[cig-commits] [commit] master: Update build instructions in manual, and added list of cases to regenerate (3c28fba)

cig_noreply at geodynamics.org cig_noreply at geodynamics.org
Fri May 9 15:23:34 PDT 2014 

Repository : https://github.com/geodynamics/cigma

On branch  : master
Link       : https://github.com/geodynamics/cigma/compare/65c02138d3ae8b87c088cc14fe4f98e21e3f0805...a26f592c25c89a40622404999ba1effcdf6df9e3

>---------------------------------------------------------------

commit 3c28fba2e1bbf4295fc4d9a26b1c17161f30e5a2
Author: Luis Armendariz <luis>
Date:   Tue Jan 29 17:18:09 2008 +0000

    Update build instructions in manual, and added list of cases to regenerate


>---------------------------------------------------------------

3c28fba2e1bbf4295fc4d9a26b1c17161f30e5a2
 cigma.lyx        | 140 +++++++++++++++++++++++++++----------------------------
 figures/list.txt |  26 +++++++++++
 2 files changed, 96 insertions(+), 70 deletions(-)

diff --git a/cigma.lyx b/cigma.lyx
index a78e46f..4f398f1 100644
--- a/cigma.lyx
+++ b/cigma.lyx
@@ -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
@@ -219,23 +219,10 @@ Lastly, as an automated tool, Cigma can help developers in creating regression
 \end_layout
 
 \begin_layout Standard
-At its core, Cigma draws from a variety of libraries, particularly the 
-\begin_inset LatexCommand htmlurl
-name "Tetrahedral Mesh Comparator (TMC)"
-target "www.sci.utah.edu/~bavoil/research/tetsimp/tmc/"
-
-\end_inset
-
- from the University of Utah, which itself draws from the 
-\begin_inset LatexCommand htmlurl
-name "GTB Graphics Toolbox library"
-target "sf.net/projects/gtb"
-
-\end_inset
-
-.
- Cigma extends and generalizes the functionality therein to handle other
- types of elements as well as adding the ability to compare vector fields.
+At its core, Cigma draws from a variety of libraries, particularly the FIAT
+ Python Library from Cigma extends and generalizes the functionality therein
+ to handle other types of elements as well as adding the ability to compare
+ vector fields.
 \end_layout
 
 \begin_layout Section
@@ -345,6 +332,18 @@ target "geodynamics.org/cig/software/packages/cs/cigma"
 \end_layout
 
 \begin_layout LyX-Code
+$ tar xvfz cigma-0.9.1
+\end_layout
+
+\begin_layout LyX-Code
+$ cd cigma-0.9.1
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure --with-hdf5=$HDF5_PREFIX
+\end_layout
+
+\begin_layout LyX-Code
 $ make
 \end_layout
 
@@ -412,8 +411,8 @@ target "www.vtk.org/get-software.php"
 .
  If you obtain the binaries from a package manager, make sure to install
  the associated development headers along with the library.
- To enable VTK support in Cigma, use the following flags in the configure
- step:
+ To enable VTK support in Cigma, use the following additional flag in the
+ configure step for Cigma.
 \end_layout
 
 \begin_layout LyX-Code
@@ -421,6 +420,42 @@ target "www.vtk.org/get-software.php"
 \end_layout
 
 \begin_layout Subsection
+NumPy
+\end_layout
+
+\begin_layout Standard
+NumPy is a Python module which adds support for large multi-dimensional
+ arrays and matrices, and is available for download from [TODO]numpy.scipy.org.
+ To install this extension module from source, download it and issue the
+ following command in the NumPy source directory
+\end_layout
+
+\begin_layout Standard
+$ sudo python setup.py install[TODO:lyxcode]
+\end_layout
+
+\begin_layout Subsection
+FIAT
+\end_layout
+
+\begin_layout Standard
+The Finite Element Automatic Tabulator (FIAT) Python module supports generation
+ of arbitrary order instances of the Lagrange elements, as well as arbitrary
+ order instances of the Jacobi-type quadrature rules on the same element
+ shapes.
+ It is available from [TODO]http://www.fenics.org/wiki/FIAT
+\end_layout
+
+\begin_layout Standard
+To install this module, download it and issue the following command inside
+ the FIAT source directory:
+\end_layout
+
+\begin_layout Standard
+$ sudo python setup.py install[TODO:lyxcode]
+\end_layout
+
+\begin_layout Subsection
 PyTables
 \end_layout
 
@@ -791,6 +826,8 @@ This release of Cigma provides you with two built-in finite element spaces
  shown below.
  The location of each element is indexed into a spatial database in order
  to speed up the evaluation process.
+ [TODO: drop the tet4, hex8 images but keep the formulas --adding more element
+ types, so will use single image]
 \end_layout
 
 \begin_layout Standard
@@ -1465,10 +1502,6 @@ cigma set --target=file.h5:/model/vars/pressure/t10 --attribute=FunctionSpace
  --value=tet4
 \end_layout
 
-\begin_layout Standard
-
-\end_layout
-
 \begin_layout Section
 Comparing Two Fields
 \end_layout
@@ -1667,18 +1700,9 @@ cigma extract --mesh=field1.h5:/model/mesh/
 \end_layout
 
 \begin_layout Standard
-[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.
+At this point, one possibility would be to copy 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 LyX-Code
@@ -1714,10 +1738,6 @@ cigma copy --source=values.txt
 \end_layout
 
 \begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
 Lastly, you can provide the path to the explicit set of values with
 \end_layout
 
@@ -1733,10 +1753,6 @@ cigma compare --output=squared-residuals.vtk
               --second=values.h5:/stepN_values
 \end_layout
 
-\begin_layout Standard
-
-\end_layout
-
 \begin_layout Subsection
 Against a Known Function
 \end_layout
@@ -1840,22 +1856,6 @@ cigma compare --output=squared-residuals.vtk
 
 \end_layout
 
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-
-\end_layout
-
-\begin_layout Standard
-
-\end_layout
-
 \begin_layout Chapter
 Visualization
 \end_layout
@@ -1963,7 +1963,7 @@ reference "fig:Cube-domain-of"
 placement H
 wide false
 sideways false
-status collapsed
+status open
 
 \begin_layout Standard
 \noindent
@@ -2015,7 +2015,7 @@ The first benchmark problem (left) consists of a vertical right-lateral
 placement H
 wide false
 sideways false
-status collapsed
+status open
 
 \begin_layout Standard
 \noindent
@@ -2095,7 +2095,7 @@ reference "fig:PyLith-solution"
 placement H
 wide false
 sideways false
-status collapsed
+status open
 
 \begin_layout Standard
 \noindent
@@ -2156,7 +2156,7 @@ Slightly different behavior can be observed in the velocity field residuals.
 placement H
 wide false
 sideways false
-status collapsed
+status open
 
 \begin_layout Standard
 \noindent
@@ -2208,7 +2208,7 @@ n mesh (left: t=0 years, right: t=1 year).
 placement H
 wide false
 sideways false
-status collapsed
+status open
 
 \begin_layout Standard
 \noindent
@@ -2270,7 +2270,7 @@ Finally, here is a higher resolution comparison of the displacement residuals
 placement H
 wide false
 sideways false
-status collapsed
+status open
 
 \begin_layout Standard
 \noindent
@@ -2328,7 +2328,7 @@ You can also visualize the distribution of errors by plotting the residual
 placement H
 wide false
 sideways false
-status collapsed
+status open
 
 \begin_layout Standard
 \noindent
@@ -2380,7 +2380,7 @@ Reverse-slip: PyLith-GeoFEST comparison of velocity residuals on a 500m
 placement H
 wide false
 sideways false
-status collapsed
+status open
 
 \begin_layout Standard
 \noindent
@@ -2439,7 +2439,7 @@ tic layer.
 placement H
 wide false
 sideways false
-status collapsed
+status open
 
 \begin_layout Standard
 \noindent
@@ -2491,7 +2491,7 @@ Reverse-slip: PyLith-GeoFEST comparison of displacement residuals on a 500m
 placement H
 wide false
 sideways false
-status collapsed
+status open
 
 \begin_layout Standard
 \noindent
diff --git a/figures/list.txt b/figures/list.txt
new file mode 100644
index 0000000..06e6424
--- /dev/null
+++ b/figures/list.txt
@@ -0,0 +1,26 @@
+
+p0500 -> /pylith/tet4_0500m
+g0500 -> /pylith/tet4_0250m
+
+
+ssng-p0500-g0500-isosurf-disp-000.png
+ssng-p0500-g0500-isosurf-disp-100.png
+
+ssng-p0500-g0500-point-isosurf-velo-000.png
+ssng-p0500-g0500-point-isosurf-velo-010.png
+
+ssng-p0500-g0500-point-isosurf-velo-010.png
+ssng-p0500-g0500-point-isosurf-velo-100.png
+
+ssng-p0250-g0500-point-isosurf-disp-000.png
+
+rsng-p0500-g0500-cell-threshold-velo-010.png
+rsng-p0500-g0500-cell-threshold-velo-000.png
+
+rsng-p0500-g0500-cell-threshold-velo-050.png
+rsng-p0500-g0500-cell-threshold-velo-100.png
+
+rsng-p0500-g0500-point-isosurf-res-disp-000.png
+rsng-p0500-g0500-point-isosurf-res-disp-010.png
+rsng-p0500-g0500-point-isosurf-res-disp-050.png
+rsng-p0500-g0500-point-isosurf-res-disp-100.png

More information about the CIG-COMMITS mailing list