[cig-commits] r7300 - in short/3D/PyLith/trunk/doc/userguide/intro:
. figs
brad at geodynamics.org
brad at geodynamics.org
Tue Jun 19 09:22:51 PDT 2007
Author: brad
Date: 2007-06-19 09:22:50 -0700 (Tue, 19 Jun 2007)
New Revision: 7300
Added:
short/3D/PyLith/trunk/doc/userguide/intro/figs/workflow.eps
short/3D/PyLith/trunk/doc/userguide/intro/figs/workflow.fig
Modified:
short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
Log:
Cleaned up introduction. Updated workflow figure.
Added: short/3D/PyLith/trunk/doc/userguide/intro/figs/workflow.eps
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/intro/figs/workflow.eps 2007-06-19 14:31:16 UTC (rev 7299)
+++ short/3D/PyLith/trunk/doc/userguide/intro/figs/workflow.eps 2007-06-19 16:22:50 UTC (rev 7300)
@@ -0,0 +1,742 @@
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Added: short/3D/PyLith/trunk/doc/userguide/intro/figs/workflow.fig
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/intro/figs/workflow.fig 2007-06-19 14:31:16 UTC (rev 7299)
+++ short/3D/PyLith/trunk/doc/userguide/intro/figs/workflow.fig 2007-06-19 16:22:50 UTC (rev 7300)
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Modified: short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2007-06-19 14:31:16 UTC (rev 7299)
+++ short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2007-06-19 16:22:50 UTC (rev 7300)
@@ -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
@@ -84,30 +84,23 @@
Material properties and parameters for boundary and fault conditions are
specified using a spatial database, which permits easy precsription of
complex spatial variations of properties and parameters.
- Simulation parameters are generally specified through the use of
-\family sans
-.cfg
-\family default
- files, although they can also be specified using
-\family typewriter
-.pml
-\family default
- files or from the command line.
- At present, mesh information may be provided using a simple ASCII format
+ Simulation parameters are generally specified through the use of simple
+ ASCII files or the command line.
+ At present, mesh information may be provided using a simple ASCII file
(PyLith ASCII format) or imported from CUBIT or LaGriT, two widely-used
meshing packages.
The elements currently available include a linear bar in 1-D, linear triangles
- and quadrilaterals in 2-D, and linear tetrahedra and hexahedra in 3-D)
+ and quadrilaterals in 2-D, and linear tetrahedra and hexahedra in 3-D.
Higher-order (quadratic) elements are also supported, but it is not presently
possible to create a quadratic mesh from the linear meshes provided by
most meshing packages.
Materials presently available include isotropic elastic and linear Maxwell
viscoelastic (3-D only).
- Cohesive elements are used to represent faults.
+ Cohesive elements are used to implement slip across interior surfaces (faults).
At present, only kinematically-specified fault slip is available.
In the near future, we will provide several constitutive models for cohesive
- elements, which will allow slip to occur using several different fault
- constitutive models.
+ elements, which will allow slip to occur using various fault constitutive
+ models.
\end_layout
\begin_layout Standard
@@ -139,26 +132,19 @@
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.
- In the case of PyLith, this task is performed by translating external formats
- into Sieve mesh data structures.
PyLith presently provides three mesh importing options: CUBIT Exodus format,
LaGriT GMV + Pset files, and PyLith 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 translated
+ Once the computations have been performed, the results must be exported
into a format that can be used by a visualization code.
- For PyLith, this task is performed by translating the Sieve data structures
- into an appropriate form.
Present output consists of VTK files which can be used by a number of visualiza
tion codes (e.g., ParaView and MayaVi).
In the near future, a more flexible HDF5 format is planned.
- [
-\series bold
-BRAD
-\series default
- -- need new figure to replace this placeholder.
- If you give me the original xfig (or whatever you used), I can modify it
- accordingly)]
+
+\end_layout
+
+\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
@@ -166,7 +152,7 @@
\begin_layout Standard
\begin_inset Graphics
- filename figs/workflow.pdf
+ filename figs/workflow.eps
\end_inset
@@ -193,44 +179,32 @@
\begin_layout Standard
PyLith is separated into modules to encapsulate behavior and facilitate
use across multiple applications.
- That way expert users can replace functionality of a wide variety of components
- without recompiling or polluting the main code.
- External packages reduce development time and enhance computational efficiency;
- for example, PyLith 0.8 ran two times faster when the PETSc linear solver
- was used.
+ This allows expert users to replace functionality of a wide variety of
+ components without recompiling or polluting the main code.
+ PyLith employs external packages to reduce development time and enhance
+ computational efficiency; for example, PyLith 0.8 ran two times faster when
+ the PETSc linear solver was used.
\end_layout
\begin_layout Standard
-PyLith employs two programming languages.
+PyLith is written in two programming languages.
High-level code is written in Python; this rich, expressive interpreted
language with dynamic typing reduces development time and permits flexible
addition of user-contributed modules.
+ This high-level code makes use of Pyre, a science-neutral simulation framework
+ developed at Caltech, to link the modules together at runtime and gather
+ user-input.
Low-level code is written in C++, providing fast execution while still
- allowing object-oriented code.
+ allowing an object-oriented implementation.
+ This low-level code relies on PETSc to perform operations on matrices and
+ vectors in parallel.
We also make extensive use of two Python packages.
Pyrex is a package that simplifies the task of adding C extensions to Python
- code.
- We also use pyrexembed, which extends the use of Pyrex to handle C++ code.
+ code, and pyrexembed extends Pyrex to handle C++ code.
\end_layout
\begin_layout Standard
-PyLith makes extensive use of external software.
- Pyre is a science-neutral simulation framework being developed at Caltech.
- PETSc is used to perform operations on matrices and vectors in parallel.
-\end_layout
-
-\begin_layout Standard
-[
-\series bold
-BRAD, MATT
-\series default
- -- This section needs to be completely rewritten, since it came from PyLith
- 0.8.
- Any help would be appreciated.]
-\end_layout
-
-\begin_layout Standard
-In rewriting PyLith, the code was completely redesigned to be object-oriented
+In writing PyLith 1.0, the code was completely redesigned to be object-oriented
and modular.
Each type of module is accessed through a specified interface (set of functions
).
@@ -254,10 +228,10 @@
\end_layout
\begin_layout Standard
-During development tests were constructed for nearly every module function.
+During development, tests were constructed for nearly every module function.
These unit tests are distributed with the source code.
- During development these tests were run on a frequent basis to expose bugs
- and isolate their origin.
+ These tests are run continuously during development to expose bugs and
+ isolate their origin.
As additional changes are made to the code, the tests are rerun to help
prevent introduction of bugs.
A number of simple, full scale tests, such as axial compression, simple
@@ -265,28 +239,22 @@
\end_layout
\begin_layout Standard
-[ADD DESCRIPTION OF WHAT HAPPENS WHEN EXECUTING PYLITH IN PARALLEL, next
- paragraph is too technical (too much nomenclature)]
-\end_layout
-
-\begin_layout Standard
Our new design begins with the
\family typewriter
Sieve
\family default
to represent the topology of our domain.
Zero volume elements are inserted along all fault surfaces which can implement
- both split node and cohesive element schemes.
- Material properties and other parameters are represented as
+ both kinematic (prescribed) and 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
+ retrived by restricting the section to the vertex or cell.
+ For each problem, functions are provided to calculate the residual and
+ its Jacobian.
+ All numerical integration is done in these functions, and parallel assembly
+ is accomplished using the restrict/update paradigm of the
\family typewriter
- Sections
-\family default
- over the sieve, and values can be retrieved by restriction.
- For each problem, methods are provided to calculate the residual and its
- Jacobian.
- All analytic work is done in these functions, and parallel assembly is
- accomplished using the restrict/update paradigm from the
-\family typewriter
Sieve
\family default
framework.
@@ -306,7 +274,7 @@
Pyre allows the binding of multiple components such as solid and fluid
models used in Earth science simulations, and different meshers.
The Pyre framework enables the elegant setup, modification and launching
- of massively parallel three-dimensional solver applications.
+ of massively parallel solver applications.
\end_layout
\begin_layout Standard
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