# [cig-commits] r13263 - in doc/snac: . figures

echoi at geodynamics.org echoi at geodynamics.org
Thu Nov 6 08:09:19 PST 2008

Author: echoi
Date: 2008-11-06 08:09:19 -0800 (Thu, 06 Nov 2008)
New Revision: 13263

doc/snac/figures/Remeshing.png
Modified:
doc/snac/snac.lyx
Log:
1. Replaced the figure in the remeshing section.
2. Removed Pyre-related contents.
3. References updated.

===================================================================
(Binary files differ)

Property changes on: doc/snac/figures/Remeshing.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream

Modified: doc/snac/snac.lyx
===================================================================
--- doc/snac/snac.lyx	2008-11-05 23:47:01 UTC (rev 13262)
+++ doc/snac/snac.lyx	2008-11-06 16:09:19 UTC (rev 13263)
@@ -26,7 +26,7 @@
\spacing single
\papersize default
\use_geometry true
-\use_amsmath 0
+\use_amsmath 1
\use_esint 0
\cite_engine basic
\use_bibtopic false
@@ -454,7 +454,6 @@
\begin_layout Standard
\noindent
\align center
-
\begin_inset Graphics
filename figures/snac-mesh.pdf
scale 60
@@ -591,18 +590,13 @@
\end_layout

\begin_layout Standard
-\begin_inset Formula $$-\begin{array}{cc} -f_{,i} & =\frac{1}{V}\sum_{l=1}^{4}\bar{f}^{l}n_{i}^{l}A^{l}=\frac{1}{V}\sum_{l=1}^{4}\frac{1}{3}\sum_{m=1,\neq l}^{4}f^{m}n_{i}^{l}A^{l}\\ - & =\frac{1}{3V}\sum_{m=1}^{4}f^{m}\sum_{l=1,\neq m}^{4}n_{i}^{l}A^{l}\\ - & =-\frac{1}{3V}\sum_{m=1}^{4}f^{m}n_{i}^{m}A^{m},\end{array}\label{eq:formula_fi}$$
+\begin_inset Formula \begin{align}
+f_{,i} & =\frac{1}{V}\sum_{l=1}^{4}\bar{f}^{l}n_{i}^{l}A^{l}=\frac{1}{V}\sum_{l=1}^{4}\frac{1}{3}\sum_{m=1,\neq l}^{4}f^{m}n_{i}^{l}A^{l}\nonumber \\
+ & =\frac{1}{3V}\sum_{m=1}^{4}f^{m}\sum_{l=1,\neq m}^{4}n_{i}^{l}A^{l}\nonumber \\
+ & =-\frac{1}{3V}\sum_{m=1}^{4}f^{m}n_{i}^{m}A^{m},\label{eq:formula_fi}\end{align}

\end_inset

-
-\end_layout
-
-\begin_layout Standard
where
\begin_inset Formula $l$
\end_inset
@@ -987,22 +981,25 @@
\end_layout

\begin_layout Standard
-\begin_inset Formula $$-\begin{array}{cc} -\frac{1}{3}T_{i} & =-ku_{i}\Rightarrow\\ -\frac{1}{3}\left(\lambda+2\mu\right)\left(\dot{\epsilon_{ii}}dt\right)n_{i}A & =-k\left(v_{i}dt\right)\,\,(\mathrm{no\, sum}),\end{array}\label{eq:eqfork}$$
+\begin_inset Formula \begin{align}
+ & \frac{1}{3}T_{i}=-ku_{i}\nonumber \\
+\Rightarrow & \frac{1}{3}\left(\lambda+2\mu\right)\left(\dot{\epsilon_{ii}}dt\right)n_{i}A=-k\left(v_{i}dt\right)\,\,(\mathrm{no\, sum}),\label{eq:eqfork}\end{align}

\end_inset

where only the volumetric contribution from internal forces is taken into
account.
- By substituting the approximation for the partial derivative (
+ By substituting the approximation (
\begin_inset LatexCommand ref
reference "eq:formula_fi"

\end_inset

-) into the above equation and dividing both sides by
+) for the partial derivative,
+\begin_inset Formula $\dot{\epsilon_{ii}}$
+\end_inset
+
+, into the above equation and dividing both sides by
\begin_inset Formula $v_{i}dt$
\end_inset

@@ -1265,7 +1262,11 @@
\end_inset

is cohesive strength of the material.
- In the case of Drucker-Prager material
+ In the case of Drucker-Prager material,
+\begin_inset Formula $\tau$
+\end_inset
+
+is defined as the second invariant of the deviatoric tensor
\end_layout

\begin_layout Standard
@@ -1274,36 +1275,25 @@

\end_inset

-the second invariant of the deviatoric stress tensor (
+where
\begin_inset Formula $S$
\end_inset

-), while
-\begin_inset Formula $\sigma_{p}=\frac{1}{3}\sigma_{kk}$
-\end_inset
+ is the deviatoric part of stress tensor.
+ Similarly in the case of Mohr-Coulomb material,
+\end_layout

-, the first invariant of stress tensor (
-\begin_inset Formula $\sigma$
-\end_inset
+\begin_layout Standard
+\begin_inset Formula $$+\tau=\frac{1}{2}\left(\sigma_{3}-\sigma_{1}\right)\text{ and }\sigma_{p}=\frac{1}{2}\left(\sigma_{3}+\sigma_{1}\right),\label{eq:Mohr-Coulomb material}$$

-).
- Similarly in the case of Mohr-Coulomb material,
-\begin_inset Formula $\tau=\frac{1}{2}\left(\sigma_{3}-\sigma_{1}\right)$
\end_inset

- and
-\begin_inset Formula $\sigma_{p}=\frac{1}{2}\left(\sigma_{3}+\sigma_{1}\right)$
-\end_inset
-
-, where
+where
\begin_inset Formula $\sigma_{1}\leq\sigma_{2}\leq\sigma_{3}$
\end_inset

- are the principal stresses of stress tensor (
-\begin_inset Formula $\sigma$
-\end_inset
-
-).
+ are the principal stresses of stress tensor.

\end_layout

@@ -1387,6 +1377,8 @@
\end_inset

which provides stress correction.
+ More details of calculations for the Mohr-Coulomb model are available in
+ the benchmark section.
\end_layout

\begin_layout Subsection
@@ -1419,7 +1411,32 @@
\end_inset

.
+ Figure
+\begin_inset LatexCommand ref
+reference "fig:Remeshing.-Lagrangian-mesh"
+
+\end_inset
+
+ demonstrates how remeshing actually works.
+ Note that Fig.

+\begin_inset LatexCommand ref
+reference "fig:Remeshing.-Lagrangian-mesh"
+
+\end_inset
+
+(b) shows that remeshing can not only generate a more regular mesh but also
+ change the boundary.
+ Although useful in some cases, this
+\begin_inset Quotes sld
+\end_inset
+
+boundary restoring
+\begin_inset Quotes srd
+\end_inset
+
+ technique should be used with caution.
+ SNAC keeps the deformed boundary by default.
\end_layout

\begin_layout Standard
@@ -1434,9 +1451,8 @@
\noindent
\align center
\begin_inset Graphics
-	filename figures/remeshing1.png
+	filename figures/Remeshing.png
lyxscale 101
-	scale 101

\end_inset

@@ -1444,19 +1460,6 @@
\end_layout

\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
-	filename figures/remeshing2.png
-	lyxscale 39
-	scale 39
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
\begin_inset Caption

\begin_layout Standard
@@ -1465,11 +1468,9 @@

\end_inset

-Remeshing.
- Lagrangian mesh deforms severely as deformation accumulates.
- This degrades accuracy of the solution, which eventually leads to crash.
- The nodal values are interpolated on the new regular mesh and the element
- values are transferred to the nearest neighbor element in the new mesh.
+(a) Meshes and velocity fields before (blue) and after (red) remeshing.
+ (b) Plastic strain, an element-associated variable, is shown on the meshed
+ before and after remeshing.

\end_layout

@@ -1478,10 +1479,6 @@

\end_layout

-\begin_layout Standard
-
-\end_layout
-
\end_inset

@@ -1629,9 +1626,8 @@
my code, how do I share it with my collaborators with the optional inclusion
of their additions?'' This capability is inherent to StGermain and provides
an important feature lacking in most scientific codes.
- As of the end of 2004 [TODO update this year?], StGermain is still under
- active development and its interfaces are unlikely to be frozen in the
- near future.
+ As of the end of 2008, StGermain is still under active development and
+ its interfaces are unlikely to be frozen in the near future.

\end_layout

@@ -1720,219 +1716,11 @@

\end_layout

-\begin_layout Standard
-StGermain facilitates the coupling of SNAC with regional CitcomS through
- Pyre.
- To couple two different scientific codes, Pyre presupposes the proper structuri
-ng of the codes.
- Specifically, a code should be composed of units abstracted from common
- features of numerical modeling programs, such as initialization (allocating
- memory, or assigning values of variables), time marching, application of
- the boundary conditions, and output [Tan, et al., 2004].
- Since the integration of SNAC into StGermain inherently includes structuring
- SNAC according to this general architecture, SNAC can be easily coupled
- with another structured software, such as regional CitomS, within Pyre.
-
-\end_layout
-
-\begin_layout Section
-Pyre
-\end_layout
-
-\begin_layout Standard
-Pyre is a full-featured, object oriented environment that is capable of
- handling all aspects of the specification and launching of numerical investigat
-ions, and operates on massively parallel supercomputers including both shared
- memory computers and Beowulf clusters.
- Pyre is written in Python, an open source, well maintained and widely used
- interpretive environment.
- Python is a modern, object-oriented programming language that is well documente
-d and easily extensible.
- The Python interpreter has been ported to a wide variety of machines, including
- massively parallel systems, and comes with interfaces to a wide array of
- system calls and libraries.
- In fact, it is the ease with which interfaces to new facilities can be
- constructed that makes writing a simulation framework in Python such an
- attractive choice.
-
-\end_layout
-
-\begin_layout Standard
-In the Pyre framework, computational facilities are represented in terms
- of abstract base classes that encapsulate their interaction with the rest
- of the framework and define the interface that actual instances of these
- facilities must provide in order to become functional framework components.
- Pyre simulations are themselves Python programs that execute on each computatio
-nal node and have complete access to the capabilities of the interpreter.
-
-\end_layout
-
-\begin_layout Standard
-In order to perform a simulation, the user constructs the various components
- of the physical model by specifying their geometry.
- Boundary and initial conditions can be specified by providing a high-level
- geometrical description of the affected regions of space.
- This insulates the user from the particular representation of that region
- of space by any particular solver and allows transparent access to the
- underlying data structures.
- Constitutive models and material properties are selected and attached to
- regions of space in a similar manner.
- Subsequently, the user selects the solvers that are responsible for the
- simulation of the behavior of each component.
- All these activities take place through the programmatic construction of
- the simulation model (an instance of the class Application), which acts
- as a convenient repository of the relevant information.
- The model is handed to the simulation Controller, which is responsible
- for partitioning the parallel machine into groups of processors, each with
- its own instance of the relevant Solver descendant, and launches the simulation.
-
-\end_layout
-
-\begin_layout Standard
-The user has full control over the structure and implementation of the main
- simulation loop.
- A complete specification is provided that governs the interaction between
- the simulation driver and the various engines and guarantees consistency,
- but the user is free to add arbitrary operations at any part of the time
- step.
- Activities such as checkpoints and on-the-fly visualization are supported
- with minimal effort on the part of the user.
-
-\end_layout
-
-\begin_layout Standard
-Currently (as of October 2001 [TODO--update this year? and information following
-?]), Pyre consists of approximately 35,000 lines of Python and 15,000 lines
- of C++ in the form of bindings and infrastructure.
- Examples of third party computational facilities that are already integrated
- into the framework include MPI from ANL, HDF5, the scalable IO subsystem
- from NCSA, ACIS, a commercial, industrial strength solid modeler, the visualiza
-tion capabilities of IRIS Explorer28 from NAG, Metis, the graph partitioning
- package, and GrACE, the adaptive mesh refinement package.
-
-\end_layout
-
-\begin_layout Standard
-Computational scientists face the challenge of assimilating large quantities
- of data that are starting to become available in a variety of formats.
- Easy access to data stores from within our software package is very important
- for the validation effort.
- Pyre provides good support for the construction of data format converters,
- both in terms of parsing infrastructure and flexible output generation.
-
-\end_layout
-
-\begin_layout Standard
-Pyre leverages the extensibility of the Python interpreter to allow for
- the seamless integration of rather diverse computational facilities.
- The framework provides enough flexibility to allow the dynamic discovery
- of available facilities as part of simulation staging.
- The former implies that there is a well defined and well documented method
- by which a new solver or a new material model can be made available to
- the framework, while the latter allows the user to specify solvers and
- algorithms in the simulation script, without the need for recompilation
- The combination promotes experimentation with new algorithms by lowering
- the overall overhead associated with trying out new approaches.
-
-\end_layout
-
-\begin_layout Section
-Coupling through GeoFramework
-\end_layout
-
-\begin_layout Standard
-GeoFramework is a framework that relies on Pyre for coupling codes [TODO
- -- I removed URL as it is not working].
- Elements (distinct applications) can collaborate within it, coupling two
- spatially overlapping geophysical applications in such a way that interaction
- occurs through sharing physical quantities (such as velocity, temperature,
- or traction) at interfaces.
- Coupling can solve problems of multi-scale and multi-material nature.
- For example, modeling localization in crust and the large-scale mantle
- flow at the same time.
-
-\end_layout
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
-	filename figures/citcoms-coupling.png
-	lyxscale 65
-	scale 65
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:CitcomS-Couping.-Within"
-
-\end_inset
-
-CitcomS Couping.
- Within the containing mesh (blue) within the CitcomS domain (dimension:
- 45°
-\begin_inset Formula $\times$
-\end_inset
-
- 45°
-\begin_inset Formula $\times$
-\end_inset
-
- 1200 km) a spherical thermal anomaly drives mantle flow.
- The embedded mesh of the SNAC domain (yellow) occupies an area within the
- CitcomS domain (dimension: 20°
-\begin_inset Formula $\times$
-\end_inset
-
- 20°
-\begin_inset Formula $\times$
-\end_inset
-
- 40 km).
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Chapter
Installation
\end_layout

\begin_layout Standard
-First you will install StGermain and SNAC, which will be followed by the
- installation of Pyre.
-
-\end_layout
-
-\begin_layout Section
-StGermain and SNAC
-\end_layout
-
-\begin_layout Standard
StGermain and SNAC are both available at the
\begin_inset LatexCommand htmlurl
name "Geodynamics Software Packages web page"
@@ -2021,105 +1809,6 @@
\end_layout

\begin_layout Subsection
-Obtaining the StGermain Source (in the future)
-\end_layout
-
-\begin_layout Enumerate
- Computing's Computational Software Development Portal.
-
-\end_layout
-
-\begin_layout Enumerate
-Register as a VPAC collaborator at: http://csd.vpac.org/portal/admin/registration.p
-hp.
- [TODO -- need URL (this doesn't work) or procedure needs updating]
-\end_layout
-
-\begin_layout Enumerate
-Login to the CSD portal at
-\begin_inset LatexCommand htmlurl
-name "VPAC Computational Software Development"
-target "csd.vpac.org"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Enumerate
-Click on the download'' link on the left of the page, and download the
- latest available version.
-
-\end_layout
-
-\begin_layout Enumerate
-Unzip and untar the file you just downloaded into a suitable directory.
-\end_layout
-
-\begin_layout Subsection
-Obtaining the StGermain Source (current Subversion checkout)
-\end_layout
-
-\begin_layout Standard
-To download the StGermain and SNAC packages via a content version system
- called Subversion, first you must install the Subversion client software,
- which, in turn, relies on the installation of a package called neon.
- Neon is an HTTP and WebDAV client library, with a C interface.
-\begin_inset LatexCommand htmlurl
-name "neon HTTP and WebDAV client library"
-target "www.webdav.org/neon"
-
-\end_inset
-
-.
-
-\end_layout
-
-\begin_layout Standard
-After installing neon, you will be ready to install the Subversion client,
- which is available through http://subversion.tigris.org.
-
-\end_layout
-
-\begin_layout Standard
-Once you have the subversion client installed, you will need to register
- at http://csd.vpac.org/twiki/bin/view/TWiki/TWikiRegistration [TODO -- URL
- is wrong, gives strange error] for permission to download software from
- the repository at http://rd01.vpac.org/svn/StGermain [TODO -- URL is not
- found].
- Both Snark and SNAC repositories are only available bundled with the StGermain
- repository to create an all-encompassing repository.
-
-\end_layout
-
-\begin_layout Standard
-To obtain the combined StGermain, Snark and SNAC repository:
-\end_layout
-
-\begin_layout LyX-Code
-$svn --username=UserName co http://rd01.vpac.org/svn/StGermain/trunk StGermain - -\end_layout - -\begin_layout Enumerate -replace UserName'' with your VPAC twiki user name, -\end_layout - -\begin_layout Enumerate -trunk'' says to obtain only the main trunk, not all branches and tags - (this is the default in CVS), -\end_layout - -\begin_layout Enumerate -the last StGermain'' says to check the repository out into a local directory - StGermain'' (else it would have been named trunk''). - -\end_layout - -\begin_layout Subsection Configuring using the VMake build system \end_layout @@ -2186,689 +1875,6 @@$ ./configure.sh --options=cautious,memory_stats
\end_layout

-\begin_layout Section
-Pyre
-\end_layout
-
-\begin_layout Subsection
-Basics
-\end_layout
-
-\begin_layout Standard
-Pyre is included within a larger package called Pythia.
- Within the Pyre directory you will find a set of subdirectories, each one
- of which contains a dedicated piece of infrastructure designed to solve
- a specific problem.
-
-\end_layout
-
-\begin_layout Standard
-Installation requires three steps.
- First you will need to checkout the most recent version of Pythia, config,
- and templates from the CVS server.
- Then you will need to configure your environment.
- Finally you will run a custom installer script, mm, based on GNU Make.
-
-\end_layout
-
-\begin_layout Standard
-The build procedure compiles and links the package and is designed to make
- codes easily portable to a wide variety of compiler and platform targets.
- Furthermore, it allows for customization of the compilation process at
- several different levels.
- The core of the build procedure is embodied in the shell script mm.
- Code packages are built and installed by invoking this script, which automatica
-lly determines the host target, locates the appropriate compiler commands
- and options for this target platform, and issues the necessary commands
- to build the code packages.
- The mm script relies on a layered set of definition files that customize
- behavior and recursive processing of makefiles that describe a package
- and any subpackages it may contain.
-
-\end_layout
-
-\begin_layout Subsection
-Hardware and Software Requirements
-\end_layout
-
-\begin_layout Standard
-\end_layout
-
-\begin_layout Standard
-15 MB for compiled package
-\end_layout
-
-\begin_layout Standard
-Pythia package (which includes Pyre)
-\end_layout
-
-\begin_layout Standard
-config package (includes make files)
-\end_layout
-
-\begin_layout Standard
-Python 2.3+
-\end_layout
-
-\begin_layout Subsection
-Supported Platforms
-\end_layout
-
-\begin_layout Standard
-As of May 2004 [TODO update this month/year] the following platforms are
- supported [TODO -- update this list]:
-\end_layout
-
-\begin_layout Standard
-11AIX-3.0
-\end_layout
-
-\begin_layout Standard
-AIX-4.3
-\end_layout
-
-\begin_layout Standard
-AIX-5.1
-\end_layout
-
-\begin_layout Standard
-CompaqTru64Unix-5.0
-\end_layout
-
-\begin_layout Standard
-Darwin-6.x
-\end_layout
-
-\begin_layout Standard
-Darwin-7.x
-\end_layout
-
-\begin_layout Standard
-DigitalUnix-4.0
-\end_layout
-
-\begin_layout Standard
-HPUX-10.0
-\end_layout
-
-\begin_layout Standard
-HPUX-11.1
-\end_layout
-
-\begin_layout Standard
-Irix-6.2
-\end_layout
-
-\begin_layout Standard
-Irix-6.4
-\end_layout
-
-\begin_layout Standard
-Irix-6.5
-\end_layout
-
-\begin_layout Standard
-Linux-2.0
-\end_layout
-
-\begin_layout Standard
-SunOS-5.5
-\end_layout
-
-\begin_layout Standard
-SunOS-5.6
-\end_layout
-
-\begin_layout Standard
-SunOS-5.7
-\end_layout
-
-\begin_layout Standard
-SunOS-5.8
-\end_layout
-
-\begin_layout Standard
-TFLOPS
-\end_layout
-
-\begin_layout Standard
-Win32-4.0
-\end_layout
-
-\begin_layout Standard
-Win32-5.1
-\end_layout
-
-\begin_layout Subsection
-\end_layout
-
-\begin_layout Standard
-Pyre is available via a Concurrent Versions System (CVS) server located
- at the California Institute of Technology.
- This allows users to check out the most recent version of the software.
- Pyre uses an anonymous CVS server so that anyone can check out the code
-
-\end_layout
-
-\begin_layout Standard
-Prior to checking out the code, you should have both CVS and SSH running
- on the machine where you will be working with Pyre.
- To check, type
-\family typewriter
-cvs
-\family default
- and
-\family typewriter
-ssh
-\family default
-; both should return a usage message and options.
-
-\end_layout
-
-\begin_layout LyX-Code
-$cvs Usage: cvs [cvs-options] command [command-options-and-arguments] more - ... - -\end_layout - -\begin_layout LyX-Code -$ ssh Usage: ssh [options] host [command] more ...
-
-\end_layout
-
-\begin_layout Standard
-Since you will be using SSH to retrieve files, you may need to set the
-\family typewriter
-CVS_RSH
-\family default
- environment variable.
-
-\end_layout
-
-\begin_layout LyX-Code
-$setenv CVS_RSH ssh -\end_layout - -\begin_layout Standard -If you have not used a remote repository before, you will need to set the - variable -\family typewriter -CVS_RSH -\family default - to equal "ssh". - If you use the bash shell, this means adding the following to your -\family typewriter -$HOME/.bashrc
-\family default
- file:
-\end_layout
-
-\begin_layout LyX-Code
-$export CVS_RSH="ssh" -\end_layout - -\begin_layout Standard -Or, if you use a C shell derivative, you should add the following to your - -\family typewriter -.cshrc -\family default -: -\end_layout - -\begin_layout LyX-Code -$ setenv SVS_RSH "ssh"
-\end_layout
-
-\begin_layout Standard
-To check out the Pyre source code, login to the CVS server, then retrieve
-\family typewriter
-pyre
-\family default
-.
- and templates.
-\family typewriter
-config
-\family default
- separately.
-
-\family typewriter
-config
-\family default
- contains the make system required for installation.
-
-\family typewriter
-config
-\family default
- is a system of makefiles that simplifies program construction and deployment.
- config includes support for dozens of platforms and compilers, including
- those available at the ASCI supercomputers, permits easy access to external
- libraries and tools in a portable manner, and allows libraries and executables
- built from the same sources with different options or different compilers
- to co-exist.
- Other features include automatic dependency generation and sensible support
- for mixed language programming.
-
-\end_layout
-
-\begin_layout Standard
-The dialog between you and the server will look something like this:
-\end_layout
-
-\begin_layout LyX-Code
-$cvs -d :pserver:pyre at cvs.cacr.caltech.edu:/pyre login -\end_layout - -\begin_layout LyX-Code -(Logging in to pyre at cvs.cacr.caltech.edu) -\end_layout - -\begin_layout LyX-Code -CVS password: (password is pyre) -\end_layout - -\begin_layout LyX-Code -$ cvs -d :pserver:pyre at cvs.cacr.caltech.edu:/pyre co pythia-0.6
-\end_layout
-
-\begin_layout LyX-Code
-$cvs -d :pserver:pyre at cvs.cacr.caltech.edu:/pyre co templates -\end_layout - -\begin_layout LyX-Code -$ cvs -d :pserver:config at cvs.cacr.caltech.edu:/config login
-\end_layout
-
-\begin_layout LyX-Code
-(Logging in to config at cvs.cacr.caltech.edu)
-\end_layout
-
-\begin_layout LyX-Code
-\end_layout
-
-\begin_layout LyX-Code
-$cvs -d :pserver:config at cvs.cacr.caltech.edu:/config co config -\end_layout - -\begin_layout Subsection -Create New Directories -\end_layout - -\begin_layout Standard -You will need to create two directories for the installation, one for the - build and one for finished product. - In this example, the directories build and export were created in the pathway - /Users/username/dv/. -$ mkdir build $mkdir export -\end_layout - -\begin_layout Subsubsection -Set the Environment -\end_layout - -\begin_layout Standard -Product libraries and binaries are built in subdirectories lib and bin beneath - -\family typewriter -BLD_ROOT -\family default -. - Once a code package has been built, the make target export can be used - to install it in a directory below -\family typewriter -EXPORT_ROOT -\family default -. - The source code for any package to be built using the build procedure is - typically stored in a directory below the common root -\family typewriter -BLD_ROOT -\family default -. - The files for the build system itself are also assumed to be located beneath - this common root directory in -\family typewriter -$BLD_ROOT/config
-\family default
-, although this can be overridden by setting the environment variable
-\family typewriter
-BLD_CONFIG
-\family default
- to a different path.
-
-\end_layout
-
-\begin_layout Standard
-Key environment variables:
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-BLD_ROOT
-\family default
- is the location of installation and build
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-EXPORT_ROOT
-\family default
- is the location of the finished products
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-TARGET
-\family default
- can be followed by a comma-delineated list of desired compilation option
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-BLD_CONFIG
-\family default
- points to a non-default location for the build files
-\end_layout
-
-\begin_layout Standard
-You must set the
-\family typewriter
-BLD_ROOT
-\family default
- and
-\family typewriter
-EXPORT_ROOT
-\family default
-.
- First you should name where you would like the code to be built.
-
-\end_layout
-
-\begin_layout LyX-Code
-$export BLD_ROOT=/Users/username/dv/build/ -\end_layout - -\begin_layout Standard -Then you should name the directory where the installation will wind up. - -\end_layout - -\begin_layout LyX-Code -$ export EXPORT_ROOT=/Users/username/pythia-0.6/
-\end_layout
-
-\begin_layout Standard
-Note:
-\family typewriter
-BLD_ROOT
-\family default
- and
-\family typewriter
-EXPORT_ROOT
-\family default
- should not point to the same location!
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-TARGET
-\family default
- and
-\family typewriter
-BLD_CONFIG
-\family default
- are optional.
- If you would like to indicate any special compile options, this is done
- with
-\family typewriter
-TARGET
-\family default
-.
- These targets are not the same as the make targets, which are defined within
- the makefiles of a code package in the standard way.
- The current valid target options are:
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-debug
-\family default
- allows you to compile with debugging on
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-opt
-\family default
- will compile with optimization on
-\end_layout
-
-\begin_layout Description
-
-\family typewriter
-insure
-\family default
- will invoke the Insure++ code checking tool to detect errors
-\end_layout
-
-\begin_layout Description
-purify will link with Purify memory analysis libraries
-\end_layout
-
-\begin_layout Description
-prof generates extra code to write profiling information
-\end_layout
-
-\begin_layout Description
-mpi includes MPI header and library files
-\end_layout
-
-\begin_layout Standard
-For example:
-\end_layout
-
-\begin_layout LyX-Code
-$export TARGET=debug,mpi -\end_layout - -\begin_layout Standard -If you would prefer to not point to the files located in the build directory, - you can point to another location. - -\end_layout - -\begin_layout LyX-Code -$ export BLD_CONFIG=/Users/username/dv/config/make
-\end_layout
-
-\begin_layout Subsection
-Build with
-\family typewriter
-mm
-\family default
-
-\end_layout
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-\family typewriter
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-\family default
-, for example:
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-
-\begin_layout LyX-Code
-$mm [-f <makefile>] [target] -\end_layout - -\begin_layout Standard -The default target is -\family typewriter -all -\family default -. - Other targets can be defined in -\family typewriter -std-targets.def -\family default - or the local makefile. - -\end_layout - -\begin_layout Standard -The -\family typewriter --f -\family default - option allows a code package to use makefiles with a different name other - than the default name, which is -\family typewriter -Make.mm -\family default -. - If any target is specified, then mm will build that target rather than - the default target given by the makefiles. - -\end_layout - -\begin_layout Standard -Change to the -\family typewriter -/Users/username/dv/pythia-0.6/packages -\family default - and invoke the -\family typewriter -mm -\family default - script. - -\end_layout - -\begin_layout LyX-Code -$ cd /Users/username/dv/pythia-0.6/packages
-\end_layout
-
-\begin_layout LyX-Code
-$mm -\end_layout - -\begin_layout Standard -The script will first check for the existence of the directories indicated - by -\family typewriter -BLD_ROOT -\family default - and -\family typewriter -EXPORT_ROOT -\family default -. - Next, it uses the uname utility to determine the operating system and machine - type. - This information is later used to select a platform-specific definitions - file, which indicates what compilers and standard options to use. - -\end_layout - -\begin_layout Standard -Once this is done, -\family typewriter -mm -\family default - parses the contents of -\family typewriter -TARGET -\family default - and looks for corresponding target-specific definitions files. - These files contain the special flags and definitions that are needed for - these compilation options. - In addition, a target tag is constructed by combining the name of the target - platform with any user-specified targets, and this tag is later used to - create target-specific subdirectories where the code package will be built. - This allows the build system to simultaneously maintain builds of a code - package for many different potential targets. - The final setup step is to get the user's name and check for any user-specific - file of definitions that may override the standard settings and behaviors. - -\end_layout - -\begin_layout Paragraph* -Example Installation on Mac OS 10.3 (Panther) -\end_layout - -\begin_layout LyX-Code -$ cd dv
-\end_layout
-
-\begin_layout LyX-Code
-$mkdir build -\end_layout - -\begin_layout LyX-Code -$ mkdir export
-\end_layout
-
-\begin_layout LyX-Code
-$export BLD_ROOT=/Users/username/dv/build/ -\end_layout - -\begin_layout LyX-Code -$ export EXPORT_ROOT=/Users/username/pythia-0.6/
-\end_layout
-
-\begin_layout LyX-Code
-$export BLD_CONFIG=~/dv/config -\end_layout - -\begin_layout LyX-Code -$ export PATH=$BLD_CONFIG/make:$PATH
-\end_layout
-
-\begin_layout LyX-Code
-$cd pythia-0.6 -\end_layout - -\begin_layout LyX-Code -$ mm
-\end_layout
-
-\begin_layout Subsection
-Test the Installation
-\end_layout
-
-\begin_layout Standard
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- installation or various tools in the installation.
- For example, you can run
-\family typewriter
-diagnostics.py
-\family default
- in
-\family typewriter
-~/pythia-0.6/tests/jtest/tests
-\family default
-.
-\end_layout
-
\begin_layout Chapter
Running SNAC
\end_layout
@@ -4654,7 +3660,7 @@
\begin_inset Float figure
wide false
sideways false
-status collapsed
+status open

\begin_layout Standard
\noindent
@@ -4711,7 +3717,7 @@
\begin_inset Float figure
wide false
sideways false
-status collapsed
+status open

\begin_layout Standard
\noindent
@@ -5412,15 +4418,25 @@
\end_layout

\begin_layout Chapter
-ViscoElasticRheology (from TWiki)
+ViscoElasticRheology
\end_layout

\begin_layout Standard
-Problem Description Parallel-Plate Viscometer (excerpted from FLAC3D manual)
- Suppose that a material with viscosity is steadily squeezed between two
- parallel plates that are moving at a constant velocity V0.
- The two plates have length 2L and are a distance 2h apart.
- The material is prevented from slipping at the plates.
+We solve a parallel-plate viscometer problem (
+\begin_inset LatexCommand cite
+key "Jaeger 1969"
+
+\end_inset
+
+) is simulated, in which viscoelastic material is squeezed between two parallel
+ plates.
+ The plates are moving at a constant velocity,
+\begin_inset Formula $v_{0}$
+\end_inset
+
+.
+ Each plate has the length of 2L and is at a distance 2h from the other.
+ No slip is assumed between the material and the plates.
The approximate analytical solution is given by Jaeger (1969, Elasticity,
Fracture and Flow, 3rd Ed.
New York: John Wiley & Sons, Inc.)
@@ -5618,67 +4634,8 @@

\end_layout

-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Paragraph*
-Other sections from the TWiki include
-\end_layout
-
-\begin_layout Standard
-ElastoViscoPlasticRheologyI - Introduction and benchmarking
-\end_layout
-
-\begin_layout Standard
-ElastoViscoPlasticRheologyII - Comparison of two different yield criterion
-
-\end_layout
-
-\begin_layout Standard
-TemperatureSolverPlugin - design issues around the temperature solver plugin
-
-\end_layout
-
-\begin_layout Standard
-ReMeshing - plans & strategies for remeshing.
-
-\end_layout
-
-\begin_layout Standard
-ParallelBenchmarks - results of parallel runs
-\end_layout
-
-\begin_layout Standard
-SnacCitComSCoupling - notes on the coupling with CitComS project
-\end_layout
-
-\begin_layout Standard
-PossibleRoundOffIssue
-\end_layout
-
-\begin_layout Standard
-GcubedPaperProblems
-\end_layout
-
-\begin_layout Standard
-DomainDecompositionin2D
-\end_layout
-
-\begin_layout Standard
-NaturalBCVerification
-\end_layout
-
-\begin_layout Standard
-
-\end_layout
-
\begin_layout Chapter
-10 Parameters
+Parameters
\end_layout

\begin_layout Standard
@@ -6936,380 +5893,12 @@
.
\end_layout

-\begin_layout Section
-\begin_inset LatexCommand label
-name "sec:Exchanger-Configuration-(Optional)"
-
-\end_inset
-
-Exchanger Configuration (Optional)
-\end_layout
-
-\begin_layout Standard
-This version of CitcomS is capable of solver coupling.
- Two or more instances of CitcomS solvers can be coupled together to solve
- a problem with different length and time scales
-\begin_inset LatexCommand cite
-key "Tan et al GeoFramework Part I"
-
-\end_inset
-
-.
- An external Exchanger package is needed for solver coupling.
-\begin_inset LatexCommand htmlurl
-name "CIG's Exchanger web page"
-target "geodynamics.org/cig/software/packages/cs/exchanger"
-
-\end_inset
-
-.
- After you download and untar the package, you can configure and install
- Exchanger using these commands:
-\end_layout
-
\begin_layout LyX-Code
-$cd Exchanger-1.0.0/ -\end_layout -\begin_layout LyX-Code -$ ./configure --prefix=$HOME/cig \end_layout -\begin_layout LyX-Code -$ make
-\end_layout
-
-\begin_layout LyX-Code
-$make install -\end_layout - -\begin_layout Standard -By default, CitcomS will attempt to auto-detect your Exchanger installation - and will disable Exchanger support if it is not found. - You may specify the location of your Exchanger installation by setting - the PYTHONPATH environment variable to the appropriate installation prefix. -\end_layout - -\begin_layout LyX-Code -$ cd CitcomS-3.0.3/
-\end_layout
-
-\begin_layout LyX-Code
-$export PYTHONPATH=$HOME/cig/lib/python2.3/site-packages:$PYTHONPATH -\end_layout - -\begin_layout LyX-Code -$ ./configure --with-exchanger
-\end_layout
-
\begin_layout Section
\begin_inset LatexCommand label
-name "sec:HDF5-Configuration"
-
-\end_inset
-
-HDF5 Configuration (Optional)
-\end_layout
-
-\begin_layout Standard
-For writing its output in binary format, CitcomS requires parallel HDF5
- (PHDF5).
- In turn, PHDF5 requires an MPI compiler with MPI-IO support and a parallel
- file system.
- If an existing installation of the PHDF5 library is not available on your
- cluster, you can compile it from source by following the instructions in
- the file
-\family typewriter
-\size small
-release_docs/INSTALL_parallel
-\family default
-\size default
- under the HDF5 source tree.
- Under Debian Linux, you may simply install the
-\family typewriter
-libhdf5-mpich
-\family default
-,
-\family typewriter
-libhdf5-mpich-dev
-\family default
- and
-\family typewriter
-hdf5-tools
-\family default
- packages.
-\end_layout
-
-\begin_layout Standard
-By default, CitcomS will attempt to auto-detect your PHDF5 installation,
- You may specify the location of your PHDF5 installation by setting the
- PHDF5_HOME environment variable to the appropriate installation prefix.
-\end_layout
-
-\begin_layout LyX-Code
-$export PHDF5_HOME=/opt/phdf5/1.6.5 -\end_layout - -\begin_layout LyX-Code -$ ./configure --with-hdf5
-\end_layout
-
-\begin_layout Subsection
-\end_layout
-
-\begin_layout Standard
-While the following software is not necessary for the normal operation of
- CitcomS, you may find it useful for accessing CitcomS data in HDF5 files.
-\end_layout
-
-\begin_layout Subsubsection
-NumPy
-\end_layout
-
-\begin_layout Standard
-NumPy is an extension to Python which adds support for multi-dimensional
- arrays for use in scientific computing.
-\begin_inset LatexCommand htmlurl
-target "numpy.scipy.org"
-
-\end_inset
-
-.
- To compile and install this extension, download it and issue the following
- commands after extracting it:
-\end_layout
-
-\begin_layout LyX-Code
-$cd numpy-1.0 -\end_layout - -\begin_layout LyX-Code -$ python setup.py install --prefix=$HOME/cig -\end_layout - -\begin_layout Standard -Alternatively, under Debian Linux you can install the -\family typewriter -python-numpy -\family default - package. - On Gentoo Linux, NumPy is available in the -\family typewriter -dev-python/numpy -\family default - ebuild. -\end_layout - -\begin_layout Subsubsection -\begin_inset LatexCommand label -name "sub:PyTables" - -\end_inset - -PyTables -\end_layout - -\begin_layout Standard -PyTables is an extension to Python and can expose HDF5 array datasets as - Python NumPy arrays. - It is available at -\begin_inset LatexCommand htmlurl -name "PyTables" -target "www.pytables.org" - -\end_inset - -. -\end_layout - -\begin_layout Standard -To compile and install this extension, download the latest stable version - and issue the following commands: -\end_layout - -\begin_layout LyX-Code -$ cd pytables-1.3.3
-\end_layout
-
-\begin_layout LyX-Code
-$python setup.py install --prefix=$HOME/cig
-\end_layout
-
-\begin_layout Standard
-To install on Debian Linux, you may use the
-\family typewriter
-python-tables
-\family default
- On Gentoo Linux, it is available in the
-\family typewriter
-dev-python/pytables
-\family default
- ebuild.
-\end_layout
-
-\begin_layout Subsubsection
-HDFView
-\end_layout
-
-\begin_layout Standard
-HDFView is a visual tool written in Java for browsing and editing HDF5 files.
-\begin_inset LatexCommand htmlurl
-target "hdf.ncsa.uiuc.edu/hdf-java-html/hdfview"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Subsubsection
-\begin_inset LatexCommand label
-name "sub:OpenDXutils"
-
-\end_inset
-
-OpenDXutils
-\end_layout
-
-\begin_layout Standard
-In order to import HDF5 files into OpenDX, you need the OpenDXutils package
- from the Cactus project.
- Go to the
-\begin_inset LatexCommand url
-name "OpenDXutils package website"
-target "www.cactuscode.org/Visualization/openDX"
-
-\end_inset
-
- Note that you will need to set both
-\family typewriter
-DXMODULES
-\family default
- and
-\family typewriter
-DXMDF
-\family default
- environment variables before running OpenDX to load the package.
-\end_layout
-
-\begin_layout Section
-\begin_inset LatexCommand label
-name "sec:Batch-System-Configuration"
-
-\end_inset
-
-Batch System Configuration
-\end_layout
-
-\begin_layout Standard
-If you are installing CitcomS on a cluster with a batch system, you can
- configure Pyre such that the
-\family typewriter
-citcoms
-\family default
- command automatically submits jobs to the batch queue.
- Pyre contains support for the LSF, PBS, and Globus batch systems.
-\end_layout
-
-\begin_layout Standard
-The command to submit a batch job depends upon the particular batch system
- used.
- Further, the command used in a batch script to launch an MPI program varies
- from one cluster to the next.
- This command can vary between two clusters, even if the clusters use the
- same batch system! On some systems,
-\family typewriter
-mpirun
-\family default
- is invoked directly from the batch script.
- On others, a special wrapper is used instead.
-\end_layout
-
-\begin_layout Standard
-Properly configured, Pyre can handle job submissions automatically, insulating
- users from the details of the batch system and the site configuration.
- This feature has the most value when the system administrator installs
- a global Pyre configuration file on the cluster (under
-\family typewriter
-/etc/pythia-0.8
-\family default
-), for the benefit of all users and all Pyre-based applications.
-\end_layout
-
-\begin_layout Standard
-
-\begin_inset LatexCommand htmlurl
-name "Pythia page"
-target "geodynamics.org/cig/software/packages/cs/pythia"
-
-\end_inset
-
-.
- For more information on batch system configuration as it pertains to running
- CitcomS, see Section
-\begin_inset LatexCommand vref
-reference "sub:Launchers-and-Schedulers"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Section
-\begin_inset LatexCommand label
-name "sec:Installing-without-Pyre"
-
-\end_inset
-
-Installing without Pyre
-\end_layout
-
-\begin_layout Standard
-To build just the CitcomS tools (or drivers'') from the legacy C code,
- give
-\family typewriter
-configure
-\family default
- the
-\family typewriter
---without-pyre
-\family default
- option:
-\end_layout
-
-\begin_layout LyX-Code
-$./configure --without-pyre -\end_layout - -\begin_layout Standard -The only system requirements for this configuration are an MPI library and - a C compiler. - The -\family typewriter -make -\family default - command will build two command-line tools, -\family typewriter -CitcomSFull -\family default - and -\family typewriter -CitcomSRegional -\family default -, for running the full solver and the regional solver, respectively. -\end_layout - -\begin_layout Section -\begin_inset LatexCommand label name "sec:Software-Repository" \end_inset @@ -7420,22 +6009,22 @@ \end_layout \begin_layout LyX-Code -$ svn checkout http://geodynamics.org/svn/cig/mc/3D/CitcomS/trunk CitcomS
+$svn checkout http://geodynamics.org/svn/cig/long/3D/SNAC/trunk SNAC \end_layout \begin_layout Standard This will create the local directory \family typewriter -CitcomS +SNAC \family default - (if it doesn't already exist) and fill it with the latest CitcomS source - from the CIG software repository. + (if it doesn't already exist) and fill it with the latest SNAC source from + the CIG software repository. \end_layout \begin_layout Standard The \family typewriter -CitcomS +SNAC \family default directory thus created is called a \emph on @@ -7450,7 +6039,7 @@ \end_layout \begin_layout LyX-Code -$ cd CitcomS
+\$ cd SNAC
\end_layout

\begin_layout LyX-Code
@@ -8214,7 +6803,8 @@

\end_inset

+ and Gurnis, M.
Seismic tomography, surface uplift, and the breakup of Gondwanaland: Integratin
g mantle convection backwards in time.
Geochem., Geophys., Geosys.
@@ -8229,9 +6819,7 @@

\end_inset

-Hughes, T.
- J.
- R.
+Hughes, T.J.R.
The Finite Element Method: Linear Static and Dynamic Finite Element Analysis
(Prentice-Hall, Inc., Englewood Cliffs, New Jersey, 1987).

@@ -8245,8 +6833,7 @@
\end_inset

Ramage, A.
- & Wathen, A.
- J.
+ and Wathen, A.J.
Iterative solution techniques for the Stokes and Navier-Stokes equations.
Int.
J.
@@ -8276,7 +6863,7 @@
\end_inset

Cahouet, J.
- & Chabard, J.-P.
+ and Chabard, J.-P.
Some fast 3D finite element solvers for the generalized Stokes problem.
Int.
J.
@@ -8294,7 +6881,7 @@
\end_inset

Atanga, J.
- & Silvester, D.
+ and Silvester, D.
Iterative methods for stabilized mixed velocity-pressure finite elements.
Int.
J.
@@ -8311,10 +6898,8 @@

\end_inset

-Hager, B.
- H.
- & O'Connell, R.
- J.
+Hager, B.H.
+ and O'Connell, R.J.
A simple global model of plate dynamics and mantle convection.
J.
Geophys.
@@ -8329,7 +6914,14 @@

\end_inset

-MARTI AND CUNDALL 1982 -- TODO
+Marti, J.
+ and Cundall, P.
+ Mixed discretization procecure for accurate modelling of plastic collapse.
+ Int.
+ J.
+ Numer.
+ Anal.
+ Methods Geomech., 6, 129-139 (1982).
\end_layout

\begin_layout Bibliography
@@ -8339,7 +6931,9 @@

\end_inset

-CUNDALL 1989 -- TODO
+Cundall, P.
+ Numerical experiments on localization in frictional materials.
+ Ingenieur Archiv., 58, 148-159 (1989).
\end_layout

\begin_layout Bibliography
@@ -8349,7 +6943,10 @@

\end_inset

-WILKINS 1964 -- TODO
+Wilkins, M.L.
+ Calculation of elastic-plastic flow Meth.
+ Comput.
+ Phys., 3, 211-263 (1964).
\end_layout

\begin_layout Bibliography
@@ -8359,7 +6956,13 @@

\end_inset

-NEEDLEMAN 1988 -- TODO
+Needleman, A.
+ Material rate dependence and mesh sensitivity in localization problems.
+ Comp.
+ Meth.
+ App.
+ Mech.
+ Eng., 67, 69-85 (1988).
\end_layout

\begin_layout Bibliography
@@ -8369,7 +6972,15 @@

\end_inset

-Ortiz and Simo, 1986 -- TODO
+Ortiz, M.
+ and Simo, J.C.
+ An analysis of a new class of integration algorithms for elastoplastic
+ constitutive relations.
+ Int.
+ J.
+ Num.
+ Meth.
+ Eng., 23, 353-366 (1986).
\end_layout

\begin_layout Bibliography
@@ -8379,7 +6990,13 @@

\end_inset

-Ortiz and Quigley, 1991 -- TODO
+Ortiz, M.
+ and Quigley, J.J.
+ Adaptive mesh refinement in strain localization problems.
+ Comput.
+ Methods Appl.
+ Mech.
+ Engrg., 90, 781-804, (1991).
\end_layout

\begin_layout Bibliography
@@ -8389,8 +7006,12 @@

\end_inset

-Quenette, et al.
- -- TODO, find citation and insert year too
+Quenette, S., Appelbe, B., Gurnis, M., Hodkinson, L., Moresi, L., and Sunter,
+ P.
+ An investigation into design for performace and code maintainability in
+ high performance computing.
+ ANZIAM J.
+ 46 (E), C101–C116 (2005).
\end_layout

\begin_layout Bibliography
@@ -8400,7 +7021,11 @@

\end_inset

-Tan, et al., 2004 -- TODO
+Tan, E., Choi, E., Thoutireddy, P., Gurnis, M., and Aivazis, M.
+ GeoFramework: Coupling multiple models of mantle convection within a computatio
+nal framework Geochem.
+ Geophys.
+ Geosyst., 7, Q06001, doi:10.1029/2005GC001155 (2004).
\end_layout

\begin_layout Bibliography
@@ -8432,7 +7057,15 @@

\end_inset

- Zien_etal1995 -- TODO
+ Zienkiewicz, O.
+ C., Huang, M., and Pastor, M.
+ Localization problems in plasticity using finite elements with adaptive
+ remeshing.
+ Int.
+ J.
+ Numer.
+ Anal.
+ Methods Geomech., 19, 127-148 (1995)
\end_layout

\begin_layout Bibliography
@@ -8442,7 +7075,9 @@

\end_inset

-Bathe1996 -- TODO
+Bathe, K.-J.
+ Finite Element Procedure Prentice-Hall, Upper Saddle River, New Jersey
+ (1996).
\end_layout

\begin_layout Bibliography
@@ -8452,7 +7087,12 @@

\end_inset

-Albe_etal2000 -- TODO
+Albert, R., Phillips, R., Dombard, A., and Brown, C.
+ A test of the validity of yield strength envelope with an elastoviscoplastic
+ finite element model.
+ Geophys.
+ J.
+ Int., 140, 399-409 (2000).
\end_layout

\begin_layout Bibliography
@@ -8462,7 +7102,15 @@

\end_inset

-Poli_etal1993a -- TODO
+Poliakov, A.N.B., Cundall, P.A., Podladchikov, Y.Y., and Lyakhovsky, V.A.
+ An explicit inertial method for the simulation of viscoelastic flow: An
+ evaluation of elastic effects on diapiric flow in two- and three-layers
+ models.
+
+\emph on
+Flow and Creep in the Solar Systems: Observations, Modeling and Theory
+\emph default
+, Kluwer Academic Publishers, 175-195 (1993).
\end_layout

\begin_layout Bibliography
@@ -8472,7 +7120,9 @@

\end_inset

-SimoHugh2004 -- TODO
+Simo, J.
+ and Hughes, T.
+ Computational Inelasticity Springer, New York (2004).
\end_layout

\begin_layout Bibliography
@@ -8482,7 +7132,14 @@

\end_inset

-RudnRice1975 -- TODO
+Rudnicki, J.
+ and Rice, J.
+ Conditions for the localization of deformation in pressure-sensitive dilatant
+ materials.
+ J.
+ Mech.
+ Phys.
+ Solids., 1975, 23, 371-394 (1975).
\end_layout

\begin_layout Bibliography
@@ -8492,8 +7149,16 @@

\end_inset

-Cundall 1987 (or is the date just wrong in the text? this was from your
- ERT notation) -- TODO
+Cundall, P.A.
+ Distinct Element Models of Rock and Soil Structure, in Analytical and Computati
+onal.
+ Methods in Engineering Rock Mechanics, Chapter 4, pp.
+ 129-163.
+ E.
+ T.
+ Brown, Ed.
+ London: George Allen.
+ & Unwin, (1987).
\end_layout

\end_body