[cig-commits] r6600 - in
short/3D/PyLith/branches/pylith-0.8/doc/userguide: materials
runpylith
willic3 at geodynamics.org
willic3 at geodynamics.org
Wed Apr 18 17:02:52 PDT 2007
Author: willic3
Date: 2007-04-18 17:02:52 -0700 (Wed, 18 Apr 2007)
New Revision: 6600
Modified:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.lyx
short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx
Log:
Checked in current version of documentation, which still needs work.
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.lyx 2007-04-19 00:01:29 UTC (rev 6599)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.lyx 2007-04-19 00:02:52 UTC (rev 6600)
@@ -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
@@ -40,6 +40,175 @@
Material Models
\end_layout
+\begin_layout Standard
+There are six material models presently available in PyLith.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Tabular
+<lyxtabular version="3" rows="7" columns="2">
+<features>
+<column alignment="center" valignment="top" leftline="true" width="0">
+<column alignment="center" valignment="top" leftline="true" rightline="true" width="0">
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Model Name
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Description
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+IsotropicLinearElastic
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Isotropic linear elastic material
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+IsotropicLinearMaxwellViscoelastic
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Isotropic Maxwell material with linear viscous rheology
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+IsotropicLinearGenMaxwellViscoelastic
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Generalized model consisting of 3 Maxwell models in parallel
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+IsotropicPowerLawMaxwellViscoelastic
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Isotropic Maxwell material with power-law viscous rheology
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+IsotropicLinearMaxwellViscoelasticESF
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Another linear Maxwell model formulated with an Effective Stress Function
+ (ESF) approach
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row topline="true" bottomline="true">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+IsotropicPowerLawMaxwellViscoelasticZT
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Standard
+Another power-law Maxwell model using a formulation based on that of Zienkiewicz
+ & Taylor
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+Note that there are two formulations for two of the material models (linear
+ and power-law Maxwell viscoelastic).
+ The alternate formulations are still being evaluated, and at present it
+ is still unclear which formulations are most effective.
+ It is likely that the performance of each formulation will depend on the
+ loading conditions, so users may wish to try different formulations for
+ each particular problem.
+\end_layout
+
\begin_layout Section
Effective Stress Function Formulation for Viscoelastic Materials
\end_layout
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx 2007-04-19 00:01:29 UTC (rev 6599)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.lyx 2007-04-19 00:02:52 UTC (rev 6600)
@@ -70,10 +70,6 @@
status open
\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
\align center
\begin_inset Graphics
filename figs/tet4.eps
@@ -108,10 +104,6 @@
status open
\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
\align center
\begin_inset Graphics
filename figs/hex8.eps
@@ -191,20 +183,14 @@
\begin_layout Standard
In some cases, a user may want to run the same simulation using different
numbers of processors.
- In this case, iAs a result, the user must create copies of each one for
- each of the processors.
- By default PyLith expects the names of these files to follow the same form,
-
-\family typewriter
-xx.PROC.ext
-\family default
-.
+ In this case, users may wish to provide distinctive sets of filenames 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
-runbm.py
+mklinks.py
\family default
in section\InsetSpace ~
@@ -214,7 +200,7 @@
for a simple example.
You can also choose your own filename template by setting the appropriate
- command-line argument.
+ parameters.
See section\InsetSpace ~
\begin_inset LatexCommand \ref{sec:setting:parameters}
@@ -343,7 +329,6 @@
\family default
\color none
Traction boundary condition information.
-
\end_layout
\begin_layout Description
@@ -355,6 +340,9 @@
\color none
Local coordinate rotation information for boundary conditions.
+\shape italic
+\color inherit
+Not yet implemented.
\end_layout
\begin_layout Description
@@ -395,7 +383,7 @@
xx.hist
\family default
\color none
- Time histories for split node and Winkler boundary conditions (if necessary).
+ Time histories for split nodes and boundary conditions (if necessary).
\emph on
Not yet tested.
@@ -417,92 +405,87 @@
\end_layout
\begin_layout Standard
-In general, PyLith's command-line arguments fall into three categories:
- MPI settings, Pyre properties and facilities, and PETSc settings.
+There are several methods for setting input parameters for pylith3dapp.py:
+ via the command line, or by using a configuration file in
+\family typewriter
+.cfg
+\family default
+ or
+\family typewriter
+.pml
+\family default
+ format.
+ PyLith gathers many simulation parameters and settings using Pyre properties
+ and facilities.
+ Properties correspond to simple settings in the form of strings, integers,
+ and real numbers.
+ Facilities correspond to software modules.
+ Both facilities and properties have default values provided, so you only
+ need to set values when you want to deviate from the default behavior.
+ Unless you write a module that extends PyLith's functionality, you will
+ never need to change any of the facilities from the defaults.
\end_layout
+\begin_layout Subsection
+Using the Command Line
+\end_layout
+
\begin_layout Standard
-If using the MPICH implementation of the Message Passing Interface (MPI),
- as is done for the CIG distributed binaries, the synopsis for running PyLith
- is
-\newline
+Pyre uses the following syntax to change properties from the command line.
+ To change the value of a property of a component, use:
+\end_layout
-\newline
+\begin_layout LyX-Code
\family typewriter
- $ mpirun {-np
-\emph on
-NPROCS
-\emph default
-} pylith3dapp.py
-\emph on
-[PyLith settings]
-\emph default
-
-\emph on
-[PETSc settings]
+--[component].[property]=[value]
\end_layout
-\begin_layout Subsection
-MPI Settings
+\begin_layout Standard
+Each component is attached to a facility, so the option above can also be
+ written as:
\end_layout
-\begin_layout Quote
+\begin_layout LyX-Code
-\series bold
-\color red
-Warning:
-\series default
-\color none
- This section applies only to PyLith compiled using the MPICH implementation
- of the Message Passing Interface (MPI).
-
+\family typewriter
+--[facility].[property]=[value]
\end_layout
\begin_layout Standard
-The MPI settings define how many processors are used and other parallel
- processing parameters.
- The number of processors is specified using
-\family typewriter
-\color black
--np NPROCS
-\family default
-\color none
-, where
-\family typewriter
-\color black
-NPROCS
-\family default
-\color none
- corresponds to the number of processors.
+Each facility has a default component attached to it.
+ A different component can be attached to a facility by:
\end_layout
-\begin_layout Subsection
-Properties and Facilities
+\begin_layout LyX-Code
+
+\family typewriter
+--[facility]=[new_component]
\end_layout
\begin_layout Standard
-PyLith gathers many simulation parameters and settings using Pyre properties
- and facilities.
- Properties correspond to simple settings in the form of strings, integers,
- and real numbers.
- Facilities correspond to software modules.
- Both facilities and properties have default values provided, so you only
- need to set values when you want to deviate from the default behavior.
- Unless you write a module that extends PyLith's functionality, you will
- never need to change any of the facilities from the defaults.
+In general, PyLith's command-line arguments fall into three categories:
+ MPI settings, Pyre/PyLith properties and facilities, 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
+\end_layout
+
\begin_layout Standard
-In the current version of PyLith, all of the properties are associated with
- the scanner component.
+All PyLith-related properties are associated with the
+\family typewriter
+pylith3d
+\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
-\color black
---scanner.help-properties
+--pylith3d.help-properties
\family default
-\color none
command-line argument.
\end_layout
@@ -518,19 +501,15 @@
\family typewriter
\color black
-$ mpirun\InsetSpace ~
-\InsetSpace ~
- -np
+$ pylith3dapp.py --pylith3d.help-properties --pylith3d.fileRoot=
+\shape italic
+test
+\shape default
+ --pylith3d.asciiOutput=
\emph on
-1
-\emph default
- \InsetSpace ~
-\InsetSpace ~
-pylith3dapp.py --scanner.help-properties --scanner.asciiOutput=
-\emph on
none
\emph default
- --scanner.title=
+ --pylith3d.title=
\emph on
"My simulation"
\emph default
@@ -538,7 +517,7 @@
\end_layout
\begin_layout Caption
-Setting scanner properties from the command line.
+Setting pylith properties from the command line.
\end_layout
\end_inset
@@ -547,6 +526,187 @@
\end_layout
\begin_layout Subsection
+Using a
+\family typewriter
+.cfg
+\family default
+ File
+\end_layout
+
+\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
+\family typewriter
+.cfg
+\family default
+ input file that contains the parameters.
+ This file has a format similar to a Windows INI file.
+ The file is composed of one or more sections which are formatted as follows:
+\end_layout
+
+\begin_layout LyX-Code
+[pylith3d.component1.component2]
+\end_layout
+
+\begin_layout LyX-Code
+# this is a comment
+\end_layout
+
+\begin_layout LyX-Code
+property1 = value1
+\end_layout
+
+\begin_layout LyX-Code
+property2 = value2 ; this is another comment
+\end_layout
+
+\begin_layout Standard
+We strongly recommend that you use
+\family typewriter
+.cfg
+\family default
+ files for your work.
+ The files are syntax-colored by the vim editor.
+\end_layout
+
+\begin_layout Subsection
+Using a
+\family typewriter
+.pml
+\family default
+ File
+\end_layout
+
+\begin_layout Standard
+A
+\family typewriter
+.pml
+\family default
+ file is an XML file that specifies parameter values in a highly structured
+ format.
+ It is composed of nested sections which are formatted as follows:
+\end_layout
+
+\begin_layout LyX-Code
+<component name='component1'>
+\end_layout
+
+\begin_layout LyX-Code
+ <component name='component2'>
+\end_layout
+
+\begin_layout LyX-Code
+ <property name='property1'>value1</property>
+\end_layout
+
+\begin_layout LyX-Code
+ <property name='property2'>value2</property>
+\end_layout
+
+\begin_layout LyX-Code
+ </component>
+\end_layout
+
+\begin_layout LyX-Code
+</component>
+\end_layout
+
+\begin_layout Standard
+XML files are intended to be read and written by machines, not edited manually
+ by humans.
+ The
+\family typewriter
+.pml
+\family default
+ 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 in using
+\family typewriter
+.pml
+\family default
+ files, note that
+\family typewriter
+.pml
+\family default
+ files and
+\family typewriter
+.cfg
+\family default
+ files can be used interchangeably; in the following discussion, a file
+ with a
+\family typewriter
+.pml
+\family default
+ extension can be substituted anywhere a
+\family typewriter
+.cfg
+\family default
+ file can be used.
+\end_layout
+
+\begin_layout Subsection
+Specification and Placement of Configuration Files
+\end_layout
+
+\begin_layout Standard
+Configuration files may be specified on the command line:
+\end_layout
+
+\begin_layout LyX-Code
+$ pylith3dapp.py example.cfg
+\end_layout
+
+\begin_layout Standard
+In addition, the Pyre framework searches for configuration files named
+\family typewriter
+pylith3d.cfg
+\family default
+ in several predefined locations.
+ You may put settings in any or all of these locations, depending on the
+ scope you want the settings to have:
+\end_layout
+
+\begin_layout Enumerate
+
+\family typewriter
+PREFIX/etc/pylith3d.cfg
+\family default
+, for system-wide settings;
+\end_layout
+
+\begin_layout Enumerate
+
+\family typewriter
+$HOME/.pyre/pylith3d/pylith3d.cfg
+\family default
+, for user settings and preferences;
+\end_layout
+
+\begin_layout Enumerate
+the current directory (
+\family typewriter
+./pylith3d.cfg
+\family default
+), for local overrides.
+
+\end_layout
+
+\begin_layout Standard
+Parameters given directly on the command line will override any input contained
+ in a configuration file.
+ Configuration files given on the command line override all others.
+ The
+\family typewriter
+pylith3d.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 Standard
PETSc Settings
\end_layout
@@ -570,10 +730,6 @@
status open
\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="7" columns="2">
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