[cig-commits] r14798 - in doc/cigma/manual: . figures figures/bm1 figures/bm2 figures/bm2/out figures/bm3 figures/bm3/out figures/bm4 figures/bm4/scripts figures/misc figures/old figures/scripts figures2 figures3 figures3/bm1 figures3/bm2 figures3/bm2/out figures3/bm3 figures3/bm3/out

luis at geodynamics.org luis at geodynamics.org
Mon Apr 27 11:39:19 PDT 2009


Author: luis
Date: 2009-04-27 11:39:11 -0700 (Mon, 27 Apr 2009)
New Revision: 14798

Added:
   doc/cigma/manual/figures/bm1/
   doc/cigma/manual/figures/bm1/alpha.png
   doc/cigma/manual/figures/bm1/alpha_2d.png
   doc/cigma/manual/figures/bm1/alpha_3d.png
   doc/cigma/manual/figures/bm1/process-images.sh
   doc/cigma/manual/figures/bm2/
   doc/cigma/manual/figures/bm2/heatflux.png
   doc/cigma/manual/figures/bm2/log_error_temperature_64_08_20000_2100_y099.png
   doc/cigma/manual/figures/bm2/log_error_temperature_64_16_20000_4700_y099.png
   doc/cigma/manual/figures/bm2/log_error_temperature_64_32_20000_9900_y099.png
   doc/cigma/manual/figures/bm2/log_error_velocity_64_08_20000_2100_y099.png
   doc/cigma/manual/figures/bm2/log_error_velocity_64_16_20000_4700_y099.png
   doc/cigma/manual/figures/bm2/log_error_velocity_64_32_20000_9900_y099.png
   doc/cigma/manual/figures/bm2/out/
   doc/cigma/manual/figures/bm2/out/.keep
   doc/cigma/manual/figures/bm2/out/fig_fields_64_20000_y099.png
   doc/cigma/manual/figures/bm2/out/fig_log_error_temperature_64_16_64_32_y099.png
   doc/cigma/manual/figures/bm2/out/fig_log_error_velocity_64_16_64_32_y099.png
   doc/cigma/manual/figures/bm2/process-images.sh
   doc/cigma/manual/figures/bm2/temperature_64_20000_y099.png
   doc/cigma/manual/figures/bm2/velocity_64_20000_y099.png
   doc/cigma/manual/figures/bm3/
   doc/cigma/manual/figures/bm3/full_log_error_pressure_128.png
   doc/cigma/manual/figures/bm3/full_log_error_pressure_256.png
   doc/cigma/manual/figures/bm3/full_log_error_pressure_512.png
   doc/cigma/manual/figures/bm3/full_log_error_pressure_512_128.png
   doc/cigma/manual/figures/bm3/full_log_error_pressure_512_256.png
   doc/cigma/manual/figures/bm3/full_log_error_velocity_128.png
   doc/cigma/manual/figures/bm3/full_log_error_velocity_256.png
   doc/cigma/manual/figures/bm3/full_log_error_velocity_512.png
   doc/cigma/manual/figures/bm3/full_log_error_velocity_512_128.png
   doc/cigma/manual/figures/bm3/full_log_error_velocity_512_256.png
   doc/cigma/manual/figures/bm3/full_pressure_512.png
   doc/cigma/manual/figures/bm3/full_velocity_512.png
   doc/cigma/manual/figures/bm3/inc_log_error_pressure_128.png
   doc/cigma/manual/figures/bm3/inc_log_error_pressure_256.png
   doc/cigma/manual/figures/bm3/inc_log_error_pressure_512.png
   doc/cigma/manual/figures/bm3/inc_log_error_pressure_512_128.png
   doc/cigma/manual/figures/bm3/inc_log_error_pressure_512_256.png
   doc/cigma/manual/figures/bm3/inc_log_error_velocity_512.png
   doc/cigma/manual/figures/bm3/inc_log_error_velocity_512_128.png
   doc/cigma/manual/figures/bm3/inc_log_error_velocity_512_256.png
   doc/cigma/manual/figures/bm3/inc_pressure_512.png
   doc/cigma/manual/figures/bm3/inc_velocity_512.png
   doc/cigma/manual/figures/bm3/inclusion_setup.eps
   doc/cigma/manual/figures/bm3/out/
   doc/cigma/manual/figures/bm3/out/.keep
   doc/cigma/manual/figures/bm3/out/fig_full_log_error_pressure_256_512.png
   doc/cigma/manual/figures/bm3/out/fig_full_log_error_pressure_512_128_512_256.png
   doc/cigma/manual/figures/bm3/out/fig_inc_log_error_pressure_256_512.png
   doc/cigma/manual/figures/bm3/out/fig_inc_log_error_pressure_512_128_512_256.png
   doc/cigma/manual/figures/bm3/out/fig_pressure_512.png
   doc/cigma/manual/figures/bm3/process-images.sh
   doc/cigma/manual/figures/bm4/
   doc/cigma/manual/figures/bm4/reverse-slip-fault.png
   doc/cigma/manual/figures/bm4/rsng-p0500-g0500-cell-threshold-velo-000.png
   doc/cigma/manual/figures/bm4/rsng-p0500-g0500-cell-threshold-velo-010.png
   doc/cigma/manual/figures/bm4/rsng-p0500-g0500-cell-threshold-velo-050.png
   doc/cigma/manual/figures/bm4/rsng-p0500-g0500-cell-threshold-velo-100.png
   doc/cigma/manual/figures/bm4/rsng-p0500-g0500-point-isosurf-res-disp-000.png
   doc/cigma/manual/figures/bm4/rsng-p0500-g0500-point-isosurf-res-disp-010.png
   doc/cigma/manual/figures/bm4/rsng-p0500-g0500-point-isosurf-res-disp-050.png
   doc/cigma/manual/figures/bm4/rsng-p0500-g0500-point-isosurf-res-disp-100.png
   doc/cigma/manual/figures/bm4/scripts/
   doc/cigma/manual/figures/bm4/scripts/bottom-layer.vtk
   doc/cigma/manual/figures/bm4/scripts/faults.mv2
   doc/cigma/manual/figures/bm4/scripts/full-list.txt
   doc/cigma/manual/figures/bm4/scripts/generate-cases.py
   doc/cigma/manual/figures/bm4/scripts/list.txt
   doc/cigma/manual/figures/bm4/scripts/reference-hex8.mv2
   doc/cigma/manual/figures/bm4/scripts/reference-hex8.vtk
   doc/cigma/manual/figures/bm4/scripts/reference-tet4.mv2
   doc/cigma/manual/figures/bm4/scripts/reference-tet4.vtk
   doc/cigma/manual/figures/bm4/scripts/reverse-slip-fault.vtk
   doc/cigma/manual/figures/bm4/scripts/rsng-p0500-g0500-cell-threshold-velo.mv2
   doc/cigma/manual/figures/bm4/scripts/rsng-p0500-g0500-point-isosurf-res-disp.mv2
   doc/cigma/manual/figures/bm4/scripts/rsng-p0500-g0500.sh
   doc/cigma/manual/figures/bm4/scripts/ssng-p0250-g0500-point-isosurf-disp.mv2
   doc/cigma/manual/figures/bm4/scripts/ssng-p0250-g0500.sh
   doc/cigma/manual/figures/bm4/scripts/ssng-p0500-g0500-isosurf-disp.mv2
   doc/cigma/manual/figures/bm4/scripts/ssng-p0500-g0500-point-isosurf-velo.mv2
   doc/cigma/manual/figures/bm4/scripts/ssng-p0500-g0500.sh
   doc/cigma/manual/figures/bm4/scripts/ssng-p0500-g0500.velo-010.mv2
   doc/cigma/manual/figures/bm4/scripts/strike-slip-fault.vtk
   doc/cigma/manual/figures/bm4/scripts/top-layer.vtk
   doc/cigma/manual/figures/bm4/ssng-p0250-g0500-point-isosurf-disp-000.png
   doc/cigma/manual/figures/bm4/ssng-p0500-g0500-isosurf-disp-000.png
   doc/cigma/manual/figures/bm4/ssng-p0500-g0500-isosurf-disp-010.png
   doc/cigma/manual/figures/bm4/ssng-p0500-g0500-isosurf-disp-050.png
   doc/cigma/manual/figures/bm4/ssng-p0500-g0500-isosurf-disp-100.png
   doc/cigma/manual/figures/bm4/ssng-p0500-g0500-point-isosurf-velo-000.png
   doc/cigma/manual/figures/bm4/ssng-p0500-g0500-point-isosurf-velo-010.png
   doc/cigma/manual/figures/bm4/ssng-p0500-g0500-point-isosurf-velo-050.png
   doc/cigma/manual/figures/bm4/ssng-p0500-g0500-point-isosurf-velo-100.png
   doc/cigma/manual/figures/bm4/ssng-p0500-g0500.velo-010.png
   doc/cigma/manual/figures/bm4/ssng_tet4_1000m_geofest_disp_t00.png
   doc/cigma/manual/figures/bm4/ssng_tet4_1000m_pylith_disp_t00.png
   doc/cigma/manual/figures/bm4/strike-slip-fault.png
   doc/cigma/manual/figures/common.sh
   doc/cigma/manual/figures/misc/
   doc/cigma/manual/figures/misc/hex.svg
   doc/cigma/manual/figures/misc/quad.svg
   doc/cigma/manual/figures/misc/tet.svg
   doc/cigma/manual/figures/misc/tri.svg
   doc/cigma/manual/figures/old/cigma-a2h-cube.jpg
   doc/cigma/manual/figures/old/cigma-abcd-triangle.jpg
   doc/cigma/manual/figures/old/degrees-freedom.gif
   doc/cigma/manual/figures/old/element-IDs.png
   doc/cigma/manual/figures/old/hdfview-bmrsnog.png
   doc/cigma/manual/figures/old/layers.png
   doc/cigma/manual/figures/old/mapping1.gif
   doc/cigma/manual/figures/old/mapping2.gif
   doc/cigma/manual/figures/old/mapping3.gif
   doc/cigma/manual/figures/old/meshA-diagram.gif
   doc/cigma/manual/figures/old/node-ordering-for-standard-ele-types.png
   doc/cigma/manual/figures/old/quadrature-rule-diagram.jpg
   doc/cigma/manual/figures/old/reference-hex8.png
   doc/cigma/manual/figures/old/reference-tet4.png
   doc/cigma/manual/subversion.cfg
   doc/cigma/manual/svn-autoprops.config
Removed:
   doc/cigma/manual/figures/cigma-a2h-cube.jpg
   doc/cigma/manual/figures/cigma-abcd-triangle.jpg
   doc/cigma/manual/figures/degrees-freedom.gif
   doc/cigma/manual/figures/element-IDs.png
   doc/cigma/manual/figures/hdfview-bmrsnog.png
   doc/cigma/manual/figures/layers.png
   doc/cigma/manual/figures/mapping1.gif
   doc/cigma/manual/figures/mapping2.gif
   doc/cigma/manual/figures/mapping3.gif
   doc/cigma/manual/figures/meshA-diagram.gif
   doc/cigma/manual/figures/node-ordering-for-standard-ele-types.png
   doc/cigma/manual/figures/old/rsng-p0500-g0500-cell-threshold-velo-000.png
   doc/cigma/manual/figures/old/rsng-p0500-g0500-cell-threshold-velo-010.png
   doc/cigma/manual/figures/old/rsng-p0500-g0500-cell-threshold-velo-050.png
   doc/cigma/manual/figures/old/rsng-p0500-g0500-cell-threshold-velo-100.png
   doc/cigma/manual/figures/old/rsng-p0500-g0500-point-isosurf-res-disp-000.png
   doc/cigma/manual/figures/old/rsng-p0500-g0500-point-isosurf-res-disp-010.png
   doc/cigma/manual/figures/old/rsng-p0500-g0500-point-isosurf-res-disp-050.png
   doc/cigma/manual/figures/old/rsng-p0500-g0500-point-isosurf-res-disp-100.png
   doc/cigma/manual/figures/old/ssng-p0250-g0500-point-isosurf-disp-000.png
   doc/cigma/manual/figures/old/ssng-p0500-g0500-isosurf-disp-000.png
   doc/cigma/manual/figures/old/ssng-p0500-g0500-isosurf-disp-010.png
   doc/cigma/manual/figures/old/ssng-p0500-g0500-isosurf-disp-050.png
   doc/cigma/manual/figures/old/ssng-p0500-g0500-isosurf-disp-100.png
   doc/cigma/manual/figures/old/ssng-p0500-g0500-point-isosurf-velo-000.png
   doc/cigma/manual/figures/old/ssng-p0500-g0500-point-isosurf-velo-010.png
   doc/cigma/manual/figures/old/ssng-p0500-g0500-point-isosurf-velo-050.png
   doc/cigma/manual/figures/old/ssng-p0500-g0500-point-isosurf-velo-100.png
   doc/cigma/manual/figures/old/ssng-p0500-g0500.velo-010.png
   doc/cigma/manual/figures/old/ssng_tet4_1000m_geofest_disp_t00.png
   doc/cigma/manual/figures/old/ssng_tet4_1000m_pylith_disp_t00.png
   doc/cigma/manual/figures/quadrature-rule-diagram.jpg
   doc/cigma/manual/figures/reference-hex8.png
   doc/cigma/manual/figures/reference-tet4.png
   doc/cigma/manual/figures/reverse-slip-fault.png
   doc/cigma/manual/figures/scripts/bottom-layer.vtk
   doc/cigma/manual/figures/scripts/faults.mv2
   doc/cigma/manual/figures/scripts/full-list.txt
   doc/cigma/manual/figures/scripts/generate-cases.py
   doc/cigma/manual/figures/scripts/list.txt
   doc/cigma/manual/figures/scripts/reference-hex8.mv2
   doc/cigma/manual/figures/scripts/reference-hex8.vtk
   doc/cigma/manual/figures/scripts/reference-tet4.mv2
   doc/cigma/manual/figures/scripts/reference-tet4.vtk
   doc/cigma/manual/figures/scripts/reverse-slip-fault.vtk
   doc/cigma/manual/figures/scripts/rsng-p0500-g0500-cell-threshold-velo.mv2
   doc/cigma/manual/figures/scripts/rsng-p0500-g0500-point-isosurf-res-disp.mv2
   doc/cigma/manual/figures/scripts/rsng-p0500-g0500.sh
   doc/cigma/manual/figures/scripts/ssng-p0250-g0500-point-isosurf-disp.mv2
   doc/cigma/manual/figures/scripts/ssng-p0250-g0500.sh
   doc/cigma/manual/figures/scripts/ssng-p0500-g0500-isosurf-disp.mv2
   doc/cigma/manual/figures/scripts/ssng-p0500-g0500-point-isosurf-velo.mv2
   doc/cigma/manual/figures/scripts/ssng-p0500-g0500.sh
   doc/cigma/manual/figures/scripts/ssng-p0500-g0500.velo-010.mv2
   doc/cigma/manual/figures/scripts/strike-slip-fault.vtk
   doc/cigma/manual/figures/scripts/top-layer.vtk
   doc/cigma/manual/figures/strike-slip-fault.png
   doc/cigma/manual/figures2/alpha_cube.png
   doc/cigma/manual/figures2/alpha_square.png
   doc/cigma/manual/figures2/inclusion_setup.eps
   doc/cigma/manual/figures2/log_res_circular_inclusion_256_064.png
   doc/cigma/manual/figures2/log_res_circular_inclusion_256_128.png
   doc/cigma/manual/figures2/log_res_citcomcu_velocity_32_08.png
   doc/cigma/manual/figures2/log_res_citcomcu_velocity_32_16.png
   doc/cigma/manual/figures2/log_res_square_6_2.png
   doc/cigma/manual/figures2/log_res_square_6_3.png
   doc/cigma/manual/figures2/log_res_square_6_4.png
   doc/cigma/manual/figures2/log_res_square_6_5.png
   doc/cigma/manual/figures2/res_circular_inclusion_256_064.png
   doc/cigma/manual/figures2/res_circular_inclusion_256_128.png
   doc/cigma/manual/figures3/bm1/alpha.png
   doc/cigma/manual/figures3/bm1/alpha_2d.png
   doc/cigma/manual/figures3/bm1/alpha_3d.png
   doc/cigma/manual/figures3/bm1/process-images.sh
   doc/cigma/manual/figures3/bm2/heatflux.png
   doc/cigma/manual/figures3/bm2/log_error_temperature_64_08_20000_2100_y099.png
   doc/cigma/manual/figures3/bm2/log_error_temperature_64_16_20000_4700_y099.png
   doc/cigma/manual/figures3/bm2/log_error_temperature_64_32_20000_9900_y099.png
   doc/cigma/manual/figures3/bm2/log_error_velocity_64_08_20000_2100_y099.png
   doc/cigma/manual/figures3/bm2/log_error_velocity_64_16_20000_4700_y099.png
   doc/cigma/manual/figures3/bm2/log_error_velocity_64_32_20000_9900_y099.png
   doc/cigma/manual/figures3/bm2/out/.keep
   doc/cigma/manual/figures3/bm2/out/fig_fields_64_20000_y099.png
   doc/cigma/manual/figures3/bm2/out/fig_log_error_temperature_64_16_64_32_y099.png
   doc/cigma/manual/figures3/bm2/out/fig_log_error_velocity_64_16_64_32_y099.png
   doc/cigma/manual/figures3/bm2/process-images.sh
   doc/cigma/manual/figures3/bm2/temperature_64_20000_y099.png
   doc/cigma/manual/figures3/bm2/velocity_64_20000_y099.png
   doc/cigma/manual/figures3/bm3/full_log_error_pressure_128.png
   doc/cigma/manual/figures3/bm3/full_log_error_pressure_256.png
   doc/cigma/manual/figures3/bm3/full_log_error_pressure_512.png
   doc/cigma/manual/figures3/bm3/full_log_error_pressure_512_128.png
   doc/cigma/manual/figures3/bm3/full_log_error_pressure_512_256.png
   doc/cigma/manual/figures3/bm3/full_log_error_velocity_128.png
   doc/cigma/manual/figures3/bm3/full_log_error_velocity_256.png
   doc/cigma/manual/figures3/bm3/full_log_error_velocity_512.png
   doc/cigma/manual/figures3/bm3/full_log_error_velocity_512_128.png
   doc/cigma/manual/figures3/bm3/full_log_error_velocity_512_256.png
   doc/cigma/manual/figures3/bm3/full_pressure_512.png
   doc/cigma/manual/figures3/bm3/full_velocity_512.png
   doc/cigma/manual/figures3/bm3/inc_log_error_pressure_128.png
   doc/cigma/manual/figures3/bm3/inc_log_error_pressure_256.png
   doc/cigma/manual/figures3/bm3/inc_log_error_pressure_512.png
   doc/cigma/manual/figures3/bm3/inc_log_error_pressure_512_128.png
   doc/cigma/manual/figures3/bm3/inc_log_error_pressure_512_256.png
   doc/cigma/manual/figures3/bm3/inc_log_error_velocity_512.png
   doc/cigma/manual/figures3/bm3/inc_log_error_velocity_512_128.png
   doc/cigma/manual/figures3/bm3/inc_log_error_velocity_512_256.png
   doc/cigma/manual/figures3/bm3/inc_pressure_512.png
   doc/cigma/manual/figures3/bm3/inc_velocity_512.png
   doc/cigma/manual/figures3/bm3/out/.keep
   doc/cigma/manual/figures3/bm3/out/fig_full_log_error_pressure_256_512.png
   doc/cigma/manual/figures3/bm3/out/fig_full_log_error_pressure_512_128_512_256.png
   doc/cigma/manual/figures3/bm3/out/fig_inc_log_error_pressure_256_512.png
   doc/cigma/manual/figures3/bm3/out/fig_inc_log_error_pressure_512_128_512_256.png
   doc/cigma/manual/figures3/bm3/out/fig_pressure_512.png
   doc/cigma/manual/figures3/bm3/process-images.sh
   doc/cigma/manual/figures3/common.sh
   doc/cigma/manual/hex.svg
   doc/cigma/manual/quad.svg
   doc/cigma/manual/tet.svg
   doc/cigma/manual/tri.svg
Modified:
   doc/cigma/manual/cigma.lyx
   doc/cigma/manual/main.lyx
Log:
Fixing failed git-svn dcommit operation (from svn:mime-type issue with images).

Modified: doc/cigma/manual/cigma.lyx
===================================================================
--- doc/cigma/manual/cigma.lyx	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/cigma.lyx	2009-04-27 18:39:11 UTC (rev 14798)
@@ -280,21 +280,21 @@
 \begin_layout Bibliography
 \begin_inset CommandInset bibitem
 LatexCommand bibitem
-label "8"
-key "Schmid Podladchikov 2003"
+label "6"
+key "Uesu 2005"
 
 \end_inset
 
-Schmid, D.W., and Y.Y.
- Podladchikov (2003), Analytical solutions for deformable elliptical inclusions
- in general shear, 
+Uesu, D., L.
+ Bavoil, S.
+ Fleishman, J.
+ Shepherd, and C.
+ Silva (2005), Simplification of Unstructured Tetrahedral Meshes by Point-Sampli
+ng, 
 \emph on
-Geophys.
- J.
- Int.
- 155
+Proceedings of the 2005 International Workshop on Volume Graphics,
 \emph default
-(1), 269-288, doi: 10.1046/j.1365-246X.2003.02042.x.
+ 157-165, doi: 10.2312/VG/VG05/157-165.
 \end_layout
 
 \begin_layout Bibliography
@@ -319,21 +319,21 @@
 \begin_layout Bibliography
 \begin_inset CommandInset bibitem
 LatexCommand bibitem
-label "6"
-key "Uesu 2005"
+label "8"
+key "Schmid Podladchikov 2003"
 
 \end_inset
 
-Uesu, D., L.
- Bavoil, S.
- Fleishman, J.
- Shepherd, and C.
- Silva (2005), Simplification of Unstructured Tetrahedral Meshes by Point-Sampli
-ng, 
+Schmid, D.W., and Y.Y.
+ Podladchikov (2003), Analytical solutions for deformable elliptical inclusions
+ in general shear, 
 \emph on
-Proceedings of the 2005 International Workshop on Volume Graphics,
+Geophys.
+ J.
+ Int.
+ 155
 \emph default
- 157-165, doi: 10.2312/VG/VG05/157-165.
+(1), 269-288, doi: 10.1046/j.1365-246X.2003.02042.x.
 \end_layout
 
 \end_body

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   + image/png

Copied: doc/cigma/manual/figures/bm1/alpha_2d.png (from rev 14797, doc/cigma/manual/figures3/bm1/alpha_2d.png)
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Copied: doc/cigma/manual/figures/bm1/alpha_3d.png (from rev 14797, doc/cigma/manual/figures3/bm1/alpha_3d.png)
===================================================================
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Property changes on: doc/cigma/manual/figures/bm1/alpha_3d.png
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   + image/png

Copied: doc/cigma/manual/figures/bm1/process-images.sh (from rev 14797, doc/cigma/manual/figures3/bm1/process-images.sh)
===================================================================
--- doc/cigma/manual/figures/bm1/process-images.sh	                        (rev 0)
+++ doc/cigma/manual/figures/bm1/process-images.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,19 @@
+#!/bin/bash
+set -x
+source ../common.sh
+
+img-caption '(a) 2D Poisson Problem' \
+    alpha_2d.png \
+    rm_alpha_2d.png
+
+img-caption '(b) 3D Poisson Problem' \
+    alpha_3d.png \
+    rm_alpha_3d.png
+
+cat-pair \
+    rm_alpha_2d.png \
+    rm_alpha_3d.png \
+    alpha.png
+
+rm -f rm_*.png
+

Copied: doc/cigma/manual/figures/bm2/heatflux.png (from rev 14797, doc/cigma/manual/figures3/bm2/heatflux.png)
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Property changes on: doc/cigma/manual/figures/bm2/heatflux.png
___________________________________________________________________
Name: svn:mime-type
   + image/png

Copied: doc/cigma/manual/figures/bm2/log_error_temperature_64_08_20000_2100_y099.png (from rev 14797, doc/cigma/manual/figures3/bm2/log_error_temperature_64_08_20000_2100_y099.png)
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Copied: doc/cigma/manual/figures/bm2/process-images.sh (from rev 14797, doc/cigma/manual/figures3/bm2/process-images.sh)
===================================================================
--- doc/cigma/manual/figures/bm2/process-images.sh	                        (rev 0)
+++ doc/cigma/manual/figures/bm2/process-images.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,93 @@
+#!/bin/bash
+
+# Include some common image processing functions
+source ../common.sh
+
+# Enable bash debugging
+set -x
+
+#
+# List of the original images
+#
+imglist="
+    temperature_64_20000_y099.png
+    velocity_64_20000_y099.png
+    log_error_temperature_64_08_20000_2100_y099.png
+    log_error_temperature_64_16_20000_4700_y099.png
+    log_error_temperature_64_32_20000_9900_y099.png
+    log_error_velocity_64_08_20000_2100_y099.png
+    log_error_velocity_64_16_20000_4700_y099.png
+    log_error_velocity_64_32_20000_9900_y099.png
+"
+
+#
+# Operate on copies of the original images
+#
+orig=${PWD}
+tmp=/tmp/bm2
+mkdir -p $tmp
+for img in ${imglist}; do
+    cp -f -v ${img} ${tmp}
+done
+cd ${tmp}
+
+
+# 
+# Start processing the images
+#
+
+for img in ${imglist}; do
+    img-trim ${img}
+    img-add-border ${img} 100
+done
+
+img-caption '(a) Temperature                           ' \
+    temperature_64_20000_y099.png \
+    temperature_64_20000_y099.png
+
+img-caption '(b) Velocity                     ' \
+    velocity_64_20000_y099.png \
+    velocity_64_20000_y099.png
+
+img-caption '(a) log (temperature error for 16 x 16 x 16 case)             ' \
+    log_error_temperature_64_16_20000_4700_y099.png \
+    log_error_temperature_64_16_20000_4700_y099.png
+
+img-caption '(b) log (temperature error for 32 x 32 x 32 case)         ' \
+    log_error_temperature_64_32_20000_9900_y099.png \
+    log_error_temperature_64_32_20000_9900_y099.png
+
+img-caption '(a) log (velocity error for 16 x 16 x 16 case)                ' \
+    log_error_velocity_64_16_20000_4700_y099.png \
+    log_error_velocity_64_16_20000_4700_y099.png
+
+img-caption '(b) log (velocity error for 32 x 32 x 32 case)            ' \
+    log_error_velocity_64_32_20000_9900_y099.png \
+    log_error_velocity_64_32_20000_9900_y099.png
+
+cat-pair \
+    temperature_64_20000_y099.png \
+    velocity_64_20000_y099.png \
+    fig_fields_64_20000_y099.png
+
+cat-pair \
+    log_error_temperature_64_16_20000_4700_y099.png \
+    log_error_temperature_64_32_20000_9900_y099.png \
+    fig_log_error_temperature_64_16_64_32_y099.png
+    
+cat-pair \
+    log_error_velocity_64_16_20000_4700_y099.png \
+    log_error_velocity_64_32_20000_9900_y099.png \
+    fig_log_error_velocity_64_16_64_32_y099.png
+
+# finally, resize the images that will be included in the manual
+for img in fig_*; do
+    img-resize ${img}
+done
+
+#
+# Copy the images back
+#
+cd ${orig}
+cp -f -v ${tmp}/fig_* ${orig}/out
+

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===================================================================

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Copied: doc/cigma/manual/figures/bm3/process-images.sh (from rev 14797, doc/cigma/manual/figures3/bm3/process-images.sh)
===================================================================
--- doc/cigma/manual/figures/bm3/process-images.sh	                        (rev 0)
+++ doc/cigma/manual/figures/bm3/process-images.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,132 @@
+#!/bin/bash
+#
+
+# Include some common image processing functions
+source ../common.sh
+
+# Enable bash debugging
+set -x
+
+#
+# List of the original image names
+#
+imglist="
+    full_pressure_512.png
+    full_velocity_512.png
+    full_log_error_pressure_128.png
+    full_log_error_pressure_256.png
+    full_log_error_pressure_512.png
+    full_log_error_pressure_512_128.png
+    full_log_error_pressure_512_256.png
+    full_log_error_velocity_128.png
+    full_log_error_velocity_256.png
+    full_log_error_velocity_512.png
+    full_log_error_velocity_512_128.png
+    full_log_error_velocity_512_256.png
+    inc_pressure_512.png
+    inc_velocity_512.png
+    inc_log_error_pressure_128.png
+    inc_log_error_pressure_256.png
+    inc_log_error_pressure_512.png
+    inc_log_error_pressure_512_128.png
+    inc_log_error_pressure_512_256.png
+    inc_log_error_velocity_512.png
+    inc_log_error_velocity_512_128.png
+    inc_log_error_velocity_512_256.png
+"
+
+# 
+# Operate on copies of the original images
+#
+orig=${PWD}
+tmp=/tmp/bm3
+mkdir -p $tmp
+for img in ${imglist}; do
+    cp -f -v ${img} ${tmp}
+done
+cd ${tmp}
+
+
+#
+# Start processing the images
+#
+
+for img in ${imglist}; do
+    img-trim ${img}
+    img-add-border ${img} 100
+done
+
+
+img-caption '(a) Pressure' \
+    full_pressure_512.png \
+    full_pressure_512.png
+img-caption '(b) Pressure near inclusion' \
+    inc_pressure_512.png \
+    inc_pressure_512.png
+
+img-caption '(a) log (pressure error for 256 x 256 case)' \
+    full_log_error_pressure_256.png \
+    full_log_error_pressure_256.png
+img-caption '(b) log (pressure error for 512 x 512 case)' \
+    full_log_error_pressure_512.png \
+    full_log_error_pressure_512.png
+
+img-caption '(a) log (pressure error for 128 x 128 case)' \
+    full_log_error_pressure_512_128.png \
+    full_log_error_pressure_512_128.png
+img-caption '(a) log (pressure error for 256 x 256 case)' \
+    full_log_error_pressure_512_256.png \
+    full_log_error_pressure_512_256.png
+
+img-caption '(a) log (pressure error for 256 x 256 case)' \
+    inc_log_error_pressure_256.png \
+    inc_log_error_pressure_256.png
+img-caption '(b) log (pressure error for 512 x 512 case)' \
+    inc_log_error_pressure_512.png \
+    inc_log_error_pressure_512.png
+
+img-caption '(a) log (pressure error for 128 x 128 case)' \
+    inc_log_error_pressure_512_128.png \
+    inc_log_error_pressure_512_128.png
+img-caption '(a) log (pressure error for 256 x 256 case)' \
+    inc_log_error_pressure_512_256.png \
+    inc_log_error_pressure_512_256.png
+
+
+cat-pair \
+    full_pressure_512.png \
+    inc_pressure_512.png \
+    fig_pressure_512.png
+
+cat-pair \
+    full_log_error_pressure_256.png \
+    full_log_error_pressure_512.png \
+    fig_full_log_error_pressure_256_512.png
+
+cat-pair \
+    full_log_error_pressure_512_128.png \
+    full_log_error_pressure_512_256.png \
+    fig_full_log_error_pressure_512_128_512_256.png
+
+cat-pair \
+    inc_log_error_pressure_256.png \
+    inc_log_error_pressure_512.png \
+    fig_inc_log_error_pressure_256_512.png \
+
+cat-pair \
+    inc_log_error_pressure_512_128.png \
+    inc_log_error_pressure_512_256.png \
+    fig_inc_log_error_pressure_512_128_512_256.png
+
+
+# finally, resize the images that will be included in the manual
+for img in fig_*; do
+    resize-image ${img}
+done
+
+#
+# Copy the images back
+#
+cd ${orig}
+cp -f -v ${tmp}/fig_* ${orig}/out
+

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Copied: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-cell-threshold-velo-010.png (from rev 14797, doc/cigma/manual/figures/old/rsng-p0500-g0500-cell-threshold-velo-010.png)
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Property changes on: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-cell-threshold-velo-010.png
___________________________________________________________________
Name: svn:mime-type
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Copied: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-cell-threshold-velo-050.png (from rev 14797, doc/cigma/manual/figures/old/rsng-p0500-g0500-cell-threshold-velo-050.png)
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Property changes on: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-cell-threshold-velo-050.png
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Name: svn:mime-type
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Copied: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-cell-threshold-velo-100.png (from rev 14797, doc/cigma/manual/figures/old/rsng-p0500-g0500-cell-threshold-velo-100.png)
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Property changes on: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-cell-threshold-velo-100.png
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Name: svn:mime-type
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Copied: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-point-isosurf-res-disp-000.png (from rev 14797, doc/cigma/manual/figures/old/rsng-p0500-g0500-point-isosurf-res-disp-000.png)
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Property changes on: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-point-isosurf-res-disp-000.png
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Name: svn:mime-type
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Copied: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-point-isosurf-res-disp-010.png (from rev 14797, doc/cigma/manual/figures/old/rsng-p0500-g0500-point-isosurf-res-disp-010.png)
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Property changes on: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-point-isosurf-res-disp-010.png
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Name: svn:mime-type
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Copied: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-point-isosurf-res-disp-050.png (from rev 14797, doc/cigma/manual/figures/old/rsng-p0500-g0500-point-isosurf-res-disp-050.png)
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Property changes on: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-point-isosurf-res-disp-050.png
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Name: svn:mime-type
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Copied: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-point-isosurf-res-disp-100.png (from rev 14797, doc/cigma/manual/figures/old/rsng-p0500-g0500-point-isosurf-res-disp-100.png)
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Property changes on: doc/cigma/manual/figures/bm4/rsng-p0500-g0500-point-isosurf-res-disp-100.png
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Name: svn:mime-type
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Copied: doc/cigma/manual/figures/bm4/scripts/bottom-layer.vtk (from rev 14797, doc/cigma/manual/figures/scripts/bottom-layer.vtk)
===================================================================
--- doc/cigma/manual/figures/bm4/scripts/bottom-layer.vtk	                        (rev 0)
+++ doc/cigma/manual/figures/bm4/scripts/bottom-layer.vtk	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,20 @@
+# vtk DataFile Version 1.0
+This line is a comment
+ASCII
+DATASET POLYDATA
+POINTS 8 float
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+4  0 2 6 4
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+4  0 4 5 1
+4  2 3 7 6
+4  0 1 3 2
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Copied: doc/cigma/manual/figures/bm4/scripts/faults.mv2 (from rev 14797, doc/cigma/manual/figures/scripts/faults.mv2)
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Copied: doc/cigma/manual/figures/bm4/scripts/full-list.txt (from rev 14797, doc/cigma/manual/figures/scripts/full-list.txt)
===================================================================
--- doc/cigma/manual/figures/bm4/scripts/full-list.txt	                        (rev 0)
+++ doc/cigma/manual/figures/bm4/scripts/full-list.txt	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,288 @@
+rsng-pylith_tet4_1000m-pylith_tet4_1000m
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+ssng-geofest_tet4_0250m-pylith_hex8_0250m
+ssng-geofest_tet4_0250m-geofest_tet4_1000m
+ssng-geofest_tet4_0250m-geofest_tet4_0500m
+ssng-geofest_tet4_0250m-geofest_tet4_0250m
+ssng-geofest_tet4_0250m-geofest_hex8_1000m
+ssng-geofest_tet4_0250m-geofest_hex8_0500m
+ssng-geofest_tet4_0250m-geofest_hex8_0250m
+ssng-geofest_hex8_1000m-pylith_tet4_1000m
+ssng-geofest_hex8_1000m-pylith_tet4_0500m
+ssng-geofest_hex8_1000m-pylith_tet4_0250m
+ssng-geofest_hex8_1000m-pylith_hex8_1000m
+ssng-geofest_hex8_1000m-pylith_hex8_0500m
+ssng-geofest_hex8_1000m-pylith_hex8_0250m
+ssng-geofest_hex8_1000m-geofest_tet4_1000m
+ssng-geofest_hex8_1000m-geofest_tet4_0500m
+ssng-geofest_hex8_1000m-geofest_tet4_0250m
+ssng-geofest_hex8_1000m-geofest_hex8_1000m
+ssng-geofest_hex8_1000m-geofest_hex8_0500m
+ssng-geofest_hex8_1000m-geofest_hex8_0250m
+ssng-geofest_hex8_0500m-pylith_tet4_1000m
+ssng-geofest_hex8_0500m-pylith_tet4_0500m
+ssng-geofest_hex8_0500m-pylith_tet4_0250m
+ssng-geofest_hex8_0500m-pylith_hex8_1000m
+ssng-geofest_hex8_0500m-pylith_hex8_0500m
+ssng-geofest_hex8_0500m-pylith_hex8_0250m
+ssng-geofest_hex8_0500m-geofest_tet4_1000m
+ssng-geofest_hex8_0500m-geofest_tet4_0500m
+ssng-geofest_hex8_0500m-geofest_tet4_0250m
+ssng-geofest_hex8_0500m-geofest_hex8_1000m
+ssng-geofest_hex8_0500m-geofest_hex8_0500m
+ssng-geofest_hex8_0500m-geofest_hex8_0250m
+ssng-geofest_hex8_0250m-pylith_tet4_1000m
+ssng-geofest_hex8_0250m-pylith_tet4_0500m
+ssng-geofest_hex8_0250m-pylith_tet4_0250m
+ssng-geofest_hex8_0250m-pylith_hex8_1000m
+ssng-geofest_hex8_0250m-pylith_hex8_0500m
+ssng-geofest_hex8_0250m-pylith_hex8_0250m
+ssng-geofest_hex8_0250m-geofest_tet4_1000m
+ssng-geofest_hex8_0250m-geofest_tet4_0500m
+ssng-geofest_hex8_0250m-geofest_tet4_0250m
+ssng-geofest_hex8_0250m-geofest_hex8_1000m
+ssng-geofest_hex8_0250m-geofest_hex8_0500m
+ssng-geofest_hex8_0250m-geofest_hex8_0250m

Copied: doc/cigma/manual/figures/bm4/scripts/generate-cases.py (from rev 14797, doc/cigma/manual/figures/scripts/generate-cases.py)
===================================================================
--- doc/cigma/manual/figures/bm4/scripts/generate-cases.py	                        (rev 0)
+++ doc/cigma/manual/figures/bm4/scripts/generate-cases.py	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,27 @@
+#!/usr/bin/env python
+
+benchmarks = ['rsng', 'ssng']
+codes = ['pylith', 'geofest']
+
+resolutions = ['1000m', '0500m', '0250m']
+elements = ['tet4', 'hex8']
+
+cases = []
+for code in codes:
+    for elt in elements:
+        for res in resolutions:
+            cases.append("%s_%s_%s" % (code,elt,res))
+
+comparisons = []
+for a in cases:
+    for b in cases:
+        comparisons.append('%s-%s' % (a,b))
+
+benchmark_comparisons = []
+for bm in benchmarks:
+    for cmp in comparisons:
+        benchmark_comparisons.append('%s-%s' % (bm,cmp))
+
+for bm in benchmark_comparisons:
+    print bm
+

Copied: doc/cigma/manual/figures/bm4/scripts/list.txt (from rev 14797, doc/cigma/manual/figures/scripts/list.txt)
===================================================================
--- doc/cigma/manual/figures/bm4/scripts/list.txt	                        (rev 0)
+++ doc/cigma/manual/figures/bm4/scripts/list.txt	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,26 @@
+
+p0500 -> /pylith/tet4_0500m
+g0500 -> /geofest/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

Copied: doc/cigma/manual/figures/bm4/scripts/reference-hex8.mv2 (from rev 14797, doc/cigma/manual/figures/scripts/reference-hex8.mv2)
===================================================================
(Binary files differ)

Copied: doc/cigma/manual/figures/bm4/scripts/reference-hex8.vtk (from rev 14797, doc/cigma/manual/figures/scripts/reference-hex8.vtk)
===================================================================
--- doc/cigma/manual/figures/bm4/scripts/reference-hex8.vtk	                        (rev 0)
+++ doc/cigma/manual/figures/bm4/scripts/reference-hex8.vtk	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,20 @@
+# vtk DataFile Version 1.0
+This line is a comment
+ASCII
+DATASET POLYDATA
+POINTS 8 float
+ -1 -1 -1
+ +1 -1 -1
+ -1 +1 -1
+ +1 +1 -1
+ -1 -1 +1
+ +1 -1 +1
+ -1 +1 +1
+ +1 +1 +1
+POLYGONS 6 30
+4  0 1 5 4
+4  2 6 7 3
+4  0 4 6 2
+4  1 3 7 5
+4  0 2 3 1
+4  4 5 7 6

Copied: doc/cigma/manual/figures/bm4/scripts/reference-tet4.mv2 (from rev 14797, doc/cigma/manual/figures/scripts/reference-tet4.mv2)
===================================================================
(Binary files differ)

Copied: doc/cigma/manual/figures/bm4/scripts/reference-tet4.vtk (from rev 14797, doc/cigma/manual/figures/scripts/reference-tet4.vtk)
===================================================================
--- doc/cigma/manual/figures/bm4/scripts/reference-tet4.vtk	                        (rev 0)
+++ doc/cigma/manual/figures/bm4/scripts/reference-tet4.vtk	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,14 @@
+# vtk DataFile Version 1.0
+This line is a comment
+ASCII
+DATASET POLYDATA
+POINTS 4 float
+ -1 -1 -1
+ +1 -1 -1
+ -1 +1 -1
+ -1 -1 +1
+POLYGONS 4 16
+3 0 2 1
+3 0 1 3
+3 0 3 2
+3 1 2 3

Copied: doc/cigma/manual/figures/bm4/scripts/reverse-slip-fault.vtk (from rev 14797, doc/cigma/manual/figures/scripts/reverse-slip-fault.vtk)
===================================================================
--- doc/cigma/manual/figures/bm4/scripts/reverse-slip-fault.vtk	                        (rev 0)
+++ doc/cigma/manual/figures/bm4/scripts/reverse-slip-fault.vtk	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,11 @@
+# vtk DataFile Version 1.0
+This line is a comment
+ASCII
+DATASET POLYDATA
+POINTS 4 float
+ 4000.0      0.0       0.0
+ 4000.0  16000.0       0.0
+20000.0  16000.0  -16000.0
+20000.0      0.0  -16000.0
+POLYGONS 1 5
+4  0 1 2 3

Copied: doc/cigma/manual/figures/bm4/scripts/rsng-p0500-g0500-cell-threshold-velo.mv2 (from rev 14797, doc/cigma/manual/figures/scripts/rsng-p0500-g0500-cell-threshold-velo.mv2)
===================================================================
(Binary files differ)

Copied: doc/cigma/manual/figures/bm4/scripts/rsng-p0500-g0500-point-isosurf-res-disp.mv2 (from rev 14797, doc/cigma/manual/figures/scripts/rsng-p0500-g0500-point-isosurf-res-disp.mv2)
===================================================================
(Binary files differ)

Copied: doc/cigma/manual/figures/bm4/scripts/rsng-p0500-g0500.sh (from rev 14797, doc/cigma/manual/figures/scripts/rsng-p0500-g0500.sh)
===================================================================
--- doc/cigma/manual/figures/bm4/scripts/rsng-p0500-g0500.sh	                        (rev 0)
+++ doc/cigma/manual/figures/bm4/scripts/rsng-p0500-g0500.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,82 @@
+#!/bin/bash
+
+bm=bmrsnog
+bmfile=$HOME/benchmarks/$bm.h5
+prefix=rsng-p0500-g0500
+
+#########
+
+echo "---------------------------------------------------------------"
+var=variables/displacement/step00000
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var          \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var      \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
+              --output=$prefix.disp-000.vtk
+
+echo "---------------------------------------------------------------"
+var=variables/displacement/step00010
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var          \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var      \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
+              --output=$prefix.disp-010.vtk
+
+echo "---------------------------------------------------------------"
+var=variables/displacement/step00050
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var          \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var      \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
+              --output=$prefix.disp-050.vtk
+
+echo "---------------------------------------------------------------"
+var=variables/displacement/step00100
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var          \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var      \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
+              --output=$prefix.disp-100.vtk
+
+#########
+
+echo "---------------------------------------------------------------"
+t=step00000
+var1=variables/velocity/$t
+var2=variables/del_displacement/$t
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var1         \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var2     \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
+              --output=$prefix.velo-000.vtk
+
+echo "---------------------------------------------------------------"
+t=step00010
+var1=variables/velocity/$t
+var2=variables/del_displacement/$t
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var1         \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var2     \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
+              --output=$prefix.velo-010.vtk
+
+echo "---------------------------------------------------------------"
+t=step00050
+var1=variables/velocity/$t
+var2=variables/del_displacement/$t
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var1         \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var2     \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
+              --output=$prefix.velo-050.vtk
+
+echo "---------------------------------------------------------------"
+t=step00100
+var1=variables/velocity/$t
+var2=variables/del_displacement/$t
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var1         \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var2     \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
+              --output=$prefix.velo-100.vtk
+

Copied: doc/cigma/manual/figures/bm4/scripts/ssng-p0250-g0500-point-isosurf-disp.mv2 (from rev 14797, doc/cigma/manual/figures/scripts/ssng-p0250-g0500-point-isosurf-disp.mv2)
===================================================================
(Binary files differ)

Copied: doc/cigma/manual/figures/bm4/scripts/ssng-p0250-g0500.sh (from rev 14797, doc/cigma/manual/figures/scripts/ssng-p0250-g0500.sh)
===================================================================
--- doc/cigma/manual/figures/bm4/scripts/ssng-p0250-g0500.sh	                        (rev 0)
+++ doc/cigma/manual/figures/bm4/scripts/ssng-p0250-g0500.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,31 @@
+#!/bin/bash
+
+bm=bmssnog
+bmfile=$HOME/benchmarks/$bm.h5
+prefix=ssng-p0250-g0500
+
+#########
+
+echo "---------------------------------------------"
+var=variables/displacement/step00000
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0250m/$var     \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var   \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0250m       \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m      \
+              --verbose --output-frequency=10000                \
+              --output=$prefix.disp-000.vtk
+
+
+#########
+
+echo "---------------------------------------------"
+t=step00000
+var1=variables/velocity/$t
+var2=variables/del_displacement/$t
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0250m/$var1    \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var2  \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0250m       \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m      \
+              --verbose --output-frequency=10000                \
+              --output=$prefix.velo-000.vtk 
+

Copied: doc/cigma/manual/figures/bm4/scripts/ssng-p0500-g0500-isosurf-disp.mv2 (from rev 14797, doc/cigma/manual/figures/scripts/ssng-p0500-g0500-isosurf-disp.mv2)
===================================================================
(Binary files differ)

Copied: doc/cigma/manual/figures/bm4/scripts/ssng-p0500-g0500-point-isosurf-velo.mv2 (from rev 14797, doc/cigma/manual/figures/scripts/ssng-p0500-g0500-point-isosurf-velo.mv2)
===================================================================
(Binary files differ)

Copied: doc/cigma/manual/figures/bm4/scripts/ssng-p0500-g0500.sh (from rev 14797, doc/cigma/manual/figures/scripts/ssng-p0500-g0500.sh)
===================================================================
--- doc/cigma/manual/figures/bm4/scripts/ssng-p0500-g0500.sh	                        (rev 0)
+++ doc/cigma/manual/figures/bm4/scripts/ssng-p0500-g0500.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,90 @@
+#!/bin/bash
+
+bm=bmssnog
+bmfile=$HOME/benchmarks/$bm.h5
+prefix=ssng-p0500-g0500
+
+#########
+
+echo "---------------------------------------------"
+var=variables/displacement/step00000
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var    \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var         \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --verbose --output-frequency=10000                      \
+              --output=$prefix.disp-000.vtk 
+
+echo "---------------------------------------------" 
+var=variables/displacement/step00010
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var    \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var         \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --verbose --output-frequency=10000                      \
+              --output=$prefix.disp-010.vtk 
+
+echo "---------------------------------------------" 
+var=variables/displacement/step00050
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var    \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var         \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --verbose --output-frequency=10000                      \
+              --output=$prefix.disp-050.vtk 
+
+echo "---------------------------------------------" 
+var=variables/displacement/step00100
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var    \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var         \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --verbose --output-frequency=10000                      \
+              --output=$prefix.disp-100.vtk 
+
+#########
+
+echo "---------------------------------------------" 
+t=step00000
+var1=variables/velocity/$t
+var2=variables/del_displacement/$t
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var1   \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var2        \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --verbose --output-frequency=10000                      \
+              --output=$prefix.velo-000.vtk 
+
+echo "---------------------------------------------" 
+t=step00010
+var1=variables/velocity/$t
+var2=variables/del_displacement/$t
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var1   \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var2        \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --verbose --output-frequency=10000                      \
+              --output=$prefix.velo-010.vtk 
+
+echo "---------------------------------------------" 
+t=step00050
+var1=variables/velocity/$t
+var2=variables/del_displacement/$t
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var1   \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var2        \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --verbose --output-frequency=10000                      \
+              --output=$prefix.velo-050.vtk
+
+echo "---------------------------------------------" 
+t=step00100
+var1=variables/velocity/$t
+var2=variables/del_displacement/$t
+cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var1   \
+              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var2        \
+              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
+              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
+              --verbose --output-frequency=10000                      \
+              --output=$prefix.velo-100.vtk 
+

Copied: doc/cigma/manual/figures/bm4/scripts/ssng-p0500-g0500.velo-010.mv2 (from rev 14797, doc/cigma/manual/figures/scripts/ssng-p0500-g0500.velo-010.mv2)
===================================================================
(Binary files differ)

Copied: doc/cigma/manual/figures/bm4/scripts/strike-slip-fault.vtk (from rev 14797, doc/cigma/manual/figures/scripts/strike-slip-fault.vtk)
===================================================================
--- doc/cigma/manual/figures/bm4/scripts/strike-slip-fault.vtk	                        (rev 0)
+++ doc/cigma/manual/figures/bm4/scripts/strike-slip-fault.vtk	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,11 @@
+# vtk DataFile Version 1.0
+This line is a comment
+ASCII
+DATASET POLYDATA
+POINTS 4 float
+12000.0      0.0       0.0
+12000.0  16000.0       0.0
+12000.0  16000.0  -16000.0
+12000.0      0.0  -16000.0
+POLYGONS 1 5
+4  0 1 2 3

Copied: doc/cigma/manual/figures/bm4/scripts/top-layer.vtk (from rev 14797, doc/cigma/manual/figures/scripts/top-layer.vtk)
===================================================================
--- doc/cigma/manual/figures/bm4/scripts/top-layer.vtk	                        (rev 0)
+++ doc/cigma/manual/figures/bm4/scripts/top-layer.vtk	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,20 @@
+# vtk DataFile Version 1.0
+This line is a comment
+ASCII
+DATASET POLYDATA
+POINTS 8 float
+    0.0      0.0       0.0
+24000.0      0.0       0.0
+    0.0  24000.0       0.0
+24000.0  24000.0       0.0
+    0.0      0.0  -12000.0
+24000.0      0.0  -12000.0
+    0.0  24000.0  -12000.0
+24000.0  24000.0  -12000.0
+POLYGONS 6 30
+4  0 2 6 4
+4  1 5 7 3
+4  0 4 5 1
+4  2 3 7 6
+4  0 1 3 2
+4  4 5 7 6

Copied: doc/cigma/manual/figures/bm4/ssng-p0250-g0500-point-isosurf-disp-000.png (from rev 14797, doc/cigma/manual/figures/old/ssng-p0250-g0500-point-isosurf-disp-000.png)
===================================================================
(Binary files differ)


Property changes on: doc/cigma/manual/figures/bm4/ssng-p0250-g0500-point-isosurf-disp-000.png
___________________________________________________________________
Name: svn:mime-type
   + image/png

Copied: doc/cigma/manual/figures/bm4/ssng-p0500-g0500-isosurf-disp-000.png (from rev 14797, doc/cigma/manual/figures/old/ssng-p0500-g0500-isosurf-disp-000.png)
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--- doc/cigma/manual/figures/common.sh	                        (rev 0)
+++ doc/cigma/manual/figures/common.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,71 @@
+#!/bin/bash
+
+#
+# In this file we define a few useful functions for
+# processing multiple images, based on the ImageMagick
+# manipulation programs
+#
+# Some useful links:
+#
+#   http://www.imagemagick.org/Usage/crop/
+#   http://www.imagemagick.org/Usage/annotating/
+#   http://personal.cscs.ch/~mvalle/postprocessing/ImageTools.html
+#
+
+function img-caption0
+{
+    #echo $1 ...adding caption
+    convert \
+        -gravity south  \
+        -stroke '#000C' \
+        -strokewidth 2  \
+        -font Arial-Regular \
+        -pointsize 30 \
+        -annotate 0 "$1" \
+        $2 $3
+}
+
+function img-caption
+{
+    #echo $1 ...adding caption
+    montage \
+        -geometry +0+0 \
+        -background White \
+        -font Arial-Regular \
+        -pointsize 35 \
+        -label "$1" \
+        $2 $3
+}
+
+function img-cat
+{
+    local tile=$1
+    shift
+    montage -tile ${tile} -mode Concatenate $*
+}
+
+function cat-pair
+{
+    #echo Concatenating $1 $2
+    img-cat 2x1 $1 $2 $3
+}
+
+
+function img-trim
+{
+    #echo $1 ...trimming
+    convert -trim $1 $1
+}
+
+function img-add-border
+{
+    #echo $1 ...adding border
+    convert -border $2 -bordercolor white $1 $1
+}
+
+function img-resize
+{
+    #echo $1 ...resizing
+    convert -resize '80%' $1 $1
+}
+

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Copied: doc/cigma/manual/figures/misc/quad.svg (from rev 14797, doc/cigma/manual/quad.svg)
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--- doc/cigma/manual/figures/misc/quad.svg	                        (rev 0)
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===================================================================
--- doc/cigma/manual/figures/misc/tet.svg	                        (rev 0)
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-ssng-pylith_hex8_0500m-pylith_hex8_0500m
-ssng-pylith_hex8_0500m-pylith_hex8_0250m
-ssng-pylith_hex8_0500m-geofest_tet4_1000m
-ssng-pylith_hex8_0500m-geofest_tet4_0500m
-ssng-pylith_hex8_0500m-geofest_tet4_0250m
-ssng-pylith_hex8_0500m-geofest_hex8_1000m
-ssng-pylith_hex8_0500m-geofest_hex8_0500m
-ssng-pylith_hex8_0500m-geofest_hex8_0250m
-ssng-pylith_hex8_0250m-pylith_tet4_1000m
-ssng-pylith_hex8_0250m-pylith_tet4_0500m
-ssng-pylith_hex8_0250m-pylith_tet4_0250m
-ssng-pylith_hex8_0250m-pylith_hex8_1000m
-ssng-pylith_hex8_0250m-pylith_hex8_0500m
-ssng-pylith_hex8_0250m-pylith_hex8_0250m
-ssng-pylith_hex8_0250m-geofest_tet4_1000m
-ssng-pylith_hex8_0250m-geofest_tet4_0500m
-ssng-pylith_hex8_0250m-geofest_tet4_0250m
-ssng-pylith_hex8_0250m-geofest_hex8_1000m
-ssng-pylith_hex8_0250m-geofest_hex8_0500m
-ssng-pylith_hex8_0250m-geofest_hex8_0250m
-ssng-geofest_tet4_1000m-pylith_tet4_1000m
-ssng-geofest_tet4_1000m-pylith_tet4_0500m
-ssng-geofest_tet4_1000m-pylith_tet4_0250m
-ssng-geofest_tet4_1000m-pylith_hex8_1000m
-ssng-geofest_tet4_1000m-pylith_hex8_0500m
-ssng-geofest_tet4_1000m-pylith_hex8_0250m
-ssng-geofest_tet4_1000m-geofest_tet4_1000m
-ssng-geofest_tet4_1000m-geofest_tet4_0500m
-ssng-geofest_tet4_1000m-geofest_tet4_0250m
-ssng-geofest_tet4_1000m-geofest_hex8_1000m
-ssng-geofest_tet4_1000m-geofest_hex8_0500m
-ssng-geofest_tet4_1000m-geofest_hex8_0250m
-ssng-geofest_tet4_0500m-pylith_tet4_1000m
-ssng-geofest_tet4_0500m-pylith_tet4_0500m
-ssng-geofest_tet4_0500m-pylith_tet4_0250m
-ssng-geofest_tet4_0500m-pylith_hex8_1000m
-ssng-geofest_tet4_0500m-pylith_hex8_0500m
-ssng-geofest_tet4_0500m-pylith_hex8_0250m
-ssng-geofest_tet4_0500m-geofest_tet4_1000m
-ssng-geofest_tet4_0500m-geofest_tet4_0500m
-ssng-geofest_tet4_0500m-geofest_tet4_0250m
-ssng-geofest_tet4_0500m-geofest_hex8_1000m
-ssng-geofest_tet4_0500m-geofest_hex8_0500m
-ssng-geofest_tet4_0500m-geofest_hex8_0250m
-ssng-geofest_tet4_0250m-pylith_tet4_1000m
-ssng-geofest_tet4_0250m-pylith_tet4_0500m
-ssng-geofest_tet4_0250m-pylith_tet4_0250m
-ssng-geofest_tet4_0250m-pylith_hex8_1000m
-ssng-geofest_tet4_0250m-pylith_hex8_0500m
-ssng-geofest_tet4_0250m-pylith_hex8_0250m
-ssng-geofest_tet4_0250m-geofest_tet4_1000m
-ssng-geofest_tet4_0250m-geofest_tet4_0500m
-ssng-geofest_tet4_0250m-geofest_tet4_0250m
-ssng-geofest_tet4_0250m-geofest_hex8_1000m
-ssng-geofest_tet4_0250m-geofest_hex8_0500m
-ssng-geofest_tet4_0250m-geofest_hex8_0250m
-ssng-geofest_hex8_1000m-pylith_tet4_1000m
-ssng-geofest_hex8_1000m-pylith_tet4_0500m
-ssng-geofest_hex8_1000m-pylith_tet4_0250m
-ssng-geofest_hex8_1000m-pylith_hex8_1000m
-ssng-geofest_hex8_1000m-pylith_hex8_0500m
-ssng-geofest_hex8_1000m-pylith_hex8_0250m
-ssng-geofest_hex8_1000m-geofest_tet4_1000m
-ssng-geofest_hex8_1000m-geofest_tet4_0500m
-ssng-geofest_hex8_1000m-geofest_tet4_0250m
-ssng-geofest_hex8_1000m-geofest_hex8_1000m
-ssng-geofest_hex8_1000m-geofest_hex8_0500m
-ssng-geofest_hex8_1000m-geofest_hex8_0250m
-ssng-geofest_hex8_0500m-pylith_tet4_1000m
-ssng-geofest_hex8_0500m-pylith_tet4_0500m
-ssng-geofest_hex8_0500m-pylith_tet4_0250m
-ssng-geofest_hex8_0500m-pylith_hex8_1000m
-ssng-geofest_hex8_0500m-pylith_hex8_0500m
-ssng-geofest_hex8_0500m-pylith_hex8_0250m
-ssng-geofest_hex8_0500m-geofest_tet4_1000m
-ssng-geofest_hex8_0500m-geofest_tet4_0500m
-ssng-geofest_hex8_0500m-geofest_tet4_0250m
-ssng-geofest_hex8_0500m-geofest_hex8_1000m
-ssng-geofest_hex8_0500m-geofest_hex8_0500m
-ssng-geofest_hex8_0500m-geofest_hex8_0250m
-ssng-geofest_hex8_0250m-pylith_tet4_1000m
-ssng-geofest_hex8_0250m-pylith_tet4_0500m
-ssng-geofest_hex8_0250m-pylith_tet4_0250m
-ssng-geofest_hex8_0250m-pylith_hex8_1000m
-ssng-geofest_hex8_0250m-pylith_hex8_0500m
-ssng-geofest_hex8_0250m-pylith_hex8_0250m
-ssng-geofest_hex8_0250m-geofest_tet4_1000m
-ssng-geofest_hex8_0250m-geofest_tet4_0500m
-ssng-geofest_hex8_0250m-geofest_tet4_0250m
-ssng-geofest_hex8_0250m-geofest_hex8_1000m
-ssng-geofest_hex8_0250m-geofest_hex8_0500m
-ssng-geofest_hex8_0250m-geofest_hex8_0250m

Deleted: doc/cigma/manual/figures/scripts/generate-cases.py
===================================================================
--- doc/cigma/manual/figures/scripts/generate-cases.py	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures/scripts/generate-cases.py	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,27 +0,0 @@
-#!/usr/bin/env python
-
-benchmarks = ['rsng', 'ssng']
-codes = ['pylith', 'geofest']
-
-resolutions = ['1000m', '0500m', '0250m']
-elements = ['tet4', 'hex8']
-
-cases = []
-for code in codes:
-    for elt in elements:
-        for res in resolutions:
-            cases.append("%s_%s_%s" % (code,elt,res))
-
-comparisons = []
-for a in cases:
-    for b in cases:
-        comparisons.append('%s-%s' % (a,b))
-
-benchmark_comparisons = []
-for bm in benchmarks:
-    for cmp in comparisons:
-        benchmark_comparisons.append('%s-%s' % (bm,cmp))
-
-for bm in benchmark_comparisons:
-    print bm
-

Deleted: doc/cigma/manual/figures/scripts/list.txt
===================================================================
--- doc/cigma/manual/figures/scripts/list.txt	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures/scripts/list.txt	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,26 +0,0 @@
-
-p0500 -> /pylith/tet4_0500m
-g0500 -> /geofest/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

Deleted: doc/cigma/manual/figures/scripts/reference-hex8.mv2
===================================================================
(Binary files differ)

Deleted: doc/cigma/manual/figures/scripts/reference-hex8.vtk
===================================================================
--- doc/cigma/manual/figures/scripts/reference-hex8.vtk	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures/scripts/reference-hex8.vtk	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,20 +0,0 @@
-# vtk DataFile Version 1.0
-This line is a comment
-ASCII
-DATASET POLYDATA
-POINTS 8 float
- -1 -1 -1
- +1 -1 -1
- -1 +1 -1
- +1 +1 -1
- -1 -1 +1
- +1 -1 +1
- -1 +1 +1
- +1 +1 +1
-POLYGONS 6 30
-4  0 1 5 4
-4  2 6 7 3
-4  0 4 6 2
-4  1 3 7 5
-4  0 2 3 1
-4  4 5 7 6

Deleted: doc/cigma/manual/figures/scripts/reference-tet4.mv2
===================================================================
(Binary files differ)

Deleted: doc/cigma/manual/figures/scripts/reference-tet4.vtk
===================================================================
--- doc/cigma/manual/figures/scripts/reference-tet4.vtk	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures/scripts/reference-tet4.vtk	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,14 +0,0 @@
-# vtk DataFile Version 1.0
-This line is a comment
-ASCII
-DATASET POLYDATA
-POINTS 4 float
- -1 -1 -1
- +1 -1 -1
- -1 +1 -1
- -1 -1 +1
-POLYGONS 4 16
-3 0 2 1
-3 0 1 3
-3 0 3 2
-3 1 2 3

Deleted: doc/cigma/manual/figures/scripts/reverse-slip-fault.vtk
===================================================================
--- doc/cigma/manual/figures/scripts/reverse-slip-fault.vtk	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures/scripts/reverse-slip-fault.vtk	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,11 +0,0 @@
-# vtk DataFile Version 1.0
-This line is a comment
-ASCII
-DATASET POLYDATA
-POINTS 4 float
- 4000.0      0.0       0.0
- 4000.0  16000.0       0.0
-20000.0  16000.0  -16000.0
-20000.0      0.0  -16000.0
-POLYGONS 1 5
-4  0 1 2 3

Deleted: doc/cigma/manual/figures/scripts/rsng-p0500-g0500-cell-threshold-velo.mv2
===================================================================
(Binary files differ)

Deleted: doc/cigma/manual/figures/scripts/rsng-p0500-g0500-point-isosurf-res-disp.mv2
===================================================================
(Binary files differ)

Deleted: doc/cigma/manual/figures/scripts/rsng-p0500-g0500.sh
===================================================================
--- doc/cigma/manual/figures/scripts/rsng-p0500-g0500.sh	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures/scripts/rsng-p0500-g0500.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,82 +0,0 @@
-#!/bin/bash
-
-bm=bmrsnog
-bmfile=$HOME/benchmarks/$bm.h5
-prefix=rsng-p0500-g0500
-
-#########
-
-echo "---------------------------------------------------------------"
-var=variables/displacement/step00000
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var          \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var      \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
-              --output=$prefix.disp-000.vtk
-
-echo "---------------------------------------------------------------"
-var=variables/displacement/step00010
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var          \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var      \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
-              --output=$prefix.disp-010.vtk
-
-echo "---------------------------------------------------------------"
-var=variables/displacement/step00050
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var          \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var      \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
-              --output=$prefix.disp-050.vtk
-
-echo "---------------------------------------------------------------"
-var=variables/displacement/step00100
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var          \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var      \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
-              --output=$prefix.disp-100.vtk
-
-#########
-
-echo "---------------------------------------------------------------"
-t=step00000
-var1=variables/velocity/$t
-var2=variables/del_displacement/$t
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var1         \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var2     \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
-              --output=$prefix.velo-000.vtk
-
-echo "---------------------------------------------------------------"
-t=step00010
-var1=variables/velocity/$t
-var2=variables/del_displacement/$t
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var1         \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var2     \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
-              --output=$prefix.velo-010.vtk
-
-echo "---------------------------------------------------------------"
-t=step00050
-var1=variables/velocity/$t
-var2=variables/del_displacement/$t
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var1         \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var2     \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
-              --output=$prefix.velo-050.vtk
-
-echo "---------------------------------------------------------------"
-t=step00100
-var1=variables/velocity/$t
-var2=variables/del_displacement/$t
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m/$var1         \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m_A/$var2     \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m           \
-              --output=$prefix.velo-100.vtk
-

Deleted: doc/cigma/manual/figures/scripts/ssng-p0250-g0500-point-isosurf-disp.mv2
===================================================================
(Binary files differ)

Deleted: doc/cigma/manual/figures/scripts/ssng-p0250-g0500.sh
===================================================================
--- doc/cigma/manual/figures/scripts/ssng-p0250-g0500.sh	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures/scripts/ssng-p0250-g0500.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,31 +0,0 @@
-#!/bin/bash
-
-bm=bmssnog
-bmfile=$HOME/benchmarks/$bm.h5
-prefix=ssng-p0250-g0500
-
-#########
-
-echo "---------------------------------------------"
-var=variables/displacement/step00000
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0250m/$var     \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var   \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0250m       \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m      \
-              --verbose --output-frequency=10000                \
-              --output=$prefix.disp-000.vtk
-
-
-#########
-
-echo "---------------------------------------------"
-t=step00000
-var1=variables/velocity/$t
-var2=variables/del_displacement/$t
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0250m/$var1    \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var2  \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0250m       \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m      \
-              --verbose --output-frequency=10000                \
-              --output=$prefix.velo-000.vtk 
-

Deleted: doc/cigma/manual/figures/scripts/ssng-p0500-g0500-isosurf-disp.mv2
===================================================================
(Binary files differ)

Deleted: doc/cigma/manual/figures/scripts/ssng-p0500-g0500-point-isosurf-velo.mv2
===================================================================
(Binary files differ)

Deleted: doc/cigma/manual/figures/scripts/ssng-p0500-g0500.sh
===================================================================
--- doc/cigma/manual/figures/scripts/ssng-p0500-g0500.sh	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures/scripts/ssng-p0500-g0500.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,90 +0,0 @@
-#!/bin/bash
-
-bm=bmssnog
-bmfile=$HOME/benchmarks/$bm.h5
-prefix=ssng-p0500-g0500
-
-#########
-
-echo "---------------------------------------------"
-var=variables/displacement/step00000
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var    \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var         \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --verbose --output-frequency=10000                      \
-              --output=$prefix.disp-000.vtk 
-
-echo "---------------------------------------------" 
-var=variables/displacement/step00010
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var    \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var         \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --verbose --output-frequency=10000                      \
-              --output=$prefix.disp-010.vtk 
-
-echo "---------------------------------------------" 
-var=variables/displacement/step00050
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var    \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var         \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --verbose --output-frequency=10000                      \
-              --output=$prefix.disp-050.vtk 
-
-echo "---------------------------------------------" 
-var=variables/displacement/step00100
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var    \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var         \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --verbose --output-frequency=10000                      \
-              --output=$prefix.disp-100.vtk 
-
-#########
-
-echo "---------------------------------------------" 
-t=step00000
-var1=variables/velocity/$t
-var2=variables/del_displacement/$t
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var1   \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var2        \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --verbose --output-frequency=10000                      \
-              --output=$prefix.velo-000.vtk 
-
-echo "---------------------------------------------" 
-t=step00010
-var1=variables/velocity/$t
-var2=variables/del_displacement/$t
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var1   \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var2        \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --verbose --output-frequency=10000                      \
-              --output=$prefix.velo-010.vtk 
-
-echo "---------------------------------------------" 
-t=step00050
-var1=variables/velocity/$t
-var2=variables/del_displacement/$t
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var1   \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var2        \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --verbose --output-frequency=10000                      \
-              --output=$prefix.velo-050.vtk
-
-echo "---------------------------------------------" 
-t=step00100
-var1=variables/velocity/$t
-var2=variables/del_displacement/$t
-cigma compare --first=$bmfile:/pylith/${bm}_tet4_0500m_new_bc/$var1   \
-              --second=$bmfile:/geofest/${bm}_tet4_0500m/$var2        \
-              --first-mesh=$bmfile:/mesh/${bm}_tet4_0500m             \
-              --second-mesh=$bmfile:/mesh/${bm}_tet4_0500m            \
-              --verbose --output-frequency=10000                      \
-              --output=$prefix.velo-100.vtk 
-

Deleted: doc/cigma/manual/figures/scripts/ssng-p0500-g0500.velo-010.mv2
===================================================================
(Binary files differ)

Deleted: doc/cigma/manual/figures/scripts/strike-slip-fault.vtk
===================================================================
--- doc/cigma/manual/figures/scripts/strike-slip-fault.vtk	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures/scripts/strike-slip-fault.vtk	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,11 +0,0 @@
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Deleted: doc/cigma/manual/figures/scripts/top-layer.vtk
===================================================================
--- doc/cigma/manual/figures/scripts/top-layer.vtk	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures/scripts/top-layer.vtk	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,20 +0,0 @@
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Deleted: doc/cigma/manual/figures/strike-slip-fault.png
===================================================================
(Binary files differ)

Deleted: doc/cigma/manual/figures2/alpha_cube.png
===================================================================
(Binary files differ)

Deleted: doc/cigma/manual/figures2/alpha_square.png
===================================================================
(Binary files differ)

Deleted: doc/cigma/manual/figures2/inclusion_setup.eps
===================================================================
--- doc/cigma/manual/figures2/inclusion_setup.eps	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures2/inclusion_setup.eps	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,990 +0,0 @@
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-n 6750 4815 m
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-15.00 15.00 sc P6 [16 0 0 -16 420.00 321.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6432 4816 m 6316 4858 l 6438 4875 l  col0 s
-% Polyline
-gs  clippath
-6422 5376 m 6277 5420 l 6294 5478 l 6439 5434 l 6439 5434 l 6316 5440 l 6422 5376 l cp
-eoclip
-n 6750 5310 m
- 6300 5445 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 420.00 354.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6422 5376 m 6316 5440 l 6439 5434 l  col0 s
-% Polyline
-gs  clippath
-6401 6158 m 6271 6236 l 6302 6288 l 6432 6209 l 6432 6209 l 6314 6246 l 6401 6158 l cp
-eoclip
-n 6750 5985 m
- 6300 6255 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 420.00 399.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6401 6158 m 6314 6246 l 6432 6209 l  col0 s
-% Polyline
-gs  clippath
-6387 6551 m 6269 6645 l 6307 6692 l 6425 6598 l 6425 6598 l 6313 6650 l 6387 6551 l cp
-eoclip
-n 6750 6300 m
- 6300 6660 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 420.00 420.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6387 6551 m 6313 6650 l 6425 6598 l  col0 s
-% Polyline
-gs  clippath
-5487 1908 m 5420 1773 l 5366 1800 l 5433 1935 l 5433 1935 l 5407 1815 l 5487 1908 l cp
-eoclip
-n 5625 2250 m
- 5400 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 360.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 5487 1908 m 5407 1815 l 5433 1935 l  col0 s
-% Polyline
-gs  clippath
-6138 1887 m 6044 1769 l 5997 1807 l 6091 1925 l 6091 1925 l 6040 1813 l 6138 1887 l cp
-eoclip
-n 6390 2250 m
- 6030 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 402.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6138 1887 m 6040 1813 l 6091 1925 l  col0 s
-% Polyline
-gs  clippath
-5811 1901 m 5733 1771 l 5681 1802 l 5760 1932 l 5760 1932 l 5724 1814 l 5811 1901 l cp
-eoclip
-n 5985 2250 m
- 5715 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 381.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 5811 1901 m 5724 1814 l 5760 1932 l  col0 s
-% Polyline
-gs  clippath
-5118 1915 m 5062 1774 l 5006 1797 l 5062 1937 l 5062 1937 l 5046 1815 l 5118 1915 l cp
-eoclip
-n 5220 2250 m
- 5040 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 336.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 5118 1915 m 5046 1815 l 5062 1937 l  col0 s
-% Polyline
-gs  clippath
-4825 1927 m 4796 1779 l 4737 1791 l 4767 1939 l 4767 1939 l 4773 1816 l 4825 1927 l cp
-eoclip
-n 4860 2250 m
- 4770 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 318.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 4825 1927 m 4773 1816 l 4767 1939 l  col0 s
-% Polyline
-gs  clippath
-3566 1935 m 3633 1800 l 3579 1773 l 3512 1908 l 3512 1908 l 3593 1815 l 3566 1935 l cp
-eoclip
-n 3375 2250 m
- 3600 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 225.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 3566 1935 m 3593 1815 l 3512 1908 l  col0 s
-% Polyline
-gs  clippath
-2908 1925 m 3002 1807 l 2955 1769 l 2861 1887 l 2861 1887 l 2960 1813 l 2908 1925 l cp
-eoclip
-n 2610 2250 m
- 2970 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 174.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 2908 1925 m 2960 1813 l 2861 1887 l  col0 s
-% Polyline
-gs  clippath
-3239 1932 m 3318 1802 l 3266 1771 l 3188 1901 l 3188 1901 l 3276 1814 l 3239 1932 l cp
-eoclip
-n 3015 2250 m
- 3285 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 201.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 3239 1932 m 3276 1814 l 3188 1901 l  col0 s
-% Polyline
-gs  clippath
-3937 1937 m 3993 1797 l 3937 1774 l 3881 1915 l 3881 1915 l 3954 1815 l 3937 1937 l cp
-eoclip
-n 3780 2250 m
- 3960 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 252.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 3937 1937 m 3954 1815 l 3881 1915 l  col0 s
-% Polyline
-gs  clippath
-4232 1939 m 4262 1791 l 4203 1779 l 4174 1927 l 4174 1927 l 4227 1816 l 4232 1939 l cp
-eoclip
-n 4140 2250 m
- 4230 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 276.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 4232 1939 m 4227 1816 l 4174 1927 l  col0 s
-% Polyline
-gs  clippath
-4530 1937 m 4530 1785 l 4470 1785 l 4470 1937 l 4470 1937 l 4500 1817 l 4530 1937 l cp
-eoclip
-n 4500 2250 m
- 4500 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 300.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 4530 1937 m 4500 1817 l 4470 1937 l  col0 s
-% Polyline
-gs  clippath
-3512 7091 m 3579 7226 l 3633 7200 l 3566 7064 l 3566 7064 l 3593 7185 l 3512 7091 l cp
-eoclip
-n 3375 6750 m
- 3600 7200 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 225.00 450.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 3512 7091 m 3593 7185 l 3566 7064 l  col0 s
-% Polyline
-gs  clippath
-2861 7112 m 2955 7230 l 3002 7192 l 2908 7074 l 2908 7074 l 2960 7187 l 2861 7112 l cp
-eoclip
-n 2610 6750 m
- 2970 7200 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 174.00 450.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 2861 7112 m 2960 7187 l 2908 7074 l  col0 s
-% Polyline
-gs  clippath
-3188 7098 m 3266 7228 l 3318 7197 l 3239 7067 l 3239 7067 l 3276 7186 l 3188 7098 l cp
-eoclip
-n 3015 6750 m
- 3285 7200 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 201.00 450.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 3188 7098 m 3276 7186 l 3239 7067 l  col0 s
-% Polyline
-gs  clippath
-3881 7084 m 3937 7225 l 3993 7202 l 3937 7062 l 3937 7062 l 3954 7185 l 3881 7084 l cp
-eoclip
-n 3780 6750 m
- 3960 7200 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 252.00 450.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 3881 7084 m 3954 7185 l 3937 7062 l  col0 s
-% Polyline
-gs  clippath
-4174 7072 m 4203 7220 l 4262 7208 l 4232 7060 l 4232 7060 l 4227 7184 l 4174 7072 l cp
-eoclip
-n 4140 6750 m
- 4230 7200 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 276.00 450.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 4174 7072 m 4227 7184 l 4232 7060 l  col0 s
-% Polyline
-gs  clippath
-5433 7064 m 5366 7200 l 5420 7226 l 5487 7091 l 5487 7091 l 5407 7185 l 5433 7064 l cp
-eoclip
-n 5625 6750 m
- 5400 7200 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 360.00 450.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 5433 7064 m 5407 7185 l 5487 7091 l  col0 s
-% Polyline
-gs  clippath
-6091 7074 m 5997 7192 l 6044 7230 l 6138 7112 l 6138 7112 l 6040 7187 l 6091 7074 l cp
-eoclip
-n 6390 6750 m
- 6030 7200 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 402.00 450.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6091 7074 m 6040 7187 l 6138 7112 l  col0 s
-% Polyline
-gs  clippath
-5760 7067 m 5681 7197 l 5733 7228 l 5811 7098 l 5811 7098 l 5724 7186 l 5760 7067 l cp
-eoclip
-n 5985 6750 m
- 5715 7200 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 381.00 450.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 5760 7067 m 5724 7186 l 5811 7098 l  col0 s
-% Polyline
-gs  clippath
-5062 7062 m 5006 7202 l 5062 7225 l 5118 7084 l 5118 7084 l 5046 7185 l 5062 7062 l cp
-eoclip
-n 5220 6750 m
- 5040 7200 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 336.00 450.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 5062 7062 m 5046 7185 l 5118 7084 l  col0 s
-% Polyline
-gs  clippath
-4767 7060 m 4737 7208 l 4796 7220 l 4825 7072 l 4825 7072 l 4773 7184 l 4767 7060 l cp
-eoclip
-n 4860 6750 m
- 4770 7200 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 318.00 450.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 4767 7060 m 4773 7184 l 4825 7072 l  col0 s
-% Polyline
-gs  clippath
-4470 7063 m 4470 7215 l 4530 7215 l 4530 7063 l 4530 7063 l 4500 7183 l 4470 7063 l cp
-eoclip
-n 4500 6750 m
- 4500 7200 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 300.00 450.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 4470 7063 m 4500 7183 l 4530 7063 l  col0 s
-% Ellipse
-n 4500 4500 450 450 0 360 DrawEllipse gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 270.00 270.00] PATmp PATsp ef gr PATusp gs col0 s gr
-
-% Polyline
-gs  clippath
-6437 4470 m 6285 4470 l 6285 4530 l 6437 4530 l 6437 4530 l 6317 4500 l 6437 4470 l cp
-eoclip
-n 6750 4500 m
- 6300 4500 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 420.00 300.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6437 4470 m 6317 4500 l 6437 4530 l  col0 s
-% Polyline
-n 2250 2250 m 6750 2250 l 6750 6750 l 2250 6750 l
- cp gs col0 s gr 
-% Polyline
-gs  clippath
-2563 4530 m 2715 4530 l 2715 4470 l 2563 4470 l 2563 4470 l 2683 4500 l 2563 4530 l cp
-eoclip
-n 2250 4500 m
- 2700 4500 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 150.00 300.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 2563 4530 m 2683 4500 l 2563 4470 l  col0 s
-% Polyline
-gs  clippath
-2624 1918 m 2731 1810 l 2689 1768 l 2581 1875 l 2581 1875 l 2688 1812 l 2624 1918 l cp
-eoclip
-n 2250 2250 m
- 2700 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 150.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 2624 1918 m 2688 1812 l 2581 1875 l  col0 s
-% Polyline
-gs  clippath
-2591 3237 m 2726 3170 l 2700 3116 l 2564 3183 l 2564 3183 l 2685 3157 l 2591 3237 l cp
-eoclip
-n 2250 3375 m
- 2700 3150 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 150.00 210.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 2591 3237 m 2685 3157 l 2564 3183 l  col0 s
-% Polyline
-gs  clippath
-2577 3893 m 2722 3849 l 2705 3791 l 2560 3835 l 2560 3835 l 2684 3830 l 2577 3893 l cp
-eoclip
-n 2250 3960 m
- 2700 3825 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 150.00 255.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 2577 3893 m 2684 3830 l 2560 3835 l  col0 s
-% Polyline
-gs  clippath
-2567 4183 m 2717 4168 l 2711 4108 l 2561 4124 l 2561 4124 l 2684 4142 l 2567 4183 l cp
-eoclip
-n 2250 4185 m
- 2700 4140 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 150.00 276.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 2567 4183 m 2684 4142 l 2561 4124 l  col0 s
-% Polyline
-gs  clippath
-2577 3623 m 2722 3579 l 2705 3521 l 2560 3565 l 2560 3565 l 2684 3560 l 2577 3623 l cp
-eoclip
-n 2250 3690 m
- 2700 3555 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 150.00 237.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 2577 3623 m 2684 3560 l 2560 3565 l  col0 s
-% Polyline
-gs  clippath
-2598 2841 m 2728 2763 l 2697 2711 l 2567 2790 l 2567 2790 l 2686 2754 l 2598 2841 l cp
-eoclip
-n 2250 3015 m
- 2700 2745 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 150.00 183.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 2598 2841 m 2686 2754 l 2567 2790 l  col0 s
-% Polyline
-gs  clippath
-2612 2448 m 2730 2354 l 2692 2307 l 2574 2401 l 2574 2401 l 2687 2350 l 2612 2448 l cp
-eoclip
-n 2250 2700 m
- 2700 2340 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 150.00 156.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 2612 2448 m 2687 2350 l 2574 2401 l  col0 s
-% Polyline
-gs  clippath
-6418 1875 m 6310 1768 l 6268 1810 l 6375 1918 l 6375 1918 l 6312 1812 l 6418 1875 l cp
-eoclip
-n 6750 2250 m
- 6300 1800 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 420.00 120.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6418 1875 m 6312 1812 l 6375 1918 l  col0 s
-% Polyline
-gs  clippath
-6435 3183 m 6300 3116 l 6273 3170 l 6408 3237 l 6408 3237 l 6315 3157 l 6435 3183 l cp
-eoclip
-n 6750 3375 m
- 6300 3150 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 420.00 210.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6435 3183 m 6315 3157 l 6408 3237 l  col0 s
-% Polyline
-gs  clippath
-6439 3835 m 6294 3791 l 6277 3849 l 6422 3893 l 6422 3893 l 6316 3830 l 6439 3835 l cp
-eoclip
-n 6750 3960 m
- 6300 3825 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 420.00 255.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6439 3835 m 6316 3830 l 6422 3893 l  col0 s
-% Polyline
-gs  clippath
-6438 4124 m 6288 4108 l 6282 4168 l 6432 4183 l 6432 4183 l 6316 4142 l 6438 4124 l cp
-eoclip
-n 6750 4185 m
- 6300 4140 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 420.00 276.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6438 4124 m 6316 4142 l 6432 4183 l  col0 s
-% Polyline
-gs  clippath
-6439 3565 m 6294 3521 l 6277 3579 l 6422 3623 l 6422 3623 l 6316 3560 l 6439 3565 l cp
-eoclip
-n 6750 3690 m
- 6300 3555 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 420.00 237.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6439 3565 m 6316 3560 l 6422 3623 l  col0 s
-% Polyline
-gs  clippath
-6432 2790 m 6302 2711 l 6271 2763 l 6401 2841 l 6401 2841 l 6314 2754 l 6432 2790 l cp
-eoclip
-n 6750 3015 m
- 6300 2745 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 420.00 183.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6432 2790 m 6314 2754 l 6401 2841 l  col0 s
-% Polyline
-gs  clippath
-6425 2401 m 6307 2307 l 6269 2354 l 6387 2448 l 6387 2448 l 6313 2350 l 6425 2401 l cp
-eoclip
-n 6750 2700 m
- 6300 2340 l gs /PC [[0.00 1.00 0.00] [0.00 0.00 0.00]] def
-15.00 15.00 sc P6 [16 0 0 -16 420.00 156.00] PATmp PATsp ef gr PATusp gs col0 s gr gr
-
-% arrowhead
-n 6425 2401 m 6313 2350 l 6387 2448 l  col0 s
-% here ends figure;
-pagefooter
-showpage
-%%Trailer
-end
-%EOF

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--- doc/cigma/manual/figures3/bm1/process-images.sh	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures3/bm1/process-images.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,19 +0,0 @@
-#!/bin/bash
-set -x
-source ../common.sh
-
-img-caption '(a) 2D Poisson Problem' \
-    alpha_2d.png \
-    rm_alpha_2d.png
-
-img-caption '(b) 3D Poisson Problem' \
-    alpha_3d.png \
-    rm_alpha_3d.png
-
-cat-pair \
-    rm_alpha_2d.png \
-    rm_alpha_3d.png \
-    alpha.png
-
-rm -f rm_*.png
-

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===================================================================

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Deleted: doc/cigma/manual/figures3/bm2/process-images.sh
===================================================================
--- doc/cigma/manual/figures3/bm2/process-images.sh	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures3/bm2/process-images.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,93 +0,0 @@
-#!/bin/bash
-
-# Include some common image processing functions
-source ../common.sh
-
-# Enable bash debugging
-set -x
-
-#
-# List of the original images
-#
-imglist="
-    temperature_64_20000_y099.png
-    velocity_64_20000_y099.png
-    log_error_temperature_64_08_20000_2100_y099.png
-    log_error_temperature_64_16_20000_4700_y099.png
-    log_error_temperature_64_32_20000_9900_y099.png
-    log_error_velocity_64_08_20000_2100_y099.png
-    log_error_velocity_64_16_20000_4700_y099.png
-    log_error_velocity_64_32_20000_9900_y099.png
-"
-
-#
-# Operate on copies of the original images
-#
-orig=${PWD}
-tmp=/tmp/bm2
-mkdir -p $tmp
-for img in ${imglist}; do
-    cp -f -v ${img} ${tmp}
-done
-cd ${tmp}
-
-
-# 
-# Start processing the images
-#
-
-for img in ${imglist}; do
-    img-trim ${img}
-    img-add-border ${img} 100
-done
-
-img-caption '(a) Temperature                           ' \
-    temperature_64_20000_y099.png \
-    temperature_64_20000_y099.png
-
-img-caption '(b) Velocity                     ' \
-    velocity_64_20000_y099.png \
-    velocity_64_20000_y099.png
-
-img-caption '(a) log (temperature error for 16 x 16 x 16 case)             ' \
-    log_error_temperature_64_16_20000_4700_y099.png \
-    log_error_temperature_64_16_20000_4700_y099.png
-
-img-caption '(b) log (temperature error for 32 x 32 x 32 case)         ' \
-    log_error_temperature_64_32_20000_9900_y099.png \
-    log_error_temperature_64_32_20000_9900_y099.png
-
-img-caption '(a) log (velocity error for 16 x 16 x 16 case)                ' \
-    log_error_velocity_64_16_20000_4700_y099.png \
-    log_error_velocity_64_16_20000_4700_y099.png
-
-img-caption '(b) log (velocity error for 32 x 32 x 32 case)            ' \
-    log_error_velocity_64_32_20000_9900_y099.png \
-    log_error_velocity_64_32_20000_9900_y099.png
-
-cat-pair \
-    temperature_64_20000_y099.png \
-    velocity_64_20000_y099.png \
-    fig_fields_64_20000_y099.png
-
-cat-pair \
-    log_error_temperature_64_16_20000_4700_y099.png \
-    log_error_temperature_64_32_20000_9900_y099.png \
-    fig_log_error_temperature_64_16_64_32_y099.png
-    
-cat-pair \
-    log_error_velocity_64_16_20000_4700_y099.png \
-    log_error_velocity_64_32_20000_9900_y099.png \
-    fig_log_error_velocity_64_16_64_32_y099.png
-
-# finally, resize the images that will be included in the manual
-for img in fig_*; do
-    img-resize ${img}
-done
-
-#
-# Copy the images back
-#
-cd ${orig}
-cp -f -v ${tmp}/fig_* ${orig}/out
-

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===================================================================

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Deleted: doc/cigma/manual/figures3/bm3/process-images.sh
===================================================================
--- doc/cigma/manual/figures3/bm3/process-images.sh	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures3/bm3/process-images.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,132 +0,0 @@
-#!/bin/bash
-#
-
-# Include some common image processing functions
-source ../common.sh
-
-# Enable bash debugging
-set -x
-
-#
-# List of the original image names
-#
-imglist="
-    full_pressure_512.png
-    full_velocity_512.png
-    full_log_error_pressure_128.png
-    full_log_error_pressure_256.png
-    full_log_error_pressure_512.png
-    full_log_error_pressure_512_128.png
-    full_log_error_pressure_512_256.png
-    full_log_error_velocity_128.png
-    full_log_error_velocity_256.png
-    full_log_error_velocity_512.png
-    full_log_error_velocity_512_128.png
-    full_log_error_velocity_512_256.png
-    inc_pressure_512.png
-    inc_velocity_512.png
-    inc_log_error_pressure_128.png
-    inc_log_error_pressure_256.png
-    inc_log_error_pressure_512.png
-    inc_log_error_pressure_512_128.png
-    inc_log_error_pressure_512_256.png
-    inc_log_error_velocity_512.png
-    inc_log_error_velocity_512_128.png
-    inc_log_error_velocity_512_256.png
-"
-
-# 
-# Operate on copies of the original images
-#
-orig=${PWD}
-tmp=/tmp/bm3
-mkdir -p $tmp
-for img in ${imglist}; do
-    cp -f -v ${img} ${tmp}
-done
-cd ${tmp}
-
-
-#
-# Start processing the images
-#
-
-for img in ${imglist}; do
-    img-trim ${img}
-    img-add-border ${img} 100
-done
-
-
-img-caption '(a) Pressure' \
-    full_pressure_512.png \
-    full_pressure_512.png
-img-caption '(b) Pressure near inclusion' \
-    inc_pressure_512.png \
-    inc_pressure_512.png
-
-img-caption '(a) log (pressure error for 256 x 256 case)' \
-    full_log_error_pressure_256.png \
-    full_log_error_pressure_256.png
-img-caption '(b) log (pressure error for 512 x 512 case)' \
-    full_log_error_pressure_512.png \
-    full_log_error_pressure_512.png
-
-img-caption '(a) log (pressure error for 128 x 128 case)' \
-    full_log_error_pressure_512_128.png \
-    full_log_error_pressure_512_128.png
-img-caption '(a) log (pressure error for 256 x 256 case)' \
-    full_log_error_pressure_512_256.png \
-    full_log_error_pressure_512_256.png
-
-img-caption '(a) log (pressure error for 256 x 256 case)' \
-    inc_log_error_pressure_256.png \
-    inc_log_error_pressure_256.png
-img-caption '(b) log (pressure error for 512 x 512 case)' \
-    inc_log_error_pressure_512.png \
-    inc_log_error_pressure_512.png
-
-img-caption '(a) log (pressure error for 128 x 128 case)' \
-    inc_log_error_pressure_512_128.png \
-    inc_log_error_pressure_512_128.png
-img-caption '(a) log (pressure error for 256 x 256 case)' \
-    inc_log_error_pressure_512_256.png \
-    inc_log_error_pressure_512_256.png
-
-
-cat-pair \
-    full_pressure_512.png \
-    inc_pressure_512.png \
-    fig_pressure_512.png
-
-cat-pair \
-    full_log_error_pressure_256.png \
-    full_log_error_pressure_512.png \
-    fig_full_log_error_pressure_256_512.png
-
-cat-pair \
-    full_log_error_pressure_512_128.png \
-    full_log_error_pressure_512_256.png \
-    fig_full_log_error_pressure_512_128_512_256.png
-
-cat-pair \
-    inc_log_error_pressure_256.png \
-    inc_log_error_pressure_512.png \
-    fig_inc_log_error_pressure_256_512.png \
-
-cat-pair \
-    inc_log_error_pressure_512_128.png \
-    inc_log_error_pressure_512_256.png \
-    fig_inc_log_error_pressure_512_128_512_256.png
-
-
-# finally, resize the images that will be included in the manual
-for img in fig_*; do
-    resize-image ${img}
-done
-
-#
-# Copy the images back
-#
-cd ${orig}
-cp -f -v ${tmp}/fig_* ${orig}/out
-

Deleted: doc/cigma/manual/figures3/common.sh
===================================================================
--- doc/cigma/manual/figures3/common.sh	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/figures3/common.sh	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,71 +0,0 @@
-#!/bin/bash
-
-#
-# In this file we define a few useful functions for
-# processing multiple images, based on the ImageMagick
-# manipulation programs
-#
-# Some useful links:
-#
-#   http://www.imagemagick.org/Usage/crop/
-#   http://www.imagemagick.org/Usage/annotating/
-#   http://personal.cscs.ch/~mvalle/postprocessing/ImageTools.html
-#
-
-function img-caption0
-{
-    #echo $1 ...adding caption
-    convert \
-        -gravity south  \
-        -stroke '#000C' \
-        -strokewidth 2  \
-        -font Arial-Regular \
-        -pointsize 30 \
-        -annotate 0 "$1" \
-        $2 $3
-}
-
-function img-caption
-{
-    #echo $1 ...adding caption
-    montage \
-        -geometry +0+0 \
-        -background White \
-        -font Arial-Regular \
-        -pointsize 35 \
-        -label "$1" \
-        $2 $3
-}
-
-function img-cat
-{
-    local tile=$1
-    shift
-    montage -tile ${tile} -mode Concatenate $*
-}
-
-function cat-pair
-{
-    #echo Concatenating $1 $2
-    img-cat 2x1 $1 $2 $3
-}
-
-
-function img-trim
-{
-    #echo $1 ...trimming
-    convert -trim $1 $1
-}
-
-function img-add-border
-{
-    #echo $1 ...adding border
-    convert -border $2 -bordercolor white $1 $1
-}
-
-function img-resize
-{
-    #echo $1 ...resizing
-    convert -resize '80%' $1 $1
-}
-

Deleted: doc/cigma/manual/hex.svg
===================================================================
--- doc/cigma/manual/hex.svg	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/hex.svg	2009-04-27 18:39:11 UTC (rev 14798)
@@ -1,702 +0,0 @@
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-<!-- Created with Inkscape (http://www.inkscape.org/) -->
-<svg
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-   xmlns:svg="http://www.w3.org/2000/svg"
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-   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
-   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
-   width="744.09448819"
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-   id="svg2822"
-   sodipodi:version="0.32"
-   inkscape:version="0.46"
-   sodipodi:docname="hex.svg"
-   inkscape:output_extension="org.inkscape.output.svg.inkscape">
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Modified: doc/cigma/manual/main.lyx
===================================================================
--- doc/cigma/manual/main.lyx	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/main.lyx	2009-04-27 18:39:11 UTC (rev 14798)
@@ -48,7 +48,7 @@
 
 \begin_layout Standard
 \begin_inset ERT
-status collapsed
+status open
 
 \begin_layout Plain Layout
 
@@ -248,37 +248,59 @@
 \end_layout
 
 \begin_layout LyX-Code
-    --with-boost=$BOOST_PREFIX      
+    --with-boost=
+\emph on
+$BOOST_PREFIX
+\emph default
+      
 \backslash
 
 \end_layout
 
 \begin_layout LyX-Code
-    --with-hdf5=$HDF5_PREFIX        
+    --with-hdf5=
+\emph on
+$HDF5_PREFIX
+\emph default
+        
 \backslash
 
 \end_layout
 
 \begin_layout LyX-Code
-    --with-netcdf=$NETCDF_PREFIX    
+    --with-vtk=
+\emph on
+$VTK_PREFIX
+\emph default
+          
 \backslash
 
 \end_layout
 
 \begin_layout LyX-Code
-    --with-vtk=$VTK_PREFIX          
+    --with-vtk-version=
+\emph on
+$VTK_VERSION
+\emph default
+ 
 \backslash
 
 \end_layout
 
 \begin_layout LyX-Code
-    --with-vtk-version=$VTK_VERSION 
+    --with-netcdf=
+\emph on
+$NETCDF_PREFIX
+\emph default
+    
 \backslash
 
 \end_layout
 
 \begin_layout LyX-Code
-    --with-cppunit-prefix=$CPPUNIT_PREFIX
+    --with-cppunit-prefix=
+\emph on
+$CPPUNIT_PREFIX
 \end_layout
 
 \begin_layout LyX-Code
@@ -290,27 +312,54 @@
 \end_layout
 
 \begin_layout Standard
-Only the Boost and HDF5 libraries are required components for this step.
- The additional configure flag 
+In general, the installation prefixes given to the configure options should
+ be used if you have installed the corresponding library in a custom location.
+ For demonstration purposes, the instructions in the next few sections use
+ a subdirectory of 
 \family typewriter
---with-vtk-version
+$HOME/opt
 \family default
- is required if you wish to enable VTK support.
+ as the installation prefix for each of the libraries.
 \end_layout
 
 \begin_layout Standard
-In general, the installation prefixes specified above should be used if
- you have installed the corresponding library in a custom location.
- In the instructions below, we use a subdirectory of 
+The only required options in this step are the ones for the Boost and HDF5
+ libraries.
+ If you wish to enable VTK library support, you will also have to select
+ a specific version number by providing the configure flag 
 \family typewriter
-$HOME/opt
+--with-vtk-version
 \family default
- as the installation prefix, but you may change it to something else.
- After all these steps are complete, you should be able to run the 
+, whose value defaults to 
+\begin_inset Quotes eld
+\end_inset
+
+
 \family typewriter
+5.0
+\family default
+
+\begin_inset Quotes erd
+\end_inset
+
+.
+ The NetCDF option is disabled by default, but if you wish to use a ExodusII
+ mesh files, you can provide an installation prefix to the corresponding
+ configure option.
+ Lastly, the CppUnit configure option will allow you to use 
+\family typewriter
+make check
+\family default
+ to compile and run a basic set of unit tests which verify that Cigma is
+ giving internally consistent results.
+\end_layout
+
+\begin_layout Standard
+After all these steps are complete, you should be able to run the 
+\family typewriter
 cigma
 \family default
- binary and start comparing arbitrary functions.
+ binary and proceed to compare.
 \end_layout
 
 \begin_layout Subsection
@@ -323,9 +372,9 @@
  Cigma uses Boost for its smart pointer facilities, lexical conversions,
  as well as for parsing command-line options, and for providing cross-platform
  filesystem operations.
- If Boost is not available for your platform as a binary package, you may
- choose to avoid long compilation times by building Boost with only the
- necessary components that Cigma needs,
+ If Boost is not available for your platform as a binary package that can
+ be readily installed, you may choose to install Boost with only the components
+ that Cigma will need,
 \end_layout
 
 \begin_layout LyX-Code
@@ -355,8 +404,8 @@
 \end_layout
 
 \begin_layout Standard
-Other components of Boost that need to be built can be chosen from the list
- generated by the command
+Just as a reference, the full list of Boost components can be obtained with
+ the command
 \end_layout
 
 \begin_layout LyX-Code
@@ -364,12 +413,8 @@
 \end_layout
 
 \begin_layout Standard
-These additional components can be passed as a comma-delimited list to the
- option 
-\family typewriter
---with-libraries
-\family default
- as in the build procedure specified in
+Enabling all components will certainly increase the compilation time of
+ the Boost code, since some of those components will require compilation.
 \end_layout
 
 \begin_layout Subsection
@@ -379,8 +424,8 @@
 \begin_layout Standard
 The Hierarchical Data Format is a library and multi-object file format for
  the transfer of numerical data between computers.
- Cigma depends on the C++ API of the HDF5 library, so it is important to
- enable C++ support when running the configure script below.
+ Since Cigma depends on the C++ API of the HDF5 library, it is important
+ to enable C++ support when running the configure script below.
  We recommend you install the library version 1.8 or higher, due to the improved
  metadata API in those versions.
  The latest source can be obtained from The HDF Group 
@@ -431,8 +476,9 @@
 \end_layout
 
 \begin_layout Standard
-If it is not already available on your system, you must build the zlib compressi
-on library before building HDF5 above 
+In the rare case that the zlib compression library is not already available
+ on your system, you must install it before running the installation procedure
+ given above, 
 \end_layout
 
 \begin_layout LyX-Code
@@ -1648,6 +1694,13 @@
 \end_layout
 
 \begin_layout Standard
+\begin_inset VSpace defskip
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
 We use this final form to calculate the global and localized errors on arbitrary
  discretizations.
 \end_layout
@@ -1823,7 +1876,7 @@
 
 \end_inset
 
-with regression variables 
+over the transformed variables 
 \begin_inset Formula $X_{i}=\log h_{i}$
 \end_inset
 
@@ -1832,23 +1885,26 @@
 \end_inset
 
 .
- The slope of the regression line will result in an estimate of 
+ The slope of that regression line gives an estimate of 
 \begin_inset Formula $\alpha.$
 \end_inset
 
- For this purpose, a short script called 
+ This process can be expedited using the the SciPy and Matplotlib Python
+ modules.
+\end_layout
+
+\begin_layout Standard
+A short script called 
 \family typewriter
 power-plot.py
 \family default
-, based on the SciPy and Matplotlib Python modules, is provided in the Cigma
- source code.
- You can use it for both calculating and plotting the regression line associated
- with the points 
-\begin_inset Formula $(X_{i},Y_{i})$
+ is provided in the Cigma source code.
+ It expects a file containing the points 
+\begin_inset Formula $(h_{i},\varepsilon_{i})$
 \end_inset
 
-, given an input file containing the points 
-\begin_inset Formula $(h_{i},\varepsilon_{i})$
+, and plots the regression line associated with the points 
+\begin_inset Formula $(\log h_{i},\log\varepsilon_{i})$
 \end_inset
 
 .
@@ -1867,27 +1923,20 @@
 
 \size footnotesize
 $ cigma compare 
-\series bold
-\bar under
+\emph on
 FunctionA
-\series default
-\bar default
+\emph default
  
-\series bold
-\bar under
+\emph on
 FunctionB
-\series default
-\bar default
+\emph default
  -m 
-\series bold
-\bar under
+\emph on
 IntegrationMesh
-\series default
-\bar default
- -o 
-\series bold
-\bar under
-LocalResiduals
+\emph default
+ -o
+\emph on
+ L2_Error_on_IntegrationCells
 \end_layout
 
 \begin_layout Standard
@@ -1896,13 +1945,15 @@
  Typically, you will also want to specify a particular discretization to
  use as the integration mesh.
  The output file will be used to store the results of the comparison, which
- are defined relative to the integration mesh.
+ consists of the 
+\begin_inset Formula $L_{2}$
+\end_inset
+
+-error over each of the cells in the integration mesh.
 \end_layout
 
 \begin_layout Standard
-In this chapter, we give a general overview of the options used in Cigma,
- and show actual usage examples in the next Chapter.
- To access the full list of options simply run the 
+The full list of options can be obtain by running the 
 \family typewriter
 cigma help
 \family default
@@ -1958,12 +2009,6 @@
 \begin_layout LyX-Code
 
 \size footnotesize
-   extract        Extract quadrature points from a mesh
-\end_layout
-
-\begin_layout LyX-Code
-
-\size footnotesize
    list           List file contents (fields, dimensions, ...)
 \end_layout
 
@@ -2002,12 +2047,22 @@
 \end_layout
 
 \begin_layout Standard
-For the remainder of this chapter, we will focus on the 
-\family typewriter
-compare 
-\family default
-command, as well as on a few other convenience commands that you can use
- for querying the fields themselves.
+In this Chapter, we give a general overview of each of these subcommands,
+ explain the meaning of each of their command line options, and give hypothetica
+l examples of typical usage patterns.
+ We delay discussion of actual examples until the next Chapter, where we
+ rely on publically available data files can be downloaded from the Cigma
+ software page 
+\begin_inset Note Greyedout
+status open
+
+\begin_layout Plain Layout
+URL here
+\end_layout
+
+\end_inset
+
+.
  
 \end_layout
 
@@ -3704,7 +3759,7 @@
 
 \begin_layout Standard
 \begin_inset Note Note
-status collapsed
+status open
 
 \begin_layout Plain Layout
 For example, querying 
@@ -4211,7 +4266,7 @@
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename figures3/bm1/alpha.png
+	filename figures/bm1/alpha.png
 	lyxscale 60
 	scale 30
 
@@ -4313,7 +4368,7 @@
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename figures3/bm2/out/fig_fields_64_20000_y099.png
+	filename figures/bm2/out/fig_fields_64_20000_y099.png
 	lyxscale 40
 	scale 29
 
@@ -4385,7 +4440,7 @@
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename figures3/bm2/heatflux.png
+	filename figures/bm2/heatflux.png
 	lyxscale 80
 	scale 40
 
@@ -4725,7 +4780,7 @@
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename figures3/bm2/out/fig_log_error_temperature_64_16_64_32_y099.png
+	filename figures/bm2/out/fig_log_error_temperature_64_16_64_32_y099.png
 	lyxscale 40
 	scale 28
 
@@ -4771,7 +4826,7 @@
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename figures3/bm2/out/fig_log_error_velocity_64_16_64_32_y099.png
+	filename figures/bm2/out/fig_log_error_velocity_64_16_64_32_y099.png
 	lyxscale 40
 	scale 28
 
@@ -4828,7 +4883,7 @@
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename figures2/inclusion_setup.eps
+	filename figures/bm3/inclusion_setup.eps
 	scale 60
 	rotateOrigin center
 
@@ -4926,7 +4981,7 @@
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename figures3/bm3/out/fig_pressure_512.png
+	filename figures/bm3/out/fig_pressure_512.png
 	lyxscale 40
 	scale 22
 
@@ -5015,7 +5070,7 @@
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename figures3/bm3/out/fig_full_log_error_pressure_512_128_512_256.png
+	filename figures/bm3/out/fig_full_log_error_pressure_512_128_512_256.png
 	lyxscale 40
 	scale 25
 
@@ -5049,7 +5104,7 @@
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename figures3/bm3/out/fig_inc_log_error_pressure_512_128_512_256.png
+	filename figures/bm3/out/fig_inc_log_error_pressure_512_128_512_256.png
 	lyxscale 40
 	scale 25
 
@@ -5097,9 +5152,9 @@
 
 \begin_layout LyX-Code
       -b 
-\bar under
+\series bold
 bm.circular_inclusion.pressure
-\bar default
+\series default
  
 \backslash
 
@@ -5135,7 +5190,7 @@
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename figures3/bm3/out/fig_full_log_error_pressure_256_512.png
+	filename figures/bm3/out/fig_full_log_error_pressure_256_512.png
 	lyxscale 40
 	scale 25
 
@@ -5170,7 +5225,7 @@
 \begin_layout Plain Layout
 \align center
 \begin_inset Graphics
-	filename figures3/bm3/out/fig_inc_log_error_pressure_256_512.png
+	filename figures/bm3/out/fig_inc_log_error_pressure_256_512.png
 	lyxscale 40
 	scale 25
 
@@ -7889,12 +7944,9 @@
  and groups are analagous to folders.
  One important difference, however, is that you can attach supporting metadata
  to both kinds of objects.
- The metadata objects are called 
+ These associated metadata are known as 
 \emph on
-attribute
-\emph default
-s.
- [TODO: citation for all this HDF5 explanation?]
+attributes.
 \end_layout
 
 \begin_layout Standard
@@ -7910,15 +7962,14 @@
 \end_layout
 
 \begin_layout Standard
-In Cigma you may always provide an explicit path to every dataset, so you
- have a fair amount of flexibility for how you organize your datasets inside
- HDF5 files.
- For example, a typical Cigma HDF5 file could have the following structure.
- 
+With Cigma you always provide an explicit path to specific datasets, so
+ you have a fair amount of flexibility in how you organize datasets into
+ groups inside your HDF5 files.
+ For example, a typical file could have the following structure,
 \end_layout
 
 \begin_layout LyX-Code
-model.h5
+file.h5
 \end_layout
 
 \begin_layout LyX-Code
@@ -8003,26 +8054,133 @@
 ...
 \end_layout
 
+\begin_layout LyX-Code
+
+\end_layout
+
 \begin_layout Standard
-Generally, Cigma will only require you to specify the path to a specific
- field dataset.
- If a small amount of metadata is present in your field dataset, the rest
- of the required information, such as which mesh and finite elements to
- use, will be deduced from that metadata.
+where the structure of the mesh does not change from timestep to timestep.
 \end_layout
 
+\begin_layout Standard
+Alternatively, a file which stores data associated with a mesh that changes
+ over time would have a different structure,
+\end_layout
+
+\begin_layout LyX-Code
+file.h5
+\end_layout
+
+\begin_layout LyX-Code
+
+\backslash
+__ model
+\end_layout
+
+\begin_layout LyX-Code
+    |__ step00000
+\end_layout
+
+\begin_layout LyX-Code
+    |   |__ mesh
+\end_layout
+
+\begin_layout LyX-Code
+    |   |   |__ coordinates
+\end_layout
+
+\begin_layout LyX-Code
+    |   |   
+\backslash
+__ connectivity
+\end_layout
+
+\begin_layout LyX-Code
+    |   |__ variables
+\end_layout
+
+\begin_layout LyX-Code
+    |       |__ temperature
+\end_layout
+
+\begin_layout LyX-Code
+    |       |__ displacement
+\end_layout
+
+\begin_layout LyX-Code
+    |       
+\backslash
+__ velocity
+\end_layout
+
+\begin_layout LyX-Code
+    |__ step00010
+\end_layout
+
+\begin_layout LyX-Code
+    |   |__ mesh
+\end_layout
+
+\begin_layout LyX-Code
+    |   |   |__ coordinates
+\end_layout
+
+\begin_layout LyX-Code
+    |   |   
+\backslash
+__ connectivity
+\end_layout
+
+\begin_layout LyX-Code
+    |   |__ variables
+\end_layout
+
+\begin_layout LyX-Code
+    |       |__ temperature
+\end_layout
+
+\begin_layout LyX-Code
+    |       |__ displacement
+\end_layout
+
+\begin_layout LyX-Code
+    |       
+\backslash
+__ velocity
+\end_layout
+
+\begin_layout LyX-Code
+    
+\backslash
+__ ...
+\end_layout
+
+\begin_layout Standard
+where we have allowed for each.
+\end_layout
+
+\begin_layout Standard
+To summarize, Cigma requires you to specify a full path to a specific dataset.
+ Moreover, by attaching a small amount of metadata to your datasets, it
+ becomes possible to reduce the amount of information that must be provided
+ to the comparison routine, such as what mesh to use in conjunction with
+ a given set of coefficients, and which set of shape functions to use in
+ the respective evaluations.
+\end_layout
+
 \begin_layout Description
-MeshLocation points to the HDF5 group which contains the appropriate coordinates
- and connectivity datasets.
+MeshLocation is a string representing the HDF5 path pointing to the mesh
+ group which contains the coordinates and connectivity datasets.
  This attribute should be attached to the array corresponding to your degrees
  of freedom (shape function coefficients).
 \end_layout
 
 \begin_layout Description
-CellType is a string identifier to determine which shape functions to use
- for interpolating values inside the element (e.g., tet4, hex8, quad4, tri3,
- ...).
- This attribute should be attached to the mesh dataset.
+CellType is a string identifier used to determine which shape functions
+ to use for interpolating values inside the element (e.g., tet4, hex8, quad4,
+ tri3, ...).
+ This attribute should be attached to the mesh group that contains the coordinat
+es and connectivity datasets.
 \end_layout
 
 \begin_layout Standard

Deleted: doc/cigma/manual/quad.svg
===================================================================
--- doc/cigma/manual/quad.svg	2009-04-27 18:29:17 UTC (rev 14797)
+++ doc/cigma/manual/quad.svg	2009-04-27 18:39:11 UTC (rev 14798)
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Added: doc/cigma/manual/subversion.cfg
===================================================================
--- doc/cigma/manual/subversion.cfg	                        (rev 0)
+++ doc/cigma/manual/subversion.cfg	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,20 @@
+#
+# NOTE: In order to use git-svn to manage this repository, first we need to properly set
+# the svn:mime-type of a specific set of files by enabling the following options in
+# the file "~/.subversion/config". (Should in principle work).
+#
+# This is because a pre-commit script on the svn server will not accept binary files
+# that don't have the appropriate mime-type set. This will prevent binary files, often
+# large, from being included in the body of the email notifications sent to the
+# cig-commit mailing list.
+#
+# Refer to
+#  http://kerneltrap.org/mailarchive/git/2008/5/14/1815914
+#  http://kerneltrap.org/mailarchive/git/2008/7/8/2391314
+#
+[miscellany]
+enable-auto-props=yes
+[auto-props]
+*.png = svn:mime-type=application/octet-stream
+*.jpg = svn:mime-type=application/octet-stream
+*.gif = svn:mime-type=application/octet-stream

Added: doc/cigma/manual/svn-autoprops.config
===================================================================
--- doc/cigma/manual/svn-autoprops.config	                        (rev 0)
+++ doc/cigma/manual/svn-autoprops.config	2009-04-27 18:39:11 UTC (rev 14798)
@@ -0,0 +1,38 @@
+
+[miscellany]
+enable-auto-props = yes
+
+[auto-props]
+*.ai = svn:mime-type=application/postscript
+*.bmp = svn:mime-type=image/bmp
+*.bz2 = svn:mime-type=application/x-bzip2
+*.doc = svn:mime-type=application/msword
+*.eps = svn:mime-type=application/postscript
+*.gif = svn:mime-type=image/gif
+*.gz = svn:mime-type=application/x-gzip
+*.h5 = svn:mime-type=application/x-hdf
+*.hdf = svn:mime-type=application/x-hdf
+*.ico = svn:mime-type=image/x-icon
+*.jpeg = svn:mime-type=image/jpeg
+*.jpg = svn:mime-type=image/jpeg
+*.odc = svn:mime-type=application/vnd.oasis.opendocument.chart
+*.odf = svn:mime-type=application/vnd.oasis.opendocument.formula
+*.odg = svn:mime-type=application/vnd.oasis.opendocument.graphics
+*.odi = svn:mime-type=application/vnd.oasis.opendocument.image
+*.odp = svn:mime-type=application/vnd.oasis.opendocument.presentation
+*.ods = svn:mime-type=application/vnd.oasis.opendocument.spreadsheet
+*.odt = svn:mime-type=application/vnd.oasis.opendocument.text
+*.pdf = svn:mime-type=application/pdf
+*.png = svn:mime-type=image/png
+*.ppm = svn:mime-type=image/x-portable-pixmap
+*.ppt = svn:mime-type=application/vnd.ms-powerpoint
+*.ps = svn:mime-type=application/postscript
+*.psd = svn:mime-type=application/octet-stream
+*.tar = svn:mime-type=application/x-tar
+*.tif = svn:mime-type=image/tiff
+*.tiff = svn:mime-type=image/tiff
+*.tgz = svn:mime-type=application/x-compressed
+*.xls = svn:mime-type=application/vnd.ms-excel
+*.zip = svn:mime-type=application/zip
+
+

Deleted: doc/cigma/manual/tet.svg
===================================================================
--- doc/cigma/manual/tet.svg	2009-04-27 18:29:17 UTC (rev 14797)
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