[cig-commits] r13296 - in doc/snac: . figures
echoi at geodynamics.org
echoi at geodynamics.org
Wed Nov 12 09:08:36 PST 2008
Author: echoi
Date: 2008-11-12 09:08:35 -0800 (Wed, 12 Nov 2008)
New Revision: 13296
Added:
doc/snac/figures/EP_hierarchy.png
Modified:
doc/snac/snac.lyx
Log:
1. Work ongoing on the sections, "SNAC design" and "StGermain". 2. Irrelevant references have been removed.
Added: doc/snac/figures/EP_hierarchy.png
===================================================================
(Binary files differ)
Property changes on: doc/snac/figures/EP_hierarchy.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: doc/snac/snac.lyx
===================================================================
--- doc/snac/snac.lyx 2008-11-12 01:07:56 UTC (rev 13295)
+++ doc/snac/snac.lyx 2008-11-12 17:08:35 UTC (rev 13296)
@@ -1,4 +1,4 @@
-#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+#LyX 1.5.3 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -54,7 +54,6 @@
\begin_layout Standard
\noindent
\align center
-d
\begin_inset Float figure
placement H
wide false
@@ -792,7 +791,7 @@
Instead of adding a usual velocity-dependent friction term, we adopt a
local non-viscous damping scheme
\begin_inset LatexCommand cite
-key "Cundall 1987"
+key "Cundall_1987"
\end_inset
@@ -910,7 +909,7 @@
we use a criterion that does not explicitly include length scale and P
wave velocity; see Chapter 9 in Bathe
\begin_inset LatexCommand cite
-key "Bathe1996"
+key "Bathe_1996"
\end_inset
@@ -1512,13 +1511,22 @@
, below).
Although primarily implemented in C, it is object-oriented, and makes use
of extensibility and inheritance.
- Having StGermain as a framework, SNAC code must follow certain conventions.
- It means that many abilities are available in generic forms: XML input,
- extensible data structures, classified output streams, etc.
- SNAC is readily customizable through writing a ``plugin,'' a shared object
+ Having StGermain as a framework, SNAC can use directly or extend many abilities
+ of StGermain available in generic forms: XML input, extensible data structures,
+ classified output streams, etc.
+ The three key design ideas relevant to SNAC are the plugins, SNAC Context
+ and Entry Points.
+\end_layout
+
+\begin_layout Subsection
+Plugins
+\end_layout
+
+\begin_layout Standard
+SNAC is readily customizable through writing a ``plugin,'' a shared object
that can be loaded dynamically at run-time.
- The two key design ideas relevant to SNAC are the ``SNAC Context'' and
- ``Entry Points.''
+ A plugin is typically stored in Snac/plugins directory and Together with
+ the Entry Point design, the time and effort to
\end_layout
\begin_layout Subsection
@@ -1543,8 +1551,15 @@
\end_layout
\begin_layout Standard
-The SNAC Context inherits from the StGermain Mesh and Abstract Contexts,
- which provide much of the default functionality.
+The SNAC Context inherits from the
+\emph on
+StGermain Mesh
+\emph default
+ and
+\emph on
+Abstract Context
+\emph default
+, which provide much of the default functionality.
\end_layout
@@ -1553,12 +1568,12 @@
\end_layout
\begin_layout Standard
-An Entry Point is essentially a list of function pointers, which can be
- dynamically modified.
- When an entry point is called, it runs each of the function pointers in
- its list sequentially, with the same arguments.
- Since the SNAC Context calls the entry points in a specific hierarchy,
- an application's set of entry points define the call-tree for an application.
+An entry point (EP) is essentially a list of function pointers, which can
+ be dynamically modified.
+ When an EP is called, it runs each of the function pointers in its list
+ sequentially, with the same arguments.
+ Since the SNAC Context calls the EPs in a specific hierarchy, an application's
+ set of EPs define the call-tree for an application.
\end_layout
\begin_layout Standard
@@ -1568,13 +1583,21 @@
In SNAC, this is simply a matter of adding pointers to their custom functions
to the relevant entry points.
For instance, to add a contribution from the Winkler foundation to the
- residual force at each node, one can simply include a plugin called ``SnacWinkl
-erForce.'' What this plugins does is to add (or ``hook up'') its own force
- computing routine to the entry point that already has a pointer to the
- function computing internal residual forces.
- It is possible to determined which function should be called first.
- This way, the core structure of the code does not need to be modified every
- time new operations on nodes or elements are added.
+ residual force at each node on the bottom surface, one can simply include
+ a plugin called ``SnacWinklerForce.'' What this plugins does is to add (or
+ ``hook up'') a pointer to its own force computing routine to the entry
+ point that already has a pointer to the function computing internal residual
+ forces.
+ While being a part of the loop over all the nodes (local to a processor),
+ this plugin's function takes care of deciding if a node is on the bottom
+ and adding the computed restoring force.
+ In this way, the core structure of the code does not need to be modified
+ every time new operations on nodes or elements are added.
+ StGermain provides a flexible way of managing hooked-up function pointers
+ such that one can create a new entry point, set a default function for
+ it, insert one function pointer before or after another within an Entry
+ Point., etc.
+
\end_layout
\begin_layout Standard
@@ -1595,20 +1618,12 @@
\begin_layout Standard
\begin_inset Graphics
- filename figures/SNACCallHierarchyArch.png
+ filename figures/EP_hierarchy.png
lyxscale 40
\end_inset
-\begin_inset Graphics
- filename figures/SNACSolveDetails.png
- lyxscale 40
- scale 110
-
-\end_inset
-
-
\end_layout
\end_inset
@@ -1616,18 +1631,6 @@
\end_layout
-\begin_layout Subsection
-SNAC History
-\end_layout
-
-\begin_layout Standard
-A long, long time ago …
-\end_layout
-
-\begin_layout Chapter
-SNAC-Related Software
-\end_layout
-
\begin_layout Section
\begin_inset LatexCommand label
name "sec:StGermain"
@@ -1664,21 +1667,15 @@
\end_layout
\begin_layout Standard
-SNAC is built up from the StGermain framework, an environment for the developmen
-t of physically based scientific codes [Quenette, et al., 2005].
- As frameworks, StGermain and Pyre differ in that StGermain provides the
- infrastructural components needed to build complete codes while Pyre provides
- the superstructure to couple codes together; for this reason the former
- is considered an infrastructure framework and the later as a superstructure
- framework.
-
-\end_layout
-
-\begin_layout Standard
StGermain provides a suite of libraries needed by general physical modeling
software such as flow control, domain discretization, and initial/boundary
- condition management [Quenette, et al.
- TODO--need year].
+ condition management
+\begin_inset LatexCommand cite
+key "Quen_etal2005"
+
+\end_inset
+
+.
One of the advantages of using the StGermain framework is that a code can
be easily extended through entry points and plugins.
By adding or removing entry points, a problem-specific algorithm can be
@@ -1692,7 +1689,15 @@
\end_layout
+\begin_layout Section
+SNAC History
+\end_layout
+
\begin_layout Standard
+A long, long time ago …
+\end_layout
+
+\begin_layout Standard
\noindent
\align center
\begin_inset Float figure
@@ -1737,7 +1742,7 @@
\end_layout
\begin_layout Standard
-StGermain and SNAC are both available at the
+StGermain and SNAC are bundled as SNAC and available at the
\begin_inset LatexCommand htmlurl
name "Geodynamics Software Packages web page"
target "geodynamics.org/cig/software/packages"
@@ -1745,9 +1750,6 @@
\end_inset
.
- You will download StGermain and SNAC (along with Snark, an extensible framework
- for building Finite Element Method-Particle In Cell applications) at the
- same time.
First, you will need to have MPI available on your machine.
\end_layout
@@ -4440,7 +4442,7 @@
\begin_layout Standard
We solve a parallel-plate viscometer problem (
\begin_inset LatexCommand cite
-key "Jaeger 1969"
+key "Jaeger_1969"
\end_inset
@@ -6692,239 +6694,6 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
-label "1"
-key "Moresi et al 2000"
-
-\end_inset
-
-Moresi, L., Gurnis, M., and Zhong, S.
- Plate tectonics and convection in the Earth's mantle: Toward a numerical
- simulation.
-
-\emph on
- Comp.
- Sci.
- Engin.
- 2,
-\emph default
- 22-33 (2000).
-
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "2"
-key "Moresi Solomatov 1995"
-
-\end_inset
-
-Moresi, L.N., and Solomatov, V.S.
- Numerical investigation of 2D convection with extremely large viscosity
- variations.
-
-\emph on
-Phys.
- Fluid 7,
-\emph default
-2154-2162 (1995).
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "3"
-key "Moresi Gurnis 1996"
-
-\end_inset
-
-Moresi, L.N., and Gurnis, M.
- Constraints on the lateral strength of slabs from three-dimensional dynamic
- flow models.
-
-\emph on
- Earth Planet.
- Sci.
- Lett.
- 138,
-\emph default
-15-28 (1996).
-
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "4"
-key "Zhong et al 1998"
-
-\end_inset
-
-Zhong, S., Gurnis, M., and Moresi, L.
- The role of faults, nonlinear rheology, and viscosity structure in generating
- plates from instantaneous mantle flow models.
-
-\emph on
-J.
- Geophys.
- Res.
- 103,
-\emph default
- 15,255-15,268 (1998).
-
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "5"
-key "Zhong et al 2000"
-
-\end_inset
-
-Zhong, S., Zuber, M.T., Moresi, L.N., and Gurnis, M.
- The role of temperature-dependent viscosity and surface plates in spherical
- shell models of mantle convection.
-
-\emph on
- J.
- Geophys.
- Res.
- 105,
-\emph default
-11,063-11,082 (2000).
-
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "6"
-key "Tan et al 2002"
-
-\end_inset
-
-Tan, E., Gurnis, M., and Han, L.
- Slabs in the lower mantle and their modulation of plume formation.
-
-\emph on
-Geochem.
- Geophys.
- Geosyst.
- 3,
-\emph default
- 1067 (2002).
-
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "7"
-key "Conrad Gurnis 2001"
-
-\end_inset
-
-Conrad, C.P.
- and Gurnis, M.
- Seismic tomography, surface uplift, and the breakup of Gondwanaland: Integratin
-g mantle convection backwards in time.
- Geochem., Geophys., Geosys.
- (2001).
-
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "8"
-key "Hughes 1987"
-
-\end_inset
-
-Hughes, T.J.R.
- The Finite Element Method: Linear Static and Dynamic Finite Element Analysis
- (Prentice-Hall, Inc., Englewood Cliffs, New Jersey, 1987).
-
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "9"
-key "Ramage Wathen 1994"
-
-\end_inset
-
-Ramage, A.
- and Wathen, A.J.
- Iterative solution techniques for the Stokes and Navier-Stokes equations.
- Int.
- J.
- Numer.
- Methods.
- Fluids 19, 67-83 (1994).
-
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "10"
-key "Brooks 1981"
-
-\end_inset
-
-Brooks, A.N., TODO: TITLE (California Institute of Technology, Pasadena, CA,
- 1981).
-
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "11"
-key "Cahoet Chabard 1988"
-
-\end_inset
-
-Cahouet, J.
- and Chabard, J.-P.
- Some fast 3D finite element solvers for the generalized Stokes problem.
- Int.
- J.
- Numer.
- Methods.
- Fluids 8, 869-895 (1988).
-
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "12"
-key "Atanga Silvester 1992"
-
-\end_inset
-
-Atanga, J.
- and Silvester, D.
- Iterative methods for stabilized mixed velocity-pressure finite elements.
- Int.
- J.
- Numer.
- Methods.
- Fluids 14, 71-81 (1992).
-
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "13"
-key "Hager OConnell 1981"
-
-\end_inset
-
-Hager, B.H.
- and O'Connell, R.J.
- A simple global model of plate dynamics and mantle convection.
- J.
- Geophys.
- Res.
- 86, 4843-4867 (1981).
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
label "14"
key "MartCund1982"
@@ -6943,7 +6712,7 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
label "15"
-key "Cundall 1989"
+key "Cundall1989"
\end_inset
@@ -6968,7 +6737,7 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
label "17"
-key "Needleman 1988"
+key "Needleman1988"
\end_inset
@@ -6984,7 +6753,7 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
label "18"
-key "Ortiz and Simo, 1986"
+key "OrtiSimo1986"
\end_inset
@@ -7002,7 +6771,7 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
label "19"
-key "Ortiz and Quigley, 1991"
+key "OrtiQuig1991"
\end_inset
@@ -7018,7 +6787,7 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
label "20"
-key "Quenette, et al"
+key "Quen_etal2005"
\end_inset
@@ -7033,7 +6802,7 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
label "21"
-key "Tan, et al., 2004"
+key "Tan_etal2004"
\end_inset
@@ -7047,7 +6816,7 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
label "22"
-key "Jaeger 1969"
+key "Jaeger_1969"
\end_inset
@@ -7059,16 +6828,6 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
label "23"
-key "FLAC3D Manual"
-
-\end_inset
-
-FLAC3D Manual -- TODO
-\end_layout
-
-\begin_layout Bibliography
-\begin_inset LatexCommand bibitem
-label "24"
key "Zien_etal1995"
\end_inset
@@ -7086,8 +6845,8 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
-label "25"
-key "Bathe1996"
+label "24"
+key "Bathe_1996"
\end_inset
@@ -7098,7 +6857,7 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
-label "26"
+label "25"
key "Albe_etal2000"
\end_inset
@@ -7113,7 +6872,7 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
-label "27"
+label "26"
key "Poli_etal1993a"
\end_inset
@@ -7131,7 +6890,7 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
-label "28"
+label "27"
key "SimoHugh2004"
\end_inset
@@ -7143,7 +6902,7 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
-label "29"
+label "28"
key "RudnRice1975"
\end_inset
@@ -7160,8 +6919,8 @@
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
-label "30"
-key "Cundall 1987"
+label "29"
+key "Cundall_1987"
\end_inset
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