[cig-commits] r14795 - doc/cigma/manual
luis at geodynamics.org
luis at geodynamics.org
Mon Apr 27 11:29:10 PDT 2009
Author: luis
Date: 2009-04-27 11:29:10 -0700 (Mon, 27 Apr 2009)
New Revision: 14795
Modified:
doc/cigma/manual/main2.lyx
Log:
Some suggestions from Walter
Modified: doc/cigma/manual/main2.lyx
===================================================================
--- doc/cigma/manual/main2.lyx 2009-04-27 18:29:00 UTC (rev 14794)
+++ doc/cigma/manual/main2.lyx 2009-04-27 18:29:10 UTC (rev 14795)
@@ -364,21 +364,12 @@
\end_layout
\begin_layout Standard
-[TODO something wrong with second half of this sentence.
-
-\begin_inset Quotes eld
-\end_inset
-
-and by modifying
-\begin_inset Quotes erd
-\end_inset
-
-?] and modifying the comma-delimited list passed to the
+These additional components can be passed as a comma-delimited list to the
+ option
\family typewriter
--with-libraries
\family default
- option when repeating the build procedure above.
-
+ as in the build procedure specified in
\end_layout
\begin_layout Subsection
@@ -2025,9 +2016,8 @@
\end_layout
\begin_layout Standard
-In general, you will provide data to Cigma as a simple two dimensional array
- of values.
- Now, because most scientific formats are capable of storing multiple datasets
+In general, you will provide data to Cigma as a simple array of values.
+ Because most scientific formats are capable of storing multiple datasets
in the same file, you will need a consistent way to select a specific array
on a given data file.
Therefore, all option arguments to Cigma that expect a dataset can be specified
@@ -2047,15 +2037,57 @@
location
\emph default
part of the option argument may be omitted.
- There are a number of different file formats available for specifying and
- storing your data, according to how Cigma was configured at build time.
- The file format will be derived directly from the
-\emph on
-filename
-\emph default
- extension.
+ For example, consider two HDF5 files,
+\begin_inset Quotes eld
+\end_inset
+
+low_res.h5
+\begin_inset Quotes erd
+\end_inset
+
+ and
+\begin_inset Quotes eld
+\end_inset
+
+high_res.h5
+\begin_inset Quotes erd
+\end_inset
+
+ which each have fields
+\begin_inset Quotes eld
+\end_inset
+
+density
+\begin_inset Quotes erd
+\end_inset
+
+ and
+\begin_inset Quotes eld
+\end_inset
+
+pressure
+\begin_inset Quotes erd
+\end_inset
+
+.
+ Then the command
\end_layout
+\begin_layout Standard
+cigma compare low_res.h5:density high_res.h5:density -o low_high.h5
+\end_layout
+
+\begin_layout Standard
+will compare the density fields between the two files on the mesh defined
+ in low_res.h5.
+\end_layout
+
+\begin_layout Standard
+Depending on how it was configured, Cigma understands a number of different
+ file formats.
+ The file format is determined by the filename extension.
+\end_layout
+
\begin_layout Section
Mesh Options
\end_layout
@@ -2125,7 +2157,6 @@
\family typewriter
\series bold
\size scriptsize
-\bar under
MeshA
\end_layout
@@ -2139,7 +2170,6 @@
\family typewriter
\series bold
\size scriptsize
-\bar under
MeshB
\end_layout
@@ -2153,7 +2183,6 @@
\family typewriter
\series bold
\size scriptsize
-\bar under
IntegrationMesh
\end_layout
@@ -2165,7 +2194,7 @@
\begin_layout Plain Layout
\size scriptsize
-Items Read
+Item
\end_layout
\end_inset
@@ -2437,17 +2466,17 @@
\begin_layout Standard
There are a number of rules determining which of these options are required.
For any of the
-\bar under
+\series bold
MeshA
-\bar default
+\series default
,
-\bar under
+\series bold
MeshB
-\bar default
+\series default
, and
-\bar under
+\series bold
IntegrationMesh
-\bar default
+\series default
columns in the table above, the relationship between these options is as
follows:
\end_layout
@@ -2525,11 +2554,7 @@
\end_layout
\begin_layout LyX-Code
-File
-\emph on
-
-\bar under
-filename
+File mesh.h5
\end_layout
\begin_layout LyX-Code
@@ -2540,37 +2565,24 @@
`Group
\emph on
-\bar under
-location
+\emph default
+/mesh
\end_layout
\begin_layout LyX-Code
- |--
-\emph on
-Attribute
-\emph default
-
+ |-- Attribute
\series bold
-\emph on
CellType
\end_layout
\begin_layout LyX-Code
- |--
-\emph on
-Array
-\emph default
-
+ |-- Array
\series bold
coordinates
\end_layout
\begin_layout LyX-Code
- `--
-\emph on
-Array
-\emph default
-
+ `-- Array
\series bold
connectivity
\end_layout
@@ -2650,55 +2662,19 @@
\end_layout
\begin_layout Enumerate
-At least one of
-\bar under
-MeshA
-\bar default
-,
-\bar under
-MeshB
-\bar default
-, or
-\bar under
-IntegrationMesh
-\bar default
- must be given.
+At least one of MeshA, MeshB, or IntegrationMesh must be given.
\end_layout
\begin_layout Enumerate
-If
-\bar under
-IntegrationMesh
-\bar default
- is specified, then it is always used.
+If IntegrationMesh is specified, then it is always used.
\end_layout
\begin_layout Enumerate
-If
-\bar under
-IntegrationMesh
-\bar default
- is missing, then
-\bar under
-MeshA
-\bar default
- is copied to
-\bar under
-IntegrationMesh
-\bar default
-.
+If IntegrationMesh is missing, then MeshA is copied to IntegrationMesh.
\end_layout
\begin_layout Enumerate
-If only
-\bar under
-MeshB
-\bar default
- is given, then it is copied to
-\bar under
-IntegrationMesh
-\bar default
-.
+If only MeshB is given, then it is copied to IntegrationMesh.
\end_layout
\begin_layout Standard
@@ -2974,8 +2950,16 @@
File
\emph on
-\bar under
-filename
+\emph default
+
+\begin_inset Quotes eld
+\end_inset
+
+model.h5
+\begin_inset Quotes erd
+\end_inset
+
+
\end_layout
\begin_layout LyX-Code
@@ -2983,59 +2967,40 @@
\emph on
\emph default
-
+ Group
\emph on
-Group
-\bar under
+
+\series bold
+\emph default
variables
\end_layout
\begin_layout LyX-Code
- |--
-\emph on
-Group
-\emph default
-
+ |-- Group
\series bold
temperature
\end_layout
\begin_layout LyX-Code
- | |--
-\emph on
-Array
-\emph default
-
+ | |-- Array
\series bold
step000
\end_layout
\begin_layout LyX-Code
- | | `--
-\emph on
-Attribute
-\emph default
-
+ | | `-- Attribute
\series bold
MeshLocation
\end_layout
\begin_layout LyX-Code
- | |--
-\emph on
-Array
-\emph default
-
+ | |-- Array
\series bold
step001
\end_layout
\begin_layout LyX-Code
- | | `--
-\emph on
-Attribute
-\emph default
-
+ | | `-- Attribute
\series bold
MeshLocation
\end_layout
@@ -3045,11 +3010,7 @@
\end_layout
\begin_layout LyX-Code
- `--
-\emph on
-Group
-\emph default
-
+ `-- Group
\series bold
displacements
\end_layout
@@ -3169,15 +3130,15 @@
\end_layout
\begin_layout LyX-Code
-$ cigma compare
+$ cigma compare A
\series bold
-A
-\series default
-\series bold
+\series default
B
+\series bold
+
\series default
- --verbose
+--verbose
\end_layout
\begin_layout Standard
@@ -3194,15 +3155,15 @@
\end_layout
\begin_layout LyX-Code
-$ cigma compare
+$ cigma compare A
\series bold
-A
-\series default
-\series bold
+\series default
B
+\series bold
+
\series default
- --verbose --timer-frequency=1000
+--verbose --timer-frequency=1000
\end_layout
\begin_layout Standard
@@ -3219,15 +3180,11 @@
\end_layout
\begin_layout LyX-Code
-$ cigma compare
+$ cigma compare A
\series bold
-A
-\series default
-\series bold
-B
\series default
- --debug
+B --debug
\end_layout
\begin_layout Standard
@@ -3248,15 +3205,11 @@
\end_layout
\begin_layout LyX-Code
-$ cigma compare
+$ cigma compare A
\series bold
-A
-\series default
-\series bold
-B
\series default
- --quiet --global-threshold=0.001
+B --quiet --global-threshold=0.001
\end_layout
\begin_layout Standard
@@ -3322,29 +3275,19 @@
\end_layout
\begin_layout LyX-Code
- -m
-\bar under
-MeshFile
-\bar default
-
+ -m MeshFile.h5
\backslash
\end_layout
\begin_layout LyX-Code
- -i
-\bar under
-InputResiduals.h5:/path
-\bar default
-
+ -i InputResiduals.h5:/path
\backslash
\end_layout
\begin_layout LyX-Code
- -o
-\bar under
-OutputResiduals.vtk
+ -o OutputResiduals.vtk
\end_layout
\begin_layout Standard
@@ -3401,9 +3344,7 @@
\end_layout
\begin_layout LyX-Code
-$ cigma mesh-info
-\series bold
-MESH
+$ cigma mesh-info MESH
\end_layout
\begin_layout Standard
@@ -3413,11 +3354,7 @@
\end_layout
\begin_layout LyX-Code
-$ cigma mesh-info
-\series bold
-MESH
-\series default
- --cell-id=N
+$ cigma mesh-info MESH --cell-id=N
\end_layout
\begin_layout Standard
@@ -3425,11 +3362,7 @@
\end_layout
\begin_layout LyX-Code
-$ cigma mesh-info
-\series bold
-MESH
-\series default
- --query-point=
+$ cigma mesh-info MESH --query-point=
\begin_inset Quotes erd
\end_inset
@@ -3489,11 +3422,7 @@
\end_layout
\begin_layout LyX-Code
-$ cigma function-info
-\series bold
-FUNCTION
-\series default
- --query-point=
+$ cigma function-info FUNCTION --query-point=
\begin_inset Quotes erd
\end_inset
@@ -3775,7 +3704,7 @@
\begin_layout Standard
\begin_inset Note Note
-status open
+status collapsed
\begin_layout Plain Layout
For example, querying
@@ -3950,9 +3879,14 @@
.
We summarize that information in the following tables,
+\begin_inset VSpace defskip
+\end_inset
+
+
\end_layout
\begin_layout Standard
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="7">
<features>
@@ -4243,6 +4177,13 @@
\end_layout
\begin_layout Standard
+\begin_inset VSpace defskip
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
It should become apparent from these results that the global error metric
\begin_inset Formula $\varepsilon$
@@ -4949,18 +4890,8 @@
\family default
.
-\begin_inset Note Note
-status open
-
-\begin_layout Plain Layout
-TODO: Include source code listing?
\end_layout
-\end_inset
-
-
-\end_layout
-
\begin_layout Standard
We can use Gale, a CIG code for long-term crustal dynamics, to obtain an
approximate solution to this circular inclusion problem.
@@ -5418,7 +5349,7 @@
Cigma can understand a number of file formats, depending on how it is configured
(see Chapter 2).
By default it will read and write all information in binary form as HDF5
- files, which is format optimal for archiving data with minimal redundancy.
+ files, which is a format optimal for archiving data with minimal redundancy.
VTK files are also sometimes used by finite element software, due to the
ease with which the solution fields can be visualized.
Lastly, ExodusII mesh files generated by the CUBIT mesh generation package
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