end_layout
-
-\begin_layout LyX-Code
quadrature.cell = pylith.feassemble.FIATLagrange
\end_layout
@@ -419,10 +431,6 @@
\end_layout
\begin_layout LyX-Code
-quadrature = pylith.feassemble.quadrature.Quadrature3D
-\end_layout
-
-\begin_layout LyX-Code
quadrature.cell = pylith.feassemble.FIATLagrange
\end_layout
@@ -433,7 +441,8 @@
\begin_layout Standard
The two material groups correspond to the two different colors in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:3dhex8-mesh"
\end_inset
@@ -689,7 +698,8 @@
, so they are quadrilaterals rather than hexahedra.
If the problem ran correctly, you should be able to generate a figure such
as
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:3dhex8-shear"
\end_inset
@@ -703,7 +713,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/shear.jpg
@@ -715,13 +725,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the axial displacement example
using a mesh composed of trilinear hexahedral cells generated by CUBIT.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:3dhex8-shear"
\end_inset
@@ -849,7 +860,8 @@
\begin_layout Standard
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:3dhex-disloc"
\end_inset
@@ -865,7 +877,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/dislocation.jpg
@@ -877,13 +889,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the kinematic fault example
using a mesh composed of trilinear hexahedral cells generated by CUBIT.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:3dhex-disloc"
\end_inset
@@ -978,13 +991,15 @@
), providing the label (defined in
\family typewriter
box_hex8_
-\newline
+\begin_inset Newline newline
+\end_inset
+
1000m.exo
\family default
) defining the points desired, and assigning a label to the boundary condition
set.
Rather than specifying a spatial database file to define the boundary condition
-s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+s, we use the default spatial database (ZeroDispDB) for the Dirichlet boundary
condition, which sets the displacements to zero.
\end_layout
@@ -998,13 +1013,15 @@
), providing the label (defined in
\family typewriter
box_hex8_
-\newline
+\begin_inset Newline newline
+\end_inset
+
1000m.exo
\family default
) defining the points desired, and assigning a label to the boundary condition
set.
Rather than specifying a spatial database file to define the boundary condition
-s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+s, we use the default spatial database (ZeroDispDB) for the Dirichlet boundary
condition, which sets the displacements to zero.
\end_layout
@@ -1022,7 +1039,7 @@
) defining the points desired, and assigning a label to the boundary condition
set.
Rather than specifying a spatial database file to define the boundary condition
-s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+s, we use the default spatial database (ZeroDispDB) for the Dirichlet boundary
condition, which sets the displacements to zero.
\end_layout
@@ -1040,7 +1057,7 @@
) defining the points desired, and assigning a label to the boundary condition
set.
Rather than specifying a spatial database file to define the boundary condition
-s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+s, we use the default spatial database (ZeroDispDB) for the Dirichlet boundary
condition, which sets the displacements to zero.
\end_layout
@@ -1054,13 +1071,15 @@
), providing the label (defined in
\family typewriter
box_hex8_1000m.
-\newline
+\begin_inset Newline newline
+\end_inset
+
exo
\family default
) defining the points desired, and assigning a label to the boundary condition
set.
Rather than specifying a spatial database file to define the boundary condition
-s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+s, we use the default spatial database (ZeroDispDB) for the Dirichlet boundary
condition, which sets the displacements to zero.
\end_layout
@@ -1082,7 +1101,9 @@
,
\family typewriter
mat_
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscoelastic.spatialdb
\family default
) along with the problem-specific file (
@@ -1102,7 +1123,8 @@
\begin_layout Standard
If the problem ran correctly, you should be able to generate a figure such
as
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:3dhex-gravity"
\end_inset
@@ -1121,7 +1143,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -1134,11 +1156,12 @@
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours of vertical stress and vectors of displacement for the gravitatio
nal body force example using a mesh composed of trilinear hexahedral cells
generated by CUBIT.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:3dhex-gravity"
\end_inset
@@ -1220,7 +1243,9 @@
) as the filename for
\family typewriter
initial_state_db.iohandler.
-\newline
+\begin_inset Newline newline
+\end_inset
+
filename
\family default
.
@@ -1242,7 +1267,9 @@
) as the filename for
\family typewriter
initial_state_db.
-\newline
+\begin_inset Newline newline
+\end_inset
+
iohandler.filename
\family default
.
@@ -1266,7 +1293,9 @@
,
\family typewriter
mat_
-\newline
+\begin_inset Newline newline
+\end_inset
+
viscoelastic.spatialdb
\family default
,
@@ -1290,7 +1319,8 @@
\begin_layout Standard
If the problem ran correctly, you should be able to generate a figure such
as
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:3dhex-gravity_istress"
\end_inset
@@ -1306,7 +1336,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/hex8-gravity_istress.jpg
@@ -1318,14 +1348,15 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours of vertical displacement for the gravitational body force
example with initial stresses using a mesh composed of trilinear hexahedral
cells generated by CUBIT.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:3dhex-gravity_istress"
\end_inset
@@ -1410,7 +1441,7 @@
) defining the points desired, and assigning a label to the boundary condition
set.
Rather than specifying a spatial database file to define the boundary condition
-s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+s, we use the default spatial database (ZeroDispDB) for the Dirichlet boundary
condition, which sets the displacements to zero.
We also assign nonzero rates for the y degree of freedom, corresponding
to a velocity of -1.0 cm/year.
@@ -1434,7 +1465,7 @@
) defining the points desired, and assigning a label to the boundary condition
set.
Rather than specifying a spatial database file to define the boundary condition
-s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+s, we use the default spatial database (ZeroDispDB) for the Dirichlet boundary
condition, which sets the displacements to zero.
We also assign nonzero rates for the y degree of freedom, corresponding
to a velocity of 1.0 cm/year.
@@ -1446,13 +1477,15 @@
(z), providing the label (defined in
\family typewriter
box_hex8_1000m.
-\newline
+\begin_inset Newline newline
+\end_inset
+
exo
\family default
) defining the points desired, and assigning a label to the boundary condition
set.
Rather than specifying a spatial database file to define the boundary condition
-s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+s, we use the default spatial database (ZeroDispDB) for the Dirichlet boundary
condition, which sets the displacements to zero.
\end_layout
@@ -1507,7 +1540,7 @@
pylithapp.timedependent.materials.elastic.output Gives the base filename for
state variable output files for the elastic material (
\family typewriter
-savageprescott-statevars-elastic.vtk
+savageprescott-elastic.vtk
\family default
), and causes state variables to be averaged over all quadrature points
in each cell.
@@ -1519,7 +1552,7 @@
pylithapp.timedependent.materials.viscoelastic.output Gives the base filename
for state variable output files for the viscoelastic material (
\family typewriter
-savageprescott-statevars-viscoelastic.vtk
+savageprescott-viscoelastic.vtk
\family default
), and causes state variables to be averaged over all quadrature points
in each cell.
@@ -1586,7 +1619,9 @@
,
\family typewriter
finalslip_
-\newline
+\begin_inset Newline newline
+\end_inset
+
rupture.spatialdb
\family default
,
@@ -1620,7 +1655,7 @@
contain the displacement values at the mesh vertices.
The files of the form
\family typewriter
-savageprescott-statevars-elastic_tXXXX.vtk
+savageprescott-elastic_tXXXX.vtk
\family default
contain the state variables for each cell in the material group
\family typewriter
@@ -1633,16 +1668,16 @@
that these values be averaged, so there is a single set of values per cell.
The file
\family typewriter
-savageprescott-statevars-elastic_info.vtk
+savageprescott-elastic_info.vtk
\family default
gives the material properties used for the elastic material.
The files for the viscoelastic material (
\family typewriter
-savageprescott-statevars-viscoelastic_tXXXX.vtk
+savageprescott-viscoelastic_tXXXX.vtk
\family default
and
\family typewriter
-savageprescott-statevars-viscoelastic_info.vtk
+savageprescott-viscoelastic_info.vtk
\family default
) are exactly analogous to the corresponding files for the elastic material.
The files of the form
@@ -1658,7 +1693,9 @@
The files of the form
\family typewriter
savageprescott-fault
-\newline
+\begin_inset Newline newline
+\end_inset
+
_tXXXX.vtk
\family default
give the fault slip for each vertex on the fault, along with the computed
@@ -1680,7 +1717,8 @@
.
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:3dhex:savageprescott"
\end_inset
@@ -1696,7 +1734,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/savageprescott-t100.jpg
@@ -1708,14 +1746,15 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement at t = 100 years for the multiple
kinematic fault rupture example using a mesh composed of trilinear hexahedral
cells generated by CUBIT.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:3dhex:savageprescott"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 0
@@ -47,7 +50,8 @@
\begin_body
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Tutorial-3d-tet4"
\end_inset
@@ -100,7 +104,7 @@
\end_layout
\begin_layout Itemize
-FixedDOFDB spatial database
+ZeroDispDB spatial database
\end_layout
\begin_layout Subsection
@@ -111,11 +115,16 @@
This tutorial is a simple 3D example of a quasi-static finite element problem.
It is a mesh composed of 852 linear tetrahedra subject to displacement
boundary conditions.
- This example demonstrates the usage of the
-\begin_inset LatexCommand htmlurl
-name "LaGriT mesh generation package"
-target "lagrit.lanl.gov"
+ This example demonstrates the usage of the LaGriT mesh generation package
+
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+lagrit.lanl.gov
+\end_layout
+
\end_inset
to create a mesh, as well as describing how to use a LaGriT-generated mesh
@@ -132,7 +141,8 @@
\begin_layout Standard
The mesh for these examples is a simple rectangular solid (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:3dtet4-mesh"
\end_inset
@@ -147,11 +157,16 @@
\family default
Investigation of this command file should provide some insight into how
to use LaGriT with PyLith.
- For more detailed information on using LaGriT, refer to the
-\begin_inset LatexCommand htmlurl
-name "LaGriT web site"
-target "lagrit.lanl.gov"
+ For more detailed information on using LaGriT, refer to the LaGriT web
+ site
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+lagrit.lanl.gov
+\end_layout
+
\end_inset
.
@@ -247,11 +262,15 @@
.gmv
\family default
files define the mesh information, and they may be read directly by the
-
-\begin_inset LatexCommand htmlurl
-name "GMV"
-target "laws.lanl.gov/XCM/gmv/GMVHome.html"
+ GMV
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+laws.lanl.gov/XCM/gmv/GMVHome.html
+\end_layout
+
\end_inset
mesh visualization package.
@@ -272,7 +291,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/tet4-mesh.jpg
@@ -284,14 +303,15 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Mesh composed of linear tetrahedral cells generated by LaGriT used for the
example problems.
The different colors represent the different material groups.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:3dtet4-mesh"
\end_inset
@@ -376,7 +396,7 @@
\end_layout
\begin_layout LyX-Code
-importer = pylith.meshio.MeshIOLagrit
+reader = pylith.meshio.MeshIOLagrit
\end_layout
\begin_layout LyX-Code
@@ -384,7 +404,7 @@
\end_layout
\begin_layout LyX-Code
-[pylithapp.mesh_generator.importer]
+[pylithapp.mesh_generator.reader]
\end_layout
\begin_layout LyX-Code
@@ -459,10 +479,6 @@
\end_layout
\begin_layout LyX-Code
-quadrature = pylith.feassemble.quadrature.Quadrature3D
-\end_layout
-
-\begin_layout LyX-Code
quadrature.cell = pylith.feassemble.FIATSimplex
\end_layout
@@ -491,10 +507,6 @@
\end_layout
\begin_layout LyX-Code
-quadrature = pylith.feassemble.quadrature.Quadrature3D
-\end_layout
-
-\begin_layout LyX-Code
quadrature.cell = pylith.feassemble.FIATSimplex
\end_layout
@@ -512,7 +524,8 @@
\begin_layout Standard
The two materials correspond to the two different colors in Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:3dtet4-mesh"
\end_inset
@@ -660,7 +673,7 @@
\family default
material set (
\family typewriter
-shearxy-statevars-elastic.vtk
+shearxy-elastic.vtk
\family default
), and causes state variables to be averaged over all quadrature points
in each cell.
@@ -674,7 +687,7 @@
\family default
material set (
\family typewriter
-shearxy-statevars-viscoelastic.vtk
+shearxy-viscoelastic.vtk
\family default
), and causes state variables to be averaged over all quadrature points
in each cell.
@@ -816,7 +829,8 @@
files may be used with a number of visualization packages.
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:3dtet4-shear"
\end_inset
@@ -831,7 +845,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/shear.jpg
@@ -843,13 +857,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the axial displacement example
using a mesh composed of linear tetrahedral cells generated by LaGriT.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:3dtet4-shear"
\end_inset
@@ -936,7 +951,7 @@
pset) defining the points desired, and assigning a label to the boundary
condition set.
Rather than specifying a spatial database file to define the boundary condition
-s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+s, we use the default spatial database (ZeroDispDB) for the Dirichlet boundary
condition, which sets the displacements to zero.
\end_layout
@@ -962,7 +977,7 @@
pset) defining the points desired, and assigning a label to the boundary
condition set.
Rather than specifying a spatial database file to define the boundary condition
-s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+s, we use the default spatial database (ZeroDispDB) for the Dirichlet boundary
condition, which sets the displacements to zero.
\end_layout
@@ -1089,7 +1104,9 @@
\family typewriter
\size small
dislocation
-\newline
+\begin_inset Newline newline
+\end_inset
+
.cfg
\family default
,
@@ -1199,7 +1216,8 @@
files may be used with a number of visualization packages.
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:3dtet-disloc"
\end_inset
@@ -1215,7 +1233,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/dislocation.jpg
@@ -1227,13 +1245,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the kinematic fault example
using a mesh composed of linear tetrahedral cells generated by LaGriT.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:3dtet-disloc"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 1
@@ -47,7 +50,8 @@
\begin_body
\begin_layout Chapter
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "cha:Tutorials"
\end_inset
@@ -70,9 +74,13 @@
\begin_layout Standard
Before you begin any of the tutorials, you will need to install PyLith following
- the instructions in Chapter\InsetSpace ~
+ the instructions in Chapter
+\begin_inset space ~
+\end_inset
-\begin_inset LatexCommand ref
+
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:Installation-and-Getting"
\end_inset
@@ -80,38 +88,54 @@
.
\color none
- For more complex tutorials, you will also need either
-\begin_inset LatexCommand htmlurl
-name "CUBIT"
-target "cubit.sandia.gov"
+ For more complex tutorials, you will also need either CUBIT
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+cubit.sandia.gov
+\end_layout
+
\end_inset
- or
-\begin_inset LatexCommand htmlurl
-name "LaGriT"
-target "meshing.lanl.gov"
+ or LaGriT
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+meshing.lanl.gov
+\end_layout
+
\end_inset
mesh generation software to create the meshes.
If you do not wish to create your own mesh at this time, the meshes are
also provided as part of the tutorial.
- The
-\begin_inset LatexCommand htmlurl
-name "ParaView"
-target "www.paraview.org"
+ The ParaView
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+www.paraview.org
+\end_layout
+
\end_inset
visualization package may be used to view simulation results.
ParaView 3 includes built-in documentation that is accessed by clicking
on the Help menu item.
- Some additional documentation is available on the
-\begin_inset LatexCommand htmlurl
-name "ParaView Wiki site"
-target "paraview.org/Wiki/ParaView"
+ Some additional documentation is available on the ParaView Wiki site
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+paraview.org/Wiki/ParaView
+\end_layout
+
\end_inset
.
@@ -147,44 +171,51 @@
\end_layout
\begin_layout Standard
-\begin_inset Include \input{twotri3/twotri3.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "twotri3/twotri3.lyx"
\end_inset
-\begin_inset Include \input{twoquad4/twoquad4.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "twoquad4/twoquad4.lyx"
\end_inset
-\begin_inset Include \input{twotet4/twotet4.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "twotet4/twotet4.lyx"
\end_inset
-\begin_inset Include \input{twohex8/twohex8.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "twohex8/twohex8.lyx"
\end_inset
-\begin_inset Include \input{twotet4-geoproj/twotet4-geoproj.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "twotet4-geoproj/twotet4-geoproj.lyx"
\end_inset
-\begin_inset Include \input{3dhex8/3dhex8.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "3dhex8/3dhex8.lyx"
\end_inset
-\begin_inset Include \input{3dtet4/3dtet4.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "3dtet4/3dtet4.lyx"
\end_inset
@@ -224,18 +255,18 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="2">
<features>
-<column alignment="left" valignment="top" leftline="true" width="1.75in">
-<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">
+<column alignment="left" valignment="top" width="1.75in">
+<column alignment="left" valignment="top" width="4in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Directory
@@ -243,10 +274,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\series bold
Description
@@ -255,11 +286,11 @@
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
bar_shearwave/tri3
@@ -270,18 +301,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Wave propagation in a 2D bar discretized with triangular cells
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
bar_shearwave/quad4
@@ -292,18 +323,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Wave propagation in a 2D bar discretized with quadrilateral cells
\end_layout
\end_inset
</cell>
</row>
-<row topline="true">
+<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
bar_shearwave/tet4
@@ -314,18 +345,18 @@
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Wave propagation in a 3D bar discretized with tetrahedral cells
\end_layout
\end_inset
</cell>
</row>
-<row topline="true" bottomline="true">
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
\family typewriter
bar_shearwave/hex8
@@ -333,10 +364,10 @@
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
-\begin_layout Standard
+\begin_layout Plain Layout
Wave propagation in a 3D bar discretized with hexahedral cells
\end_layout
@@ -350,11 +381,12 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
-\begin_inset LatexCommand label
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
name "tab:additional:examples"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/twohex8.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/twohex8.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/twohex8.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 0
@@ -47,7 +50,8 @@
\begin_body
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Tutorial-Two-hexahedra"
\end_inset
@@ -92,7 +96,7 @@
\end_layout
\begin_layout Itemize
-FixedDOFDB spatial database
+ZeroDispDB spatial database
\end_layout
\begin_layout Itemize
@@ -128,7 +132,8 @@
\begin_layout Standard
The mesh consists of two hexahedra forming a rectangular prism (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:twohex8-mesh"
\end_inset
@@ -149,7 +154,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/twohex8-mesh.eps
@@ -159,12 +164,13 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Mesh composed of two trilinear hexahedral cells used for the example problems.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twohex8-mesh"
\end_inset
@@ -242,7 +248,7 @@
\end_layout
\begin_layout LyX-Code
-db.data = [5773.502691896258, 3333.333333333333, 2700.0, 1.0e18]
+db.data = [5773.502691896258*m/s, 3333.333333333333*m/s, 2700.0*kg/m**3, 1.0e18*Pa*s]
\end_layout
\begin_layout LyX-Code
@@ -250,10 +256,6 @@
\end_layout
\begin_layout LyX-Code
-quadrature = pylith.feassemble.quadrature.Quadrature3D
-\end_layout
-
-\begin_layout LyX-Code
quadrature.cell = pylith.feassemble.FIATLagrange
\end_layout
@@ -446,7 +448,8 @@
).
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:twohex8-axial"
\end_inset
@@ -460,7 +463,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/axialdisp.jpg
@@ -472,13 +475,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the axial displacement example
using a mesh composed of two trilinear hexahedral cells.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twohex8-axial"
\end_inset
@@ -591,7 +595,8 @@
\begin_layout Standard
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:twohex8-shear"
\end_inset
@@ -605,7 +610,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/sheardisp.jpg
@@ -617,13 +622,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the shear displacement example
using a mesh composed of two trilinear hexahedral cells.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twohex8-shear"
\end_inset
@@ -636,7 +642,7 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\end_layout
@@ -677,7 +683,7 @@
\family default
) defining the points desired, and assigns a label to the boundary condition
set.
- In this case, we use the default spatial database (FixedDOFDB) for the
+ In this case, we use the default spatial database (ZeroDispDB) for the
Dirichlet boundary condition, which sets the displacements to zero.
\end_layout
@@ -765,7 +771,8 @@
\begin_layout Standard
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:twohex8-disloc"
\end_inset
@@ -781,7 +788,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -794,13 +801,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the kinematic fault example
using a mesh composed of two trilinear hexahedral cells.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twohex8-disloc"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/twoquad4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/twoquad4.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/twoquad4.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 0
@@ -47,7 +50,8 @@
\begin_body
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Tutorial-Two-quad4"
\end_inset
@@ -96,7 +100,7 @@
\end_layout
\begin_layout Itemize
-FixedDOFDB spatial database
+ZeroDispDB spatial database
\end_layout
\begin_layout Subsection
@@ -123,7 +127,8 @@
\begin_layout Standard
The mesh consists of two square cells with edge lengths of one unit forming
a regular region (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:twoquad4-mesh"
\end_inset
@@ -149,7 +154,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/twoquad4-mesh.eps
@@ -159,12 +164,13 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Mesh composed of two bilinear quadrilateral cells used for the example problems.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twoquad4-mesh"
\end_inset
@@ -315,7 +321,8 @@
As in the two triangle axial displacement example, three files will be produced.
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:twoquad4-axial"
\end_inset
@@ -332,7 +339,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/axialdisp.jpg
@@ -344,13 +351,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the axial displacement example
using a mesh composed of two bilinear quadrilateral cells.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twoquad4-axial"
\end_inset
@@ -478,7 +486,8 @@
As in the previous example, three files will be produced.
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:twoquad4-shear"
\end_inset
@@ -492,7 +501,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/sheardispl.jpg
@@ -504,13 +513,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the shear displacement example
using a mesh composed of two bilinear quadrilateral cells.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twoquad4-shear"
\end_inset
@@ -562,7 +572,7 @@
) defining the points desired, and assigning a label to the boundary condition
set.
Instead of specifying a spatial database file for the values of the Dirichlet
- boundary condition, we use the default spatial database (FixedDOFDB) for
+ boundary condition, we use the default spatial database (ZeroDispDB) for
the Dirichlet boundary condition, which sets the displacements to zero
for all time.
\end_layout
@@ -580,7 +590,7 @@
\family default
) defining the points desired, and assigning a label to the boundary condition
set.
- We use the FixedDOFDB for this boundary condition as well, which sets the
+ We use the ZeroDispDB for this boundary condition as well, which sets the
displacements to zero for all time.
\end_layout
@@ -672,7 +682,8 @@
each vertex on the fault.
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:twoquad4-disloc"
\end_inset
@@ -686,7 +697,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/dislocation.jpg
@@ -698,13 +709,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the kinematic fault example
using a mesh composed of two bilinear quadrilateral cells.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twoquad4-disloc"
\end_inset
@@ -723,7 +735,8 @@
\end_layout
\begin_layout Subsection
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sub:Tutorial-twoquad4-traction"
\end_inset
@@ -777,7 +790,7 @@
) defining the points desired.
In this case, rather than specifying a spatial database file with values
for the Dirichlet boundary conditions, we use the default spatial database
- (FixedDOFDB) for the Dirichlet boundary condition, which sets the displacements
+ (ZeroDispDB) for the Dirichlet boundary condition, which sets the displacements
to zero for all time.
\end_layout
@@ -804,14 +817,16 @@
twoquad4.mesh
\family default
) defining the points desired.
- In this case, we again use the FixedDOFDB, which sets the displacements
+ In this case, we again use the ZeroDispDB, which sets the displacements
to zero for all time.
\end_layout
\begin_layout Description
pylithapp.problem.formulation.output.output.writer Gives the base filename for
VTK output
-\newline
+\begin_inset Newline newline
+\end_inset
+
(
\family typewriter
axialtract.vtk
@@ -896,7 +911,8 @@
components of traction applied at each integration point.
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:twoquad4-axialtract"
\end_inset
@@ -904,7 +920,8 @@
, which was generated using ParaView.
The results may be compared against the analytical solution derived in
Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sub:Analytical-Constant-Traction"
\end_inset
@@ -918,7 +935,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/axialtract.jpg
@@ -930,13 +947,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the axial traction example
using a mesh composed of two bilinear quadrilateral cells.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twoquad4-axialtract"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/twotet4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/twotet4.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/twotet4.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 0
@@ -47,7 +50,8 @@
\begin_body
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Tutorial-Two-tet4"
\end_inset
@@ -92,7 +96,7 @@
\end_layout
\begin_layout Itemize
-FixedDOFDB spatial database
+ZeroDispDB spatial database
\end_layout
\begin_layout Subsection
@@ -118,7 +122,8 @@
\begin_layout Standard
The mesh consists of two tetrahedra forming a pyramid shape (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:twotet4-mesh"
\end_inset
@@ -139,7 +144,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/twotet4-mesh.eps
@@ -149,12 +154,13 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Mesh composed of two linear tetrahedral cells used for example problems.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twotet4-mesh"
\end_inset
@@ -278,7 +284,8 @@
\begin_layout Standard
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:twotet4-axial"
\end_inset
@@ -292,7 +299,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/axialdisp.jpg
@@ -304,13 +311,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the axial displacement example
using a mesh composed of two linear tetrahedral cells.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twotet4-axial"
\end_inset
@@ -381,7 +389,7 @@
) defining the points desired, and assigns a label to the boundary condition
set.
Rather than specifying a spatial database file to define the boundary condition
-s, we use the default spatial database (FixedDOFDB) for the Dirichlet boundary
+s, we use the default spatial database (ZeroDispDB) for the Dirichlet boundary
condition, which sets the displacements to zero.
\end_layout
@@ -460,7 +468,8 @@
\begin_layout Standard
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:twotet4-disloc"
\end_inset
@@ -474,7 +483,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/dislocation.jpg
@@ -486,13 +495,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the kinematic fault example
using a mesh composed of two linear tetrahedral cells.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twotet4-disloc"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4-geoproj/twotet4-geoproj.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4-geoproj/twotet4-geoproj.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4-geoproj/twotet4-geoproj.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 0
@@ -47,7 +50,8 @@
\begin_body
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Tutorial-Two-tet4-geoproj"
\end_inset
@@ -96,7 +100,7 @@
\end_layout
\begin_layout Itemize
-FixedDOFDB spatial database
+ZeroDispDB spatial database
\end_layout
\begin_layout Subsection
@@ -106,7 +110,8 @@
\begin_layout Standard
This tutorial is virtually identical to the other tutorial using two linear
tetrahedra (See Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Tutorial-Two-tet4"
\end_inset
@@ -115,7 +120,8 @@
The primary difference is in how the material properties are assigned.
For this tutorial, the physical properties come from the SCEC CVM-H database
(described in Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sub:SCECCVMH-Impl"
\end_inset
@@ -139,7 +145,8 @@
properly.
Since all aspects of this problem other than the material database and
the coordinate system are identical to the examples in Section
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Tutorial-Two-tet4"
\end_inset
@@ -153,7 +160,8 @@
\begin_layout Standard
The mesh consists of two tetrahedra forming a pyramid shape (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:twotet4-geoproj-mesh"
\end_inset
@@ -165,7 +173,8 @@
\family default
, which is in PyLith mesh ASCII format.
If you compare this mesh against the one used in
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Tutorial-Two-tet4"
\end_inset
@@ -177,7 +186,8 @@
have also used any another geographic projection supported by spatialdata
and Proj.4.
See Appendix
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "sec:Spatialdata:SimpleIOAscii"
\end_inset
@@ -194,7 +204,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/twotet4-mesh.eps
@@ -204,13 +214,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Mesh composed of two linear tetrahedral cells in a georeferenced coordinate
system used for the example problems.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twotet4-geoproj-mesh"
\end_inset
@@ -343,11 +354,16 @@
\family default
data files, and must be changed to the location specified by the user when
the package is installed.
- The package may be obtained from
-\begin_inset LatexCommand htmlurl
-name "Harvard's Structural Geology and Tectonics"
-target "structure.harvard.edu/cvm-h"
+ The package may be obtained from Harvard's Structural Geology and Tectonics
+
+\begin_inset Flex URL
+status collapsed
+\begin_layout Plain Layout
+
+structure.harvard.edu/cvm-h
+\end_layout
+
\end_inset
.
@@ -479,7 +495,8 @@
\begin_layout Standard
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:twotet4-geoproj-disloc"
\end_inset
@@ -493,7 +510,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/dislocation.jpg
@@ -505,14 +522,15 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the kinematic fault example
using a mesh composed of two linear tetrahedral cells in a georeferenced
coordinate system.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twotet4-geoproj-disloc"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,11 +1,12 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
\begin_preamble
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
\font_roman default
@@ -16,9 +17,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 0
@@ -47,7 +50,8 @@
\begin_body
\begin_layout Section
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "sec:Tutorial-Two-triangle"
\end_inset
@@ -92,7 +96,7 @@
\end_layout
\begin_layout Itemize
-FixedDOFDB spatial database
+ZeroDispDB spatial database
\end_layout
\begin_layout Subsection
@@ -119,7 +123,8 @@
\begin_layout Standard
The mesh consists of two triangles forming a square with edge lengths of
one unit (Figure
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "fig:twotri3-mesh"
\end_inset
@@ -131,7 +136,8 @@
\family default
, which is in PyLith mesh ASCII format.
This file format is described in Appendix
-\begin_inset LatexCommand ref
+\begin_inset CommandInset ref
+LatexCommand ref
reference "cha:File-Formats"
\end_inset
@@ -150,7 +156,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/twotri3-mesh.eps
@@ -160,12 +166,13 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Mesh composed of two linear triangular cells used in the example problems.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twotri3-mesh"
\end_inset
@@ -316,7 +323,9 @@
\begin_layout Description
pylithapp.problem.formulation.output.output.writer Gives the base filename for
VTK output
-\newline
+\begin_inset Newline newline
+\end_inset
+
(
\family typewriter
axialdisp.vtk
@@ -430,7 +439,8 @@
files may be used with a number of visualization packages.
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:twotri3-axial"
\end_inset
@@ -446,7 +456,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/axialdisp.jpg
@@ -458,13 +468,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the axial displacement example
using a mesh composed of two linear triangular cells.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twotri3-axial"
\end_inset
@@ -575,7 +586,8 @@
example.
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:twotri-shear"
\end_inset
@@ -591,7 +603,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/sheardisp.jpg
@@ -603,13 +615,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the shear displacement example
using a mesh composed of two linear triangular cells.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twotri-shear"
\end_inset
@@ -665,7 +678,7 @@
set.
In this case, rather than specifying a spatial database file with the values
for the Dirichlet boundary condition.
- The default database (FixedDOFDB) for Dirichlet boundary conditions is
+ The default database (ZeroDispDB) for Dirichlet boundary conditions is
used, which sets the displacements to zero.
\end_layout
@@ -774,7 +787,8 @@
time for each vertex on the fault.
If the problem ran correctly, you should be able to generate a figure such
as Figure
-\begin_inset LatexCommand vref
+\begin_inset CommandInset ref
+LatexCommand vref
reference "fig:twotri-disloc"
\end_inset
@@ -790,7 +804,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename figs/dislocation.jpg
@@ -802,13 +816,14 @@
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
\begin_inset Caption
-\begin_layout Standard
+\begin_layout Plain Layout
Color contours and vectors of displacement for the kinematic fault example
using a mesh composed of two linear triangular cells.
-\begin_inset LatexCommand label
+\begin_inset CommandInset label
+LatexCommand label
name "fig:twotri-disloc"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/userguide.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/userguide.lyx 2009-06-10 17:49:35 UTC (rev 15171)
+++ short/3D/PyLith/trunk/doc/userguide/userguide.lyx 2009-06-10 18:19:15 UTC (rev 15172)
@@ -1,5 +1,5 @@
-#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
-\lyxformat 276
+#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
\begin_document
\begin_header
\textclass book
@@ -10,6 +10,7 @@
\renewcommand{\url}[1]{(\myUrl{#1})}
\newcommand\Prefix[3]{\vphantom{#3}#1#2#3}
\end_preamble
+\use_default_options false
\language english
\inputencoding latin1
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@@ -20,9 +21,11 @@
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
+
\graphics default
\paperfontsize default
\spacing single
+\use_hyperref false
\papersize default
\use_geometry true
\use_amsmath 1
@@ -59,7 +62,7 @@
sideways false
status open
-\begin_layout Standard
+\begin_layout Plain Layout
\noindent
\align center
\begin_inset Graphics
@@ -80,14 +83,14 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
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thispagestyle{empty}
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
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@@ -102,8 +105,10 @@
\begin_layout Author
© California Institute of Technology
-\newline
-Version 1.3.1
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+
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@@ -111,7 +116,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
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@@ -127,7 +132,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
+\begin_layout Plain Layout
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@@ -137,7 +142,8 @@
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-\begin_inset LatexCommand tableofcontents
+\begin_inset CommandInset toc
+LatexCommand tableofcontents
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@@ -161,8 +167,9 @@
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\begin_layout Standard
-\begin_inset Include \input{preface.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "preface.lyx"
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@@ -170,7 +177,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
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@@ -183,7 +190,7 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
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@@ -196,50 +203,58 @@
\end_layout
\begin_layout Standard
-\begin_inset Include \input{intro/intro.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "intro/intro.lyx"
\end_inset
-\begin_inset Include \input{governingeqns/governingeqns.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "governingeqns/governingeqns.lyx"
\end_inset
-\begin_inset Include \input{install/install.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "install/install.lyx"
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-\begin_inset Include \input{runpylith/runpylith.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "runpylith/runpylith.lyx"
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-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "materials/materials.lyx"
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-\begin_inset Include \input{boundaryconditions/boundaryconditions.lyx}
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+\begin_inset CommandInset include
+LatexCommand input
+filename "boundaryconditions/boundaryconditions.lyx"
\end_inset
-\begin_inset Include \input{tutorials/tutorials.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "tutorials/tutorials.lyx"
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-\begin_inset Include \input{benchmarks/benchmarks.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "benchmarks/benchmarks.lyx"
\end_inset
@@ -251,39 +266,43 @@
\begin_inset ERT
status collapsed
-\begin_layout Standard
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%dummy comment inserted by tex2lyx to ensure that this paragraph is not
empty
\end_layout
-\begin_layout Standard
+\begin_layout Plain Layout
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\end_inset
-\begin_inset Include \input{glossary.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "glossary.lyx"
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-\begin_inset Include \input{fileformats/fileformats.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "fileformats/fileformats.lyx"
\end_inset
-\begin_inset Include \input{analyticalsolns/analyticalsolns.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "analyticalsolns/analyticalsolns.lyx"
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-\begin_inset Include \input{license.lyx}
-preview false
+\begin_inset CommandInset include
+LatexCommand input
+filename "license.lyx"
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@@ -291,7 +310,8 @@
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\begin_layout Bibliography
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+LatexCommand bibitem
key "Williams:etal:2005"
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@@ -310,7 +330,8 @@
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\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
key "Williams:2006"
\end_inset
@@ -332,7 +353,8 @@
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\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
key "Aagaard:etal:2001a"
\end_inset
@@ -348,7 +370,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
key "Aagaard:etal:2001b"
\end_inset
@@ -365,7 +388,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
key "Aagaard:etal:2007"
\end_inset
@@ -383,7 +407,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
key "Brune:1970"
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@@ -398,7 +423,8 @@
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\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
key "Kojic:Bathe:1987"
\end_inset
@@ -422,7 +448,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "7"
key "Zienkiewicz:Taylor:2000"
@@ -438,7 +465,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "8"
key "Taylor:2003"
@@ -453,7 +481,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "9"
key "Timoshenko:Goodier:1987"
@@ -469,7 +498,8 @@
\end_layout
\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
+\begin_inset CommandInset bibitem
+LatexCommand bibitem
label "10"
key "Okada:1992"
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