[cig-commits] r14906 - in short/3D/PyLith/trunk/doc/presentations: . pylith1.3 pylith1.3/figs
brad at geodynamics.org
brad at geodynamics.org
Wed May 6 15:47:24 PDT 2009
Author: brad
Date: 2009-05-06 15:47:23 -0700 (Wed, 06 May 2009)
New Revision: 14906
Added:
short/3D/PyLith/trunk/doc/presentations/pylith1.3/
short/3D/PyLith/trunk/doc/presentations/pylith1.3/figs/
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short/3D/PyLith/trunk/doc/presentations/pylith1.3/figs/benchmark_error_tet4_0500m.png
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short/3D/PyLith/trunk/doc/presentations/pylith1.3/makefile_pdf
short/3D/PyLith/trunk/doc/presentations/pylith1.3/pylith_overview.tex
Log:
Started working on slides for tutorial.
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===================================================================
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Added: short/3D/PyLith/trunk/doc/presentations/pylith1.3/makefile_pdf
===================================================================
--- short/3D/PyLith/trunk/doc/presentations/pylith1.3/makefile_pdf (rev 0)
+++ short/3D/PyLith/trunk/doc/presentations/pylith1.3/makefile_pdf 2009-05-06 22:47:23 UTC (rev 14906)
@@ -0,0 +1,58 @@
+MASTERROOT = pylith_overview
+
+TEXMASTER = $(MASTERROOT).tex
+
+TEXSRCS =
+
+TEXFILES = $(TEXMASTER) $(TEXSRCS)
+
+AUXFILES = $(TEXMASTER:.tex=.aux)
+
+PDFFILE = $(TEXMASTER:.tex=.pdf)
+
+DVIFILE = $(TEXMASTER:.tex=.dvi)
+
+PSFILE = $(TEXMASTER:.tex=.ps)
+
+PDFTMPFILE = tmp.pdf
+
+default:
+
+pdf: $(PDFFILE)
+ps: $(PSFILE)
+dvi: $(DVIFILE)
+
+again:
+ pdflatex $(TEXMASTER) && mv $(PDFFILE) $(PDFTMPFILE)
+ ppower4 $(PDFTMPFILE) $(PDFFILE)
+
+$(PDFTMPFILE): $(TEXFILES) $(AUXFILES)
+ pdflatex $(TEXMASTER) && mv $(PDFFILE) $(PDFTMPFILE)
+
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+ ppower4 $(PDFTMPFILE) $(PDFFILE)
+
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+
+$(DVIFILE): $(TEXFILES) $(AUXFILES)
+ latex $(TEXMASTER)
+
+$(AUXFILES):
+ touch $(AUXFILES)
+
+clean:
+ rm -f $(AUXFILES) $(DVIFILE) $(PSFILE) $(PDFFILE) $(PDFTMPFILE)\
+ $(MASTERROOT).log $(MASTERROOT).out *~
+ rm -fr auto
+ rm `find figs -name "*.pdf"`
+
+pdffigs:
+ for i in `find figs -name "*.eps"`; do ~/bin/epstopdf $$i; done
+
+compressfigs:
+ gzip `find figs -name "*.eps"`
+
+uncompressfigs:
+ gunzip `find figs -name "*.eps.gz"`
+
Added: short/3D/PyLith/trunk/doc/presentations/pylith1.3/pylith_overview.tex
===================================================================
--- short/3D/PyLith/trunk/doc/presentations/pylith1.3/pylith_overview.tex (rev 0)
+++ short/3D/PyLith/trunk/doc/presentations/pylith1.3/pylith_overview.tex 2009-05-06 22:47:23 UTC (rev 14906)
@@ -0,0 +1,479 @@
+\documentclass[pdftex,cig,slideColor]{pp4slides}
+\usepackage{amsmath}
+\usepackage{mpmulti}
+\usepackage{multirow}
+\usepackage{amsfonts}
+\usepackage{pifont}
+\usepackage{rotating} % use turn environment
+
+\title{PyLith}
+\subtitle{}
+\author{Brad Aagaard, Charles Williams, Matthew Knepley, \\[10pt]
+ Sue Kientz and Leif Strand}
+\institution{\includegraphics[height=2cm]{../logos/cig}}
+\date{May 12, 2009}
+
+% --------------------------------------------------------- DOCUMENT
+\begin{document}
+
+% ------------------------------------------------------------ SLIDE
+\maketitle
+\vfill
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Outline}
+ \summary{}
+
+ \begin{itemize}
+ \item Introduction to PyLith
+ \begin{itemize}
+ \item Motivation \& development objective
+ \item What does PyLith do?
+ \end{itemize}
+ \item PyLith Design
+ \begin{itemize}
+ \item Architecture and programming languages
+ \item Development strategy
+ \end{itemize}
+ \item Features
+ \begin{itemize}
+ \item Current release
+ \item Planned releases
+ \end{itemize}
+ \item Benchmark results
+ \item Current development
+ \end{itemize}
+
+\bgadd{\vspace*{7.9in}%
+ \begin{center}%
+ \includegraphics[height=14mm]{../logos/cig}
+ \end{center}}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Motivation for Developing PyLith}
+ \summary{}
+
+ \begin{itemize}
+ \item Available modeling codes
+ \begin{itemize}
+ \item rarely solve the problem {\bf you} want to solve
+ \item are often poorly documented
+ \item may not work correctly
+ \end{itemize}
+ \item Current research demands larger, more complex simulations
+ \item Want to avoid multiple, incompatible versions of the same code
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{PyLith}
+ \summary{What is it good for?}
+
+ \begin{itemize}
+ \item Elasticity problems where geometry does not change significantly
+ \item Quasi-static crustal deformation
+ \begin{itemize}
+ \item Strain accumulation associated with interseismic deformation
+ \item Post-seismic relaxation of the crust
+ \item Volcanic deformation due to ??
+ \end{itemize}
+ \item Dynamic rupture and wave propagation
+ \begin{itemize}
+ \item Kinematic (prescribed) earthquake ruptures
+ \item Local/regional ground-motion modeling
+ \end{itemize}
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Features in PyLith 1.3}
+ \summary{}
+
+ \begin{itemize}
+ \item Spatial dimensions: 1-D, 2-D, or 3-D
+ \item Time integration schemes
+ \begin{itemize}
+ \item Implicit time stepping for quasi-static problems
+ \item Explicit time stepping for dynamic problems
+ \end{itemize}
+ \item Bulk constitutive models
+ \begin{itemize}
+ \item Elastic model (1-D, 2-D, and 3-D)
+ \item Linear and Generalized Maxwell viscoelastic models (3-D)
+ \end{itemize}
+ \item Boundary and interface conditions
+ \begin{itemize}
+ \item Dirichlet (prescribed displacement and velocity) boundary conditions
+ \item Neumann (traction) boundary conditions
+ \item Absorbing boundary conditions
+ \item Kinematic (prescribed slip) fault interfaces w/multiple ruptures
+ \item Gravitational body forces
+ \end{itemize}
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Features in PyLith 1.3 (cont.)}
+ \summary{}
+
+ \begin{itemize}
+ \item Automatic and user-controlled time stepping
+ \item Solution as perturbation from an initial stress state
+ \item Importing meshes
+ \begin{itemize}
+ \item LaGriT: GMV/Pset
+ \item CUBIT: Exodus II
+ \item ASCII: PyLith mesh ASCII format (intended for toy problems only)
+ \end{itemize}
+ \item Output: VTK files
+ \begin{itemize}
+ \item Solution over volume
+ \item Solution over surface boundary
+ \item State variables (e.g., stress and strain) for each material
+ \item Fault information (e.g., slip and tractions)
+ \end{itemize}
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{PyLith Design Objective}
+ \summary{Want a code developed for and by the community}
+
+ \begin{itemize}
+ \item Modular
+ \begin{itemize}
+ \item Users can swap modules to run the problem of interest
+ \end{itemize}
+ \item Scalable
+ \begin{itemize}
+ \item Code runs on one to a thousand processors efficiently
+ \end{itemize}
+ \item Extensible
+ \begin{itemize}
+ \item Expert users can add functionality to solve their problem
+ without polluting main code
+ \end{itemize}
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Crustal Deformation Modeling}
+ \summary{Overview of workflow for typical research problem}
+
+ \vfill
+ \begin{center}
+ \includegraphics[scale=0.9]{figs/workflow}
+ \end{center}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{PyLith Design: Focus on Geodynamics}
+ \summary{Leverage packages developed by computational scientists}
+
+ \vfill
+ \begin{center}
+ \includegraphics[scale=1.23]{figs/packages}
+ \end{center}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{PyLith Design: Code Architecture}
+ \summary{Flexible and modular with good performance}
+
+ \begin{itemize}
+ \item Top-level code written in Python
+ \begin{itemize}
+ \item Expressive, high-level,, object-oriented language
+ \item Dynamic typing allows adding additional modules at runtime
+ \item Convenient scripting
+ \end{itemize}
+ \item Low-level code written in C++
+ \begin{itemize}
+ \item Compiled (fast execution), object oriented language
+ \end{itemize}
+ \item Bindings to glue Python \& C++ together
+ \begin{itemize}
+ \item Pyrex/pyrexembed generate C code for calling C++ from Python
+ \end{itemize}
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{PyLith Design}
+ \summary{Tests, tests, and more tests ($>$1100 in all)}
+
+ \begin{itemize}
+ \item Create tests for nearly every function during development
+ \begin{itemize}
+ \item Remove most bugs during initial implementation
+ \item Isolate and expose bugs at origin
+ \end{itemize}
+ \item Create new tests to expose bugs reported
+ \begin{itemize}
+ \item Prevent bugs from reoccurring
+ \end{itemize}
+ \item Rerun tests whenever code is changed
+ \begin{itemize}
+ \item Allows optimization of performance with quality control
+ \item Code continually improves
+ \end{itemize}
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Example of Automated Building and Testing}
+ \summary{Test written to expose bug, buildbot shows tests fail}
+
+ \begin{center}
+ \includegraphics[scale=0.68]{figs/buildbotfail}
+ \end{center}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Automated Building and Testing}
+ \summary{Bug is fixed, buildbot shows tests pass}
+
+ \begin{center}
+ \includegraphics[scale=0.68]{figs/buildbotsuccess}
+ \end{center}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{PyLith 1.x: Planned Releases}
+ \summary{First add features present in Tecton and EqSim}
+
+ \begin{itemize}
+ \item PyLith 1.4: June 2009
+ \begin{itemize}
+ \item Power-law viscoelastic rheology and PETSc nonlinear solvers
+ \item Ability to specify initial stress, strain, and state variables
+ \item Automatic, transparent nondimensionalization
+ \item Use SWIG for Python/C++ interface
+ \end{itemize}
+ \item PyLith 1.5: anticipate release in Fall 2009
+ \begin{itemize}
+ \item Fault constitutive behavior with several widely used friction models
+ \end{itemize}
+ \item PyLith 1.6: anticipate release in Spring/Summer 2010
+ \begin{itemize}
+ \item Time dependent boundary conditions
+ \item Large deformations and finite strain
+ \end{itemize}
+ \item PyLith 1.7: Automation of 4-D Green's functions
+ \item PyLith 1.8: Coupling of quasi-static and dynamic simulations
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Implementation: Finite-Element Data Structures}
+ \summary{Use Sieve for storage and manipulating mesh information}
+
+ \begin{itemize}
+ \item PyLith makes only a few MPI calls
+ \item Data structures are independent of basis functions and
+ reference cells
+ \begin{itemize}
+ \item Same code for many cell shapes and types
+ \item Physics implementation limits code, not data structures
+ \end{itemize}
+ \item Sieve routines force adhering to finite-element formulation
+ \begin{itemize}
+ \item Do not have access to underlying storage
+ \item Manipulations must be done using Sieve interface
+ \item Only valid finite-element manipulation is allowed
+ \end{itemize}
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Implementation: Fault Interfaces}
+ \summary{Use cohesive cells to control fault behavior}
+
+ \vfill
+ \begin{center}
+ \includegraphics[scale=1.5]{figs/quad4cohesive}
+ \end{center}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Kinematic (prescribed) slip earthquake ruptures}
+ \summary{Use Lagrange multipliers to specify slip}
+
+ \begin{itemize}
+ \item System without cohesive cells
+ \begin{equation}
+ \underbar{A} \vec{u} = \vec{b} \nonumber
+ \end{equation}
+ \item System with cohesive cells
+ \begin{equation}
+ \left( \begin{array}{cc}
+ \underbar{A} & \underbar{C}^T\\
+ \underbar{C} & 0
+ \end{array} \right)
+ \left( \begin{array}{c}
+ \vec{u}\\
+ \vec{L}
+ \end{array}\right)
+ =
+ \left( \begin{array}{c}
+ \vec{b}\\
+ \vec{D}
+ \end{array} \right)
+ \nonumber
+ \end{equation}
+ \item System with cohesive cells \& conditioning
+ \begin{equation}
+ \left( \begin{array}{cc}
+ \underbar{A} & a \underbar{C}^T\\
+ \underbar{C} & 0
+ \end{array} \right)
+ \left( \begin{array}{c}
+ \vec{u}\\
+ \frac{1}{a} \vec{L}
+ \end{array}\right)
+ =
+ \left( \begin{array}{c}
+ \vec{b}\\
+ \vec{D}
+ \end{array} \right)
+ \nonumber
+ \end{equation}
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Implementing Fault Slip with Lagrange multipliers}
+
+ \begin{itemize}
+ \item Advantages
+ \begin{itemize}
+ \item Fault implementation is local to cohesive cell
+ \item Solution includes forces generating slip (Lagrange multipliers)
+ \item Retains block structure of matrix (same number of DOF per vertex)
+ \item Offsets in mesh mimic slip on natural faults
+ \end{itemize}
+ \item Disadvantages
+ \begin{itemize}
+ \item Conditioned matrix is non-symmetric (eliminated through
+ nondimensionalization)
+ \item Mixes displacements and forces in solution
+ \end{itemize}
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Benchmarking PyLith}
+ \summary{Elastic solution for strike-slip benchmark}
+
+ \vfill
+ \begin{center}
+ \includegraphics[scale=0.6]{figs/benchmark_soln}
+ \end{center}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Tet4 500m Mesh: Local Error}
+ \summary{Error largest around edges of fault}
+
+ \vfill
+ \begin{center}
+ \includegraphics[scale=0.6]{figs/benchmark_error_tet4_0500m}
+ \end{center}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Hex8 500m Mesh: Local Error}
+ \summary{Error concentrated around change in slip gradient}
+
+ \vfill
+ \begin{center}
+ \includegraphics[scale=0.6]{figs/benchmark_error_hex8_0500m}
+ \end{center}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Strike-Slip Benchmark: Performance Summary}
+ \summary{Hex8 cells outperform tet4 cells}
+
+ \vfill
+ \begin{center}
+ \includegraphics[scale=0.5]{figs/benchmark_summary}
+ \end{center}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Running PyLith}
+ \summary{Ingredients}
+
+ \begin{itemize}
+ \item Simulation parameters
+ \item Finite-element mesh
+ \begin{itemize}
+ \item Mesh exported from LaGriT
+ \item Mesh exported from CUBIT
+ \item Mesh constructed by hand (PyLith mesh ASCII format)
+ \end{itemize}
+ \item Spatial databases for boundary and fault conditions
+ \begin{itemize}
+ \item Simple ASCII files specify spatial variation of parameters
+ \item Independent of discretization scheme and size
+ \end{itemize}
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Useful Tips/Tricks}
+ \summary{}
+
+ \begin{itemize}
+ \item Command line arguments
+ \begin{itemize}
+ \item {\tt --help}
+ \item {\tt --help-components}
+ \item {\tt --help-properties}
+ \item {\tt --petsc.start\_in\_debugger} (run in xterm)
+ \item {\tt --nodes=N} (to run on N processors on local machine)
+ \end{itemize}
+ \item PyLith User Manual
+ \item CIG Short-Term Tectonics mailing list
+ \begin{itemize}
+ \item {\tt cig-short at geodynamics.org}
+ \end{itemize}
+ \item CIG bug tracking system
+ \begin{itemize}
+ \item {\tt http://www.geodynamics.org/roundup}
+ \end{itemize}
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{PyLith is a Community Code}
+ \summary{Success of code depends on community participation}
+
+ \begin{itemize}
+ \item End-users (anyone who uses the code)
+ \begin{itemize}
+ \item Help define and prioritize features that should be added
+ \item Report bugs/problems and suggest improvements
+ \end{itemize}
+ \item Expert users
+ \begin{itemize}
+ \item Help test alpha versions of releases
+ \item Run benchmarks and report results
+ \item Contribute meshing and visualization examples to documentation
+ \item Add features following template (e.g., constitutive models)
+ \end{itemize}
+ \item Developer
+ \begin{itemize}
+ \item Define development strategy
+ \item Implement new features and tests
+ \item Write documentation
+ \end{itemize}
+ \end{itemize}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Example: Slip on a Vertical Strike-Slip Fault}
+ \summary{examples/3d/hex8}
+
+ \vfill
+ \begin{center}
+ \includegraphics[scale=0.7]{figs/examplehex8}
+ \end{center}
+
+% ------------------------------------------------------------ SLIDE
+\foilhead{Workflow for Example}
+ \summary{}
+
+ \begin{enumerate}
+ \item Generate finite-element mesh using CUBIT (hex8 cells)
+ \item Create {\tt .cfg} file with simulation parameters
+ \item Create spatial database files with parameters for boundary
+ conditions and faults
+ \item Run PyLith
+ \item Visualize results with ParaView
+ \end{enumerate}
+
+
+% --------------------------------------------------------- DOCUMENT
+\end{document}
+
+
+% End of file
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