[cig-commits] r6760 - in short/3D/PyLith/branches/pylith-0.8/pylith3d/examples: . linhex/patchtest linhex/ps1 linhex/slip1 linhex/splittest linhex/timeslip1 lintet/bm1a lintet/bm1b lintet/bm1c lintet/bm2a lintet/bm5 lintet/patchtest quadhex/bm1a quadhex/patchtest quadtet/bm1a quadtet/patchtest

leif at geodynamics.org leif at geodynamics.org
Wed May 2 17:05:56 PDT 2007


Author: leif
Date: 2007-05-02 17:05:55 -0700 (Wed, 02 May 2007)
New Revision: 6760

Removed:
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runpt1.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest-debug.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest-lithomop.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest-test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-lithomop.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-lithomop.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-lithomop.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-lithomop.sh
Modified:
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/Makefile.am
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-bbar-comp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-bbar-incomp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-full-comp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-full-incomp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-red-comp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-red-incomp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/ps1/test.sh.in
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/slip1/test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/timeslip1/test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-debug.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-debug.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-debug.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-debug.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-bbar-comp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-bbar-incomp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-full-comp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-full-incomp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-red-comp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-red-incomp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-bbar-comp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-bbar-incomp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-full-comp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-full-incomp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-red-comp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-red-incomp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-bbar-comp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-bbar-incomp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-full-comp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-full-incomp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-red-comp.com
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-red-incomp.com
Log:
Using a Perl script, updated all shell scripts to use the new
property/facility/component layout.  Removed shell scripts that still
used 'mpiexec' or had 'lithomop' in the filename.


Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/Makefile.am
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/Makefile.am	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/Makefile.am	2007-05-03 00:05:55 UTC (rev 6760)
@@ -67,7 +67,6 @@
 	linhex/patchtest/pt7.bc \
 	linhex/patchtest/pt8.bc \
 	linhex/patchtest/pt9.bc \
-	linhex/patchtest/runpt1.sh \
 	linhex/patchtest/runtests-bbar-comp.com \
 	linhex/patchtest/runtests-bbar-incomp.com \
 	linhex/patchtest/runtests-full-comp.com \
@@ -184,10 +183,6 @@
 	linhex/slip1/slip1.time \
 	linhex/slip1/slip1.winkx \
 	linhex/slip1/test.sh \
-	linhex/splittest/runsplittest-debug.sh \
-	linhex/splittest/runsplittest-lithomop.sh \
-	linhex/splittest/runsplittest-test.sh \
-	linhex/splittest/runsplittest.sh \
 	linhex/splittest/splittest.bc \
 	linhex/splittest/splittest.cfg \
 	linhex/splittest/splittest.connect \
@@ -239,7 +234,6 @@
 	lintet/bm1a/bm1a.time \
 	lintet/bm1a/pylith3d.cfg \
 	lintet/bm1a/runbm1a-debug.sh \
-	lintet/bm1a/runbm1a-lithomop.sh \
 	lintet/bm1a/runbm1a-test.sh \
 	lintet/bm1a/runbm1a.sh \
 	lintet/bm1a/test.sh \
@@ -253,7 +247,6 @@
 	lintet/bm1b/bm1b.time \
 	lintet/bm1b/pylith3d.cfg \
 	lintet/bm1b/runbm1b-debug.sh \
-	lintet/bm1b/runbm1b-lithomop.sh \
 	lintet/bm1b/runbm1b-test.sh \
 	lintet/bm1b/runbm1b.sh \
 	lintet/bm1b/test.sh \
@@ -267,7 +260,6 @@
 	lintet/bm1c/bm1c.time \
 	lintet/bm1c/pylith3d.cfg \
 	lintet/bm1c/runbm1c-debug.sh \
-	lintet/bm1c/runbm1c-lithomop.sh \
 	lintet/bm1c/runbm1c-test.sh \
 	lintet/bm1c/runbm1c.sh \
 	lintet/bm2a/bm2a.bc \
@@ -284,7 +276,6 @@
 	lintet/bm5/bm5.time \
 	lintet/bm5/pylith3d.cfg \
 	lintet/bm5/runbm5-debug.sh \
-	lintet/bm5/runbm5-lithomop.sh \
 	lintet/bm5/runbm5-test.sh \
 	lintet/bm5/runbm5.sh \
 	lintet/bm5/test.sh \

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1 +1 @@
-time pylith3dapp.py --pl3dscan.fileRoot=bm1/bm1 --pl3dscan.keywordEqualsValueFile=bm2/bm2.keyval --pl3dscan.bcInputFile=bm2/bm2.bc --pl3dscan.timeStepInputFile=bm2/bm2.time --pl3dscan.asciiOutputFile=bm2/bm2.ascii --pl3dscan.plotOutputFile=bm2/bm2.plot
+time pylith3dapp.py --fileRoot=bm1/bm1 --keywordEqualsValueFile=bm2/bm2.keyval --bcInputFile=bm2/bm2.bc --timeStepInputFile=bm2/bm2.time --asciiOutputFile=bm2/bm2.ascii --plotOutputFile=bm2/bm2.plot

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runpt1.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runpt1.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runpt1.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,56 +0,0 @@
-#!/bin/bash
-# ======================================================================
-#
-# Shell script to run PyLith using small split node test.
-#
-# ======================================================================
-
-if [ $# != 1 ]; then
-  echo "usage: runpt1-test.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="pt1"
-dupext="fuldat prop statevar time"
-sinext="coord connect bc split"
-
-pyreflags="-typos=relaxed"
-echo "Pyre flags:"
-echo $pyreflags
-
-pylithflags="-pl3dscan.fileRoot=${simroot}_$nprocs \
-  -pl3dscan.asciiOutput=full \
-  -pl3dscan.ucdOutput=ascii"
-# Do not use pythonTimestep for now until all the bugs are worked out.
-#  -pl3dscan.ucdOutput=ascii \
-#  -pl3dscan.pythonTimestep=1 "
-echo "PyLith flags:"
-echo $pylithflags
-
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09 "
-#  -start_in_debugger "
-echo "PETSc flags:"
-echo $petscflags
-
-echo "Setting up symbolic links with prefix ${simroot}_${nprocs}..."
-for ext in $sinext; do
-  ln -s $simroot.$ext ${simroot}_$nprocs.$ext
-done
-for ext in $dupext; do
-  for (( i=0; i < $nprocs; i+=1 )); do
-    ln -s $simroot.$ext ${simroot}_$nprocs.$i.$ext
-  done
-done
-
-echo "Running PyLith..."
-cmd="mpiexec -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
-# end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-bbar-comp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-bbar-comp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-bbar-comp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt1.bc --pl3dscan.asciiOutputFile=pt1-bbar-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt1.bc --asciiOutputFile=pt1-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt2.bc --pl3dscan.asciiOutputFile=pt2-bbar-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt2.bc --asciiOutputFile=pt2-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt3.bc --pl3dscan.asciiOutputFile=pt3-bbar-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt3.bc --asciiOutputFile=pt3-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt4.bc --pl3dscan.asciiOutputFile=pt4-bbar-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt4.bc --asciiOutputFile=pt4-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt5.bc --pl3dscan.asciiOutputFile=pt5-bbar-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt5.bc --asciiOutputFile=pt5-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt6.bc --pl3dscan.asciiOutputFile=pt6-bbar-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt6.bc --asciiOutputFile=pt6-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt7.bc --pl3dscan.asciiOutputFile=pt7-bbar-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt7.bc --asciiOutputFile=pt7-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt8.bc --pl3dscan.asciiOutputFile=pt8-bbar-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt8.bc --asciiOutputFile=pt8-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt9.bc --pl3dscan.asciiOutputFile=pt9-bbar-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt9.bc --asciiOutputFile=pt9-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt10.bc --pl3dscan.asciiOutputFile=pt10-bbar-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt10.bc --asciiOutputFile=pt10-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt11.bc --pl3dscan.asciiOutputFile=pt11-bbar-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt11.bc --asciiOutputFile=pt11-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt12.bc --pl3dscan.asciiOutputFile=pt12-bbar-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt12.bc --asciiOutputFile=pt12-bbar-comp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-bbar-incomp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-bbar-incomp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-bbar-incomp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt1-bbar-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt1.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt1-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt2-bbar-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt2.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt2-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt3-bbar-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt3.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt3-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt4-bbar-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt4.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt4-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt5-bbar-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt5.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt5-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt6-bbar-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt6.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt6-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt7-bbar-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt7.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt7-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt8-bbar-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt8.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt8-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt9-bbar-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt9.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt9-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt10-bbar-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt10.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt10-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt11-bbar-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt11.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt11-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-bbar.keyval --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-bbar-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-bbar.keyval --bcInputFile=pt12.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt12-bbar-incomp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-full-comp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-full-comp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-full-comp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt1.bc --pl3dscan.asciiOutputFile=pt1-full-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt1.bc --asciiOutputFile=pt1-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt2.bc --pl3dscan.asciiOutputFile=pt2-full-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt2.bc --asciiOutputFile=pt2-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt3.bc --pl3dscan.asciiOutputFile=pt3-full-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt3.bc --asciiOutputFile=pt3-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt4.bc --pl3dscan.asciiOutputFile=pt4-full-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt4.bc --asciiOutputFile=pt4-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt5.bc --pl3dscan.asciiOutputFile=pt5-full-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt5.bc --asciiOutputFile=pt5-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt6.bc --pl3dscan.asciiOutputFile=pt6-full-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt6.bc --asciiOutputFile=pt6-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt7.bc --pl3dscan.asciiOutputFile=pt7-full-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt7.bc --asciiOutputFile=pt7-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt8.bc --pl3dscan.asciiOutputFile=pt8-full-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt8.bc --asciiOutputFile=pt8-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt9.bc --pl3dscan.asciiOutputFile=pt9-full-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt9.bc --asciiOutputFile=pt9-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt10.bc --pl3dscan.asciiOutputFile=pt10-full-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt10.bc --asciiOutputFile=pt10-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt11.bc --pl3dscan.asciiOutputFile=pt11-full-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt11.bc --asciiOutputFile=pt11-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt12.bc --pl3dscan.asciiOutputFile=pt12-full-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt12.bc --asciiOutputFile=pt12-full-comp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-full-incomp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-full-incomp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-full-incomp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt1-full-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt1.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt1-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt2-full-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt2.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt2-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt3-full-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt3.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt3-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt4-full-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt4.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt4-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt5-full-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt5.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt5-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt6-full-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt6.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt6-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt7-full-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt7.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt7-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt8-full-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt8.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt8-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt9-full-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt9.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt9-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt10-full-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt10.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt10-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt11-full-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt11.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt11-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-full.keyval --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-full-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-full.keyval --bcInputFile=pt12.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt12-full-incomp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-red-comp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-red-comp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-red-comp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt1.bc --pl3dscan.asciiOutputFile=pt1-red-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt1.bc --asciiOutputFile=pt1-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt2.bc --pl3dscan.asciiOutputFile=pt2-red-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt2.bc --asciiOutputFile=pt2-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt3.bc --pl3dscan.asciiOutputFile=pt3-red-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt3.bc --asciiOutputFile=pt3-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt4.bc --pl3dscan.asciiOutputFile=pt4-red-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt4.bc --asciiOutputFile=pt4-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt5.bc --pl3dscan.asciiOutputFile=pt5-red-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt5.bc --asciiOutputFile=pt5-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt6.bc --pl3dscan.asciiOutputFile=pt6-red-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt6.bc --asciiOutputFile=pt6-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt7.bc --pl3dscan.asciiOutputFile=pt7-red-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt7.bc --asciiOutputFile=pt7-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt8.bc --pl3dscan.asciiOutputFile=pt8-red-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt8.bc --asciiOutputFile=pt8-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt9.bc --pl3dscan.asciiOutputFile=pt9-red-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt9.bc --asciiOutputFile=pt9-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt10.bc --pl3dscan.asciiOutputFile=pt10-red-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt10.bc --asciiOutputFile=pt10-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt11.bc --pl3dscan.asciiOutputFile=pt11-red-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt11.bc --asciiOutputFile=pt11-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt12.bc --pl3dscan.asciiOutputFile=pt12-red-comp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt12.bc --asciiOutputFile=pt12-red-comp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-red-incomp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-red-incomp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/patchtest/runtests-red-incomp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt1-red-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt1.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt1-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt2-red-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt2.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt2-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt3-red-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt3.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt3-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt4-red-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt4.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt4-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt5-red-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt5.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt5-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt6-red-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt6.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt6-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt7-red-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt7.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt7-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt8-red-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt8.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt8-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt9-red-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt9.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt9-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt10-red-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt10.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt10-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt11-red-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt11.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt11-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.fileRoot=pt1 --pl3dscan.keywordEqualsValueFile=pt-red.keyval --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-red-incomp.ascii
+pylith3dapp.py --fileRoot=pt1 --keywordEqualsValueFile=pt-red.keyval --bcInputFile=pt12.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt12-red-incomp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/ps1/test.sh.in
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/ps1/test.sh.in	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/ps1/test.sh.in	2007-05-03 00:05:55 UTC (rev 6760)
@@ -2,6 +2,6 @@
 
 common="linhex/ps1"
 
-pylith3dapp.py --pl3dscan.fileRoot=@fileRoot@ --pl3dscan.coordinateInputFile=$common/ps1.coord --pl3dscan.bcInputFile=$common/ps1.bc --pl3dscan.stateVariableInputFile=$common/ps1.statevar --pl3dscan.connectivityInputFile=$common/ps1.connect --pl3dscan.fullOutputInputFile=$common/ps1.fuldat
+pylith3dapp.py --fileRoot=@fileRoot@ --coordinateInputFile=$common/ps1.coord --bcInputFile=$common/ps1.bc --stateVariableInputFile=$common/ps1.statevar --connectivityInputFile=$common/ps1.connect --fullOutputInputFile=$common/ps1.fuldat
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/slip1/test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/slip1/test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/slip1/test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-pylith3dapp.py -typos=relaxed -pl3dscan.fileRoot=linhex/slip1/slip1 -pl3dscan.asciiOutput=full -pl3dscan.autoRotateSlipperyNodes=False -log_summary -petsc_solver 1 -pc_type ilu -ksp_monitor -ksp_view -ksp_rtol 1e-9
+pylith3dapp.py -typos=relaxed -fileRoot=linhex/slip1/slip1 -asciiOutput=full -autoRotateSlipperyNodes=False -petsc.log_summary -petsc.pc_type=ilu -petsc.ksp_monitor -petsc.ksp_view -petsc.ksp_rtol=1e-9
 
 # end of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest-debug.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest-debug.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest-debug.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,57 +0,0 @@
-#!/bin/bash
-# ======================================================================
-#
-# Shell script to run PyLith using small split node test.
-#
-# ======================================================================
-
-if [ $# != 1 ]; then
-  echo "usage: runsplittest-debug.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="splittest"
-dupext="fuldat prop statevar time"
-sinext="coord connect bc split"
-
-pyreflags="-typos=relaxed"
-echo "Pyre flags:"
-echo $pyreflags
-
-pylithflags="-pl3dscan.fileRoot=${simroot}_$nprocs \
-  -pl3dscan.asciiOutput=full \
-  -pl3dscan.ucdOutput=ascii"
-# Do not use pythonTimestep for now until all the bugs are worked out.
-#  -pl3dscan.ucdOutput=ascii \
-#  -pl3dscan.pythonTimestep=1 "
-echo "PyLith flags:"
-echo $pylithflags
-
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_view \
-  -ksp_rtol 1e-09 \
-  -start_in_debugger"
-echo "PETSc flags:"
-echo $petscflags
-
-echo "Setting up symbolic links with prefix ${simroot}_${nprocs}..."
-for ext in $sinext; do
-  ln -s $simroot.$ext ${simroot}_$nprocs.$ext
-done
-for ext in $dupext; do
-  for (( i=0; i < $nprocs; i+=1 )); do
-    ln -s $simroot.$ext ${simroot}_$nprocs.$i.$ext
-  done
-done
-
-echo "Running PyLith..."
-cmd="mpiexec -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
-# end of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest-lithomop.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest-lithomop.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest-lithomop.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,50 +0,0 @@
-#!/bin/bash
-# ======================================================================
-#
-# Shell script to run LithoMop using small split node test.
-#
-# ======================================================================
-
-if [ $# != 0 ]; then
-  echo "usage: runsplittest-lithomop.sh"
-  exit 1
-fi
-suff="lm"
-
-simroot="splittest"
-dupext="fuldat prop statevar time"
-sinext="coord connect bc split"
-
-pyreflags="-typos=relaxed"
-echo "Pyre flags:"
-echo $pyreflags
-
-lithomopflags="-lm3dscan.fileRoot=${simroot}_$suff \
-  -lm3dscan.asciiOutput=none \
-  -lm3dscan.ucdOutput=binary"
-echo "LithoMop flags:"
-echo $lithomopflags
-
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
-
-echo "Setting up symbolic links with prefix ${simroot}_${suff}..."
-for ext in $sinext; do
-  ln -s $simroot.$ext ${simroot}_$suff.$ext
-done
-for ext in $dupext; do
-  ln -s $simroot.$ext ${simroot}_$suff.$ext
-done
-
-echo "Running LithoMop..."
-cmd="lithomop3dapp.py $pyreflags $lithomopflags $petscflags"
-
-echo $cmd
-eval $cmd
-
-# end of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest-test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest-test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest-test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,55 +0,0 @@
-#!/bin/bash
-# ======================================================================
-#
-# Shell script to run PyLith using small split node test.
-#
-# ======================================================================
-
-if [ $# != 1 ]; then
-  echo "usage: runsplittest-test.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="splittest"
-dupext="fuldat prop statevar time"
-sinext="coord connect bc split"
-
-pyreflags="-typos=relaxed"
-echo "Pyre flags:"
-echo $pyreflags
-
-pylithflags="-pl3dscan.fileRoot=${simroot}_$nprocs \
-  -pl3dscan.asciiOutput=echo \
-  -pl3dscan.ucdOutput=ascii"
-# Do not use pythonTimestep for now until all the bugs are worked out.
-#  -pl3dscan.ucdOutput=ascii \
-#  -pl3dscan.pythonTimestep=1 "
-echo "PyLith flags:"
-echo $pylithflags
-
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
-
-echo "Setting up symbolic links with prefix ${simroot}_${nprocs}..."
-for ext in $sinext; do
-  ln -s $simroot.$ext ${simroot}_$nprocs.$ext
-done
-for ext in $dupext; do
-  for (( i=0; i < $nprocs; i+=1 )); do
-    ln -s $simroot.$ext ${simroot}_$nprocs.$i.$ext
-  done
-done
-
-echo "Running PyLith..."
-cmd="mpiexec -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
-# end of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/runsplittest.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,55 +0,0 @@
-#!/bin/bash
-# ======================================================================
-#
-# Shell script to run PyLith using small split node test.
-#
-# ======================================================================
-
-if [ $# != 1 ]; then
-  echo "usage: runsplittest.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="splittest"
-dupext="fuldat prop statevar time"
-sinext="coord connect bc split"
-
-pyreflags="-typos=relaxed"
-echo "Pyre flags:"
-echo $pyreflags
-
-pylithflags="-pl3dscan.fileRoot=${simroot}_$nprocs \
-  -pl3dscan.asciiOutput=none \
-  -pl3dscan.ucdOutput=binary"
-# Do not use pythonTimestep for now until all the bugs are worked out.
-#  -pl3dscan.ucdOutput=ascii \
-#  -pl3dscan.pythonTimestep=1 "
-echo "PyLith flags:"
-echo $pylithflags
-
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
-
-echo "Setting up symbolic links with prefix ${simroot}_${nprocs}..."
-for ext in $sinext; do
-  ln -s $simroot.$ext ${simroot}_$nprocs.$ext
-done
-for ext in $dupext; do
-  for (( i=0; i < $nprocs; i+=1 )); do
-    ln -s $simroot.$ext ${simroot}_$nprocs.$i.$ext
-  done
-done
-
-echo "Running PyLith..."
-cmd="mpiexec -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
-# end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/splittest/test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-pylith3dapp.py -typos=relaxed -pl3dscan.fileRoot=lintet/splittest/splittest -pl3dscan.ucdOutput=binary -log_summary -pc_type ilu -ksp_monitor -ksp_view -ksp_rtol 1e-9
+pylith3dapp.py -typos=relaxed -fileRoot=lintet/splittest/splittest -ucdOutput=binary -petsc.log_summary -petsc.pc_type=ilu -petsc.ksp_monitor -petsc.ksp_view -petsc.ksp_rtol=1e-9
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/timeslip1/test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/timeslip1/test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/timeslip1/test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-pylith3dapp.py -typos=relaxed -pl3dscan.fileRoot=linhex/timeslip1/timeslip1 -pl3dscan.asciiOutput=full -pl3dscan.autoRotateSlipperyNodes=False -log_summary -petsc_solver 1 -pc_type ilu -ksp_monitor -ksp_view -ksp_rtol 1e-09
+pylith3dapp.py -typos=relaxed -fileRoot=linhex/timeslip1/timeslip1 -asciiOutput=full -autoRotateSlipperyNodes=False -petsc.log_summary -petsc.pc_type=ilu -petsc.ksp_monitor -petsc.ksp_view -petsc.ksp_rtol=1e-09
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-debug.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-debug.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-debug.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -6,9 +6,9 @@
 # ======================================================================
 
 # Do not use pythonTimestep for now until all the bugs are worked out.
-#pyts="-pl3dscan.pythonTimestep=1"
+#pyts="-pythonTimestep=1"
 
 set -x
-pylith3dapp.py -pl3dscan.asciiOutput=full -pl3dscan.ucdOutput=ascii $pyts
+pylith3dapp.py -asciiOutput=full -ucdOutput=ascii $pyts
 
 # end of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-lithomop.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-lithomop.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-lithomop.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,50 +0,0 @@
-#!/bin/bash
-# ======================================================================
-#
-# Shell script to run LithoMop using SCEC benchmark 1 (medium resolution).
-#
-# ======================================================================
-
-if [ $# != 0 ]; then
-  echo "usage: runbm1a-lithomop.sh"
-  exit 1
-fi
-suff="lm"
-
-simroot="bm1a"
-dupext="fuldat prop statevar time"
-sinext="coord connect bc split"
-
-pyreflags="-typos=relaxed"
-echo "Pyre flags:"
-echo $pyreflags
-
-lithomopflags="-lm3dscan.fileRoot=${simroot}_$suff \
-  -lm3dscan.asciiOutput=none \
-  -lm3dscan.ucdOutput=binary"
-echo "LithoMop flags:"
-echo $lithomopflags
-
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
-
-echo "Setting up symbolic links with prefix ${simroot}_${suff}..."
-for ext in $sinext; do
-  ln -s $simroot.$ext ${simroot}_$suff.$ext
-done
-for ext in $dupext; do
-  ln -s $simroot.$ext ${simroot}_$suff.$ext
-done
-
-echo "Running LithoMop..."
-cmd="lithomop3dapp.py $pyreflags $lithomopflags $petscflags"
-
-echo $cmd
-eval $cmd
-
-# end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -6,9 +6,9 @@
 # ======================================================================
 
 # Do not use pythonTimestep for now until all the bugs are worked out.
-#pyts="-pl3dscan.pythonTimestep=1"
+#pyts="-pythonTimestep=1"
 
 set -x
-pylith3dapp.py -pl3dscan.asciiOutput=echo -pl3dscan.ucdOutput=ascii $pyts
+pylith3dapp.py -asciiOutput=echo -ucdOutput=ascii $pyts
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -6,9 +6,9 @@
 # ======================================================================
 
 # Do not use pythonTimestep for now until all the bugs are worked out.
-#pyts="-pl3dscan.pythonTimestep=1"
+#pyts="-pythonTimestep=1"
 
 set -x
-pylith3dapp.py -pl3dscan.asciiOutput=none -pl3dscan.ucdOutput=binary $pyts
+pylith3dapp.py -asciiOutput=none -ucdOutput=binary $pyts
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-pylith3dapp.py -pl3dscan.fileRoot=lintet/bm1a/bm1a -log_summary -petsc_solver 1 -pc_type ilu -ksp_monitor -ksp_view -ksp_rtol 1e-9
+pylith3dapp.py -fileRoot=lintet/bm1a/bm1a -petsc.log_summary -petsc.pc_type=ilu -petsc.ksp_monitor -petsc.ksp_view -petsc.ksp_rtol=1e-9
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-debug.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-debug.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-debug.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -6,9 +6,9 @@
 # ======================================================================
 
 # Do not use pythonTimestep for now until all the bugs are worked out.
-#pyts="-pl3dscan.pythonTimestep=1"
+#pyts="-pythonTimestep=1"
 
 set -x
-pylith3dapp.py -pl3dscan.asciiOutput=full -pl3dscan.ucdOutput=ascii $pyts
+pylith3dapp.py -asciiOutput=full -ucdOutput=ascii $pyts
 
 # end of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-lithomop.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-lithomop.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-lithomop.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,50 +0,0 @@
-#!/bin/bash
-# ======================================================================
-#
-# Shell script to run LithoMop using SCEC benchmark 1 (low resolution).
-#
-# ======================================================================
-
-if [ $# != 0 ]; then
-  echo "usage: runbm1b-lithomop.sh"
-  exit 1
-fi
-suff="lm"
-
-simroot="bm1b"
-dupext="fuldat prop statevar time"
-sinext="coord connect bc split"
-
-pyreflags="-typos=relaxed"
-echo "Pyre flags:"
-echo $pyreflags
-
-lithomopflags="-lm3dscan.fileRoot=${simroot}_$suff \
-  -lm3dscan.asciiOutput=none \
-  -lm3dscan.ucdOutput=binary"
-echo "LithoMop flags:"
-echo $lithomopflags
-
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
-
-echo "Setting up symbolic links with prefix ${simroot}_${suff}..."
-for ext in $sinext; do
-  ln -s $simroot.$ext ${simroot}_$suff.$ext
-done
-for ext in $dupext; do
-  ln -s $simroot.$ext ${simroot}_$suff.$ext
-done
-
-echo "Running LithoMop..."
-cmd="lithomop3dapp.py $pyreflags $lithomopflags $petscflags"
-
-echo $cmd
-eval $cmd
-
-# end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -6,9 +6,9 @@
 # ======================================================================
 
 # Do not use pythonTimestep for now until all the bugs are worked out.
-#pyts="-pl3dscan.pythonTimestep=1"
+#pyts="-pythonTimestep=1"
 
 set -x
-pylith3dapp.py -pl3dscan.asciiOutput=echo -pl3dscan.ucdOutput=ascii $pyts
+pylith3dapp.py -asciiOutput=echo -ucdOutput=ascii $pyts
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -6,9 +6,9 @@
 # ======================================================================
 
 # Do not use pythonTimestep for now until all the bugs are worked out.
-#pyts="-pl3dscan.pythonTimestep=1"
+#pyts="-pythonTimestep=1"
 
 set -x
-pylith3dapp.py -pl3dscan.asciiOutput=none -pl3dscan.ucdOutput=binary $pyts
+pylith3dapp.py -asciiOutput=none -ucdOutput=binary $pyts
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-pylith3dapp.py -pl3dscan.fileRoot=lintet/bm1b/bm1b -log_summary -petsc_solver 1 -pc_type ilu -ksp_monitor -ksp_view -ksp_rtol 1e-9
+pylith3dapp.py -fileRoot=lintet/bm1b/bm1b -petsc.log_summary -petsc.pc_type=ilu -petsc.ksp_monitor -petsc.ksp_view -petsc.ksp_rtol=1e-9
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-debug.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-debug.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-debug.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -7,6 +7,6 @@
 # ======================================================================
 
 set -x
-pylith3dapp.py -pl3dscan.asciiOutput=full -pl3dscan.ucdOutput=ascii $pyts
+pylith3dapp.py -asciiOutput=full -ucdOutput=ascii $pyts
 
 # end of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-lithomop.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-lithomop.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-lithomop.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,51 +0,0 @@
-#!/bin/bash
-# ======================================================================
-#
-# Shell script to run LithoMop using SCEC benchmark 1 (low resolution,
-# 2 materials).
-#
-# ======================================================================
-
-if [ $# != 0 ]; then
-  echo "usage: runbm1c-lithomop.sh"
-  exit 1
-fi
-suff="lm"
-
-simroot="bm1c"
-dupext="fuldat prop statevar time"
-sinext="coord connect bc split"
-
-pyreflags="-typos=relaxed"
-echo "Pyre flags:"
-echo $pyreflags
-
-lithomopflags="-lm3dscan.fileRoot=${simroot}_$suff \
-  -lm3dscan.asciiOutput=none \
-  -lm3dscan.ucdOutput=binary"
-echo "LithoMop flags:"
-echo $lithomopflags
-
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
-
-echo "Setting up symbolic links with prefix ${simroot}_${suff}..."
-for ext in $sinext; do
-  ln -s $simroot.$ext ${simroot}_$suff.$ext
-done
-for ext in $dupext; do
-  ln -s $simroot.$ext ${simroot}_$suff.$ext
-done
-
-echo "Running LithoMop..."
-cmd="lithomop3dapp.py $pyreflags $lithomopflags $petscflags"
-
-echo $cmd
-eval $cmd
-
-# end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -7,9 +7,9 @@
 # ======================================================================
 
 # Do not use pythonTimestep for now until all the bugs are worked out.
-#pyts="-pl3dscan.pythonTimestep=1"
+#pyts="-pythonTimestep=1"
 
 set -x
-pylith3dapp.py -pl3dscan.asciiOutput=echo -pl3dscan.ucdOutput=ascii $pyts
+pylith3dapp.py -asciiOutput=echo -ucdOutput=ascii $pyts
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -7,9 +7,9 @@
 # ======================================================================
 
 # Do not use pythonTimestep for now until all the bugs are worked out.
-#pyts="-pl3dscan.pythonTimestep=1"
+#pyts="-pythonTimestep=1"
 
 set -x
-pylith3dapp.py -pl3dscan.asciiOutput=none -pl3dscan.ucdOutput=binary $pyts
+pylith3dapp.py -asciiOutput=none -ucdOutput=binary $pyts
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-pylith3dapp.py -pl3dscan.fileRoot=lintet/bm1a/bm1a -pl3dscan.bcInputFile=lintet/bm2a/bm2a.bc -pl3dscan.keywordEqualsValueFile=lintet/bm2a/bm2a.keyval -pl3dscan.timeStepInputFile=lintet/bm2a/bm2a.time -pl3dscan.asciiOutputFile=lintet/bm2a/bm2a.ascii -pl3dscan.ucdOutputRoot=lintet/bm2a/bm2a
+pylith3dapp.py -fileRoot=lintet/bm1a/bm1a -bcInputFile=lintet/bm2a/bm2a.bc -keywordEqualsValueFile=lintet/bm2a/bm2a.keyval -timeStepInputFile=lintet/bm2a/bm2a.time -asciiOutputFile=lintet/bm2a/bm2a.ascii -ucdOutputRoot=lintet/bm2a/bm2a
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-debug.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-debug.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-debug.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -6,9 +6,9 @@
 # ======================================================================
 
 # Do not use pythonTimestep for now until all the bugs are worked out.
-#pyts="-pl3dscan.pythonTimestep=1"
+#pyts="-pythonTimestep=1"
 
 set -x
-pylith3dapp.py -pl3dscan.asciiOutput=full -pl3dscan.ucdOutput=ascii $pyts
+pylith3dapp.py -asciiOutput=full -ucdOutput=ascii $pyts
 
 # end of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-lithomop.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-lithomop.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-lithomop.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,50 +0,0 @@
-#!/bin/bash
-# ======================================================================
-#
-# Shell script to run LithoMop using SCEC benchmark 5 (low resolution).
-#
-# ======================================================================
-
-if [ $# != 0 ]; then
-  echo "usage: runbm5-lithomop.sh"
-  exit 1
-fi
-suff="lm"
-
-simroot="bm5"
-dupext="fuldat prop statevar time"
-sinext="coord connect bc split"
-
-pyreflags="-typos=relaxed"
-echo "Pyre flags:"
-echo $pyreflags
-
-lithomopflags="-lm3dscan.fileRoot=${simroot}_$suff \
-  -lm3dscan.asciiOutput=none \
-  -lm3dscan.ucdOutput=binary"
-echo "LithoMop flags:"
-echo $lithomopflags
-
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
-
-echo "Setting up symbolic links with prefix ${simroot}_${suff}..."
-for ext in $sinext; do
-  ln -s $simroot.$ext ${simroot}_$suff.$ext
-done
-for ext in $dupext; do
-  ln -s $simroot.$ext ${simroot}_$suff.$ext
-done
-
-echo "Running LithoMop..."
-cmd="lithomop3dapp.py $pyreflags $lithomopflags $petscflags"
-
-echo $cmd
-eval $cmd
-
-# end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -6,9 +6,9 @@
 # ======================================================================
 
 # Do not use pythonTimestep for now until all the bugs are worked out.
-#pyts="-pl3dscan.pythonTimestep=1"
+#pyts="-pythonTimestep=1"
 
 set -x
-pylith3dapp.py -pl3dscan.asciiOutput=echo -pl3dscan.ucdOutput=ascii $pyts
+pylith3dapp.py -asciiOutput=echo -ucdOutput=ascii $pyts
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -6,9 +6,9 @@
 # ======================================================================
 
 # Do not use pythonTimestep for now until all the bugs are worked out.
-#pyts="-pl3dscan.pythonTimestep=1"
+#pyts="-pythonTimestep=1"
 
 set -x
-pylith3dapp.py -pl3dscan.asciiOutput=none -pl3dscan.ucdOutput=binary $pyts
+pylith3dapp.py -asciiOutput=none -ucdOutput=binary $pyts
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-pylith3dapp.py -pl3dscan.fileRoot=lintet/bm5/bm5 -pl3dscan.ucdOutput=binary -log_summary -pc_type ilu -ksp_monitor -ksp_view -ksp_rtol 1e-9
+pylith3dapp.py -fileRoot=lintet/bm5/bm5 -ucdOutput=binary -petsc.log_summary -petsc.pc_type=ilu -petsc.ksp_monitor -petsc.ksp_view -petsc.ksp_rtol=1e-9
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-bbar-comp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-bbar-comp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-bbar-comp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt1.bc --pl3dscan.asciiOutputFile=pt1-bbar-comp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt1.bc --asciiOutputFile=pt1-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt2.bc --pl3dscan.asciiOutputFile=pt2-bbar-comp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt2.bc --asciiOutputFile=pt2-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt3.bc --pl3dscan.asciiOutputFile=pt3-bbar-comp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt3.bc --asciiOutputFile=pt3-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt4.bc --pl3dscan.asciiOutputFile=pt4-bbar-comp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt4.bc --asciiOutputFile=pt4-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt5.bc --pl3dscan.asciiOutputFile=pt5-bbar-comp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt5.bc --asciiOutputFile=pt5-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt6.bc --pl3dscan.asciiOutputFile=pt6-bbar-comp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt6.bc --asciiOutputFile=pt6-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt7.bc --pl3dscan.asciiOutputFile=pt7-bbar-comp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt7.bc --asciiOutputFile=pt7-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt8.bc --pl3dscan.asciiOutputFile=pt8-bbar-comp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt8.bc --asciiOutputFile=pt8-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt9.bc --pl3dscan.asciiOutputFile=pt9-bbar-comp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt9.bc --asciiOutputFile=pt9-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt10.bc --pl3dscan.asciiOutputFile=pt10-bbar-comp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt10.bc --asciiOutputFile=pt10-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt11.bc --pl3dscan.asciiOutputFile=pt11-bbar-comp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt11.bc --asciiOutputFile=pt11-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt12.bc --pl3dscan.asciiOutputFile=pt12-bbar-comp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt12.bc --asciiOutputFile=pt12-bbar-comp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-bbar-incomp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-bbar-incomp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-bbar-incomp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt1-bbar-incomp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt1.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt1-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt2-bbar-incomp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt2.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt2-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt3-bbar-incomp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt3.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt3-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt4-bbar-incomp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt4.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt4-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt5-bbar-incomp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt5.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt5-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt6-bbar-incomp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt6.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt6-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt7-bbar-incomp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt7.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt7-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt8-bbar-incomp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt8.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt8-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt9-bbar-incomp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt9.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt9-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt10-bbar-incomp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt10.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt10-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt11-bbar-incomp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt11.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt11-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-bbar.cfg --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-bbar-incomp.ascii
+pylith3dapp.py pt-bbar.cfg --bcInputFile=pt12.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt12-bbar-incomp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-full-comp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-full-comp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-full-comp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt1.bc --pl3dscan.asciiOutputFile=pt1-full-comp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt1.bc --asciiOutputFile=pt1-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt2.bc --pl3dscan.asciiOutputFile=pt2-full-comp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt2.bc --asciiOutputFile=pt2-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt3.bc --pl3dscan.asciiOutputFile=pt3-full-comp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt3.bc --asciiOutputFile=pt3-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt4.bc --pl3dscan.asciiOutputFile=pt4-full-comp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt4.bc --asciiOutputFile=pt4-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt5.bc --pl3dscan.asciiOutputFile=pt5-full-comp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt5.bc --asciiOutputFile=pt5-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt6.bc --pl3dscan.asciiOutputFile=pt6-full-comp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt6.bc --asciiOutputFile=pt6-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt7.bc --pl3dscan.asciiOutputFile=pt7-full-comp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt7.bc --asciiOutputFile=pt7-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt8.bc --pl3dscan.asciiOutputFile=pt8-full-comp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt8.bc --asciiOutputFile=pt8-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt9.bc --pl3dscan.asciiOutputFile=pt9-full-comp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt9.bc --asciiOutputFile=pt9-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt10.bc --pl3dscan.asciiOutputFile=pt10-full-comp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt10.bc --asciiOutputFile=pt10-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt11.bc --pl3dscan.asciiOutputFile=pt11-full-comp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt11.bc --asciiOutputFile=pt11-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt12.bc --pl3dscan.asciiOutputFile=pt12-full-comp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt12.bc --asciiOutputFile=pt12-full-comp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-full-incomp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-full-incomp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-full-incomp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt1-full-incomp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt1.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt1-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt2-full-incomp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt2.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt2-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt3-full-incomp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt3.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt3-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt4-full-incomp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt4.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt4-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt5-full-incomp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt5.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt5-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt6-full-incomp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt6.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt6-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt7-full-incomp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt7.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt7-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt8-full-incomp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt8.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt8-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt9-full-incomp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt9.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt9-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt10-full-incomp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt10.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt10-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt11-full-incomp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt11.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt11-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-full.cfg --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-full-incomp.ascii
+pylith3dapp.py pt-full.cfg --bcInputFile=pt12.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt12-full-incomp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-red-comp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-red-comp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-red-comp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt1.bc --pl3dscan.asciiOutputFile=pt1-red-comp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt1.bc --asciiOutputFile=pt1-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt2.bc --pl3dscan.asciiOutputFile=pt2-red-comp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt2.bc --asciiOutputFile=pt2-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt3.bc --pl3dscan.asciiOutputFile=pt3-red-comp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt3.bc --asciiOutputFile=pt3-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt4.bc --pl3dscan.asciiOutputFile=pt4-red-comp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt4.bc --asciiOutputFile=pt4-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt5.bc --pl3dscan.asciiOutputFile=pt5-red-comp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt5.bc --asciiOutputFile=pt5-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt6.bc --pl3dscan.asciiOutputFile=pt6-red-comp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt6.bc --asciiOutputFile=pt6-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt7.bc --pl3dscan.asciiOutputFile=pt7-red-comp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt7.bc --asciiOutputFile=pt7-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt8.bc --pl3dscan.asciiOutputFile=pt8-red-comp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt8.bc --asciiOutputFile=pt8-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt9.bc --pl3dscan.asciiOutputFile=pt9-red-comp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt9.bc --asciiOutputFile=pt9-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt10.bc --pl3dscan.asciiOutputFile=pt10-red-comp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt10.bc --asciiOutputFile=pt10-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt11.bc --pl3dscan.asciiOutputFile=pt11-red-comp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt11.bc --asciiOutputFile=pt11-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt12.bc --pl3dscan.asciiOutputFile=pt12-red-comp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt12.bc --asciiOutputFile=pt12-red-comp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-red-incomp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-red-incomp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-red-incomp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt1-red-incomp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt1.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt1-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt2-red-incomp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt2.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt2-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt3-red-incomp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt3.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt3-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt4-red-incomp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt4.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt4-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt5-red-incomp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt5.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt5-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt6-red-incomp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt6.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt6-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt7-red-incomp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt7.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt7-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt8-red-incomp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt8.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt8-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt9-red-incomp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt9.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt9-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt10-red-incomp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt10.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt10-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt11-red-incomp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt11.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt11-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py pt-red.cfg --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-red-incomp.ascii
+pylith3dapp.py pt-red.cfg --bcInputFile=pt12.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt12-red-incomp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-pylith3dapp.py -pl3dscan.fileRoot=quadhex/bm1a/bm1a
+pylith3dapp.py -fileRoot=quadhex/bm1a/bm1a
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-bbar-comp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-bbar-comp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-bbar-comp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt1.bc --pl3dscan.asciiOutputFile=pt1-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt1.bc --asciiOutputFile=pt1-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt2.bc --pl3dscan.asciiOutputFile=pt2-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt2.bc --asciiOutputFile=pt2-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt3.bc --pl3dscan.asciiOutputFile=pt3-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt3.bc --asciiOutputFile=pt3-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt4.bc --pl3dscan.asciiOutputFile=pt4-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt4.bc --asciiOutputFile=pt4-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt5.bc --pl3dscan.asciiOutputFile=pt5-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt5.bc --asciiOutputFile=pt5-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt6.bc --pl3dscan.asciiOutputFile=pt6-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt6.bc --asciiOutputFile=pt6-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt7.bc --pl3dscan.asciiOutputFile=pt7-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt7.bc --asciiOutputFile=pt7-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt8.bc --pl3dscan.asciiOutputFile=pt8-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt8.bc --asciiOutputFile=pt8-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt9.bc --pl3dscan.asciiOutputFile=pt9-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt9.bc --asciiOutputFile=pt9-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt10.bc --pl3dscan.asciiOutputFile=pt10-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt10.bc --asciiOutputFile=pt10-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt11.bc --pl3dscan.asciiOutputFile=pt11-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt11.bc --asciiOutputFile=pt11-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt12.bc --pl3dscan.asciiOutputFile=pt12-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt12.bc --asciiOutputFile=pt12-bbar-comp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-bbar-incomp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-bbar-incomp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-bbar-incomp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt1-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt1.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt1-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt2-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt2.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt2-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt3-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt3.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt3-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt4-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt4.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt4-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt5-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt5.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt5-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt6-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt6.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt6-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt7-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt7.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt7-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt8-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt8.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt8-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt9-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt9.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt9-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt10-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt10.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt10-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt11-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt11.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt11-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt12.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt12-bbar-incomp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-full-comp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-full-comp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-full-comp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.bcInputFile=pt1.bc --pl3dscan.asciiOutputFile=pt1-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt1.bc --asciiOutputFile=pt1-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt2.bc --pl3dscan.asciiOutputFile=pt2-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt2.bc --asciiOutputFile=pt2-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt3.bc --pl3dscan.asciiOutputFile=pt3-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt3.bc --asciiOutputFile=pt3-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt4.bc --pl3dscan.asciiOutputFile=pt4-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt4.bc --asciiOutputFile=pt4-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt5.bc --pl3dscan.asciiOutputFile=pt5-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt5.bc --asciiOutputFile=pt5-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt6.bc --pl3dscan.asciiOutputFile=pt6-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt6.bc --asciiOutputFile=pt6-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt7.bc --pl3dscan.asciiOutputFile=pt7-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt7.bc --asciiOutputFile=pt7-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt8.bc --pl3dscan.asciiOutputFile=pt8-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt8.bc --asciiOutputFile=pt8-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt9.bc --pl3dscan.asciiOutputFile=pt9-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt9.bc --asciiOutputFile=pt9-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt10.bc --pl3dscan.asciiOutputFile=pt10-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt10.bc --asciiOutputFile=pt10-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt11.bc --pl3dscan.asciiOutputFile=pt11-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt11.bc --asciiOutputFile=pt11-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt12.bc --pl3dscan.asciiOutputFile=pt12-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt12.bc --asciiOutputFile=pt12-full-comp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-full-incomp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-full-incomp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-full-incomp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt1-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt1.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt1-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt2-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt2.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt2-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt3-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt3.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt3-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt4-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt4.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt4-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt5-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt5.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt5-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt6-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt6.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt6-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt7-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt7.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt7-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt8-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt8.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt8-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt9-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt9.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt9-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt10-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt10.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt10-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt11-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt11.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt11-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt12.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt12-full-incomp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-red-comp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-red-comp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-red-comp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt1.bc --pl3dscan.asciiOutputFile=pt1-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt1.bc --asciiOutputFile=pt1-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt2.bc --pl3dscan.asciiOutputFile=pt2-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt2.bc --asciiOutputFile=pt2-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt3.bc --pl3dscan.asciiOutputFile=pt3-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt3.bc --asciiOutputFile=pt3-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt4.bc --pl3dscan.asciiOutputFile=pt4-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt4.bc --asciiOutputFile=pt4-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt5.bc --pl3dscan.asciiOutputFile=pt5-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt5.bc --asciiOutputFile=pt5-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt6.bc --pl3dscan.asciiOutputFile=pt6-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt6.bc --asciiOutputFile=pt6-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt7.bc --pl3dscan.asciiOutputFile=pt7-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt7.bc --asciiOutputFile=pt7-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt8.bc --pl3dscan.asciiOutputFile=pt8-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt8.bc --asciiOutputFile=pt8-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt9.bc --pl3dscan.asciiOutputFile=pt9-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt9.bc --asciiOutputFile=pt9-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt10.bc --pl3dscan.asciiOutputFile=pt10-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt10.bc --asciiOutputFile=pt10-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt11.bc --pl3dscan.asciiOutputFile=pt11-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt11.bc --asciiOutputFile=pt11-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt12.bc --pl3dscan.asciiOutputFile=pt12-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt12.bc --asciiOutputFile=pt12-red-comp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-red-incomp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-red-incomp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-red-incomp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt1-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt1.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt1-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt2-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt2.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt2-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt3-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt3.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt3-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt4-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt4.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt4-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt5-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt5.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt5-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt6-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt6.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt6-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt7-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt7.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt7-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt8-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt8.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt8-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt9-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt9.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt9-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt10-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt10.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt10-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt11-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt11.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt11-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt12.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt12-red-incomp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/test.sh	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/test.sh	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-pylith3dapp.py -pl3dscan.fileRoot=quadtet/bm1a/bm1a
+pylith3dapp.py -fileRoot=quadtet/bm1a/bm1a
 
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-bbar-comp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-bbar-comp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-bbar-comp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt1.bc --pl3dscan.asciiOutputFile=pt1-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt1.bc --asciiOutputFile=pt1-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt2.bc --pl3dscan.asciiOutputFile=pt2-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt2.bc --asciiOutputFile=pt2-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt3.bc --pl3dscan.asciiOutputFile=pt3-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt3.bc --asciiOutputFile=pt3-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt4.bc --pl3dscan.asciiOutputFile=pt4-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt4.bc --asciiOutputFile=pt4-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt5.bc --pl3dscan.asciiOutputFile=pt5-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt5.bc --asciiOutputFile=pt5-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt6.bc --pl3dscan.asciiOutputFile=pt6-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt6.bc --asciiOutputFile=pt6-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt7.bc --pl3dscan.asciiOutputFile=pt7-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt7.bc --asciiOutputFile=pt7-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt8.bc --pl3dscan.asciiOutputFile=pt8-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt8.bc --asciiOutputFile=pt8-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt9.bc --pl3dscan.asciiOutputFile=pt9-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt9.bc --asciiOutputFile=pt9-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt10.bc --pl3dscan.asciiOutputFile=pt10-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt10.bc --asciiOutputFile=pt10-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt11.bc --pl3dscan.asciiOutputFile=pt11-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt11.bc --asciiOutputFile=pt11-bbar-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt12.bc --pl3dscan.asciiOutputFile=pt12-bbar-comp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt12.bc --asciiOutputFile=pt12-bbar-comp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-bbar-incomp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-bbar-incomp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-bbar-incomp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt1-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt1.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt1-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt2-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt2.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt2-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt3-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt3.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt3-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt4-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt4.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt4-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt5-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt5.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt5-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt6-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt6.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt6-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt7-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt7.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt7-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt8-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt8.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt8-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt9-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt9.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt9-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt10-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt10.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt10-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt11-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt11.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt11-bbar-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-bbar-incomp.ascii
+pylith3dapp.py --quadratureOrder=Selective --bcInputFile=pt12.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt12-bbar-incomp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-full-comp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-full-comp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-full-comp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.bcInputFile=pt1.bc --pl3dscan.asciiOutputFile=pt1-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt1.bc --asciiOutputFile=pt1-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt2.bc --pl3dscan.asciiOutputFile=pt2-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt2.bc --asciiOutputFile=pt2-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt3.bc --pl3dscan.asciiOutputFile=pt3-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt3.bc --asciiOutputFile=pt3-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt4.bc --pl3dscan.asciiOutputFile=pt4-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt4.bc --asciiOutputFile=pt4-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt5.bc --pl3dscan.asciiOutputFile=pt5-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt5.bc --asciiOutputFile=pt5-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt6.bc --pl3dscan.asciiOutputFile=pt6-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt6.bc --asciiOutputFile=pt6-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt7.bc --pl3dscan.asciiOutputFile=pt7-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt7.bc --asciiOutputFile=pt7-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt8.bc --pl3dscan.asciiOutputFile=pt8-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt8.bc --asciiOutputFile=pt8-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt9.bc --pl3dscan.asciiOutputFile=pt9-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt9.bc --asciiOutputFile=pt9-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt10.bc --pl3dscan.asciiOutputFile=pt10-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt10.bc --asciiOutputFile=pt10-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt11.bc --pl3dscan.asciiOutputFile=pt11-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt11.bc --asciiOutputFile=pt11-full-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt12.bc --pl3dscan.asciiOutputFile=pt12-full-comp.ascii
+pylith3dapp.py --bcInputFile=pt12.bc --asciiOutputFile=pt12-full-comp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-full-incomp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-full-incomp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-full-incomp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt1-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt1.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt1-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt2-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt2.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt2-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt3-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt3.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt3-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt4-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt4.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt4-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt5-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt5.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt5-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt6-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt6.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt6-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt7-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt7.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt7-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt8-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt8.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt8-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt9-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt9.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt9-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt10-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt10.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt10-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt11-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt11.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt11-full-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-full-incomp.ascii
+pylith3dapp.py --bcInputFile=pt12.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt12-full-incomp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-red-comp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-red-comp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-red-comp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt1.bc --pl3dscan.asciiOutputFile=pt1-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt1.bc --asciiOutputFile=pt1-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt2.bc --pl3dscan.asciiOutputFile=pt2-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt2.bc --asciiOutputFile=pt2-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt3.bc --pl3dscan.asciiOutputFile=pt3-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt3.bc --asciiOutputFile=pt3-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt4.bc --pl3dscan.asciiOutputFile=pt4-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt4.bc --asciiOutputFile=pt4-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt5.bc --pl3dscan.asciiOutputFile=pt5-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt5.bc --asciiOutputFile=pt5-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt6.bc --pl3dscan.asciiOutputFile=pt6-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt6.bc --asciiOutputFile=pt6-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt7.bc --pl3dscan.asciiOutputFile=pt7-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt7.bc --asciiOutputFile=pt7-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt8.bc --pl3dscan.asciiOutputFile=pt8-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt8.bc --asciiOutputFile=pt8-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt9.bc --pl3dscan.asciiOutputFile=pt9-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt9.bc --asciiOutputFile=pt9-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt10.bc --pl3dscan.asciiOutputFile=pt10-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt10.bc --asciiOutputFile=pt10-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt11.bc --pl3dscan.asciiOutputFile=pt11-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt11.bc --asciiOutputFile=pt11-red-comp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt12.bc --pl3dscan.asciiOutputFile=pt12-red-comp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt12.bc --asciiOutputFile=pt12-red-comp.ascii
 /bin/rm pt1.plot

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-red-incomp.com
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-red-incomp.com	2007-05-03 00:02:06 UTC (rev 6759)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-red-incomp.com	2007-05-03 00:05:55 UTC (rev 6760)
@@ -1,24 +1,24 @@
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt1-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt1.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt1-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt2-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt2.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt2-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt3-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt3.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt3-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt4-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt4.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt4-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt5-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt5.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt5-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt6-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt6.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt6-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt7-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt7.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt7-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt8-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt8.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt8-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt9-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt9.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt9-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt10-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt10.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt10-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt11-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt11.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt11-red-incomp.ascii
 /bin/rm pt1.plot
-pylith3dapp.py --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-red-incomp.ascii
+pylith3dapp.py --quadratureOrder=Reduced --bcInputFile=pt12.bc --materialPropertiesInputFile=pt-incomp.prop --asciiOutputFile=pt12-red-incomp.ascii
 /bin/rm pt1.plot



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