[cig-commits] r3917 - in short/3D/PyLith/branches/pylith-0.8/doc/userguide: fileformats install runpylith runpylith/figs

baagaard at geodynamics.org baagaard at geodynamics.org
Wed Jul 5 11:14:54 PDT 2006


Author: baagaard
Date: 2006-07-05 11:14:54 -0700 (Wed, 05 Jul 2006)
New Revision: 3917

Added:
   short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/hex8.eps
   short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/hex8.fig
   short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/hex8.png
Modified:
   short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/connect.xml
   short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.xml
   short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/tet4.eps
   short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/tet4.fig
   short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/tet4.png
   short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.xml
Log:
User guide. Added instructions for building developers version. Added info on support for hex element.

Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/connect.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/connect.xml	2006-07-04 00:55:20 UTC (rev 3916)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/connect.xml	2006-07-05 18:14:54 UTC (rev 3917)
@@ -22,10 +22,9 @@
 # Columns:
 #   (1) Element number
 #   (2) Element type
-#        1 = Linear hexahedron (8 vertices) [NOT IMPLEMENTED]
+#        1 = Linear hexahedron (8 vertices)
 #        2 = Linear hexahedron with 1 set of collapsed vertices
-#            (7 vertices)
-#            [NOT IMPLEMENTED]
+#            (7 vertices) [NOT IMPLEMENTED]
 #        3 = Linear hexahedron with 2 sets of collapsed vertices
 #           (6 vertices) [NOT IMPLEMENTED]
 #        4 = Linear hexahedron with 4 vertices collapsed to a point

Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.xml	2006-07-04 00:55:20 UTC (rev 3916)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.xml	2006-07-05 18:14:54 UTC (rev 3917)
@@ -232,7 +232,7 @@
 
     <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++ -->
     <section>
-      <title>Building from source</title>
+      <title>Building using source tarball</title>
 
       <para>
         Building PyLith from the source code is not a trivial task
@@ -315,6 +315,296 @@
 
     </section>
 
+    <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++ -->
+    <section>
+      <title>Building using source repositories</title>
+
+      <warning>
+	<para>
+          Building PyLith using the source repositories is recommended
+          only for expert users who are willing to work with a moving
+          target and rebuild on a frequent basis. The installation
+          instructions cover the basic steps and assume the user has
+          experience building and installing software.
+        </para>
+      </warning>
+
+      <para>
+        The PyLith-0.8 source code is available from the <ulink
+        url="http://www.geodynamics.org:8080/cig/software/Repository/">Geodynamics
+        subversion repository</ulink> under <filename
+        classname="directory">cig/short/3D/PyLith/branches/pylith-0.8</filename>.
+      </para>
+
+      <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++ -->
+      <section>
+	<title>System Requirements</title>
+
+	<itemizedlist>
+	  <listitem>
+	    <para>Unix flavored operating system</para>
+	  </listitem>
+	  <listitem>
+	    <para>Fortran, C, and C++ compilers</para>
+	  </listitem>
+	  <listitem>
+	    <para>Python (2.3 or later)</para>
+	  </listitem>
+	  <listitem>
+	    <para>Subversion</para>
+	  </listitem>
+	  <listitem>
+	    <para>Mercurial (0.90 or later)</para>
+	  </listitem>
+	</itemizedlist>
+
+	<tip>
+	  <para>
+            Many flavors of Unix have Subversion packages. In most
+            cases you do not need anything but the basic subversion
+            package. You will likely have to build Mercurial from
+            source, but this is a very easy task that takes only a
+            couple of minutes.
+          </para>
+	</tip>
+
+      </section>
+
+      <para>
+        The software must be built starting from the bottom of the
+        dependency list and working upwards. The steps below describe
+        the recommended way to build PyLith and the external packages
+        on which it depends.
+      </para>
+
+      <orderedlist>
+	<listitem>
+	  <para>
+            Build <ulink
+            url="http://www-unix.mcs.anl.gov/petsc/petsc-as/developers/index.html">PETSc (developers version)</ulink>
+            and MPI.
+          </para>
+	  <para>
+            If you have an MPI implementation installed, you can use
+            it or let PETSc download and install one for you. If you
+            have an architecture optimized version of BLAS/LAPACK
+            (e.g., veclib on a Mac or ATLAS on a PC), you should use those
+            instead of asking PETSc to download and build one for you.
+          </para>
+	  <orderedlist numeration="lowerroman">
+	    <listitem>
+	      <para>
+                Pull the source code from ANL and place the source
+                tree in a suitable location. The steps below will
+                create a <filename
+                class="directory">petsc-dev</filename> sub-directory
+                in the current directory.
+              </para>
+	      <screen>
+<prompt>bash$ </prompt><userinput>hg clone http://mercurial.mcs.anl.gov/petsc/petsc-dev</userinput>
+<prompt>bash$ </prompt><userinput>cd petsc-dev/python</userinput>
+<prompt>bash$ </prompt><userinput>hg clone http://mercurial.mcs.anl.gov/petsc/BuildSystem \
+BuildSystem</userinput>
+              </screen>
+	    </listitem>
+	    <listitem>
+	      <para>
+                Set the <envar>PETSC_DIR</envar> and
+                <envar>PETSC_ARCH</envar> environment
+                variables. <envar>PETSC_DIR</envar> corresponds to
+                the top-level directory in the PETSc source tree and
+                <envar>PETSC_ARCH</envar> is a tag for this
+                configuration of PETSc (e.g., linux_gcc-4.0_debug,
+                darwin_gcc-3.4_opt, etc). You will want to set these
+                environment variables in your
+                <filename>.bashrc</filename>,
+                <filename>.cshrc</filename>, or similar file.
+              </para>
+	      <screen>
+<prompt>bash$ </prompt><userinput>export PETSC_DIR=<replaceable>replace_with_absolute_path</replaceable>/petsc-dev</userinput>
+<prompt>bash$ </prompt><userinput>export PETSC_ARCH=<replaceable>replace_with_PETSc_arch_tag</replaceable></userinput>
+              </screen>
+	    </listitem>
+	    <listitem>
+	      <para>
+                Configure PETSc.
+              </para>
+	      <para>
+                Run <command>config/configure.py</command> with the
+                appropriate arguments to configure PETSc for your
+                computer. Run <command>config/configure.py
+                --help</command> to see the long list of possible
+                options. Building PETSc for use with PyLith requires
+                the following arguments:
+              </para>
+	      <screen>
+<option>--with-clanguage=c++</option>
+<option>--with-c-support</option>
+<option>--with-shared=1</option>
+<option>--with-boost=1</option>
+<option>--download-boost=1</option>
+<option>--with-sieve=1</option>
+              </screen>
+	      <para>
+                Be sure to include flags indicating where MPI and
+                BLAS/LAPACK are if you want to use a preinstalled
+                implementation. If not, be sure to tell PETSc to
+                download those packages. If you do not want build
+                PETSc using the gnu compilers, be sure to let PETSc
+                know which compilers you want to use instead.
+              </para>
+	      <para>
+                After several minutes, the configure script should
+                finish and display the PETSc settings. Check to make
+                sure these match your expectations before continuing.
+              </para>
+	    </listitem>
+	    <listitem>
+	      <para>
+                Build PETSc.
+              </para>
+	      <screen>
+<prompt>bash$ </prompt><userinput>make</userinput>
+              </screen>
+	    </listitem>
+	    <listitem>
+	      <para>
+                Test PETSc installation.
+              </para>
+	      <para>
+                One of the tests will attempt to display some X
+                windows. If X windows is not available from the shell
+                in which you run <command>make test</command>, then
+                that test will fail.
+              </para>
+	      <screen>
+<prompt>bash$ </prompt><userinput>make test</userinput>
+              </screen>
+	    </listitem>
+	    <listitem>
+	      <para>
+                In the future, you will likely want to update the
+                PETSc source tree to include bug fixes, new features
+                etc.
+              </para>
+              <para>
+                To update PETSc (use to <command>hg update
+                -v</command> to see what files are being updated):
+              </para>
+	      <screen>
+<prompt>bash$ </prompt><userinput>cd petsc-dev</userinput>
+<prompt>bash$ </prompt><userinput>hg pull</userinput>
+<prompt>bash$ </prompt><userinput>hg update</userinput>
+<prompt>bash$ </prompt><userinput>cd python/BuildSystem</userinput>
+<prompt>bash$ </prompt><userinput>hg pull</userinput>
+<prompt>bash$ </prompt><userinput>hg update</userinput>
+              </screen>
+	    </listitem>
+	  </orderedlist>
+	</listitem>
+	<listitem>
+	  <para>
+            Build Pythia.
+          </para>
+	  <orderedlist numeration="lowerroman">
+	    <listitem>
+	      <para>
+                Pull the source code from CIG and place the source
+                tree in a suitable location. The steps below will
+                create a <filename
+                class="directory">pythia-0.8</filename> sub-directory
+                in the current directory.
+              </para>
+	      <screen>
+<prompt>bash$ </prompt><userinput>svn co svn://geodynamics.org/cig/vendor/pythia [cont.]
+/v0.8/pythia-0.8</userinput>
+              </screen>
+	    </listitem>
+	    <listitem>
+	      <para>
+                Configure Pythia.
+              </para>
+	      <para>
+                Run <command>configure</command> with the appropriate
+                arguments. Run <command>configure --help</command> to
+                see a list of possible options. You may want to
+                specify compilers and/or an install location.
+              </para>
+	      <screen>
+<prompt>bash$ </prompt><userinput>cd pythia-0.8</userinput>
+<prompt>bash$ </prompt><userinput>autoreconf -i</userinput>
+<prompt>bash$ </prompt><userinput>./configure</userinput>
+              </screen>
+	    </listitem>
+	    <listitem>
+	      <para>
+                Build Pythia.
+              </para>
+	      <para>
+                Run <command>make</command> and <command>make install</command>.
+              </para>
+	      <screen>
+<prompt>bash$ </prompt><userinput>make</userinput>
+<prompt>bash$ </prompt><userinput>make install</userinput>
+              </screen>
+	    </listitem>
+	  </orderedlist>
+	</listitem>
+	<listitem>
+	  <para>
+            Build PyLith.
+          </para>
+	  <orderedlist numeration="lowerroman">
+	    <listitem>
+	      <para>
+                Pull the source code from CIG and place the source
+                tree in a suitable location. The steps below will
+                create a <filename
+                class="directory">pylith-0.8</filename> sub-directory
+                in the current directory.
+              </para>
+	      <screen>
+<prompt>bash$ </prompt><userinput>svn co svn://geodynamics.org/cig/short/3D/PyLith [cont.]
+/branches/pylith-0.8</userinput>
+              </screen>
+	    </listitem>
+	    <listitem>
+	      <para>
+                Configure PyLith.
+              </para>
+	      <para>
+                Run <command>configure</command> with the appropriate
+                arguments. Run <command>configure --help</command> to
+                see a list of possible options. You may want to
+                specify compilers and/or an install location. If you
+                installed pythia-0.8 in a non-system location, you
+                will need to set <envar>CPPFLAGS</envar> and
+                <envar>LDFLAGS</envar> appropriately.
+              </para>
+	      <screen>
+<prompt>bash$ </prompt><userinput>cd pylith-0.8</userinput>
+<prompt>bash$ </prompt><userinput>autoreconf -i</userinput>
+<prompt>bash$ </prompt><userinput>./configure</userinput>
+              </screen>
+	    </listitem>
+	    <listitem>
+	      <para>
+                Build PyLith.
+              </para>
+	      <para>
+                Run <command>make</command> and <command>make install</command>.
+              </para>
+	      <screen>
+<prompt>bash$ </prompt><userinput>make</userinput>
+<prompt>bash$ </prompt><userinput>make install</userinput>
+              </screen>
+	    </listitem>
+	  </orderedlist>
+	</listitem>
+      </orderedlist>
+
+    </section>
+
   </section>
 
 </chapter>

Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/hex8.eps
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/hex8.eps	2006-07-04 00:55:20 UTC (rev 3916)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/hex8.eps	2006-07-05 18:14:54 UTC (rev 3917)
@@ -0,0 +1,198 @@
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Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/hex8.fig
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/hex8.fig	2006-07-04 00:55:20 UTC (rev 3916)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/hex8.fig	2006-07-05 18:14:54 UTC (rev 3917)
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+1 3 0 1 39 39 40 -1 20 0.000 1 0.0000 4350 1950 37 37 4350 1950 4387 1950
+4 0 0 40 -1 18 12 0.0000 4 135 105 4425 3225 3\001
+4 0 0 40 -1 18 12 0.0000 4 135 105 3525 2775 4\001
+4 0 0 40 -1 18 12 0.0000 4 135 105 2175 1875 5\001
+4 0 0 40 -1 18 12 0.0000 4 135 105 2175 3225 1\001
+4 0 0 40 -1 18 12 0.0000 4 135 105 3300 3675 2\001
+4 0 0 40 -1 18 12 0.0000 4 135 105 4425 1950 7\001
+4 0 0 40 -1 18 12 0.0000 4 135 105 3525 1500 8\001
+4 0 0 40 -1 18 12 0.0000 4 135 105 3225 2250 6\001

Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/hex8.png
===================================================================
(Binary files differ)


Property changes on: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/hex8.png
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/tet4.eps
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/tet4.eps	2006-07-04 00:55:20 UTC (rev 3916)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/tet4.eps	2006-07-05 18:14:54 UTC (rev 3917)
@@ -1,7 +1,7 @@
 %!PS-Adobe-2.0 EPSF-2.0
 %%Title: tet4.fig
 %%Creator: fig2dev Version 3.2 Patchlevel 4
-%%CreationDate: Fri Jun 16 16:36:02 2006
+%%CreationDate: Wed Jul  5 11:04:17 2006
 %%For: brad at arling (Brad Aagaard)
 %%BoundingBox: 0 0 119 144
 %%Magnification: 1.0000
@@ -42,6 +42,22 @@
 /col29 {1.000 0.750 0.750 srgb} bind def
 /col30 {1.000 0.880 0.880 srgb} bind def
 /col31 {1.000 0.840 0.000 srgb} bind def
+/col32 {0.004 0.004 0.004 srgb} bind def
+/col33 {0.988 0.988 0.988 srgb} bind def
+/col34 {0.184 0.207 0.281 srgb} bind def
+/col35 {0.445 0.496 0.672 srgb} bind def
+/col36 {0.992 0.250 0.250 srgb} bind def
+/col37 {0.781 0.000 0.012 srgb} bind def
+/col38 {0.992 0.730 0.410 srgb} bind def
+/col39 {0.957 0.496 0.000 srgb} bind def
+/col40 {0.992 0.992 0.449 srgb} bind def
+/col41 {0.895 0.895 0.000 srgb} bind def
+/col42 {0.375 0.793 0.055 srgb} bind def
+/col43 {0.230 0.488 0.031 srgb} bind def
+/col44 {0.199 0.730 0.992 srgb} bind def
+/col45 {0.117 0.430 0.582 srgb} bind def
+/col46 {0.801 0.562 0.992 srgb} bind def
+/col47 {0.379 0.004 0.684 srgb} bind def
 
 end
 save
@@ -108,16 +124,31 @@
 % Polyline
 2 slj
 7.500 slw
+n 3600 1650 m 4275 2925 l 3525 3600 l
+ cp gs col45 s gr 
+% Polyline
 n 3600 1650 m 2625 3075 l 3525 3600 l
- cp gs col1 s gr 
+ cp gs col45 s gr 
 % Polyline
-n 3600 1650 m 4275 2925 l 3525 3600 l
- cp gs col1 s gr 
-% Polyline
-0 slj
  [60] 0 sd
 n 2625 3075 m
- 4275 2925 l gs col1 s gr  [] 0 sd
+ 4275 2925 l gs col45 s gr  [] 0 sd
+% here ends figure;
+% 
+% here starts figure with depth 40
+% Ellipse
+7.500 slw
+n 3525 3600 37 37 0 360 DrawEllipse gs col39 1.00 shd ef gr gs col39 s gr
+
+% Ellipse
+n 2625 3075 37 37 0 360 DrawEllipse gs col39 1.00 shd ef gr gs col39 s gr
+
+% Ellipse
+n 3600 1650 37 37 0 360 DrawEllipse gs col39 1.00 shd ef gr gs col39 s gr
+
+% Ellipse
+n 4275 2925 37 37 0 360 DrawEllipse gs col39 1.00 shd ef gr gs col39 s gr
+
 /Helvetica-Bold ff 180.00 scf sf
 2475 3225 m
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@@ -131,22 +162,6 @@
 3600 1575 m
 gs 1 -1 sc (4) col0 sh gr
 % here ends figure;
-% 
-% here starts figure with depth 40
-% Ellipse
-7.500 slw
-n 2625 3075 37 37 0 360 DrawEllipse gs col4 1.00 shd ef gr gs col4 s gr
-
-% Ellipse
-n 3600 1650 37 37 0 360 DrawEllipse gs col4 1.00 shd ef gr gs col4 s gr
-
-% Ellipse
-n 4275 2925 37 37 0 360 DrawEllipse gs col4 1.00 shd ef gr gs col4 s gr
-
-% Ellipse
-n 3525 3600 37 37 0 360 DrawEllipse gs col4 1.00 shd ef gr gs col4 s gr
-
-% here ends figure;
 $F2psEnd
 rs
 showpage

Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/tet4.fig
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/tet4.fig	2006-07-04 00:55:20 UTC (rev 3916)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/tet4.fig	2006-07-05 18:14:54 UTC (rev 3917)
@@ -7,17 +7,33 @@
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-1 3 0 1 4 4 40 -1 20 0.000 1 0.0000 4275 2925 37 37 4275 2925 4312 2925
-1 3 0 1 4 4 40 -1 20 0.000 1 0.0000 3525 3600 37 37 3525 3600 3562 3600
-2 3 0 1 1 7 50 -1 -1 0.000 2 0 -1 0 0 4
+0 32 #010101
+0 33 #fdfdfd
+0 34 #2f3548
+0 35 #727fac
+0 36 #fe4040
+0 37 #c80003
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+0 40 #fefe73
+0 41 #e5e500
+0 42 #60cb0e
+0 43 #3b7d08
+0 44 #33bbfe
+0 45 #1e6e95
+0 46 #cd90fe
+0 47 #6101af
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+1 3 0 1 39 39 40 -1 20 0.000 1 0.0000 2625 3075 37 37 2625 3075 2662 3075
+1 3 0 1 39 39 40 -1 20 0.000 1 0.0000 3600 1650 37 37 3600 1650 3637 1650
+1 3 0 1 39 39 40 -1 20 0.000 1 0.0000 4275 2925 37 37 4275 2925 4312 2925
+2 3 0 1 45 7 50 -1 -1 0.000 2 0 -1 0 0 4
+	 3600 1650 4275 2925 3525 3600 3600 1650
+2 3 0 1 45 7 50 -1 -1 0.000 2 0 -1 0 0 4
 	 3600 1650 2625 3075 3525 3600 3600 1650
-2 3 0 1 1 7 50 -1 -1 0.000 2 0 -1 0 0 4
-	 3600 1650 4275 2925 3525 3600 3600 1650
-2 1 1 1 1 7 50 -1 -1 4.000 0 0 -1 0 0 2
+2 1 1 1 45 7 50 -1 -1 4.000 2 0 -1 0 0 2
 	 2625 3075 4275 2925
-4 0 0 50 -1 18 12 0.0000 4 135 105 2475 3225 1\001
-4 0 0 50 -1 18 12 0.0000 4 135 105 3450 3825 2\001
-4 0 0 50 -1 18 12 0.0000 4 135 105 4350 3075 3\001
-4 0 0 50 -1 18 12 0.0000 4 135 105 3600 1575 4\001
+4 0 0 40 -1 18 12 0.0000 4 135 105 2475 3225 1\001
+4 0 0 40 -1 18 12 0.0000 4 135 105 3450 3825 2\001
+4 0 0 40 -1 18 12 0.0000 4 135 105 4350 3075 3\001
+4 0 0 40 -1 18 12 0.0000 4 135 105 3600 1575 4\001

Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/figs/tet4.png
===================================================================
(Binary files differ)

Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.xml
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.xml	2006-07-04 00:55:20 UTC (rev 3916)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.xml	2006-07-05 18:14:54 UTC (rev 3917)
@@ -8,11 +8,10 @@
   <section>
     <title>Supported Finite Elements</title>
     <para>
-      PyLith currently only supports the 4-node linear tetrahedral
-      element. The node ordering must follow the convention shown in
-      <xref linkend="fig_tet4" />. Support for the 8-node linear
-      hexahedral element will be included in PyLith version 0.8.1,
-      expected to be released in July 2006.
+      PyLith currently only supports the 4-node linear tetrahedral and
+      8-node linear hexahedral elements. The node ordering must follow
+      the convention shown in <xref linkend="fig_tet4" /> and <xref
+      linkend="fig_hex8" />.
     </para>
 
     <figure id="fig_tet4">
@@ -26,6 +25,18 @@
 	</imageobject>
       </mediaobject>
     </figure>
+
+    <figure id="fig_hex8">
+      <title>Linear hexahedral finite element.</title>
+      <mediaobject>
+	<imageobject role="fo">
+	  <imagedata fileref="figs/hex8.eps" format="EPS" />
+	</imageobject>
+	<imageobject role="xhtml,html">
+	  <imagedata fileref="figs/hex8.png" format="PNG" />
+	</imageobject>
+      </mediaobject>
+    </figure>
   </section>
 
   <!-- SECTION +++++++++++++++++++++++++++++++++++++++++++++++++++ -->



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