[cig-commits] r22348 - in short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro: . figs
brad at geodynamics.org
brad at geodynamics.org
Mon Jun 17 16:01:41 PDT 2013
Author: brad
Date: 2013-06-17 16:01:41 -0700 (Mon, 17 Jun 2013)
New Revision: 22348
Modified:
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro/figs/workflow.svg
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro/intro.lyx
Log:
Added Relax to workflow diagram.
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro/figs/workflow.svg
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro/figs/workflow.svg 2013-06-17 21:49:15 UTC (rev 22347)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro/figs/workflow.svg 2013-06-17 23:01:41 UTC (rev 22348)
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Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro/intro.lyx 2013-06-17 21:49:15 UTC (rev 22347)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro/intro.lyx 2013-06-17 23:01:41 UTC (rev 22348)
@@ -1,542 +1,541 @@
-#LyX 2.0 created this file. For more info see http://www.lyx.org/
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-\end_header
-
-\begin_body
-
-\begin_layout Chapter
-Introduction
-\end_layout
-
-\begin_layout Section
-Overview
-\end_layout
-
-\begin_layout Standard
-PyLith is a multi-scale simulation software package for earthquake physics.
- It is portable, scalable software for simulation of crustal deformation
- across spatial scales ranging from meters to hundreds of kilometers and
- temporal scales ranging from milliseconds to thousands of years.
-\end_layout
-
-\begin_layout Section
-History
-\end_layout
-
-\begin_layout Standard
-PyLith 1.0 was the first version to allow the solution of both implicit (quasi-st
-atic) and explicit (dynamic) problems and was a complete rewrite of the
- original PyLith (version 0.8).
- PyLith 1.0 combines the functionality of EqSim
-\begin_inset CommandInset citation
-LatexCommand cite
-key "Aagaard:etal:2001a,Aagaard:etal:2001b"
-
-\end_inset
-
- 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.
- 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
- 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.
-\end_layout
-
-\begin_layout Standard
-The release of PyLith 1.0 has been followed by additional releases that expand
- the number of features as well as improve performance.
- The PyLith 1.x series of releases allows the solution of both quasi-static
- and dynamic problems in one, two, or three dimensions.
- The code runs in either serial or parallel, and the design allows for relativel
-y easy scripting using the Python programming language.
- Material properties and values for boundary and fault conditions are specified
- 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.
- At present, mesh information may be provided using a simple ASCII file
- (PyLith mesh ASCII format) or imported from CUBIT or LaGriT, two widely-used
- meshing packages.
- The elements currently available include a linear bar in 1D, linear triangles
- and quadrilaterals in 2D, and linear tetrahedra and hexahedra in 3D.
- Materials presently available include isotropic elastic, linear Maxwell
- viscoelastic, generalized Maxwell viscoelastic, power-law viscoelastic,
- and Drucker-Prager elastoplastic.
- Boundary conditions include Dirichlet (prescribed displacements and velocities)
-, Neumann (traction), point forces, and absorbing boundaries.
- Cohesive elements are used to implement slip across interior surfaces (faults)
- with both kinematically-specified fault slip and slip governed by fault
- constitutive models.
- PyLith also includes an interface for computing static Green's functions
- for fault slip.
-\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 additional bulk and fault constitutive
- models, coupled quasi-static and dynamic simulations for earthquake cycle
- modeling, and coupling between elasticity, heat flow, and/or fluid flow.
-\end_layout
-
-\begin_layout Section
-PyLith Workflow
-\end_layout
-
-\begin_layout Standard
-PyLith is one component in the process of investigating problems in tectonics
- (Figure
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "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.
- PyLith presently provides three mesh importing options: CUBIT Exodus 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.
- Present output consists of VTK or HDF5/Xdmf files which can be used by
- a number of visualization codes (e.g., ParaView, Visit, MayaVi, and Matlab).
-
-\end_layout
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-\begin_layout Standard
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-name "fig:Workflow-summary"
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-\end_inset
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-Workflow involved in going from geologic structure to problem analysis.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Section
-PyLith Design
-\end_layout
-
-\begin_layout Standard
-PyLith is separated into modules to encapsulate behavior and facilitate
- use across multiple applications.
- This allows expert users to replace functionality of a wide variety of
- components without recompiling or polluting the main code.
- PyLith employs external packages (see Figure
-\begin_inset CommandInset ref
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-reference "fig:pylith-dependencies"
-
-\end_inset
-
-) to reduce development time and enhance computational efficiency; for example,
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-name "fig:pylith-dependencies"
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-
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- own dependencies.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-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 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.
- SWIG is a package that simplifies the task of adding C++ extensions to
- Python code, and FIAT provides tabulated basis functions and numerical
- quadrature points.
-
-\end_layout
-
-\begin_layout Standard
-In writing PyLith 1.0, the code was designed to be object-oriented and modular.
- Each type of module is accessed through a specified interface (set of functions
-).
- This permits adding, replacing, and rewriting modules without affecting
- other parts of the code.
- This code structure simplifies code maintenance and development.
- Extending the set of code features is also easier, since developers can
- create new modules derived from the existing ones.
-\end_layout
-
-\begin_layout Standard
-The new code design leverages Pyre, Sieve, and PETSc much more extensively
- than the previous version.
- Pyre is used to glue together the various modules used to construct a
- simulation and specify the parameters.
- Sieve is used for all finite-element storage and manipulation and handles
- the creation of the PETSc matrices and vectors.
- As a result, most of the PyLith source code pertains to implementing the
- geodynamics, such as bulk rheology, boundary conditions, and slip on faults.
-
-\end_layout
-
-\begin_layout Standard
-PyLith also uses FIAT to tabulate the finite-element basis functions at
- the numerical integration (quadrature) points.
- Nemesis allows PyLith to run Python using the Message Passing Interface
- (MPI) for parallel processing.
- Additional, indirect dependencies (see Figure
-\begin_inset CommandInset ref
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-reference "fig:pylith-dependencies"
-
-\end_inset
-
-) include numpy (efficient operations on numerical arrays in Python), Proj.4
- (geographic projections), and SWIG (calling C++ functions from Python).
-\end_layout
-
-\begin_layout Standard
-During development, tests were constructed for nearly every module function.
- These unit tests are distributed with the source code.
- These tests are run throughout the development cycle to expose bugs and
- isolate their origin.
- As additional changes are made to the code, the tests are rerun to help
- prevent introduction of new bugs.
- A number of simple, full-scale tests, such as axial compression and extension,
- simple shear, and slip on through-going faults, have been used to test
- the code.
- Additionally, we have run the Southern California Earthquake Center crustal
- deformation and several of the spontaneous rupture benchmarks for strike-slip
- and reverse-slip to determine the relative local and global error (see
- Chapter
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "cha:Benchmarks"
-
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Subsection
-Pyre
-\end_layout
-
-\begin_layout Standard
-Pyre is an object-oriented environment capable of specifying and launching
- numerical simulations on multiple platforms, including Beowulf-class parallel
- computers and grid computing systems.
- 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 solver applications.
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status open
-
-\begin_layout Plain Layout
-\align center
-\begin_inset Graphics
- filename figs/pyre_overview.png
- width 4in
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Plain Layout
-\begin_inset Caption
-
-\begin_layout Plain Layout
-\begin_inset CommandInset label
-LatexCommand label
-name "fig:Pyre:Architecture"
-
-\end_inset
-
-Pyre Architecture.
- The integration framework is a set of cooperating abstract services.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-Pyre is a framework, a combination of software and design philosophy that
- promotes the reuse of code.
- In their canonical software design book,
-\emph on
-Design Patterns
-\emph default
-, Erich Gamma
-\shape italic
-et al
-\shape default
-.
- condense the concept of a framework concept down to, ``When you use a framework
-, you reuse the main body and write the code it calls.'' In the context of
- frameworks and object-oriented programming, Pyre can be thought of as a
- collection of classes and the way their instances interact.
- Programming applications based on Pyre will look similar to those written
- in any other object-oriented language.
- The Pyre framework contains a subset of parts that make up the overall
- framework.
- Each of those parts is designed to solve a specific problem.
-\end_layout
-
-\begin_layout Standard
-The framework approach to computation offers many advantages.
- It permits the exchange of codes and promotes the reuse of standardized
- software while preserving efficiency.
- Frameworks are also an efficient way to handle changes in computer architecture.
- They present programmers and scientists with a unified and well-defined
- task and allow for shared costs of the housekeeping aspects of software
- development.
- They provide greater institutional continuity to model development than
- piecemeal approaches.
-\end_layout
-
-\begin_layout Standard
-The Pyre framework incorporates features aimed at enabling the scientific
- non-expert to perform tasks easily without hindering the expert.
- Target features for end users allow complete and intuitive simulation specifica
-tion, reasonable defaults, consistency checks of input, good diagnostics,
- easy access to remote facilities, and status monitoring.
- Target features for developers include easy access to user input, a shorter
- development cycle, and good debugging support.
-\end_layout
-
-\begin_layout Subsection
-Sieve and PETSc
-\end_layout
-
-\begin_layout Standard
-PyLith 1.x makes use of a set of data structures and routines in PETSc called
-
-\family typewriter
-Sieve
-\family default
-, which is still under active development.
-
-\family typewriter
-Sieve
-\family default
- provides data structures and routines for for representing and manipulating
- computational meshes, and it greatly simplifies finite-element computations.
-
-\family typewriter
- Sieve
-\family default
- represents the topology of the domain.
- 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
- retrieved 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
-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.
-\end_layout
-
-\begin_layout Standard
-PETSc
-\begin_inset Flex URL
-status collapsed
-
-\begin_layout Plain Layout
-
-www-unix.mcs.anl.gov/petsc/petsc-as
-\end_layout
-
-\end_inset
-
-, the Portable, Extensible Toolkit for Scientific computation, provides
- a suite of routines for parallel, numerical solution of partial differential
- equations for linear and nonlinear systems with large, sparse systems of
- equations.
- 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
- and interaction with other software packages.
-\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 can be built with user-supplied, highly optimized linear algebra
- routines (e.g., ATLAS and commercial versions of BLAS/LAPACK), thereby improving
- application performance.
- Users can use PETSc parallel matrices, vectors, and other data structures
- for most parallel operations, eliminating the need for explicit calls to
- Message Passing Interface (MPI) routines.
- Many settings and options can be controlled with PETSc-specific command-line
- arguments, including selection of preconditions, solvers, and generation
- of performance logs.
-\end_layout
-
-\end_body
-\end_document
+#LyX 2.0 created this file. For more info see http://www.lyx.org/
+\lyxformat 413
+\begin_document
+\begin_header
+\textclass book
+\begin_preamble
+\usepackage{tikz}
+\end_preamble
+\use_default_options false
+\maintain_unincluded_children false
+\language english
+\language_package default
+\inputencoding latin1
+\fontencoding global
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\use_non_tex_fonts false
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
+
+\graphics default
+\default_output_format default
+\output_sync 0
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+\spacing single
+\use_hyperref false
+\papersize default
+\use_geometry true
+\use_amsmath 1
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+\use_mhchem 1
+\use_mathdots 1
+\cite_engine basic
+\use_bibtopic false
+\use_indices false
+\paperorientation portrait
+\suppress_date false
+\use_refstyle 0
+\index Index
+\shortcut idx
+\color #008000
+\end_index
+\leftmargin 1in
+\topmargin 1in
+\rightmargin 1in
+\bottommargin 2in
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\paragraph_indentation default
+\quotes_language english
+\papercolumns 1
+\papersides 2
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\html_math_output 0
+\html_css_as_file 0
+\html_be_strict false
+\end_header
+
+\begin_body
+
+\begin_layout Chapter
+Introduction
+\end_layout
+
+\begin_layout Section
+Overview
+\end_layout
+
+\begin_layout Standard
+PyLith is a multi-scale simulation software package for earthquake physics.
+ It is portable, scalable software for simulation of crustal deformation
+ across spatial scales ranging from meters to hundreds of kilometers and
+ temporal scales ranging from milliseconds to thousands of years.
+\end_layout
+
+\begin_layout Section
+History
+\end_layout
+
+\begin_layout Standard
+PyLith 1.0 was the first version to allow the solution of both implicit (quasi-st
+atic) and explicit (dynamic) problems and was a complete rewrite of the
+ original PyLith (version 0.8).
+ PyLith 1.0 combines the functionality of EqSim
+\begin_inset CommandInset citation
+LatexCommand cite
+key "Aagaard:etal:2001a,Aagaard:etal:2001b"
+
+\end_inset
+
+ 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.
+ 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
+ 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.
+\end_layout
+
+\begin_layout Standard
+The release of PyLith 1.0 has been followed by additional releases that expand
+ the number of features as well as improve performance.
+ The PyLith 1.x series of releases allows the solution of both quasi-static
+ and dynamic problems in one, two, or three dimensions.
+ The code runs in either serial or parallel, and the design allows for relativel
+y easy scripting using the Python programming language.
+ Material properties and values for boundary and fault conditions are specified
+ 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.
+ At present, mesh information may be provided using a simple ASCII file
+ (PyLith mesh ASCII format) or imported from CUBIT or LaGriT, two widely-used
+ meshing packages.
+ The elements currently available include a linear bar in 1D, linear triangles
+ and quadrilaterals in 2D, and linear tetrahedra and hexahedra in 3D.
+ Materials presently available include isotropic elastic, linear Maxwell
+ viscoelastic, generalized Maxwell viscoelastic, power-law viscoelastic,
+ and Drucker-Prager elastoplastic.
+ Boundary conditions include Dirichlet (prescribed displacements and velocities)
+, Neumann (traction), point forces, and absorbing boundaries.
+ Cohesive elements are used to implement slip across interior surfaces (faults)
+ with both kinematically-specified fault slip and slip governed by fault
+ constitutive models.
+ PyLith also includes an interface for computing static Green's functions
+ for fault slip.
+\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 additional bulk and fault constitutive
+ models, coupled quasi-static and dynamic simulations for earthquake cycle
+ modeling, and coupling between elasticity, heat flow, and/or fluid flow.
+\end_layout
+
+\begin_layout Section
+PyLith Workflow
+\end_layout
+
+\begin_layout Standard
+PyLith is one component in the process of investigating problems in tectonics
+ (Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "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.
+ PyLith presently provides three mesh importing options: CUBIT Exodus 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.
+ Present output consists of VTK or HDF5/Xdmf files which can be used by
+ a number of visualization codes (e.g., ParaView, Visit, MayaVi, and Matlab).
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/workflow.pdf
+ scale 67
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:Workflow-summary"
+
+\end_inset
+
+Workflow involved in going from geologic structure to problem analysis.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section
+PyLith Design
+\end_layout
+
+\begin_layout Standard
+PyLith is separated into modules to encapsulate behavior and facilitate
+ use across multiple applications.
+ This allows expert users to replace functionality of a wide variety of
+ components without recompiling or polluting the main code.
+ PyLith employs external packages (see Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:pylith-dependencies"
+
+\end_inset
+
+) 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
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/packages.eps
+ scale 40
+
+\end_inset
+
+
+\begin_inset Caption
+
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:pylith-dependencies"
+
+\end_inset
+
+PyLith dependencies.
+ PyLith makes direct use of several other packages, some of which have their
+ own dependencies.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+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 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.
+ SWIG is a package that simplifies the task of adding C++ extensions to
+ Python code, and FIAT provides tabulated basis functions and numerical
+ quadrature points.
+
+\end_layout
+
+\begin_layout Standard
+In writing PyLith 1.0, the code was designed to be object-oriented and modular.
+ Each type of module is accessed through a specified interface (set of functions
+).
+ This permits adding, replacing, and rewriting modules without affecting
+ other parts of the code.
+ This code structure simplifies code maintenance and development.
+ Extending the set of code features is also easier, since developers can
+ create new modules derived from the existing ones.
+\end_layout
+
+\begin_layout Standard
+The new code design leverages Pyre, Sieve, and PETSc much more extensively
+ than the previous version.
+ Pyre is used to glue together the various modules used to construct a
+ simulation and specify the parameters.
+ Sieve is used for all finite-element storage and manipulation and handles
+ the creation of the PETSc matrices and vectors.
+ As a result, most of the PyLith source code pertains to implementing the
+ geodynamics, such as bulk rheology, boundary conditions, and slip on faults.
+
+\end_layout
+
+\begin_layout Standard
+PyLith also uses FIAT to tabulate the finite-element basis functions at
+ the numerical integration (quadrature) points.
+ Nemesis allows PyLith to run Python using the Message Passing Interface
+ (MPI) for parallel processing.
+ Additional, indirect dependencies (see Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:pylith-dependencies"
+
+\end_inset
+
+) include numpy (efficient operations on numerical arrays in Python), Proj.4
+ (geographic projections), and SWIG (calling C++ functions from Python).
+\end_layout
+
+\begin_layout Standard
+During development, tests were constructed for nearly every module function.
+ These unit tests are distributed with the source code.
+ These tests are run throughout the development cycle to expose bugs and
+ isolate their origin.
+ As additional changes are made to the code, the tests are rerun to help
+ prevent introduction of new bugs.
+ A number of simple, full-scale tests, such as axial compression and extension,
+ simple shear, and slip on through-going faults, have been used to test
+ the code.
+ Additionally, we have run the Southern California Earthquake Center crustal
+ deformation and several of the spontaneous rupture benchmarks for strike-slip
+ and reverse-slip to determine the relative local and global error (see
+ Chapter
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "cha:Benchmarks"
+
+\end_inset
+
+).
+\end_layout
+
+\begin_layout Subsection
+Pyre
+\end_layout
+
+\begin_layout Standard
+Pyre is an object-oriented environment capable of specifying and launching
+ numerical simulations on multiple platforms, including Beowulf-class parallel
+ computers and grid computing systems.
+ 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 solver applications.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+ filename figs/pyre_overview.png
+ width 4in
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:Pyre:Architecture"
+
+\end_inset
+
+Pyre Architecture.
+ The integration framework is a set of cooperating abstract services.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+Pyre is a framework, a combination of software and design philosophy that
+ promotes the reuse of code.
+ In their canonical software design book,
+\emph on
+Design Patterns
+\emph default
+, Erich Gamma
+\shape italic
+et al
+\shape default
+.
+ condense the concept of a framework concept down to, ``When you use a framework
+, you reuse the main body and write the code it calls.'' In the context of
+ frameworks and object-oriented programming, Pyre can be thought of as a
+ collection of classes and the way their instances interact.
+ Programming applications based on Pyre will look similar to those written
+ in any other object-oriented language.
+ The Pyre framework contains a subset of parts that make up the overall
+ framework.
+ Each of those parts is designed to solve a specific problem.
+\end_layout
+
+\begin_layout Standard
+The framework approach to computation offers many advantages.
+ It permits the exchange of codes and promotes the reuse of standardized
+ software while preserving efficiency.
+ Frameworks are also an efficient way to handle changes in computer architecture.
+ They present programmers and scientists with a unified and well-defined
+ task and allow for shared costs of the housekeeping aspects of software
+ development.
+ They provide greater institutional continuity to model development than
+ piecemeal approaches.
+\end_layout
+
+\begin_layout Standard
+The Pyre framework incorporates features aimed at enabling the scientific
+ non-expert to perform tasks easily without hindering the expert.
+ Target features for end users allow complete and intuitive simulation specifica
+tion, reasonable defaults, consistency checks of input, good diagnostics,
+ easy access to remote facilities, and status monitoring.
+ Target features for developers include easy access to user input, a shorter
+ development cycle, and good debugging support.
+\end_layout
+
+\begin_layout Subsection
+Sieve and PETSc
+\end_layout
+
+\begin_layout Standard
+PyLith 1.x makes use of a set of data structures and routines in PETSc called
+
+\family typewriter
+Sieve
+\family default
+, which is still under active development.
+
+\family typewriter
+Sieve
+\family default
+ provides data structures and routines for for representing and manipulating
+ computational meshes, and it greatly simplifies finite-element computations.
+
+\family typewriter
+ Sieve
+\family default
+ represents the topology of the domain.
+ 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
+ retrieved 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
+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.
+\end_layout
+
+\begin_layout Standard
+PETSc
+\begin_inset Flex URL
+status collapsed
+
+\begin_layout Plain Layout
+
+www-unix.mcs.anl.gov/petsc/petsc-as
+\end_layout
+
+\end_inset
+
+, the Portable, Extensible Toolkit for Scientific computation, provides
+ a suite of routines for parallel, numerical solution of partial differential
+ equations for linear and nonlinear systems with large, sparse systems of
+ equations.
+ 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
+ and interaction with other software packages.
+\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 can be built with user-supplied, highly optimized linear algebra
+ routines (e.g., ATLAS and commercial versions of BLAS/LAPACK), thereby improving
+ application performance.
+ Users can use PETSc parallel matrices, vectors, and other data structures
+ for most parallel operations, eliminating the need for explicit calls to
+ Message Passing Interface (MPI) routines.
+ Many settings and options can be controlled with PETSc-specific command-line
+ arguments, including selection of preconditions, solvers, and generation
+ of performance logs.
+\end_layout
+
+\end_body
+\end_document
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