[cig-commits] r7131 - in
short/3D/PyLith/trunk/doc/userguide/runpylith: . figs
willic3 at geodynamics.org
willic3 at geodynamics.org
Mon Jun 11 14:01:02 PDT 2007
Author: willic3
Date: 2007-06-11 14:01:01 -0700 (Mon, 11 Jun 2007)
New Revision: 7131
Added:
short/3D/PyLith/trunk/doc/userguide/runpylith/figs/bar2.eps
short/3D/PyLith/trunk/doc/userguide/runpylith/figs/bar2.fig
short/3D/PyLith/trunk/doc/userguide/runpylith/figs/hex8.fig.bak
short/3D/PyLith/trunk/doc/userguide/runpylith/figs/quad4.eps
short/3D/PyLith/trunk/doc/userguide/runpylith/figs/quad4.fig
short/3D/PyLith/trunk/doc/userguide/runpylith/figs/quad4.fig.bak
short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tet4.fig.bak
short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tri3.eps
short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tri3.fig
short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tri3.fig.bak
Modified:
short/3D/PyLith/trunk/doc/userguide/runpylith/figs/hex8.fig
short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tet4.fig
short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
Log:
Figures and incomplete documentation for running PyLith.
Added: short/3D/PyLith/trunk/doc/userguide/runpylith/figs/bar2.eps
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/figs/bar2.eps 2007-06-11 19:06:11 UTC (rev 7130)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/figs/bar2.eps 2007-06-11 21:01:01 UTC (rev 7131)
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Added: short/3D/PyLith/trunk/doc/userguide/runpylith/figs/bar2.fig
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/figs/bar2.fig 2007-06-11 19:06:11 UTC (rev 7130)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/figs/bar2.fig 2007-06-11 21:01:01 UTC (rev 7131)
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Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/figs/hex8.fig
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/figs/hex8.fig 2007-06-11 19:06:11 UTC (rev 7130)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/figs/hex8.fig 2007-06-11 21:01:01 UTC (rev 7131)
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===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/figs/hex8.fig.bak 2007-06-11 19:06:11 UTC (rev 7130)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/figs/hex8.fig.bak 2007-06-11 21:01:01 UTC (rev 7131)
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===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/figs/quad4.eps 2007-06-11 19:06:11 UTC (rev 7130)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/figs/quad4.eps 2007-06-11 21:01:01 UTC (rev 7131)
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Added: short/3D/PyLith/trunk/doc/userguide/runpylith/figs/quad4.fig
===================================================================
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+++ short/3D/PyLith/trunk/doc/userguide/runpylith/figs/quad4.fig 2007-06-11 21:01:01 UTC (rev 7131)
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===================================================================
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+++ short/3D/PyLith/trunk/doc/userguide/runpylith/figs/quad4.fig.bak 2007-06-11 21:01:01 UTC (rev 7131)
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Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tet4.fig
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tet4.fig 2007-06-11 19:06:11 UTC (rev 7130)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tet4.fig 2007-06-11 21:01:01 UTC (rev 7131)
@@ -1,4 +1,4 @@
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Added: short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tet4.fig.bak
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tet4.fig.bak 2007-06-11 19:06:11 UTC (rev 7130)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tet4.fig.bak 2007-06-11 21:01:01 UTC (rev 7131)
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Added: short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tri3.eps
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tri3.eps 2007-06-11 19:06:11 UTC (rev 7130)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tri3.eps 2007-06-11 21:01:01 UTC (rev 7131)
@@ -0,0 +1,157 @@
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Added: short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tri3.fig
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tri3.fig 2007-06-11 19:06:11 UTC (rev 7130)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tri3.fig 2007-06-11 21:01:01 UTC (rev 7131)
@@ -0,0 +1,33 @@
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Added: short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tri3.fig.bak
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tri3.fig.bak 2007-06-11 19:06:11 UTC (rev 7130)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/figs/tri3.fig.bak 2007-06-11 21:01:01 UTC (rev 7131)
@@ -0,0 +1,33 @@
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Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2007-06-11 19:06:11 UTC (rev 7130)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2007-06-11 21:01:01 UTC (rev 7131)
@@ -1,4 +1,4 @@
-#LyX 1.4.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.4.4 created this file. For more info see http://www.lyx.org/
\lyxformat 245
\begin_document
\begin_header
@@ -40,349 +40,41 @@
Running PyLith
\end_layout
-\begin_layout Section
-Supported Finite Elements
-\end_layout
-
\begin_layout Standard
-PyLith currently only supports the 4-node linear tetrahedral and 8-node
- linear hexahedral elements.
- The node ordering must follow the convention shown in Figures\InsetSpace ~
-
-\begin_inset LatexCommand \ref{fig:tet4}
-
-\end_inset
-
- and\InsetSpace ~
-
-\begin_inset LatexCommand \ref{fig:hex8}
-
-\end_inset
-
-.
+There are essentially three major pieces needed to run a problem with PyLith:
\end_layout
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status collapsed
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename figs/tet4.eps
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Caption
-Linear tetrahedral finite element.
-\end_layout
-
-\begin_layout Standard
-\begin_inset LatexCommand \label{fig:tet4}
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Float figure
-placement t
-wide false
-sideways false
-status collapsed
-
-\begin_layout Standard
-\align center
-\begin_inset Graphics
- filename figs/hex8.eps
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Caption
-Linear hexahedral finite element.
-\end_layout
-
-\begin_layout Standard
-\begin_inset LatexCommand \label{fig:hex8}
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
-Input Files
-\end_layout
-
-\begin_layout Standard
-PyLith gets its input from a variety of files.
- Most of these are associated with different kinds of boundary conditions.
- As a result only six files are required.
- The remaining files are only used when the associated boundary condition
- is used.
- See Appendix\InsetSpace ~
-
-\begin_inset LatexCommand \ref{cha:File-Formats}
-
-\end_inset
-
- for a detailed discussion of the file formats.
-\end_layout
-
-\begin_layout Standard
-The first step in the simulation process involves partitioning the mesh
- among the processors.
- In this phase, PyLith reads in the entire mesh and then writes out processor-sp
-ecific pieces with one file for each processor.
- The file names for these follow the convention
+\begin_layout Enumerate
+A set of parameters describing the problem.
+ These parameters describe the type of problem to be run, solver information,
+ time-stepping information, etc.
+ This information can be provided from the command-line or using a
\family typewriter
-xx.PROC.ext
-\family default
- where
-\family typewriter
-PROC
-\family default
- refers to the processor number and
-\family typewriter
-xx.ext
-\family default
- is the original file name.
- This procedure is applied to files with the following extensions:
-\family typewriter
- coord, connect, split, bc
-\family default
-, and
-\family typewriter
-traction
-\family default
-.
- The remaining files provide information common to all processors, and thus
- do not require separate files for each processor.
-\end_layout
-
-\begin_layout Standard
-In some cases, a user may want to run the same simulation using different
- numbers of processors.
- In this case, users may wish to provide distinctive sets of file names
- to distinguish between the different runs.
- Setting up this naming scheme is most easily done using symbolic links
- or copying files to local directories on each machine using a shell script
- that starts a simulation.
- See
-\family typewriter
-mklinks.py
-\family default
- in Section\InsetSpace ~
-
-\begin_inset LatexCommand \ref{sec:Tutorial-Using-Reverse-Slip}
-
-\end_inset
-
- for a simple example.
- You can also choose your own file-name template by setting the appropriate
- parameters.
- See Section\InsetSpace ~
-
-\begin_inset LatexCommand \ref{sec:setting:parameters}
-
-\end_inset
-
- for more information.
-\end_layout
-
-\begin_layout Subsection
-Required Input Files
-\end_layout
-
-\begin_layout Standard
-The required input files define the finite-element mesh, boundary conditions,
- time-step information, output, and material properties.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-xx.coord
-\family default
- Coordinates of finite-element vertices.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-xx.connect
-\family default
- Topology and material information for the finite-element mesh.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-xx.bc
-\family default
- Boundary conditions at vertices on external boundaries.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-xx.time
-\family default
-Time stepping information.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-xx.statevar
-\family default
- State variables to be output for the elastic and (time-dependent) viscoelastic
- solution.
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-xx.prop
-\family default
- Properties for each material.
-
-\end_layout
-
-\begin_layout Subsection
-Optional Input Files
-\end_layout
-
-\begin_layout Standard
-The optional input files are only read when a file exists matching the name
- of an input file PyLith expects to read.
- Note that explicit file names for each of the files can be specified using
- command-line arguments, with
-\family typewriter
.cfg
\family default
- files, or with
+ or
\family typewriter
.pml
\family default
- files, as discussed in Section\InsetSpace ~
-
-\begin_inset LatexCommand \ref{sec:setting:parameters}
-
-\end_inset
-
-.
+ file.
\end_layout
-\begin_layout Description
-
-\family typewriter
-\color black
-xx.fuldat
-\family default
-\color none
-Time steps for which full output is requested.
-
-\shape italic
-Required for time-dependent problems.
+\begin_layout Enumerate
+Mesh information.
+ This includes nodal coordinates, element connectivities, and flagged sets
+ of nodes to which boundary conditions can be implied.
+ This information can be provided using a simple ascii format, or by importing
+ the information from the LaGriT or CUBIT meshing packages.
\end_layout
-\begin_layout Description
-
-\family typewriter
-\color black
-xx.split
-\family default
-\color none
- Dislocation boundary condition information (implemented using split nodes).
-
+\begin_layout Enumerate
+Databases specifying the material properties and boundary conditions to
+ be used.
+ Arbitrarily complex spatial variations in boundary conditions (including
+ fault specifications) and material properties may be given in the spatial
+ database.
\end_layout
-\begin_layout Description
-
-\family typewriter
-\color black
-xx.traction
-\family default
-\color none
- Traction boundary condition information.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-\color black
-xx.skew
-\family default
-\color none
- Local coordinate rotation information for boundary conditions.
-
-\shape italic
-Not yet implemented.
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-\color black
-xx.wink
-\family default
-\color none
- Winkler spring element boundary condition information.
-
-\emph on
- Not yet implemented.
-
-\emph default
-
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-\color black
-xx.hist
-\family default
-\color none
- Time histories for split nodes and boundary conditions (if necessary).
-
-\emph on
-Not yet tested.
-
-\emph default
-
-\end_layout
-
\begin_layout Section
Setting Parameters for PyLith
\end_layout
@@ -396,11 +88,14 @@
\end_layout
\begin_layout Standard
-There are several methods for setting input parameters for
+The most basic information for setting up a PyLith simulation is the problem
+ parameters, since these also describe the characteristics of the mesh and
+ database information.
+ There are several methods for setting input parameters for the
\family typewriter
-pylith3dapp.py
+pylith
\family default
-: via the command line, or by using a configuration file in
+ executable: via the command line, or by using a configuration file in
\family typewriter
.cfg
\family default
@@ -458,69 +153,47 @@
\end_layout
\begin_layout Standard
-In general, PyLith's command-line arguments fall into three categories:
- MPI settings, Pyre/PyLith properties and facilities, and PETSc settings.
+PyLith's command-line arguments can control Pyre and PyLith properties and
+ facilities, MPI settings, and PETSc settings.
You can get more information on the available options by typing
\end_layout
\begin_layout LyX-Code
\family typewriter
-$ pylith3dapp.py --help
+$ pylith --help
\end_layout
\begin_layout Standard
All PyLith-related properties are associated with the
\family typewriter
-pylith3d
+pylithapp
\family default
component.
You can get a list of all of these properties along with a description
of what they do by running PyLith with the
\family typewriter
---pylith3d.help-properties
+--help-properties
\family default
command-line argument.
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status open
-
-\begin_layout Quote
-\noindent
-
+ To get information on user settable facilities and components, you can
+ run PyLith with the
\family typewriter
-\color black
-$ pylith3dapp.py --pylith3d.help-properties --pylith3d.fileRoot=
-\shape italic
-test
-\shape default
- --pylith3d.asciiOutput=
-\emph on
-none
-\emph default
- --pylith3d.title=
-\emph on
-"My simulation"
-\emph default
-
+--help-components
+\family default
+ command-line argument.
+ To find out about the properties associated with a given component, you
+ can run PyLith with the
+\family typewriter
+--[component].help-properties
+\family default
+ flag:
\end_layout
-\begin_layout Caption
-Setting PyLith properties from the command line.
+\begin_layout LyX-Code
+$ pylith --problem.help-properties
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Subsection
Using a
\family typewriter
@@ -532,7 +205,7 @@
\begin_layout Standard
Entering all those parameters via the command line involves the risk of
typographical errors, which can lead to undesired results.
- You may find it easier to write a brief
+ You will generally find it easier to write a brief
\family typewriter
.cfg
\family default
@@ -542,7 +215,7 @@
\end_layout
\begin_layout LyX-Code
-[pylith3d.component1.component2]
+[pylithapp.component1.component2]
\end_layout
\begin_layout LyX-Code
@@ -652,13 +325,13 @@
\end_layout
\begin_layout LyX-Code
-$ pylith3dapp.py example.cfg
+$ pylith example.cfg
\end_layout
\begin_layout Standard
In addition, the Pyre framework searches for configuration files named
\family typewriter
-pylith3d.cfg
+pylithapp.cfg
\family default
in several predefined locations.
You may put settings in any or all of these locations, depending on the
@@ -668,7 +341,7 @@
\begin_layout Enumerate
\family typewriter
-PREFIX/etc/pylith3d.cfg
+PREFIX/etc/pylithapp.cfg
\family default
, for system-wide settings;
\end_layout
@@ -676,7 +349,7 @@
\begin_layout Enumerate
\family typewriter
-$HOME/.pyre/pylith3d/pylith3d.cfg
+$HOME/.pyre/pylithapp/pylithapp.cfg
\family default
, for user settings and preferences;
\end_layout
@@ -684,7 +357,7 @@
\begin_layout Enumerate
the current directory (
\family typewriter
-./pylith3d.cfg
+./pylithapp.cfg
\family default
), for local overrides.
@@ -696,13 +369,37 @@
Configuration files given on the command line override all others.
The
\family typewriter
-pylith3d.cfg
+pylithapp.cfg
\family default
files placed in (3) will override those in (2), (2) overrides (1), and
(1) overrides only the built-in defaults.
\end_layout
+\begin_layout Subsection
+PETSc Settings
+\end_layout
+
\begin_layout Standard
+PyLith relies on PETSc for the linear algebra computations.
+ PETSc options can be set in
+\family typewriter
+.cfg
+\family default
+ files in sections beginning with
+\family typewriter
+[pylithapp.petsc]
+\family default
+.
+ The ones of primary interest in the case of PyLith are shown in Table\InsetSpace ~
+
+\begin_inset LatexCommand \ref{tab:Useful-command-line-arguments}
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Standard
\noindent
\align center
\begin_inset Float table
@@ -976,29 +673,123 @@
\end_layout
-\begin_layout Subsection
-PETSc Settings
+\begin_layout Section
+Mesh Information
\end_layout
\begin_layout Standard
-PyLith relies on PETSc for the linear algebra computations.
- Many PETSc options can be set in
-\family typewriter
-.cfg
-\family default
- files.
- The ones of primary interest in the case of PyLith are shown in Table\InsetSpace ~
+Geometrical and topological information for the finite element mesh may
+ be provided using CUBIT (exported using EXODUS format), LaGriT (exported
+ using a GMV and a pset file), or by specifying the information in PyLith
+ ascii format.
+ **Put in references to tutorials and appendix.**
+\end_layout
-\begin_inset LatexCommand \ref{tab:Useful-command-line-arguments}
+\begin_layout Standard
+**Maybe mention higher-order elements.** Quadratic elements are supported,
+ but not automatic generation of a quadratic mesh from a linear mesh.
+\end_layout
+\begin_layout Standard
+PyLith currently only supports the 4-node linear tetrahedral and 8-node
+ linear hexahedral elements.
+ The node ordering must follow the convention shown in Figures\InsetSpace ~
+
+\begin_inset LatexCommand \ref{fig:tet4}
+
\end_inset
+ and\InsetSpace ~
+
+\begin_inset LatexCommand \ref{fig:hex8}
+
+\end_inset
+
.
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Graphics
+ filename figs/tet4.eps
+
+\end_inset
+
+
\end_layout
+\begin_layout Caption
+Linear tetrahedral finite element.
+\end_layout
+
+\begin_layout Standard
+\begin_inset LatexCommand \label{fig:tet4}
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement t
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename figs/hex8.eps
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+Linear hexahedral finite element.
+\end_layout
+
+\begin_layout Standard
+\begin_inset LatexCommand \label{fig:hex8}
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
\end_body
\end_document
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