[cig-commits] r18986 - short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d
brad at geodynamics.org
brad at geodynamics.org
Wed Sep 28 17:40:03 PDT 2011
Author: brad
Date: 2011-09-28 17:40:03 -0700 (Wed, 28 Sep 2011)
New Revision: 18986
Added:
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/gradient.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/plot_faultth.py
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_050m_gradient.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_050m_gradient.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_gradient.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_gradient.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_uniform.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_uniform.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_gradient.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_gradient.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_050m_gradient.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_050m_gradient.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_gradient.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_gradient.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_uniform.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_uniform.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_gradient.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_gradient.jou
Removed:
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/geometry_refine.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_refine.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_refine.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_refine.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_refine.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/refinecells.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_refine.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_refine.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_refine.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_refine.jou
Modified:
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/createbc.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/friction.spatialdb
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/geometry.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/pylithapp.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tabulate_onfaultdata.py
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tractions.spatialdb
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3.cfg
Log:
Updated meshes and config files.
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/createbc.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/createbc.jou 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/createbc.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -2,17 +2,12 @@
# Create blocks for materials
# ----------------------------------------------------------------------
block 1 surface 8 9
-#block 1 surface 11 12 13 14
block 1 name "elastic"
# ----------------------------------------------------------------------
# Create nodeset for fault
# ----------------------------------------------------------------------
group "fault" add node in fault_surface
-#group "fault" add node in fault_surface at A
-#group "fault" add node in fault_surface at B
-group "fault" remove node with y_coord > +15.0001e+3
-group "fault" remove node with y_coord < -15.0001e+3
nodeset 10 group fault
nodeset 10 name "fault"
@@ -45,11 +40,3 @@
group "face_yneg" add node in curve 20
nodeset 14 group face_yneg
nodeset 14 name "face_yneg"
-
-# ----------------------------------------------------------------------
-# Create nodeset for Off-Fault stations
-# ----------------------------------------------------------------------
-#group "off_fault_stat" add node in vertex 15
-#group "off_fault_stat" add node in vertex 16
-#nodeset 15 group off_fault_stat
-#nodeset 15 name "off_fault_stat"
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/friction.spatialdb
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/friction.spatialdb 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/friction.spatialdb 2011-09-29 00:40:03 UTC (rev 18986)
@@ -11,7 +11,7 @@
space-dim = 2
}
}
-0.0 -15.01 10000.0 0.525 0.4 0.0
-0.0 -14.99 0.677 0.525 0.4 0.0
-0.0 +14.99 0.677 0.525 0.4 0.0
-0.0 +15.01 10000.0 0.525 0.4 0.0
+0.0 -15.000 10000.0 0.525 0.4 0.0
+0.0 -14.999 0.677 0.525 0.4 0.0
+0.0 +14.999 0.677 0.525 0.4 0.0
+0.0 +15.000 10000.0 0.525 0.4 0.0
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/geometry.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/geometry.jou 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/geometry.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,13 +1,41 @@
+# -*- Python -*- (syntax highlighting)
# ----------------------------------------------------------------------
+#
+# Brad T. Aagaard, U.S. Geological Survey
+#
+# ----------------------------------------------------------------------
+#
+# CUBIT journal file with geometry for TPV205-2D.
+#
+# ----------------------------------------------------------------------
+# Set units to SI.
+# ----------------------------------------------------------------------
+# {Units('si')}
+#
+# ----------------------------------------------------------------------
+# Reset geometry.
+# ----------------------------------------------------------------------
+reset
+
+# Make sure undo is off to prevent errors in stitching volumes.
+undo off
+
+# ----------------------------------------------------------------------
# Create block
# ----------------------------------------------------------------------
-# Block is 24.0 km x 48.0 km
-# -12.0 km <= x <= 12.0 km
-# -24.0 km <= y <= 24.0 km
+# Block is 48.0 km x 64.0 km
+# -24.0 km <= x <= 24.0 km
+# -32.0 km <= y <= 32.0 km
#
-# We create the 2-D mesh by extracting the mid-surface from a 3-D mesh.
+#{Units('si')}
+#
reset
-brick x 24000 y 48000 z 24000
+
+#{blockWidth=48*km}
+#{blockLength=64*km}
+#{blockHeight=32*km}
+#
+brick x {blockWidth} y {blockLength} z {blockHeight}
create midsurface volume 1 surface 1 2
delete volume 1
@@ -16,25 +44,13 @@
# ----------------------------------------------------------------------
# Create fault (yz plane) at x = 0.0
-split surface 7 across location position 0 -24000 0 location position 0 24000 0
-curve 17 name "fault_surface"
+split surface 7 across location position 0 {-blockLength/2.0} 0 location position 0 {blockLength/2.0} 0
+split curve 17 at position 0.0 {15.0*km} 0.0
+split curve 23 at position 0.0 {-15.0*km} 0.0
+curve 25 name "fault_surface"
# ----------------------------------------------------------------------
-# Create surface for Off-Fault stations
-# ----------------------------------------------------------------------
-
-#create vertex 3000 12000 0
-#create vertex 3000 -12000 0
-#create vertex -3000 -12000 0
-#create vertex -3000 12000 0
-
-#create surface vertex 15 16 17 18
-
-# ----------------------------------------------------------------------
# Imprint all volumes, merging surfaces
# ----------------------------------------------------------------------
imprint all
merge all
-
-
-
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/geometry_refine.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/geometry_refine.jou 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/geometry_refine.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,26 +0,0 @@
-# ----------------------------------------------------------------------
-# Create block
-# ----------------------------------------------------------------------
-# Block is 128.0 km x 128.0 km
-# -64.0 km <= x <= 64.0 km
-# -64.0 km <= y <= 64.0 km
-#
-# We create the 2-D mesh by extracting the mid-surface from a 3-D mesh.
-reset
-brick x 128000 y 128000 z 128000
-create midsurface volume 1 surface 1 2
-delete volume 1
-
-# ----------------------------------------------------------------------
-# Create interface surfaces
-# ----------------------------------------------------------------------
-
-# Create fault (yz plane) at x = 0.0
-split surface 7 across location position 0 -64000 0 location position 0 64000 0
-curve 17 name "fault_surface"
-
-# ----------------------------------------------------------------------
-# Imprint all volumes, merging surfaces
-# ----------------------------------------------------------------------
-imprint all
-merge all
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/gradient.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/gradient.jou (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/gradient.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,44 @@
+# ----------------------------------------------------------------------
+# Set vertex spacing with increasing spacing away from fault
+# ----------------------------------------------------------------------
+#{bias_factor=1.015}
+
+# Function for computing discretization size at end of curve with bias
+#{fun_dx='dxStart*bias_factor**ceil( ln(1-curveL/dxStart*(1-bias_factor))/ln(bias_factor))'}
+
+# ----------------------------------------------------------------------
+# Compute sizes at curve endpoints
+# ----------------------------------------------------------------------
+
+# dxA - size at vertex 13 14
+#{dxStart=dx}{curveL=Length(22)}{execute("dxA="//fun_dx)}
+
+# dxB - size at vertex 9 10 11 12
+#{dxStart=dxA}{curveL=Length(21)}{execute("dxC="//fun_dx)}
+
+# ----------------------------------------------------------------------
+# Reset sizes
+# ----------------------------------------------------------------------
+curve all scheme default
+surface all sizing function none
+
+# Set size on faults
+curve fault_surface size {dx}
+
+# Set bias on curves extending from faults
+curve 22 scheme bias fine size {dx} factor {bias_factor} start vertex 15
+curve 24 scheme bias fine size {dx} factor {bias_factor} start vertex 16
+
+# A to B
+curve 18 scheme bias fine size {dxA} factor {bias_factor} start vertex 13
+curve 21 scheme bias fine size {dxA} factor {bias_factor} start vertex 13
+curve 19 scheme bias fine size {dxA} factor {bias_factor} start vertex 14
+curve 20 scheme bias fine size {dxA} factor {bias_factor} start vertex 14
+
+# B to B
+curve 16 size {dxC}
+curve 14 size {dxC}
+
+
+# End of file
+
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/plot_faultth.py
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/plot_faultth.py (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/plot_faultth.py 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,107 @@
+#!/usr/bin/env python
+#
+# ======================================================================
+#
+# Brad T. Aagaard
+# U.S. Geological Survey
+#
+# {LicenseText}
+#
+# ======================================================================
+#
+
+cell = "quad4"
+dx = 200
+
+inputRoot = "output/%s_%3dm_%s-fault" % (cell,dx,"gradient")
+
+# ======================================================================
+import tables
+import numpy
+import pylab
+from mypylab.Figure import Figure
+
+if dx == 200:
+ targets = numpy.array([[0.0, -12000.0, 0.0],
+ [0.0, -7600.0, 0.0],
+ [0.0, -4400.0, 0.0],
+ [0.0, 0.0, 0.0],
+ [0.0, +4400.0, 0.0],
+ [0.0, +7600.0, 0.0],
+ [0.0, +12000.0, 0.0]])
+elif dx == 100 or dx == 50:
+ targets = numpy.array([[0.0, -12000.0, 0.0],
+ [0.0, -7500.0, 0.0],
+ [0.0, -4500.0, 0.0],
+ [0.0, 0.0, 0.0],
+ [0.0, +4500.0, 0.0],
+ [0.0, +7500.0, 0.0],
+ [0.0, +12000.0, 0.0]])
+
+# ----------------------------------------------------------------------
+tolerance = 1.0e-6
+
+h5 = tables.openFile("%s.h5" % inputRoot, 'r')
+vertices = h5.root.geometry.vertices[:]
+ntargets = targets.shape[0]
+indices = []
+for target in targets:
+ dist = ( (vertices[:,0]-target[0])**2 +
+ (vertices[:,1]-target[1])**2 )**0.5
+ min = numpy.min(dist)
+ indices.append(numpy.where(dist <= min+tolerance)[0][0])
+
+print "Indices: ", indices
+print "Coordinates of selected points:\n",vertices[indices,:]
+
+
+# Get datasets
+slip = h5.root.vertex_fields.slip[:]
+slip_rate = h5.root.vertex_fields.slip_rate[:]
+traction = h5.root.vertex_fields.traction[:]
+timeStamps = h5.root.time[:].ravel()
+nsteps = timeStamps.shape[0]
+dt = timeStamps[1] - timeStamps[0]
+
+h5.close()
+
+
+nrows = 2
+ncols = 2
+irow = 1
+icol = 1
+
+fig = Figure(fontsize=8, color="lightbg")
+fig.open(7.0, 7.25, margins=[[0.6, 0.6, 0.2],
+ [0.6, 0.5, 0.2]])
+
+ax = fig.axes(nrows, ncols, irow, icol)
+ax.plot(timeStamps, slip_rate[:,indices,0])
+ax.set_xlabel("Time (s)")
+ax.set_ylabel("Slip Rate (m/s)")
+icol += 1
+
+ax = fig.axes(nrows, ncols, irow, icol)
+ax.plot(timeStamps, -traction[:,indices,0]/traction[:,indices,1])
+ax.set_xlabel("Time (s)")
+ax.set_ylabel("Shear/Normal Traction")
+icol += 1
+
+irow = 2
+icol = 1
+ax = fig.axes(nrows, ncols, irow, icol)
+ax.plot(timeStamps, -traction[:,indices,0])
+ax.set_xlabel("Time (s)")
+ax.set_ylabel("Shear Traction (MPa)")
+icol += 1
+
+ax = fig.axes(nrows, ncols, irow, icol)
+ax.plot(timeStamps, traction[:,indices,1])
+ax.set_xlabel("Time (s)")
+ax.set_ylabel("Normal Traction (MPa)")
+icol += 1
+
+pylab.show()
+
+
+# End of file
Property changes on: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/plot_faultth.py
___________________________________________________________________
Name: svn:executable
+ *
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/pylithapp.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/pylithapp.cfg 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/pylithapp.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -17,7 +17,7 @@
faultcohesivedyn = 1
[pylithapp.journal.debug]
-#pylithapp = 1
+pylithapp = 1
#problem = 1
#explicit = 1
@@ -26,7 +26,10 @@
# ----------------------------------------------------------------------
[pylithapp.mesh_generator]
reader = pylith.meshio.MeshIOCubit
-reorder_mesh = True
+#reorder_mesh = True
+distributor.partitioner = parmetis
+distributor.write_partition = True
+distributor.data_writer.filename = partition.vtk
[pylithapp.mesh_generator.reader]
coordsys.space_dim = 2
@@ -35,58 +38,39 @@
# problem
# ----------------------------------------------------------------------
[pylithapp.timedependent]
-
dimension = 2
-# Set interfaces to an array with 1 faults: 'fault'.
-interfaces = [fault]
-
-# Set materials to an array with 1 material 'elastic'.
-materials = [elastic]
-
-#formulation = pylith.problems.Explicit
-#formulation.solver = pylith.problems.SolverNonlinear
formulation = pylith.problems.ExplicitLumped
-
-# Nondimensionalize problem using wave propagation parameters.
+formulation.norm_viscosity = 0.2
normalizer = spatialdata.units.NondimElasticDynamic
-#normalizer.mass_density = 1000.0*kg/m**3
-#normalizer.shear_wave_speed = 1.0*m/s
-#normalizer.wave_period = 1.0*s
-bc = [x_neg,x_pos,y_neg,y_pos]
-
-# Change the DirichletPoints BC to the AbsorbingDampers BC
-bc.x_neg = pylith.bc.AbsorbingDampers
-bc.x_pos = pylith.bc.AbsorbingDampers
-bc.y_neg = pylith.bc.AbsorbingDampers
-bc.y_pos = pylith.bc.AbsorbingDampers
-
[pylithapp.timedependent.formulation.time_step]
-total_time = 12.01*s
+total_time = 12.001*s
dt = 0.01*s
-
-# Set subdomain component to OutputSolnSubset (subset of domain).
-#output.subdomain = pylith.meshio.OutputSolnSubset
-
-
# ----------------------------------------------------------------------
# materials
# ----------------------------------------------------------------------
[pylithapp.timedependent]
-
materials = [elastic]
materials.elastic = pylith.materials.ElasticPlaneStrain
[pylithapp.timedependent.materials.elastic]
label = Elastic material
id = 1
+db_properties.label = Elastic properties
db_properties.iohandler.filename = matprops.spatialdb
# ----------------------------------------------------------------------
# boundary conditions
# ----------------------------------------------------------------------
+[pylithapp.timedependent]
+bc = [x_neg,x_pos,y_neg,y_pos]
+bc.x_neg = pylith.bc.AbsorbingDampers
+bc.x_pos = pylith.bc.AbsorbingDampers
+bc.y_neg = pylith.bc.AbsorbingDampers
+bc.y_pos = pylith.bc.AbsorbingDampers
+
[pylithapp.timedependent.bc.x_pos]
label = face_xpos
db.label = Absorbing BC +x
@@ -110,25 +94,20 @@
# ----------------------------------------------------------------------
# faults
# ----------------------------------------------------------------------
+[pylithapp.timedependent]
+interfaces = [fault]
+interfaces.fault = pylith.faults.FaultCohesiveDyn
-# Provide information on the fault (interface).
-[pylithapp.timedependent.interfaces]
-
-fault = pylith.faults.FaultCohesiveDyn
-
[pylithapp.timedependent.interfaces.fault]
-
-# Material id
id = 10
-
-# Name of nodeset from CUBIT
label = fault
db_initial_tractions = spatialdata.spatialdb.SimpleDB
db_initial_tractions.iohandler.filename = tractions.spatialdb
-db_initial_tractions.label = "Initial fault tractions"
+db_initial_tractions.label = Initial fault tractions
friction = pylith.friction.SlipWeakening
+friction.label = Slip weakening
friction.db_properties = spatialdata.spatialdb.SimpleDB
friction.db_properties.iohandler.filename = friction.spatialdb
@@ -137,61 +116,31 @@
# ----------------------------------------------------------------------
# output
# ----------------------------------------------------------------------
-# Give basename for VTK domain output of solution over domain.
[pylithapp.problem.formulation.output.output]
vertex_data_fields=[displacement,velocity]
output_freq = time_step
time_step = 0.04999*s
-writer.time_format = %06.3f
+writer = pylith.meshio.DataWriterHDF5ExtMesh
-# Give basename for VTK fault output.
[pylithapp.timedependent.interfaces.fault.output]
vertex_info_fields = [strike_dir,normal_dir,initial_traction]
vertex_data_fields = [slip,slip_rate,traction]
output_freq = time_step
time_step = 0.04999*s
-writer.time_format = %06.3f
+writer = pylith.meshio.DataWriterHDF5ExtSubSubMesh
-# Give basename for VTK output of state variables.
[pylithapp.timedependent.materials.elastic.output]
+cell_data_fields = []
cell_filter = pylith.meshio.CellFilterAvgMesh
output_freq = time_step
time_step = 12.0*s
-writer.time_format = %06.3f
+writer = pylith.meshio.DataWriterHDF5ExtMesh
# ----------------------------------------------------------------------
# PETSc
# ----------------------------------------------------------------------
[pylithapp.petsc]
-pc_type = asm
-
-# Change the preconditioner settings.
-sub_pc_factor_shift_type = nonzero
-
-ksp_rtol = 1.0e-8
-ksp_atol = 1.0e-15
-ksp_max_it = 100
-ksp_gmres_restart = 50
-snes_max_it = 200
-
-ksp_monitor = true
-ksp_view = true
-ksp_converged_reason = true
-
-snes_monitor = true
-snes_view = true
-snes_converged_reason = true
-
log_summary = true
-# Friction sensitivity solve
-friction_pc_type = asm
-friction_sub_pc_factor_shift_type = nonzero
-friction_ksp_max_it = 25
-friction_ksp_gmres_restart = 30
-
-friction_ksp_monitor = true
-friction_ksp_view = true
-friction_ksp_converged_reason = true
-
+# End of file
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4.cfg 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -7,6 +7,7 @@
[pylithapp.timedependent.materials.elastic]
quadrature.cell = pylith.feassemble.FIATLagrange
quadrature.cell.dimension = 2
+quadrature.cell.quad_order = 2
# ----------------------------------------------------------------------
@@ -40,3 +41,6 @@
quadrature.cell = pylith.feassemble.FIATLagrange
quadrature.cell.dimension = 1
quadrature.cell.quad_order = 2
+
+
+# End of file
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_050m_gradient.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_050m_gradient.cfg (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_050m_gradient.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,29 @@
+# -*- Python -*-
+[pylithapp]
+
+# ----------------------------------------------------------------------
+# mesh_generator
+# ----------------------------------------------------------------------
+[pylithapp.mesh_generator.reader]
+filename = quad4_050m_gradient.exo
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.formulation.time_step]
+dt = 0.005*s
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+[pylithapp.problem.formulation.output.output]
+writer.filename = output/quad4_050m_gradient.h5
+
+[pylithapp.timedependent.interfaces.fault.output]
+writer.filename = output/quad4_050m_gradient-fault.h5
+
+[pylithapp.timedependent.materials.elastic.output]
+writer.filename = output/quad4_050m_gradient-elastic.h5
+
+
+# End of file
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_050m_gradient.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_050m_gradient.jou (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_050m_gradient.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,40 @@
+# ----------------------------------------------------------------------
+# Create tri3 mesh at 100m resolution.
+# ----------------------------------------------------------------------
+
+# ----------------------------------------------------------------------
+# Generate geometry
+# ----------------------------------------------------------------------
+playback 'geometry.jou'
+
+# ----------------------------------------------------------------------
+# Set discretization size and scheme
+# ----------------------------------------------------------------------
+#{dx=50*m}
+surface all scheme pave
+playback 'gradient.jou'
+
+# ----------------------------------------------------------------------
+# Generate the mesh
+# ----------------------------------------------------------------------
+mesh surface all
+
+# ----------------------------------------------------------------------
+# Smooth mesh to improve quality
+# ----------------------------------------------------------------------
+surface all smooth scheme laplacian
+smooth surface all
+surface all smooth scheme condition number beta 1.5 cpu 10
+smooth surface all
+
+# ----------------------------------------------------------------------
+# Setup boundary conditions.
+# ----------------------------------------------------------------------
+playback 'createbc.jou'
+
+# ----------------------------------------------------------------------
+# Export exodus file
+# ----------------------------------------------------------------------
+export mesh "quad4_050m_gradient.exo" dimension 2 overwrite
+
+
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m.cfg 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,29 +0,0 @@
-# -*- Python -*-
-[pylithapp]
-
-# ----------------------------------------------------------------------
-# mesh_generator
-# ----------------------------------------------------------------------
-[pylithapp.mesh_generator.reader]
-filename = quad4_100m.exo
-
-# ----------------------------------------------------------------------
-# problem
-# ----------------------------------------------------------------------
-[pylithapp.timedependent.formulation.time_step]
-dt = 0.01*s
-
-# ----------------------------------------------------------------------
-# output
-# ----------------------------------------------------------------------
-# Give basename for VTK domain output of solution over domain.
-[pylithapp.problem.formulation.output.output]
-writer.filename = output/quad4_100m.vtk
-
-# Give basename for VTK fault output.
-[pylithapp.timedependent.interfaces.fault.output]
-writer.filename = output/quad4_100m-fault.vtk
-
-# Give basename for VTK output of state variables.
-[pylithapp.timedependent.materials.elastic.output]
-writer.filename = output/quad4_100m-elastic.vtk
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m.jou 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,28 +0,0 @@
-# ----------------------------------------------------------------------
-# Create quad4 mesh at 100m resolution.
-# ----------------------------------------------------------------------
-
-# ----------------------------------------------------------------------
-# Generate geometry
-# ----------------------------------------------------------------------
-playback 'geometry.jou'
-
-# ----------------------------------------------------------------------
-# Set discretization size
-# ----------------------------------------------------------------------
-surface all size 100
-
-# ----------------------------------------------------------------------
-# Generate the mesh
-# ----------------------------------------------------------------------
-mesh surface all
-
-# ----------------------------------------------------------------------
-# Setup boundary conditions.
-# ----------------------------------------------------------------------
-playback 'createbc.jou'
-
-# ----------------------------------------------------------------------
-# Export exodus file
-# ----------------------------------------------------------------------
-export mesh "quad4_100m.exo" dimension 2 overwrite
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_gradient.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_gradient.cfg (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_gradient.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,29 @@
+# -*- Python -*-
+[pylithapp]
+
+# ----------------------------------------------------------------------
+# mesh_generator
+# ----------------------------------------------------------------------
+[pylithapp.mesh_generator.reader]
+filename = quad4_100m_gradient.exo
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.formulation.time_step]
+dt = 0.01*s
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+[pylithapp.problem.formulation.output.output]
+writer.filename = output/quad4_100m_gradient.h5
+
+[pylithapp.timedependent.interfaces.fault.output]
+writer.filename = output/quad4_100m_gradient-fault.h5
+
+[pylithapp.timedependent.materials.elastic.output]
+writer.filename = output/quad4_100m_gradient-elastic.h5
+
+
+# End of file
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_gradient.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_gradient.jou (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_gradient.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,39 @@
+# ----------------------------------------------------------------------
+# Create tri3 mesh at 100m resolution.
+# ----------------------------------------------------------------------
+
+# ----------------------------------------------------------------------
+# Generate geometry
+# ----------------------------------------------------------------------
+playback 'geometry.jou'
+
+# ----------------------------------------------------------------------
+# Set discretization size and scheme
+# ----------------------------------------------------------------------
+#{dx=100*m}
+surface all scheme pave
+playback 'gradient.jou'
+
+# ----------------------------------------------------------------------
+# Generate the mesh
+# ----------------------------------------------------------------------
+mesh surface all
+
+# ----------------------------------------------------------------------
+# Smooth mesh to improve quality
+# ----------------------------------------------------------------------
+surface all smooth scheme laplacian
+smooth surface all
+surface all smooth scheme condition number beta 1.3 cpu 10
+smooth surface all
+
+# ----------------------------------------------------------------------
+# Setup boundary conditions.
+# ----------------------------------------------------------------------
+playback 'createbc.jou'
+
+# ----------------------------------------------------------------------
+# Export exodus file
+# ----------------------------------------------------------------------
+export mesh "quad4_100m_gradient.exo" dimension 2 overwrite
+
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_refine.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_refine.cfg 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_refine.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,30 +0,0 @@
-# -*- Python -*-
-[pylithapp]
-
-# ----------------------------------------------------------------------
-# mesh_generator
-# ----------------------------------------------------------------------
-[pylithapp.mesh_generator.reader]
-filename = quad4_100m_refine.exo
-
-# ----------------------------------------------------------------------
-# problem
-# ----------------------------------------------------------------------
-[pylithapp.timedependent.formulation.time_step]
-dt = 0.01*s
-
-
-# ----------------------------------------------------------------------
-# output
-# ----------------------------------------------------------------------
-# Give basename for VTK domain output of solution over domain.
-[pylithapp.problem.formulation.output.output]
-writer.filename = output/quad4_100m_refine.vtk
-
-# Give basename for VTK fault output.
-[pylithapp.timedependent.interfaces.fault.output]
-writer.filename = output/quad4_100m_refine-fault.vtk
-
-# Give basename for VTK output of state variables.
-[pylithapp.timedependent.materials.elastic.output]
-writer.filename = output/quad4_100m_refine-elastic.vtk
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_refine.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_refine.jou 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_refine.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,39 +0,0 @@
-# ----------------------------------------------------------------------
-# Create quad4 mesh at 100m resolution.
-# ----------------------------------------------------------------------
-
-# ----------------------------------------------------------------------
-# Generate geometry
-# ----------------------------------------------------------------------
-playback 'geometry_refine.jou'
-
-# ----------------------------------------------------------------------
-# Set discretization size
-# ----------------------------------------------------------------------
-surface all size 400
-
-# ----------------------------------------------------------------------
-# Generate the mesh
-# ----------------------------------------------------------------------
-mesh surface all
-
-# ----------------------------------------------------------------------
-# Refine elements within 1/2 of rupture width
-# ----------------------------------------------------------------------
-playback 'refinecells.jou'
-
-# ----------------------------------------------------------------------
-# Smooth mesh to improve quality
-# ----------------------------------------------------------------------
-surface all smooth scheme condition number beta 1.3 cpu 10
-smooth surface all
-
-# ----------------------------------------------------------------------
-# Setup boundary conditions.
-# ----------------------------------------------------------------------
-playback 'createbc.jou'
-
-# ----------------------------------------------------------------------
-# Export exodus file
-# ----------------------------------------------------------------------
-export mesh "quad4_100m_refine.exo" dimension 2 overwrite
Copied: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_uniform.cfg (from rev 17829, short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m.cfg)
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_uniform.cfg (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_uniform.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,29 @@
+# -*- Python -*-
+[pylithapp]
+
+# ----------------------------------------------------------------------
+# mesh_generator
+# ----------------------------------------------------------------------
+[pylithapp.mesh_generator.reader]
+filename = quad4_100m_uniform.exo
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.formulation.time_step]
+dt = 0.01*s
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+[pylithapp.problem.formulation.output.output]
+writer.filename = output/quad4_100m_uniform.h5
+
+[pylithapp.timedependent.interfaces.fault.output]
+writer.filename = output/quad4_100m_uniform-fault.h5
+
+[pylithapp.timedependent.materials.elastic.output]
+writer.filename = output/quad4_100m_uniform-elastic.h5
+
+
+# End of file
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_uniform.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_uniform.jou (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_100m_uniform.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,32 @@
+# ----------------------------------------------------------------------
+# Create tri3 mesh at 100m resolution.
+# ----------------------------------------------------------------------
+
+# ----------------------------------------------------------------------
+# Generate geometry
+# ----------------------------------------------------------------------
+playback 'geometry.jou'
+
+# ----------------------------------------------------------------------
+# Set discretization size and scheme
+# ----------------------------------------------------------------------
+#{dx=100*m}
+surface all scheme map
+surface all size {dx}
+
+# ----------------------------------------------------------------------
+# Generate the mesh
+# ----------------------------------------------------------------------
+mesh surface all
+
+# ----------------------------------------------------------------------
+# Setup boundary conditions.
+# ----------------------------------------------------------------------
+playback 'createbc.jou'
+
+# ----------------------------------------------------------------------
+# Export exodus file
+# ----------------------------------------------------------------------
+export mesh "quad4_100m_uniform.exo" dimension 2 overwrite
+
+
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m.cfg 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,39 +0,0 @@
-# -*- Python -*-
-[pylithapp]
-
-# ----------------------------------------------------------------------
-# mesh_generator
-# ----------------------------------------------------------------------
-[pylithapp.mesh_generator.reader]
-filename = quad4_200m.exo
-
-# ----------------------------------------------------------------------
-# problem
-# ----------------------------------------------------------------------
-[pylithapp.timedependent.formulation.time_step]
-dt = 0.01666666666666666666666667*s
-
-
-# ----------------------------------------------------------------------
-# output
-# ----------------------------------------------------------------------
-# Give basename for VTK domain output of solution over domain.
-[pylithapp.problem.formulation.output.output]
-writer.filename = output/quad4_200m.vtk
-
-# Give basename for VTK domain output of solution over Off-fault stations.
-#[pylithapp.problem.formulation.output.subdomain]
-#label = 15 ; nodeset for subdomain
-#vertex_data_fields=[displacement,velocity]
-#output_freq = time_step
-#time_step = 0.04999*s
-#writer.filename = output/quad4_200m_OffFault.vtk
-#writer.time_format = %05.2f
-
-# Give basename for VTK fault output.
-[pylithapp.timedependent.interfaces.fault.output]
-writer.filename = output/quad4_200m-fault.vtk
-
-# Give basename for VTK output of state variables.
-[pylithapp.timedependent.materials.elastic.output]
-writer.filename = output/quad4_200m-elastic.vtk
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m.jou 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,29 +0,0 @@
-# ----------------------------------------------------------------------
-# Create quad4 mesh at 200m resolution.
-# ----------------------------------------------------------------------
-
-# ----------------------------------------------------------------------
-# Generate geometry
-# ----------------------------------------------------------------------
-playback 'geometry.jou'
-
-# ----------------------------------------------------------------------
-# Set discretization size
-# ----------------------------------------------------------------------
-surface all size 200
-
-# ----------------------------------------------------------------------
-# Generate the mesh
-# ----------------------------------------------------------------------
-mesh surface all
-
-# ----------------------------------------------------------------------
-# Setup boundary conditions.
-# ----------------------------------------------------------------------
-playback 'createbc.jou'
-
-# ----------------------------------------------------------------------
-# Export exodus file
-# ----------------------------------------------------------------------
-export mesh "quad4_200m.exo" dimension 2 overwrite
-
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_gradient.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_gradient.cfg (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_gradient.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,29 @@
+# -*- Python -*-
+[pylithapp]
+
+# ----------------------------------------------------------------------
+# mesh_generator
+# ----------------------------------------------------------------------
+[pylithapp.mesh_generator.reader]
+filename = quad4_200m_gradient.exo
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.formulation.time_step]
+dt = 0.02*s
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+[pylithapp.problem.formulation.output.output]
+writer.filename = output/quad4_200m_gradient.h5
+
+[pylithapp.timedependent.interfaces.fault.output]
+writer.filename = output/quad4_200m_gradient-fault.h5
+
+[pylithapp.timedependent.materials.elastic.output]
+writer.filename = output/quad4_200m_gradient-elastic.h5
+
+
+# End of file
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_gradient.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_gradient.jou (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_gradient.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,40 @@
+# ----------------------------------------------------------------------
+# Create tri3 mesh at 100m resolution.
+# ----------------------------------------------------------------------
+
+# ----------------------------------------------------------------------
+# Generate geometry
+# ----------------------------------------------------------------------
+playback 'geometry.jou'
+
+# ----------------------------------------------------------------------
+# Set discretization size and scheme
+# ----------------------------------------------------------------------
+#{dx=200*m}
+surface all scheme pave
+playback 'gradient.jou'
+
+# ----------------------------------------------------------------------
+# Generate the mesh
+# ----------------------------------------------------------------------
+mesh surface all
+
+# ----------------------------------------------------------------------
+# Smooth mesh to improve quality
+# ----------------------------------------------------------------------
+surface all smooth scheme laplacian
+smooth surface all
+surface all smooth scheme condition number beta 1.3 cpu 10
+smooth surface all
+
+# ----------------------------------------------------------------------
+# Setup boundary conditions.
+# ----------------------------------------------------------------------
+playback 'createbc.jou'
+
+# ----------------------------------------------------------------------
+# Export exodus file
+# ----------------------------------------------------------------------
+export mesh "quad4_200m_gradient.exo" dimension 2 overwrite
+
+
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_refine.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_refine.cfg 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_refine.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,30 +0,0 @@
-# -*- Python -*-
-[pylithapp]
-
-# ----------------------------------------------------------------------
-# mesh_generator
-# ----------------------------------------------------------------------
-[pylithapp.mesh_generator.reader]
-filename = quad4_200m_refine.exo
-
-# ----------------------------------------------------------------------
-# problem
-# ----------------------------------------------------------------------
-[pylithapp.timedependent.formulation.time_step]
-dt = 0.01666666666666666666666667*s
-
-
-# ----------------------------------------------------------------------
-# output
-# ----------------------------------------------------------------------
-# Give basename for VTK domain output of solution over domain.
-[pylithapp.problem.formulation.output.output]
-writer.filename = output/quad4_200m_refine.vtk
-
-# Give basename for VTK fault output.
-[pylithapp.timedependent.interfaces.fault.output]
-writer.filename = output/quad4_200m_refine-fault.vtk
-
-# Give basename for VTK output of state variables.
-[pylithapp.timedependent.materials.elastic.output]
-writer.filename = output/quad4_200m_refine-elastic.vtk
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_refine.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_refine.jou 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/quad4_200m_refine.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,39 +0,0 @@
-# ----------------------------------------------------------------------
-# Create quad4 mesh at 200m resolution.
-# ----------------------------------------------------------------------
-
-# ----------------------------------------------------------------------
-# Generate geometry
-# ----------------------------------------------------------------------
-playback 'geometry_refine.jou'
-
-# ----------------------------------------------------------------------
-# Set discretization size
-# ----------------------------------------------------------------------
-surface all size 800
-
-# ----------------------------------------------------------------------
-# Generate the mesh
-# ----------------------------------------------------------------------
-mesh surface all
-
-# ----------------------------------------------------------------------
-# Refine elements within 1/2 of rupture width
-# ----------------------------------------------------------------------
-playback 'refinecells.jou'
-
-# ----------------------------------------------------------------------
-# Smooth mesh to improve quality
-# ----------------------------------------------------------------------
-surface all smooth scheme condition number beta 1.3 cpu 10
-smooth surface all
-
-# ----------------------------------------------------------------------
-# Setup boundary conditions.
-# ----------------------------------------------------------------------
-playback 'createbc.jou'
-
-# ----------------------------------------------------------------------
-# Export exodus file
-# ----------------------------------------------------------------------
-export mesh "quad4_200m_refine.exo" dimension 2 overwrite
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/refinecells.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/refinecells.jou 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/refinecells.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,7 +0,0 @@
-# ----------------------------------------------------------------------
-# Refine elements within 1/2 of rupture width
-# ----------------------------------------------------------------------
-group "refinecells1" add node with x_min >= -24.001e+3 and x_max <= 24.001e+3 and y_min >= -36.001e+3 and y_max <= 36.001e+3
-refine node in refinecells1 depth 1
-group "refinecells2" add node with x_min >= -12.001e+3 and x_max <= 12.001e+3 and y_min >= -24.001e+3 and y_max <= 24.001e+3
-refine node in refinecells2 depth 1
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tabulate_onfaultdata.py
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tabulate_onfaultdata.py 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tabulate_onfaultdata.py 2011-09-29 00:40:03 UTC (rev 18986)
@@ -12,18 +12,16 @@
cell = "quad4"
dx = 100
-dt = 0.05
-outputRoot = "output/%s_%3dm_%s" % (cell,dx,"refine")
-outdir = "scecfiles/%s_%3dm_%s/" % (cell,dx,"refine")
+inputRoot = "output/%s_%3dm_%s-fault" % (cell,dx,"gradient")
+outdir = "scecfiles/%s_%3dm_%s/" % (cell,dx,"gradient")
+# ----------------------------------------------------------------------
+import tables
import numpy
import time
-from pylith.utils.VTKDataReader import VTKDataReader
-
# ----------------------------------------------------------------------
-timestamps = numpy.arange(50,12001,50)
if dx == 200:
targets = numpy.array([[0.0, -12000.0, 0.0],
[0.0, -7600.0, 0.0],
@@ -32,7 +30,7 @@
[0.0, +4400.0, 0.0],
[0.0, +7600.0, 0.0],
[0.0, +12000.0, 0.0]])
-elif dx == 100:
+elif dx == 100 or dx == 50:
targets = numpy.array([[0.0, -12000.0, 0.0],
[0.0, -7500.0, 0.0],
[0.0, -4500.0, 0.0],
@@ -42,49 +40,44 @@
[0.0, +12000.0, 0.0]])
-reader = VTKDataReader()
tolerance = 1.0e-6
-# Get vertices and find indices of target locations
-filename = "%s-fault_t%05d.vtk" % (outputRoot,timestamps[0])
-data = reader.read(filename)
-
-vertices = numpy.array(data['vertices'])
+h5 = tables.openFile("%s.h5" % inputRoot, 'r')
+vertices = h5.root.geometry.vertices[:]
ntargets = targets.shape[0]
indices = []
for target in targets:
dist = ( (vertices[:,0]-target[0])**2 +
- (vertices[:,1]-target[1])**2 +
- (vertices[:,2]-target[2])**2 )**0.5
+ (vertices[:,1]-target[1])**2 )**0.5
min = numpy.min(dist)
- indices.append(numpy.where(dist <= min+tolerance)[0])
+ indices.append(numpy.where(dist <= min+tolerance)[0][0])
-print "Indices", indices
-print "Coordinates of selected points:",vertices[indices,:]
+print "Indices: ", indices
+print "Coordinates of selected points:\n",vertices[indices,:]
-# Extract values
-nsteps = timestamps.shape[0]
-slip = numpy.zeros((nsteps,ntargets,3)) # 3-D array (time, targets, components)
-slip_rate = numpy.zeros((nsteps,ntargets,3))
-traction = numpy.zeros((nsteps,ntargets,3))
-itime = 0
-for timestamp in timestamps:
- filename = "%s-fault_t%05d.vtk" % (outputRoot,timestamp)
- data = reader.read(filename)
- fields = data['vertex_fields']
- slip[itime,0:ntargets,:] = fields['slip'][indices,:].squeeze()
- slip_rate[itime,0:ntargets,:] = fields['slip_rate'][indices,:].squeeze()
- traction[itime,0:ntargets,:] = fields['traction'][indices,:].squeeze()
- itime += 1
+# Get datasets
+slip = h5.root.vertex_fields.slip[:]
+slip_rate = h5.root.vertex_fields.slip_rate[:]
+traction = h5.root.vertex_fields.traction[:]
+timeStamps = h5.root.time[:].ravel()
+nsteps = timeStamps.shape[0]
+dt = timeStamps[1] - timeStamps[0]
+h5.close()
+
+# Extract locations
+slip = slip[:,indices,:]
+slip_rate = slip_rate[:,indices,:]
+traction = traction[:,indices,:]
+
# Write data
headerA = \
- "# problem = TPV205\n" + \
- "# author = Surendra N. Somala\n" + \
+ "# problem = TPV205-2D\n" + \
+ "# author = Brad Aagaard\n" + \
"# date = %s\n" % (time.asctime()) + \
"# code = PyLith\n" + \
- "# code_version = 1.5.0a\n" + \
+ "# code_version = 1.6.2\n" + \
"# element_size = %s\n" % dx
headerB = \
"# Time series in 7 columns of E14.6:\n" + \
@@ -107,8 +100,6 @@
timeScale = 1000.0
dip = 7.5
strike = targets[:,1] / lengthScale
-time = timestamps / timeScale
-print "time", time
for iloc in xrange(ntargets):
pt = locName % (round(10*strike[iloc]),
@@ -120,12 +111,12 @@
fout.write("# num_timesteps = %8d\n" % nsteps)
fout.write(locHeader % (strike[iloc], dip))
fout.write(headerB)
- data = numpy.transpose((time,
+ data = numpy.transpose((timeStamps,
-slip[:,iloc,0],
-slip_rate[:,iloc,0],
-traction[:,iloc,0]/1e+6,
- +slip[:,iloc,2],
- +slip_rate[:,iloc,2],
- +traction[:,iloc,2]/1e+6))
+ +slip[:,iloc,1],
+ +slip_rate[:,iloc,1],
+ +traction[:,iloc,1]/1e+6))
numpy.savetxt(fout, data, fmt='%14.6e')
fout.close()
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tractions.spatialdb
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tractions.spatialdb 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tractions.spatialdb 2011-09-29 00:40:03 UTC (rev 18986)
@@ -3,7 +3,7 @@
num-values = 2
value-names = traction-shear traction-normal
value-units = MPa MPa
- num-locs = 12
+ num-locs = 12
data-dim = 2
space-dim = 2
cs-data = cartesian {
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3.cfg 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -2,35 +2,52 @@
[pylithapp]
# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent]
+formulation = pylith.problems.ExplicitLumpedTri3
+
+
+# ----------------------------------------------------------------------
# materials
# ----------------------------------------------------------------------
[pylithapp.timedependent.materials.elastic]
quadrature.cell = pylith.feassemble.FIATSimplex
quadrature.cell.shape = triangle
+quadrature.cell.quad_order = 2
+
# ----------------------------------------------------------------------
# boundary conditions
# ----------------------------------------------------------------------
[pylithapp.timedependent.bc.x_pos]
quadrature.cell = pylith.feassemble.FIATSimplex
quadrature.cell.shape = line
+quadrature.cell.quad_order = 2
[pylithapp.timedependent.bc.x_neg]
quadrature.cell = pylith.feassemble.FIATSimplex
quadrature.cell.shape = line
+quadrature.cell.quad_order = 2
[pylithapp.timedependent.bc.y_pos]
quadrature.cell = pylith.feassemble.FIATSimplex
quadrature.cell.shape = line
+quadrature.cell.quad_order = 2
[pylithapp.timedependent.bc.y_neg]
quadrature.cell = pylith.feassemble.FIATSimplex
quadrature.cell.shape = line
+quadrature.cell.quad_order = 2
+
# ----------------------------------------------------------------------
# faults
# ----------------------------------------------------------------------
[pylithapp.timedependent.interfaces.fault]
quadrature.cell = pylith.feassemble.FIATSimplex
quadrature.cell.shape = line
+quadrature.cell.quad_order = 2
+
+# End of file
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_050m_gradient.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_050m_gradient.cfg (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_050m_gradient.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,32 @@
+# -*- Python -*-
+[pylithapp]
+
+# ----------------------------------------------------------------------
+# mesh_generator
+# ----------------------------------------------------------------------
+[pylithapp.mesh_generator.reader]
+filename = tri3_050m_gradient.exo
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.formulation.time_step]
+dt = 0.005*s
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+# Give basename for VTK domain output of solution over domain.
+[pylithapp.problem.formulation.output.output]
+writer.filename = output/tri3_050m_gradient.h5
+
+# Give basename for VTK fault output.
+[pylithapp.timedependent.interfaces.fault.output]
+writer.filename = output/tri3_050m_gradient-fault.h5
+
+# Give basename for VTK output of state variables.
+[pylithapp.timedependent.materials.elastic.output]
+writer.filename = output/tri3_050m_gradient-elastic.h5
+
+
+# End of file
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_050m_gradient.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_050m_gradient.jou (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_050m_gradient.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,38 @@
+# ----------------------------------------------------------------------
+# Create tri3 mesh at 100m resolution.
+# ----------------------------------------------------------------------
+
+# ----------------------------------------------------------------------
+# Generate geometry
+# ----------------------------------------------------------------------
+playback 'geometry.jou'
+
+# ----------------------------------------------------------------------
+# Set discretization size and scheme
+# ----------------------------------------------------------------------
+#{dx=50*m}
+surface all scheme trimesh
+playback 'gradient.jou'
+
+# ----------------------------------------------------------------------
+# Generate the mesh
+# ----------------------------------------------------------------------
+mesh surface all
+
+# ----------------------------------------------------------------------
+# Smooth mesh to improve quality
+# ----------------------------------------------------------------------
+surface all smooth scheme laplacian
+smooth surface all
+surface all smooth scheme condition number beta 1.3 cpu 10
+smooth surface all
+
+# ----------------------------------------------------------------------
+# Setup boundary conditions.
+# ----------------------------------------------------------------------
+playback 'createbc.jou'
+
+# ----------------------------------------------------------------------
+# Export exodus file
+# ----------------------------------------------------------------------
+export mesh "tri3_050m_gradient.exo" dimension 2 overwrite
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m.cfg 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,29 +0,0 @@
-# -*- Python -*-
-[pylithapp]
-
-# ----------------------------------------------------------------------
-# mesh_generator
-# ----------------------------------------------------------------------
-[pylithapp.mesh_generator.reader]
-filename = tri3_100m.exo
-
-# ----------------------------------------------------------------------
-# problem
-# ----------------------------------------------------------------------
-[pylithapp.timedependent.formulation.time_step]
-dt = 0.01*s
-
-# ----------------------------------------------------------------------
-# output
-# ----------------------------------------------------------------------
-# Give basename for VTK domain output of solution over domain.
-[pylithapp.problem.formulation.output.output]
-writer.filename = output/tri3_100m.vtk
-
-# Give basename for VTK fault output.
-[pylithapp.timedependent.interfaces.fault.output]
-writer.filename = output/tri3_100m-fault.vtk
-
-# Give basename for VTK output of state variables.
-[pylithapp.timedependent.materials.elastic.output]
-writer.filename = output/tri3_100m-elastic.vtk
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m.jou 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,32 +0,0 @@
-# ----------------------------------------------------------------------
-# Create tri3 mesh at 100m resolution.
-# ----------------------------------------------------------------------
-
-# ----------------------------------------------------------------------
-# Generate geometry
-# ----------------------------------------------------------------------
-playback 'geometry.jou'
-
-# ----------------------------------------------------------------------
-# Set discretization size and scheme
-# ----------------------------------------------------------------------
-surface all size 100
-surface all scheme trimesh
-
-# ----------------------------------------------------------------------
-# Generate the mesh
-# ----------------------------------------------------------------------
-mesh surface all
-
-# ----------------------------------------------------------------------
-# Setup boundary conditions.
-# ----------------------------------------------------------------------
-playback 'createbc.jou'
-
-# ----------------------------------------------------------------------
-# Export exodus file
-# ----------------------------------------------------------------------
-export mesh "tri3_100m.exo" dimension 2 overwrite
-
-
-
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_gradient.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_gradient.cfg (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_gradient.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,32 @@
+# -*- Python -*-
+[pylithapp]
+
+# ----------------------------------------------------------------------
+# mesh_generator
+# ----------------------------------------------------------------------
+[pylithapp.mesh_generator.reader]
+filename = tri3_100m_gradient.exo
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.formulation.time_step]
+dt = 0.01*s
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+# Give basename for VTK domain output of solution over domain.
+[pylithapp.problem.formulation.output.output]
+writer.filename = output/tri3_100m_gradient.h5
+
+# Give basename for VTK fault output.
+[pylithapp.timedependent.interfaces.fault.output]
+writer.filename = output/tri3_100m_gradient-fault.h5
+
+# Give basename for VTK output of state variables.
+[pylithapp.timedependent.materials.elastic.output]
+writer.filename = output/tri3_100m_gradient-elastic.h5
+
+
+# End of file
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_gradient.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_gradient.jou (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_gradient.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,38 @@
+# ----------------------------------------------------------------------
+# Create tri3 mesh at 100m resolution.
+# ----------------------------------------------------------------------
+
+# ----------------------------------------------------------------------
+# Generate geometry
+# ----------------------------------------------------------------------
+playback 'geometry.jou'
+
+# ----------------------------------------------------------------------
+# Set discretization size and scheme
+# ----------------------------------------------------------------------
+#{dx=100*m}
+surface all scheme trimesh
+playback 'gradient.jou'
+
+# ----------------------------------------------------------------------
+# Generate the mesh
+# ----------------------------------------------------------------------
+mesh surface all
+
+# ----------------------------------------------------------------------
+# Smooth mesh to improve quality
+# ----------------------------------------------------------------------
+surface all smooth scheme laplacian
+smooth surface all
+surface all smooth scheme condition number beta 1.3 cpu 10
+smooth surface all
+
+# ----------------------------------------------------------------------
+# Setup boundary conditions.
+# ----------------------------------------------------------------------
+playback 'createbc.jou'
+
+# ----------------------------------------------------------------------
+# Export exodus file
+# ----------------------------------------------------------------------
+export mesh "tri3_100m_gradient.exo" dimension 2 overwrite
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_refine.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_refine.cfg 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_refine.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,29 +0,0 @@
-# -*- Python -*-
-[pylithapp]
-
-# ----------------------------------------------------------------------
-# mesh_generator
-# ----------------------------------------------------------------------
-[pylithapp.mesh_generator.reader]
-filename = tri3_100m_refine.exo
-
-# ----------------------------------------------------------------------
-# problem
-# ----------------------------------------------------------------------
-[pylithapp.timedependent.formulation.time_step]
-dt = 0.01*s
-
-# ----------------------------------------------------------------------
-# output
-# ----------------------------------------------------------------------
-# Give basename for VTK domain output of solution over domain.
-[pylithapp.problem.formulation.output.output]
-writer.filename = output/tri3_100m_refine.vtk
-
-# Give basename for VTK fault output.
-[pylithapp.timedependent.interfaces.fault.output]
-writer.filename = output/tri3_100m_refine-fault.vtk
-
-# Give basename for VTK output of state variables.
-[pylithapp.timedependent.materials.elastic.output]
-writer.filename = output/tri3_100m_refine-elastic.vtk
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_refine.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_refine.jou 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_refine.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,46 +0,0 @@
-# ----------------------------------------------------------------------
-# Create tri3 mesh at 100m resolution.
-# ----------------------------------------------------------------------
-
-# ----------------------------------------------------------------------
-# Generate geometry
-# ----------------------------------------------------------------------
-playback 'geometry_refine.jou'
-
-# ----------------------------------------------------------------------
-# Set discretization size and scheme
-# ----------------------------------------------------------------------
-surface all size 400
-surface all scheme trimesh
-
-# ----------------------------------------------------------------------
-# Generate the mesh
-# ----------------------------------------------------------------------
-mesh surface all
-
-# ----------------------------------------------------------------------
-# Refine elements within 1/2 of rupture width
-# ----------------------------------------------------------------------
-playback 'refinecells.jou'
-
-# ----------------------------------------------------------------------
-# Smooth mesh to improve quality
-# ----------------------------------------------------------------------
-surface all smooth scheme laplacian
-smooth surface all
-surface all smooth scheme condition number beta 1.3 cpu 10
-smooth surface all
-
-# ----------------------------------------------------------------------
-# Setup boundary conditions.
-# ----------------------------------------------------------------------
-playback 'createbc.jou'
-
-# ----------------------------------------------------------------------
-# Export exodus file
-# ----------------------------------------------------------------------
-export mesh "tri3_100m_refine.exo" dimension 2 overwrite
-
-
-
-
Copied: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_uniform.cfg (from rev 17829, short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m.cfg)
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_uniform.cfg (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_uniform.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,32 @@
+# -*- Python -*-
+[pylithapp]
+
+# ----------------------------------------------------------------------
+# mesh_generator
+# ----------------------------------------------------------------------
+[pylithapp.mesh_generator.reader]
+filename = tri3_100m_uniform.exo
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.formulation.time_step]
+dt = 0.01*s
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+# Give basename for VTK domain output of solution over domain.
+[pylithapp.problem.formulation.output.output]
+writer.filename = output/tri3_100m_uniform.h5
+
+# Give basename for VTK fault output.
+[pylithapp.timedependent.interfaces.fault.output]
+writer.filename = output/tri3_100m_uniform-fault.h5
+
+# Give basename for VTK output of state variables.
+[pylithapp.timedependent.materials.elastic.output]
+writer.filename = output/tri3_100m_uniform-elastic.h5
+
+
+# End of file
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_uniform.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_uniform.jou (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_100m_uniform.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,39 @@
+# ----------------------------------------------------------------------
+# Create tri3 mesh at 100m resolution.
+# ----------------------------------------------------------------------
+
+# ----------------------------------------------------------------------
+# Generate geometry
+# ----------------------------------------------------------------------
+playback 'geometry.jou'
+
+# ----------------------------------------------------------------------
+# Set discretization size and scheme
+# ----------------------------------------------------------------------
+#{dx=100*m}
+surface all scheme trimesh
+surface all size {dx}
+
+# ----------------------------------------------------------------------
+# Generate the mesh
+# ----------------------------------------------------------------------
+mesh surface all
+
+# ----------------------------------------------------------------------
+# Smooth mesh to improve quality
+# ----------------------------------------------------------------------
+surface all smooth scheme laplacian
+smooth surface all
+surface all smooth scheme condition number beta 1.3 cpu 10
+smooth surface all
+
+# ----------------------------------------------------------------------
+# Setup boundary conditions.
+# ----------------------------------------------------------------------
+playback 'createbc.jou'
+
+# ----------------------------------------------------------------------
+# Export exodus file
+# ----------------------------------------------------------------------
+export mesh "tri3_100m_uniform.exo" dimension 2 overwrite
+
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m.cfg 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,29 +0,0 @@
-# -*- Python -*-
-[pylithapp]
-
-# ----------------------------------------------------------------------
-# mesh_generator
-# ----------------------------------------------------------------------
-[pylithapp.mesh_generator.reader]
-filename = tri3_200m.exo
-
-# ----------------------------------------------------------------------
-# problem
-# ----------------------------------------------------------------------
-[pylithapp.timedependent.formulation.time_step]
-dt = 0.01666666666666666666666667*s
-
-# ----------------------------------------------------------------------
-# output
-# ----------------------------------------------------------------------
-# Give basename for VTK domain output of solution over domain.
-[pylithapp.problem.formulation.output.output]
-writer.filename = output/tri3_200m.vtk
-
-# Give basename for VTK fault output.
-[pylithapp.timedependent.interfaces.fault.output]
-writer.filename = output/tri3_200m-fault.vtk
-
-# Give basename for VTK output of state variables.
-[pylithapp.timedependent.materials.elastic.output]
-writer.filename = output/tri3_200m-elastic.vtk
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m.jou 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,32 +0,0 @@
-# ----------------------------------------------------------------------
-# Create tri3 mesh at 200m resolution.
-# ----------------------------------------------------------------------
-
-# ----------------------------------------------------------------------
-# Generate geometry
-# ----------------------------------------------------------------------
-playback 'geometry.jou'
-
-# ----------------------------------------------------------------------
-# Set discretization size and scheme
-# ----------------------------------------------------------------------
-surface all size 200
-surface all scheme trimesh
-
-# ----------------------------------------------------------------------
-# Generate the mesh
-# ----------------------------------------------------------------------
-mesh surface all
-
-# ----------------------------------------------------------------------
-# Setup boundary conditions.
-# ----------------------------------------------------------------------
-playback 'createbc.jou'
-
-# ----------------------------------------------------------------------
-# Export exodus file
-# ----------------------------------------------------------------------
-export mesh "tri3_200m.exo" dimension 2 overwrite
-
-
-
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_gradient.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_gradient.cfg (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_gradient.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,32 @@
+# -*- Python -*-
+[pylithapp]
+
+# ----------------------------------------------------------------------
+# mesh_generator
+# ----------------------------------------------------------------------
+[pylithapp.mesh_generator.reader]
+filename = tri3_200m_gradient.exo
+
+# ----------------------------------------------------------------------
+# problem
+# ----------------------------------------------------------------------
+[pylithapp.timedependent.formulation.time_step]
+dt = 0.02*s
+
+# ----------------------------------------------------------------------
+# output
+# ----------------------------------------------------------------------
+# Give basename for VTK domain output of solution over domain.
+[pylithapp.problem.formulation.output.output]
+writer.filename = output/tri3_200m_gradient.h5
+
+# Give basename for VTK fault output.
+[pylithapp.timedependent.interfaces.fault.output]
+writer.filename = output/tri3_200m_gradient-fault.h5
+
+# Give basename for VTK output of state variables.
+[pylithapp.timedependent.materials.elastic.output]
+writer.filename = output/tri3_200m_gradient-elastic.h5
+
+
+# End of file
Added: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_gradient.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_gradient.jou (rev 0)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_gradient.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -0,0 +1,38 @@
+# ----------------------------------------------------------------------
+# Create tri3 mesh at 100m resolution.
+# ----------------------------------------------------------------------
+
+# ----------------------------------------------------------------------
+# Generate geometry
+# ----------------------------------------------------------------------
+playback 'geometry.jou'
+
+# ----------------------------------------------------------------------
+# Set discretization size and scheme
+# ----------------------------------------------------------------------
+#{dx=200*m}
+surface all scheme trimesh
+playback 'gradient.jou'
+
+# ----------------------------------------------------------------------
+# Generate the mesh
+# ----------------------------------------------------------------------
+mesh surface all
+
+# ----------------------------------------------------------------------
+# Smooth mesh to improve quality
+# ----------------------------------------------------------------------
+surface all smooth scheme laplacian
+smooth surface all
+surface all smooth scheme condition number beta 1.3 cpu 10
+smooth surface all
+
+# ----------------------------------------------------------------------
+# Setup boundary conditions.
+# ----------------------------------------------------------------------
+playback 'createbc.jou'
+
+# ----------------------------------------------------------------------
+# Export exodus file
+# ----------------------------------------------------------------------
+export mesh "tri3_200m_gradient.exo" dimension 2 overwrite
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_refine.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_refine.cfg 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_refine.cfg 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,29 +0,0 @@
-# -*- Python -*-
-[pylithapp]
-
-# ----------------------------------------------------------------------
-# mesh_generator
-# ----------------------------------------------------------------------
-[pylithapp.mesh_generator.reader]
-filename = tri3_200m_refine.exo
-
-# ----------------------------------------------------------------------
-# problem
-# ----------------------------------------------------------------------
-[pylithapp.timedependent.formulation.time_step]
-dt = 0.01666666666666666666666667*s
-
-# ----------------------------------------------------------------------
-# output
-# ----------------------------------------------------------------------
-# Give basename for VTK domain output of solution over domain.
-[pylithapp.problem.formulation.output.output]
-writer.filename = output/tri3_200m_refine.vtk
-
-# Give basename for VTK fault output.
-[pylithapp.timedependent.interfaces.fault.output]
-writer.filename = output/tri3_200m_refine-fault.vtk
-
-# Give basename for VTK output of state variables.
-[pylithapp.timedependent.materials.elastic.output]
-writer.filename = output/tri3_200m_refine-elastic.vtk
Deleted: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_refine.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_refine.jou 2011-09-29 00:23:34 UTC (rev 18985)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205-2d/tri3_200m_refine.jou 2011-09-29 00:40:03 UTC (rev 18986)
@@ -1,46 +0,0 @@
-# ----------------------------------------------------------------------
-# Create tri3 mesh at 200m resolution.
-# ----------------------------------------------------------------------
-
-# ----------------------------------------------------------------------
-# Generate geometry
-# ----------------------------------------------------------------------
-playback 'geometry_refine.jou'
-
-# ----------------------------------------------------------------------
-# Set discretization size and scheme
-# ----------------------------------------------------------------------
-surface all size 800
-surface all scheme trimesh
-
-# ----------------------------------------------------------------------
-# Generate the mesh
-# ----------------------------------------------------------------------
-mesh surface all
-
-# ----------------------------------------------------------------------
-# Refine elements within 1/2 of rupture width
-# ----------------------------------------------------------------------
-playback 'refinecells.jou'
-
-# ----------------------------------------------------------------------
-# Smooth mesh to improve quality
-# ----------------------------------------------------------------------
-surface all smooth scheme laplacian
-smooth surface all
-surface all smooth scheme condition number beta 1.3 cpu 10
-smooth surface all
-
-# ----------------------------------------------------------------------
-# Setup boundary conditions.
-# ----------------------------------------------------------------------
-playback 'createbc.jou'
-
-# ----------------------------------------------------------------------
-# Export exodus file
-# ----------------------------------------------------------------------
-export mesh "tri3_200m_refine.exo" dimension 2 overwrite
-
-
-
-
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