[cig-commits] r12746 - in short/3D/PyLith/trunk/doc/userguide: . install intro materials runpylith
brad at geodynamics.org
brad at geodynamics.org
Fri Aug 29 10:27:25 PDT 2008
Author: brad
Date: 2008-08-29 10:27:25 -0700 (Fri, 29 Aug 2008)
New Revision: 12746
Modified:
short/3D/PyLith/trunk/doc/userguide/install/install.lyx
short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx
short/3D/PyLith/trunk/doc/userguide/preface.lyx
short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
Log:
Minor cleanup with some very minor updates for v1.3.
Modified: short/3D/PyLith/trunk/doc/userguide/install/install.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/install/install.lyx 2008-08-28 20:20:22 UTC (rev 12745)
+++ short/3D/PyLith/trunk/doc/userguide/install/install.lyx 2008-08-29 17:27:25 UTC (rev 12746)
@@ -198,6 +198,17 @@
\end_deeper
\begin_layout Enumerate
Set environment variables.
+ The provided
+\family typewriter
+setup.sh
+\family default
+ script only works if you are using bash shell.
+ If you are using a different shell, you will need to alter how the environment
+ variables are set in
+\family typewriter
+setup.sh
+\family default
+.
\end_layout
\begin_deeper
@@ -257,6 +268,17 @@
\end_deeper
\begin_layout Enumerate
Set environment variables.
+ The provided
+\family typewriter
+setup.sh
+\family default
+ script only works if you are using bash shell.
+ If you are using a different shell, you will need to alter how the environment
+ variables are set in
+\family typewriter
+setup.sh
+\family default
+.
\end_layout
\begin_deeper
@@ -786,16 +808,19 @@
\emph default
\family typewriter
-configure.log
+\shape italic
+$PETSC_ARCH
+\shape default
+/conf/configure.log
\family default
and
\family typewriter
-make_log_
-\emph on
+\shape italic
$PETSC_ARCH
+\shape default
+/conf/make.log
\family default
-\emph default
- to
+to
\begin_inset LatexCommand url
name "PETSc Maintenance Mailing List"
target "petsc-maint at mcs.anl.gov"
@@ -832,7 +857,7 @@
\family typewriter
petsc-dev
\family default
- for PyLith 1.2.0 from
+ for PyLith from
\begin_inset LatexCommand htmlurl
name "PyLith PETSc tarball"
target "www.geodynamics.org/cig/software/packages/short/pylith/petsc-dev-pylith-1_1_0.tgz"
@@ -848,7 +873,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf petsc-dev-pylith-1_1_0.tgz
+$ tar xzf petsc-dev-pylith-1.3.0.tgz
\end_layout
\begin_layout Standard
@@ -856,7 +881,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c petsc-dev-pylith-1_1_0.tgz | tar xf -
+$ gunzip -c petsc-dev-pylith-1.3.0.tgz | tar xf -
\end_layout
\begin_layout Standard
@@ -1604,7 +1629,7 @@
package available at the
\begin_inset LatexCommand htmlurl
name "PROJ.4 web page"
-target "www.remotesensing.org/proj"
+target "trac.osgeo.org/proj"
\end_inset
@@ -1629,7 +1654,7 @@
Download Proj.4 from the
\begin_inset LatexCommand htmlurl
name "Proj.4 website"
-target "www.remotesensing.org/proj"
+target "trac.osgeo.org/proj"
\end_inset
@@ -1666,7 +1691,7 @@
\end_layout
\begin_layout LyX-Code
-$ cd proj-4.6.0/nad$ unzip proj-datumgrid-1.3.zip
+$ cd proj-4.6.0/nad$ unzip proj-datumgrid-1.4.zip
\end_layout
\begin_layout Subsubsection
@@ -2998,7 +3023,7 @@
\end_layout
\begin_layout Subsubsection
-Pyre Configuration on a Personal Computer
+Pyre Configuration on a Laptop of Desktop Computer
\end_layout
\begin_layout Standard
Modified: short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2008-08-28 20:20:22 UTC (rev 12745)
+++ short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2008-08-29 17:27:25 UTC (rev 12746)
@@ -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
@@ -81,7 +81,7 @@
LithoMop.
LithoMop was the product of major reengineering of Tecton, a finite-element
code for simulating static and quasi-static crustal deformation.
- The major new features present in Lithomop included dynamic memory allocation
+ The major new features present in LithoMop included dynamic memory allocation
and the use of the Pyre simulation framework and PETSc solvers.
EqSim was written by Brad Aagaard to solve problems in earthquake dynamics,
including rupture propagation and seismic wave propagation.
@@ -95,7 +95,7 @@
The code runs in either serial or parallel mode, and the design allows
for relatively easy scripting using the Python programming language.
Material properties and values for boundary and fault conditions are specified
- using a spatial database, which permits easy prescription of complex spatial
+ using spatial databases, which permit easy prescription of complex spatial
variations of properties and parameters.
Simulation parameters are generally specified through the use of simple
ASCII files or the command line.
@@ -145,14 +145,10 @@
Given a geological problem of interest, a scientist must first provide
a geometrical representation of the desired structure.
Once the structure has been defined, a computational mesh must be created.
- Since there are a wide variety of mesh formats, this information must then
- be translated into something that the computational physics code can understand.
PyLith presently provides three mesh importing options: CUBIT Exodus format,
- LaGriT GMV + Pset files, and PyLith mesh ASCII format.
+ LaGriT GMV and Pset files, and PyLith mesh ASCII format.
The modeling of the physical processes of interest is performed by a code
such as PyLith.
- Once the computations have been performed, the results must be exported
- into a format that can be used by a visualization code.
Present output consists of VTK files which can be used by a number of visualiza
tion codes (e.g., ParaView, Visit, and MayaVi).
In the near future, PyLith will also use the HDF5 format.
@@ -457,8 +453,8 @@
Sieve
\family default
represents the topology of the domain.
- Zero volume elements are inserted along all fault surfaces which can implement
- both kinematic (prescribed) and dynamic (constitutive model) implementations
+ Zero volume elements are inserted along all fault surfaces to implement
+ kinematic (prescribed) or dynamic (constitutive model) implementations
of fault slip.
Material properties and other parameters are represented as sections (scalar
and vector fields) over the mesh, and values for a vertex or cell can be
@@ -490,7 +486,7 @@
PETSc includes solvers that implement a variety of Newton and Krylov subspace
methods.
It can also interface with many external packages, including ESSL, MUMPS,
- Matlab, ParMeTis, PVODE, and Hypre, thereby providing additional solvers
+ Matlab, ParMETIS, PVODE, and Hypre, thereby providing additional solvers
and interaction with other software packages.
\end_layout
Modified: short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx 2008-08-28 20:20:22 UTC (rev 12745)
+++ short/3D/PyLith/trunk/doc/userguide/materials/materials.lyx 2008-08-29 17:27:25 UTC (rev 12746)
@@ -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
@@ -155,16 +155,23 @@
are no longer available (or necessary).
If a set of material groups is not specified, a single material model is
used for the entire problem.
- The examples in
-\family typewriter
-examples/3d/hex8
-\family default
+ See Sections
+\begin_inset LatexCommand ref
+reference "sec:Tutorial-3d-hex8"
+
+\end_inset
+
and
+\begin_inset LatexCommand ref
+reference "sec:Tutorial-3d-tet4"
+
+\end_inset
+
+for examples
\family typewriter
-examples/3d/tet4
+that
\family default
- demonstrate how to specify more than one material model for a problem,
- while the remainder of the example problems assume a single material model.
+ demonstrate how to specify more than one material model.
\end_layout
\begin_layout Subsection
@@ -174,8 +181,6 @@
\begin_layout Standard
For each material group, there is a single component defining the material
model to be used.
- If no groups are specified, a single material model is assumed for the
- problem.
The default material model is
\family typewriter
elasticisotropic3d
@@ -186,7 +191,7 @@
\begin_layout Description
db Spatial database specifying the spatial variation in the parameters of
- the bulk constitutive model.
+ the bulk constitutive model (default is a SimpleDB).
\end_layout
\begin_layout Description
@@ -225,7 +230,7 @@
\end_layout
\begin_layout LyX-Code
-materials = [elastic_upper,elastic_lower]
+materials = [elastic,viscoelastic]
\end_layout
\begin_layout LyX-Code
@@ -233,11 +238,11 @@
\end_layout
\begin_layout LyX-Code
-[pylithapp.timedependent.materials.elastic_upper]
+[pylithapp.timedependent.materials.elastic]
\end_layout
\begin_layout LyX-Code
-label = Upper elastic material
+label = Elastic material
\end_layout
\begin_layout LyX-Code
@@ -265,11 +270,11 @@
\end_layout
\begin_layout LyX-Code
-[pylithapp.timedependent.materials.elastic_lower]
+[pylithapp.timedependent.materials.viscoelastic]
\end_layout
\begin_layout LyX-Code
-label = Lower elastic material
+label = Viscoelastic material
\end_layout
\begin_layout LyX-Code
@@ -277,7 +282,7 @@
\end_layout
\begin_layout LyX-Code
-db.iohandler.filename = mat_elastic.spatialdb
+db.iohandler.filename = mat_viscoelastic.spatialdb
\end_layout
\begin_layout LyX-Code
@@ -295,15 +300,25 @@
\begin_layout Standard
These settings correspond to the the problem in
\family typewriter
-examples/3d/hex8
+Section
\family default
+
+\begin_inset LatexCommand ref
+reference "sec:Tutorial-3d-hex8"
+
+\end_inset
+
.
- The parameters for each bulk constitutive model are specified using the
- same spatial database (
+ The parameters for the bulk constitutive models are specified using the
+ spatial databases
\family typewriter
mat_elastic.spatialdb
\family default
-).
+ and
+\family typewriter
+mat_viscoelastic.spatialdb
+\family default
+.
Refer to the discussion of each material model to find the parameters that
must be specified in the spatial database.
Appendix
@@ -312,7 +327,7 @@
\end_inset
- describes the format of the spatial database files.
+ describes the format of the SimpleDB spatial database files.
In a more realistic problem, a different spatial database, and possibly
a different material model, would be used for each material group.
\end_layout
@@ -324,7 +339,7 @@
\end_layout
\begin_layout LyX-Code
-[pylithapp.timedependent.materials.elastic_upper.output]
+[pylithapp.timedependent.materials.elastic.output]
\end_layout
\begin_layout LyX-Code
@@ -340,7 +355,7 @@
\end_layout
\begin_layout LyX-Code
-[pylithapp.timedependent.materials.elastic_lower.output]
+[pylithapp.timedependent.materials.viscoelastic.output]
\end_layout
\begin_layout LyX-Code
@@ -354,8 +369,14 @@
\begin_layout Standard
These settings again correspond to the problem in
\family typewriter
-examples/3d/hex8
+Section
\family default
+
+\begin_inset LatexCommand ref
+reference "sec:Tutorial-3d-hex8"
+
+\end_inset
+
.
The specification of a state variable base filename (
\family typewriter
@@ -391,8 +412,14 @@
Additional output may be requested for a material model, as in this example
(
\family typewriter
-examples/twocells/twohex8
+see Section
\family default
+
+\begin_inset LatexCommand ref
+reference "sec:Tutorial-Two-hexahedra"
+
+\end_inset
+
):
\end_layout
@@ -443,12 +470,30 @@
\begin_layout Standard
\align center
+\begin_inset Caption
+
+\begin_layout Standard
\begin_inset LatexCommand label
name "tab:material-model-output"
\end_inset
+Properties and state variables available for output for existing material
+ models.
+ Physical properties are available for output as
+\family typewriter
+cell_info_fields
+\family default
+ and state variables are available for output as
+\family typewriter
+cell_data_fields
+\family default
+.
+\end_layout
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="3">
<features>
@@ -584,31 +629,9 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Properties and state variables available for output for existing material
- models.
- Physical properties are available for output as
-\family typewriter
-cell_info_fields
-\family default
- and state variables are available for output as
-\family typewriter
-cell_data_fields
-\family default
-.
-\end_layout
-
\end_inset
-\end_layout
-
-\end_inset
-
-
\begin_inset Float table
placement H
wide false
@@ -617,12 +640,20 @@
\begin_layout Standard
\align center
+\begin_inset Caption
+
+\begin_layout Standard
\begin_inset LatexCommand label
name "tab:material-model-statevars"
\end_inset
+Order of components in tensor state-variables for material models.
+\end_layout
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="4">
<features>
@@ -833,23 +864,11 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Order of components in tensor state-variables for material models.
-\end_layout
-
\end_inset
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Section
Elastic Material Models
\end_layout
@@ -939,6 +958,16 @@
\begin_layout Standard
\noindent
\align center
+\begin_inset Caption
+
+\begin_layout Standard
+Values in spatial database used as parameters in the elastic material constituti
+ve models.
+\end_layout
+
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="2">
<features>
@@ -1051,24 +1080,11 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-Values in spatial database used as parameters in the elastic material constituti
-ve models.
-\end_layout
-
\end_inset
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Subsection
1D Elastic Material Models
\end_layout
@@ -1277,9 +1293,8 @@
\end_layout
\begin_layout Standard
-At present, there are two viscoelastic material models available in PyLith
- 1.1, with at least one additional model planned for the near future (Table
-
+At present, there are two viscoelastic material models available in PyLith,
+ with at least one additional model planned for the near future (Table
\begin_inset LatexCommand ref
reference "tab:Material-models-available"
@@ -1310,6 +1325,20 @@
\begin_layout Standard
\noindent
\align center
+\begin_inset Caption
+
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "tab:Material-models-available"
+
+\end_inset
+
+Planned and available 3D viscoelastic materials for PyLith.
+\end_layout
+
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="3">
<features>
@@ -1445,28 +1474,11 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "tab:Material-models-available"
-
\end_inset
-Planned and available 3D viscoelastic materials for PyLith.
-\end_layout
-\end_inset
-
-
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Standard
\noindent
\align center
@@ -1477,6 +1489,14 @@
status open
\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename figs/pylith-materials.ai
+ scale 75
+
+\end_inset
+
+
\begin_inset Caption
\begin_layout Standard
@@ -1486,8 +1506,8 @@
\end_inset
-Spring-dashpot 1D representations of the planned and available 3D elastic
- and viscoelastic material models for PyLith.
+Spring-dashpot 1D representations of the available 3D elastic and viscoelastic
+ material models for PyLith.
The top model is a linear elastic model, the middle model is a Maxwell
model, and the bottom model is a generalized Maxwell model.
For the generalized Maxwell model,
@@ -1510,23 +1530,11 @@
\end_layout
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename figs/pylith-materials.ai
- scale 75
-
\end_inset
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Subsection
Definitions
\end_layout
@@ -1654,6 +1662,20 @@
\begin_layout Standard
\noindent
\align center
+\begin_inset Caption
+
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "tab:Mathematical-notation"
+
+\end_inset
+
+Mathematical notation used in this section.
+\end_layout
+
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="3" columns="3">
<features>
@@ -1766,28 +1788,11 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "tab:Mathematical-notation"
-
\end_inset
-Mathematical notation used in this section.
-\end_layout
-\end_inset
-
-
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Subsection
Formulation for Generalized Maxwell Models
\end_layout
@@ -2748,7 +2753,7 @@
\end_layout
\begin_layout Standard
-PyLith 1.1 does not presently include power-law viscoelasticity, but we plan
+PyLith does not presently include power-law viscoelasticity, but we plan
to provide the effective stress function formulation as one possible implementa
tion of a power-law Maxwell viscoelastic material.
\end_layout
Modified: short/3D/PyLith/trunk/doc/userguide/preface.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/preface.lyx 2008-08-28 20:20:22 UTC (rev 12745)
+++ short/3D/PyLith/trunk/doc/userguide/preface.lyx 2008-08-29 17:27:25 UTC (rev 12746)
@@ -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
@@ -152,13 +152,13 @@
Williams.
\emph on
-PyLith User Manual, Version 1.1.
+PyLith User Manual, Version 1.3.
\emph default
Pasadena, CA: Computational Infrastructure of Geodynamics, 2008.
URL: geodynamics.org/cig/software/
\newline
-short/pylith/pylith_book-1.1.pdf
+short/pylith/pylith_book-1.3.pdf
\end_layout
\begin_layout Section
Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2008-08-28 20:20:22 UTC (rev 12745)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2008-08-29 17:27:25 UTC (rev 12746)
@@ -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
@@ -75,7 +75,7 @@
and how the vertices are connected into cells), a material identifier for
each cell, and sets of vertices associated with boundary conditions, faults,
and output (for subsets of the mesh).
- This information can be provided using the PyLith mesh ASCII format (See
+ This information can be provided using the PyLith mesh ASCII format (see
Chapter
\begin_inset LatexCommand ref
reference "cha:Tutorials"
@@ -89,15 +89,13 @@
\end_inset
for the format specification) or by importing the information from the
- LaGriT or CUBIT meshing packages (see
-\family typewriter
-examples/3d/hex8
-\family default
- and
-\family typewriter
-examples/3d/tet4
-\family default
-).
+ LaGriT or CUBIT meshing packages (see Chapter
+\begin_inset LatexCommand ref
+reference "cha:Tutorials"
+
+\end_inset
+
+ for examples).
\end_layout
\begin_layout Enumerate
@@ -566,6 +564,20 @@
\begin_layout Standard
\align center
+\begin_inset Caption
+
+\begin_layout Standard
+\begin_inset LatexCommand label
+name "tab:petsc:options:defaults"
+
+\end_inset
+
+Useful command-line arguments for setting PETSc options.
+\end_layout
+
+\end_inset
+
+
\begin_inset Tabular
<lyxtabular version="3" rows="6" columns="3">
<features>
@@ -778,34 +790,32 @@
\end_layout
+\end_inset
+
+
+\begin_inset Float table
+placement H
+wide false
+sideways false
+status open
+
\begin_layout Standard
+\align center
\begin_inset Caption
\begin_layout Standard
\begin_inset LatexCommand label
-name "tab:petsc:options:defaults"
+name "tab:petsc:options:quasistatic"
\end_inset
-Useful command-line arguments for setting PETSc options.
+PETSc options that often result in improved performance in quasi-static
+ and dynamic elasticity problems.
\end_layout
\end_inset
-\end_layout
-
-\end_inset
-
-
-\begin_inset Float table
-placement H
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\align center
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="3">
<features>
@@ -984,29 +994,11 @@
\end_layout
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "tab:petsc:options:quasistatic"
-
\end_inset
-PETSc options that often result in improved performance in quasi-static
- and dynamic elasticity problems.
-\end_layout
-\end_inset
-
-
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Section
Mesh Information
\end_layout
@@ -1538,15 +1530,23 @@
\end_layout
\begin_layout Standard
-The SimpleDB spatial database is quite general.
- When the values are uniform, it is often easier to use the UniformDB spatial
- database and specify the values directly (either on the command line or
- in a parameters settings file).
- However, if the values are used in more than one place, it is easier to
- place the values in a SimpleDB file, because they can then be referred
- to using the filename of the spatial database rather than having to repeatedly
- list all of the values on the command line or in a parameter settings (.cfg)
- file.
+The SimpleDB spatial database is quite general, but when the values are
+ uniform, it is often easier to use the UniformDB spatial database instead.
+ With the UniformDB, you specify the values directly either on the command
+ line or in a parameter settings (
+\family typewriter
+.cfg
+\family default
+) file.
+ On the other hand, if the values are used in more than one place, it is
+ easier to place the values in a SimpleDB file, because they can then be
+ referred to using the filename of the spatial database rather than having
+ to repeatedly list all of the values on the command line or in a parameter
+ settings (
+\family typewriter
+.cfg
+\family default
+) file.
The Pyre properties for a UniformDB are:
\end_layout
@@ -1651,7 +1651,7 @@
\end_layout
\begin_layout Description
-squash Squash topography/bathymetry to sea level (make the Earth's surface
+squash Squash topography/bathymetry to sea level (make the earth's surface
flat)
\end_layout
@@ -1696,7 +1696,7 @@
squash_limit = -1000.0 ; Only distort the geometry above z = -1 km in flattening
the
\newline
-Earth
+earth
\end_layout
\begin_layout Section
@@ -1711,18 +1711,28 @@
material model and quadrature rule.
For boundary conditions the ``label'' is a string used to associate groups
of vertices (psets in LaGriT and nodesets in CUBIT) with a boundary condition.
- PyLith 1.0 had an ``id'' for boundary conditions, but we removed it because
- it was not used.
- For faults the ``label'' is a string used to associate groups of vertices
- (psets in LaGriT and nodesets in CUBIT) with vertices on the fault.
Note that some mesh generators use strings (LaGriT) to identify groups
of nodes while others use integers (CUBIT Exodus files).
Although CUBIT permits associated strings with nodesets, they are not included
- in the Exodus files.
+ in the Exodus files, so we must rely on the nodset ID.
+ PyLith 1.0 had an ``id'' for boundary conditions, but we removed it from
+ subsequent releases because it was not used.
+ For faults the ``label'' is used in the same manner as the
+\begin_inset Quotes eld
+\end_inset
+
+label
+\begin_inset Quotes erd
+\end_inset
+
+ for boundary conditions.
+ That is, it associates a string with a group of vertices (pset in LaGriT
+ and nodeset in CUBIT).
The fault ``id'' is a integer used to tag the cohesive cells in the mesh
with a specific fault and quadrature rule.
- Because we use the fault ``id'' to tag the cohesive cells in the mesh,
- it must be unique among the faults as well as the materials.
+ Because we use the fault ``id'' to tag cohesive cells in the mesh the same
+ way we tag normal cells to materials, it must be unique among the faults
+ as well as the materials.
\end_layout
\begin_layout Section
@@ -1958,8 +1968,8 @@
\begin_layout Standard
PyLith currently supports output to VTK files, which can be imported directly
into a number of visualization tools, such as ParaView, Visit, and MayaVi.
- PyLith 1.1 significantly expands the information available for output, including
- fault information and state variables.
+ PyLith 1.1 significantly expanded the information available for output,
+ including fault information and state variables.
Output of solution information for the domain, faults, materials, and boundary
conditions is controlled by an output manager for each module.
This allows the user to tailor the output to the problem.
@@ -1970,7 +1980,8 @@
For a fault the fields include the final slip, the slip initiation time,
and the fault normal vector.
For a material the fields include the density and the elastic constants.
- Additional diagnostic can be included by setting the output parameters.
+ Additional diagnostic information can be included by setting the appropriate
+ output parameters.
See Chapters
\begin_inset LatexCommand ref
reference "cha:material:models"
@@ -2001,7 +2012,7 @@
\begin_layout Standard
The OutputManager object controls the type of files written, the fields
included in the output, and how often output is written.
- PyLith includes some specialized OutputManagers that prescribe while fields
+ PyLith includes some specialized OutputManagers that prescribe what fields
are output by default.
In some cases, additional fields are available but not included by default.
For example, in 3D problems, the along-strike and up-dip directions over
@@ -2140,8 +2151,8 @@
\begin_layout Standard
Output fields may not directly correspond to the information a user desires.
- For example, the state variables of the materials, the default output includes
- the state variables (or physical properties) at each quadrature point.
+ For example, the default output for the state variables includes the physical
+ properties at each quadrature point.
Most visualization packages cannot handle cell fields with multiple points
in a cell (the locations of the points within the cell are not included
in the data file).
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