[cig-commits] [commit] master: fixed some formatting that somehow disappeared; some typos; added TODO for Luis regarding prob w/sentence; improved figure placement and relation to captions (610f2d4)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Fri May 9 15:23:28 PDT 2014
Repository : https://github.com/geodynamics/cigma
On branch : master
Link : https://github.com/geodynamics/cigma/compare/65c02138d3ae8b87c088cc14fe4f98e21e3f0805...a26f592c25c89a40622404999ba1effcdf6df9e3
>---------------------------------------------------------------
commit 610f2d46c726849791f513210c00b1228f2560ae
Author: Sue Kientz <sue>
Date: Tue Jan 22 19:57:48 2008 +0000
fixed some formatting that somehow disappeared; some typos; added TODO for Luis regarding prob w/sentence; improved figure placement and relation to captions
>---------------------------------------------------------------
610f2d46c726849791f513210c00b1228f2560ae
cigma.lyx | 325 +++++++++++++++++++++++++++++++++-----------------------------
cigma.pdf | Bin 6336492 -> 6354835 bytes
2 files changed, 175 insertions(+), 150 deletions(-)
diff --git a/cigma.lyx b/cigma.lyx
index 29e064d..34bd313 100644
--- a/cigma.lyx
+++ b/cigma.lyx
@@ -250,7 +250,7 @@ Computational Infrastructure for Geodynamics (CIG) is making this source
for use as citations other than this manual, which is cited as follows:
\end_layout
-\begin_layout Standard
+\begin_layout Itemize
Armendariz, L., and S.
Kientz.
@@ -344,11 +344,11 @@ target "geodynamics.org/cig/software/packages/cs/cigma"
commands
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$ make
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$ sudo make install
\end_layout
@@ -377,23 +377,23 @@ target "hdfgroup.org/HDF5/release/obtain5.html"
(currently 1.6.5) and issue the following commands
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$ tar xvfz hdf5-1.6.5
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$ cd hdf5-1.6.5
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$ ./configure
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$ make
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$ sudo make install
\end_layout
@@ -416,7 +416,7 @@ target "www.vtk.org/get-software.php"
step:
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
./configure --with-vtk=/path/to/vtk
\end_layout
@@ -443,15 +443,15 @@ To install this extension from source, download the latest stable version
(currently 2.0) and issue the following commands
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$ tar xvfz pytables-2.x
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$ cd pytables-2.x
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$ sudo python setup.py install
\end_layout
@@ -484,12 +484,12 @@ sideways false
status collapsed
\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-With HFDFView, you can view the internal file hierarchy in a tree structure,
- add new datasets, and modify or delete existing datasets.
-\end_layout
+\noindent
+\align center
+\begin_inset Graphics
+ filename figures/hdfview-bmrsnog.png
+ lyxscale 70
+ width 70page%
\end_inset
@@ -497,12 +497,12 @@ With HFDFView, you can view the internal file hierarchy in a tree structure,
\end_layout
\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename figures/hdfview-bmrsnog.png
- lyxscale 70
- width 70page%
+\begin_inset Caption
+
+\begin_layout Standard
+With HFDFView, you can view the internal file hierarchy in a tree structure,
+ add new datasets, and modify or delete existing datasets
+\end_layout
\end_inset
@@ -703,7 +703,7 @@ In calculating the norm of the residual field
.
\end_layout
-\begin_layout Standard
+\begin_layout Chapter
Cigma Components
\end_layout
@@ -812,7 +812,20 @@ tet4
placement H
wide false
sideways false
-status collapsed
+status open
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Graphics
+ filename figures/reference-tet4.png
+ lyxscale 35
+ width 35page%
+
+\end_inset
+
+
+\end_layout
\begin_layout Standard
\begin_inset Caption
@@ -827,16 +840,6 @@ Reference tetrahedral element
\end_layout
\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename figures/reference-tet4.png
- lyxscale 35
- width 35page%
-
-\end_inset
-
-
\begin_inset Formula \begin{eqnarray*}
TN_{a} & = & \frac{1}{2}(-1-x-y-z)\\
TN_{b} & = & \frac{1}{2}(1+x)\\
@@ -872,7 +875,20 @@ hex8
placement H
wide false
sideways false
-status collapsed
+status open
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Graphics
+ filename figures/reference-hex8.png
+ lyxscale 35
+ width 35page%
+
+\end_inset
+
+
+\end_layout
\begin_layout Standard
\begin_inset Caption
@@ -887,16 +903,6 @@ Reference hexahedral element
\end_layout
\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename figures/reference-hex8.png
- lyxscale 35
- width 35page%
-
-\end_inset
-
-
\begin_inset Formula \begin{eqnarray*}
HN_{a} & = & \frac{1}{8}\left(1-x\right)\left(1-y\right)\left(1-z\right)\\
HN_{b} & = & \frac{1}{8}\left(1+x\right)\left(1-y\right)\left(1-z\right)\\
@@ -1230,9 +1236,8 @@ Since Cigma relies so much on being able to specify dataset paths, we have
\family typewriter
list
\family default
- for viewing the structure of input file.
- Its usage is very simple:
-\newline
+ for viewing the structure of the input file.
+ Its usage is very simple.
\end_layout
@@ -1240,54 +1245,58 @@ list
To view the structure of an HDF5 file:
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$
\series bold
cigma list file.h5
\end_layout
-\begin_layout Standard
+\begin_deeper
+\begin_layout LyX-Code
/mesh/coordinates Dataset {119827, 3}
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
/mesh/connectivity Dataset {661929, 4}
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
/vars/displacement/step0 Dataset {119827, 3}
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
/residuals/comparison0 Dataset {661929, 1}
\end_layout
+\end_deeper
\begin_layout Standard
If VTK support is enabled, you can view the structure of a VTK file with:
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
$
\series bold
cigma list file.vtk
\end_layout
-\begin_layout Standard
+\begin_deeper
+\begin_layout LyX-Code
Reading file.vtk
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
Points = 119827
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
Cells = 661929
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
PointDataArray[0] = displacements_t0 (119827 x 3)
\end_layout
+\end_deeper
\begin_layout Section
Converting Data
\end_layout
@@ -1302,27 +1311,25 @@ cigma copy
By default, it relies on the file extension to detect what format to use
when reading or writing data.
Various examples are given below.
-\newline
-
\end_layout
\begin_layout Standard
Usage is typically
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma copy <source-path> <destination-path>
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma copy --source=<path> --destination=<path>
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma copy -s <path> -d <path>
@@ -1332,13 +1339,13 @@ cigma copy -s <path> -d <path>
To dump the mesh information into a text file:
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma copy --source=file.h5:/model/mesh/coords --destination=model-coords.txt
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma copy --source=file.h5:/model/mesh/connect --destination=model-connect.txt
@@ -1352,7 +1359,7 @@ pressure0
from a VTK file into an HDF5 file:
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma copy --source=file.vtk:pressure0 --destination=file.h5:/model/variables/pres
@@ -1367,7 +1374,7 @@ displacement15
from a VTK file into an HDF5 file:
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma copy --source=file.vtk:displacement15 --destination=file.h5:/model/variables
@@ -1378,23 +1385,19 @@ cigma copy --source=file.vtk:displacement15 --destination=file.h5:/model/variabl
To convert residual data into a VTK file, and then into ASCII:
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma copy --source=file.h5:/model/residuals/pressure0 --destination=pressure0-re
siduals.vtk
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma copy --source=pressure0-residuals.vtk --destination=residuals.txt
\end_layout
-\begin_layout Standard
-
-\end_layout
-
\begin_layout Section
Metadata
\end_layout
@@ -1411,13 +1414,13 @@ As described in a previous chapter on the HDF5 input files, you can attach
Usage is typically:
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma set <target-object-path> <attribute-name>[:<type>] <value>
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma get <target-object-path> [<attribute>]
@@ -1429,33 +1432,33 @@ cigma get <target-object-path> [<attribute>]
For example,
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma set --target=file.h5:/model/ --attribute=AUTHOR --value='John Doe'
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma set --target=file.h5:/model/vars/pressure --attribute=Units --value=MPa
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma set --target=file.h5:/model/vars/pressure/t10 --attribute=Step:int32
--value=10
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma set --target=file.h5:/model/vars/pressure/t10 --attribute=MeshID:int32
--value=1234
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\size small
cigma set --target=file.h5:/model/vars/pressure/t10 --attribute=FunctionSpace
@@ -1474,7 +1477,7 @@ Comparing Two Fields
Comparing two arbitrary finite element fields can be accomplished with the
\family typewriter
-`cigma compare'
+cigma compare
\family default
command line utility.
By default, the comparison will take place over the elements in the mesh
@@ -1489,25 +1492,27 @@ Comparing two arbitrary finite element fields can be accomplished with the
A basic comparison can be as simple as specifying the following arguments:
\end_layout
-\begin_layout Standard
-
-\series bold
+\begin_layout LyX-Code
cigma compare --output=squared-residuals.vtk
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\series bold
+
+\series default
--first=field1.h5:/field1/stepN
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\series bold
+
+\series default
--second=field2.h5:/field2/stepN
\end_layout
@@ -1520,17 +1525,17 @@ To override the mesh used in the integration, you can specify an extra argument
providing the location of the mesh:
\end_layout
-\begin_layout Standard
-
-\series bold
+\begin_layout LyX-Code
cigma compare --mesh=mesh.h5:/model/mesh/
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\series bold
+
+\series default
[...]
\end_layout
@@ -1539,25 +1544,27 @@ You can also specify the coordinates and connectivity arrays separately,
in case they reside in separate files.
\end_layout
-\begin_layout Standard
-
-\series bold
+\begin_layout LyX-Code
cigma compare --mesh-coordinates=file1.h5:/model/mesh/coordinates
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\series bold
+
+\series default
--mesh-connectivity=file2.h5:/model/mesh/connectivity
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\series bold
+
+\series default
[...]
\end_layout
@@ -1571,17 +1578,17 @@ If you wish to specify your own quadrature rule, you will have to provide
This can be done with the following additional argument:
\end_layout
-\begin_layout Standard
-
-\series bold
+\begin_layout LyX-Code
cigma compare --rule=quadrature-rules.h5:/path/to/rule
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\series bold
+
+\series default
[...]
\end_layout
@@ -1589,30 +1596,28 @@ cigma compare --rule=quadrature-rules.h5:/path/to/rule
You may also specify the location of the points and weights separately:
\end_layout
-\begin_layout Standard
-
-\series bold
+\begin_layout LyX-Code
cigma compare --rule-points=file.h5:/path/to/rule/points
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\series bold
+
+\series default
--rule-weights=file.h5:/path/to/rule/weights
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\series bold
- [...]
-\end_layout
-
-\begin_layout Standard
+\series default
+ [...]
\end_layout
\begin_layout Standard
@@ -1620,17 +1625,17 @@ Alternatively, to perform a pointwise comparison at random sample points
inside each element in the first mesh,
\end_layout
-\begin_layout Standard
-
-\series bold
+\begin_layout LyX-Code
cigma compare --samples-per-element=1
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\series bold
+
+\series default
[...]
\end_layout
@@ -1651,51 +1656,60 @@ First, extract the global coordinates of the integration points.
field.
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
cigma extract --mesh=field1.h5:/model/mesh/
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
--output=points.h5:/points
\end_layout
\begin_layout Standard
-At this point, one possibility would be to dump explicit the list of points
- to a text file, generate the corresponding list of values on your own and
- import that lsit of values back into an HDF5 file that Cigma can understand.
+[TODO: Luis, word
+\begin_inset Quotes sld
+\end_inset
+
+explicit
+\begin_inset Quotes srd
+\end_inset
+
+ here seems misplaced.] At this point, one possibility would be to dump explicit
+ the list of points to a text file, generate the corresponding list of values
+ on your own and import that list of values back into an HDF5 file that
+ Cigma can understand.
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
cigma copy --source=points.h5:/points
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
--destination=points.txt
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
# create values.txt
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
cigma copy --source=values.txt
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
--destination=values.h5:/stepN_values
\end_layout
@@ -1707,15 +1721,15 @@ cigma copy --source=values.txt
Lastly, you can provide the path to the explicit set of values with
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
cigma compare --output=squared-residuals.vtk
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
--first=field1.h5:/field1/stepN
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
--second=values.h5:/stepN_values
\end_layout
@@ -1729,7 +1743,7 @@ Against a Known Function
\begin_layout Standard
If one of your fields is easily described by an analytic expression, then
- you also have the option to compile your analytic function into cigma,
+ you also have the option to compile your analytic function into Cigma,
which will enable the
\family typewriter
compare
@@ -1737,82 +1751,92 @@ compare
command to reference your function by name:
\end_layout
-\begin_layout Standard
-
-\series bold
+\begin_layout LyX-Code
cigma compare --output=squared-residuals.vtk
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\series bold
+
+\series default
--first=field1.h5:/vars/displacement/step0
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\series bold
+
+\series default
--second=
\bar under
disloc3d
-\series default
+\series bold
\bar default
-\series bold
+\series default
\end_layout
\begin_layout Standard
You may also interact with your analytic function by using the
\family typewriter
-cigma eval
+cigma
+\family default
+
+\family typewriter
+eval
\family default
command, and obtain a set of values which may then be passed back to the
- compare command.
+
+\family typewriter
+compare
+\family default
+ command.
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
cigma eval --function=disloc3d
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
--points=points.h5:/points
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
--values=values.h5:/disloc3d_values
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
cigma compare --output=squared-residuals.vtk
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
--first=field1.h5:/vars/displacement/step0
\backslash
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
--second=values.h5:/disloc3d_values
\end_layout
-\begin_layout Standard
+\begin_layout LyX-Code
\end_layout
@@ -1846,8 +1870,8 @@ reference "fig:PyLith-solution"
, 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.
+ a better idea of how the local contributions to the global error are distribute
+d both spatially and temporally.
\end_layout
\begin_layout Standard
@@ -1857,7 +1881,7 @@ ed both spatially and temporally.
placement H
wide false
sideways false
-status collapsed
+status open
\begin_layout Standard
\align center
@@ -2973,6 +2997,7 @@ Applying these to our shape functions on a tetrahedron, we obtain
\end_layout
\begin_layout Standard
+\align center
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="5">
<features>
diff --git a/cigma.pdf b/cigma.pdf
index 2313489..68d5ae0 100644
Binary files a/cigma.pdf and b/cigma.pdf differ
More information about the CIG-COMMITS
mailing list