[cig-commits] r7697 - cs/cigma/branches/cigma-0.9b1/doc/manual
sue at geodynamics.org
sue at geodynamics.org
Wed Jul 18 11:41:03 PDT 2007
Author: sue
Date: 2007-07-18 11:41:03 -0700 (Wed, 18 Jul 2007)
New Revision: 7697
Modified:
cs/cigma/branches/cigma-0.9b1/doc/manual/cigma.lyx
Log:
edits and additions of todos
Modified: cs/cigma/branches/cigma-0.9b1/doc/manual/cigma.lyx
===================================================================
--- cs/cigma/branches/cigma-0.9b1/doc/manual/cigma.lyx 2007-07-18 18:37:29 UTC (rev 7696)
+++ cs/cigma/branches/cigma-0.9b1/doc/manual/cigma.lyx 2007-07-18 18:41:03 UTC (rev 7697)
@@ -193,10 +193,17 @@
\end_layout
\begin_layout Standard
-At its core, Cigma draws from a variety of libraries, particularly the Tetrahedr
-al Mesh Comparator (TMC) from the University of Utah (TODO: link to http://www.sc
-i.utah.edu/~bavoil/research/tetsimp/tmc/), which itself draws from the GTB
- Graphics Toolbox library (TODO: link to http://sf.net/projects/gtb).
+At its core, Cigma draws from a variety of libraries, particularly the
+\begin_inset LatexCommand \htmlurl[Tetrahedral Mesh Comparator (TMC)]{www.sci.utah.edu/~bavoil/research/tetsimp/tmc/}
+
+\end_inset
+
+ from the University of Utah, which itself draws from the
+\begin_inset LatexCommand \htmlurl[GTB Graphics Toolbox library]{sf.net/projects/gtb}
+
+\end_inset
+
+.
Cigma extends and generalizes the functionality therein to handle other
types of elements and be able to compare vector fields.
\end_layout
@@ -228,7 +235,7 @@
CIG requests that in your oral presentations and in your papers that you
indicate your use of this code and acknowledge the author of the code and
-\begin_inset LatexCommand \htmlurl[CIG]{www.geodynamics.org}
+\begin_inset LatexCommand \htmlurl[CIG]{geodynamics.org}
\end_inset
@@ -374,7 +381,7 @@
placement H
wide false
sideways false
-status open
+status collapsed
\begin_layout Caption
With HFDFView, you can view the internal file hierarchy in a tree structure,
@@ -555,8 +562,12 @@
\end_inset
by applying an appropriate quadrature rule with a tolerable truncation
- error (TODO: add Encyclopedia of Cubature Formulas to bibliography, link
- http://www.cs.kuleuven.be/~nines/research/ecf/).
+ error
+\begin_inset LatexCommand \cite{Encyclopaedia of Cubature Formulas 2005}
+
+\end_inset
+
+.
\end_layout
\begin_layout Standard
@@ -582,7 +593,7 @@
\end_layout
\begin_layout Standard
-and thus we arrive at the final form
+thus we arrive at the final form
\end_layout
\begin_layout Standard
@@ -599,7 +610,7 @@
\begin_inset Formula $\rho$
\end_inset
-, Cigma will output of each the local contributions
+, Cigma will output each of the local contributions
\begin_inset Formula $\varepsilon_{e}^{2}$
\end_inset
@@ -653,8 +664,8 @@
\begin_inset Formula $\Omega_{e}=\{ n_{1},n_{2},\ldots\}$
\end_inset
-among them which define each individual element in the corresponding discretizat
-ion.
+ among them which define each individual element in the corresponding discretiza
+tion.
\end_layout
\begin_layout Section
@@ -691,6 +702,12 @@
\end_layout
+\begin_layout Standard
+
+\newpage
+
+\end_layout
+
\begin_layout Subsubsection*
Function Space
\bar under
@@ -740,6 +757,12 @@
\end_layout
+\begin_layout Standard
+
+\newpage
+
+\end_layout
+
\begin_layout Subsubsection*
Function Space
\bar under
@@ -756,7 +779,7 @@
status open
\begin_layout Caption
-Need reference-hex8.png caption.
+TODO: Need reference-hex8.png caption.
\end_layout
\begin_layout Standard
@@ -798,7 +821,7 @@
\end_layout
\begin_layout Standard
-There are various reasons to use We use HDF5 for the following reasons
+There are various reasons to use HDF5:
\end_layout
\begin_layout Enumerate
@@ -808,6 +831,7 @@
\begin_layout Enumerate
In order to support large finite element meshes efficiently...
+ [Luis TODO]
\end_layout
\begin_layout Enumerate
@@ -863,7 +887,7 @@
\begin_layout Standard
Each field keeps a certain amount of metadata that allows Cigma to correctly
- interpret the meaning of the field data
+ interpret the meaning of the field data.
\end_layout
\begin_layout Description
@@ -876,8 +900,8 @@
\end_layout
\begin_layout Description
-FunctionSpace identifies which shape functions for interpolating values
- inside the element.
+FunctionSpace identifies which shape functions to use for interpolating
+ values inside the element.
\end_layout
\begin_layout Chapter
@@ -889,9 +913,12 @@
\end_layout
\begin_layout Standard
-To compare two fields, use the cigma-compare (TODO: tty font) command line
- utility.
- The
+To compare two fields, use the
+\family typewriter
+cigma-compare
+\family default
+ command line utility.
+ The [Luis TODO]
\end_layout
\begin_layout LyX-Code
@@ -1005,7 +1032,7 @@
\end_layout
\begin_layout Standard
-The effect of this command is to create a file with the following structure
+The effect of this command is to create a file with the following structure:
\end_layout
\begin_layout LyX-Code
@@ -1045,56 +1072,324 @@
\end_layout
\begin_layout Standard
-(TODO: move file formats from appendix to here)
+Cigma can easily import datasets from simple text files consisting of a
+ single header line followed by data.
+ The header consists of two numbers, the first of which consists of the
+ number of lines to read next, and the second number representing the number
+ of columns to read on each line.
+ Thus, after the header, each of the lines begin with the appropriate row
+ number, followed by the requisite number of columns.
+ For simplicity, the maximum line size is 1024, and lines beginning with
+ the '#' character are skipped.
+\newline
+
+\newline
+Mesh coordinates can be specified in the following
+ format
\end_layout
+\begin_layout LyX-Code
+nno nsd
+\end_layout
+
+\begin_layout LyX-Code
+1 x1 y1 z1
+\end_layout
+
+\begin_layout LyX-Code
+2 x2 y2 z2
+\end_layout
+
+\begin_layout LyX-Code
+3 x3 y3 z3
+\end_layout
+
+\begin_layout LyX-Code
+...
+\end_layout
+
+\begin_layout Standard
+Mesh connectivity with
+\end_layout
+
+\begin_layout LyX-Code
+nel ndof
+\end_layout
+
+\begin_layout LyX-Code
+1 node_1 node_2 node_3 node_4 ...
+\end_layout
+
+\begin_layout LyX-Code
+2 node_1 node_2 node_3 node_4 ...
+\end_layout
+
+\begin_layout LyX-Code
+3 node_1 node_2 node_3 node_4 ...
+\end_layout
+
+\begin_layout LyX-Code
+...
+\end_layout
+
+\begin_layout Standard
+A generic field with
+\family typewriter
+ndim
+\family default
+ components is specified by
+\end_layout
+
+\begin_layout LyX-Code
+nno ndim
+\end_layout
+
+\begin_layout LyX-Code
+1 f1 f2 f3 ..
+\end_layout
+
+\begin_layout LyX-Code
+2 f1 f2 f3 ..
+\end_layout
+
+\begin_layout LyX-Code
+...
+\end_layout
+
+\begin_layout Standard
+A quadrature rule may be explicitly specified by
+\end_layout
+
+\begin_layout LyX-Code
+nq nsd
+\end_layout
+
+\begin_layout LyX-Code
+w1 x1 y1 z1
+\end_layout
+
+\begin_layout LyX-Code
+w2 x2 y2 z2
+\end_layout
+
+\begin_layout LyX-Code
+...
+\end_layout
+
\begin_layout Chapter
Visualization
\end_layout
\begin_layout Standard
-As can be seen from Figures X and Y (TODO: insert ssng_tet4_1000m_pylith_disp_t0
-0.png and ssng_tet4_1000m_pylith_disp_t00.png), simply visualizing two different
- solutions side by side does not give you enough insight into their actual
- differences.
+As can be seen from Figures
+\begin_inset LatexCommand \ref{fig:PyLith-solution}
+
+\end_inset
+
+ and
+\begin_inset LatexCommand \ref{fig:GeoFEST-solution}
+
+\end_inset
+
+, simply visualizing two different solutions side by side does not give
+ you enough insight into their actual differences.
By using Cigma to calculate the residual field between them, you can get
a better idea for how the local contributions to the global error are distribut
ed both spatially and temporally.
\end_layout
+\begin_layout Standard
+\noindent
+\align left
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\align left
+\begin_inset Graphics
+ filename figures/ssng_tet4_1000m_pylith_disp_t00.png
+ lyxscale 30
+ width 30page%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+\noindent
+\begin_inset LatexCommand \label{fig:PyLith-solution}
+
+\end_inset
+
+PyLith solution.
+ [TODO: check caption, is this enough?]
+\end_layout
+
+\end_inset
+
+
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Standard
+\noindent
+\align left
+\begin_inset Graphics
+ filename figures/ssng_tet4_1000m_geofest_disp_t00.png
+ lyxscale 30
+ width 30page%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Caption
+\noindent
+\begin_inset LatexCommand \label{fig:GeoFEST-solution}
+
+\end_inset
+
+GeoFEST solution.
+ [TODO: check caption, is this enough?]
+\end_layout
+
+\end_inset
+
+ [Sue TODO: make these solutions side-by-side]
+\end_layout
+
\begin_layout Section
Benchmark cases
\end_layout
\begin_layout Standard
Here we compare the output from two codes, PyLith-0.8 and GeoFEST-4.5, on
- two benchmark cases defined by the CIG Short-Term Tectonics working group
- (TODO: link to http://www.geodynamics.org/cig/workinggroups/short/workarea/benchm
-arks/).
- They are both defined on cube domain (TODO: Figure X) with sides of length
- of 24 km, consisting of two layers of different material types.
+ two
+\begin_inset LatexCommand \htmlurl[benchmark cases]{geodynamics.org/cig/workinggroups/short/workarea/benchmarks}
+
+\end_inset
+
+ defined by the CIG Short-Term Tectonics working group.
+ They are both defined on cube domain (Figure
+\begin_inset LatexCommand \ref{fig:PyLith-solution}
+
+\end_inset
+
+) with sides having a length of 24 km, consisting of two layers of different
+ material types.
The top layer is nearly elastic while the bottom layer is viscoelastic.
A symmetric boundary condition is also imposed on the y=0 plane.
\end_layout
\begin_layout Standard
-(TODO: insert figures/layers.png)
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+\noindent
+Cube domain of 24 km length consisting of two layers of different material
+ types.
\end_layout
\begin_layout Standard
+\noindent
+\align center
+\begin_inset Graphics
+ filename figures/layers.png
+ lyxscale 50
+ scale 50
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
The first benchmark problem consists of a vertical right-lateral strike-slip
- fault (TODO: insert figures/strike-slip-fault.png).
+ fault.
\end_layout
\begin_layout Standard
-The second benchmark problem consists of a 45 degree dipping reverse fault
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Benchmark problem consisting of a vertical right-lateral strike-slip fault.
\end_layout
\begin_layout Standard
-(TODO: insert figures/reverse-slip-fault.png).
+\begin_inset Graphics
+ filename figures/strike-slip-fault.png
+ lyxscale 50
+ scale 50
+
+\end_inset
+
+
\end_layout
+\end_inset
+
+
+\end_layout
+
\begin_layout Standard
+The second benchmark problem consists of a 45-degree dipping reverse fault.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Benchmark problem consisting of a 45-degree dipping reverse fault.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Graphics
+ filename figures/reverse-slip-fault.png
+ lyxscale 50
+ scale 50
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
In both cases we solve for the displacement and vector fields at various
time steps, namely 0, 10, 50, and 100 years.
All plots show the distribution of the squared residual error
@@ -1107,10 +1402,14 @@
\begin_layout Standard
Here, we show ten equally spaced isosurfaces of the displacement field residuals
for the strike-slip benchmark (0 and 100 years shown).
- In Figure X (TODO), we see that the differences are very localized at t=0
- years.
+ In Figure
+\begin_inset LatexCommand \ref{fig:PyLith-solution}
+
+\end_inset
+
+, we see that the differences are very localized at t=0 years.
There is not much difference between time steps at t=10, 50 and 100 years,
- so we only show the last time step.
+ so we are only showing the last time step.
Note that the maximum errors are localized to the interface between the
two layers and the symmetric boundary.
\end_layout
@@ -1369,7 +1668,7 @@
\begin_layout Standard
You can also visualize the distribution of errors by plotting the residual
field value over the surface of each cell and applying a threshold filter
- which eliminates cells outside an threshold interval.
+ which eliminates cells outside a threshold interval.
Here, we show how velocity field residuals in the reverse-slip benchmark
are distributed temporally by throwing away all squared residuals lower
than
@@ -1644,111 +1943,6 @@
\begin_layout Chapter
\start_of_appendix
-Text Input File Formats
-\end_layout
-
-\begin_layout Standard
-Cigma can easily import datasets from simple text files consisting of a
- single header line followed by data.
- The header consists of two numbers, the first of which consists of the
- number of lines to read next, and the second number representing the number
- of columns to read on each line.
- Thus, after the header, each of the lines begin with the appropriate row
- number, followed by the requisite number of columns.
- For simplicity, the maximum line size is 1024, and lines beginning with
- the '#' character are skipped.
-\newline
-
-\newline
-Mesh coordinates can specified in the following
- format
-\end_layout
-
-\begin_layout LyX-Code
-nno nsd
-\end_layout
-
-\begin_layout LyX-Code
-1 x1 y1 z1
-\end_layout
-
-\begin_layout LyX-Code
-2 x2 y2 z2
-\end_layout
-
-\begin_layout LyX-Code
-3 x3 y3 z3
-\end_layout
-
-\begin_layout LyX-Code
-...
-\end_layout
-
-\begin_layout Standard
-Mesh connectivity with
-\end_layout
-
-\begin_layout LyX-Code
-nel ndof
-\end_layout
-
-\begin_layout LyX-Code
-1 node_1 node_2 node_3 node_4 ...
-\end_layout
-
-\begin_layout LyX-Code
-2 node_1 node_2 node_3 node_4 ...
-\end_layout
-
-\begin_layout LyX-Code
-3 node_1 node_2 node_3 node_4 ...
-\end_layout
-
-\begin_layout LyX-Code
-...
-\end_layout
-
-\begin_layout Standard
-A generic field with ndim components would be specified by
-\end_layout
-
-\begin_layout LyX-Code
-nno ndim
-\end_layout
-
-\begin_layout LyX-Code
-1 f1 f2 f3 ..
-\end_layout
-
-\begin_layout LyX-Code
-2 f1 f2 f3 ..
-\end_layout
-
-\begin_layout LyX-Code
-...
-\end_layout
-
-\begin_layout Standard
-A quadrature rule may be explicitly specified by
-\end_layout
-
-\begin_layout LyX-Code
-nq nsd
-\end_layout
-
-\begin_layout LyX-Code
-w1 x1 y1 z1
-\end_layout
-
-\begin_layout LyX-Code
-w2 x2 y2 z2
-\end_layout
-
-\begin_layout LyX-Code
-...
-\end_layout
-
-\begin_layout Chapter
Shape Functions
\end_layout
@@ -3024,7 +3218,7 @@
\begin_layout Bibliography
-\bibitem [Akin2005]{key-1}
+\bibitem [1]{Akin 2005}
Akin, J.E.
(2005),
\emph on
@@ -3036,7 +3230,26 @@
\begin_layout Bibliography
-\bibitem [Karniadakis-Sherwin2005]{key-2}
+\bibitem [2]{Encyclopaedia of Cubature Formulas 2005}
+Encyclopaedia of Cubature Formulas (1998-2005), Katholieke Universiteit
+ Leuven, Dept.
+ Computerwetenschappen, www.cs.kuleuven.be/~nines/research/ecf/
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [3]{Hughes 2000}
+Hughes, Thomas J.R.
+ (2000),
+\emph on
+The Finite Element Method: Linear Static and Dynamic Finite Element Analysis
+\emph default
+, Dover, 672 pp.
+\end_layout
+
+\begin_layout Bibliography
+
+\bibitem [4]{KarniadakisSherwin2005}
Karniadakis, George E.
and Spencer J.
Sherwin (2005),
@@ -3052,7 +3265,7 @@
\begin_layout Bibliography
-\bibitem [Uesu-etal2005]{key-3}
+\bibitem [5]{Uesu-etal2005}
Uesu, D., L.
Bavoil, S.
Fleishman, J.
@@ -3065,12 +3278,5 @@
157-165, doi: 10.2312/VG/VG05/157-165.
\end_layout
-\begin_layout Bibliography
-
-\bibitem {key-4}
-TODO: Add Hughes book as first bibliography entry (see http://www.amazon.com/Finit
-e-Element-Method-Dynamic-Analysis/dp/0486411818 for info)
-\end_layout
-
\end_body
\end_document
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