[cig-commits] r4254 - long/3D/Gale/trunk/documentation
sue at geodynamics.org
sue at geodynamics.org
Wed Aug 9 14:59:43 PDT 2006
Author: sue
Date: 2006-08-09 14:59:43 -0700 (Wed, 09 Aug 2006)
New Revision: 4254
Modified:
long/3D/Gale/trunk/documentation/gale.lyx
Log:
added use and modify info
Modified: long/3D/Gale/trunk/documentation/gale.lyx
===================================================================
--- long/3D/Gale/trunk/documentation/gale.lyx 2006-08-09 19:45:49 UTC (rev 4253)
+++ long/3D/Gale/trunk/documentation/gale.lyx 2006-08-09 21:59:43 UTC (rev 4254)
@@ -33,8 +33,30 @@
GALE
\end_layout
+\begin_layout Author
+California Institute of Technology
+\newline
+Walter Landry and Luke Hodkinson
+\end_layout
+
+\begin_layout Date
+08.09.06
+\end_layout
+
+\begin_layout Author
+Version 0.2.0 (BETA)
+\end_layout
+
\begin_layout Standard
+\begin_inset LatexCommand \tableofcontents{}
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+
\newpage
\end_layout
@@ -57,9 +79,57 @@
\end_layout
\begin_layout Standard
-TBD
+Computational Infrastructure for Geodynamics (CIG) is making this source
+ code available to you in the hope that the software will enhance your research
+ in geophysics.
+ The underlying C code for the finite element package were donated to CIG
+ in July of 2005.
+ A number of individuals have contributed a significant portion of their
+ careers toward the development of GALE.
+ It is essential that you recognize these individuals in the normal scientific
+ practice by making appropriate acknowledgements.
+
\end_layout
+\begin_layout Standard
+The code is based on the method described in Moresi, L.
+ N., Dufour, F., Mühlhaus, H.-B.
+ A Lagrandian integration point finite element method for large deformation
+ modeling of viscoelastic geomaterials.
+
+\emph on
+J.
+ Comp.
+ Phys.
+
+\series bold
+\emph default
+184
+\series default
+, 476-497 (2003).
+ The developers are Walter Landry of CIG and Luke Hodkinson of the Victorian
+ Partnership for Advanced Computing (VPAC), as well as Louis Moresi's group
+ at Monash University.
+ The GALE team requests that in your oral presentations and in your paper
+ acknowledgements that you indicate your use of this code, the authors of
+ the code,
+\begin_inset LatexCommand \htmlurl[CIG]{<http://www.geodynamics.org/>}
+
+\end_inset
+
+,
+\begin_inset LatexCommand \htmlurl[Victoria Partnership for Advanced Computing]{<http://www.vpac.org/>}
+
+\end_inset
+
+, and
+\begin_inset LatexCommand \htmlurl[Monash University]{<http://www.monash.edu/>}
+
+\end_inset
+
+.
+\end_layout
+
\begin_layout Section
Support
\end_layout
@@ -289,7 +359,7 @@
\begin_layout Standard
Walter Landry of CIG and Luke Hodkinson of the Victorian Partnership for
- Advanced Computing(VPAC) are the primary developers of GALE.
+ Advanced Computing (VPAC) are the primary developers of GALE.
Roger Buck and Robert Bialis of Columbia University and Chris Fuller of
the University of Washington assisted in making the code useful to geoscientist
s.
@@ -666,10 +736,140 @@
\end_layout
\begin_layout Standard
-This should run for 29 time steps and then crash.
+This should run for 500 time steps and then exit.
\end_layout
\begin_layout Section
+Output Format
+\end_layout
+
+\begin_layout Standard
+The file
+\family typewriter
+simple-extension.xml
+\family default
+ will produce the directory
+\family typewriter
+output.sandbox
+\family default
+ in which you will find a number of different output files.
+ The default setting is to print once for every time step.
+ You can change the frequency of that setting, e.g., have it print more frequently
+, by modifying
+\family typewriter
+simple-extension.xml
+\family default
+ so the parameter
+\family typewriter
+checkpointEvery
+\family default
+ has a different value, e.g.:
+\end_layout
+
+\begin_layout LyX-Code
+<param name=
+\begin_inset Quotes erd
+\end_inset
+
+checkpointEvery
+\begin_inset Quotes erd
+\end_inset
+
+>25</param>
+\end_layout
+
+\begin_layout Standard
+You can change the value to any number you want.
+
+\end_layout
+
+\begin_layout Standard
+Also found in
+\family typewriter
+output.sandbox
+\family default
+ are a number of .dat and .txt files.
+ The .dat files are ASCII and self-explanatory, e.g., pressurefield.dat contains
+ pressure field output information.
+ Inside each .dat file is found several columns of data:
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+0 0.0312539624080715 0.0109361134145122 0 -9.81467103200287
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+1 0.0937630718938361 0.0109356986189374 0 17.7373201951569
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+2 0.156270066350344 0.0109368543031399 0 -37.0281780188199
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+3 0.218780947570009 0.0109343376815161 0 45.6263762140766
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+4 0.28128858838265 0.010937987088561 0 -65.2132484518426
+\end_layout
+
+\begin_layout Standard
+The first column (0,1,2,3, ...) is the node number, and the second, third,
+ and fourth columns are the x, y, and z coordinates.
+ The last column(s) show the value.
+ Note: If performing a 2D run, you will still obtain the z data, but that
+ can be ignored.
+\end_layout
+
+\begin_layout Standard
+The .txt files exist for the output of DumpSwarm, explained below.
+\end_layout
+
+\begin_layout Section
+Using DumpSwarm for Particle Information
+\end_layout
+
+\begin_layout Standard
+Several binary files are found in
+\family typewriter
+output.sandbox
+\family default
+, but they are not useful to examine.
+ While they contain checkpointing, or a dump of the memory, accessing it
+ depends on how the memory is set up.
+ Since all particle information is there, which has the material properties,
+ we provide a plug-in called DumpSwarm to access that information.
+ DumpSwarm is found in the CIG Software Repository at
+\end_layout
+
+\begin_layout LyX-Code
+/cig/long/3D/Gale/trunk/src/Underworld/plugins/Output/DumpSwarm/
+\end_layout
+
+\begin_layout Standard
+There you can get info about particles; the rest is about the mesh.
+ Using
+\family typewriter
+DumpSwarm.c
+\family default
+ you can find out whether a particular particle has yielded or not.
+ If you want to print out some other property of the material, e.g., viscosity,
+ you can check DumpSwarm which will provide that information in addition
+ to whether the particle has yielded.
+\end_layout
+
+\begin_layout Section
Postprocessing
\end_layout
@@ -678,6 +878,173 @@
\end_layout
\begin_layout Chapter
+Modifying GALE
+\end_layout
+
+\begin_layout Section
+Introduction
+\end_layout
+
+\begin_layout Standard
+If you wish to change material properties, here is a brief overview of how
+ to modify the code.
+ The following is currently lacking in many areas, but will be expanded
+ and refined in future releases.
+
+\end_layout
+
+\begin_layout Section
+System Decription
+\end_layout
+
+\begin_layout Standard
+GALE, like StG_FEM, formulates implicit finite element systems, with the
+ bulk of the information placed in a stiffness matrix and a force vector.
+ Depending on the type of solver used there may be several matrices and
+ vectors.
+ The stiffness matrix class has a member whose purpose is to assemble the
+ entire matrix.
+ It does this through the use of
+\begin_inset Quotes eld
+\end_inset
+
+stiffness matrix terms.
+\begin_inset Quotes erd
+\end_inset
+
+ The
+\family typewriter
+StiffnessMatrixTerm
+\family default
+ class provides an interface through which the elemental contributions to
+ the matrix may be influenced.
+ In typical fluid flow systems, the majority of the physics is applied to
+ the model through constitutive laws which modify the stiffness matrix to
+ reflect certain physical situations.
+ The
+\family typewriter
+ConstitutiveMatrix
+\family default
+ class inherits from
+\family typewriter
+StiffnessMatrixTerm
+\family default
+, providing an interface tailored to implementing material based continuum
+ physics.
+
+\end_layout
+
+\begin_layout Standard
+So, where do the actual physics take place? The answer is in the Rheology
+ class, but first we need to look at the PIC (particle in cell) scheme.
+ There are a number of benefits to using a PIC scheme, but the main use
+ is to store material properties on each particle.
+ We can then use these properties to drive our constitutive laws, in turn
+ modifying the produced stiffness matrices.
+ For each defined material in the domain, there may be a number of associated
+ rheological laws.
+ Whenever an element in the system is assembled, each stiffness matrix term
+ is evaluated, implying that the consitutive matrix will be evaluated for
+ each element.
+ For each particle internal to an element, the
+\family typewriter
+ConstitutiveMatrix
+\family default
+ class will evaluate all associated rheologies, each rheology modifying
+ the constitutive matrix.
+
+\end_layout
+
+\begin_layout Standard
+Modifying the constitutive matrix takes place in the form of viscosity values.
+ In this, probably the simplest of rheological laws, the
+\family typewriter
+ModifyConstitutiveMatrix
+\family default
+ method simply sets a specific viscosity value for the current element/material
+ point tuple.
+
+\end_layout
+
+\begin_layout Section
+Sample Rheologies
+\end_layout
+
+\begin_layout Subsection
+Simple Viscous
+\end_layout
+
+\begin_layout Standard
+This excerpt is taken from the
+\family typewriter
+MaterialViscosity.c
+\family default
+ rheology file.
+ It has been inherited from the Rheology class and thus possesses a virtual
+ method named
+\family typewriter
+MaterialViscosity_ModifyConstitutiveMatrix
+\family default
+, which has been overridden to set the viscosity in the constitutive matrix,
+ as follows:
+\end_layout
+
+\begin_layout LyX-Code
+void _MaterialViscosity_ModifyConstitutiveMatrix(
+\end_layout
+
+\begin_layout LyX-Code
+ void* rheology,
+\end_layout
+
+\begin_layout LyX-Code
+ ConstitutiveMatrix* constitutiveMatrix,
+\end_layout
+
+\begin_layout LyX-Code
+ MaterialPointsSwarm* swarm,
+\end_layout
+
+\begin_layout LyX-Code
+ Element_LocalIndex lElement_I,
+\end_layout
+
+\begin_layout LyX-Code
+ MaterialPoint* materialPoint,
+\end_layout
+
+\begin_layout LyX-Code
+ Coord xi )
+\end_layout
+
+\begin_layout LyX-Code
+{
+\end_layout
+
+\begin_layout LyX-Code
+ MaterialViscosity* self = (MaterialViscosity*)rheology;
+\end_layout
+
+\begin_layout LyX-Code
+ ConstitutiveMatrix_SetIsotropicViscosity( constitutiveMatrix,
+\end_layout
+
+\begin_layout LyX-Code
+ self->eta0 );
+\end_layout
+
+\begin_layout LyX-Code
+}
+\end_layout
+
+\begin_layout Standard
+The parameters passed to this method provide access to the rheology class's
+ members/methods, the constitutive matrix, the swarm (material points),
+ the index of the element currently being assembled, the material point
+ currently being evaluated and the material point's elemental coordinates.
+\end_layout
+
+\begin_layout Chapter
Cookbook Examples
\end_layout
@@ -1483,5 +1850,25 @@
instead of this License.
\end_layout
+\begin_layout Bibliography
+
+\bibitem {key-1}
+ Moresi, L.
+ N., Dufour, F., Mühlhaus, H.-B.
+ A Lagrandian integration point finite element method for large deformation
+ modeling of viscoelastic geomaterials.
+
+\emph on
+J.
+ Comp.
+ Phys.
+
+\series bold
+\emph default
+184
+\series default
+, 476-497 (2003).
+\end_layout
+
\end_body
\end_document
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