[cig-commits] r12748 - in short/3D/PyLith/trunk/doc/userguide: . benchmarks benchmarks/strikeslip boundaryconditions fileformats install intro materials runpylith tutorials tutorials/3dhex8 tutorials/twohex8 tutorials/twoquad4 tutorials/twotet4 tutorials/twotet4-geoproj tutorials/twotri3
brad at geodynamics.org
brad at geodynamics.org
Fri Aug 29 13:52:05 PDT 2008
Author: brad
Date: 2008-08-29 13:52:04 -0700 (Fri, 29 Aug 2008)
New Revision: 12748
Modified:
short/3D/PyLith/trunk/doc/userguide/TODO
short/3D/PyLith/trunk/doc/userguide/benchmarks/benchmarks.lyx
short/3D/PyLith/trunk/doc/userguide/benchmarks/strikeslip/strikeslip.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/glossary.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/runpylith/runpylith.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.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
Log:
Spell checking. Finished cleaning up manual for v1.3. Removed superfluous repetition of material in tutorials (to make them easier to maintain).
Modified: short/3D/PyLith/trunk/doc/userguide/TODO
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/TODO 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/TODO 2008-08-29 20:52:04 UTC (rev 12748)
@@ -1,73 +1,4 @@
-6. Intro [DONE (for now)]
+1. Running PyLith
- PyLith Diagram [future: Brad]
- Pyre
- PyLith
- Faults, Topology, BC, FEAssemble, Problems, MeshIO, Solver, Materials
- PETSc
- Sieve
- MPI
-
-7. Governing equations [MOSTLY DONE]
-
- Remove margin notes, check if possible. [CHARLES]
-
-8. Running PyLith
-
- Insert cross-references.
Could use an overview of what happens when you run PyLith.
-9. Installing binary PyLith
-
- [CHARLES- NEED TO GET BINARY AND WRITE INSTRUCTIONS]
-
- Installation from source [Leif will write after CFEM]
-
-
-11. Tutorials (all using ascii mesh format?) [CHARLES]
-
- a. Two-triangle problem.
-
- i. Dirichlet boundary conditions (shear)
-
- ii. Dirichlet boundary conditions (fixed) and fault
-
- b. Two-quad problem.
-
- i. Dirichlet boundary conditions (fixed) and fault
-
- c. Two-tet shear viscoelastic problem?
-
- d. Two-hex element shear viscoelastic problem?
-
- e. LaGrit/CUBIT problem with fault and Dirichlet (fixed) BC
-
- i. Provide LaGriT and CUBIT scripts with comments.
- ii. Describe process for setting up meshes for export from LaGriT/CUBIT.
-
-12. Material models (should be able to copy from 0.8 with some editing) [Charles]
-
- * MaxwellIsotropic3D [Charles]
-
- [CHARLES - need to rewrite formulation in terms of mu and lambda]
-
- [CHARLES - also list material modesl that will be added soon]
-
- [CHARLES - Create table with spatial database parameter names]
-
- c. List material models in 0.8 that will be added soon.
-
-13. Boundary and interface conditions (includes faults)
-
- [BRAD]
-
- d. Fault
-
- i. Conventions (sign, orientation info)
-
- ii. Cohesive cells (described how faults implemented)
-
- iii. Kinematic earthquake source
-
-14. Appendix [DONE]
-
Modified: short/3D/PyLith/trunk/doc/userguide/benchmarks/benchmarks.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/benchmarks/benchmarks.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/benchmarks/benchmarks.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -1,4 +1,4 @@
-#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -62,7 +62,7 @@
\begin_layout Standard
The Crustal Deformation Modeling Working Group within the Southern California
Earthquake Center and the Short-Term Tectonics Working Group within CIG
- developed a suite of benchmarks to test the accuracy and peformance of
+ 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
Modified: short/3D/PyLith/trunk/doc/userguide/benchmarks/strikeslip/strikeslip.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/benchmarks/strikeslip/strikeslip.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/benchmarks/strikeslip/strikeslip.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -1,4 +1,4 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -87,7 +87,7 @@
\end_inset
- shows the geometry of the strike-slip fault (red surface) embeded in the
+ shows the geometry of the strike-slip fault (red surface) embedded in the
cube consisting of an elastic material (yellow block) over a Maxwell viscoelast
ic material (blue block).
@@ -235,7 +235,7 @@
quasistatic/strikeslip
\family default
directory.
- Uncompress the gzipped files in the meshes and parameters directories,
+ Decompress the gzipped files in the meshes and parameters directories,
\end_layout
\begin_layout LyX-Code
@@ -738,7 +738,7 @@
\begin_layout Standard
Convergence rate for the strike-slip benchmark problem with tetrahedral
cells and linear basis functions and with hexahedral cells with trilinear
- basis funtions.
+ basis functions.
\begin_inset LatexCommand label
name "fig:benchmark:strikeslip:convergence"
Modified: short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -1,4 +1,4 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -110,9 +110,9 @@
Note also that we currently associate boundary conditions with string identifie
rs, so even if the mesh generator uses integers, the name is specified as
the digits of the integer value.
- Finally, note that every vertex set used to specify boundary conditions
- must correspond to a simply-connected surface, meaning that all vertices
- in the set must be connected to each other.
+ Finally, note that every vertex set that ultimately is associated with
+ a boundary condition on a cell face (e.g., Neumann boundary conditions and
+ fault interface conditions) must correspond to a simply-connected surface.
\end_layout
\begin_layout Subsection
@@ -377,6 +377,20 @@
\begin_layout Standard
\noindent
\align center
+\begin_inset Caption
+
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "tab:dirichlet:output"
+
+\end_inset
+
+Fields available in output of DirichletBoundary boundary condition information.
+\end_layout
+
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="3">
<features>
@@ -489,29 +503,11 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Fields available in output of DirichletBoundary boundary condition information.
-\begin_inset LatexCommand label
-name "tab:dirichlet:output"
-
\end_inset
\end_layout
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Subsection
Dirichlet Boundary Condition Spatial Database Files
\end_layout
@@ -547,6 +543,15 @@
\begin_layout Standard
\noindent
\align center
+\begin_inset Caption
+
+\begin_layout Standard
+Values in spatial database used for Dirichlet boundary conditions.
+\end_layout
+
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
<features>
@@ -654,23 +659,11 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Values in spatial database used for Dirichlet boundary conditions.
-\end_layout
-
\end_inset
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Section
Neumann Boundary Conditions
\end_layout
@@ -855,6 +848,20 @@
\begin_layout Standard
\noindent
\align center
+\begin_inset Caption
+
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "tab:neumann:output"
+
+\end_inset
+
+Fields available in output of Neumann boundary condition information.
+\end_layout
+
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="3">
<features>
@@ -936,29 +943,11 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Fields available in output of Neumann boundary condition information.
-\begin_inset LatexCommand label
-name "tab:neumann:output"
-
\end_inset
\end_layout
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Subsection
Neumann Boundary Condition Spatial Database Files
\end_layout
@@ -1739,9 +1728,9 @@
Typically, the additional degrees of freedom associated with the Lagrange
multipliers result in a complex implementation.
However, the use of Lagrange multiplier constraints with cohesive cells
- makes this very easy; we simply add the additional degrees of freedom associate
-d with the Lagrange multipliers to the cohesive cells as shown in Figure
-
+ 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
reference "fig:fault:cohesive:quad4:kin"
@@ -1891,6 +1880,20 @@
\begin_layout Standard
\noindent
\align center
+\begin_inset Caption
+
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "tab:fault:kin:output"
+
+\end_inset
+
+Fields available in output of fault information.
+\end_layout
+
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="8" columns="3">
<features>
@@ -2165,29 +2168,11 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Fields available in output of fault information.
-\begin_inset LatexCommand label
-name "tab:fault:kin:output"
-
\end_inset
\end_layout
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Subsubsection
Kinematic Earthquake Rupture Parameters
\end_layout
@@ -2247,7 +2232,7 @@
\begin_layout Standard
The current release of PyLith supports specification of the evolution of
fault slip using analytical expressions for the slip time history at each
- point where the parameters for the slip time function may vary over the
+ point, where the parameters for the slip time function may vary over the
fault surface.
Currently, three slip time functions are available: (1) a step-function
for quasi-static modeling of earthquake rupture, (2) a constant slip rate
@@ -2369,6 +2354,21 @@
\begin_layout Standard
\noindent
\align center
+\begin_inset Caption
+
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "tab:step-function-db-params"
+
+\end_inset
+
+Values in spatial database used as parameters in the step function slip
+ time function.
+\end_layout
+
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="3">
<features>
@@ -2554,30 +2554,11 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Values in spatial database used as parameters in the step function slip
- time function.
-\end_layout
-
\end_inset
-\begin_inset LatexCommand label
-name "tab:step-function-db-params"
-
-\end_inset
-
-
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Paragraph
Constant Slip Rate Slip Time Function
\end_layout
@@ -2685,6 +2666,21 @@
\begin_layout Standard
\noindent
\align center
+\begin_inset Caption
+
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "tab:const-slip-rate-db-params"
+
+\end_inset
+
+Values in spatial database used as parameters in the constant slip rate
+ slip time function.
+\end_layout
+
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="3">
<features>
@@ -2870,30 +2866,11 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Values in spatial database used as parameters in the constant slip rate
- slip time function.
-\end_layout
-
\end_inset
-\begin_inset LatexCommand label
-name "tab:const-slip-rate-db-params"
-
-\end_inset
-
-
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Paragraph
Brune Slip Time Function
\end_layout
@@ -3021,6 +2998,20 @@
\begin_layout Standard
\noindent
\align center
+\begin_inset Caption
+
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "tab:Brune-slip-db-params"
+
+\end_inset
+
+Values in spatial database used as parameters in the Brune slip time function.
+\end_layout
+
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="6" columns="3">
<features>
@@ -3243,29 +3234,11 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Values in spatial database used as parameters in the Brune slip time function.
-\end_layout
-
\end_inset
-\begin_inset LatexCommand label
-name "tab:Brune-slip-db-params"
-
-\end_inset
-
-
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Section
Gravitational Body Forces
\end_layout
@@ -3326,8 +3299,8 @@
This is appropriate for three-dimensional problems where the gravity vector
is aligned with the negative z-axis, as would be the case in a geographic-proje
cted coordinate system or a generic Cartesian coordinate system.
- For cases in which the curvature of the Earth should be considered, the
- spatialdata package provides an Earth-centered, Earth-fixed (ECEF) coordinate
+ For cases in which the curvature of the earth should be considered, the
+ spatialdata package provides an earth-centered, earth-fixed (ECEF) coordinate
system and a local georeferenced Cartesian system; in each of these cases
the orientation vector is computed automatically, although this feature
has not been tested.
@@ -3335,7 +3308,7 @@
the vector will need to be explicitly specified.
For example, in a two-dimensional problem, the vector might be specified
as (0, -1, 0).
- The vector still has three components, although the extra components are
+ The vector still has three components, although the extra component is
not used.
\end_layout
Modified: short/3D/PyLith/trunk/doc/userguide/fileformats/fileformats.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/fileformats/fileformats.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/fileformats/fileformats.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -1,4 +1,4 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -454,7 +454,7 @@
\end_layout
\begin_layout Standard
-SimplDB spatial database files contain a header describing the set of points
+SimpleDB spatial database files contain a header describing the set of points
and then the data with each line listing the coordinates of a point followed
by the values of the fields for that point.
@@ -520,7 +520,7 @@
\end_layout
\begin_layout LyX-Code
- num-values = 3 // number of values in the databasae
+ num-values = 3 // number of values in the database
\end_layout
\begin_layout LyX-Code
@@ -702,7 +702,7 @@
Alternatively, refer to the documentation for the
\begin_inset LatexCommand htmlurl
name "Proj.4 Cartographic Projections library"
-target "proj.maptools.org"
+target "trac.osgeo.org/proj"
\end_inset
@@ -763,7 +763,7 @@
\end_layout
\begin_layout Standard
-This coordinate system is for geographic coordinates, such as longtitude
+This coordinate system is for geographic coordinates, such as longitude
and latitude.
Specification of the location in three-dimensions is supported.
The vertical datum can be either the reference ellipsoid or mean sea level.
@@ -811,7 +811,7 @@
\end_layout
\begin_layout LyX-Code
- ellipspod = WGS84
+ ellipsoid = WGS84
\end_layout
\begin_layout LyX-Code
@@ -954,7 +954,7 @@
\end_layout
\begin_layout LyX-Code
- ellipspod = WGS84
+ ellipsoid = WGS84
\end_layout
\begin_layout LyX-Code
@@ -1179,7 +1179,7 @@
\end_layout
\begin_layout LyX-Code
- ellipspod = WGS84
+ ellipsoid = WGS84
\end_layout
\begin_layout LyX-Code
@@ -1248,7 +1248,7 @@
\end_layout
\begin_layout LyX-Code
- // roundoff errors it is best to pick a location near the center of
+ // round-off errors it is best to pick a location near the center of
\end_layout
\begin_layout LyX-Code
Modified: short/3D/PyLith/trunk/doc/userguide/glossary.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/glossary.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/glossary.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -1,4 +1,4 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -41,6 +41,7 @@
\tracking_changes false
\output_changes false
\author ""
+\author ""
\end_header
\begin_body
@@ -59,7 +60,7 @@
finite element mesh based upon a covering relation.
For example, segments are covered by their endpoints, faces by their bounding
edges, etc.
- Geometry is absent from the sieve, and is repesented instead by a coordinate
+ Geometry is absent from the sieve, and is represented instead by a coordinate
section.
Sieves can also be understood as directed acyclic graphs, where we call
the constituents points and arrows.
Modified: short/3D/PyLith/trunk/doc/userguide/install/install.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/install/install.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/install/install.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -763,7 +763,7 @@
\end_layout
\begin_layout Standard
-PETSc itself depends upon several other sofware packages.
+PETSc itself depends upon several other software packages.
Fortunately, PETSc's configuration script can automatically download and
build these software packages for you.
\end_layout
@@ -2231,12 +2231,12 @@
.
After unpacking the source, run the prepackaged shell script to configure
- Spacialdata for your system.
+ Spatialdata for your system.
Finally, use the
\family typewriter
make
\family default
- utility to build and install Spacialdata.
+ utility to build and install Spatialdata.
\end_layout
\begin_layout Subsubsection
@@ -2244,7 +2244,7 @@
\end_layout
\begin_layout Standard
-Download Spacialdata from the
+Download Spatialdata from the
\begin_inset LatexCommand htmlurl
name "PyLith web page"
target "geodynamics.org/cig/software/packages/short/pylith"
@@ -2271,7 +2271,7 @@
\end_layout
\begin_layout Subsubsection
-Spacialdata Installation Procedure
+Spatialdata Installation Procedure
\end_layout
\begin_layout Quote
Modified: short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -280,7 +280,7 @@
).
This permits adding, replacing, and rewriting modules without affecting
other parts of the code.
- This code structure simplifies code maintenance and developement.
+ This code structure simplifies code maintenance and development.
Extending the set of code features is also easier, since developers can
create new modules derived from the existing ones.
\end_layout
Modified: short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -2809,8 +2809,9 @@
In a more general sense, initial values for state variables may be used
to provide values that are consistent with any set of conditions that occurred
prior to the beginning of a simulation.
- In PyLith 1.3, we presently only allow the specification of initial stresses.
- In future versions, however, we will allow a more general specification
+ The current release of PyLith only allows the specification of initial
+ stresses.
+ In future releases, however, we will allow a more general specification
of initial state values.
\end_layout
@@ -2826,22 +2827,17 @@
\family typewriter
use_initial_state
\family default
- flag may be set to true:
-\end_layout
+ 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
+reference "sec:Tutorial-3d-hex8"
-\begin_layout LyX-Code
-[pylithapp.problem.materials.material]
-\end_layout
+\end_inset
-\begin_layout LyX-Code
-use_initial_state = True
+:
\end_layout
-\begin_layout Standard
-Initial state values are specified using a spatial database, so it is necessary
- to provide the name of the database as well:
-\end_layout
-
\begin_layout LyX-Code
[pylithapp.timedependent.materials.elastic]
\end_layout
@@ -2854,19 +2850,5 @@
initial_state_db.iohandler.filename = initial_state.spatialdb
\end_layout
-\begin_layout Standard
-The settings above are from an example in the
-\family typewriter
-3D/hex8
-\family default
- directory, which is described in
-\begin_inset LatexCommand ref
-reference "sec:Tutorial-3d-hex8"
-
-\end_inset
-
-.
-\end_layout
-
\end_body
\end_document
Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -363,7 +363,7 @@
file format is intended for applications in which PyLith input files are
generated by another program, e.g., a GUI, web application, or a high-level
structured editor.
- This file fomat will not be discussed further here, but if you are interested
+ This file format will not be discussed further here, but if you are interested
in using
\family typewriter
.pml
@@ -1400,8 +1400,8 @@
one value included in a search query, the interpolation of each value will
be done independently.
Time dependent variations of a field are not supported in these files.
- Spatial database files can specifiy spatial variations over zero, one,
- two, and three dimensions.
+ Spatial database files can specify spatial variations over zero, one, two,
+ and three dimensions.
Zero dimensional variations correspond to uniform values.
One-dimensional spatial variations correspond to piecewise linear variations,
which need not coincide with coordinate axes.
@@ -1424,7 +1424,7 @@
system as the mesh coordinate system, provided the two coordinate systems
are compatible.
Examples of compatible coordinate systems include geographic coordinates
- (longitude/latitude/elevation), and projected coordiates (e.g., coordinates
+ (longitude/latitude/elevation), and projected coordinates (e.g., coordinates
in a transverse Mercator projection).
Spatial database queries use the
\begin_inset LatexCommand htmlurl
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -316,57 +316,14 @@
\begin_layout Standard
In addition to the mesh, the example problems share additional information.
- For problems of this type, it is generally useful to create a file named
-
+ As in previous examples, we place this information in
\family typewriter
pylithapp.cfg
\family default
- in the run directory, since this file is read automatically every time
- PyLith is run.
- Settings specific to a particular problem may be placed in other
+.
+ Since these examples use CUBIT format, in this file we set the importer
+ to
\family typewriter
-.cfg
-\family default
- files, as described later, and then those files are placed on the command
- line.
- The settings contained in
-\family typewriter
-pylithapp.cfg
-\family default
- for this problem consist of:
-\end_layout
-
-\begin_layout Description
-pylithapp.journal.info Settings that control the verbosity of the output for
- the different components.
-\end_layout
-
-\begin_layout Description
-pylithapp.mesh_generator Settings that control mesh importing, such as the
- importer type, the filename, and the spatial dimension of the mesh.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent Settings that control the problem, such as the total
- time, time step size, and spatial dimension.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials Settings that control the material type,
- specify which material IDs are to be associated with a particular material
- type, and give the name of the spatial database containing material parameters
- for the mesh.
- The quadrature information is also given.
-\end_layout
-
-\begin_layout Description
-pylithapp.petsc PETSc settings to use for the problem, such as the preconditioner
- type.
-\end_layout
-
-\begin_layout Standard
-Since these examples use CUBIT format, we set the importer to
-\family typewriter
MeshIOCubit
\family default
:
@@ -518,15 +475,10 @@
shearxy.cfg
\family default
.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem
- and specifies the array of boundary conditions.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.implicit Specifies an array of two output managers,
one for the full domain, and another for a subdomain corresponding to the
ground surface.
@@ -605,15 +557,6 @@
\end_layout
\begin_layout Description
-pylithapp.problem.formulation.output.domain.writer Gives the base filename for
- VTK output over the entire domain (
-\family typewriter
-shearxy.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
pylithapp.problem.formulation.output.subdomain Gives the label of the nodeset
defining the subdomain and gives the base filename for VTK output over
the subdomain corresponding to the ground surface (
@@ -654,13 +597,7 @@
shearxy.cfg
\family default
.
- The format of all spatial database files is similar.
- Because data are being specified using two control points (rather than
- being uniform over the mesh, for example), the data dimension is one.
-\end_layout
-
-\begin_layout Standard
-The files containing common information (
+ The files containing common information (
\family typewriter
box_hex8_1000m.exo
\family default
@@ -693,33 +630,17 @@
\end_layout
\begin_layout Standard
-Once the problem has run, six files will be produced.
- The first file is named
+The output file
\family typewriter
-shearxy_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
shearxy-statevars-elastic_t0000000.vtk
\family default
-.
- This file contains the state variables for each cell in the material group
-
+ contains the state variables for each cell in the material group
\family typewriter
elastic
\family default
.
- The default fields are the total strain and stress fields.
- These values are computed at each quadrature point in the cell.
+ The default fields are the total strain and stress fields and are computed
+ at each quadrature point in the cell.
There are eight quadrature points for each cell; however, we have requested
that these values be averaged, so there is a single set of values per cell.
The third file (
@@ -750,11 +671,11 @@
shearxy-statevars-viscoelastic_info.vtk
\family default
) are exactly analogous to the corresponding files for the elastic material.
- The final file (
+ The file
\family typewriter
shearxy-groundsurf_t0000000.vtk
\family default
-) is analogous to
+ is analogous to
\family typewriter
shearxy_t0000000.vtk
\family default
@@ -765,12 +686,7 @@
\family typewriter
shearxy_t0000000.vtk
\family default
-, so they are quadrilaterials rather than hexahedra.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
+, 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
@@ -856,136 +772,9 @@
dislocation.cfg
\family default
.
- These settings are:
+
\end_layout
-\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem,
- the array of boundary conditions, and the array of interfaces.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.implicit Specifies an array of two output managers,
- one for the full domain, and another for a subdomain corresponding to the
- ground surface.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.bc.x_pos Specifies the boundary conditions for the
- right side of the mesh, defining which degrees of freedom are being constrained
- (
-\family typewriter
-x
-\family default
- and
-\family typewriter
-y
-\family default
-), providing the label (defined in
-\family typewriter
-box_hex8_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
- condition, which sets the displacements to zero.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.bc.x_neg Specifies the boundary conditions for the
- left side of the mesh, defining which degrees of freedom are being constrained
- (
-\family typewriter
-x
-\family default
- and
-\family typewriter
-y
-\family default
-), providing the label (defined in
-\family typewriter
-box_hex8_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
- condition, which sets the displacements to zero.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.bc.z_neg Specifies the boundary conditions for the
- bottom of the mesh, defining which degrees of freedom are being constrained
- (z), providing the label (defined in
-\family typewriter
-box_hex8_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
- condition, which sets the displacements to zero.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.interfaces Gives the label (defined in
-\family typewriter
-box_hex8_1000m.exo
-\family default
-) defining the points on the fault, provides quadrature information, and
- then gives database names for material properties (needed for conditioning),
- fault slip, peak fault slip rate, and fault slip time.
-\end_layout
-
-\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output over the entire domain (
-\family typewriter
-dislocation.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.problem.formulation.output.subdomain Gives the label of the nodeset
- defining the subdomain and gives the base filename for VTK output over
- the subdomain corresponding to the ground surface (
-\family typewriter
-dislocation-groundsurf.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.interfaces.fault.output.writer Gives the base filename
- for cohesive cell output files (
-\family typewriter
-dislocation-fault.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.elastic.output Gives the base filename for
- state variable output files for the elastic material (
-\family typewriter
-dislocation-statevars-elastic.vtk
-\family default
-), and causes state variables to be averaged over all quadrature points
- in each cell.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.viscoelastic.output Gives the base filename
- for state variable output files for the viscoelastic material (
-\family typewriter
-dislocation-statevars-viscoelastic.vtk
-\family default
-), and causes state variables to be averaged over all quadrature points
- in each cell.
-\end_layout
-
\begin_layout Standard
The fault example requires three additional database files that were not
needed for the simple displacement example.
@@ -1058,103 +847,7 @@
\end_layout
\begin_layout Standard
-Once the problem has run, eight files will be produced.
- The first file is named
-\family typewriter
-dislocation_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-dislocation-statevars-elastic_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell in the material group
-
-\family typewriter
-elastic
-\family default
-.
- The default fields are the total strain and stress fields.
- These values are computed at each quadrature point in the cell.
- There are eight quadrature points for each cell; however, we have requested
- that these values be averaged, so there is a single set of values per cell.
- The third file (
-\family typewriter
-dislocation-statevars-elastic_info.vtk
-\family default
-) gives the material properties used for the elastic material.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- The files are for the viscoelastic material (
-\family typewriter
-dislocation-statevars-viscoelastic_t0000000.vtk
-\family default
- and
-\family typewriter
-dislocation-statevars-viscoelastic_info.vtk
-\family default
-) are exactly analogous to the corresponding files for the elastic material.
- The sixth file (
-\family typewriter
-dislocation-groundsurf_t0000000.vtk
-\family default
-) is analogous to
-\family typewriter
-dislocation_
-\newline
-t0000000.vtk
-\family default
-, but in this case the results are only given for a subset of the mesh correspon
-ding to the ground surface.
- Also, the cells in this file are one dimension lower than the cells described
- in
-\family typewriter
-dislocation_t0000000
-\newline
-.vtk
-\family default
-, so they are quadrilaterials rather than hexahedra.
- The seventh file (
-\family typewriter
-dislocation-fault_t0000000.
-\newline
-vtk
-\family default
-) gives the specified fault slip for each vertex on the fault, along with
- the computed traction change for the cohesive cell.
- The final file (
-\family typewriter
-dislocation-fault_info.vtk
-\family default
-) provides information such as the normal direction, final slip, and slip
- time for each vertex on the fault.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
- If the problem ran correctly, you should be able to generate a figure such
+If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset LatexCommand vref
reference "fig:3dhex-disloc"
@@ -1223,7 +916,7 @@
\end_inset
-wherev
+where
\begin_inset Formula $\rho$
\end_inset
@@ -1250,7 +943,7 @@
gravity.cfg
\family default
.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
@@ -1276,12 +969,6 @@
\end_layout
\begin_layout Description
-pylithapp.timedependent.implicit Specifies an array of two output managers,
- one for the full domain, and another for a subdomain corresponding to the
- ground surface.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.x_pos Specifies the boundary conditions for the
right side of the mesh, defining which degrees of freedom are being constrained
(
@@ -1377,45 +1064,6 @@
condition, which sets the displacements to zero.
\end_layout
-\begin_layout Description
-pylithapp.problem.formulation.output.domain.writer Gives the base filename for
- VTK output over the entire domain (
-\family typewriter
-gravity.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.problem.formulation.output.subdomain Gives the label of the nodeset
- defining the subdomain and gives the base filename for VTK output over
- the subdomain corresponding to the ground surface (
-\family typewriter
-gravity-groundsurf.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.elastic.output Gives the base filename for
- state variable output files for the elastic material (
-\family typewriter
-gravity-statevars-elastic.vtk
-\family default
-), and causes state variables to be averaged over all quadrature points
- in each cell.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.viscoelastic.output Gives the base filename
- for state variable output files for the viscoelastic material (
-\family typewriter
-gravity-statevars-viscoelastic.vtk
-\family default
-), and causes state variables to be averaged over all quadrature points
- in each cell.
-\end_layout
-
\begin_layout Standard
The files containing common information (
\family typewriter
@@ -1452,89 +1100,7 @@
\end_layout
\begin_layout Standard
-Once the problem has run, six files will be produced.
- The first file is named
-\family typewriter
-gravity_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-gravity-statevars-elastic_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell in the material group
-
-\family typewriter
-elastic
-\family default
-.
- The default fields are the total strain and stress fields.
- These values are computed at each quadrature point in the cell.
- There are eight quadrature points for each cell; however, we have requested
- that these values be averaged, so there is a single set of values per cell.
- The third file (
-\family typewriter
-gravity-statevars-elastic_info.vtk
-\family default
-) gives the material properties used for the elastic material.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- The files for the
-\family typewriter
-
-\family default
-viscoelastic material
-\family typewriter
- (gravity-statevars-viscoelastic_t0000000.vtk
-\family default
- and
-\family typewriter
-gravity-statevars-viscoelastic_info.vtk
-\family default
-) are exactly analogous to the corresponding files for the elastic material.
- The sixth file (
-\family typewriter
-gravity-groundsurf_t0000000.vtk
-\family default
-) is analogous to
-\family typewriter
-gravity_t0000000.vtk
-\family default
-, but in this case the results are only given for a subset of the mesh correspon
-ding to the ground surface.
- Also, the cells in this file are one dimension lower than the cells described
- in
-\family typewriter
-gravity_t0000000.vtk
-\family default
-, so they are quadrilaterals rather than hexahedra.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
- If the problem ran correctly, you should be able to generate a figure such
+If the problem ran correctly, you should be able to generate a figure such
as
\begin_inset LatexCommand vref
reference "fig:3dhex-gravity"
@@ -1602,7 +1168,8 @@
balance the stresses due to gravitational body forces.
The problem is identical to the previous problem, except for the use of
initial stresses.
- The stress solution should be identical, but there should be no displacements.
+ The stress solution should be identical, but there should be no displacements
+ or strains.
Parameter settings that override or augment those in
\family typewriter
pylithapp.cfg
@@ -1612,7 +1179,7 @@
gravity_istress.cfg
\family default
.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
@@ -1638,115 +1205,6 @@
\end_layout
\begin_layout Description
-pylithapp.timedependent.implicit Specifies an array of two output managers,
- one for the full domain, and another for a subdomain corresponding to the
- ground surface.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.bc.x_pos Specifies the boundary conditions for the
- right side of the mesh, defining which degrees of freedom are being constrained
- (
-\family typewriter
-x
-\family default
-), providing the label (defined in
-\family typewriter
-box_hex8_
-\newline
-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
- condition, which sets the displacements to zero.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.bc.x_neg Specifies the boundary conditions for the
- left side of the mesh, defining which degrees of freedom are being constrained
- (
-\family typewriter
-x
-\family default
-), providing the label (defined in
-\family typewriter
-box_hex8_
-\newline
-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
- condition, which sets the displacements to zero.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.bc.y_pos Specifies the boundary conditions for the
- back of the mesh, defining which degrees of freedom are being constrained
- (y), providing the label (defined in
-\family typewriter
-box_hex8_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
- condition, which sets the displacements to zero.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.bc.y_neg Specifies the boundary conditions for the
- front of the mesh, defining which degrees of freedom are being constrained
- (y), providing the label (defined in
-\family typewriter
-box_hex8_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
- condition, which sets the displacements to zero.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.bc.z_neg Specifies the boundary conditions for the
- bottom of the mesh, defining which degrees of freedom are being constrained
- (z), providing the label (defined in
-\family typewriter
-box_hex8_1000m.
-\newline
-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
- condition, which sets the displacements to zero.
-\end_layout
-
-\begin_layout Description
-pylithapp.problem.formulation.output.domain.writer Gives the base filename for
- VTK output over the entire domain (
-\family typewriter
-gravity.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.problem.formulation.output.subdomain Gives the label of the nodeset
- defining the subdomain and gives the base filename for VTK output over
- the subdomain corresponding to the ground surface (
-\family typewriter
-gravity-groundsurf.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.materials.elastic Sets the
\family typewriter
use_initial_state
@@ -1786,26 +1244,6 @@
.
\end_layout
-\begin_layout Description
-pylithapp.timedependent.materials.elastic.output Gives the base filename for
- state variable output files for the elastic material (
-\family typewriter
-gravity-statevars-elastic.vtk
-\family default
-), and causes state variables to be averaged over all quadrature points
- in each cell.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.viscoelastic.output Gives the base filename
- for state variable output files for the viscoelastic material (
-\family typewriter
-gravity-statevars-viscoelastic.vtk
-\family default
-), and causes state variables to be averaged over all quadrature points
- in each cell.
-\end_layout
-
\begin_layout Standard
The files containing common information (
\family typewriter
@@ -1846,89 +1284,7 @@
\end_layout
\begin_layout Standard
-Once the problem has run, six files will be produced.
- The first file is named
-\family typewriter
-gravity_istress_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-gravity_istress-statevars-elastic_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell in the material group
-
-\family typewriter
-elastic
-\family default
-.
- The default fields are the total strain and stress fields.
- These values are computed at each quadrature point in the cell.
- There are eight quadrature points for each cell; however, we have requested
- that these values be averaged, so there is a single set of values per cell.
- The third file (
-\family typewriter
-gravity_istress-statevars-elastic_info.vtk
-\family default
-) gives the material properties used for the elastic material.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- The files
-\family typewriter
-for the
-\family default
-viscoelastic material
-\family typewriter
- (gravity_istress-statevars-viscoelastic_t0000000.vtk
-\family default
- and
-\family typewriter
-gravity_istress-statevars-viscoelastic_info.vtk
-\family default
-) are exactly analogous to the corresponding files for the elastic material.
- The sixth file (
-\family typewriter
-gravity_istress-groundsurf_t0000000.vtk
-\family default
-) is analogous to
-\family typewriter
-gravity_istress_t0000000.vtk
-\family default
-, but in this case the results are only given for a subset of the mesh correspon
-ding to the ground surface.
- Also, the cells in this file are one dimension lower than the cells described
- in
-\family typewriter
-gravity_t0000000.vtk
-\family default
-, so they are quadrilaterials rather than hexahedra.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
- If the problem ran correctly, you should be able to generate a figure such
+If the problem ran correctly, you should be able to generate a figure such
as
\begin_inset LatexCommand vref
reference "fig:3dhex-gravity_istress"
@@ -2023,7 +1379,7 @@
savageprescott.cfg
\family default
.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
@@ -2033,12 +1389,6 @@
\end_layout
\begin_layout Description
-pylithapp.timedependent.implicit Specifies an array of two output managers,
- one for the full domain, and another for a subdomain corresponding to the
- ground surface.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.x_pos Specifies the boundary conditions for the
right side of the mesh, defining which degrees of freedom are being constrained
(
@@ -2282,22 +1632,8 @@
savageprescott-statevars-elastic_info.vtk
\family default
gives the material properties used for the elastic material.
- Since we have not specified which properties to write, the default properties
- (
+ The files for the viscoelastic material (
\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- The files are for the viscoelastic material (
-\family typewriter
savageprescott-statevars-viscoelastic_tXXXX.vtk
\family default
and
@@ -2315,12 +1651,6 @@
\family default
, but in this case the results are only given for a subset of the mesh correspon
ding to the ground surface (and are output more frequently).
- Also, the cells in this file are one dimension lower than the cells described
- in
-\family typewriter
-savageprescott_tXXXX.vtk
-\family default
-, so they are quadrilaterials rather than hexahedra.
The files of the form
\family typewriter
savageprescott-fault_tXXXX.vtk
@@ -2344,11 +1674,6 @@
cfg
\family default
.
- All of the
-\family typewriter
-.vtk
-\family default
- 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
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -117,7 +117,7 @@
.
You may use other visualization software, but some adaption from what is
described here will be necessary.
- Alternatively, you can complete a subset of the tutorial using files provided
+ Furthermore, you can complete a subset of the tutorial using files provided
(as described below), skipping the steps for which you do not have the
proper software packages installed.
\end_layout
@@ -127,7 +127,7 @@
\family typewriter
examples
\family default
- directory in the top-level PyLith directory.
+ directory under the top-level PyLith directory.
There are five examples in
\family typewriter
examples/twocells
@@ -143,7 +143,7 @@
\family default
, use external mesh generation software to create the meshes.
All of the files used in the example problems are extensively documented
- with commented files.
+ with comments.
\end_layout
\begin_layout Standard
@@ -196,16 +196,20 @@
\end_layout
\begin_layout Standard
-The examples directory also contains other examples which are not described
- in this chapter.
+The
+\family typewriter
+examples
+\family default
+ directory also contains other examples which are not described in this
+ chapter.
The files associated with these examples contain comments to explain the
problems they solve.
Once you understand the examples described in detail in the previous sections
of this chapter, you should have little trouble understanding these additional
- examples.
- Currently, these problems are very simple examples of using dynamic time
- stepping with absorbing boundaries to simulate shear wave propagation in
- a 2D or 3D bar.
+ ones.
+ Currently, these problems are very simple cases of using dynamic time stepping
+ with absorbing boundaries to simulate shear wave propagation in a 2D or
+ 3D bar.
More complex examples of wave propagation problems will be included in
future releases.
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/twohex8.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/twohex8.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twohex8/twohex8.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -139,18 +139,6 @@
twohex8.mesh
\family default
, which is in PyLith mesh ASCII format.
- This file format is described in Appendix
-\begin_inset LatexCommand ref
-reference "cha:File-Formats"
-
-\end_inset
-
-.
- This file describes the dimensionality of the problem (1D, 2D, or 3D),
- the coordinates of the vertices (nodes), the vertices composing each cell
- (element), the material ID to be associated with each cell, and then provides
- groups of vertices that may be used to define faults or surfaces to which
- boundary conditions may be applied.
\end_layout
\begin_layout Standard
@@ -199,73 +187,11 @@
\end_layout
\begin_layout Standard
-In addition to the mesh, the three example problems share additional information.
- For problems of this type, it is generally useful to create a file named
-
+In addition to the mesh, the three example problems share additional information
+, which we place in
\family typewriter
pylithapp.cfg
\family default
- in the run directory, since this file is read automatically every time
- PyLith is run.
- Settings specific to a particular problem may be placed in other
-\family typewriter
-.cfg
-\family default
- files, as described later, and then those files are placed on the command
- line.
- The settings contained in
-\family typewriter
-pylithapp.cfg
-\family default
- for this problem consist of:
-\end_layout
-
-\begin_layout Description
-pylithapp.journal.info Settings that control the verbosity of the output for
- the different components.
-\end_layout
-
-\begin_layout Description
-pylithapp.mesh_generator Settings that control mesh importing, such as the
- importer type, the filename, and the spatial dimension of the mesh.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent Settings that control the problem, such as the total
- time, time step size, and spatial dimension.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials Settings that control the material type,
- specify which material IDs are to be associated with a particular material
- type, and give the name of the spatial database containing material parameters
- for the mesh.
- The quadrature information is also given.
-\end_layout
-
-\begin_layout Description
-pylithapp.petsc PETSc settings to use for the problem, such as the preconditioner
- type.
-\end_layout
-
-\begin_layout Standard
-All of the problems in this directory use the same material database, as
- specified under
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
-pylithapp.timedependent.materials
-\family default
-
-\end_layout
-
-\begin_layout Standard
-in
-\family typewriter
-pylithapp.cfg
-\family default
.
Note that in this example we make use of the UniformDB spatial database,
rather than the SimpleDB implementation used to specify the physical properties
@@ -335,20 +261,6 @@
quadrature.cell.dimension = 3
\end_layout
-\begin_layout Standard
-Rather than specifying a database file, as for the other examples, the propertie
-s are specified directly in the
-\family typewriter
-.cfg
-\family default
- file.
- In
-\family typewriter
-pylithapp.cfg
-\family default
-.
-\end_layout
-
\begin_layout Subsection
Axial Displacement Example
\end_layout
@@ -365,23 +277,10 @@
axialdisp.cfg
\family default
.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem
- and defines two boundary condition groups with the names
-\family typewriter
-x_neg
-\family default
- and
-\family typewriter
-x_pos
-\family default
-.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.x_neg Defines which degrees of freedom are being
constrained (x, y, and z), gives the label (
\family typewriter
@@ -420,18 +319,6 @@
\end_layout
\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output
-\newline
-(
-\family typewriter
-axialdisp.vtk
-\family default
-) and defines the format to use when defining the output filenames for each
- time step.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.materials.material.output Defines the filter to be used
when writing cell state variables (average over the quadrature points of
the cell), specifies which state variables and properties to output, gives
@@ -451,9 +338,8 @@
.
Since data are being specified using two control points (rather than being
uniform over the mesh, for example), the data dimension is one.
- Note that since we are using a Maxwell viscoelastic model, additional state
- variables and properties may be output if they are specified.
- Otherwise, the default values will be used:
+ Note that since we are using a Maxwell viscoelastic model, we request that
+ additional state variables and properties be output:
\end_layout
\begin_layout LyX-Code
@@ -517,7 +403,7 @@
(recall that the decimal point is removed in the filename).
As a result, the filenames contain the time in tenths of a year.
These files will contain mesh information as well as displacement values
- at the mesh vertices.
+ for the mesh vertices at the given time.
The second set of files will have names such as
\family typewriter
axialdisp-statevars_txxxx.vtk
@@ -558,11 +444,6 @@
maxwell_time
\family default
).
- All of the
-\family typewriter
-.vtk
-\family default
- 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
@@ -630,23 +511,10 @@
sheardisp.cfg
\family default
.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem
- and defines two boundary condition groups with the names
-\family typewriter
-x_neg
-\family default
- and
-\family typewriter
-x_pos
-\family default
-.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.x_neg Defines which degrees of freedom are being
constrained (x, y, and z), gives the label (
\family typewriter
@@ -684,26 +552,6 @@
).
\end_layout
-\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output
-\newline
-(
-\family typewriter
-sheardisp.vtk
-\family default
-) and defines the format to use when defining the output filenames for each
- time step.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.material.output Defines the filter to be used
- when writing cell state variables (average over the quadrature points of
- the cell), specifies which state variables and properties to output, gives
- the base filename for state variable output files, and defines the format
- to use when defining the output filenames for each time step.
-\end_layout
-
\begin_layout Standard
The values for the Dirichlet boundary conditions are given in the file
\family typewriter
@@ -716,25 +564,7 @@
.
Data are being specified at two control points (rather than being uniform
over the mesh, for example), so the data dimension is one.
- Note that since we are using a Maxwell viscoelastic model, additional state
- variables and properties may be output if they are specified.
- Otherwise, the default values will be used:
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.materials.material.output]
-\end_layout
-
-\begin_layout LyX-Code
-cell_data_fields = [total_strain,viscous_strain,stress]
-\end_layout
-
-\begin_layout LyX-Code
-cell_info_fields = [mu,lambda,density,maxwell_time]
-\end_layout
-
-\begin_layout Standard
-The files containing common information (
+ The files containing common information (
\family typewriter
twohex8.mesh
\family default
@@ -759,65 +589,7 @@
\end_layout
\begin_layout Standard
-Once the problem has run, two sets of files will be produced, along with
- one additional file.
- The first set will have filenames such as
-\family typewriter
-sheardisp_txxxx.vtk
-\family default
-, where
-\family typewriter
-xxxx
-\family default
- is the time in tenths of a year (as in the previous example).
- These files will contain mesh information as well as displacement values
- at the mesh vertices.
- The second set of files will have names such as
-\family typewriter
-axialdisp-statevars_txxxx.vtk
-\family default
-, where
-\family typewriter
-xxxx
-\family default
- is the time in tenths of a year.
- These files contain the state variables for each cell at the given time.
- The default fields are the total strain and stress fields; however, we
- have also requested the viscous strains.
- As specified in
-\family typewriter
-sheardisp.cfg
-\family default
-, these values are averaged over each cell.
- The final file (
-\family typewriter
-sheardisp-statevars_info.vtk
-\family default
-) gives the material properties used for the problem.
- We have requested all of the properties available for this material model
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-,
-\family typewriter
-maxwell_time
-\family default
-).
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
- If the problem ran correctly, you should be able to generate a figure such
+If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset LatexCommand ref
reference "fig:twohex8-shear"
@@ -825,6 +597,9 @@
\end_inset
, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
@@ -887,32 +662,10 @@
dislocation.cfg
\family default
.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
-pylithapp.journal.info Turns on journaling for 2D quadrature (used for 3D
- faults) and for cohesive kinematic faults.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem,
- defines two boundary condition groups with the names
-\family typewriter
-x_neg
-\family default
- and
-\family typewriter
-x_pos
-\family default
-, and defines a single fault group,
-\family typewriter
-fault
-\family default
-.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.x_neg Defines which degrees of freedom are being
constrained (x, y, and z), gives the label (
\family typewriter
@@ -952,32 +705,6 @@
fault slip, peak fault slip rate, and fault slip time.
\end_layout
-\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output
-\newline
-(
-\family typewriter
-dislocation.vtk
-\family default
-) and defines the format to use when defining the output filenames for each
- time step.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.interfaces.fault.output.writer Gives the base filename
- for cohesive cell output files, and defines the format to use when defining
- the output filenames for each time step.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.material.output Defines the filter to be used
- when writing cell state variables (average the quadrature points for the
- cell), specifies which state variables and properties to output, gives
- the base filename for state variable output files, and defines the format
- to use when defining the output filenames for each time step.
-\end_layout
-
\begin_layout Standard
The fault example requires three additional database files that were not
needed for the simple displacement examples.
@@ -1003,25 +730,7 @@
dislocation_sliptime.spatialdb
\family default
.
- Note that since we are using a Maxwell viscoelastic model, additional state
- variables and properties may be output if they are specified.
- Otherwise, the default values will be used:
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.materials.material.output]
-\end_layout
-
-\begin_layout LyX-Code
-cell_data_fields = [total_strain,viscous_strain,stress]
-\end_layout
-
-\begin_layout LyX-Code
-cell_info_fields = [mu,lambda,density,maxwell_time]
-\end_layout
-
-\begin_layout Standard
-The files containing common information (
+ The files containing common information (
\family typewriter
\size small
twohex8.mesh
@@ -1054,78 +763,7 @@
\end_layout
\begin_layout Standard
-Once the problem has run, three sets of files are produced, along with two
- additional files.
- The first set will have filenames such as
-\family typewriter
-dislocation_txxxx.vtk
-\family default
-, where
-\family typewriter
-xxxx
-\family default
- is the time in tenths of a year.
- These files will contain mesh information as well as displacement values
- at the mesh vertices.
- The second set of files will have names such as
-\family typewriter
-dislocation-statevars_txxxx.vtk
-\family default
-, where
-\family typewriter
-xxxx
-\family default
- is the time in tenths of a year.
- These files contain the state variables for each cell at the given time.
- The default fields are the total strain and stress fields; however, we
- have also requested the viscous strains.
- As specified in
-\family typewriter
-dislocation.cfg
-\family default
-, these values are averaged over each cell.
- The final set of files will have names such as
-\family typewriter
-dislocation-fault_txxxx.vtk
-\family default
-.
- These files give the specified fault slip for each vertex on the fault,
- along with the computed traction change for the cohesive cell.
- One of the additional files (
-\family typewriter
-dislocation-statevars_info.vtk
-\family default
-) gives the material properties used for the problem.
- We have requested all of the properties available for this material model
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-,
-\family typewriter
-maxwell_time
-\family default
-).
- The final additional file (
-\family typewriter
-dislocation-fault_info.vtk
-\family default
-) provides information such as the normal direction, final slip, and slip
- time for each vertex on the fault.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
- If the problem ran correctly, you should be able to generate a figure such
+If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset LatexCommand ref
reference "fig:twohex8-disloc"
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/twoquad4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/twoquad4.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twoquad4/twoquad4.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -1,4 +1,4 @@
-#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -111,7 +111,7 @@
Due to the simple geometry of the problem, the mesh may be constructed
by hand, using PyLith mesh ASCII format to describe the mesh.
In this tutorial, we will walk through the steps necessary to construct,
- run, and view three problems that use the same mesh.
+ run, and view four problems that use the same mesh.
In addition to this manual, each of the files for the example problem includes
extensive comments.
\end_layout
@@ -134,14 +134,7 @@
twoquad4.mesh
\family default
, which is in PyLith mesh ASCII format.
- This file format is described in Appendix
-\begin_inset LatexCommand ref
-reference "cha:File-Formats"
-
-\end_inset
-
-.
- This file describes the dimensionality of the problem (1D, 2D, or 3D),
+ This file describes the dimensionality of the problem (in this case 2D),
the coordinates of the vertices (nodes), the vertices composing each cell
(element), the material ID to be associated with each cell, and then provides
groups of vertices that may be used to define faults or surfaces to which
@@ -194,92 +187,20 @@
\end_layout
\begin_layout Standard
-In addition to the mesh, the three example problems share additional information.
- For problems of this type, it is generally useful to create a file named
-
+In addition to the mesh, the four example problems share additional information.
+ As in the previous examples, we place this information in
\family typewriter
pylithapp.cfg
\family default
- in the run directory, since this file is read automatically every time
- PyLith is run.
+, since this file is read automatically every time PyLith is run.
Settings specific to a particular problem may be placed in other
\family typewriter
.cfg
\family default
files, as described later, and then those files are placed on the command
line.
- The settings contained in
-\family typewriter
-pylithapp.cfg
-\family default
- for this problem consist of:
\end_layout
-\begin_layout Description
-pylithapp.journal.info Settings that control the verbosity of the output for
- the different components.
-\end_layout
-
-\begin_layout Description
-pylithapp.mesh_generator Settings that control mesh importing, such as the
- importer type, the filename, and the spatial dimension of the mesh.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent Settings that control the problem, such as the total
- time, time step size, and spatial dimension.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials Settings that control the material type,
- specify which material IDs are to be associated with a particular material
- type, and give the name of the spatial database containing physical properties
- for the material.
- The quadrature information is also given.
-\end_layout
-
-\begin_layout Description
-pylithapp.petsc PETSc settings to use for the problem, such as the preconditioner
- type.
-\end_layout
-
-\begin_layout Standard
-All of the problems in this directory use the same material database, as
- specified under
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
-pylithapp.timedependent.materials
-\family default
-
-\end_layout
-
-\begin_layout Standard
-in
-\family typewriter
-pylithapp.cfg
-\family default
-.
- This information is contained in the file
-\family typewriter
-matprops.spatialdb
-\family default
-.
- Although the material model is specified in
-\family typewriter
-pylithapp.cfg
-\family default
-, the physical properties for the material are given in
-\family typewriter
-matprops.spatialdb
-\family default
-.
- For this example, values describing elastic plane strain material properties
- are given at a single point, resulting in uniform material properties.
-\end_layout
-
\begin_layout Subsection
Axial Displacement Example
\end_layout
@@ -295,15 +216,10 @@
axialdisp.cfg
\family default
.
- These settings are:
+ These include:
\end_layout
\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem
- and specifies the array of boundary conditions.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.x_neg Specifies the boundary conditions for the
left side of the mesh, defining which degrees of freedom are being constrained
(x), giving the label (defined in
@@ -351,28 +267,6 @@
).
\end_layout
-\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output
-\newline
-(
-\family typewriter
-axialdisp.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.material.output Defines the filter to be used
- when writing cell state variables (averages over the quadrature points
- for the cell) and gives the base filename for state variable output files
- (
-\family typewriter
-axialdisp-statevars.vtk
-\family default
-).
-\end_layout
-
\begin_layout Standard
The values for the Dirichlet boundary condition are given in the file
\family typewriter
@@ -418,56 +312,7 @@
\end_layout
\begin_layout Standard
-Once the problem has run, three files will be produced.
- The first file is named
-\family typewriter
-axialdisp_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-axialdisp-statevars_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell.
- The default fields are the total strain and stress fields.
- As specified in
-\family typewriter
-axialdisp.cfg
-\family default
-, these values are averaged over each cell.
- The final file (
-\family typewriter
-axialdisp-statevars_info.vtk
-\family default
-) gives the material properties used for the problem.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
+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
@@ -539,15 +384,10 @@
sheardisp.cfg
\family default
.
- These settings are:
+ These include:
\end_layout
\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem
- and specifies the array of boundary conditions.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.x_neg Specifies the boundary conditions for the
left side of the mesh, defining which degrees of freedom are being constrained
(x and y), giving the label (
@@ -587,28 +427,6 @@
).
\end_layout
-\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output
-\newline
-(
-\family typewriter
-sheardisp.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.material.output Defines the filter to be used
- when writing cell state variables (averages over the quadrature points
- for the cell) and gives the base filename for state variable output files
- (
-\family typewriter
-sheardisp-statevars.vtk
-\family default
-).
-\end_layout
-
\begin_layout Standard
The values for the Dirichlet boundary conditions are described in the file
@@ -657,56 +475,7 @@
\end_layout
\begin_layout Standard
-Once the problem has run, three files will be produced.
- The first file is named
-\family typewriter
-sheardisp_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-sheardisp-statevars_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell.
- The default fields are the total strain and stress fields.
- As specified in
-\family typewriter
-sheardisp.cfg
-\family default
-, these values are averaged over each cell.
- The final file (
-\family typewriter
-sheardisp-statevars_info.vtk
-\family default
-) gives the material properties used for the problem.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
+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
@@ -776,20 +545,10 @@
dislocation.cfg
\family default
.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
-pylithapp.journal.info Turns on journaling for 1D quadrature (used for 2D
- faults) and for cohesive kinematic faults.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem,
- the array of boundary conditions, and the array of interfaces.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.x_neg Specifies the boundary conditions for the
left side of the mesh, defining which degrees of freedom are being constrained
(x and y), giving the label (
@@ -835,37 +594,6 @@
fault slip, peak fault slip rate, and fault slip time.
\end_layout
-\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output
-\newline
-(
-\family typewriter
-dislocation.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.interfaces.fault.output.writer Gives the base filename
- for cohesive cell output files (
-\family typewriter
-dislocation-fault.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.material.output Defines the filter to be used
- when writing cell state variables (averages over the quadrature points
- for the cell) and gives the base filename for state variable output files
- (
-\family typewriter
-dislocation-statevars.vtk
-\family default
-).
-\end_layout
-
\begin_layout Standard
The fault example requires three additional database files that were not
needed for the simple displacement examples.
@@ -929,69 +657,19 @@
\end_layout
\begin_layout Standard
-Once the problem has run, five files are produced.
- The first file is named
+The additional of a fault results in two additional output files (as in
+ the two triangle fault example),
\family typewriter
-dislocation_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-dislocation-statevars_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell.
- The default fields are the total strain and stress fields.
- As specified in
-\family typewriter
-dislocation.cfg
-\family default
-, these values are averaged over each cell.
- The third file is named
-\family typewriter
dislocation-fault_t0000000.vtk
\family default
-.
- This file gives the specified fault slip for each vertex on the fault,
- along with the computed traction change for the cohesive cell.
- The fourth file (
+ and
\family typewriter
-dislocation-statevars_info.vtk
-\family default
-) gives the material properties used for the problem.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- The final file (
-\family typewriter
dislocation-fault_info.vtk
\family default
-) provides information such as the normal direction, final slip, and slip
- time for each vertex on the fault.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
+.
+ These files provide output of fault slip, change in tractions, and diagnostic
+ information such as the normal direction, final slip, and slip 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 ref
@@ -1054,7 +732,8 @@
\end_layout
\begin_layout Standard
-The third example demonstrates the use of Neumann (traction) boundary conditions.
+The fourth example demonstrates the use of Neumann (traction) boundary condition
+s.
Constant tractions are applied to the right edge of the mesh, while displacemen
ts normal to the boundaries are held fixed along the left and bottom edges
of the mesh.
@@ -1067,7 +746,7 @@
axialtract.cfg
\family default
.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
@@ -1141,17 +820,6 @@
\end_layout
\begin_layout Description
-pylithapp.timedependent.materials.material.output Defines the filter to be used
- when writing cell state variables (averages over the quadrature points
- for the cell) and gives the base filename for state variable output files
- (
-\family typewriter
-axialtract-statevars.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.x_pos.output Gives the field to be output for the
\family typewriter
@@ -1213,55 +881,11 @@
\begin_layout Standard
Once the problem has run, six files will be produced.
- The first file is named
+ This includes the five files as in the previous example plus
\family typewriter
-axialtract_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-axialtract-statevars_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell.
- The default fields are the total strain and stress fields.
- As specified in
-\family typewriter
-axialtract.cfg
-\family default
-, these values are averaged over each cell.
- The third file (
-\family typewriter
-axialtract-statevars_info.vtk
-\family default
-) gives the material properties used for the problem.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- The fourth file (
-\family typewriter
axialtract-tractions_info.vtk
\family default
-) gives the
+, which gives the
\family typewriter
x
\family default
@@ -1270,25 +894,6 @@
y
\family default
components of traction applied at each integration point.
- The file
-\family typewriter
-axialtract-fault_info.vtk
-\family default
- gives the fault normal direction, slip (zero) and time of slip (-1 second)
- for the fault.
- The final file
-\family typewriter
-axialtract-fault_t0000000.vtk
-\family default
- gives the slip vector and change in tractions on the fault surface in the
- fault coordinate system (along-strike and opening).
- The second component of the change in traction vector corresponds to the
- applied traction, as expected.
- All of the
-\family typewriter
-.vtk
-\family default
- 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
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/twotet4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/twotet4.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4/twotet4.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -1,4 +1,4 @@
-#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -129,18 +129,6 @@
twotet4.mesh
\family default
, which is in PyLith mesh ASCII format.
- This file format is described in Appendix
-\begin_inset LatexCommand ref
-reference "cha:File-Formats"
-
-\end_inset
-
-.
- This file describes the dimensionality of the problem (1D, 2D, or 3D),
- the coordinates of the vertices (nodes), the vertices composing each cell
- (element), and the material ID to be associated with each cell.
- It then provides groups of vertices that may be used to define faults or
- surfaces to which boundary conditions may be applied.
\end_layout
\begin_layout Standard
@@ -189,91 +177,12 @@
\end_layout
\begin_layout Standard
-In addition to the mesh, the two example problems share additional information.
- For problems of this type, it is generally useful to create a file named
-
+In addition to the mesh, the two example problems share additional information,
+ which we place in
\family typewriter
pylithapp.cfg
\family default
- in the run directory, since this file is read automatically every time
- PyLith is run.
- Settings specific to a particular problem may be placed in other
-\family typewriter
-.cfg
-\family default
- files, as described later, and then those files are placed on the command
- line.
- The settings contained in
-\family typewriter
-pylithapp.cfg
-\family default
- for this problem consist of:
-\end_layout
-
-\begin_layout Description
-pylithapp.journal.info Settings that control the verbosity of the output for
- the different components.
-\end_layout
-
-\begin_layout Description
-pylithapp.mesh_generator Settings that control mesh importing, such as the
- importer type, the filename, and the spatial dimension of the mesh.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent Settings that control the problem, such as the total
- time, time step size, and spatial dimension.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials Settings that control the material type,
- specify which material IDs are to be associated with a particular material
- type, and give the name of the spatial database containing material parameters
- for the mesh.
- The quadrature information is also given.
-\end_layout
-
-\begin_layout Description
-pylithapp.petsc PETSc settings to use for the problem, such as the preconditioner
- type.
-\end_layout
-
-\begin_layout Standard
-All of the problems in this directory use the same material database, as
- specified under
-\end_layout
-
-\begin_layout LyX-Code
-
-\family typewriter
-pylithapp.timedependent.materials
-\family default
-
-\end_layout
-
-\begin_layout Standard
-in
-\family typewriter
-pylithapp.cfg
-\family default
.
- This information is contained in the file
-\family typewriter
-matprops.spatialdb
-\family default
-.
- Although the material model is specified in
-\family typewriter
-pylithapp.cfg
-\family default
-, the physical properties for the material model are given in
-\family typewriter
-matprops.spatialdb
-\family default
-.
- For this example, values describing three-dimensional elastic material
- properties are given at a single point, resulting in uniform material propertie
-s.
\end_layout
\begin_layout Subsection
@@ -292,15 +201,10 @@
axialdisp.cfg
\family default
.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem
- and specifies the array of boundary conditions.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.bc Defines which degrees of freedom are being constraine
d (
\family typewriter
@@ -327,26 +231,6 @@
).
\end_layout
-\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output
-\newline
-(
-\family typewriter
-axialdisp.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.material.output Gives the base filename for
- state variable output files (
-\family typewriter
-axialdisp-statevars.vtk
-\family default
-).
-\end_layout
-
\begin_layout Standard
The values for the Dirichlet boundary conditions are described in the file
@@ -358,9 +242,8 @@
axialdisp.cfg
\family default
.
- The format of all spatial database files is similar.
Because data are being specified using two control points (rather than
- being uniform over the mesh, for example), the data dimension is one.
+ being uniform over the mesh), the data dimension is one.
\end_layout
\begin_layout Standard
@@ -393,55 +276,7 @@
\end_layout
\begin_layout Standard
-Once the problem has run, three files will be produced.
- The first file is named
-\family typewriter
-axialdisp_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-axialdisp-statevars_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell.
- The default fields are the total strain and stress fields.
- Since the cells are linear tetrahedra, there is a single quadrature point
- for each cell and thus a single set of stress and strain values for each
- cell.
- The final file (
-\family typewriter
-axialdisp-statevars_info.vtk
-\family default
-) gives the material properties used for the problem.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
- If the problem ran correctly, you should be able to generate a figure such
+If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset LatexCommand ref
reference "fig:twotet4-axial"
@@ -522,20 +357,10 @@
dislocation.cfg
\family default
.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
-pylithapp.journal.info Turns on journaling for 2D quadrature (used for 3D
- faults) and for cohesive kinematic faults.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem,
- the array of boundary conditions, and the array of interfaces.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.bc Defines which degrees of freedom are being constraine
d (
\family typewriter
@@ -570,35 +395,6 @@
fault slip, peak fault slip rate, and fault slip time.
\end_layout
-\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output
-\newline
-(
-\family typewriter
-dislocation.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.interfaces.fault.output.writer Gives the base filename
- for cohesive cell output files (
-\family typewriter
-dislocation-fault.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.material.output Gives the base filename for
- state variable output files (
-\family typewriter
-dislocation-statevars.vtk
-\family default
-).
-\end_layout
-
\begin_layout Standard
The fault example requires three additional database files that were not
needed for the simple displacement examples.
@@ -662,68 +458,7 @@
\end_layout
\begin_layout Standard
-Once the problem has run, five files are produced.
- The first file is named
-\family typewriter
-dislocation_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-dislocation-statevars_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell.
- The default fields are the total strain and stress fields.
- Since the cells are linear tetrahedra, there is a single quadrature point
- for each cell and thus a single set of stress and strain values for each
- cell.
- The third file is named
-\family typewriter
-dislocation-fault_t0000000.vtk
-\family default
-.
- This file gives the specified fault slip for each vertex on the fault,
- along with the computed traction change for the cohesive cell.
- The fourth file (
-\family typewriter
-dislocation-statevars_info.vtk
-\family default
-) gives the material properties used for the problem.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- The final file (
-\family typewriter
-dislocation-fault_info.vtk
-\family default
-) provides information such as the normal direction, final slip, and slip
- time for each vertex on the fault.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
- If the problem ran correctly, you should be able to generate a figure such
+If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset LatexCommand vref
reference "fig:twotet4-disloc"
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 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twotet4-geoproj/twotet4-geoproj.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -1,4 +1,4 @@
-#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -121,7 +121,7 @@
\end_inset
).
- Using the SCEC SVM-H database is straightforward, requiring only a few
+ Using the SCEC CVM-H database is straightforward, requiring only a few
modifications to
\family typewriter
pylithapp.cfg
@@ -134,8 +134,9 @@
the same.
PyLith will automatically transform from one geographic coordinate system
to another using the spatialdata package.
- The spatial databases should all use a Cartesian coordinate system, such
- as a geographic projection to insure interpolation is performed properly.
+ The spatial databases should all use a georeferenced Cartesian coordinate
+ system, such as a geographic projection to insure interpolation is performed
+ 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
@@ -163,18 +164,6 @@
twotet4.mesh
\family default
, which is in PyLith mesh ASCII format.
- This file format is described in Appendix
-\begin_inset LatexCommand ref
-reference "cha:File-Formats"
-
-\end_inset
-
-.
- This file describes the dimensionality of the problem (1D, 2D, or 3D),
- the coordinates of the vertices (nodes), the vertices composing each cell
- (element), the material ID to be associated with each cell, and then provides
- groups of vertices that may be used to define faults or surfaces to which
- boundary conditions may be applied.
If you compare this mesh against the one used in
\begin_inset LatexCommand ref
reference "sec:Tutorial-Two-tet4"
@@ -244,61 +233,6 @@
\end_layout
\begin_layout Standard
-In addition to the mesh, the three example problems share additional information.
- For problems of this type, it is generally useful to create a file named
-
-\family typewriter
-pylithapp.cfg
-\family default
- in the run directory, since this file is read automatically every time
- PyLith is run.
- Settings specific to a particular problem may be placed in other
-\family typewriter
-.cfg
-\family default
- files, as described later, and then those files are placed on the command
- line.
- The settings contained in
-\family typewriter
-pylithapp.cfg
-\family default
- for this problem consist of:
-\end_layout
-
-\begin_layout Description
-pylithapp.journal.info Settings that control the verbosity of the output for
- the different components.
-\end_layout
-
-\begin_layout Description
-pylithapp.mesh_generator Settings that control mesh importing, such as the
- importer type, the filename, and the spatial dimension of the mesh.
- These setting are particularly important for this problem, as they define
- the coordinate system used.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent Settings that control the problem, such as the total
- time, time step size, and spatial dimension.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials Settings that control the material type,
- specify which material IDs are to be associated with a particular material
- type, and define the database (
-\family typewriter
-SCECCVMH
-\family default
-) used to obtain material parameters for the mesh.
- The quadrature information is also given.
-\end_layout
-
-\begin_layout Description
-pylithapp.petsc PETSc settings to use for the problem, such as the preconditioner
- type.
-\end_layout
-
-\begin_layout Standard
This problem has some unique aspects compared to the other tutorials.
First, all of the other tutorials use a Cartesian coordinate system, while
this one uses a geographic coordinate system.
@@ -400,7 +334,7 @@
\family default
option defines
\family typewriter
-SCECCVMHDB
+SCECCVMH
\family default
as the spatial database to be used.
The next line defines the location of the
@@ -501,82 +435,8 @@
dislocation.cfg
\family default
.
- These settings are:
\end_layout
-\begin_layout Description
-pylithapp.journal.info Turns on journaling for 2D quadrature (used for 3D
- faults) and for cohesive kinematic faults.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem,
- the array of boundary conditions, and the array of interfaces.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.bc.bc Defines which degrees of freedom are being constraine
-d (
-\family typewriter
-x
-\family default
-,
-\family typewriter
-y
-\family default
-, and
-\family typewriter
-z
-\family default
-), gives the label (defined in
-\family typewriter
-twotet4.mesh
-\family default
-) defining the points desired, and assigns a label to the boundary condition
- set.
- We use the default spatial database (FixedDOFDB) for the Dirichlet boundary
- conditions, which sets the displacements to zero.
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.interfaces Gives the label (defined in
-\family typewriter
-twotet4.mesh
-\family default
-) defining the points on the fault, provides quadrature information, and
- then gives database names for material properties (needed for conditioning),
- fault slip, peak fault slip rate, and fault slip time.
-\end_layout
-
-\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output
-\newline
-(
-\family typewriter
-dislocation.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.interfaces.fault.output.writer Gives the base filename
- for cohesive cell output files (
-\family typewriter
-dislocation-fault.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.material.output Gives the base filename for
- state variable output files (
-\family typewriter
-dislocation-statevars.vtk
-\family default
-).
-\end_layout
-
\begin_layout Standard
Recall that we condition problems with the kinematic fault interface using
the material properties.
@@ -586,32 +446,6 @@
\end_layout
\begin_layout Standard
-The fault example requires three additional database files.
- The first file (
-\family typewriter
-dislocation_slip.spatialdb
-\family default
-) specifies 0.01 m of left-lateral fault slip for the entire fault.
- Since we specify a different amount of slip for every vertex on the fault,
- the data dimension is one.
- The default slip time function is a step-function, so we also must provide
- the time at which slip begins.
- The elastic solution is associated with advancing from
-\begin_inset Formula $t=-dt$
-\end_inset
-
- to
-\begin_inset Formula $t=0$
-\end_inset
-
-, so we set the slip initiation time for the step-function to 0 in
-\family typewriter
-dislocation_sliptime.spatialdb
-\family default
-.
-\end_layout
-
-\begin_layout Standard
The files containing common information (
\family typewriter
twotet4.mesh
@@ -643,68 +477,7 @@
\end_layout
\begin_layout Standard
-Once the problem has run, five files are produced.
- The first file is named
-\family typewriter
-dislocation_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-dislocation-statevars_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell.
- The default fields are the total strain and stress fields.
- Since the cells are linear tetrahedra, there is a single quadrature point
- for each cell and thus a single set of stress and strain values for each
- cell.
- The third file is named
-\family typewriter
-dislocation-fault_t0000000.vtk
-\family default
-.
- This file gives the specified fault slip for each vertex on the fault,
- along with the computed traction change for the cohesive cell.
- The fourth file (
-\family typewriter
-dislocation-statevars_info.vtk
-\family default
-) gives the material properties used for the problem.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- The final file (
-\family typewriter
-dislocation-fault_info.vtk
-\family default
-) provides information such as the normal direction, final slip, and slip
- time for each vertex on the fault.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
- If the problem ran correctly, you should be able to generate a figure such
+If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset LatexCommand vref
reference "fig:twotet4-geoproj-disloc"
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx 2008-08-29 18:25:20 UTC (rev 12747)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/twotri3/twotri3.lyx 2008-08-29 20:52:04 UTC (rev 12748)
@@ -1,4 +1,4 @@
-#LyX 1.5.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.6 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -164,7 +164,7 @@
\begin_inset Caption
\begin_layout Standard
-Mesh composed of two linear trianglular cells used in the example problems.
+Mesh composed of two linear triangular cells used in the example problems.
\begin_inset LatexCommand label
name "fig:twotri3-mesh"
@@ -498,15 +498,10 @@
sheardisp.cfg
\family default
.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem
- and specifies the array of boundary conditions.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.x_neg Specifies the boundary conditions for the
left side of the mesh, defining which degrees of freedom are being constrained
(x and y), giving the label (
@@ -546,26 +541,6 @@
).
\end_layout
-\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output
-\newline
-(
-\family typewriter
-sheardisp.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
-pylithapp.timedependent.materials.material.output Gives the base filename for
- state variable output files (
-\family typewriter
-sheardisp-statevars.vtk
-\family default
-).
-\end_layout
-
\begin_layout Standard
The files containing common information (
\family typewriter
@@ -596,54 +571,8 @@
\end_layout
\begin_layout Standard
-Once the problem has run, three files will be produced.
- The first file is named
-\family typewriter
-sheardisp_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-sheardisp-statevars_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell.
- The default fields are the total strain and stress fields.
- Since the cells are linear triangles, there is a single quadrature point
- for each cell and thus a single set of stress and strain values for each
- cell.
- The final file (
-\family typewriter
-sheardisp-statevars_info.vtk
-\family default
-) gives the material properties used for the problem.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
+Once the problem has run, three files will be produced as in the previous
+ example.
If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset LatexCommand vref
@@ -718,7 +647,7 @@
.
The solution corresponds to rigid body rotation of each triangular cell.
As a result, the tractions on the fault are zero.
- These settings are:
+ These settings include:
\end_layout
\begin_layout Description
@@ -727,11 +656,6 @@
\end_layout
\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem,
- the array of boundary conditions, and the array of interfaces.
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.bc.bc Defines which degrees of freedom are being constraine
d (x and y), gives the label (defined in
\family typewriter
@@ -756,17 +680,6 @@
\end_layout
\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output
-\newline
-(
-\family typewriter
-dislocation.vtk
-\family default
-).
-\end_layout
-
-\begin_layout Description
pylithapp.timedependent.interfaces.fault.output.writer Gives the base filename
for cohesive cell output files (
\family typewriter
@@ -775,15 +688,6 @@
).
\end_layout
-\begin_layout Description
-pylithapp.timedependent.materials.material.output Gives the base filename for
- state variable output files (
-\family typewriter
-dislocation-statevars.vtk
-\family default
-).
-\end_layout
-
\begin_layout Standard
Rather than specifying the displacement boundary conditions in a spatial
database file, we use the default behavior for Dirichlet boundary conditions,
@@ -854,66 +758,20 @@
\begin_layout Standard
Once the problem has run, five files are produced.
- The first file is named
+ In addition to the files produced in the previous two examples, this examples
+ produces two files associated with the fault interface.
+ The file
\family typewriter
-dislocation_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-dislocation-statevars_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell.
- The default fields are the total strain and stress fields.
- Since the cells are linear triangles, there is a single quadrature point
- for each cell and thus a single set of stress and strain values for each
- cell.
- The third file is named
-\family typewriter
dislocation-fault_t0000000.vtk
\family default
-.
- This file gives the specified fault slip for each vertex on the fault,
- along with the computed traction change for the cohesive cell.
- The fourth file (
+ gives the fault slip for each vertex on the fault along with the computed
+ traction change for the cohesive cell.
+ The file
\family typewriter
-dislocation-statevars_info.vtk
-\family default
-) gives the material properties used for the problem.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- The final file (
-\family typewriter
dislocation-fault_info.vtk
\family default
-) provides information such as the normal direction, final slip, and slip
+ provides information such as the normal direction, final slip, and slip
time for each vertex on the fault.
- All of the
-\family typewriter
-.vtk
-\family default
- 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
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