[cig-commits] [commit] master: Manual update (6ff07cf)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Fri May 9 15:24:28 PDT 2014
Repository : https://github.com/geodynamics/cigma
On branch : master
Link : https://github.com/geodynamics/cigma/compare/65c02138d3ae8b87c088cc14fe4f98e21e3f0805...a26f592c25c89a40622404999ba1effcdf6df9e3
>---------------------------------------------------------------
commit 6ff07cf3f61a10351ea589850bd94b1b0ecf6a9f
Author: Luis Armendariz <luis>
Date: Thu Jul 31 17:58:23 2008 +0000
Manual update
>---------------------------------------------------------------
6ff07cf3f61a10351ea589850bd94b1b0ecf6a9f
cigma.lyx | 374 ++++++++++++++++++++++++------------------------
cigma.lyx => cigma.lyx~ | 370 +++++++++++++++++++++++------------------------
2 files changed, 374 insertions(+), 370 deletions(-)
diff --git a/cigma.lyx b/cigma.lyx
index 8b7dfdd..8bd0199 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 1.5.4 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -116,7 +116,7 @@ Cigma
\begin_layout Author
© California Institute of Technology
\newline
-Version 0.9.1
+Version 1.0.0
\end_layout
\begin_layout Date
@@ -347,7 +347,8 @@ target "geodynamics.org/cig/software/packages/cs/cigma"
.
You will need the GNU C++ compiler for this step.
- The HDF5 and VTK libraries, described later in this section, are also required.
+ The Boost, HDF5, and VTK libraries, described later in this section, are
+ also required.
\end_layout
\begin_layout Standard
@@ -356,15 +357,23 @@ After installing the necessary dependencies, simply unpack the source tar
\end_layout
\begin_layout LyX-Code
-$ tar xvfz cigma-0.9.1.tar.gz
+$ tar xvfz cigma-1.0.0.tar.gz
\end_layout
\begin_layout LyX-Code
-$ cd cigma-0.9.1
+$ cd cigma-1.0.0
\end_layout
\begin_layout LyX-Code
-$ ./configure --with-hdf5=$HDF5_PREFIX --with-vtk=$VTK_PREFIX
+$ ./configure --with-boost=$BOOST_PREFIX
+\end_layout
+
+\begin_layout LyX-Code
+ --with-hdf5=$HDF5_PREFIX
+\end_layout
+
+\begin_layout LyX-Code
+ --with-vtk=$VTK_PREFIX
\end_layout
\begin_layout LyX-Code
@@ -381,6 +390,43 @@ Both HDF5 and VTK prefixes are required if you have installed these libraries
\end_layout
\begin_layout Subsection
+Boost
+\end_layout
+
+\begin_layout Standard
+The Boost C++ libraries are used in Cigma for parsing command-line options,
+ and ensuring cross-platform access to the filesystem.
+\end_layout
+
+\begin_layout LyX-Code
+$ tar xvfz boost_1_35_0.tar.gz
+\end_layout
+
+\begin_layout LyX-Code
+$ cd boost_1_35_0
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure
+\end_layout
+
+\begin_layout LyX-Code
+$ make
+\end_layout
+
+\begin_layout LyX-Code
+$ make install
+\end_layout
+
+\begin_layout Standard
+Without a custom installation prefix, Boost will target your
+\family typewriter
+/usr/local
+\family default
+ directory.
+\end_layout
+
+\begin_layout Subsection
HDF5
\end_layout
@@ -403,11 +449,11 @@ target "hdfgroup.org/HDF5/release/obtain5.html"
.
To install from source, download the latest stable 1.6 version of this library
- (currently 1.6.7) and issue the following commands
+ (1.6.7, for example) and issue the following commands
\end_layout
\begin_layout LyX-Code
-$ tar xvfz hdf5-1.6.7
+$ tar xvfz hdf5-1.6.7.tar.gz
\end_layout
\begin_layout LyX-Code
@@ -495,6 +541,22 @@ $ make
$ make install
\end_layout
+\begin_layout Standard
+You can set the installation prefix during the
+\family typewriter
+ccmake
+\family default
+ step above, which defaults to your
+\family typewriter
+/usr/local
+\family default
+ directory.
+\end_layout
+
+\begin_layout Section
+Additional Software
+\end_layout
+
\begin_layout Subsection
NumPy
\end_layout
@@ -605,20 +667,15 @@ import FIAT
\end_layout
\begin_layout Subsection
-HDFView (optional)
+HDFView
\end_layout
\begin_layout Standard
NCSA HDFView is a graphical user interface tool for accessing data in your
HDF5 files.
- You can use it for viewing the internal group hierarchy (see Figure
-\begin_inset LatexCommand ref
-reference "fig:With-HFDFView,-you"
-
-\end_inset
-
-), adding new datasets, and modifying or deleting existing datasets, or
- altering metadata on groups and datasets.
+ You can use it for viewing the internal group hierarchy, adding new datasets,
+ and modifying or deleting existing datasets, or altering metadata on groups
+ and datasets.
You can download it from the
\begin_inset LatexCommand htmlurl
name "HDFView home page"
@@ -629,51 +686,6 @@ target "hdf.ncsa.uiuc.edu/hdf-java-html/hdfview"
.
\end_layout
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status collapsed
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename figures/hdfview-bmrsnog.png
- lyxscale 70
- width 60page%
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:With-HFDFView,-you"
-
-\end_inset
-
-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
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Chapter
\begin_inset LatexCommand label
name "cha:Error-Analysis"
@@ -702,10 +714,6 @@ For assessing the quality of the solution to our equations, it is important
each other through the use of a distance measure between two functions.
\end_layout
-\begin_layout Section
-Distance Measures
-\end_layout
-
\begin_layout Standard
The simplest possible quantitative measure of the difference between two
distinct functions consists of taking the pointwise difference at a common
@@ -713,10 +721,21 @@ The simplest possible quantitative measure of the difference between two
While no finite sample of points can perfectly represent a continuum of
values, valuable information can be inferred from the statistics of the
resulting set of differences.
+ However, the fields we want to compare may not be defined at a common set
+ of points.
+ This simple measure becomes unapplicable.
+\end_layout
+
+\begin_layout Section
+Interpolation Functions
\end_layout
\begin_layout Standard
-XXX: motivate this measure..validation
+We can apply a number of interpolation
+\end_layout
+
+\begin_layout Section
+Distance Measures
\end_layout
\begin_layout Standard
@@ -1024,7 +1043,7 @@ The global error
\begin_layout Standard
We can make a number of observations based on our final expression for the
- global error, (XXX: add observations here).
+ global error,
\end_layout
\begin_layout Section
@@ -1088,13 +1107,13 @@ Cigma is primarily designed for calculating error estimates between arbitrary
\begin_layout LyX-Code
$
\series bold
-cigma compare -a
+cigma compare
\emph on
\bar under
field1
\emph default
\bar default
- -b
+
\emph on
\bar under
field2
@@ -1105,9 +1124,23 @@ field2
\begin_layout Standard
You will need to provide two datasets describing each of the two fields,
- along with an integration rule and a discretization over which to integrate,
- although these last two will have reasonable defaults if they are not specified.
- This chapter aims to summarize the information you'll need to run Cigma.
+ specify an integration rule and a domain discretization over which to integrate
+, although these last two will have reasonable defaults if they are not
+ specified.
+\end_layout
+
+\begin_layout Standard
+The default data storage format for Cigma is the Hierarchical Data Format
+ (HDF5), a portable file format developed at the
+\begin_inset LatexCommand htmlurl
+name "National Center for Supercomputing Applications (NCSA)"
+target "hdf.ncsa.uiuc.edu/HDF5"
+
+\end_inset
+
+.
+ The HDF5 is designed for storing multi-dimensional arrays together with
+ meta-data in a portable self-describing format.
\end_layout
\begin_layout Section
@@ -1171,11 +1204,7 @@ Available subcommands
\end_layout
\begin_layout Standard
-XXX Quick description of each command
-\end_layout
-
-\begin_layout Standard
-XXX: Also add the same description to the help page of the respective command
+Examples for each of these commands are given in the sections below.
\end_layout
\begin_layout Section
@@ -1183,30 +1212,12 @@ Input and Output Formats
\end_layout
\begin_layout Standard
-XXX Reformat from newfile1.lyx
-\end_layout
-
-\begin_layout Standard
-The default data storage format for Cigma is the Hierarchical Data Format
- (HDF5), a portable file format developed at the
-\begin_inset LatexCommand htmlurl
-name "National Center for Supercomputing Applications (NCSA)"
-target "hdf.ncsa.uiuc.edu/HDF5"
-
-\end_inset
-
-.
- The HDF5 is designed for storing multi-dimensional arrays together with
- meta-data in a portable self-describing format.
-\end_layout
-
-\begin_layout Standard
The underlying data storage format for Cigma is the HDF5 format, due to
its flexibility for storing and organizing large amounts of data.
The Hierarchical Data Format (HDF) is designed for storing, retrieving,
analyzing, visualizing, and converting scientific data.
- It uses a hierarchical structure that provides application programmers
- with a host of options for organizing how data is stored in HDF5 files.
+ It uses a hierarchical structure that provides users a host of options
+ for organizing how their data is stored in HDF5 files.
Using HDF5 datasets in Cigma allows us to avoid having to convert between
too many distinct formats.
Moreover, due to the amount of disk I/O, large finite element meshes can
@@ -1215,21 +1226,8 @@ The underlying data storage format for Cigma is the HDF5 format, due to
\end_layout
\begin_layout Standard
-Another VTK format for providing mesh and field inputs.
-
-\color none
-
-\color inherit
-[<-- XXX something wrong with that fragment.
- Did you mean
-\begin_inset Quotes sld
-\end_inset
-
-Another format for providing mesh and field inputs is the VTK format
-\begin_inset Quotes srd
-\end_inset
-
-?] You can easily examine the structure of an input file by using the
+Another popular format for providing mesh and field inputs.You can easily
+ examine the structure of an input file by using the
\family typewriter
cigma list
\family default
@@ -1334,17 +1332,6 @@ Cigma Datasets
\end_layout
\begin_layout Standard
-Here we describe in a bit more detail the kind of datasets that Cigma expects.
-
-\end_layout
-
-\begin_layout Standard
-The first kind of dataset required are meshes.
- In this version of Cigma, meshes are expected to be specifed as an unstructured
- grid.
-\end_layout
-
-\begin_layout Standard
A field is a function which assigns a physical quantity to every point in
a domain
\begin_inset Formula $\Omega$
@@ -1401,13 +1388,13 @@ where the global point
\begin_inset Formula $d_{e,n}$
\end_inset
-, also known as degrees of freedom, are given on.
- [<-- XXX does this sentence end correctly?] These shape functions define
- a basis for the function space on the finite element
+, also known as degrees of freedom, are given on each global node.
+ These shape functions define a basis for the function space on the finite
+ element
\begin_inset Formula $\Omega_{e}$
\end_inset
-, [<-- XXX more to this?]
+.
\end_layout
\begin_layout Standard
@@ -1658,10 +1645,12 @@ Comparing two arbitrary finite element fields can be accomplished with the
cigma compare
\family default
command-line utility.
- By default, the comparison will take place over the elements in the mesh
- of the first field.
- Finally, the square of each of the local residual values are written to
- the specified VTK output file as cell-based scalars.
+ By default, the comparison will involve a numerical integration over each
+ of the elements in the mesh associated with the first field.
+ If this discretization is inadequate, you may also specify an alternative
+ discretization over which to perform the integration.
+ The comparison operation will output the local residual values are into
+ the specified output file.
\end_layout
\begin_layout Standard
@@ -1669,7 +1658,7 @@ A basic comparison can be as simple as specifying the following arguments:
\end_layout
\begin_layout LyX-Code
-cigma compare --output=residuals.vtk
+cigma compare --first=field1.h5:/field1/stepN
\end_layout
\begin_layout LyX-Code
@@ -1677,15 +1666,11 @@ cigma compare --output=residuals.vtk
\series bold
\series default
- --first=field1.h5:/field1/stepN
+ --second=field2.h5:/field2/stepN
\end_layout
\begin_layout LyX-Code
-
-\series bold
-
-\series default
- --second=field2.h5:/field2/stepN
+ --output=residuals.vtk
\end_layout
\begin_layout LyX-Code
@@ -1710,11 +1695,7 @@ First, extract the global coordinates of the integration points.
\end_layout
\begin_layout LyX-Code
-cigma extract --mesh=field1.h5:/model/mesh/
-\end_layout
-
-\begin_layout LyX-Code
- --output=points.h5:/projected_points
+cigma extract field1.h5:/model/mesh/ -o points.h5:/projected_points
\end_layout
\begin_layout Standard
@@ -1723,19 +1704,19 @@ Now you can evaluate your function at the designated points.
\end_layout
\begin_layout LyX-Code
-cigma compare --output=residuals.vtk
+cigma compare --first=field1.h5:/field1/stepN
\end_layout
\begin_layout LyX-Code
- --first=field1.h5:/field1/stepN
+ --second-points=points.h5:/projected_points
\end_layout
\begin_layout LyX-Code
- --second-points=points.h5:/projected_points
+ --second-values=values.h5:/projected_values
\end_layout
\begin_layout LyX-Code
- --second-values=values.h5:/projected_values
+ --output=residuals.vtk
\end_layout
\begin_layout Subsection
@@ -1749,25 +1730,19 @@ Comparing 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,
- which will enable the
+ you also have the option to compile your analytic function as a builtin
+ Cigma function.
+ This will enable you to reference your function by name when using the
+
\family typewriter
compare
\family default
- command to reference your function by name.
+ command.
For example,
\end_layout
\begin_layout LyX-Code
-cigma compare --output=residuals.vtk
-\end_layout
-
-\begin_layout LyX-Code
-
-\series bold
-
-\series default
- --first=field1.h5:/vars/displacement/step0
+cigma compare --first=field1.h5:/vars/displacement/step0
\end_layout
\begin_layout LyX-Code
@@ -1778,11 +1753,10 @@ cigma compare --output=residuals.vtk
--second=
\bar under
disloc3d
-\series bold
-\bar default
-
-\series default
+\end_layout
+\begin_layout LyX-Code
+ --output=residuals.vtk
\end_layout
\begin_layout Standard
@@ -1850,7 +1824,7 @@ zero
\end_layout
\begin_layout Subsection
-Specifying an Integration Mesh
+Specifying a Integration Mesh
\end_layout
\begin_layout Standard
@@ -1955,7 +1929,7 @@ In this chapter we will use sample datasets from the strike-slip benchmark
\begin_inset Float figure
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -2060,12 +2034,51 @@ where
\end_layout
+\begin_layout Standard
+XXX: list of examples to discuss here
+\end_layout
+
+\begin_layout Standard
+Viscoelastic strikeslip example (tet vs.
+ hex elts) -- pylith-tet / pylith-hex
+\end_layout
+
+\begin_layout Standard
+Cylinder extension for maxwell material (newtonian) -- pylith / geofest
+ / analytic
+\end_layout
+
+\begin_layout Standard
+Cylinder extension for maxwell material (non-newtonian) -- pylith / geofest
+ / analytic
+\end_layout
+
+\begin_layout Standard
+Cylinder gravitation -- pylith / geofest / analytic
+\end_layout
+
+\begin_layout Standard
+Laplace example (linear, quadratic elements) -- deal.II / libmesh / analytic
+\end_layout
+
+\begin_layout Standard
+Citcom example (structured datasets) -- citcom (3d) / analytic
+\end_layout
+
+\begin_layout Standard
+Gale example (structured datasets) -- gale (2d) / analytic
+\end_layout
+
+\begin_layout Standard
+MADDs example --
+\end_layout
+
\begin_layout Section
Visualization
\end_layout
\begin_layout Standard
-Using MayaVi2, we may obtain a visualization of the Cigma datasets
+The residual field obtained in the
\end_layout
\begin_layout Chapter
@@ -2074,19 +2087,19 @@ File Formats
\end_layout
\begin_layout Standard
-To differentiate between these formats, you will need to provide an appropriate
- extension for your input and output files.
- The supported extensions are currently
+To differentiate between these input and output file formats, you will need
+ to provide an appropriate file extension.
+ Currently recognized file extensions include
\family typewriter
-.h5
+*.h5
\family default
- for HDF5,
+ for HDF5 files,
\family typewriter
-.vtk
+*.vtk
\family default
- for VTK files, and
+ for legacy VTK files, and
\family typewriter
-.txt
+*.dat
\family default
for simple text files.
\end_layout
@@ -2313,7 +2326,7 @@ The text format is always in table form, with the dimensions of the table
\end_layout
\begin_layout LyX-Code
-nno nsd
+<nno> <nsd>
\end_layout
\begin_layout LyX-Code
@@ -2410,15 +2423,6 @@ The output format for residuals consists simply of a list of scalars for
so further post-processing will be necessary.
\end_layout
-\begin_layout Standard
-\begin_inset Include \include{gpl-license.lyx}
-preview false
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
label "1"
diff --git a/cigma.lyx b/cigma.lyx~
similarity index 88%
copy from cigma.lyx
copy to cigma.lyx~
index 8b7dfdd..cafef8a 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 1.5.4 created this file. For more info see http://www.lyx.org/
\lyxformat 276
\begin_document
\begin_header
@@ -116,7 +116,7 @@ Cigma
\begin_layout Author
© California Institute of Technology
\newline
-Version 0.9.1
+Version 1.0.0
\end_layout
\begin_layout Date
@@ -347,7 +347,8 @@ target "geodynamics.org/cig/software/packages/cs/cigma"
.
You will need the GNU C++ compiler for this step.
- The HDF5 and VTK libraries, described later in this section, are also required.
+ The Boost, HDF5, and VTK libraries, described later in this section, are
+ also required.
\end_layout
\begin_layout Standard
@@ -356,15 +357,23 @@ After installing the necessary dependencies, simply unpack the source tar
\end_layout
\begin_layout LyX-Code
-$ tar xvfz cigma-0.9.1.tar.gz
+$ tar xvfz cigma-1.0.0.tar.gz
\end_layout
\begin_layout LyX-Code
-$ cd cigma-0.9.1
+$ cd cigma-1.0.0
\end_layout
\begin_layout LyX-Code
-$ ./configure --with-hdf5=$HDF5_PREFIX --with-vtk=$VTK_PREFIX
+$ ./configure --with-boost=$BOOST_PREFIX
+\end_layout
+
+\begin_layout LyX-Code
+ --with-hdf5=$HDF5_PREFIX
+\end_layout
+
+\begin_layout LyX-Code
+ --with-vtk=$VTK_PREFIX
\end_layout
\begin_layout LyX-Code
@@ -381,6 +390,43 @@ Both HDF5 and VTK prefixes are required if you have installed these libraries
\end_layout
\begin_layout Subsection
+Boost
+\end_layout
+
+\begin_layout Standard
+The Boost C++ libraries are used in Cigma for parsing command-line options,
+ and ensuring cross-platform access to the filesystem.
+\end_layout
+
+\begin_layout LyX-Code
+$ tar xvfz boost_1_35_0.tar.gz
+\end_layout
+
+\begin_layout LyX-Code
+$ cd boost_1_35_0
+\end_layout
+
+\begin_layout LyX-Code
+$ ./configure
+\end_layout
+
+\begin_layout LyX-Code
+$ make
+\end_layout
+
+\begin_layout LyX-Code
+$ make install
+\end_layout
+
+\begin_layout Standard
+Without a custom installation prefix, Boost will target your
+\family typewriter
+/usr/local
+\family default
+ directory.
+\end_layout
+
+\begin_layout Subsection
HDF5
\end_layout
@@ -403,11 +449,11 @@ target "hdfgroup.org/HDF5/release/obtain5.html"
.
To install from source, download the latest stable 1.6 version of this library
- (currently 1.6.7) and issue the following commands
+ (1.6.7, for example) and issue the following commands
\end_layout
\begin_layout LyX-Code
-$ tar xvfz hdf5-1.6.7
+$ tar xvfz hdf5-1.6.7.tar.gz
\end_layout
\begin_layout LyX-Code
@@ -495,6 +541,22 @@ $ make
$ make install
\end_layout
+\begin_layout Standard
+You can set the installation prefix during the
+\family typewriter
+ccmake
+\family default
+ step above, which defaults to your
+\family typewriter
+/usr/local
+\family default
+ directory.
+\end_layout
+
+\begin_layout Section
+Additional Software
+\end_layout
+
\begin_layout Subsection
NumPy
\end_layout
@@ -605,20 +667,15 @@ import FIAT
\end_layout
\begin_layout Subsection
-HDFView (optional)
+HDFView
\end_layout
\begin_layout Standard
NCSA HDFView is a graphical user interface tool for accessing data in your
HDF5 files.
- You can use it for viewing the internal group hierarchy (see Figure
-\begin_inset LatexCommand ref
-reference "fig:With-HFDFView,-you"
-
-\end_inset
-
-), adding new datasets, and modifying or deleting existing datasets, or
- altering metadata on groups and datasets.
+ You can use it for viewing the internal group hierarchy, adding new datasets,
+ and modifying or deleting existing datasets, or altering metadata on groups
+ and datasets.
You can download it from the
\begin_inset LatexCommand htmlurl
name "HDFView home page"
@@ -629,51 +686,6 @@ target "hdf.ncsa.uiuc.edu/hdf-java-html/hdfview"
.
\end_layout
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status collapsed
-
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Graphics
- filename figures/hdfview-bmrsnog.png
- lyxscale 70
- width 60page%
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\begin_inset Caption
-
-\begin_layout Standard
-\begin_inset LatexCommand label
-name "fig:With-HFDFView,-you"
-
-\end_inset
-
-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
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Chapter
\begin_inset LatexCommand label
name "cha:Error-Analysis"
@@ -702,10 +714,6 @@ For assessing the quality of the solution to our equations, it is important
each other through the use of a distance measure between two functions.
\end_layout
-\begin_layout Section
-Distance Measures
-\end_layout
-
\begin_layout Standard
The simplest possible quantitative measure of the difference between two
distinct functions consists of taking the pointwise difference at a common
@@ -713,10 +721,17 @@ The simplest possible quantitative measure of the difference between two
While no finite sample of points can perfectly represent a continuum of
values, valuable information can be inferred from the statistics of the
resulting set of differences.
+ However, the fields we want to compare may not be defined at a common set
+ of points.
+ This simple measure becomes unapplicable.
\end_layout
-\begin_layout Standard
-XXX: motivate this measure..validation
+\begin_layout Section
+Interpolation Functions
+\end_layout
+
+\begin_layout Section
+Distance Measures
\end_layout
\begin_layout Standard
@@ -1088,13 +1103,13 @@ Cigma is primarily designed for calculating error estimates between arbitrary
\begin_layout LyX-Code
$
\series bold
-cigma compare -a
+cigma compare
\emph on
\bar under
field1
\emph default
\bar default
- -b
+
\emph on
\bar under
field2
@@ -1105,9 +1120,23 @@ field2
\begin_layout Standard
You will need to provide two datasets describing each of the two fields,
- along with an integration rule and a discretization over which to integrate,
- although these last two will have reasonable defaults if they are not specified.
- This chapter aims to summarize the information you'll need to run Cigma.
+ specify an integration rule and a domain discretization over which to integrate
+, although these last two will have reasonable defaults if they are not
+ specified.
+\end_layout
+
+\begin_layout Standard
+The default data storage format for Cigma is the Hierarchical Data Format
+ (HDF5), a portable file format developed at the
+\begin_inset LatexCommand htmlurl
+name "National Center for Supercomputing Applications (NCSA)"
+target "hdf.ncsa.uiuc.edu/HDF5"
+
+\end_inset
+
+.
+ The HDF5 is designed for storing multi-dimensional arrays together with
+ meta-data in a portable self-describing format.
\end_layout
\begin_layout Section
@@ -1171,11 +1200,7 @@ Available subcommands
\end_layout
\begin_layout Standard
-XXX Quick description of each command
-\end_layout
-
-\begin_layout Standard
-XXX: Also add the same description to the help page of the respective command
+Examples for each of these commands are given in the sections below.
\end_layout
\begin_layout Section
@@ -1183,30 +1208,12 @@ Input and Output Formats
\end_layout
\begin_layout Standard
-XXX Reformat from newfile1.lyx
-\end_layout
-
-\begin_layout Standard
-The default data storage format for Cigma is the Hierarchical Data Format
- (HDF5), a portable file format developed at the
-\begin_inset LatexCommand htmlurl
-name "National Center for Supercomputing Applications (NCSA)"
-target "hdf.ncsa.uiuc.edu/HDF5"
-
-\end_inset
-
-.
- The HDF5 is designed for storing multi-dimensional arrays together with
- meta-data in a portable self-describing format.
-\end_layout
-
-\begin_layout Standard
The underlying data storage format for Cigma is the HDF5 format, due to
its flexibility for storing and organizing large amounts of data.
The Hierarchical Data Format (HDF) is designed for storing, retrieving,
analyzing, visualizing, and converting scientific data.
- It uses a hierarchical structure that provides application programmers
- with a host of options for organizing how data is stored in HDF5 files.
+ It uses a hierarchical structure that provides users a host of options
+ for organizing how their data is stored in HDF5 files.
Using HDF5 datasets in Cigma allows us to avoid having to convert between
too many distinct formats.
Moreover, due to the amount of disk I/O, large finite element meshes can
@@ -1215,21 +1222,8 @@ The underlying data storage format for Cigma is the HDF5 format, due to
\end_layout
\begin_layout Standard
-Another VTK format for providing mesh and field inputs.
-
-\color none
-
-\color inherit
-[<-- XXX something wrong with that fragment.
- Did you mean
-\begin_inset Quotes sld
-\end_inset
-
-Another format for providing mesh and field inputs is the VTK format
-\begin_inset Quotes srd
-\end_inset
-
-?] You can easily examine the structure of an input file by using the
+Another popular format for providing mesh and field inputs.You can easily
+ examine the structure of an input file by using the
\family typewriter
cigma list
\family default
@@ -1334,17 +1328,6 @@ Cigma Datasets
\end_layout
\begin_layout Standard
-Here we describe in a bit more detail the kind of datasets that Cigma expects.
-
-\end_layout
-
-\begin_layout Standard
-The first kind of dataset required are meshes.
- In this version of Cigma, meshes are expected to be specifed as an unstructured
- grid.
-\end_layout
-
-\begin_layout Standard
A field is a function which assigns a physical quantity to every point in
a domain
\begin_inset Formula $\Omega$
@@ -1401,13 +1384,13 @@ where the global point
\begin_inset Formula $d_{e,n}$
\end_inset
-, also known as degrees of freedom, are given on.
- [<-- XXX does this sentence end correctly?] These shape functions define
- a basis for the function space on the finite element
+, also known as degrees of freedom, are given on each global node.
+ These shape functions define a basis for the function space on the finite
+ element
\begin_inset Formula $\Omega_{e}$
\end_inset
-, [<-- XXX more to this?]
+.
\end_layout
\begin_layout Standard
@@ -1658,10 +1641,12 @@ Comparing two arbitrary finite element fields can be accomplished with the
cigma compare
\family default
command-line utility.
- By default, the comparison will take place over the elements in the mesh
- of the first field.
- Finally, the square of each of the local residual values are written to
- the specified VTK output file as cell-based scalars.
+ By default, the comparison will involve a numerical integration over each
+ of the elements in the mesh associated with the first field.
+ If this discretization is inadequate, you may also specify an alternative
+ discretization over which to perform the integration.
+ The comparison operation will output the local residual values are into
+ the specified output file.
\end_layout
\begin_layout Standard
@@ -1669,7 +1654,7 @@ A basic comparison can be as simple as specifying the following arguments:
\end_layout
\begin_layout LyX-Code
-cigma compare --output=residuals.vtk
+cigma compare --first=field1.h5:/field1/stepN
\end_layout
\begin_layout LyX-Code
@@ -1677,15 +1662,11 @@ cigma compare --output=residuals.vtk
\series bold
\series default
- --first=field1.h5:/field1/stepN
+ --second=field2.h5:/field2/stepN
\end_layout
\begin_layout LyX-Code
-
-\series bold
-
-\series default
- --second=field2.h5:/field2/stepN
+ --output=residuals.vtk
\end_layout
\begin_layout LyX-Code
@@ -1710,11 +1691,7 @@ First, extract the global coordinates of the integration points.
\end_layout
\begin_layout LyX-Code
-cigma extract --mesh=field1.h5:/model/mesh/
-\end_layout
-
-\begin_layout LyX-Code
- --output=points.h5:/projected_points
+cigma extract field1.h5:/model/mesh/ -o points.h5:/projected_points
\end_layout
\begin_layout Standard
@@ -1723,19 +1700,19 @@ Now you can evaluate your function at the designated points.
\end_layout
\begin_layout LyX-Code
-cigma compare --output=residuals.vtk
+cigma compare --first=field1.h5:/field1/stepN
\end_layout
\begin_layout LyX-Code
- --first=field1.h5:/field1/stepN
+ --second-points=points.h5:/projected_points
\end_layout
\begin_layout LyX-Code
- --second-points=points.h5:/projected_points
+ --second-values=values.h5:/projected_values
\end_layout
\begin_layout LyX-Code
- --second-values=values.h5:/projected_values
+ --output=residuals.vtk
\end_layout
\begin_layout Subsection
@@ -1749,25 +1726,19 @@ Comparing 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,
- which will enable the
+ you also have the option to compile your analytic function as a builtin
+ Cigma function.
+ This will enable you to reference your function by name when using the
+
\family typewriter
compare
\family default
- command to reference your function by name.
+ command.
For example,
\end_layout
\begin_layout LyX-Code
-cigma compare --output=residuals.vtk
-\end_layout
-
-\begin_layout LyX-Code
-
-\series bold
-
-\series default
- --first=field1.h5:/vars/displacement/step0
+cigma compare --first=field1.h5:/vars/displacement/step0
\end_layout
\begin_layout LyX-Code
@@ -1778,11 +1749,10 @@ cigma compare --output=residuals.vtk
--second=
\bar under
disloc3d
-\series bold
-\bar default
-
-\series default
+\end_layout
+\begin_layout LyX-Code
+ --output=residuals.vtk
\end_layout
\begin_layout Standard
@@ -1850,7 +1820,7 @@ zero
\end_layout
\begin_layout Subsection
-Specifying an Integration Mesh
+Specifying a Integration Mesh
\end_layout
\begin_layout Standard
@@ -1955,7 +1925,7 @@ In this chapter we will use sample datasets from the strike-slip benchmark
\begin_inset Float figure
wide false
sideways false
-status open
+status collapsed
\begin_layout Standard
\begin_inset Graphics
@@ -2060,12 +2030,51 @@ where
\end_layout
+\begin_layout Standard
+XXX: list of examples to discuss here
+\end_layout
+
+\begin_layout Standard
+Viscoelastic strikeslip example (tet vs.
+ hex elts) -- pylith-tet / pylith-hex
+\end_layout
+
+\begin_layout Standard
+Cylinder extension for maxwell material (newtonian) -- pylith / geofest
+ / analytic
+\end_layout
+
+\begin_layout Standard
+Cylinder extension for maxwell material (non-newtonian) -- pylith / geofest
+ / analytic
+\end_layout
+
+\begin_layout Standard
+Cylinder gravitation -- pylith / geofest / analytic
+\end_layout
+
+\begin_layout Standard
+Laplace example (linear, quadratic elements) -- deal.II / libmesh / analytic
+\end_layout
+
+\begin_layout Standard
+Citcom example (structured datasets) -- citcom (3d) / analytic
+\end_layout
+
+\begin_layout Standard
+Gale example (structured datasets) -- gale (2d) / analytic
+\end_layout
+
+\begin_layout Standard
+MADDs example --
+\end_layout
+
\begin_layout Section
Visualization
\end_layout
\begin_layout Standard
-Using MayaVi2, we may obtain a visualization of the Cigma datasets
+The residual field obtained in the
\end_layout
\begin_layout Chapter
@@ -2074,19 +2083,19 @@ File Formats
\end_layout
\begin_layout Standard
-To differentiate between these formats, you will need to provide an appropriate
- extension for your input and output files.
- The supported extensions are currently
+To differentiate between these input and output file formats, you will need
+ to provide an appropriate file extension.
+ Currently recognized file extensions include
\family typewriter
-.h5
+*.h5
\family default
- for HDF5,
+ for HDF5 files,
\family typewriter
-.vtk
+*.vtk
\family default
- for VTK files, and
+ for legacy VTK files, and
\family typewriter
-.txt
+*.dat
\family default
for simple text files.
\end_layout
@@ -2313,7 +2322,7 @@ The text format is always in table form, with the dimensions of the table
\end_layout
\begin_layout LyX-Code
-nno nsd
+<nno> <nsd>
\end_layout
\begin_layout LyX-Code
@@ -2410,15 +2419,6 @@ The output format for residuals consists simply of a list of scalars for
so further post-processing will be necessary.
\end_layout
-\begin_layout Standard
-\begin_inset Include \include{gpl-license.lyx}
-preview false
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Bibliography
\begin_inset LatexCommand bibitem
label "1"
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