[cig-commits] r18529 - in short/3D/PyLith/trunk/examples/3d/tet4: . mesh output spatialdb

brad at geodynamics.org brad at geodynamics.org
Thu Jun 2 15:57:10 PDT 2011


Author: brad
Date: 2011-06-02 15:57:09 -0700 (Thu, 02 Jun 2011)
New Revision: 18529

Added:
   short/3D/PyLith/trunk/examples/3d/tet4/mesh/
   short/3D/PyLith/trunk/examples/3d/tet4/mesh/mesh_tet4_1000m.lagrit
   short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4-mesh.jpg
   short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4_1000m_ascii.gmv
   short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4_1000m_ascii.pset
   short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4_1000m_binary.gmv
   short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4_1000m_binary.pset
   short/3D/PyLith/trunk/examples/3d/tet4/output/
   short/3D/PyLith/trunk/examples/3d/tet4/output/Makefile.am
   short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/
   short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/finalslip.spatialdb
   short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/fixeddisp_shear.spatialdb
   short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/mat_elastic.spatialdb
   short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/mat_viscoelastic.spatialdb
   short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/sliptime.spatialdb
   short/3D/PyLith/trunk/examples/3d/tet4/step01.cfg
   short/3D/PyLith/trunk/examples/3d/tet4/step01.jpg
   short/3D/PyLith/trunk/examples/3d/tet4/step02.cfg
   short/3D/PyLith/trunk/examples/3d/tet4/step03.cfg
   short/3D/PyLith/trunk/examples/3d/tet4/step03.jpg
   short/3D/PyLith/trunk/examples/3d/tet4/step04.cfg
Removed:
   short/3D/PyLith/trunk/examples/3d/tet4/dislocation.cfg
   short/3D/PyLith/trunk/examples/3d/tet4/dislocation.jpg
   short/3D/PyLith/trunk/examples/3d/tet4/finalslip.spatialdb
   short/3D/PyLith/trunk/examples/3d/tet4/fixeddisp_shear.spatialdb
   short/3D/PyLith/trunk/examples/3d/tet4/mat_elastic.spatialdb
   short/3D/PyLith/trunk/examples/3d/tet4/mat_viscoelastic.spatialdb
   short/3D/PyLith/trunk/examples/3d/tet4/mesh_tet4_1000m.lagrit
   short/3D/PyLith/trunk/examples/3d/tet4/shear.jpg
   short/3D/PyLith/trunk/examples/3d/tet4/shearxy.cfg
   short/3D/PyLith/trunk/examples/3d/tet4/sliptime.spatialdb
   short/3D/PyLith/trunk/examples/3d/tet4/tet4-mesh.jpg
   short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_ascii.gmv
   short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_ascii.pset
   short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_binary.gmv
   short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_binary.pset
Modified:
   short/3D/PyLith/trunk/examples/3d/tet4/Makefile.am
   short/3D/PyLith/trunk/examples/3d/tet4/README
   short/3D/PyLith/trunk/examples/3d/tet4/pylithapp.cfg
Log:
Added field split and global refinement. Split example into four steps.

Modified: short/3D/PyLith/trunk/examples/3d/tet4/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/Makefile.am	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/Makefile.am	2011-06-02 22:57:09 UTC (rev 18529)
@@ -18,21 +18,25 @@
 
 dist_noinst_DATA = \
 	README \
-	dislocation.cfg \
-	dislocation.jpg \
-	finalslip.spatialdb \
-	fixeddisp_shear.spatialdb \
-	mat_elastic.spatialdb \
-	mat_viscoelastic.spatialdb \
-	mesh_tet4_1000m.lagrit \
 	pylithapp.cfg \
-	shear.jpg \
-	shearxy.cfg \
-	sliptime.spatialdb \
-	tet4-mesh.jpg \
-	tet4_1000m_ascii.gmv \
-	tet4_1000m_ascii.pset \
-	tet4_1000m_binary.gmv \
-	tet4_1000m_binary.pset
+	step01.cfg \
+	step03.cfg \
+	step01.jpg \
+	step03.jpg \
+	mesh/mesh_tet4_1000m.lagrit \
+	mesh/tet4_1000m_ascii.gmv \
+	mesh/tet4_1000m_ascii.pset \
+	mesh/tet4_1000m_binary.gmv \
+	mesh/tet4_1000m_binary.pset \
+	mesh/tet4-mesh.jpg \
+	spatialdb/finalslip.spatialdb \
+	spatialdb/fixeddisp_shear.spatialdb \
+	spatialdb/mat_elastic.spatialdb \
+	spatialdb/mat_viscoelastic.spatialdb \
+	spatialdb/sliptime.spatialdb
 
+SUBDIRS = \
+	output
+
+
 # End of file 

Modified: short/3D/PyLith/trunk/examples/3d/tet4/README
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/README	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/README	2011-06-02 22:57:09 UTC (rev 18529)
@@ -1,8 +1,9 @@
-The examples in this directory include (1) simple shearing of a box,
-(2) slip on a through-going, vertical, strike-slip fault in a
-box, (3) a box subjected to body forces, and (4) a box subjected to body
-forces where initial stresses are used to prevent deformation. In each
-problem the domain is 6 km x 6 km x 4 km and is discretized with linear
+The examples in this directory form a step-by-step sequence of 4
+problems, each building on the one before. All of the examples use the
+same mesh, which was created using LaGriT. The first two problems
+involve simple shearing of a box, and the second two problems involve
+slip on a through-going, vertical, strike-slip fault in a box. The
+domain is 6 km x 6 km x 4 km and is discretized with linear
 tetrahedral cells that have edges nominally 1.0 km long.
 
 The box spans the volume:
@@ -11,44 +12,84 @@
   -3 km <= y <= +3 km
   -6 km <= z <= 0  km.
 
-The mesh is generated using LaGrit. A LaGrit script is included and is
-annotated to guide you through the process of generating the mesh.
+A LaGrit script is included and is annotated to guide you through the
+process of generating the mesh.
 
-See the configuration files shearxy.cfg and dislocation.cfg for
+See the configuration files step01.cfg and dislocation.cfg for
 instructions on how to run these simulations. The configuration files
 also contain information about the simulation parameters.
 
+The examples are all described in the PyLith manual. Output from each
+example is put in the output directory. Each simulation may be run by
+typing:
 
+  pylith stepxx.cfg
+
+where xx is the number of the desired example.
+
+
+----------------------------------------------------------------------
 DESCRIPTION OF FILES
+----------------------------------------------------------------------
 
-dislocation.cfg - Simulation parameters for strike-slip fault problem.
+README - This file.
 
-finalslip.spatialdb - Spatial database for spatial variation of final slip
+pylithapp.cfg - PyLith configuration file containing parameters common to
+all simulations.
 
-fixeddisp_shear.spatialdb - Spatial database for spatial variation of
-the displacement field in the Dirichlet (prescribed displacement)
-boundary conditions for the shear problem
+stepxx.cfg - PyLith configuration file containing parameters for a
+particular example. The example problems are briefly described below:
 
-mat_elastic.spatialdb - Spatial database for spatial variation of the
-elastic material properties
+step01: Dirichlet BC (static) causing shear.
+step02: step01 with mesh refinement and field split preconditioning.
+step03: DirichletBC with fault slip (static) Slip on a vertical fault
+step04: step03 with mesh refinement and field split preconditioning.
 
-mesh_tet4_1000m.lagrit - LaGriT script to generate the mesh
+----------------------------------------
+figures directory
+----------------------------------------
 
-pylithapp.cfg - General simulation parameters for the mesh
+tet4-mesh.jpg - JPEG image showing mesh (from ParaView)
 
-shearxy.cfg - Simulation parameters for the shear problem
 
-sliprate.spatialdb - Spatial database for spatial variation of peak slip rate
+----------------------------------------
+mesh directory
+----------------------------------------
 
-sliptime.spatialdb - Spatial database for spatial variation of slip
-initiation time
+mesh/mesh_tet4_1000m.lagrit - LaGriT script used to generate mesh
 
-tet4_1000m_ascii.gmv - ASCII GMV file containing the finite-element mesh
+mesh/tet4_1000m_ascii.gmv - ASCII GMV file containing node and elements
+mesh/tet4_1000m_ascii.pset - ASCII file containing point sets
 
-tet4_1000m_ascii.pset - ASCII Pset file containing the psets in the
-finite-element mesh
+mesh/tet4_1000m_binary.gmv - Binary GMV file containing node and elements
+mesh/tet4_1000m_binary.pset - Binary file containing point sets
 
-tet4_1000m_binary.gmv - Binary GMV file containing the finite-element mesh
+----------------------------------------
+spatialdb directory
+----------------------------------------
 
-tet4_1000m_binary.pset - ASCII Pset file containing the psets in the
-finite-element mesh
+fixeddisp_shear.spatialdb
+
+  Spatial database for spatial variation of the displacement field in
+  the Dirichlet (prescribed displacement) boundary conditions for the
+  shear problem (step01 and step02).
+
+mat_elastic.spatialdb
+
+  Spatial database for spatial variation of the elastic material
+  properties
+
+mat_viscoelastic.spatialdb
+
+  Spatial database for spatial variation of the Maxwell viscoelastic
+  properties.
+
+finalslip.spatialdb
+
+  Spatial database for spatial variation of final slip (step03 and
+  step04)
+
+sliptime.spatialdb
+
+  Spatial database for spatial variation of slip initiation time
+  (step03 and step04)

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/dislocation.cfg
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/dislocation.cfg	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/dislocation.cfg	2011-06-02 22:57:09 UTC (rev 18529)
@@ -1,100 +0,0 @@
-# -*- Python -*-
-[pylithapp]
-
-# This is not a self-contained simulation configuration file. This
-# file only specifies parameters specific to the boundary and
-# interface conditions. The general parameters are specificed in the
-# pylithapp.cfg file which is read by default.
-#
-# To run the simulation:
-# pylith dislocation.cfg
-
-# ----------------------------------------------------------------------
-# problem
-# ----------------------------------------------------------------------
-[pylithapp.timedependent]
-# Set the BC to an array with 2 boundary conditions.
-bc = x_pos,x_neg
-
-# Set the interfaces to an array with 1 fault.
-interfaces = fault
-
-[pylithapp.timedependent.implicit]
-# Set the output to an array of 2 output managers.
-# We will output the solution over the domain and the ground surface.
-output = [domain,subdomain]
-
-# Set subdomain component to OutputSolnSubset (subset of domain).
-output.subdomain = pylith.meshio.OutputSolnSubset
-
-# ----------------------------------------------------------------------
-# boundary conditions
-# ----------------------------------------------------------------------
-
-# We use the default spatial database for the Dirichlet BC which sets
-# the displacements to zero for all time.
-#
-# Set the parameters for the desired boundary conditions. Note that we
-# only use a subset of the boundary conditions provided in the 6 BC
-# container.
-#
-# Note: A more natural set of boundary conditions involves pinning the
-# z-DOF on the bottom (-z) face. Howver, the current release of PyLith
-# does not permit overlapping fault interfaces and Dirichlet boundary
-# conditions with the block Jacobi preconditioner.
-
-# The label corresponds to the label in LaGriT.
-
-[pylithapp.timedependent.bc.x_pos]
-bc_dof = [0, 1, 2]
-label = boundary_xp
-db_initial.label = Dirichlet BC on +x
-
-[pylithapp.timedependent.bc.x_neg]
-bc_dof = [0, 1, 2]
-label = boundary_xm
-db_initial.label = Dirichlet BC on -x
-
-# ----------------------------------------------------------------------
-# faults
-# ----------------------------------------------------------------------
-[pylithapp.timedependent.interfaces]
-# Set the type of fault interface condition.
-fault = pylith.faults.FaultCohesiveKin
-
-# Set the parameters for the fault interface condition.
-
-[pylithapp.timedependent.interfaces.fault]
-label = fault
-quadrature.cell = pylith.feassemble.FIATSimplex
-quadrature.cell.shape = triangle
-
-[pylithapp.timedependent.interfaces.fault.eq_srcs.rupture.slip_function]
-slip.iohandler.filename = finalslip.spatialdb
-slip_time.iohandler.filename = sliptime.spatialdb
-
-
-# ----------------------------------------------------------------------
-# output
-# ----------------------------------------------------------------------
-# Set the root name for output.
-[pylithapp.problem.formulation.output.domain.writer]
-filename = dislocation.vtk
-
-# Give basename for VTK domain output of solution over ground surface.
-[pylithapp.problem.formulation.output.subdomain]
-label = boundary_zp
-writer.filename = dislocation-groundsurf.vtk
-
-# Give basename for vtk fault output.
-[pylithapp.timedependent.interfaces.fault.output]
-writer.filename = dislocation-fault.vtk
-
-# Give basename for VTK output of state variables.
-[pylithapp.timedependent.materials.elastic.output]
-cell_filter = pylith.meshio.CellFilterAvgMesh
-writer.filename = dislocation-elastic.vtk
-
-[pylithapp.timedependent.materials.viscoelastic.output]
-cell_filter = pylith.meshio.CellFilterAvgMesh
-writer.filename = dislocation-viscoelastic.vtk

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/dislocation.jpg
===================================================================
(Binary files differ)

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/finalslip.spatialdb
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/finalslip.spatialdb	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/finalslip.spatialdb	2011-06-02 22:57:09 UTC (rev 18529)
@@ -1,31 +0,0 @@
-// -*- C++ -*- (tell Emacs to use C++ mode for syntax highlighting)
-//
-// This spatial database specifies the distribution of slip on the
-// fault surface. In this case we prescribe a piecewise linear, depth
-// dependent distribution of slip. The slip is 2.0 m right-lateral
-// with 0.25 m of reverse slip at the surface with a linear taper from
-// 2.0 m to 0.0 m from -2 km to -4 km.
-//
-#SPATIAL.ascii 1
-SimpleDB {
-  num-values = 3
-  value-names =  left-lateral-slip  reverse-slip  fault-opening
-  value-units =  m  m  m
-  num-locs = 3
-  data-dim = 1 // Locations of data points form a line.
-  space-dim = 3
-  cs-data = cartesian {
-    to-meters = 1.0e+3 // Specify coordinates in km for convenience.
-    space-dim = 3
-  } // cs-data
-} // SimpleDB
-// Columns are
-// (1) x coordinate (km)
-// (2) y coordinate (km)
-// (3) z coordinate (km)
-// (4) left-lateral-slip (m) (right-lateral is negative)
-// (5) reverse-slip (m)
-// (6) fault-opening (m)
-0.0  0.0  0.0    -2.00  0.25  0.00
-0.0  0.0 -2.0    -2.00  0.00  0.00
-0.0  0.0 -4.0     0.00  0.00  0.00

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/fixeddisp_shear.spatialdb
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/fixeddisp_shear.spatialdb	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/fixeddisp_shear.spatialdb	2011-06-02 22:57:09 UTC (rev 18529)
@@ -1,32 +0,0 @@
-// -*- C++ -*- (tell Emacs to use C++ mode for syntax highlighting)
-//
-// This spatial database specifies the distribution of the
-// displacement field for Dirichlet boundary conditions associated
-// with shear in the xy plane.
-//
-// dof-0: Ux(x) = 0
-// dof-1: Uy(x) = 1.0 m * x / 3 km
-// dof-2: Uz(x) = 0
-//
-#SPATIAL.ascii 1
-SimpleDB {
-  num-values = 3
-  value-names =  displacement-x  displacement-y  displacement-z
-  value-units =  m  m  m
-  num-locs = 2
-  data-dim = 1 // locations form a line
-  space-dim = 3
-  cs-data = cartesian {
-    to-meters = 1.0e+3 // specify coordinates in km
-    space-dim = 3
-  }
-}
-// Columns are
-// (1) x coordinate (km)
-// (2) y coordinate (km)
-// (3) z coordinate (km)
-// (4) Ux (m)
-// (5) Uy (m)
-// (6) Uz (m)
--3.0  0.0  0.0    0.0  -1.0  0.0
-+3.0  0.0  0.0    0.0  +1.0  0.0

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/mat_elastic.spatialdb
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/mat_elastic.spatialdb	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/mat_elastic.spatialdb	2011-06-02 22:57:09 UTC (rev 18529)
@@ -1,26 +0,0 @@
-// -*- C++ -*- (tell Emacs to use C++ mode for syntax highlighting)
-//
-// This spatial database specifies the distribution of material
-// properties. In this case, the material properties are uniform.
-//
-#SPATIAL.ascii 1
-SimpleDB {
-  num-values = 3 // number of material property values
-  value-names =  density vs vp // names of the material property values
-  value-units =  kg/m**3  m/s  m/s
-  num-locs = 1 // number of locations
-  data-dim = 0
-  space-dim = 3
-  cs-data = cartesian {
-    to-meters = 1.0
-    space-dim = 3
-  }
-}
-// Columns are
-// (1) x coordinate (m)
-// (2) y coordinate (m)
-// (3) z coordinate (m)
-// (4) density (kg/m^3)
-// (5) vs (m/s)
-// (6) vp (m/s)
-0.0  0.0  0.0   2500.0  3000.0  5291.502622129181

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/mat_viscoelastic.spatialdb
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/mat_viscoelastic.spatialdb	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/mat_viscoelastic.spatialdb	2011-06-02 22:57:09 UTC (rev 18529)
@@ -1,30 +0,0 @@
-// -*- C++ -*- (tell Emacs to use C++ mode for syntax highlighting)
-//
-// This spatial database specifies the distribution of material
-// properties for a Maxwell viscoelastic material. In this case,
-// the material properties are uniform.
-//
-// The viscosity corresponds to a Maxwell time of 100 years.
-//
-#SPATIAL.ascii 1
-SimpleDB {
-  num-values = 4 // number of material property values
-  value-names =  density vs vp viscosity // names of the material property values
-  value-units =  kg/m**3  m/s  m/s Pa*s
-  num-locs = 1 // number of locations
-  data-dim = 0
-  space-dim = 3
-  cs-data = cartesian {
-    to-meters = 1.0
-    space-dim = 3
-  }
-}
-// Columns are
-// (1) x coordinate (m)
-// (2) y coordinate (m)
-// (3) z coordinate (m)
-// (4) density (kg/m**3)
-// (5) vs (m/s)
-// (6) vp (m/s)
-// (7) viscosity (Pa*s)
-0.0  0.0  0.0   2500.0  3000.0  5291.502622129181 7.10046e+19

Copied: short/3D/PyLith/trunk/examples/3d/tet4/mesh/mesh_tet4_1000m.lagrit (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/mesh_tet4_1000m.lagrit)
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/mesh/mesh_tet4_1000m.lagrit	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/mesh/mesh_tet4_1000m.lagrit	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,232 @@
+* -*- LaGriT -*-
+*
+* Mesh of a box with a through-going, vertical, strike-slip fault.
+*
+* Block is 6 km x 6 km x 4 km
+* -3 km <= x <= 3 km
+* -3 km <= y <= 3 km
+* -4 km <= z <= 0 km
+* 
+* The domain is constructed with the region command after constructing the
+* boundaries of the domain using the surface command with the plane
+* attribute (construct the 3-D domain from boundary surfaces). The
+* fault plane is also a plane.
+*
+* ----------------------------------------------------------------------
+* PARAMETERS CONTROLLING MESH
+* ----------------------------------------------------------------------
+*
+* Boundaries of domain
+define / domain_xm / -3.0e+3
+define / domain_xp /  3.0e+3
+define / domain_ym / -3.0e+3
+define / domain_yp /  3.0e+3
+define / domain_zm / -4.0e+3
+define / domain_zp /  0.0e+3
+*
+* Mesh size and number of points along x & y
+define / dx / 1000.0
+define / nx / 7
+define / ny / 7
+*
+* ----------------------------------------------------------------------
+* CREATE GEOMETRY
+* ----------------------------------------------------------------------
+*
+* Create a mesh object and name it box
+cmo / create / box /
+*
+* Create boundary surfaces
+surface / surf_xm / reflect / plane / &
+   domain_xm   0.0e+0   0.0e+0 / &
+   domain_xm   0.0e+0  10.0e+3 / &
+   domain_xm  10.0e+3   0.0e+0
+surface / surf_xp / reflect / plane / &
+    domain_xp   0.0e+0   0.0e+0 / &
+    domain_xp  10.0e+3   0.0e+0 / &
+    domain_xp   0.0e+0  10.0e+3
+surface / surf_ym / reflect / plane / &
+     0.0e+0  domain_ym   0.0e+0 / &
+     0.0e+0  domain_ym  10.0e+3 / &
+   -10.0e+3  domain_ym   0.0e+0
+surface / surf_yp / reflect / plane / &
+     0.0e+0   domain_yp   0.0e+0 / &
+   -10.0e+3   domain_yp   0.0e+0 / &
+     0.0e+0   domain_yp  10.0e+3
+surface / surf_zm / reflect / plane / &
+     0.0e+0    0.0e+0  domain_zm / &
+   -10.0e+3    0.0e+0  domain_zm / &
+     0.0e+0   10.0e+3  domain_zm
+surface / surf_zp / reflect / plane / &
+     0.0e+0    0.0e+0    domain_zp / &
+     0.0e+0   10.0e+3    domain_zp / &
+   -10.0e+3    0.0e+0    domain_zp
+*
+* Create fault plane
+surface / surf_fault / intrface / plane / &
+  0.0  0.0  0.0 / &
+  0.0  1.0  0.0 / &
+  0.0  0.0  1.0 /
+* Create material interface
+surface / surf_mantle / intrface / plane / &
+  0.0  0.0  -2.0e+3 / &
+  1.0  0.0  -2.0e+3 / &
+  0.0  1.0  -2.0e+3 /
+
+* ----------------------------------------------------------------------
+* Create regions
+* ----------------------------------------------------------------------
+
+** Elastic on +x side of fault
+region / r_elastic_pos / &
+  le surf_xp and ge surf_fault  &
+  and le surf_yp and le surf_ym  &
+  and le surf_zp and ge surf_mantle /
+
+** Elastic on -x side of the fault
+region / r_elastic_neg / &
+  le surf_xm and lt surf_fault  &
+  and le surf_yp and le surf_ym  &
+  and le surf_zp and ge surf_mantle /
+
+** Viscoelastic on +x side of the fault
+region / r_visco_pos / &
+  le surf_xp and ge surf_fault  &
+  and le surf_yp and le surf_ym  &
+  and lt surf_mantle and le surf_zm /
+
+** Viscoelastic on -x side of the fault
+region / r_visco_neg / &
+  le surf_xm and lt surf_fault  &
+  and le surf_yp and le surf_ym  &
+  and lt surf_mantle and le surf_zm /
+
+* ----------------------------------------------------------------------
+* Create material regions
+* ----------------------------------------------------------------------
+* Material regions do not include internal interfaces (regions do)
+*
+mregion / mr_elastic_pos / &
+  le surf_xp and gt surf_fault  &
+  and le surf_yp and le surf_ym  &
+  and le surf_zp and gt surf_mantle /
+mregion / mr_elastic_neg / &
+  le surf_xm and lt surf_fault  &
+  and le surf_yp and le surf_ym  &
+  and le surf_zp and gt surf_mantle /
+mregion / mr_visco_pos / &
+  le surf_xp and gt surf_fault  &
+  and le surf_yp and le surf_ym  &
+  and lt surf_mantle and le surf_zm /
+mregion / mr_visco_neg / &
+  le surf_xm and lt surf_fault  &
+  and le surf_yp and le surf_ym  &
+  and lt surf_mantle and le surf_zm /
+*
+* ----------------------------------------------------------------------
+* CREATE MESH
+* ----------------------------------------------------------------------
+*
+createpts / xyz / nx,ny,1 / &
+  domain_xm  domain_ym  domain_zp / &
+  domain_xp  domain_yp  domain_zp / &
+  1,1,0 /
+pset / rayend / seq / 0,0,0
+*
+
+loop / foreach / iregion / &
+  r_elastic_pos r_elastic_neg r_visco_pos r_visco_neg &
+  / loop_end / &
+  regnpts / iregion / dx / pset,get,rayend / xyz / &
+    0.0e+3  0.0e+3  domain_zm / &
+    0.0e+3  1.0e+3  domain_zm / &
+    1.0e+3  0.0e+3  domain_zm / &
+    0,0
+cmo/setatt//itp/pset,get,rayend/dud
+pset / rayend / delete
+
+* ----------------------------------------------------------------------
+* Remove duplicate points
+* ----------------------------------------------------------------------
+filter / 1,0,0 / 10.0
+rmpoint / compress
+
+* ----------------------------------------------------------------------
+* Set node type and material
+* ----------------------------------------------------------------------
+setpts
+
+* ----------------------------------------------------------------------
+* Connect the points into a Delaunay tetrahedral mesh
+* ----------------------------------------------------------------------
+connect
+
+* ----------------------------------------------------------------------
+* Set elements to tetrahedra
+* ----------------------------------------------------------------------
+settets / geometry
+resetpts/cell_color
+
+* Remove parent/child hierarchy
+resetpts
+rmpoint / compress
+*
+* ----------------------------------------------------------------------
+* MESH QUALITY
+* ----------------------------------------------------------------------
+*
+quality
+*
+* ----------------------------------------------------------------------
+* IDENTIFY GROUPS
+* ----------------------------------------------------------------------
+*
+* Identify nodes on fault surface
+pset / fault / surface / surf_fault /
+*
+* Identify nodes on boundaries
+pset / boundary_xm / surface / surf_xm /
+pset / boundary_xp / surface / surf_xp /
+pset / boundary_ym / surface / surf_ym /
+pset / boundary_yp / surface / surf_yp /
+pset / boundary_zm / surface / surf_zm /
+pset / boundary_zp / surface / surf_zp /
+*
+* ----------------------------------------------------------------------
+* MERGE MATERIALS
+* ----------------------------------------------------------------------
+eltset / elastic1 / itetclr / eq / 1
+eltset / elastic2 / itetclr / eq / 2
+eltset / elastic / union / elastic1 elastic2
+cmo / setatt / box / itetclr / eltset,get,elastic / 1
+eltset / elastic1 / delete
+eltset / elastic2 / delete
+eltset / elastic / delete
+
+eltset / visco1 / itetclr / eq / 3
+eltset / visco2 / itetclr / eq / 4
+eltset / visco / union / visco1 visco2
+cmo / setatt / box / itetclr / eltset,get,visco / 2
+eltset / visco1 / delete
+eltset / visco2 / delete
+eltset / visco / delete
+cmo / printatt / box / itetclr / minmax
+
+* ----------------------------------------------------------------------
+* WRITE MESH
+* ----------------------------------------------------------------------
+*
+* Export mesh and psets to files.
+cmo / setatt / box / ipolydat / no
+dump / gmv / tet4_1000m_binary.gmv / / binary
+dump / gmv / tet4_1000m_ascii.gmv / / ascii
+
+pset / -all- / write / tet4_1000m_ascii.pset / ascii
+pset / -all- / write / tet4_1000m_binary.pset / binary
+
+*
+* Terminate processing
+finish
+
+* ======================================================================
+* End of file

Copied: short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4-mesh.jpg (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/tet4-mesh.jpg)
===================================================================
(Binary files differ)

Copied: short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4_1000m_ascii.gmv (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_ascii.gmv)
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4_1000m_ascii.gmv	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4_1000m_ascii.gmv	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,1109 @@
+gmvinput ascii
+codename LaGriT
+simdate  /19/08
+nodes          245
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+cells          852
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+endvars
+flags    
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+mr_elast
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+cycleno          0
+probtime   0.00000E+000
+endgmv

Copied: short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4_1000m_ascii.pset (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_ascii.pset)
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4_1000m_ascii.pset	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4_1000m_ascii.pset	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,38 @@
+pset ascii         7
+fault    1         35
+         1          2          3         13         14         15         25         26         27         37
+        38         39         49         50         51         61         62         63         73         74
+        75        148        149        156        157        164        165        172        173        180
+       181        188        189        196        197
+boundary_xm    2         35
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+       113        114        121        122        123        130        131        132        139        140
+       141        204        205        210        211        216        217        222        223        228
+       229        234        235        240        241
+boundary_xp    3         35
+        10         11         12         22         23         24         34         35         36         46
+        47         48         58         59         60         70         71         72         82         83
+        84        154        155        162        163        170        171        178        179        186
+       187        194        195        202        203
+boundary_ym    4         35
+         1          2          3          4          5          6          7          8          9         10
+        11         12         85         86         87         88         89         90         91         92
+        93        148        149        150        151        152        153        154        155        204
+       205        206        207        208        209
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+       147        196        197        198        199        200        201        202        203        240
+       241        242        243        244        245
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+       208        210        212        214        216        218        220        222        224        226
+       228        230        232        234        236        238        240        242        244
+boundary_zp    7         49
+         3          6          9         12         15         18         21         24         27         30
+        33         36         39         42         45         48         51         54         57         60
+        63         66         69         72         75         78         81         84         87         90
+        93         96         99        102        105        108        111        114        117        120
+       123        126        129        132        135        138        141        144        147

Copied: short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4_1000m_binary.gmv (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_binary.gmv)
===================================================================
(Binary files differ)

Copied: short/3D/PyLith/trunk/examples/3d/tet4/mesh/tet4_1000m_binary.pset (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_binary.pset)
===================================================================
(Binary files differ)

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/mesh_tet4_1000m.lagrit
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/mesh_tet4_1000m.lagrit	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/mesh_tet4_1000m.lagrit	2011-06-02 22:57:09 UTC (rev 18529)
@@ -1,232 +0,0 @@
-* -*- LaGriT -*-
-*
-* Mesh of a box with a through-going, vertical, strike-slip fault.
-*
-* Block is 6 km x 6 km x 4 km
-* -3 km <= x <= 3 km
-* -3 km <= y <= 3 km
-* -4 km <= z <= 0 km
-* 
-* The domain is constructed with the region command after constructing the
-* boundaries of the domain using the surface command with the plane
-* attribute (construct the 3-D domain from boundary surfaces). The
-* fault plane is also a plane.
-*
-* ----------------------------------------------------------------------
-* PARAMETERS CONTROLLING MESH
-* ----------------------------------------------------------------------
-*
-* Boundaries of domain
-define / domain_xm / -3.0e+3
-define / domain_xp /  3.0e+3
-define / domain_ym / -3.0e+3
-define / domain_yp /  3.0e+3
-define / domain_zm / -4.0e+3
-define / domain_zp /  0.0e+3
-*
-* Mesh size and number of points along x & y
-define / dx / 1000.0
-define / nx / 7
-define / ny / 7
-*
-* ----------------------------------------------------------------------
-* CREATE GEOMETRY
-* ----------------------------------------------------------------------
-*
-* Create a mesh object and name it box
-cmo / create / box /
-*
-* Create boundary surfaces
-surface / surf_xm / reflect / plane / &
-   domain_xm   0.0e+0   0.0e+0 / &
-   domain_xm   0.0e+0  10.0e+3 / &
-   domain_xm  10.0e+3   0.0e+0
-surface / surf_xp / reflect / plane / &
-    domain_xp   0.0e+0   0.0e+0 / &
-    domain_xp  10.0e+3   0.0e+0 / &
-    domain_xp   0.0e+0  10.0e+3
-surface / surf_ym / reflect / plane / &
-     0.0e+0  domain_ym   0.0e+0 / &
-     0.0e+0  domain_ym  10.0e+3 / &
-   -10.0e+3  domain_ym   0.0e+0
-surface / surf_yp / reflect / plane / &
-     0.0e+0   domain_yp   0.0e+0 / &
-   -10.0e+3   domain_yp   0.0e+0 / &
-     0.0e+0   domain_yp  10.0e+3
-surface / surf_zm / reflect / plane / &
-     0.0e+0    0.0e+0  domain_zm / &
-   -10.0e+3    0.0e+0  domain_zm / &
-     0.0e+0   10.0e+3  domain_zm
-surface / surf_zp / reflect / plane / &
-     0.0e+0    0.0e+0    domain_zp / &
-     0.0e+0   10.0e+3    domain_zp / &
-   -10.0e+3    0.0e+0    domain_zp
-*
-* Create fault plane
-surface / surf_fault / intrface / plane / &
-  0.0  0.0  0.0 / &
-  0.0  1.0  0.0 / &
-  0.0  0.0  1.0 /
-* Create material interface
-surface / surf_mantle / intrface / plane / &
-  0.0  0.0  -2.0e+3 / &
-  1.0  0.0  -2.0e+3 / &
-  0.0  1.0  -2.0e+3 /
-
-* ----------------------------------------------------------------------
-* Create regions
-* ----------------------------------------------------------------------
-
-** Elastic on +x side of fault
-region / r_elastic_pos / &
-  le surf_xp and ge surf_fault  &
-  and le surf_yp and le surf_ym  &
-  and le surf_zp and ge surf_mantle /
-
-** Elastic on -x side of the fault
-region / r_elastic_neg / &
-  le surf_xm and lt surf_fault  &
-  and le surf_yp and le surf_ym  &
-  and le surf_zp and ge surf_mantle /
-
-** Viscoelastic on +x side of the fault
-region / r_visco_pos / &
-  le surf_xp and ge surf_fault  &
-  and le surf_yp and le surf_ym  &
-  and lt surf_mantle and le surf_zm /
-
-** Viscoelastic on -x side of the fault
-region / r_visco_neg / &
-  le surf_xm and lt surf_fault  &
-  and le surf_yp and le surf_ym  &
-  and lt surf_mantle and le surf_zm /
-
-* ----------------------------------------------------------------------
-* Create material regions
-* ----------------------------------------------------------------------
-* Material regions do not include internal interfaces (regions do)
-*
-mregion / mr_elastic_pos / &
-  le surf_xp and gt surf_fault  &
-  and le surf_yp and le surf_ym  &
-  and le surf_zp and gt surf_mantle /
-mregion / mr_elastic_neg / &
-  le surf_xm and lt surf_fault  &
-  and le surf_yp and le surf_ym  &
-  and le surf_zp and gt surf_mantle /
-mregion / mr_visco_pos / &
-  le surf_xp and gt surf_fault  &
-  and le surf_yp and le surf_ym  &
-  and lt surf_mantle and le surf_zm /
-mregion / mr_visco_neg / &
-  le surf_xm and lt surf_fault  &
-  and le surf_yp and le surf_ym  &
-  and lt surf_mantle and le surf_zm /
-*
-* ----------------------------------------------------------------------
-* CREATE MESH
-* ----------------------------------------------------------------------
-*
-createpts / xyz / nx,ny,1 / &
-  domain_xm  domain_ym  domain_zp / &
-  domain_xp  domain_yp  domain_zp / &
-  1,1,0 /
-pset / rayend / seq / 0,0,0
-*
-
-loop / foreach / iregion / &
-  r_elastic_pos r_elastic_neg r_visco_pos r_visco_neg &
-  / loop_end / &
-  regnpts / iregion / dx / pset,get,rayend / xyz / &
-    0.0e+3  0.0e+3  domain_zm / &
-    0.0e+3  1.0e+3  domain_zm / &
-    1.0e+3  0.0e+3  domain_zm / &
-    0,0
-cmo/setatt//itp/pset,get,rayend/dud
-pset / rayend / delete
-
-* ----------------------------------------------------------------------
-* Remove duplicate points
-* ----------------------------------------------------------------------
-filter / 1,0,0 / 10.0
-rmpoint / compress
-
-* ----------------------------------------------------------------------
-* Set node type and material
-* ----------------------------------------------------------------------
-setpts
-
-* ----------------------------------------------------------------------
-* Connect the points into a Delaunay tetrahedral mesh
-* ----------------------------------------------------------------------
-connect
-
-* ----------------------------------------------------------------------
-* Set elements to tetrahedra
-* ----------------------------------------------------------------------
-settets / geometry
-resetpts/cell_color
-
-* Remove parent/child hierarchy
-resetpts
-rmpoint / compress
-*
-* ----------------------------------------------------------------------
-* MESH QUALITY
-* ----------------------------------------------------------------------
-*
-quality
-*
-* ----------------------------------------------------------------------
-* IDENTIFY GROUPS
-* ----------------------------------------------------------------------
-*
-* Identify nodes on fault surface
-pset / fault / surface / surf_fault /
-*
-* Identify nodes on boundaries
-pset / boundary_xm / surface / surf_xm /
-pset / boundary_xp / surface / surf_xp /
-pset / boundary_ym / surface / surf_ym /
-pset / boundary_yp / surface / surf_yp /
-pset / boundary_zm / surface / surf_zm /
-pset / boundary_zp / surface / surf_zp /
-*
-* ----------------------------------------------------------------------
-* MERGE MATERIALS
-* ----------------------------------------------------------------------
-eltset / elastic1 / itetclr / eq / 1
-eltset / elastic2 / itetclr / eq / 2
-eltset / elastic / union / elastic1 elastic2
-cmo / setatt / box / itetclr / eltset,get,elastic / 1
-eltset / elastic1 / delete
-eltset / elastic2 / delete
-eltset / elastic / delete
-
-eltset / visco1 / itetclr / eq / 3
-eltset / visco2 / itetclr / eq / 4
-eltset / visco / union / visco1 visco2
-cmo / setatt / box / itetclr / eltset,get,visco / 2
-eltset / visco1 / delete
-eltset / visco2 / delete
-eltset / visco / delete
-cmo / printatt / box / itetclr / minmax
-
-* ----------------------------------------------------------------------
-* WRITE MESH
-* ----------------------------------------------------------------------
-*
-* Export mesh and psets to files.
-cmo / setatt / box / ipolydat / no
-dump / gmv / tet4_1000m_binary.gmv / / binary
-dump / gmv / tet4_1000m_ascii.gmv / / ascii
-
-pset / -all- / write / tet4_1000m_ascii.pset / ascii
-pset / -all- / write / tet4_1000m_binary.pset / binary
-
-*
-* Terminate processing
-finish
-
-* ======================================================================
-* End of file

Added: short/3D/PyLith/trunk/examples/3d/tet4/output/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/output/Makefile.am	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/output/Makefile.am	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,22 @@
+# -*- Makefile -*-
+#
+# ----------------------------------------------------------------------
+#
+# Brad T. Aagaard, U.S. Geological Survey
+# Charles A. Williams, GNS Science
+# Matthew G. Knepley, University of Chicago
+#
+# This code was developed as part of the Computational Infrastructure
+# for Geodynamics (http://geodynamics.org).
+#
+# Copyright (c) 2010 University of California, Davis
+#
+# See COPYING for license information.
+#
+# ----------------------------------------------------------------------
+#
+
+dist_noinst_DATA =
+
+
+# End of file 

Modified: short/3D/PyLith/trunk/examples/3d/tet4/pylithapp.cfg
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/pylithapp.cfg	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/pylithapp.cfg	2011-06-02 22:57:09 UTC (rev 18529)
@@ -33,8 +33,8 @@
 
 [pylithapp.mesh_generator.reader]
 # Set filenames of mesh and pset files to import.
-filename_gmv = tet4_1000m_binary.gmv
-filename_pset = tet4_1000m_binary.pset
+filename_gmv = mesh/tet4_1000m_binary.gmv
+filename_pset = mesh/tet4_1000m_binary.pset
 
 # If using provided mesh or importing the mesh on a machine with a
 # different endian type than the one which created the mesh, then
@@ -70,14 +70,14 @@
 [pylithapp.timedependent.materials.elastic]
 label = Elastic material
 id = 1
-db_properties.iohandler.filename = mat_elastic.spatialdb
+db_properties.iohandler.filename = spatialdb/mat_elastic.spatialdb
 quadrature.cell = pylith.feassemble.FIATSimplex
 quadrature.cell.shape = tetrahedron
 
 [pylithapp.timedependent.materials.viscoelastic]
 label = Viscoelastic material
 id = 2
-db_properties.iohandler.filename = mat_viscoelastic.spatialdb
+db_properties.iohandler.filename = spatialdb/mat_viscoelastic.spatialdb
 quadrature.cell = pylith.feassemble.FIATSimplex
 quadrature.cell.shape = tetrahedron
 
@@ -87,15 +87,18 @@
 # Set the solver options.
 
 [pylithapp.petsc]
-ksp_rtol = 1.0e-8
+
+# Preconditioner settings.
 pc_type = asm
+sub_pc_factor_shift_type = nonzero
 
-# Change the preconditioner settings.
-sub_pc_factor_shift_type = none
-
+# Convergence parameters.
+ksp_rtol = 1.0e-8
+ksp_atol = 1.0e-12
 ksp_max_it = 100
 ksp_gmres_restart = 50
 
+# Linear solver monitoring options.
 ksp_monitor = true
 ksp_view = true
 ksp_converged_reason = true

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/shear.jpg
===================================================================
(Binary files differ)

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/shearxy.cfg
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/shearxy.cfg	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/shearxy.cfg	2011-06-02 22:57:09 UTC (rev 18529)
@@ -1,83 +0,0 @@
-# -*- Python -*-
-[pylithapp]
-
-# This is not a self-contained simulation configuration file. This
-# file only specifies parameters specific to the boundary
-# conditions. The general parameters are specificed in the pylithapp.cfg
-# file which is read by default.
-#
-# To run the simulation:
-# pylith shearxy.cfg
-
-# ----------------------------------------------------------------------
-# problem
-# ----------------------------------------------------------------------
-[pylithapp.timedependent]
-# Set the BC to an array with 3 boundary conditions.
-bc = x_pos,x_neg,z_neg
-
-[pylithapp.timedependent.implicit]
-# Set the output to an array of 2 output managers.
-# We will output the solution over the domain and the ground surface.
-output = [domain,subdomain]
-
-# Set subdomain component to OutputSolnSubset (subset of domain).
-output.subdomain = pylith.meshio.OutputSolnSubset
-
-# ----------------------------------------------------------------------
-# boundary conditions
-# ----------------------------------------------------------------------
-# We change spatial database for initial value from ZeroDispDB (which has
-# a uniform spatial distribution) to SimpleDB (which uses a data file
-# to specify a spatial variation).
-
-# Set the parameters for Dirichlet boundary conditions applied on the
-# +x and -x faces of the box. Note that we only use a subset of the
-# boundary conditions provided in the 6 BC container.
-
-# We fix the x and y degrees of freedom on the +x and -x faces, and
-# fix the z degree of freedom on the bottom face.
-
-# The label corresponds to the name of the pset in LaGriT.
-
-[pylithapp.timedependent.bc.x_pos]
-bc_dof = [0, 1]
-label = boundary_xp
-db_initial = spatialdata.spatialdb.SimpleDB
-db_initial.label = Dirichlet BC on +x
-db_initial.iohandler.filename = fixeddisp_shear.spatialdb
-
-[pylithapp.timedependent.bc.x_neg]
-bc_dof = [0, 1]
-label = boundary_xm
-db_initial = spatialdata.spatialdb.SimpleDB
-db_initial.label = Dirichlet BC on -x
-db_initial.iohandler.filename = fixeddisp_shear.spatialdb
-
-[pylithapp.timedependent.bc.z_neg]
-bc_dof = [2]
-label = boundary_zm
-db_initial = spatialdata.spatialdb.SimpleDB
-db_initial.label = Dirichlet BC on -z
-db_initial.iohandler.filename = fixeddisp_shear.spatialdb
-
-# ----------------------------------------------------------------------
-# output
-# ----------------------------------------------------------------------
-# Give basename for VTK domain output of solution over domain.
-[pylithapp.problem.formulation.output.domain.writer]
-filename = shearxy.vtk
-
-# Give basename for VTK domain output of solution over ground surface.
-[pylithapp.problem.formulation.output.subdomain]
-label = boundary_zp
-writer.filename = shearxy-groundsurf.vtk
-
-# Give basename for VTK output of state variables.
-[pylithapp.timedependent.materials.elastic.output]
-cell_filter = pylith.meshio.CellFilterAvgMesh
-writer.filename = shearxy-elastic.vtk
-
-[pylithapp.timedependent.materials.viscoelastic.output]
-cell_filter = pylith.meshio.CellFilterAvgMesh
-writer.filename = shearxy-viscoelastic.vtk

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/sliptime.spatialdb
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/sliptime.spatialdb	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/sliptime.spatialdb	2011-06-02 22:57:09 UTC (rev 18529)
@@ -1,27 +0,0 @@
-// -*- C++ -*- (tell Emacs to use C++ mode for syntax highlighting)
-//
-// This spatial database specifies the distribution of the slip
-// initiation time over the fault surface for the kinematic fault
-// rupture. Because this is a quasi-static simulation, we specify that
-// the slip initiates at t=0.0 s so that we have slip at the first
-// time step.
-//
-#SPATIAL.ascii 1
-SimpleDB {
-  num-values = 1
-  value-names =  slip-time
-  value-units =  s
-  num-locs = 1
-  data-dim = 0 // data is uniform (1 location)
-  space-dim = 3
-  cs-data = cartesian {
-    to-meters = 1.0
-    space-dim = 3
-  }
-}
-// Columns are
-// (1) x coordinate (m)
-// (2) y coordinate (m)
-// (3) z coordinate (m)
-// (4) Slip initiation time (s)
-0.0  0.0  0.0   0.0

Copied: short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/finalslip.spatialdb (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/finalslip.spatialdb)
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/finalslip.spatialdb	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/finalslip.spatialdb	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,31 @@
+// -*- C++ -*- (tell Emacs to use C++ mode for syntax highlighting)
+//
+// This spatial database specifies the distribution of slip on the
+// fault surface. In this case we prescribe a piecewise linear, depth
+// dependent distribution of slip. The slip is 2.0 m right-lateral
+// with 0.25 m of reverse slip at the surface with a linear taper from
+// 2.0 m to 0.0 m from -2 km to -4 km.
+//
+#SPATIAL.ascii 1
+SimpleDB {
+  num-values = 3
+  value-names =  left-lateral-slip  reverse-slip  fault-opening
+  value-units =  m  m  m
+  num-locs = 3
+  data-dim = 1 // Locations of data points form a line.
+  space-dim = 3
+  cs-data = cartesian {
+    to-meters = 1.0e+3 // Specify coordinates in km for convenience.
+    space-dim = 3
+  } // cs-data
+} // SimpleDB
+// Columns are
+// (1) x coordinate (km)
+// (2) y coordinate (km)
+// (3) z coordinate (km)
+// (4) left-lateral-slip (m) (right-lateral is negative)
+// (5) reverse-slip (m)
+// (6) fault-opening (m)
+0.0  0.0  0.0    -2.00  0.25  0.00
+0.0  0.0 -2.0    -2.00  0.00  0.00
+0.0  0.0 -4.0     0.00  0.00  0.00

Copied: short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/fixeddisp_shear.spatialdb (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/fixeddisp_shear.spatialdb)
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/fixeddisp_shear.spatialdb	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/fixeddisp_shear.spatialdb	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,32 @@
+// -*- C++ -*- (tell Emacs to use C++ mode for syntax highlighting)
+//
+// This spatial database specifies the distribution of the
+// displacement field for Dirichlet boundary conditions associated
+// with shear in the xy plane.
+//
+// dof-0: Ux(x) = 0
+// dof-1: Uy(x) = 1.0 m * x / 3 km
+// dof-2: Uz(x) = 0
+//
+#SPATIAL.ascii 1
+SimpleDB {
+  num-values = 3
+  value-names =  displacement-x  displacement-y  displacement-z
+  value-units =  m  m  m
+  num-locs = 2
+  data-dim = 1 // locations form a line
+  space-dim = 3
+  cs-data = cartesian {
+    to-meters = 1.0e+3 // specify coordinates in km
+    space-dim = 3
+  }
+}
+// Columns are
+// (1) x coordinate (km)
+// (2) y coordinate (km)
+// (3) z coordinate (km)
+// (4) Ux (m)
+// (5) Uy (m)
+// (6) Uz (m)
+-3.0  0.0  0.0    0.0  -1.0  0.0
++3.0  0.0  0.0    0.0  +1.0  0.0

Copied: short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/mat_elastic.spatialdb (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/mat_elastic.spatialdb)
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/mat_elastic.spatialdb	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/mat_elastic.spatialdb	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,26 @@
+// -*- C++ -*- (tell Emacs to use C++ mode for syntax highlighting)
+//
+// This spatial database specifies the distribution of material
+// properties. In this case, the material properties are uniform.
+//
+#SPATIAL.ascii 1
+SimpleDB {
+  num-values = 3 // number of material property values
+  value-names =  density vs vp // names of the material property values
+  value-units =  kg/m**3  m/s  m/s
+  num-locs = 1 // number of locations
+  data-dim = 0
+  space-dim = 3
+  cs-data = cartesian {
+    to-meters = 1.0
+    space-dim = 3
+  }
+}
+// Columns are
+// (1) x coordinate (m)
+// (2) y coordinate (m)
+// (3) z coordinate (m)
+// (4) density (kg/m^3)
+// (5) vs (m/s)
+// (6) vp (m/s)
+0.0  0.0  0.0   2500.0  3000.0  5291.502622129181

Copied: short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/mat_viscoelastic.spatialdb (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/mat_viscoelastic.spatialdb)
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/mat_viscoelastic.spatialdb	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/mat_viscoelastic.spatialdb	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,30 @@
+// -*- C++ -*- (tell Emacs to use C++ mode for syntax highlighting)
+//
+// This spatial database specifies the distribution of material
+// properties for a Maxwell viscoelastic material. In this case,
+// the material properties are uniform.
+//
+// The viscosity corresponds to a Maxwell time of 100 years.
+//
+#SPATIAL.ascii 1
+SimpleDB {
+  num-values = 4 // number of material property values
+  value-names =  density vs vp viscosity // names of the material property values
+  value-units =  kg/m**3  m/s  m/s Pa*s
+  num-locs = 1 // number of locations
+  data-dim = 0
+  space-dim = 3
+  cs-data = cartesian {
+    to-meters = 1.0
+    space-dim = 3
+  }
+}
+// Columns are
+// (1) x coordinate (m)
+// (2) y coordinate (m)
+// (3) z coordinate (m)
+// (4) density (kg/m**3)
+// (5) vs (m/s)
+// (6) vp (m/s)
+// (7) viscosity (Pa*s)
+0.0  0.0  0.0   2500.0  3000.0  5291.502622129181 7.10046e+19

Copied: short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/sliptime.spatialdb (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/sliptime.spatialdb)
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/sliptime.spatialdb	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/spatialdb/sliptime.spatialdb	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,27 @@
+// -*- C++ -*- (tell Emacs to use C++ mode for syntax highlighting)
+//
+// This spatial database specifies the distribution of the slip
+// initiation time over the fault surface for the kinematic fault
+// rupture. Because this is a quasi-static simulation, we specify that
+// the slip initiates at t=0.0 s so that we have slip at the first
+// time step.
+//
+#SPATIAL.ascii 1
+SimpleDB {
+  num-values = 1
+  value-names =  slip-time
+  value-units =  s
+  num-locs = 1
+  data-dim = 0 // data is uniform (1 location)
+  space-dim = 3
+  cs-data = cartesian {
+    to-meters = 1.0
+    space-dim = 3
+  }
+}
+// Columns are
+// (1) x coordinate (m)
+// (2) y coordinate (m)
+// (3) z coordinate (m)
+// (4) Slip initiation time (s)
+0.0  0.0  0.0   0.0

Copied: short/3D/PyLith/trunk/examples/3d/tet4/step01.cfg (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/shearxy.cfg)
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/step01.cfg	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/step01.cfg	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,83 @@
+# -*- Python -*-
+[pylithapp]
+
+# This is not a self-contained simulation configuration file. This
+# file only specifies parameters specific to the boundary
+# conditions. The general parameters are specificed in the pylithapp.cfg
+# file which is read by default.
+#
+# To run the simulation:
+# pylith step01.cfg
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent]
+# Set the BC to an array with 3 boundary conditions.
+bc = x_pos,x_neg,z_neg
+
+[pylithapp.timedependent.implicit]
+# Set the output to an array of 2 output managers.
+# We will output the solution over the domain and the ground surface.
+output = [domain,subdomain]
+
+# Set subdomain component to OutputSolnSubset (subset of domain).
+output.subdomain = pylith.meshio.OutputSolnSubset
+
+# ----------------------------------------------------------------------
+# boundary conditions
+# ----------------------------------------------------------------------
+# We change spatial database for initial value from ZeroDispDB (which has
+# a uniform spatial distribution) to SimpleDB (which uses a data file
+# to specify a spatial variation).
+
+# Set the parameters for Dirichlet boundary conditions applied on the
+# +x and -x faces of the box. Note that we only use a subset of the
+# boundary conditions provided in the 6 BC container.
+
+# We fix the x and y degrees of freedom on the +x and -x faces, and
+# fix the z degree of freedom on the bottom face.
+
+# The label corresponds to the name of the pset in LaGriT.
+
+[pylithapp.timedependent.bc.x_pos]
+bc_dof = [0, 1]
+label = boundary_xp
+db_initial = spatialdata.spatialdb.SimpleDB
+db_initial.label = Dirichlet BC on +x
+db_initial.iohandler.filename = spatialdb/fixeddisp_shear.spatialdb
+
+[pylithapp.timedependent.bc.x_neg]
+bc_dof = [0, 1]
+label = boundary_xm
+db_initial = spatialdata.spatialdb.SimpleDB
+db_initial.label = Dirichlet BC on -x
+db_initial.iohandler.filename = spatialdb/fixeddisp_shear.spatialdb
+
+[pylithapp.timedependent.bc.z_neg]
+bc_dof = [2]
+label = boundary_zm
+db_initial = spatialdata.spatialdb.SimpleDB
+db_initial.label = Dirichlet BC on -z
+db_initial.iohandler.filename = spatialdb/fixeddisp_shear.spatialdb
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+# Give basename for VTK domain output of solution over domain.
+[pylithapp.problem.formulation.output.domain.writer]
+filename = output/step01.vtk
+
+# Give basename for VTK domain output of solution over ground surface.
+[pylithapp.problem.formulation.output.subdomain]
+label = boundary_zp
+writer.filename = output/step01-groundsurf.vtk
+
+# Give basename for VTK output of state variables.
+[pylithapp.timedependent.materials.elastic.output]
+cell_filter = pylith.meshio.CellFilterAvgMesh
+writer.filename = output/step01-elastic.vtk
+
+[pylithapp.timedependent.materials.viscoelastic.output]
+cell_filter = pylith.meshio.CellFilterAvgMesh
+writer.filename = output/step01-viscoelastic.vtk

Copied: short/3D/PyLith/trunk/examples/3d/tet4/step01.jpg (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/shear.jpg)
===================================================================
(Binary files differ)

Added: short/3D/PyLith/trunk/examples/3d/tet4/step02.cfg
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/step02.cfg	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/step02.cfg	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,117 @@
+# -*- Python -*-
+[pylithapp]
+
+# This is not a self-contained simulation configuration file. This
+# file only specifies parameters specific to the boundary
+# conditions. The general parameters are specificed in the pylithapp.cfg
+# file which is read by default.
+#
+# To run the simulation:
+# pylith step02.cfg
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent]
+# Set the BC to an array with 3 boundary conditions.
+bc = x_pos,x_neg,z_neg
+
+[pylithapp.timedependent.implicit]
+# Set the output to an array of 2 output managers.
+# We will output the solution over the domain and the ground surface.
+output = [domain,subdomain]
+
+# Set subdomain component to OutputSolnSubset (subset of domain).
+output.subdomain = pylith.meshio.OutputSolnSubset
+
+# ----------------------------------------------------------------------
+# mesh_generator
+# ----------------------------------------------------------------------
+[pylithapp.mesh_generator]
+# Refine mesh by a factor of 2
+refiner = pylith.topology.RefineUniform
+
+# ----------------------------------------------------------------------
+# boundary conditions
+# ----------------------------------------------------------------------
+# We change spatial database for initial value from ZeroDispDB (which has
+# a uniform spatial distribution) to SimpleDB (which uses a data file
+# to specify a spatial variation).
+
+# Set the parameters for Dirichlet boundary conditions applied on the
+# +x and -x faces of the box. Note that we only use a subset of the
+# boundary conditions provided in the 6 BC container.
+
+# We fix the x and y degrees of freedom on the +x and -x faces, and
+# fix the z degree of freedom on the bottom face.
+
+# The label corresponds to the name of the pset in LaGriT.
+
+[pylithapp.timedependent.bc.x_pos]
+bc_dof = [0, 1]
+label = boundary_xp
+db_initial = spatialdata.spatialdb.SimpleDB
+db_initial.label = Dirichlet BC on +x
+db_initial.iohandler.filename = spatialdb/fixeddisp_shear.spatialdb
+
+[pylithapp.timedependent.bc.x_neg]
+bc_dof = [0, 1]
+label = boundary_xm
+db_initial = spatialdata.spatialdb.SimpleDB
+db_initial.label = Dirichlet BC on -x
+db_initial.iohandler.filename = spatialdb/fixeddisp_shear.spatialdb
+
+[pylithapp.timedependent.bc.z_neg]
+bc_dof = [2]
+label = boundary_zm
+db_initial = spatialdata.spatialdb.SimpleDB
+db_initial.label = Dirichlet BC on -z
+db_initial.iohandler.filename = spatialdb/fixeddisp_shear.spatialdb
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+# Give basename for VTK domain output of solution over domain.
+[pylithapp.problem.formulation.output.domain.writer]
+filename = output/step02.vtk
+
+# Give basename for VTK domain output of solution over ground surface.
+[pylithapp.problem.formulation.output.subdomain]
+label = boundary_zp
+writer.filename = output/step02-groundsurf.vtk
+
+# Give basename for VTK output of state variables.
+[pylithapp.timedependent.materials.elastic.output]
+cell_filter = pylith.meshio.CellFilterAvgMesh
+writer.filename = output/step02-elastic.vtk
+
+[pylithapp.timedependent.materials.viscoelastic.output]
+cell_filter = pylith.meshio.CellFilterAvgMesh
+writer.filename = output/step02-viscoelastic.vtk
+
+# ----------------------------------------------------------------------
+# PETSc
+# ----------------------------------------------------------------------
+[pylithapp.petsc]
+
+# Field split preconditioning. We use an algebraic multigrid
+# preconditioner from Trilinos/ML built via PETSc on each component of
+# the displacement field separately. In this way, we split the
+# fields. This method requires the 'aij' matrix type.
+[pylithapp.timedependent.formulation]
+split_fields = True
+matrix_type = aij
+
+[pylithapp.petsc]
+# We split the fields into 3, corresponding to the number of degrees
+# of freeom at each vertex.
+fs_pc_type = fieldsplit
+fs_pc_fieldsplit_real_diagonal = 
+fs_pc_fieldsplit_type = multiplicative
+fs_fieldsplit_0_pc_type = ml
+fs_fieldsplit_1_pc_type = ml
+fs_fieldsplit_2_pc_type = ml
+fs_fieldsplit_0_ksp_type = preonly
+fs_fieldsplit_1_ksp_type = preonly
+fs_fieldsplit_2_ksp_type = preonly
+

Copied: short/3D/PyLith/trunk/examples/3d/tet4/step03.cfg (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/dislocation.cfg)
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/step03.cfg	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/step03.cfg	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,100 @@
+# -*- Python -*-
+[pylithapp]
+
+# This is not a self-contained simulation configuration file. This
+# file only specifies parameters specific to the boundary and
+# interface conditions. The general parameters are specificed in the
+# pylithapp.cfg file which is read by default.
+#
+# To run the simulation:
+# pylith step03.cfg
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent]
+# Set the BC to an array with 2 boundary conditions.
+bc = x_pos,x_neg
+
+# Set the interfaces to an array with 1 fault.
+interfaces = fault
+
+[pylithapp.timedependent.implicit]
+# Set the output to an array of 2 output managers.
+# We will output the solution over the domain and the ground surface.
+output = [domain,subdomain]
+
+# Set subdomain component to OutputSolnSubset (subset of domain).
+output.subdomain = pylith.meshio.OutputSolnSubset
+
+# ----------------------------------------------------------------------
+# boundary conditions
+# ----------------------------------------------------------------------
+
+# We use the default spatial database for the Dirichlet BC which sets
+# the displacements to zero for all time.
+#
+# Set the parameters for the desired boundary conditions. Note that we
+# only use a subset of the boundary conditions provided in the 6 BC
+# container.
+#
+# Note: A more natural set of boundary conditions involves pinning the
+# z-DOF on the bottom (-z) face. Howver, the current release of PyLith
+# does not permit overlapping fault interfaces and Dirichlet boundary
+# conditions with the block Jacobi preconditioner.
+
+# The label corresponds to the label in LaGriT.
+
+[pylithapp.timedependent.bc.x_pos]
+bc_dof = [0, 1, 2]
+label = boundary_xp
+db_initial.label = Dirichlet BC on +x
+
+[pylithapp.timedependent.bc.x_neg]
+bc_dof = [0, 1, 2]
+label = boundary_xm
+db_initial.label = Dirichlet BC on -x
+
+# ----------------------------------------------------------------------
+# faults
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.interfaces]
+# Set the type of fault interface condition.
+fault = pylith.faults.FaultCohesiveKin
+
+# Set the parameters for the fault interface condition.
+
+[pylithapp.timedependent.interfaces.fault]
+label = fault
+quadrature.cell = pylith.feassemble.FIATSimplex
+quadrature.cell.shape = triangle
+
+[pylithapp.timedependent.interfaces.fault.eq_srcs.rupture.slip_function]
+slip.iohandler.filename = spatialdb/finalslip.spatialdb
+slip_time.iohandler.filename = spatialdb/sliptime.spatialdb
+
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+# Set the root name for output.
+[pylithapp.problem.formulation.output.domain.writer]
+filename = output/step03.vtk
+
+# Give basename for VTK domain output of solution over ground surface.
+[pylithapp.problem.formulation.output.subdomain]
+label = boundary_zp
+writer.filename = output/step03-groundsurf.vtk
+
+# Give basename for vtk fault output.
+[pylithapp.timedependent.interfaces.fault.output]
+writer.filename = output/step03-fault.vtk
+
+# Give basename for VTK output of state variables.
+[pylithapp.timedependent.materials.elastic.output]
+cell_filter = pylith.meshio.CellFilterAvgMesh
+writer.filename = output/step03-elastic.vtk
+
+[pylithapp.timedependent.materials.viscoelastic.output]
+cell_filter = pylith.meshio.CellFilterAvgMesh
+writer.filename = output/step03-viscoelastic.vtk

Copied: short/3D/PyLith/trunk/examples/3d/tet4/step03.jpg (from rev 18522, short/3D/PyLith/trunk/examples/3d/tet4/dislocation.jpg)
===================================================================
(Binary files differ)

Added: short/3D/PyLith/trunk/examples/3d/tet4/step04.cfg
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/step04.cfg	                        (rev 0)
+++ short/3D/PyLith/trunk/examples/3d/tet4/step04.cfg	2011-06-02 22:57:09 UTC (rev 18529)
@@ -0,0 +1,139 @@
+# -*- Python -*-
+[pylithapp]
+
+# This is not a self-contained simulation configuration file. This
+# file only specifies parameters specific to the boundary and
+# interface conditions. The general parameters are specificed in the
+# pylithapp.cfg file which is read by default.
+#
+# To run the simulation:
+# pylith step04.cfg
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent]
+# Set the BC to an array with 2 boundary conditions.
+bc = x_pos,x_neg
+
+# Set the interfaces to an array with 1 fault.
+interfaces = fault
+
+[pylithapp.timedependent.implicit]
+# Set the output to an array of 2 output managers.
+# We will output the solution over the domain and the ground surface.
+output = [domain,subdomain]
+
+# Set subdomain component to OutputSolnSubset (subset of domain).
+output.subdomain = pylith.meshio.OutputSolnSubset
+
+# ----------------------------------------------------------------------
+# mesh_generator
+# ----------------------------------------------------------------------
+[pylithapp.mesh_generator]
+# Refine mesh by a factor of 2
+refiner = pylith.topology.RefineUniform
+
+# ----------------------------------------------------------------------
+# boundary conditions
+# ----------------------------------------------------------------------
+
+# We use the default spatial database for the Dirichlet BC which sets
+# the displacements to zero for all time.
+#
+# Set the parameters for the desired boundary conditions. Note that we
+# only use a subset of the boundary conditions provided in the 6 BC
+# container.
+#
+# Note: A more natural set of boundary conditions involves pinning the
+# z-DOF on the bottom (-z) face. Howver, the current release of PyLith
+# does not permit overlapping fault interfaces and Dirichlet boundary
+# conditions with the block Jacobi preconditioner.
+
+# The label corresponds to the label in LaGriT.
+
+[pylithapp.timedependent.bc.x_pos]
+bc_dof = [0, 1, 2]
+label = boundary_xp
+db_initial.label = Dirichlet BC on +x
+
+[pylithapp.timedependent.bc.x_neg]
+bc_dof = [0, 1, 2]
+label = boundary_xm
+db_initial.label = Dirichlet BC on -x
+
+# ----------------------------------------------------------------------
+# faults
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.interfaces]
+# Set the type of fault interface condition.
+fault = pylith.faults.FaultCohesiveKin
+
+# Set the parameters for the fault interface condition.
+
+[pylithapp.timedependent.interfaces.fault]
+label = fault
+quadrature.cell = pylith.feassemble.FIATSimplex
+quadrature.cell.shape = triangle
+
+[pylithapp.timedependent.interfaces.fault.eq_srcs.rupture.slip_function]
+slip.iohandler.filename = spatialdb/finalslip.spatialdb
+slip_time.iohandler.filename = spatialdb/sliptime.spatialdb
+
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+# Set the root name for output.
+[pylithapp.problem.formulation.output.domain.writer]
+filename = output/step04.vtk
+
+# Give basename for VTK domain output of solution over ground surface.
+[pylithapp.problem.formulation.output.subdomain]
+label = boundary_zp
+writer.filename = output/step04-groundsurf.vtk
+
+# Give basename for vtk fault output.
+[pylithapp.timedependent.interfaces.fault.output]
+writer.filename = output/step04-fault.vtk
+
+# Give basename for VTK output of state variables.
+[pylithapp.timedependent.materials.elastic.output]
+cell_filter = pylith.meshio.CellFilterAvgMesh
+writer.filename = output/step04-elastic.vtk
+
+[pylithapp.timedependent.materials.viscoelastic.output]
+cell_filter = pylith.meshio.CellFilterAvgMesh
+writer.filename = output/step04-viscoelastic.vtk
+
+# ----------------------------------------------------------------------
+# PETSc
+# ----------------------------------------------------------------------
+[pylithapp.petsc]
+
+# Field split preconditioning. As in step02, we use an algebraic
+# multigrid preconditioner from Trilinos/ML built via PETSc on each
+# component of the displacement field. We also apply a custom
+# preconditioner for the Lagrange multiplier vertices. In this way, we
+# split the fields.
+[pylithapp.timedependent.formulation]
+split_fields = True
+# Use custom preconditioning for the Lagrange multiplier vertices
+use_custom_constraint_pc = True
+matrix_type = aij
+
+[pylithapp.petsc]
+# Note that with 3 displacement components plus the Lagrange
+# multiplier vertices, we have split the fields into 4.
+fs_pc_type = fieldsplit
+fs_pc_fieldsplit_real_diagonal = 
+fs_pc_fieldsplit_type = multiplicative
+fs_fieldsplit_0_pc_type = ml
+fs_fieldsplit_1_pc_type = ml
+fs_fieldsplit_2_pc_type = ml
+fs_fieldsplit_3_pc_type = ml
+fs_fieldsplit_0_ksp_type = preonly
+fs_fieldsplit_1_ksp_type = preonly
+fs_fieldsplit_2_ksp_type = preonly
+fs_fieldsplit_3_ksp_type = preonly
+

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/tet4-mesh.jpg
===================================================================
(Binary files differ)

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_ascii.gmv
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_ascii.gmv	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_ascii.gmv	2011-06-02 22:57:09 UTC (rev 18529)
@@ -1,1109 +0,0 @@
-gmvinput ascii
-codename LaGriT
-simdate  /19/08
-nodes          245
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-tet         4    188    239    197    189
-tet         4      4     17     14     13
-tet         4     13     91      2      1
-tet         4     13      1      2      4
-tet         4    223    231    121    229
-tet         4     88     94     95     85
-tet         4     95     99    105     98
-tet         4     98    108    105    104
-tet         4    223    231    229    228
-tet         4    242    234    235    237
-tet         4    193     55     67     58
-tet         4     41     54     53     44
-tet         4    213    212    214    218
-tet         4     52     50     65     53
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-tet         4     10    153    163      7
-tet         4     14     26     27    101
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-tet         4    174    173    181    183
-tet         4     62     51    138     63
-tet         4    115    125    122    121
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-tet         4    106     98    107    109
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-tet         4    215    221    164    157
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-tet         4     92     90     99    102
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-tet         4    221    109     37    165
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-tet         4    134    131    133    143
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-tet         4     65     50     62     51
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-tet         4    135    144    141    143
-tet         4     56     60     59     47
-tet         4    231    115    112    121
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-tet         4     61    189    181    191
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-tet         4    133    235    241    139
-tet         4     16     13    159     28
-tet         4    159     13    157     28
-tet         4    166    159    158    156
-tet         4    164    167    174    166
-tet         4     57     60     71     56
-tet         4     55    177     58    187
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-tet         4     31     28    177     40
-tet         4     31     28    167    177
-tet         4     19     22     10     23
-tet         4    177    187    176    179
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-tet         4    193    195    203    194
-tet         4    201    193     79     82
-tet         4     57     60     56     47
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-tet         4     56     71     68     58
-tet         4     94    106    103    211
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-tet         4     19     34    163     22
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-tet         4    234    235    241    242
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-tet         4    146    143    147    137
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-tet         4    142    145    136    146
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-tet         4     14    109     26    101
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-tet         4     14     13     92      2
-tet         4     33     45     35     48
-tet         4     28     26     41     29
-tet         4    177    171    179    170
-tet         4     19     22    163     10
-tet         4    171     31    177     34
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-tet         4     28     26     29     17
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-tet         4      7      5      4     17
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-tet         4     44     48     57     47
-tet         4     40     44     55     43
-tet         4     78     68     69     81
-tet         4     64     55     68     67
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-tet         4     54     57     53     44
-tet         4     38    120     51     39
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-tet         4    109    107    116    119
-tet         4    238    230    237    231
-tet         4    101     98    102     92
-tet         4     14     13    109    101
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-tet         4    119    120    129     51
-tet         4    116    126    119    120
-tet         4    115    116    122    125
-tet         4    109    101    107    110
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-tet         4    224    225    227    221
-tet         4    143    146    136    137
-tet         4      5      6     17     20
-tet         4     52     38     50     41
-tet         4    224    227    226    220
-tet         4    157    167    156    159
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-tet         4    156    159    158    150
-tet         4    159     19    153      7
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-tet         4    159      7    153      4
-tet         4     11      9      8     20
-tet         4    227    231    233    118
-tet         4    176    179    178    170
-tet         4     64     67     68     79
-tet         4    171     34    177    179
-tet         4    193     70     82    203
-tet         4    124    118    125    128
-tet         4     34     43    177    179
-tet         4    177    176    174    166
-tet         4    239    231    136    233
-tet         4    239    233    136    181
-tet         4    217    210    218    216
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-tet         4    218    219    221    213
-tet         4    221    215    106    109
-tet         4    225    221    106    109
-tet         4    164    167    173    174
-tet         4    215    109    221    157
-tet         4     64    197     73     61
-tet         4    191    199     79     64
-tet         4    238    242    245    239
-tet         4    188    238    245    239
-tet         4    191    197    199     64
-tet         4    188    238    239    232
-tet         4    173    165     37    167
-tet         4    164    221    173    165
-tet         4    164    165    173    167
-tet         4    160    171    170    163
-tet         4    221    165    164    157
-tet         4    165    167    164    157
-tet         4     29     30     41     44
-tet         4     17     14     27     18
-tet         4     17     21     30     20
-tet         4     57     48     60     47
-tet         4     53     57     68     56
-tet         4     44     45     48     35
-tet         4    109    165    221    157
-tet         4     40     44     43     31
-tet         4     34     31     44     35
-tet         4     52     62     61     65
-tet         4     52     61    191     64
-tet         4     61     73     74    145
-tet         4     52     61     64     65
-tet         4     61    191    181     52
-tet         4     61    239    245    136
-tet         4    208    149    156    148
-tet         4     61    197     73    145
-tet         4    148    149    156    150
-tet         4    122    131    130    133
-tet         4     38    120     39     27
-tet         4    131    140    130    133
-tet         4     78     68     81     77
-tet         4     86     89     95     85
-tet         4    116    123    126    114
-tet         4    131    140    133    143
-tet         4    106     98    104    107
-tet         4    125    132    122    131
-tet         4    113    114    116    105
-tet         4    106    217    103    211
-tet         4    116    105    114    108
-tet         4     94     88     97    213
-tet         4     98    106     94     97
-tet         4    112    103    113    106
-tet         4    129    138    137     51
-tet         4    135    147    144    143
-tet         4     98     97     94     88
-tet         4    109     97     98    101
-tet         4     62    146     75    147
-tet         4     13     91    100    101
-tet         4     97     91     98    101
-tet         4     68     80     79     82
-tet         4    154    160    163    153
-tet         4     68     71     81     80
-tet         4     19     34     22     23
-tet         4    169     31    163     19
-tet         4     68     71     80     82
-tet         4     62     75     65     63
-tet         4    220    227    172    164
-tet         4    232    227    173    172
-tet         4    183    174    182    180
-tet         4    191    190    198    188
-tet         4    191    201     79    199
-tet         4    191    199    197    198
-tet         4     52     55     65     64
-tet         4    191    201    199    198
-tet         4     62     63     65     51
-tet         4    188    197    198    191
-tet         4    215    157    214    208
-tet         4    215    157    164    214
-tet         4    167    169    160    159
-tet         4    159    160    150    153
-tet         4    172    227    173    164
-tet         4    219    106    221    213
-tet         4     13    149     91      1
-tet         4    124    115    125    118
-tet         4     63     75     65     78
-tet         4    232    227    181    173
-tet         4    227     37    181    173
-tet         4    227     37    173    221
-tet         4    232    227    231    233
-tet         4     63     66     65     54
-tet         4     92     93     90    102
-tet         4      9      6      5     20
-tet         4     34     43    179     46
-tet         4     46     43    179     58
-tet         4     86     87     96     89
-tet         4     28     29     41     31
-tet         4     92    102     14      3
-tet         4     28     17     29     31
-tet         4     30     33     44     29
-tet         4     30     33     29     20
-tet         4     29     20     32     31
-tet         4      7     20     10     11
-tet         4    169     19    163    161
-tet         4      2      6      3     17
-tet         4     20     21     35     24
-tet         4     11     21     20     24
-tet         4     29     44     41     31
-tet         4    136    231    133    124
-tet         4    181    118     49     37
-tet         4    119    129     50     51
-tet         4    177     40     52     55
-tet         4    174    180    181    173
-tet         4     37    109    227    118
-tet         4    232    227    233    181
-tet         4    173    221     37    165
-tet         4    165     13     25     28
-tet         4     11      9     24     12
-tet         4     41     45     54     44
-tet         4     53     54     65     68
-tet         4    223    217    112    225
-tet         4     51     63     65     54
-tet         4     50    129    137     51
-tet         4     68     58     71     67
-tet         4    222    225    223    228
-tet         4     68     57     69     72
-tet         4    210    204    207    206
-tet         4    193    187    195    194
-tet         4    188    181    239    189
-tet         4     89     88     95     85
-tet         4     14     13    101     92
-tet         4    188    181    189    191
-tet         4    109    215    106     97
-tet         4    102     98     99     92
-tet         4    113    123    116    114
-tet         4     92     88     98     89
-tet         4    191    189    197     61
-tet         4    225    106    115    109
-tet         4    189    239    197     61
-tet         4    180    232    173    172
-tet         4    134    143    133    137
-tet         4    133    235    139    130
-tet         4    234    228    235    231
-tet         4    154    153    163    155
-tet         4    143    142    136    146
-tet         4    155    153    163     10
-tet         4    208    157    214    156
-tet         4    214    157    164    156
-tet         4    167     31    169    159
-tet         4    157    167    164    156
-tet         4    118    109    227    115
-tet         4    232    225    231    227
-tet         4    183    182    184    190
-tet         4    232    231    239    233
-tet         4    232    233    239    181
-tet         4    174    180    173    172
-tet         4    191    193     79    201
-tet         4     62    138    147     75
-tet         4     63     78     65     66
-tet         4    200    192    193    194
-tet         4    112    115    122    121
-tet         4    211    205    207    204
-tet         4     88    207    211    205
-tet         4    106    213    217    211
-tet         4    222    217    223    225
-tet         4    222    225    228    224
-tet         4    227    109    225    115
-tet         4    218    225    224    221
-tet         4    227    225    231    115
-tet         4    224    221    227    220
-tet         4    103    104    113    106
-tet         4    237    235    242    241
-tet         4     61    145     74    146
-tet         4    103     95    104    106
-tet         4    106    104    113    116
-tet         4    177    170    176    169
-tet         4     13    149      1      4
-tet         4     95     98    105    104
-tet         4     92      3     14      2
-tet         4     92      3     93    102
-tet         4     17     18     30     21
-tet         4     29     33     32     20
-tet         4     89     87     96     99
-tet         4     17     30     29     20
-tet         4     41     42     54     45
-tet         4    193     58     70    187
-tet         4    193     67     82     70
-tet         4     44     48     47     35
-tet         4    193     67     70     58
-tet         4    193    187    194    184
-tet         4     52     55     64    191
-tet         4     68     67     71     82
-tet         4     65     64     68     79
-tet         4     65     55     68     64
-tet         4     41     44     53     55
-tet         4     44     47     56     58
-tet         4     77     68     81     80
-tet         4     52     53     65     55
-tet         4     52     41     53     55
-tet         4     13    100    109    101
-tet         4    106    107    104    116
-tet         4    101    111    108    107
-tet         4     41     50     53     54
-tet         4     89     95     98     99
-tet         4     92     98     99     89
-tet         4    223    225    231    228
-tet         4    136    124    125    128
-tet         4    115    112    116    106
-tet         4    225    112    115    106
-tet         4    115    109    116    119
-tet         4    115    106    116    109
-tet         4     53     50     65     54
-tet         4     20     19     10     23
-tet         4    132    140    131    143
-tet         4    136    133    137    125
-tet         4    159    153    151      4
-tet         4     20     34     19     23
-tet         4    153     19    163      7
-tet         4    159     19      7     16
-tet         4    149    215    208    157
-tet         4    169     19    161    159
-tet         4    159     31     19     16
-tet         4    177    187    184    176
-tet         4    177    169    176    166
-tet         4    167    177    174    166
-tet         4     19     31     34     20
-tet         4    181    183     52    191
-tet         4    181    174    183    180
-tet         4    181    183    191    180
-tet         4     40     41     52     55
-tet         4    174    173    183    175
-tet         4    183    180    182    190
-tet         4      5      6      2     17
-tet         4      4      2     14     17
-tet         4    201    203    200    194
-tet         4      2      3     14     17
-tet         4    228    224    231    230
-tet         4    230    224    231    232
-tet         4    217    103    225    106
-tet         4    218    217    225    219
-tet         4    222    217    225    218
-tet         4    213    218    217    211
-tet         4    230    234    237    231
-tet         4    236    234    237    230
-tet         4    239    231    237    133
-tet         4    215    213    214    218
-tet         4    234    241    240    242
-tet         4      6     18      3     17
-tet         4     23     20     34     35
-tet         4    219    217    225    106
-tet         4    218    213    221    215
-tet         4    213    106    221    215
-tet         4     40     37    173     52
-tet         4    167     37    173     40
-tet         4     28     41     40     31
-tet         4     40     28     37     41
-tet         4     52     40     37     41
-tet         4    174    175    183    177
-tet         4    167     28     40    177
-tet         4     53     57     56     44
-tet         4     44     45     57     48
-tet         4    211    210    207    213
-tet         4    207    206    208    214
-tet         4    215    213    207    214
-tet         4     94     97    106    213
-tet         4    188    196    198    197
-tet         4     62     75     74     65
-tet         4    188    244    196    197
-tet         4    176    187    186    179
-tet         4    177    179     58    187
-tet         4     91     88     98     92
-tet         4     13     91    101     92
-tet         4    109     97    106     98
-tet         4     13    149    215     91
-tet         4    104    105    113    116
-tet         4     98     99    105    108
-tet         4     46     43     58     47
-tet         4     61    245    197    145
-tet         4    125    126    137    129
-tet         4    119    126    125    129
-tet         4    128    118    125    119
-tet         4    116    122    125    126
-tet         4     61    136    245    145
-tet         4     49    233    127    118
-tet         4    143    142    139    133
-tet         4     61    136    145    146
-tet         4    119    125    128    129
-tet         4    142    245    133    136
-tet         4    143    142    133    136
-tet         4    166    167    159    156
-tet         4    158    159    160    150
-tet         4    166    167    160    159
-tet         4      7     20     17     16
-tet         4    167     28     31    159
-tet         4    157     28    167    159
-tet         4    169     31     19    159
-tet         4     19     31    163     34
-tet         4    128    125    137    129
-tet         4    119    129    128     50
-tet         4    177    176    184    174
-tet         4    128    129    137     50
-tet         4    119    111    108    120
-tet         4     67     58     71     70
-tet         4    193     55     58    187
-tet         4    191    184    193    190
-tet         4    191    193    201    190
-tet         4    185    177    187    184
-tet         4    191    193    183     55
-tet         4    191    184    183    193
-tet         4     27    119    120    111
-tet         4     26    119     27    111
-tet         4     26    111     27    101
-tet         4     88    213    211    207
-tet         4    227    109     37    221
-tet         4    225    109    227    221
-tet         4    118    128     49     50
-tet         4    181    227    118     37
-tet         4    227    221    173    164
-tet         4    174    172    173    164
-tet         4     26    119    111    110
-tet         4     95    106    103     94
-tet         4     85     88     94    211
-tet         4     88    215    213    207
-tet         4     16     17     13     28
-tet         4      4     17     13     16
-tet         4     31     17     16     28
-tet         4      7     17      4     16
-tet         4     16     20     17     31
-tet         4     64     73     74     61
-tet         4     65     74     64     77
-tet         4     65     77     64     79
-tet         4     24     21     35     33
-tet         4     20     21     33     35
-tet         4     62     61    136     50
-tet         4     52     50     62     65
-tet         4    118    119    128     50
-tet         4     50     37     38     52
-tet         4     49    128    136     50
-tet         4     38    119     50     51
-tet         4     41     38     50     51
-tet         4     64     55     67    193
-tet         4     64     67     79    193
-tet         4     55     58     68     67
-tet         4     67     68     79     82
-tet         4    193     67     79     82
-tet         4     77     68     80     79
-tet         4     81     71     72     84
-tet         4     65     68     78     77
-tet         4     65     68     77     79
-tet         4     65     74     77     78
-tet         4    109    110    107    119
-tet         4     98    102    108    101
-tet         4     56     47     59     58
-tet         4     14    101     27    102
-tet         4     13     14     26     28
-tet         4    136    128    137     50
-tet         4     37    119    118     50
-tet         4     61    181    136     49
-tet         4    118    115    125    119
-tet         4    136    125    137    128
-tet         4    136    127    124    128
-tet         4    118    109    115    119
-tet         4     37    109    118    119
-tet         4    135    147    143    137
-tet         4     57     60     72     71
-tet         4    126    132    125    135
-tet         4     58     43     55     44
-tet         4    126    135    137    129
-tet         4    152    150    160    153
-tet         4    154    152    160    153
-tet         4    177     43     55     58
-tet         4    169    171    170    160
-tet         4    177    171    170    169
-tet         4    169     31    171    163
-tet         4    160    169    171    163
-tet         4    169    167    177     31
-tet         4    171    169    177     31
-tet         4    184    186    187    194
-tet         4    179     43    177     58
-tet         4     34     43     46     47
-tet         4     34     44     43     47
-tet         4    201    193    203    194
-tet         4    201    193     82    203
-tet         4     43     44     58     47
-tet         4     67     70     71     82
-tet         4     41     26     38     27
-tet         4     29     32     44     31
-tet         4     17     27     26     30
-tet         4    220    214    221    164
-tet         4    218    214    221    220
-tet         4    220    221    227    164
-tet         4    142    245    237    133
-tet         4    142    237    241    133
-tet         4     26     27     41     30
-tet         4    238    237    239    231
-tet         4    242    237    239    238
-tet         4    237    231    235    133
-tet         4      4      5      2     17
-tet         4     11      8      7     20
-tet         4      9     21      6     20
-tet         4     11     21      9     20
-tet         4     28     26     38     41
-tet         4     28     14     26     17
-tet         4     17     20     29     31
-tet         4     38    119     27     26
-variable
-imt1                             1
-  2.00000E+000  2.00000E+000  2.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000  3.00000E+000
-  1.00000E+000  1.00000E+000  4.00000E+000  2.00000E+000  2.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000  1.00000E+000  1.00000E+000
-  1.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000  2.00000E+000  1.00000E+000  1.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000
-  3.00000E+000  1.00000E+000  1.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000  1.00000E+000
-  1.00000E+000  1.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000  1.00000E+000  1.00000E+000
-  2.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000  1.00000E+000  1.00000E+000  1.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000
-  1.00000E+000  2.00000E+000  2.00000E+000  1.00000E+000  1.00000E+000  1.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000  3.00000E+000
-  1.00000E+000  1.00000E+000  4.00000E+000  2.00000E+000  2.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000  3.00000E+000  1.00000E+000
-  1.00000E+000  3.00000E+000  1.00000E+000  1.00000E+000  2.00000E+000  2.00000E+000  2.00000E+000  2.00000E+000  2.00000E+000  2.00000E+000
-  2.00000E+000  2.00000E+000  2.00000E+000  2.00000E+000  2.00000E+000  2.00000E+000  4.00000E+000  2.00000E+000  2.00000E+000  4.00000E+000
-  2.00000E+000  2.00000E+000  4.00000E+000  2.00000E+000  2.00000E+000  4.00000E+000  2.00000E+000  2.00000E+000  4.00000E+000  2.00000E+000
-  2.00000E+000  2.00000E+000  2.00000E+000  2.00000E+000  4.00000E+000  2.00000E+000  2.00000E+000  4.00000E+000  2.00000E+000  2.00000E+000
-  4.00000E+000  2.00000E+000  2.00000E+000  4.00000E+000  2.00000E+000  2.00000E+000  4.00000E+000  2.00000E+000  2.00000E+000  2.00000E+000
-  2.00000E+000  2.00000E+000  2.00000E+000  2.00000E+000  2.00000E+000  4.00000E+000  2.00000E+000  2.00000E+000  4.00000E+000  2.00000E+000
-  2.00000E+000  2.00000E+000  2.00000E+000  2.00000E+000  4.00000E+000  2.00000E+000  2.00000E+000  4.00000E+000  3.00000E+000  3.00000E+000
-  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  4.00000E+000  4.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000
-  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  4.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000
-  3.00000E+000  4.00000E+000  4.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  4.00000E+000
-  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000
-  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000  3.00000E+000
-  3.00000E+000  3.00000E+000  3.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000
-  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000
-  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000
-  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000
-  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000  4.00000E+000
-itp1                             1
-  1.20000E+001  1.20000E+001  1.20000E+001  1.20000E+001  1.00000E+001  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001  1.20000E+001
-  1.00000E+001  1.00000E+001  2.00000E+000  2.00000E+000  1.20000E+001  2.00000E+000  0.00000E+000  1.00000E+001  2.00000E+000  0.00000E+000
-  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001  2.00000E+000  2.00000E+000  1.20000E+001  2.00000E+000  0.00000E+000  1.00000E+001
-  2.00000E+000  0.00000E+000  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001  2.00000E+000  2.00000E+000  1.20000E+001  2.00000E+000
-  0.00000E+000  1.00000E+001  2.00000E+000  0.00000E+000  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001  2.00000E+000  2.00000E+000
-  1.20000E+001  2.00000E+000  0.00000E+000  1.00000E+001  2.00000E+000  0.00000E+000  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001
-  2.00000E+000  2.00000E+000  1.20000E+001  2.00000E+000  0.00000E+000  1.00000E+001  2.00000E+000  0.00000E+000  1.00000E+001  1.20000E+001
-  1.00000E+001  1.00000E+001  1.20000E+001  1.20000E+001  1.20000E+001  1.20000E+001  1.00000E+001  1.00000E+001  1.20000E+001  1.00000E+001
-  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001
-  1.20000E+001  1.00000E+001  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001  2.00000E+000  0.00000E+000  1.00000E+001  2.00000E+000
-  0.00000E+000  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001  2.00000E+000  0.00000E+000  1.00000E+001  2.00000E+000  0.00000E+000
-  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001  2.00000E+000  0.00000E+000  1.00000E+001  2.00000E+000  0.00000E+000  1.00000E+001
-  1.20000E+001  1.00000E+001  1.00000E+001  2.00000E+000  0.00000E+000  1.00000E+001  2.00000E+000  0.00000E+000  1.00000E+001  1.20000E+001
-  1.00000E+001  1.00000E+001  2.00000E+000  0.00000E+000  1.00000E+001  2.00000E+000  0.00000E+000  1.00000E+001  1.20000E+001  1.00000E+001
-  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001  1.20000E+001  1.00000E+001  1.00000E+001  1.20000E+001  1.20000E+001  1.00000E+001
-  1.00000E+001  1.00000E+001  1.00000E+001  1.00000E+001  1.00000E+001  1.20000E+001  2.00000E+000  1.00000E+001  0.00000E+000  1.00000E+001
-  0.00000E+000  1.00000E+001  1.00000E+001  1.20000E+001  2.00000E+000  1.00000E+001  0.00000E+000  1.00000E+001  0.00000E+000  1.00000E+001
-  1.00000E+001  1.20000E+001  2.00000E+000  1.00000E+001  0.00000E+000  1.00000E+001  0.00000E+000  1.00000E+001  1.00000E+001  1.20000E+001
-  2.00000E+000  1.00000E+001  0.00000E+000  1.00000E+001  0.00000E+000  1.00000E+001  1.00000E+001  1.20000E+001  2.00000E+000  1.00000E+001
-  0.00000E+000  1.00000E+001  0.00000E+000  1.00000E+001  1.00000E+001  1.20000E+001  1.20000E+001  1.00000E+001  1.00000E+001  1.00000E+001
-  1.00000E+001  1.00000E+001  1.00000E+001  1.00000E+001  1.00000E+001  1.00000E+001  1.00000E+001  1.00000E+001  1.00000E+001  1.00000E+001
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-endvars
-flags    
-imt1            5         1
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-mr_visco
-ERROR
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-    4    4    4    4    4
-endflag
-material            3         0
-mr_elast
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-    1    1    1    1    1    1    1    2    2    1    1    2    1    1    1    1    1    1    1    1
-    1    1    1    1    2    1    1    1    1    1    1    1    1    1    1    2    2    2    2    2
-    2    2    2    2    2    2    1    1    2    2    1    1    1    1    1    2    2    2    2    2
-    1    2    2    2    1    1    1    1    1    1    1    1
-cycleno          0
-probtime   0.00000E+000
-endgmv

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_ascii.pset
===================================================================
--- short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_ascii.pset	2011-06-02 22:56:39 UTC (rev 18528)
+++ short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_ascii.pset	2011-06-02 22:57:09 UTC (rev 18529)
@@ -1,38 +0,0 @@
-pset ascii         7
-fault    1         35
-         1          2          3         13         14         15         25         26         27         37
-        38         39         49         50         51         61         62         63         73         74
-        75        148        149        156        157        164        165        172        173        180
-       181        188        189        196        197
-boundary_xm    2         35
-        85         86         87         94         95         96        103        104        105        112
-       113        114        121        122        123        130        131        132        139        140
-       141        204        205        210        211        216        217        222        223        228
-       229        234        235        240        241
-boundary_xp    3         35
-        10         11         12         22         23         24         34         35         36         46
-        47         48         58         59         60         70         71         72         82         83
-        84        154        155        162        163        170        171        178        179        186
-       187        194        195        202        203
-boundary_ym    4         35
-         1          2          3          4          5          6          7          8          9         10
-        11         12         85         86         87         88         89         90         91         92
-        93        148        149        150        151        152        153        154        155        204
-       205        206        207        208        209
-boundary_yp    5         35
-        73         74         75         76         77         78         79         80         81         82
-        83         84        139        140        141        142        143        144        145        146
-       147        196        197        198        199        200        201        202        203        240
-       241        242        243        244        245
-boundary_zm    6         49
-       148        150        152        154        156        158        160        162        164        166
-       168        170        172        174        176        178        180        182        184        186
-       188        190        192        194        196        198        200        202        204        206
-       208        210        212        214        216        218        220        222        224        226
-       228        230        232        234        236        238        240        242        244
-boundary_zp    7         49
-         3          6          9         12         15         18         21         24         27         30
-        33         36         39         42         45         48         51         54         57         60
-        63         66         69         72         75         78         81         84         87         90
-        93         96         99        102        105        108        111        114        117        120
-       123        126        129        132        135        138        141        144        147

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_binary.gmv
===================================================================
(Binary files differ)

Deleted: short/3D/PyLith/trunk/examples/3d/tet4/tet4_1000m_binary.pset
===================================================================
(Binary files differ)



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