[cig-commits] r7229 - in short/3D/PyLith/trunk/doc/userguide/intro: . figs

willic3 at geodynamics.org willic3 at geodynamics.org
Thu Jun 14 09:00:32 PDT 2007 

Author: willic3
Date: 2007-06-14 09:00:31 -0700 (Thu, 14 Jun 2007)
New Revision: 7229

Added:
   short/3D/PyLith/trunk/doc/userguide/intro/figs/workflow.pdf
Modified:
   short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
Log:
More work on intro.  The PyLith design section still needs to be
rewritten.  The current workflow figure is a placeholder until I can
get Brad's original xfig (or whatever he used).
I have put Brad and Matt's names in BOLD wherever I think they could
help.



Added: short/3D/PyLith/trunk/doc/userguide/intro/figs/workflow.pdf
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(Binary files differ)


Property changes on: short/3D/PyLith/trunk/doc/userguide/intro/figs/workflow.pdf
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Modified: short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx	2007-06-14 14:51:04 UTC (rev 7228)
+++ short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx	2007-06-14 16:00:31 UTC (rev 7229)
@@ -59,7 +59,11 @@
 This version of PyLith (1.0) is the first version to allow the solution of
  both implicit (quasi-static) and explicit (dynamic) problems, and represents
  a complete rewrite of the original PyLith.
- This version combines the functionality of EqSim [ref???] and PyLith 0.8.
+ This version combines the functionality of EqSim [
+\series bold
+BRAD
+\series default
+ -- ref???] and PyLith 0.8.
  PyLith 0.8 was a direct descendant of LithoMop and was the first version
  that ran in parallel, as well as providing several other improvements over
  LithoMop.
@@ -88,29 +92,101 @@
 .pml
 \family default
  files or from the command line.
- At present, mesh information may be provided using a simple ASCII format,
- and mesh data may also be imported from CUBIT or LaGriT, two widely-used
- meshing packages.
+ At present, mesh information may be provided using a simple ASCII format
+ (PyLith ASCII format), and mesh data may also be imported from CUBIT or
+ LaGriT, two widely-used meshing packages.
  The elements currently available include a linear beam (1D), linear triangles
  and quadrilaterals (2D), and linear tetrahedra and hexahedra (3D).
+ 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.
- Faults???
+ Cohesive elements are used to represent 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
+ physics models.
 \end_layout
 
 \begin_layout Standard
 PyLith is under active development and we expect a number of additions and
  improvements in the near future.
- Likely enhancements will include the addition of new material models for
- both volume elements and cohesive (fault) elements, higher-order elements,
- and the generation of Green's functions to be used in inversions.
+ Likely enhancements will include the addition of new constitutive models
+ for both volume elements and cohesive (fault) elements, automatic generation
+ of higher-order elements from linear elements, and the generation of Green's
+ functions to be used in inversions.
  Many of these features should be available by late Summer, 2007.
 \end_layout
 
+\begin_layout Section
+PyLith Workflow
+\end_layout
+
 \begin_layout Standard
+PyLith is one component in the process of investigating problems in tectonics
+ (
+\begin_inset LatexCommand \ref{fig:Workflow-summary}
 
+\end_inset
+
+).
+ 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.
+ 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
+ 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 format, which can be used by a number of
+ visualization codes.
+ 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)] 
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\begin_inset Graphics
+	filename figs/workflow.pdf
+
+\end_inset
+
+
 \end_layout
 
+\begin_layout Caption
+\begin_inset LatexCommand \label{fig:Workflow-summary}
+
+\end_inset
+
+Workflow involved in going from geologic structure to problem analysis.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
 \begin_layout Section
 Software Components
 \end_layout
@@ -167,8 +243,8 @@
 \end_layout
 
 \begin_layout Standard
-PETSc includes interfaces for Fortran 77/90, C, C++, and Python for nearly all of the
- routines, and PETSc can be installed on most Unix systems.
+PETSc includes interfaces for Fortran 77/90, C, C++, and Python for nearly
+ all of the routines, and PETSc can be installed on most Unix systems.
  PETSc can be built with user-supplied, highly optimized linear algebra
  routines (e.g., ATLAS and commercial versions of BLAS/LAPACK), thereby improving
  application performance.
@@ -300,12 +376,21 @@
 \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
  and modular.
  Each module has its own facilities and parameters that may be specified
  in a number of different ways.
- This code structure will also simplify the tasks of code maintenance and
- developement.
+ This code structure will also simplify code maintenance and developement.
  We provide unit tests for all significant code funtions, which simplifies
  the task of diagnosing problems.
  Extending the set of code features is also easier, since developers can
@@ -321,10 +406,10 @@
  Active development of purely analytic features in PyLith, such as new material
  models or discretization schemes, depends on the familiarity of application
  scientists with the traditional Fortran programming paradigm.
- Global, topological operations such as parallel assembly were strictly segregated from the preexisting
- code.
- In fact, PyLith can be run purely in serial without activating
- any of the parallel capabilities.
+ Global, topological operations such as parallel assembly were strictly
+ segregated from the preexisting code.
+ In fact, PyLith can be run purely in serial without activating any of the
+ parallel capabilities.
 \end_layout
 
 \begin_layout Standard
@@ -334,9 +419,8 @@
 \family default
  structure to create a model of the serial PyLith mesh.
  This model is then partitioned and distributed to a set of processes.
- Each process receives a self-consistent mesh, meaning the pieces are overlapping,
- and then executes a serial PyLith step on that particular mesh
- piece.
+ Each process receives a self-consistent mesh, meaning the pieces are overlappin
+g, and then executes a serial PyLith step on that particular mesh piece.
  The PETSc assembles these pieces, using the 
 \family typewriter
 Sieve
@@ -349,21 +433,24 @@
 \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
+to represent the topology of our domain.
+ Zero volume elements are inserted alongall fault surfaces which can implement
+ both split node and cohesive element schemes.Material properties and other
+ parameters are represented as
 \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
+over the sieve, and values can be retrieved by restriction.
+ For each problem, methodsare provided to calculate the residual and its
+ Jacobian.
+ All analytic work is done inthese functions, and parallel assembly is accomplis
+hed using the restrict/update paradigmfrom the
 \family typewriter
 Sieve
 \family default
-framework. We assemble into PETSc linear algebra objects and then call PETSc solvers. The solution
-is mapped back into a section, which can be output in VTK format.
+framework.
+ We assemble into PETSc linear algebra objects and then call PETSc solvers.
+ The solutionis mapped back into a section, which can be output in VTK format.
 \end_layout
 
 \end_body

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