[cig-commits] r6127 - in short/3D/PyLith/branches/pylith-0.8/pylith3d/examples: bm1 bm2 linhex/bm1a lintet/bctest lintet/bm1a lintet/bm1b lintet/bm1c lintet/bm2a lintet/bm5 lintet/patchtest lintet/powertest lintet/splittest lintet/tractest quadhex/bm1a quadhex/patchtest quadtet/bm1a quadtet/patchtest

[leif at geodynamics.org]

Author: leif
Date: 2007-02-27 17:54:26 -0800 (Tue, 27 Feb 2007)
New Revision: 6127

Added:
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm1/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bctest/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-bbar.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-red.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt1.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/powertest/ESF.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/pylith3d.cfg
Removed:
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm1/bm1.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2/bm2.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bctest/runtest.py
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/bm1a.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/bm1b.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/bm1c.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/bm2a.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/bm5.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-bbar.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-red.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt1.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/powertest/pylith3dESF.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/splittest.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/tractest/tractest.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/bm1a.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/pt1.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/bm1a.keyval
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/pt1.keyval
Modified:
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/bm1a/runex.py
   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/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/lintet/powertest/pylith3d.cfg
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/runsplittest-debug.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/runsplittest-test.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/runsplittest.sh
   short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/tractest/pylith3d.cfg
   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/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:
Updated about half of the PyLith examples to use *.cfg files instead
of *.keyval files.  The other half is linhex/*, which I will update
later.


Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm1/bm1.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm1/bm1.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm1/bm1.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,110 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for SCEC BM 2.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#self.winklerScaleX = 1.0
-#self.winklerScaleY = 1.0
-#self.winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#self.stressTolerance = 1.0e-12*Pa
-#self.minimumStrainPerturbation = 1.0e-7
-#self.initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  At present, the only solution method is preconditioned
-# conjugate gradients.  The user can select the preconditioner type,
-# the maximum number of iterations, and the factors controlling
-# convergence.  Preconditioner types are as follows:
-#    diagonalNoUpdate:      Diagonal preconditioning with an initial
-#                           guess of zero for the displacement vector.
-#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess of zero for the displacement
-#                           vector.
-#    diagonalUpdate:        Diagonal preconditioning with an initial
-#                           guess for the displacement vector corresponding
-#                           to the displacement vector from the previous
-#                           time step.
-#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess for the displacement vector
-#                           corresponding to the displacement vector from
-#                           the previous time step.
-#
-#    Note that the diagonal preconditioners generally require more iterations,
-#    but at less computational cost per iteration.  In theory, the more
-#    complex preconditioner should work better for more irregular meshes.
-#
-#self.preconditionerType = "diagonalNoUpdate"
-#self.maxPcgIterations = 3000
-#self.displacementAccuracyMult = 1.0
-#self.forceAccuracyMult = 1.0
-#self.energyAccuracyMult = 1.0
-#self.minDisplacementAccuracy = 1.0e-8
-#self.minForceAccuracy = 1.0e-8
-#self.minEnergyAccuracy = 1.0e-14
-#
-#
-# Quadrature order for the problem.  At present, only values of 1 or 2 are
-# available.
-#
-self.quadratureOrder = 1
-#
-#
-# Gravitational acceleration in each direction.
-#
-#self.gravityX = 0.0*m/(s*s)
-#self.gravityY = 0.0*m/(s*s)
-#self.gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, using an alternate
-# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
-# negative value, the original Poisson's ratio is used.  Each prestress
-# component may also be scaled.  This option is only useful if the
-# prestresses are read from a file (and not automatically computed).
-#
-#self.prestressAutoCompute = False
-#self.prestressQuadrature = 1
-#self.prestressAutoComputePoisson = -0.49
-#self.prestressScaleXx = 1.0
-#self.prestressScaleYy = 1.0
-#self.prestressScaleZz = 1.0
-#self.prestressScaleXy = 1.0
-#self.prestressScaleXz = 1.0
-#self.prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#self.winklerSlipScaleX = 1.0
-#self.winklerSlipScaleY = 1.0
-#self.winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#self.f77StandardInput = 5
-#self.f77StandardOutput = 6
-#self.f77FileInput = 10
-#self.f77AsciiOutput = 11
-#self.f77PlotOutput = 12

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm1/pylith3d.cfg (from rev 6053, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm1/bm1.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm1/bm1.keyval	2007-02-20 22:55:34 UTC (rev 6053)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm1/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,114 @@
+[pylith3d.scanner]
+fileRoot = bm1
+
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for SCEC BM 2.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  At present, the only solution method is preconditioned
+# conjugate gradients.  The user can select the preconditioner type,
+# the maximum number of iterations, and the factors controlling
+# convergence.  Preconditioner types are as follows:
+#    diagonalNoUpdate:      Diagonal preconditioning with an initial
+#                           guess of zero for the displacement vector.
+#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess of zero for the displacement
+#                           vector.
+#    diagonalUpdate:        Diagonal preconditioning with an initial
+#                           guess for the displacement vector corresponding
+#                           to the displacement vector from the previous
+#                           time step.
+#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess for the displacement vector
+#                           corresponding to the displacement vector from
+#                           the previous time step.
+#
+#    Note that the diagonal preconditioners generally require more iterations,
+#    but at less computational cost per iteration.  In theory, the more
+#    complex preconditioner should work better for more irregular meshes.
+#
+#preconditionerType = "diagonalNoUpdate"
+#maxPcgIterations = 3000
+#displacementAccuracyMult = 1.0
+#forceAccuracyMult = 1.0
+#energyAccuracyMult = 1.0
+#minDisplacementAccuracy = 1.0e-8
+#minForceAccuracy = 1.0e-8
+#minEnergyAccuracy = 1.0e-14
+#
+#
+# Quadrature order for the problem.  At present, only values of 1 or 2 are
+# available.
+#
+quadratureOrder = 1
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, using an alternate
+# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
+# negative value, the original Poisson's ratio is used.  Each prestress
+# component may also be scaled.  This option is only useful if the
+# prestresses are read from a file (and not automatically computed).
+#
+#prestressAutoCompute = False
+#prestressQuadrature = 1
+#prestressAutoComputePoisson = -0.49
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2/bm2.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2/bm2.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2/bm2.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,110 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for SCEC BM 2.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#self.winklerScaleX = 1.0
-#self.winklerScaleY = 1.0
-#self.winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#self.stressTolerance = 1.0e-12*Pa
-#self.minimumStrainPerturbation = 1.0e-7
-#self.initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  At present, the only solution method is preconditioned
-# conjugate gradients.  The user can select the preconditioner type,
-# the maximum number of iterations, and the factors controlling
-# convergence.  Preconditioner types are as follows:
-#    diagonalNoUpdate:      Diagonal preconditioning with an initial
-#                           guess of zero for the displacement vector.
-#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess of zero for the displacement
-#                           vector.
-#    diagonalUpdate:        Diagonal preconditioning with an initial
-#                           guess for the displacement vector corresponding
-#                           to the displacement vector from the previous
-#                           time step.
-#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess for the displacement vector
-#                           corresponding to the displacement vector from
-#                           the previous time step.
-#
-#    Note that the diagonal preconditioners generally require more iterations,
-#    but at less computational cost per iteration.  In theory, the more
-#    complex preconditioner should work better for more irregular meshes.
-#
-#self.preconditionerType = "diagonalNoUpdate"
-#self.maxPcgIterations = 3000
-self.displacementAccuracyMult = 0.001
-self.forceAccuracyMult = 0.001
-self.energyAccuracyMult = 0.00001
-#self.minDisplacementAccuracy = 1.0e-8
-#self.minForceAccuracy = 1.0e-8
-#self.minEnergyAccuracy = 1.0e-14
-#
-#
-# Quadrature order for the problem.  At present, only values of 1 or 2 are
-# available.
-#
-self.quadratureOrder = 1
-#
-#
-# Gravitational acceleration in each direction.
-#
-#self.gravityX = 0.0*m/(s*s)
-#self.gravityY = 0.0*m/(s*s)
-self.gravityZ = -10.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, using an alternate
-# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
-# negative value, the original Poisson's ratio is used.  Each prestress
-# component may also be scaled.  This option is only useful if the
-# prestresses are read from a file (and not automatically computed).
-#
-#self.prestressAutoCompute = False
-#self.prestressQuadrature = 1
-#self.prestressAutoComputePoisson = -0.49
-#self.prestressScaleXx = 1.0
-#self.prestressScaleYy = 1.0
-#self.prestressScaleZz = 1.0
-#self.prestressScaleXy = 1.0
-#self.prestressScaleXz = 1.0
-#self.prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#self.winklerSlipScaleX = 1.0
-#self.winklerSlipScaleY = 1.0
-#self.winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#self.f77StandardInput = 5
-#self.f77StandardOutput = 6
-#self.f77FileInput = 10
-#self.f77AsciiOutput = 11
-#self.f77PlotOutput = 12

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2/pylith3d.cfg (from rev 6122, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2/bm2.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2/bm2.keyval	2007-02-27 19:52:56 UTC (rev 6122)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/bm2/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,124 @@
+[pylith3d]
+# PETSc options
+log_summary = true
+pc_type = bjacobi
+sub_pc_type = ilu
+ksp_monitor = true
+ksp_view = true
+ksp_rtol = 1.0e-9
+# start_in_debugger = true
+# debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = bm2
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for SCEC BM 2.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  At present, the only solution method is preconditioned
+# conjugate gradients.  The user can select the preconditioner type,
+# the maximum number of iterations, and the factors controlling
+# convergence.  Preconditioner types are as follows:
+#    diagonalNoUpdate:      Diagonal preconditioning with an initial
+#                           guess of zero for the displacement vector.
+#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess of zero for the displacement
+#                           vector.
+#    diagonalUpdate:        Diagonal preconditioning with an initial
+#                           guess for the displacement vector corresponding
+#                           to the displacement vector from the previous
+#                           time step.
+#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess for the displacement vector
+#                           corresponding to the displacement vector from
+#                           the previous time step.
+#
+#    Note that the diagonal preconditioners generally require more iterations,
+#    but at less computational cost per iteration.  In theory, the more
+#    complex preconditioner should work better for more irregular meshes.
+#
+#preconditionerType = "diagonalNoUpdate"
+#maxPcgIterations = 3000
+displacementAccuracyMult = 0.001
+forceAccuracyMult = 0.001
+energyAccuracyMult = 0.00001
+#minDisplacementAccuracy = 1.0e-8
+#minForceAccuracy = 1.0e-8
+#minEnergyAccuracy = 1.0e-14
+#
+#
+# Quadrature order for the problem.  At present, only values of 1 or 2 are
+# available.
+#
+quadratureOrder = 1
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+gravityZ = -10.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, using an alternate
+# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
+# negative value, the original Poisson's ratio is used.  Each prestress
+# component may also be scaled.  This option is only useful if the
+# prestresses are read from a file (and not automatically computed).
+#
+#prestressAutoCompute = False
+#prestressQuadrature = 1
+#prestressAutoComputePoisson = -0.49
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/bm1a/runex.py
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/bm1a/runex.py	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/linhex/bm1a/runex.py	2007-02-28 01:54:26 UTC (rev 6127)
@@ -58,7 +58,7 @@
         "-ksp_monitor -ksp_view -ksp_rtol 1e-09" % (nprocs, root, nprocs)
   import os
   print cmd
-  os.system(cmd)
+  #os.system(cmd)
   return
 
 

Added: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bctest/pylith3d.cfg
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bctest/pylith3d.cfg	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bctest/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,15 @@
+[pylith3d]
+# PETSc options
+log_summary = true
+pc_type = bjacobi
+sub_pc_type = ilu
+ksp_monitor = true
+ksp_view = true
+ksp_rtol = 1.0e-9
+# start_in_debugger = true
+# debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = bctest
+asciiOutput = full
+ucdOutput = ascii

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bctest/runtest.py
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bctest/runtest.py	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bctest/runtest.py	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,85 +0,0 @@
-#!/usr/bin/env python
-#
-# ======================================================================
-#
-#                           Brad T. Aagaard
-#                        U.S. Geological Survey
-#
-# {LicenseText}
-#
-# ======================================================================
-#
-
-root="bctest"
-
-# ----------------------------------------------------------------------
-def setupInput(nprocs):
-  dupext = [".fuldat", ".prop", ".statevar", ".time"]
-  sinext = [".coord", ".connect", ".bc", ".split"]
-
-  print "Setting up symbolic links with prefix '%s_%d':" % (root, nprocs)
-  import os
-
-  dirFiles = os.listdir(os.getcwd())
-  for ext in sinext:
-    src = "%s%s" % (root, ext)
-    dest = "%s_%s%s" % (root, nprocs, ext)
-    if not dest in dirFiles:
-      print "  %s -> %s... created" % (dest, src)
-      os.symlink(src, dest)
-    else:
-      print "  %s -> %s... already exists" % (dest, src)
-
-  for ext in dupext:
-    src = "%s%s" % (root, ext)
-    for iproc in range(nprocs):
-      dest = "%s_%s.%d%s" % (root, nprocs, iproc, ext)
-      if not dest in dirFiles:
-        print "  %s -> %s... created" % (dest, src)
-        os.symlink(src, dest)
-      else:
-        print "  %s -> %s... already exists" % (dest, src)
-  return
-
-
-# ----------------------------------------------------------------------
-def run(nprocs):
-  print "Running PyLith..."
-
-  # TODO: Replace the use of launching via 'system' with use
-  # of Leif's architecture independent utility.
-
-  cmd = "mpirun -np %d `which pylith3dapp.py` " \
-        "--typos=relaxed " \
-        "--scanner.fileRoot=%s_%d " \
-        "--scanner.asciiOutput=full " \
-        "--scanner.ucdOutput=ascii " \
-        "-log_summary -pc_type bjacobi -sub_pc_type ilu " \
-        "-ksp_monitor -ksp_view -ksp_rtol 1e-09" % (nprocs, root, nprocs)
-  import os
-  print cmd
-  os.system(cmd)
-  return
-
-
-# ----------------------------------------------------------------------
-if __name__ == "__main__":
-  from optparse import OptionParser
-
-  parser = OptionParser()
-  parser.add_option("-n", "--numprocs", dest="nprocs",
-                    type="int", metavar="NPROCS",
-                    help="Set number of processors.")
-  (options, args) = parser.parse_args()
-  if len(args) != 0:
-    parser.error("Incorrent number of arguments.")
-
-  nprocs = 1
-  if not options.nprocs is None:
-    nprocs = options.nprocs
-
-  setupInput(nprocs)
-  run(nprocs)
-
-
-# End of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/bm1a.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/bm1a.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/bm1a.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,97 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for SCEC BM 2.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  This is now all controlled by PETSc command-line
-# arguments.  The only option now specified in this file is whether to
-# use the solution from the previous time step as the starting guess
-# for the current time step.
-#
-#usePreviousDisplacementFlag = 0
-#
-#
-# Quadrature order for the problem.  The options are:
-#       Full:           Quadrature order that should give the exact
-#                       element matrices when the elements are
-#                       geometrically undistorted.
-#       Reduced:        Quadrature order that is one order less than
-#                       full quadrature.  This option should be used
-#                       with caution.
-#       Selective:      Uses Hughes' b-bar formulation to perform
-#                       reduced quadrature on the dilatational parts of
-#                       the strain-displacement matrix.  This can be
-#                       useful in nearly-incompressible problems.
-#
-#quadratureOrder = "Full"
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, with the option of
-# using alternative values for Poisson's ratio and Young's modulus.
-# Each prestress component may also be scaled.  This option is only
-# useful if the prestresses are read from a file (and not automatically
-# computed).
-#
-#prestressAutoCompute = False
-#prestressAutoChangeElasticProperties = False
-#prestressAutoComputePoisson = 0.49
-#prestressAutoComputeYoungs = 1.0e30*Pa
-#
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/pylith3d.cfg (from rev 6053, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/bm1a.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/bm1a.keyval	2007-02-20 22:55:34 UTC (rev 6053)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,111 @@
+[pylith3d]
+# PETSc options
+log_summary = true
+pc_type = bjacobi
+sub_pc_type = ilu
+ksp_monitor = true
+ksp_view = true
+ksp_rtol = 1.0e-9
+# start_in_debugger = true
+# debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = bm1a
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for SCEC BM 2.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  This is now all controlled by PETSc command-line
+# arguments.  The only option now specified in this file is whether to
+# use the solution from the previous time step as the starting guess
+# for the current time step.
+#
+#usePreviousDisplacementFlag = 0
+#
+#
+# Quadrature order for the problem.  The options are:
+#       Full:           Quadrature order that should give the exact
+#                       element matrices when the elements are
+#                       geometrically undistorted.
+#       Reduced:        Quadrature order that is one order less than
+#                       full quadrature.  This option should be used
+#                       with caution.
+#       Selective:      Uses Hughes' b-bar formulation to perform
+#                       reduced quadrature on the dilatational parts of
+#                       the strain-displacement matrix.  This can be
+#                       useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, with the option of
+# using alternative values for Poisson's ratio and Young's modulus.
+# Each prestress component may also be scaled.  This option is only
+# useful if the prestresses are read from a file (and not automatically
+# computed).
+#
+#prestressAutoCompute = False
+#prestressAutoChangeElasticProps = False
+#prestressAutoComputePoisson = 0.49
+#prestressAutoComputeYoungs = 1.0e30*Pa
+#
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-debug.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -5,53 +5,10 @@
 #
 # ======================================================================
 
-if [ $# != 1 ]; then
-  echo "usage: runbm1a-debug.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="bm1a"
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-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
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=full -pl3dscan.ucdOutput=ascii $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a-test.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -5,51 +5,10 @@
 #
 # ======================================================================
 
-if [ $# != 1 ]; then
-  echo "usage: runbm1a-test.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="bm1a"
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=echo -pl3dscan.ucdOutput=ascii $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
 # 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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/runbm1a.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -5,51 +5,10 @@
 #
 # ======================================================================
 
-if [ $# != 1 ]; then
-  echo "usage: runbm1a.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="bm1a"
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=none -pl3dscan.ucdOutput=binary $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
 # 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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1a/test.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-pylith3dapp.py -typos=relaxed -pl3dscan.fileRoot=lintet/bm1a/bm1a -log_summary -petsc_solver 1 -pc_type ilu -ksp_monitor -ksp_view -ksp_rtol 1e-9
+pylith3dapp.py -pl3dscan.fileRoot=lintet/bm1a/bm1a -log_summary -petsc_solver 1 -pc_type ilu -ksp_monitor -ksp_view -ksp_rtol 1e-9
 
 # end of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/bm1b.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/bm1b.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/bm1b.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,97 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for SCEC BM 2.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  This is now all controlled by PETSc command-line
-# arguments.  The only option now specified in this file is whether to
-# use the solution from the previous time step as the starting guess
-# for the current time step.
-#
-# usePreviousDisplacementFlag = 0
-#
-#
-# Quadrature order for the problem.  The options are:
-#       Full:           Quadrature order that should give the exact
-#                       element matrices when the elements are
-#                       geometrically undistorted.
-#       Reduced:        Quadrature order that is one order less than
-#                       full quadrature.  This option should be used
-#                       with caution.
-#       Selective:      Uses Hughes' b-bar formulation to perform
-#                       reduced quadrature on the dilatational parts of
-#                       the strain-displacement matrix.  This can be
-#                       useful in nearly-incompressible problems.
-#
-#quadratureOrder = "Full"
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, with the option of
-# using alternative values for Poisson's ratio and Young's modulus.
-# Each prestress component may also be scaled.  This option is only
-# useful if the prestresses are read from a file (and not automatically
-# computed).
-#
-#prestressAutoCompute = False
-#prestressAutoChangeElasticProperties = False
-#prestressAutoComputePoisson = 0.49
-#prestressAutoComputeYoungs = 1.0e30*Pa
-#
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/pylith3d.cfg (from rev 6053, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/bm1b.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/bm1b.keyval	2007-02-20 22:55:34 UTC (rev 6053)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,111 @@
+[pylith3d]
+# PETSc options
+log_summary = true
+pc_type = bjacobi
+sub_pc_type = ilu
+ksp_monitor = true
+ksp_view = true
+ksp_rtol = 1.0e-9
+# start_in_debugger = true
+# debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = bm1b
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for SCEC BM 2.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  This is now all controlled by PETSc command-line
+# arguments.  The only option now specified in this file is whether to
+# use the solution from the previous time step as the starting guess
+# for the current time step.
+#
+# usePreviousDisplacementFlag = 0
+#
+#
+# Quadrature order for the problem.  The options are:
+#       Full:           Quadrature order that should give the exact
+#                       element matrices when the elements are
+#                       geometrically undistorted.
+#       Reduced:        Quadrature order that is one order less than
+#                       full quadrature.  This option should be used
+#                       with caution.
+#       Selective:      Uses Hughes' b-bar formulation to perform
+#                       reduced quadrature on the dilatational parts of
+#                       the strain-displacement matrix.  This can be
+#                       useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, with the option of
+# using alternative values for Poisson's ratio and Young's modulus.
+# Each prestress component may also be scaled.  This option is only
+# useful if the prestresses are read from a file (and not automatically
+# computed).
+#
+#prestressAutoCompute = False
+#prestressAutoChangeElasticProps = False
+#prestressAutoComputePoisson = 0.49
+#prestressAutoComputeYoungs = 1.0e30*Pa
+#
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-debug.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -5,53 +5,10 @@
 #
 # ======================================================================
 
-if [ $# != 1 ]; then
-  echo "usage: runbm1b-debug.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="bm1b"
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-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
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=full -pl3dscan.ucdOutput=ascii $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b-test.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -5,51 +5,10 @@
 #
 # ======================================================================
 
-if [ $# != 1 ]; then
-  echo "usage: runbm1b-test.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="bm1b"
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=echo -pl3dscan.ucdOutput=ascii $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
 # 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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/runbm1b.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -5,51 +5,10 @@
 #
 # ======================================================================
 
-if [ $# != 1 ]; then
-  echo "usage: runbm1b.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="bm1b"
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=none -pl3dscan.ucdOutput=binary $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
 # 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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1b/test.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-pylith3dapp.py -typos=relaxed -pl3dscan.fileRoot=lintet/bm1b/bm1b -log_summary -petsc_solver 1 -pc_type ilu -ksp_monitor -ksp_view -ksp_rtol 1e-9
+pylith3dapp.py -pl3dscan.fileRoot=lintet/bm1b/bm1b -log_summary -petsc_solver 1 -pc_type ilu -ksp_monitor -ksp_view -ksp_rtol 1e-9
 
 # end of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/bm1c.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/bm1c.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/bm1c.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,97 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for SCEC BM 2.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  This is now all controlled by PETSc command-line
-# arguments.  The only option now specified in this file is whether to
-# use the solution from the previous time step as the starting guess
-# for the current time step.
-#
-# usePreviousDisplacementFlag = 0
-#
-#
-# Quadrature order for the problem.  The options are:
-#       Full:           Quadrature order that should give the exact
-#                       element matrices when the elements are
-#                       geometrically undistorted.
-#       Reduced:        Quadrature order that is one order less than
-#                       full quadrature.  This option should be used
-#                       with caution.
-#       Selective:      Uses Hughes' b-bar formulation to perform
-#                       reduced quadrature on the dilatational parts of
-#                       the strain-displacement matrix.  This can be
-#                       useful in nearly-incompressible problems.
-#
-#quadratureOrder = "Full"
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, with the option of
-# using alternative values for Poisson's ratio and Young's modulus.
-# Each prestress component may also be scaled.  This option is only
-# useful if the prestresses are read from a file (and not automatically
-# computed).
-#
-#prestressAutoCompute = False
-#prestressAutoChangeElasticProperties = False
-#prestressAutoComputePoisson = 0.49
-#prestressAutoComputeYoungs = 1.0e30*Pa
-#
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/pylith3d.cfg (from rev 6116, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/bm1c.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/bm1c.keyval	2007-02-26 18:30:58 UTC (rev 6116)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,111 @@
+[pylith3d]
+# PETSc options
+log_summary = true
+pc_type = bjacobi
+sub_pc_type = ilu
+ksp_monitor = true
+ksp_view = true
+ksp_rtol = 1.0e-9
+# start_in_debugger = true
+# debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = bm1c
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for SCEC BM 2.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  This is now all controlled by PETSc command-line
+# arguments.  The only option now specified in this file is whether to
+# use the solution from the previous time step as the starting guess
+# for the current time step.
+#
+# usePreviousDisplacementFlag = 0
+#
+#
+# Quadrature order for the problem.  The options are:
+#       Full:           Quadrature order that should give the exact
+#                       element matrices when the elements are
+#                       geometrically undistorted.
+#       Reduced:        Quadrature order that is one order less than
+#                       full quadrature.  This option should be used
+#                       with caution.
+#       Selective:      Uses Hughes' b-bar formulation to perform
+#                       reduced quadrature on the dilatational parts of
+#                       the strain-displacement matrix.  This can be
+#                       useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, with the option of
+# using alternative values for Poisson's ratio and Young's modulus.
+# Each prestress component may also be scaled.  This option is only
+# useful if the prestresses are read from a file (and not automatically
+# computed).
+#
+#prestressAutoCompute = False
+#prestressAutoChangeElasticProps = False
+#prestressAutoComputePoisson = 0.49
+#prestressAutoComputeYoungs = 1.0e30*Pa
+#
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-debug.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -6,53 +6,7 @@
 #
 # ======================================================================
 
-if [ $# != 1 ]; then
-  echo "usage: runbm1c-debug.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=full -pl3dscan.ucdOutput=ascii $pyts
 
-simroot="bm1c"
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c-test.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -6,51 +6,10 @@
 #
 # ======================================================================
 
-if [ $# != 1 ]; then
-  echo "usage: runbm1c-test.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="bm1c"
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=echo -pl3dscan.ucdOutput=ascii $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
 # 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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm1c/runbm1c.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -6,51 +6,10 @@
 #
 # ======================================================================
 
-if [ $# != 1 ]; then
-  echo "usage: runbm1c.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="bm1c"
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=none -pl3dscan.ucdOutput=binary $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
 # end of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/bm2a.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/bm2a.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/bm2a.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,119 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for SCEC BM 2.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  At present, the only solution method is preconditioned
-# conjugate gradients.  The user can select the preconditioner type,
-# the maximum number of iterations, and the factors controlling
-# convergence.  Preconditioner types are as follows:
-#    diagonalNoUpdate:      Diagonal preconditioning with an initial
-#                           guess of zero for the displacement vector.
-#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess of zero for the displacement
-#                           vector.
-#    diagonalUpdate:        Diagonal preconditioning with an initial
-#                           guess for the displacement vector corresponding
-#                           to the displacement vector from the previous
-#                           time step.
-#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess for the displacement vector
-#                           corresponding to the displacement vector from
-#                           the previous time step.
-#
-#    Note that the diagonal preconditioners generally require more iterations,
-#    but at less computational cost per iteration.  In theory, the more
-#    complex preconditioner should work better for more irregular meshes.
-#
-#preconditionerType = "diagonalNoUpdate"
-#maxPcgIterations = 3000
-displacementAccuracyMult = 0.001
-forceAccuracyMult = 0.001
-energyAccuracyMult = 0.00001
-#minDisplacementAccuracy = 1.0e-8
-#minForceAccuracy = 1.0e-8
-#minEnergyAccuracy = 1.0e-14
-#
-#
-# Quadrature order for the problem.  The options are:
-#       Full:           Quadrature order that should give the exact
-#                       element matrices when the elements are
-#                       geometrically undistorted.
-#       Reduced:        Quadrature order that is one order less than
-#                       full quadrature.  This option should be used
-#                       with caution.
-#       Selective:      Uses Hughes' b-bar formulation to perform
-#                       reduced quadrature on the dilatational parts of
-#                       the strain-displacement matrix.  This can be
-#                       useful in nearly-incompressible problems.
-#
-#quadratureOrder = "Full"
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-gravityZ = -10.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, using an alternate
-# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
-# negative value, the original Poisson's ratio is used.  Each prestress
-# component may also be scaled.  This option is only useful if the
-# prestresses are read from a file (and not automatically computed).
-#
-#prestressAutoCompute = False
-#prestressQuadrature = 1
-#prestressAutoComputePoisson = -0.49
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/pylith3d.cfg (from rev 6116, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/bm2a.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/bm2a.keyval	2007-02-26 18:30:58 UTC (rev 6116)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm2a/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,136 @@
+[pylith3d]
+# PETSc options
+log_summary = true
+pc_type = bjacobi
+sub_pc_type = ilu
+ksp_monitor = true
+ksp_view = true
+ksp_rtol = 1.0e-9
+# start_in_debugger = true
+# debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = bm2a
+inputFileRoot = ../bm1a/bm1a
+bcInputFile = bm2a.bc
+timeStepInputFile = bm2a.time
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for SCEC BM 2.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  At present, the only solution method is preconditioned
+# conjugate gradients.  The user can select the preconditioner type,
+# the maximum number of iterations, and the factors controlling
+# convergence.  Preconditioner types are as follows:
+#    diagonalNoUpdate:      Diagonal preconditioning with an initial
+#                           guess of zero for the displacement vector.
+#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess of zero for the displacement
+#                           vector.
+#    diagonalUpdate:        Diagonal preconditioning with an initial
+#                           guess for the displacement vector corresponding
+#                           to the displacement vector from the previous
+#                           time step.
+#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess for the displacement vector
+#                           corresponding to the displacement vector from
+#                           the previous time step.
+#
+#    Note that the diagonal preconditioners generally require more iterations,
+#    but at less computational cost per iteration.  In theory, the more
+#    complex preconditioner should work better for more irregular meshes.
+#
+#preconditionerType = "diagonalNoUpdate"
+#maxPcgIterations = 3000
+displacementAccuracyMult = 0.001
+forceAccuracyMult = 0.001
+energyAccuracyMult = 0.00001
+#minDisplacementAccuracy = 1.0e-8
+#minForceAccuracy = 1.0e-8
+#minEnergyAccuracy = 1.0e-14
+#
+#
+# Quadrature order for the problem.  The options are:
+#       Full:           Quadrature order that should give the exact
+#                       element matrices when the elements are
+#                       geometrically undistorted.
+#       Reduced:        Quadrature order that is one order less than
+#                       full quadrature.  This option should be used
+#                       with caution.
+#       Selective:      Uses Hughes' b-bar formulation to perform
+#                       reduced quadrature on the dilatational parts of
+#                       the strain-displacement matrix.  This can be
+#                       useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+gravityZ = -10.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, using an alternate
+# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
+# negative value, the original Poisson's ratio is used.  Each prestress
+# component may also be scaled.  This option is only useful if the
+# prestresses are read from a file (and not automatically computed).
+#
+#prestressAutoCompute = False
+#prestressQuadrature = 1
+#prestressAutoComputePoisson = -0.49
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/bm5.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/bm5.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/bm5.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,98 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for SCEC BM 5.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  This is now all controlled by PETSc command-line
-# arguments.  The only option now specified in this file is whether to
-# use the solution from the previous time step as the starting guess
-# for the current time step.
-#
-#usePreviousDisplacementFlag = 0
-#
-#
-# Quadrature order for the problem.  The options are:
-#       Full:           Quadrature order that should give the exact
-#                       element matrices when the elements are
-#                       geometrically undistorted.
-#       Reduced:        Quadrature order that is one order less than
-#                       full quadrature.  This option should be used
-#                       with caution.
-#       Selective:      Uses Hughes' b-bar formulation to perform
-#                       reduced quadrature on the dilatational parts of
-#                       the strain-displacement matrix.  This can be
-#                       useful in nearly-incompressible problems.
-#
-#quadratureOrder = Full
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, with the option of
-# using alternative values for Poisson's ratio and Young's modulus.
-# Each prestress component may also be scaled.  This option is only
-# useful if the prestresses are read from a file (and not automatically
-# computed).
-#
-#prestressAutoCompute = False
-#prestressAutoChangeElasticProperties = False
-#prestressAutoComputePoisson = 0.49
-#prestressAutoComputeYoungs = 1.0e30*Pa
-#
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12
-#f77UcdOutput = 13

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/pylith3d.cfg (from rev 6116, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/bm5.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/bm5.keyval	2007-02-26 18:30:58 UTC (rev 6116)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,112 @@
+[pylith3d]
+# PETSc options
+log_summary = true
+pc_type = bjacobi
+sub_pc_type = ilu
+ksp_monitor = true
+ksp_view = true
+ksp_rtol = 1.0e-9
+# start_in_debugger = true
+# debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = bm5
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for SCEC BM 5.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  This is now all controlled by PETSc command-line
+# arguments.  The only option now specified in this file is whether to
+# use the solution from the previous time step as the starting guess
+# for the current time step.
+#
+#usePreviousDisplacementFlag = 0
+#
+#
+# Quadrature order for the problem.  The options are:
+#       Full:           Quadrature order that should give the exact
+#                       element matrices when the elements are
+#                       geometrically undistorted.
+#       Reduced:        Quadrature order that is one order less than
+#                       full quadrature.  This option should be used
+#                       with caution.
+#       Selective:      Uses Hughes' b-bar formulation to perform
+#                       reduced quadrature on the dilatational parts of
+#                       the strain-displacement matrix.  This can be
+#                       useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, with the option of
+# using alternative values for Poisson's ratio and Young's modulus.
+# Each prestress component may also be scaled.  This option is only
+# useful if the prestresses are read from a file (and not automatically
+# computed).
+#
+#prestressAutoCompute = False
+#prestressAutoChangeElasticProps = False
+#prestressAutoComputePoisson = 0.49
+#prestressAutoComputeYoungs = 1.0e30*Pa
+#
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12
+#f77UcdOutput = 13

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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-debug.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -5,53 +5,10 @@
 #
 # ======================================================================
 
-if [ $# != 1 ]; then
-  echo "usage: runbm5-debug.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="bm5"
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-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
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=full -pl3dscan.ucdOutput=ascii $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5-test.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -5,51 +5,10 @@
 #
 # ======================================================================
 
-if [ $# != 1 ]; then
-  echo "usage: runbm5-test.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="bm5"
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=echo -pl3dscan.ucdOutput=ascii $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
 # 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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/runbm5.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -5,51 +5,10 @@
 #
 # ======================================================================
 
-if [ $# != 1 ]; then
-  echo "usage: runbm5.sh NPROCS"
-  exit 1
-fi
-nprocs=$1
-
-simroot="bm5"
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=none -pl3dscan.ucdOutput=binary $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
 # 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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/bm5/test.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-pylith3dapp.py -typos=relaxed -pl3dscan.fileRoot=lintet/bm5/bm5 -pl3dscan.ucdOutput=binary -log_summary -pc_type ilu -ksp_monitor -ksp_view -ksp_rtol 1e-9
+pylith3dapp.py -pl3dscan.fileRoot=lintet/bm5/bm5 -pl3dscan.ucdOutput=binary -log_summary -pc_type ilu -ksp_monitor -ksp_view -ksp_rtol 1e-9
 
 # end of file

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-bbar.cfg (from rev 6053, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-bbar.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-bbar.keyval	2007-02-20 22:55:34 UTC (rev 6053)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-bbar.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,122 @@
+[pylith3d.scanner]
+fileRoot = pt1
+
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for patchtest 1.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  At present, the only solution method is preconditioned
+# conjugate gradients.  The user can select the preconditioner type,
+# the maximum number of iterations, and the factors controlling
+# convergence.  Preconditioner types are as follows:
+#    diagonalNoUpdate:      Diagonal preconditioning with an initial
+#                           guess of zero for the displacement vector.
+#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess of zero for the displacement
+#                           vector.
+#    diagonalUpdate:        Diagonal preconditioning with an initial
+#                           guess for the displacement vector corresponding
+#                           to the displacement vector from the previous
+#                           time step.
+#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess for the displacement vector
+#                           corresponding to the displacement vector from
+#                           the previous time step.
+#
+#    Note that the diagonal preconditioners generally require more iterations,
+#    but at less computational cost per iteration.  In theory, the more
+#    complex preconditioner should work better for more irregular meshes.
+#
+#preconditionerType = "diagonalNoUpdate"
+#maxPcgIterations = 3000
+#displacementAccuracyMult = 1.0
+#forceAccuracyMult = 1.0
+#energyAccuracyMult = 1.0
+#minDisplacementAccuracy = 1.0e-8
+#minForceAccuracy = 1.0e-8
+#minEnergyAccuracy = 1.0e-14
+#
+#
+# Quadrature order for the problem.  The options are:
+#	Full:		Quadrature order that should give the exact
+#			element matrices when the elements are
+#			geometrically undistorted.
+#	Reduced:	Quadrature order that is one order less than
+#			full quadrature.  This option should be used
+#			with caution.
+#	Selective:	Uses Hughes' b-bar formulation to perform
+#			reduced quadrature on the dilatational parts of
+#			the strain-displacement matrix.  This can be
+#			useful in nearly-incompressible problems.
+#
+quadratureOrder = Selective
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, using an alternate
+# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
+# negative value, the original Poisson's ratio is used.  Each prestress
+# component may also be scaled.  This option is only useful if the
+# prestresses are read from a file (and not automatically computed).
+#
+#prestressAutoCompute = False
+#prestressAutoComputePoisson = -0.49
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-bbar.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-bbar.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-bbar.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,118 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for patchtest 1.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  At present, the only solution method is preconditioned
-# conjugate gradients.  The user can select the preconditioner type,
-# the maximum number of iterations, and the factors controlling
-# convergence.  Preconditioner types are as follows:
-#    diagonalNoUpdate:      Diagonal preconditioning with an initial
-#                           guess of zero for the displacement vector.
-#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess of zero for the displacement
-#                           vector.
-#    diagonalUpdate:        Diagonal preconditioning with an initial
-#                           guess for the displacement vector corresponding
-#                           to the displacement vector from the previous
-#                           time step.
-#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess for the displacement vector
-#                           corresponding to the displacement vector from
-#                           the previous time step.
-#
-#    Note that the diagonal preconditioners generally require more iterations,
-#    but at less computational cost per iteration.  In theory, the more
-#    complex preconditioner should work better for more irregular meshes.
-#
-#preconditionerType = "diagonalNoUpdate"
-#maxPcgIterations = 3000
-#displacementAccuracyMult = 1.0
-#forceAccuracyMult = 1.0
-#energyAccuracyMult = 1.0
-#minDisplacementAccuracy = 1.0e-8
-#minForceAccuracy = 1.0e-8
-#minEnergyAccuracy = 1.0e-14
-#
-#
-# Quadrature order for the problem.  The options are:
-#	Full:		Quadrature order that should give the exact
-#			element matrices when the elements are
-#			geometrically undistorted.
-#	Reduced:	Quadrature order that is one order less than
-#			full quadrature.  This option should be used
-#			with caution.
-#	Selective:	Uses Hughes' b-bar formulation to perform
-#			reduced quadrature on the dilatational parts of
-#			the strain-displacement matrix.  This can be
-#			useful in nearly-incompressible problems.
-#
-quadratureOrder = "Selective"
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, using an alternate
-# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
-# negative value, the original Poisson's ratio is used.  Each prestress
-# component may also be scaled.  This option is only useful if the
-# prestresses are read from a file (and not automatically computed).
-#
-#prestressAutoCompute = False
-#prestressAutoComputePoisson = -0.49
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-red.cfg (from rev 6053, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-red.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-red.keyval	2007-02-20 22:55:34 UTC (rev 6053)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-red.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,122 @@
+[pylith3d.scanner]
+fileRoot = pt1
+
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for patchtest 1.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  At present, the only solution method is preconditioned
+# conjugate gradients.  The user can select the preconditioner type,
+# the maximum number of iterations, and the factors controlling
+# convergence.  Preconditioner types are as follows:
+#    diagonalNoUpdate:      Diagonal preconditioning with an initial
+#                           guess of zero for the displacement vector.
+#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess of zero for the displacement
+#                           vector.
+#    diagonalUpdate:        Diagonal preconditioning with an initial
+#                           guess for the displacement vector corresponding
+#                           to the displacement vector from the previous
+#                           time step.
+#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess for the displacement vector
+#                           corresponding to the displacement vector from
+#                           the previous time step.
+#
+#    Note that the diagonal preconditioners generally require more iterations,
+#    but at less computational cost per iteration.  In theory, the more
+#    complex preconditioner should work better for more irregular meshes.
+#
+#preconditionerType = "diagonalNoUpdate"
+#maxPcgIterations = 3000
+#displacementAccuracyMult = 1.0
+#forceAccuracyMult = 1.0
+#energyAccuracyMult = 1.0
+#minDisplacementAccuracy = 1.0e-8
+#minForceAccuracy = 1.0e-8
+#minEnergyAccuracy = 1.0e-14
+#
+#
+# Quadrature order for the problem.  The options are:
+#	Full:		Quadrature order that should give the exact
+#			element matrices when the elements are
+#			geometrically undistorted.
+#	Reduced:	Quadrature order that is one order less than
+#			full quadrature.  This option should be used
+#			with caution.
+#	Selective:	Uses Hughes' b-bar formulation to perform
+#			reduced quadrature on the dilatational parts of
+#			the strain-displacement matrix.  This can be
+#			useful in nearly-incompressible problems.
+#
+quadratureOrder = Reduced
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, using an alternate
+# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
+# negative value, the original Poisson's ratio is used.  Each prestress
+# component may also be scaled.  This option is only useful if the
+# prestresses are read from a file (and not automatically computed).
+#
+#prestressAutoCompute = False
+#prestressAutoComputePoisson = -0.49
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-red.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-red.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt-red.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,118 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for patchtest 1.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  At present, the only solution method is preconditioned
-# conjugate gradients.  The user can select the preconditioner type,
-# the maximum number of iterations, and the factors controlling
-# convergence.  Preconditioner types are as follows:
-#    diagonalNoUpdate:      Diagonal preconditioning with an initial
-#                           guess of zero for the displacement vector.
-#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess of zero for the displacement
-#                           vector.
-#    diagonalUpdate:        Diagonal preconditioning with an initial
-#                           guess for the displacement vector corresponding
-#                           to the displacement vector from the previous
-#                           time step.
-#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess for the displacement vector
-#                           corresponding to the displacement vector from
-#                           the previous time step.
-#
-#    Note that the diagonal preconditioners generally require more iterations,
-#    but at less computational cost per iteration.  In theory, the more
-#    complex preconditioner should work better for more irregular meshes.
-#
-#preconditionerType = "diagonalNoUpdate"
-#maxPcgIterations = 3000
-#displacementAccuracyMult = 1.0
-#forceAccuracyMult = 1.0
-#energyAccuracyMult = 1.0
-#minDisplacementAccuracy = 1.0e-8
-#minForceAccuracy = 1.0e-8
-#minEnergyAccuracy = 1.0e-14
-#
-#
-# Quadrature order for the problem.  The options are:
-#	Full:		Quadrature order that should give the exact
-#			element matrices when the elements are
-#			geometrically undistorted.
-#	Reduced:	Quadrature order that is one order less than
-#			full quadrature.  This option should be used
-#			with caution.
-#	Selective:	Uses Hughes' b-bar formulation to perform
-#			reduced quadrature on the dilatational parts of
-#			the strain-displacement matrix.  This can be
-#			useful in nearly-incompressible problems.
-#
-quadratureOrder = "Reduced"
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, using an alternate
-# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
-# negative value, the original Poisson's ratio is used.  Each prestress
-# component may also be scaled.  This option is only useful if the
-# prestresses are read from a file (and not automatically computed).
-#
-#prestressAutoCompute = False
-#prestressAutoComputePoisson = -0.49
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt1.cfg (from rev 6053, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt1.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt1.keyval	2007-02-20 22:55:34 UTC (rev 6053)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt1.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,122 @@
+[pylith3d.scanner]
+fileRoot = pt1
+
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for patchtest 1.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  At present, the only solution method is preconditioned
+# conjugate gradients.  The user can select the preconditioner type,
+# the maximum number of iterations, and the factors controlling
+# convergence.  Preconditioner types are as follows:
+#    diagonalNoUpdate:      Diagonal preconditioning with an initial
+#                           guess of zero for the displacement vector.
+#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess of zero for the displacement
+#                           vector.
+#    diagonalUpdate:        Diagonal preconditioning with an initial
+#                           guess for the displacement vector corresponding
+#                           to the displacement vector from the previous
+#                           time step.
+#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess for the displacement vector
+#                           corresponding to the displacement vector from
+#                           the previous time step.
+#
+#    Note that the diagonal preconditioners generally require more iterations,
+#    but at less computational cost per iteration.  In theory, the more
+#    complex preconditioner should work better for more irregular meshes.
+#
+#preconditionerType = "diagonalNoUpdate"
+#maxPcgIterations = 3000
+#displacementAccuracyMult = 1.0
+#forceAccuracyMult = 1.0
+#energyAccuracyMult = 1.0
+#minDisplacementAccuracy = 1.0e-8
+#minForceAccuracy = 1.0e-8
+#minEnergyAccuracy = 1.0e-14
+#
+#
+# Quadrature order for the problem.  The options are:
+#	Full:		Quadrature order that should give the exact
+#			element matrices when the elements are
+#			geometrically undistorted.
+#	Reduced:	Quadrature order that is one order less than
+#			full quadrature.  This option should be used
+#			with caution.
+#	Selective:	Uses Hughes' b-bar formulation to perform
+#			reduced quadrature on the dilatational parts of
+#			the strain-displacement matrix.  This can be
+#			useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, using an alternate
+# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
+# negative value, the original Poisson's ratio is used.  Each prestress
+# component may also be scaled.  This option is only useful if the
+# prestresses are read from a file (and not automatically computed).
+#
+#prestressAutoCompute = False
+#prestressAutoComputePoisson = -0.49
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt1.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt1.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/pt1.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,118 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for patchtest 1.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  At present, the only solution method is preconditioned
-# conjugate gradients.  The user can select the preconditioner type,
-# the maximum number of iterations, and the factors controlling
-# convergence.  Preconditioner types are as follows:
-#    diagonalNoUpdate:      Diagonal preconditioning with an initial
-#                           guess of zero for the displacement vector.
-#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess of zero for the displacement
-#                           vector.
-#    diagonalUpdate:        Diagonal preconditioning with an initial
-#                           guess for the displacement vector corresponding
-#                           to the displacement vector from the previous
-#                           time step.
-#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess for the displacement vector
-#                           corresponding to the displacement vector from
-#                           the previous time step.
-#
-#    Note that the diagonal preconditioners generally require more iterations,
-#    but at less computational cost per iteration.  In theory, the more
-#    complex preconditioner should work better for more irregular meshes.
-#
-#preconditionerType = "diagonalNoUpdate"
-#maxPcgIterations = 3000
-#displacementAccuracyMult = 1.0
-#forceAccuracyMult = 1.0
-#energyAccuracyMult = 1.0
-#minDisplacementAccuracy = 1.0e-8
-#minForceAccuracy = 1.0e-8
-#minEnergyAccuracy = 1.0e-14
-#
-#
-# Quadrature order for the problem.  The options are:
-#	Full:		Quadrature order that should give the exact
-#			element matrices when the elements are
-#			geometrically undistorted.
-#	Reduced:	Quadrature order that is one order less than
-#			full quadrature.  This option should be used
-#			with caution.
-#	Selective:	Uses Hughes' b-bar formulation to perform
-#			reduced quadrature on the dilatational parts of
-#			the strain-displacement matrix.  This can be
-#			useful in nearly-incompressible problems.
-#
-#quadratureOrder = "Full"
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, using an alternate
-# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
-# negative value, the original Poisson's ratio is used.  Each prestress
-# component may also be scaled.  This option is only useful if the
-# prestresses are read from a file (and not automatically computed).
-#
-#prestressAutoCompute = False
-#prestressAutoComputePoisson = -0.49
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12

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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-bbar-comp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 pt-bbar.cfg --pl3dscan.bcInputFile=pt1.bc --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt2.bc --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt3.bc --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt4.bc --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt5.bc --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt6.bc --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt7.bc --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt8.bc --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt9.bc --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt10.bc --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt11.bc --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt12.bc --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-bbar-incomp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 pt-bbar.cfg --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-bbar.cfg --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-full-comp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 pt-full.cfg --pl3dscan.bcInputFile=pt1.bc --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt2.bc --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt3.bc --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt4.bc --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt5.bc --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt6.bc --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt7.bc --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt8.bc --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt9.bc --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt10.bc --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt11.bc --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt12.bc --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-full-incomp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 pt-full.cfg --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-full.cfg --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-red-comp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 pt-red.cfg --pl3dscan.bcInputFile=pt1.bc --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt2.bc --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt3.bc --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt4.bc --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt5.bc --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt6.bc --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt7.bc --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt8.bc --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt9.bc --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt10.bc --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt11.bc --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt12.bc --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/patchtest/runtests-red-incomp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 pt-red.cfg --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 pt-red.cfg --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-red-incomp.ascii
 /bin/rm pt1.plot

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/powertest/ESF.cfg (from rev 6122, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/powertest/pylith3dESF.cfg)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/powertest/pylith3dESF.cfg	2007-02-27 19:52:56 UTC (rev 6122)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/powertest/ESF.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,8 @@
+# Configuration file for the older ESF-based solution method.  To use,
+# simply name this file on the command line:
+#
+#     pylith3dapp.py ESF.cfg
+
+[pylith3d.scanner]
+materialPropertiesInputFile = powertestESF.prop
+outputFileRoot = powertestESF

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/powertest/pylith3d.cfg
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/powertest/pylith3d.cfg	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/powertest/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,8 +1,4 @@
 [pylith3d]
-# scanner (pylith3d) options
-scanner.fileRoot = powertest
-scanner.asciiOutput = full
-scanner.ucdOutput = ascii
 # PETSc options
 log_summary = true
 pc_type = bjacobi
@@ -12,3 +8,106 @@
 ksp_rtol = 1.0e-9
 # start_in_debugger = true
 # debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = powertest
+asciiOutput = full
+ucdOutput = ascii
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for SCEC BM 2.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  This is now all controlled by PETSc command-line
+# arguments.  The only option now specified in this file is whether to
+# use the solution from the previous time step as the starting guess
+# for the current time step.
+#
+# usePreviousDisplacementFlag = 0
+#
+#
+# Quadrature order for the problem.  The options are:
+#       Full:           Quadrature order that should give the exact
+#                       element matrices when the elements are
+#                       geometrically undistorted.
+#       Reduced:        Quadrature order that is one order less than
+#                       full quadrature.  This option should be used
+#                       with caution.
+#       Selective:      Uses Hughes' b-bar formulation to perform
+#                       reduced quadrature on the dilatational parts of
+#                       the strain-displacement matrix.  This can be
+#                       useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, with the option of
+# using alternative values for Poisson's ratio and Young's modulus.
+# Each prestress component may also be scaled.  This option is only
+# useful if the prestresses are read from a file (and not automatically
+# computed).
+#
+#prestressAutoCompute = False
+#prestressAutoChangeElasticProps = False
+#prestressAutoComputePoisson = 0.49
+#prestressAutoComputeYoungs = 1.0e30*Pa
+#
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/powertest/pylith3dESF.cfg
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/powertest/pylith3dESF.cfg	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/powertest/pylith3dESF.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,16 +0,0 @@
-[pylith3d]
-# scanner (pylith3d) options
-scanner.fileRoot = powertest
-scanner.materialPropertiesInputFile = powertestESF.prop
-scanner.outputFileRoot = powertestESF
-scanner.asciiOutput = full
-scanner.ucdOutput = ascii
-# PETSc options
-log_summary = true
-pc_type = bjacobi
-sub_pc_type = ilu
-ksp_monitor = true
-ksp_view = true
-ksp_rtol = 1.0e-9
-# start_in_debugger = true
-# debugger_pause = 100

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/pylith3d.cfg (from rev 6116, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/splittest.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/splittest.keyval	2007-02-26 18:30:58 UTC (rev 6116)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,112 @@
+[pylith3d]
+# PETSc options
+log_summary = true
+pc_type = bjacobi
+sub_pc_type = ilu
+ksp_monitor = true
+ksp_view = true
+ksp_rtol = 1.0e-9
+# start_in_debugger = true
+# debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = splittest
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for SCEC BM 5.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  This is now all controlled by PETSc command-line
+# arguments.  The only option now specified in this file is whether to
+# use the solution from the previous time step as the starting guess
+# for the current time step.
+#
+#usePreviousDisplacementFlag = 0
+#
+#
+# Quadrature order for the problem.  The options are:
+#       Full:           Quadrature order that should give the exact
+#                       element matrices when the elements are
+#                       geometrically undistorted.
+#       Reduced:        Quadrature order that is one order less than
+#                       full quadrature.  This option should be used
+#                       with caution.
+#       Selective:      Uses Hughes' b-bar formulation to perform
+#                       reduced quadrature on the dilatational parts of
+#                       the strain-displacement matrix.  This can be
+#                       useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, with the option of
+# using alternative values for Poisson's ratio and Young's modulus.
+# Each prestress component may also be scaled.  This option is only
+# useful if the prestresses are read from a file (and not automatically
+# computed).
+#
+#prestressAutoCompute = False
+#prestressAutoChangeElasticProps = False
+#prestressAutoComputePoisson = 0.49
+#prestressAutoComputeYoungs = 1.0e30*Pa
+#
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12
+#f77UcdOutput = 13

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/runsplittest-debug.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/runsplittest-debug.sh	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/runsplittest-debug.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -5,53 +5,10 @@
 #
 # ======================================================================
 
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-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
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=full -pl3dscan.ucdOutput=ascii $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/runsplittest-test.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/runsplittest-test.sh	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/runsplittest-test.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -5,51 +5,10 @@
 #
 # ======================================================================
 
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=echo -pl3dscan.ucdOutput=ascii $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
 # end of file

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/runsplittest.sh
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/runsplittest.sh	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/runsplittest.sh	2007-02-28 01:54:26 UTC (rev 6127)
@@ -5,51 +5,10 @@
 #
 # ======================================================================
 
-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
+#pyts="-pl3dscan.pythonTimestep=1"
 
-petscflags="-log_summary \
-  -pc_type bjacobi \
-  -sub_pc_type ilu \
-  -ksp_monitor \
-  -ksp_rtol 1e-09"
-echo "PETSc flags:"
-echo $petscflags
+set -x
+pylith3dapp.py -pl3dscan.asciiOutput=none -pl3dscan.ucdOutput=binary $pyts
 
-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="mpirun -np $nprocs pylith3dapp.py $pyreflags $pylithflags $petscflags"
-
-echo $cmd
-eval $cmd
-
 # end of file

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/splittest.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/splittest.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/splittest/splittest.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,98 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for SCEC BM 5.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  This is now all controlled by PETSc command-line
-# arguments.  The only option now specified in this file is whether to
-# use the solution from the previous time step as the starting guess
-# for the current time step.
-#
-#usePreviousDisplacementFlag = 0
-#
-#
-# Quadrature order for the problem.  The options are:
-#       Full:           Quadrature order that should give the exact
-#                       element matrices when the elements are
-#                       geometrically undistorted.
-#       Reduced:        Quadrature order that is one order less than
-#                       full quadrature.  This option should be used
-#                       with caution.
-#       Selective:      Uses Hughes' b-bar formulation to perform
-#                       reduced quadrature on the dilatational parts of
-#                       the strain-displacement matrix.  This can be
-#                       useful in nearly-incompressible problems.
-#
-#quadratureOrder = Full
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, with the option of
-# using alternative values for Poisson's ratio and Young's modulus.
-# Each prestress component may also be scaled.  This option is only
-# useful if the prestresses are read from a file (and not automatically
-# computed).
-#
-#prestressAutoCompute = False
-#prestressAutoChangeElasticProperties = False
-#prestressAutoComputePoisson = 0.49
-#prestressAutoComputeYoungs = 1.0e30*Pa
-#
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12
-#f77UcdOutput = 13

Modified: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/tractest/pylith3d.cfg
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/tractest/pylith3d.cfg	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/tractest/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,8 +1,4 @@
 [pylith3d]
-# scanner (pylith3d) options
-scanner.fileRoot = tractest
-scanner.asciiOutput = full
-scanner.ucdOutput = ascii
 # PETSc options
 log_summary = true
 pc_type = bjacobi
@@ -12,3 +8,107 @@
 ksp_rtol = 1.0e-9
 # start_in_debugger = true
 # debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = tractest
+asciiOutput = full
+ucdOutput = ascii
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for SCEC BM 5.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  This is now all controlled by PETSc command-line
+# arguments.  The only option now specified in this file is whether to
+# use the solution from the previous time step as the starting guess
+# for the current time step.
+#
+#usePreviousDisplacementFlag = 0
+#
+#
+# Quadrature order for the problem.  The options are:
+#       Full:           Quadrature order that should give the exact
+#                       element matrices when the elements are
+#                       geometrically undistorted.
+#       Reduced:        Quadrature order that is one order less than
+#                       full quadrature.  This option should be used
+#                       with caution.
+#       Selective:      Uses Hughes' b-bar formulation to perform
+#                       reduced quadrature on the dilatational parts of
+#                       the strain-displacement matrix.  This can be
+#                       useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, with the option of
+# using alternative values for Poisson's ratio and Young's modulus.
+# Each prestress component may also be scaled.  This option is only
+# useful if the prestresses are read from a file (and not automatically
+# computed).
+#
+#prestressAutoCompute = False
+#prestressAutoChangeElasticProps = False
+#prestressAutoComputePoisson = 0.49
+#prestressAutoComputeYoungs = 1.0e30*Pa
+#
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12
+#f77UcdOutput = 13

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/tractest/tractest.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/tractest/tractest.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/lintet/tractest/tractest.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,98 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for SCEC BM 5.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  This is now all controlled by PETSc command-line
-# arguments.  The only option now specified in this file is whether to
-# use the solution from the previous time step as the starting guess
-# for the current time step.
-#
-#usePreviousDisplacementFlag = 0
-#
-#
-# Quadrature order for the problem.  The options are:
-#       Full:           Quadrature order that should give the exact
-#                       element matrices when the elements are
-#                       geometrically undistorted.
-#       Reduced:        Quadrature order that is one order less than
-#                       full quadrature.  This option should be used
-#                       with caution.
-#       Selective:      Uses Hughes' b-bar formulation to perform
-#                       reduced quadrature on the dilatational parts of
-#                       the strain-displacement matrix.  This can be
-#                       useful in nearly-incompressible problems.
-#
-#quadratureOrder = Full
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, with the option of
-# using alternative values for Poisson's ratio and Young's modulus.
-# Each prestress component may also be scaled.  This option is only
-# useful if the prestresses are read from a file (and not automatically
-# computed).
-#
-#prestressAutoCompute = False
-#prestressAutoChangeElasticProperties = False
-#prestressAutoComputePoisson = 0.49
-#prestressAutoComputeYoungs = 1.0e30*Pa
-#
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12
-#f77UcdOutput = 13

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/bm1a.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/bm1a.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/bm1a.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,119 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for SCEC BM 2.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  At present, the only solution method is preconditioned
-# conjugate gradients.  The user can select the preconditioner type,
-# the maximum number of iterations, and the factors controlling
-# convergence.  Preconditioner types are as follows:
-#    diagonalNoUpdate:      Diagonal preconditioning with an initial
-#                           guess of zero for the displacement vector.
-#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess of zero for the displacement
-#                           vector.
-#    diagonalUpdate:        Diagonal preconditioning with an initial
-#                           guess for the displacement vector corresponding
-#                           to the displacement vector from the previous
-#                           time step.
-#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess for the displacement vector
-#                           corresponding to the displacement vector from
-#                           the previous time step.
-#
-#    Note that the diagonal preconditioners generally require more iterations,
-#    but at less computational cost per iteration.  In theory, the more
-#    complex preconditioner should work better for more irregular meshes.
-#
-#preconditionerType = "diagonalNoUpdate"
-#maxPcgIterations = 3000
-#displacementAccuracyMult = 1.0
-#forceAccuracyMult = 1.0
-#energyAccuracyMult = 1.0
-#minDisplacementAccuracy = 1.0e-8
-#minForceAccuracy = 1.0e-8
-#minEnergyAccuracy = 1.0e-14
-#
-#
-# Quadrature order for the problem.  The options are:
-#       Full:           Quadrature order that should give the exact
-#                       element matrices when the elements are
-#                       geometrically undistorted.
-#       Reduced:        Quadrature order that is one order less than
-#                       full quadrature.  This option should be used
-#                       with caution.
-#       Selective:      Uses Hughes' b-bar formulation to perform
-#                       reduced quadrature on the dilatational parts of
-#                       the strain-displacement matrix.  This can be
-#                       useful in nearly-incompressible problems.
-#
-#quadratureOrder = "Full"
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, using an alternate
-# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
-# negative value, the original Poisson's ratio is used.  Each prestress
-# component may also be scaled.  This option is only useful if the
-# prestresses are read from a file (and not automatically computed).
-#
-#prestressAutoCompute = False
-#prestressQuadrature = 1
-#prestressAutoComputePoisson = -0.49
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/pylith3d.cfg (from rev 6122, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/bm1a.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/bm1a.keyval	2007-02-27 19:52:56 UTC (rev 6122)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/bm1a/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,133 @@
+[pylith3d]
+# PETSc options
+log_summary = true
+pc_type = bjacobi
+sub_pc_type = ilu
+ksp_monitor = true
+ksp_view = true
+ksp_rtol = 1.0e-9
+# start_in_debugger = true
+# debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = bm1a
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for SCEC BM 2.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  At present, the only solution method is preconditioned
+# conjugate gradients.  The user can select the preconditioner type,
+# the maximum number of iterations, and the factors controlling
+# convergence.  Preconditioner types are as follows:
+#    diagonalNoUpdate:      Diagonal preconditioning with an initial
+#                           guess of zero for the displacement vector.
+#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess of zero for the displacement
+#                           vector.
+#    diagonalUpdate:        Diagonal preconditioning with an initial
+#                           guess for the displacement vector corresponding
+#                           to the displacement vector from the previous
+#                           time step.
+#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess for the displacement vector
+#                           corresponding to the displacement vector from
+#                           the previous time step.
+#
+#    Note that the diagonal preconditioners generally require more iterations,
+#    but at less computational cost per iteration.  In theory, the more
+#    complex preconditioner should work better for more irregular meshes.
+#
+#preconditionerType = "diagonalNoUpdate"
+#maxPcgIterations = 3000
+#displacementAccuracyMult = 1.0
+#forceAccuracyMult = 1.0
+#energyAccuracyMult = 1.0
+#minDisplacementAccuracy = 1.0e-8
+#minForceAccuracy = 1.0e-8
+#minEnergyAccuracy = 1.0e-14
+#
+#
+# Quadrature order for the problem.  The options are:
+#       Full:           Quadrature order that should give the exact
+#                       element matrices when the elements are
+#                       geometrically undistorted.
+#       Reduced:        Quadrature order that is one order less than
+#                       full quadrature.  This option should be used
+#                       with caution.
+#       Selective:      Uses Hughes' b-bar formulation to perform
+#                       reduced quadrature on the dilatational parts of
+#                       the strain-displacement matrix.  This can be
+#                       useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, using an alternate
+# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
+# negative value, the original Poisson's ratio is used.  Each prestress
+# component may also be scaled.  This option is only useful if the
+# prestresses are read from a file (and not automatically computed).
+#
+#prestressAutoCompute = False
+#prestressQuadrature = 1
+#prestressAutoComputePoisson = -0.49
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/pt1.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/pt1.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/pt1.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,118 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for patchtest 1.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  At present, the only solution method is preconditioned
-# conjugate gradients.  The user can select the preconditioner type,
-# the maximum number of iterations, and the factors controlling
-# convergence.  Preconditioner types are as follows:
-#    diagonalNoUpdate:      Diagonal preconditioning with an initial
-#                           guess of zero for the displacement vector.
-#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess of zero for the displacement
-#                           vector.
-#    diagonalUpdate:        Diagonal preconditioning with an initial
-#                           guess for the displacement vector corresponding
-#                           to the displacement vector from the previous
-#                           time step.
-#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess for the displacement vector
-#                           corresponding to the displacement vector from
-#                           the previous time step.
-#
-#    Note that the diagonal preconditioners generally require more iterations,
-#    but at less computational cost per iteration.  In theory, the more
-#    complex preconditioner should work better for more irregular meshes.
-#
-#preconditionerType = "diagonalNoUpdate"
-#maxPcgIterations = 3000
-#displacementAccuracyMult = 1.0
-#forceAccuracyMult = 1.0
-#energyAccuracyMult = 1.0
-#minDisplacementAccuracy = 1.0e-8
-#minForceAccuracy = 1.0e-8
-#minEnergyAccuracy = 1.0e-14
-#
-#
-# Quadrature order for the problem.  The options are:
-#	Full:		Quadrature order that should give the exact
-#			element matrices when the elements are
-#			geometrically undistorted.
-#	Reduced:	Quadrature order that is one order less than
-#			full quadrature.  This option should be used
-#			with caution.
-#	Selective:	Uses Hughes' b-bar formulation to perform
-#			reduced quadrature on the dilatational parts of
-#			the strain-displacement matrix.  This can be
-#			useful in nearly-incompressible problems.
-#
-#quadratureOrder = "Full"
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, using an alternate
-# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
-# negative value, the original Poisson's ratio is used.  Each prestress
-# component may also be scaled.  This option is only useful if the
-# prestresses are read from a file (and not automatically computed).
-#
-#prestressAutoCompute = False
-#prestressAutoComputePoisson = -0.49
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/pylith3d.cfg (from rev 6122, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/pt1.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/pt1.keyval	2007-02-27 19:52:56 UTC (rev 6122)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,132 @@
+[pylith3d]
+# PETSc options
+log_summary = true
+pc_type = bjacobi
+sub_pc_type = ilu
+ksp_monitor = true
+ksp_view = true
+ksp_rtol = 1.0e-9
+# start_in_debugger = true
+# debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = pt1
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for patchtest 1.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  At present, the only solution method is preconditioned
+# conjugate gradients.  The user can select the preconditioner type,
+# the maximum number of iterations, and the factors controlling
+# convergence.  Preconditioner types are as follows:
+#    diagonalNoUpdate:      Diagonal preconditioning with an initial
+#                           guess of zero for the displacement vector.
+#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess of zero for the displacement
+#                           vector.
+#    diagonalUpdate:        Diagonal preconditioning with an initial
+#                           guess for the displacement vector corresponding
+#                           to the displacement vector from the previous
+#                           time step.
+#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess for the displacement vector
+#                           corresponding to the displacement vector from
+#                           the previous time step.
+#
+#    Note that the diagonal preconditioners generally require more iterations,
+#    but at less computational cost per iteration.  In theory, the more
+#    complex preconditioner should work better for more irregular meshes.
+#
+#preconditionerType = "diagonalNoUpdate"
+#maxPcgIterations = 3000
+#displacementAccuracyMult = 1.0
+#forceAccuracyMult = 1.0
+#energyAccuracyMult = 1.0
+#minDisplacementAccuracy = 1.0e-8
+#minForceAccuracy = 1.0e-8
+#minEnergyAccuracy = 1.0e-14
+#
+#
+# Quadrature order for the problem.  The options are:
+#	Full:		Quadrature order that should give the exact
+#			element matrices when the elements are
+#			geometrically undistorted.
+#	Reduced:	Quadrature order that is one order less than
+#			full quadrature.  This option should be used
+#			with caution.
+#	Selective:	Uses Hughes' b-bar formulation to perform
+#			reduced quadrature on the dilatational parts of
+#			the strain-displacement matrix.  This can be
+#			useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, using an alternate
+# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
+# negative value, the original Poisson's ratio is used.  Each prestress
+# component may also be scaled.  This option is only useful if the
+# prestresses are read from a file (and not automatically computed).
+#
+#prestressAutoCompute = False
+#prestressAutoComputePoisson = -0.49
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-bbar-comp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt1.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt2.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt3.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt4.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt5.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt6.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt7.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt8.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt9.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt10.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt11.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt12.bc --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-bbar-incomp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-full-comp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 --pl3dscan.bcInputFile=pt1.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt2.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt3.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt4.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt5.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt6.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt7.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt8.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt9.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt10.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt11.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt12.bc --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-full-incomp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-red-comp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt1.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt2.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt3.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt4.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt5.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt6.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt7.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt8.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt9.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt10.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt11.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt12.bc --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadhex/patchtest/runtests-red-incomp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-red-incomp.ascii
 /bin/rm pt1.plot

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/bm1a.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/bm1a.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/bm1a.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,119 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for SCEC BM 2.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  At present, the only solution method is preconditioned
-# conjugate gradients.  The user can select the preconditioner type,
-# the maximum number of iterations, and the factors controlling
-# convergence.  Preconditioner types are as follows:
-#    diagonalNoUpdate:      Diagonal preconditioning with an initial
-#                           guess of zero for the displacement vector.
-#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess of zero for the displacement
-#                           vector.
-#    diagonalUpdate:        Diagonal preconditioning with an initial
-#                           guess for the displacement vector corresponding
-#                           to the displacement vector from the previous
-#                           time step.
-#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess for the displacement vector
-#                           corresponding to the displacement vector from
-#                           the previous time step.
-#
-#    Note that the diagonal preconditioners generally require more iterations,
-#    but at less computational cost per iteration.  In theory, the more
-#    complex preconditioner should work better for more irregular meshes.
-#
-#preconditionerType = "diagonalNoUpdate"
-#maxPcgIterations = 3000
-#displacementAccuracyMult = 1.0
-#forceAccuracyMult = 1.0
-#energyAccuracyMult = 1.0
-#minDisplacementAccuracy = 1.0e-8
-#minForceAccuracy = 1.0e-8
-#minEnergyAccuracy = 1.0e-14
-#
-#
-# Quadrature order for the problem.  The options are:
-#       Full:           Quadrature order that should give the exact
-#                       element matrices when the elements are
-#                       geometrically undistorted.
-#       Reduced:        Quadrature order that is one order less than
-#                       full quadrature.  This option should be used
-#                       with caution.
-#       Selective:      Uses Hughes' b-bar formulation to perform
-#                       reduced quadrature on the dilatational parts of
-#                       the strain-displacement matrix.  This can be
-#                       useful in nearly-incompressible problems.
-#
-#quadratureOrder = "Full"
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, using an alternate
-# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
-# negative value, the original Poisson's ratio is used.  Each prestress
-# component may also be scaled.  This option is only useful if the
-# prestresses are read from a file (and not automatically computed).
-#
-#prestressAutoCompute = False
-#prestressQuadrature = 1
-#prestressAutoComputePoisson = -0.49
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/pylith3d.cfg (from rev 6122, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/bm1a.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/bm1a.keyval	2007-02-27 19:52:56 UTC (rev 6122)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/bm1a/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,133 @@
+[pylith3d]
+# PETSc options
+log_summary = true
+pc_type = bjacobi
+sub_pc_type = ilu
+ksp_monitor = true
+ksp_view = true
+ksp_rtol = 1.0e-9
+# start_in_debugger = true
+# debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = bm1a
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for SCEC BM 2.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  At present, the only solution method is preconditioned
+# conjugate gradients.  The user can select the preconditioner type,
+# the maximum number of iterations, and the factors controlling
+# convergence.  Preconditioner types are as follows:
+#    diagonalNoUpdate:      Diagonal preconditioning with an initial
+#                           guess of zero for the displacement vector.
+#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess of zero for the displacement
+#                           vector.
+#    diagonalUpdate:        Diagonal preconditioning with an initial
+#                           guess for the displacement vector corresponding
+#                           to the displacement vector from the previous
+#                           time step.
+#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess for the displacement vector
+#                           corresponding to the displacement vector from
+#                           the previous time step.
+#
+#    Note that the diagonal preconditioners generally require more iterations,
+#    but at less computational cost per iteration.  In theory, the more
+#    complex preconditioner should work better for more irregular meshes.
+#
+#preconditionerType = "diagonalNoUpdate"
+#maxPcgIterations = 3000
+#displacementAccuracyMult = 1.0
+#forceAccuracyMult = 1.0
+#energyAccuracyMult = 1.0
+#minDisplacementAccuracy = 1.0e-8
+#minForceAccuracy = 1.0e-8
+#minEnergyAccuracy = 1.0e-14
+#
+#
+# Quadrature order for the problem.  The options are:
+#       Full:           Quadrature order that should give the exact
+#                       element matrices when the elements are
+#                       geometrically undistorted.
+#       Reduced:        Quadrature order that is one order less than
+#                       full quadrature.  This option should be used
+#                       with caution.
+#       Selective:      Uses Hughes' b-bar formulation to perform
+#                       reduced quadrature on the dilatational parts of
+#                       the strain-displacement matrix.  This can be
+#                       useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, using an alternate
+# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
+# negative value, the original Poisson's ratio is used.  Each prestress
+# component may also be scaled.  This option is only useful if the
+# prestresses are read from a file (and not automatically computed).
+#
+#prestressAutoCompute = False
+#prestressQuadrature = 1
+#prestressAutoComputePoisson = -0.49
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

Deleted: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/pt1.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/pt1.keyval	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/pt1.keyval	2007-02-28 01:54:26 UTC (rev 6127)
@@ -1,118 +0,0 @@
-# Example of a keyword=value file to be used with TECTON.
-# In this example, the default values are listed, but commented out.
-# To change a default value, uncomment the appropriate entry and
-# edit the value.
-# With the present implementation, there should not be any spaces
-# before the keyword.
-#
-# Non-default parameters to be used for patchtest 1.
-#
-# Scaling factors applied to Winkler forces.  These factors may be
-# used as a quick and easy way of changing the density or gravitational
-# acceleration when Winkler forces are used to simulate gravity.
-#
-#winklerScaleX = 1.0
-#winklerScaleY = 1.0
-#winklerScaleZ = 1.0
-#
-#
-# Parameters controlling stress integration and numerical computation
-# of the tangent material matrix.  These default values should be
-# reasonable for most cases.
-#
-#stressTolerance = 1.0e-12*Pa
-#minimumStrainPerturbation = 1.0e-7
-#initialStrainPerturbation = 1.0e-1
-#
-#
-# Parameters controlling the solution of the linear problem at each
-# iteration.  At present, the only solution method is preconditioned
-# conjugate gradients.  The user can select the preconditioner type,
-# the maximum number of iterations, and the factors controlling
-# convergence.  Preconditioner types are as follows:
-#    diagonalNoUpdate:      Diagonal preconditioning with an initial
-#                           guess of zero for the displacement vector.
-#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess of zero for the displacement
-#                           vector.
-#    diagonalUpdate:        Diagonal preconditioning with an initial
-#                           guess for the displacement vector corresponding
-#                           to the displacement vector from the previous
-#                           time step.
-#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
-#                           an initial guess for the displacement vector
-#                           corresponding to the displacement vector from
-#                           the previous time step.
-#
-#    Note that the diagonal preconditioners generally require more iterations,
-#    but at less computational cost per iteration.  In theory, the more
-#    complex preconditioner should work better for more irregular meshes.
-#
-#preconditionerType = "diagonalNoUpdate"
-#maxPcgIterations = 3000
-#displacementAccuracyMult = 1.0
-#forceAccuracyMult = 1.0
-#energyAccuracyMult = 1.0
-#minDisplacementAccuracy = 1.0e-8
-#minForceAccuracy = 1.0e-8
-#minEnergyAccuracy = 1.0e-14
-#
-#
-# Quadrature order for the problem.  The options are:
-#	Full:		Quadrature order that should give the exact
-#			element matrices when the elements are
-#			geometrically undistorted.
-#	Reduced:	Quadrature order that is one order less than
-#			full quadrature.  This option should be used
-#			with caution.
-#	Selective:	Uses Hughes' b-bar formulation to perform
-#			reduced quadrature on the dilatational parts of
-#			the strain-displacement matrix.  This can be
-#			useful in nearly-incompressible problems.
-#
-#quadratureOrder = "Full"
-#
-#
-# Gravitational acceleration in each direction.
-#
-#gravityX = 0.0*m/(s*s)
-#gravityY = 0.0*m/(s*s)
-#gravityZ = 0.0*m/(s*s)
-#
-#
-# Factors controlling computation of prestresses.  When gravity is being
-# used, an automatic computation option may be used, using an alternate
-# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
-# negative value, the original Poisson's ratio is used.  Each prestress
-# component may also be scaled.  This option is only useful if the
-# prestresses are read from a file (and not automatically computed).
-#
-#prestressAutoCompute = False
-#prestressAutoComputePoisson = -0.49
-#prestressScaleXx = 1.0
-#prestressScaleYy = 1.0
-#prestressScaleZz = 1.0
-#prestressScaleXy = 1.0
-#prestressScaleXz = 1.0
-#prestressScaleYz = 1.0
-#
-#
-# Scaling factors applied to differential Winkler forces.  Differential
-# Winkler forces are those applied across a slippery node interface, and
-# are generally used to keep the fault locked at certain times.  These
-# factors control the magnitudes and provide a simple way of scaling the
-# forces so the fault remains sufficiently 'locked'.
-#
-#winklerSlipScaleX = 1.0
-#winklerSlipScaleY = 1.0
-#winklerSlipScaleZ = 1.0
-#
-#
-# Unit numbers used by f77.  These defaults should work for most Unix
-# systems, but may be altered if necessary.
-#
-#f77StandardInput = 5
-#f77StandardOutput = 6
-#f77FileInput = 10
-#f77AsciiOutput = 11
-#f77PlotOutput = 12

Copied: short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/pylith3d.cfg (from rev 6122, short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/pt1.keyval)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/pt1.keyval	2007-02-27 19:52:56 UTC (rev 6122)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/pylith3d.cfg	2007-02-28 01:54:26 UTC (rev 6127)
@@ -0,0 +1,132 @@
+[pylith3d]
+# PETSc options
+log_summary = true
+pc_type = bjacobi
+sub_pc_type = ilu
+ksp_monitor = true
+ksp_view = true
+ksp_rtol = 1.0e-9
+# start_in_debugger = true
+# debugger_pause = 100
+
+[pylith3d.scanner]
+fileRoot = pt1
+
+# Example of a keyword=value file to be used with TECTON.
+# In this example, the default values are listed, but commented out.
+# To change a default value, uncomment the appropriate entry and
+# edit the value.
+# With the present implementation, there should not be any spaces
+# before the keyword.
+#
+# Non-default parameters to be used for patchtest 1.
+#
+# Scaling factors applied to Winkler forces.  These factors may be
+# used as a quick and easy way of changing the density or gravitational
+# acceleration when Winkler forces are used to simulate gravity.
+#
+#winklerScaleX = 1.0
+#winklerScaleY = 1.0
+#winklerScaleZ = 1.0
+#
+#
+# Parameters controlling stress integration and numerical computation
+# of the tangent material matrix.  These default values should be
+# reasonable for most cases.
+#
+#stressTolerance = 1.0e-12*Pa
+#minimumStrainPerturbation = 1.0e-7
+#initialStrainPerturbation = 1.0e-1
+#
+#
+# Parameters controlling the solution of the linear problem at each
+# iteration.  At present, the only solution method is preconditioned
+# conjugate gradients.  The user can select the preconditioner type,
+# the maximum number of iterations, and the factors controlling
+# convergence.  Preconditioner types are as follows:
+#    diagonalNoUpdate:      Diagonal preconditioning with an initial
+#                           guess of zero for the displacement vector.
+#    gaussSeidelNoUpdate:   Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess of zero for the displacement
+#                           vector.
+#    diagonalUpdate:        Diagonal preconditioning with an initial
+#                           guess for the displacement vector corresponding
+#                           to the displacement vector from the previous
+#                           time step.
+#    gaussSeidelUpdate:     Symmetrized Gauss-Seidel preconditioner with
+#                           an initial guess for the displacement vector
+#                           corresponding to the displacement vector from
+#                           the previous time step.
+#
+#    Note that the diagonal preconditioners generally require more iterations,
+#    but at less computational cost per iteration.  In theory, the more
+#    complex preconditioner should work better for more irregular meshes.
+#
+#preconditionerType = "diagonalNoUpdate"
+#maxPcgIterations = 3000
+#displacementAccuracyMult = 1.0
+#forceAccuracyMult = 1.0
+#energyAccuracyMult = 1.0
+#minDisplacementAccuracy = 1.0e-8
+#minForceAccuracy = 1.0e-8
+#minEnergyAccuracy = 1.0e-14
+#
+#
+# Quadrature order for the problem.  The options are:
+#	Full:		Quadrature order that should give the exact
+#			element matrices when the elements are
+#			geometrically undistorted.
+#	Reduced:	Quadrature order that is one order less than
+#			full quadrature.  This option should be used
+#			with caution.
+#	Selective:	Uses Hughes' b-bar formulation to perform
+#			reduced quadrature on the dilatational parts of
+#			the strain-displacement matrix.  This can be
+#			useful in nearly-incompressible problems.
+#
+#quadratureOrder = Full
+#
+#
+# Gravitational acceleration in each direction.
+#
+#gravityX = 0.0*m/(s*s)
+#gravityY = 0.0*m/(s*s)
+#gravityZ = 0.0*m/(s*s)
+#
+#
+# Factors controlling computation of prestresses.  When gravity is being
+# used, an automatic computation option may be used, using an alternate
+# value for Poisson's ratio.  If prestressAutoComputePoisson is set to a
+# negative value, the original Poisson's ratio is used.  Each prestress
+# component may also be scaled.  This option is only useful if the
+# prestresses are read from a file (and not automatically computed).
+#
+#prestressAutoCompute = False
+#prestressAutoComputePoisson = -0.49
+#prestressScaleXx = 1.0
+#prestressScaleYy = 1.0
+#prestressScaleZz = 1.0
+#prestressScaleXy = 1.0
+#prestressScaleXz = 1.0
+#prestressScaleYz = 1.0
+#
+#
+# Scaling factors applied to differential Winkler forces.  Differential
+# Winkler forces are those applied across a slippery node interface, and
+# are generally used to keep the fault locked at certain times.  These
+# factors control the magnitudes and provide a simple way of scaling the
+# forces so the fault remains sufficiently 'locked'.
+#
+#winklerSlipScaleX = 1.0
+#winklerSlipScaleY = 1.0
+#winklerSlipScaleZ = 1.0
+#
+#
+# Unit numbers used by f77.  These defaults should work for most Unix
+# systems, but may be altered if necessary.
+#
+#f77StandardInput = 5
+#f77StandardOutput = 6
+#f77FileInput = 10
+#f77AsciiOutput = 11
+#f77PlotOutput = 12

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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-bbar-comp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt1.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt2.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt3.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt4.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt5.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt6.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt7.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt8.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt9.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt10.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt11.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt12.bc --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-bbar-incomp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Selective --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-full-comp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 --pl3dscan.bcInputFile=pt1.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt2.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt3.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt4.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt5.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt6.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt7.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt8.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt9.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt10.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt11.bc --pl3dscan.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 --pl3dscan.bcInputFile=pt12.bc --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-full-incomp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-red-comp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt1.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt2.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt3.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt4.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt5.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt6.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt7.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt8.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt9.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt10.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt11.bc --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt12.bc --pl3dscan.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	2007-02-28 01:29:08 UTC (rev 6126)
+++ short/3D/PyLith/branches/pylith-0.8/pylith3d/examples/quadtet/patchtest/runtests-red-incomp.com	2007-02-28 01:54:26 UTC (rev 6127)
@@ -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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt1.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt2.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt3.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt4.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt5.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt6.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt7.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt8.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt9.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt10.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt11.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.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 --pl3dscan.quadratureOrder=Reduced --pl3dscan.bcInputFile=pt12.bc --pl3dscan.materialPropertiesInputFile=pt-incomp.prop --pl3dscan.asciiOutputFile=pt12-red-incomp.ascii
 /bin/rm pt1.plot