[cig-commits] r19126 - short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205
brad at geodynamics.org
brad at geodynamics.org
Fri Oct 28 16:49:25 PDT 2011
Author: brad
Date: 2011-10-28 16:49:25 -0700 (Fri, 28 Oct 2011)
New Revision: 19126
Modified:
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/createbc.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/geometry.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/gradient.jou
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/pylithapp.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tabulate_onfaultdata.py
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tabulate_ruptime.py
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tet4_200m.cfg
short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tractions.spatialdb
Log:
Added marking asperity locations on fault surface to ensure mesh is aligned with asperity boundaries.
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/createbc.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/createbc.jou 2011-10-28 23:48:01 UTC (rev 19125)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/createbc.jou 2011-10-28 23:49:25 UTC (rev 19126)
@@ -8,6 +8,9 @@
# 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" add node in fault_surface at C
nodeset 20 group fault
nodeset 20 name "fault"
@@ -68,3 +71,4 @@
nodeset 17 group face_zpos_subset
nodeset 17 name "face zpos_subset"
+
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/geometry.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/geometry.jou 2011-10-28 23:48:01 UTC (rev 19125)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/geometry.jou 2011-10-28 23:49:25 UTC (rev 19126)
@@ -51,14 +51,27 @@
split surface 18 across location vertex {vAp} location vertex {vBp}
split surface 21 across location vertex {vCn} location vertex {vCp}
surface 22 name "fault_surface"
+delete vertex all
+# asperities (to ensure exact alignment with mesh)
+brick x {3.0*km} y {3.0*km} z {3.0*km}
+{idChopper=Id("volume")}
+volume {idChopper} move x 0 y 0 z {-7.5*km}
+chop volume 2 with volume {idChopper} keep
+volume {idChopper} move x 0 y {7.5*km} z 0
+chop volume 2 with volume {idChopper} keep
+volume {idChopper} move x 0 y {-15.0*km} z 0
+chop volume 2 with volume {idChopper} keep
+delete volume {idChopper}
+
# ----------------------------------------------------------------------
# Imprint all volumes, merging surfaces
# ----------------------------------------------------------------------
imprint all
merge all
-delete body 2
+delete body 2 5 6 7 8 9 10
+
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/gradient.jou
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/gradient.jou 2011-10-28 23:48:01 UTC (rev 19125)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/gradient.jou 2011-10-28 23:49:25 UTC (rev 19126)
@@ -12,7 +12,7 @@
# dxA - size at vertex 9 12
#{dxStart=dx}{curveL=Length(40)}{execute("dxA="//fun_dx)}
-# dxB - size at vertex 23 24
+# dxB - size at vertex 27 29
#{dxStart=dx}{curveL=Length(46)}{execute("dxB="//fun_dx)}
# dxC - size at vertex 10 11
@@ -29,15 +29,15 @@
# ----------------------------------------------------------------------
curve all scheme default
surface all sizing function none
-surface fault_surface size {dx}
+surface fault_surface fault_surface at A fault_surface at B fault_surface at C size {dx}
# Set bias on curves extending from faults
-curve 40 scheme bias fine size {dx} factor {bias_factor} start vertex 22
-curve 36 scheme bias fine size {dx} factor {bias_factor} start vertex 21
+curve 40 scheme bias fine size {dx} factor {bias_factor} start vertex 30
+curve 36 scheme bias fine size {dx} factor {bias_factor} start vertex 28
-curve 46 scheme bias fine size {dx} factor {bias_factor} start vertex 26
-curve 47 scheme bias fine size {dx} factor {bias_factor} start vertex 25
+curve 46 scheme bias fine size {dx} factor {bias_factor} start vertex 31
+curve 47 scheme bias fine size {dx} factor {bias_factor} start vertex 32
# ----------------------------------------------------------------------
# B to B
@@ -55,8 +55,8 @@
curve 15 scheme bias fine size {dxA} coarse size {dxC} start vertex 12
# bias starting at B
-curve 39 scheme bias fine size {dxB} factor {bias_factor} start vertex 24
-curve 37 scheme bias fine size {dxB} factor {bias_factor} start vertex 23
+curve 39 scheme bias fine size {dxB} factor {bias_factor} start vertex 29
+curve 37 scheme bias fine size {dxB} factor {bias_factor} start vertex 27
# bias starting at C
curve 24 scheme bias fine size {dxC} factor {bias_factor} start vertex 11
@@ -81,3 +81,4 @@
# End of file
+
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/pylithapp.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/pylithapp.cfg 2011-10-28 23:48:01 UTC (rev 19125)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/pylithapp.cfg 2011-10-28 23:49:25 UTC (rev 19126)
@@ -27,7 +27,7 @@
# ----------------------------------------------------------------------
[pylithapp.mesh_generator]
reader = pylith.meshio.MeshIOCubit
-#reorder_mesh = True
+reorder_mesh = True
distributor.partitioner = parmetis
distributor.write_partition = True
@@ -43,7 +43,7 @@
dimension = 3
formulation = pylith.problems.ExplicitLumped
-formulation.norm_viscosity = 0.2
+formulation.norm_viscosity = 0.3
normalizer = spatialdata.units.NondimElasticDynamic
[pylithapp.timedependent.formulation.time_step]
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tabulate_onfaultdata.py
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tabulate_onfaultdata.py 2011-10-28 23:48:01 UTC (rev 19125)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tabulate_onfaultdata.py 2011-10-28 23:49:25 UTC (rev 19126)
@@ -5,72 +5,60 @@
# Brad T. Aagaard
# U.S. Geological Survey
#
-# <LicenseText>
-#
# ----------------------------------------------------------------------
#
cell = "tet4"
dx = 200
-dt = 0.05
-outputRoot = "output/%s_%3dm" % (cell,dx)
+inputRoot = "output/%s_%3dm-fault" % (cell,dx)
outdir = "scecfiles/%s_%3dm/" % (cell,dx)
+# ----------------------------------------------------------------------
+import tables
import numpy
import time
-from pylith.utils.VTKDataReader import VTKDataReader
-
# ----------------------------------------------------------------------
-timestamps = numpy.arange(50,12001,50)
-
if dx == 200:
- targets = numpy.array([[-12000.0, 0.0, 0.0],
- [ -7400.0, 0.0, 0.0],
- [ -4600.0, 0.0, 0.0],
- [ 0.0, 0.0, 0.0],
- [ 4600.0, 0.0, 0.0],
- [ 7400.0, 0.0, 0.0],
- [ 12000.0, 0.0, 0.0],
- [ 0.0, 0.0, -3000.0],
- [-12000.0, 0.0, -7600.0],
- [ -7400.0, 0.0, -7600.0],
- [ -4600.0, 0.0, -7600.0],
- [ 0.0, 0.0, -7600.0],
- [ 4600.0, 0.0, -7600.0],
- [ 7400.0, 0.0, -7600.0],
- [ 12000.0, 0.0, -7600.0],
- [ 0.0, 0.0, -12000.0]])
+ targets = numpy.array([[ 0.0,-12000.0, 0.0],
+ [ 0.0, -7400.0, 0.0],
+ [ 0.0, -4600.0, 0.0],
+ [ 0.0, 0.0, 0.0],
+ [ 0.0, 4600.0, 0.0],
+ [ 0.0, 7400.0, 0.0],
+ [ 0.0, 12000.0, 0.0],
+ [ 0.0, 0.0, -3000.0],
+ [ 0.0,-12000.0, -7600.0],
+ [ 0.0, -7400.0, -7600.0],
+ [ 0.0, -4600.0, -7600.0],
+ [ 0.0, 0.0, -7600.0],
+ [ 0.0, 4600.0, -7600.0],
+ [ 0.0, 7400.0, -7600.0],
+ [ 0.0, 12000.0, -7600.0],
+ [ 0.0, 0.0, -12000.0]])
elif dx == 100:
- targets = numpy.array([[-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, 0.0],
- [ 0.0, 0.0, -3000.0],
- [-12000.0, 0.0, -7500.0],
- [ -7500.0, 0.0, -7500.0],
- [ -4500.0, 0.0, -7500.0],
- [ 0.0, 0.0, -7500.0],
- [ 4500.0, 0.0, -7500.0],
- [ 7500.0, 0.0, -7500.0],
- [ 12000.0, 0.0, -7500.0],
- [ 0.0, 0.0, -12000.0]])
+ 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],
+ [ 0.0, 0.0, -3000.0],
+ [ 0.0,-12000.0, -7500.0],
+ [ 0.0, -7500.0, -7500.0],
+ [ 0.0, -4500.0, -7500.0],
+ [ 0.0, 0.0, -7500.0],
+ [ 0.0, 4500.0, -7500.0],
+ [ 0.0, 7500.0, -7500.0],
+ [ 0.0, 12000.0, -7500.0],
+ [ 0.0, 0.0, -12000.0]])
-
-
-
-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:
@@ -80,32 +68,32 @@
min = numpy.min(dist)
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" + \
+ "# 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" + \
@@ -124,12 +112,9 @@
locHeader = "# location = on fault, %3.1f km along strike and %3.1f km depth\n"
locName = "st%+04ddp%03d"
-lengthScale = 1000.0
-timeScale = 1000.0
+lengthScale = 1.0e+3
+strike = targets[:,1] / lengthScale
dip = -targets[:,2] / lengthScale
-strike = targets[:,0] / lengthScale
-time = timestamps / timeScale
-print "time", time
for iloc in xrange(ntargets):
pt = locName % (round(10*strike[iloc]),
@@ -141,12 +126,12 @@
fout.write("# num_timesteps = %8d\n" % nsteps)
fout.write(locHeader % (strike[iloc], dip[iloc]))
fout.write(headerB)
- data = numpy.transpose((time,
+ data = numpy.transpose((timeStamps,
-slip[:,iloc,0],
- -slip_rate[:,iloc,0],
+ +slip_rate[:,iloc,0],
-traction[:,iloc,0]/1e+6,
+slip[:,iloc,1],
- +slip_rate[:,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/tabulate_ruptime.py
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tabulate_ruptime.py 2011-10-28 23:48:01 UTC (rev 19125)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tabulate_ruptime.py 2011-10-28 23:49:25 UTC (rev 19126)
@@ -5,92 +5,65 @@
# Brad T. Aagaard
# U.S. Geological Survey
#
-# <LicenseText>
-#
# ----------------------------------------------------------------------
#
cell = "tet4"
dx = 200
-dt = 0.05
-outputRoot = "output/%s_%3dm" % (cell,dx)
+inputRoot = "output/%s_%3dm-fault" % (cell,dx)
outdir = "scecfiles/%s_%3dm/" % (cell,dx)
+# ----------------------------------------------------------------------
+import tables
import numpy
import time
-from pylith.utils.VTKDataReader import VTKDataReader
-
# ----------------------------------------------------------------------
-timestamps = numpy.arange(50,12001,50)
-
-
-reader = VTKDataReader()
threshold = 0.001 # threshold for detecting slip has started
+maxTime = 1.0e+10 # Large value for default rupture time
-filename = "%s-fault_t%05d.vtk" % (outputRoot,timestamps[0])
-data = reader.read(filename)
-vertices = numpy.array(data['vertices'])
-npts = vertices.shape[0]
+h5 = tables.openFile("%s.h5" % inputRoot, 'r')
+vertices = h5.root.geometry.vertices[:]
+slip = h5.root.vertex_fields.slip[:]
+slipRate = h5.root.vertex_fields.slip_rate[:]
+timeStamps = h5.root.time[:].ravel()
+dt = timeStamps[1] - timeStamps[0]
-# Extract values
-nsteps = timestamps.shape[0]
+h5.close()
-# Set default rupture time to a large value (1.0e+9)
-rupTime = 1.0e+9 * numpy.ones( (npts,), dtype=numpy.float64)
-#rupTime = numpy.zeros( (npts,), dtype=numpy.float64)
+nsteps = timeStamps.shape[0]
+npts = vertices.shape[0]
+rupTime = maxTime * numpy.ones( (npts,), dtype=numpy.float64)
+
# Create buffer for current rupture time
tmpTime = numpy.zeros( (npts,), dtype=numpy.float64)
itime = 0
-for timestamp in timestamps:
- t = (itime+1)*dt # itime=0, t=dt
+for timestamp in timeStamps:
+ t = timeStamps[itime]
- # Get slip rate field
- filename = "%s-fault_t%05d.vtk" % (outputRoot,timestamp)
- data = reader.read(filename)
- fields = data['vertex_fields']
- slipRate = fields['slip'][:,:].squeeze()
-
# Compute magnitude of slip rate
- slipRateMag = (slipRate[:,0]**2 + slipRate[:,1]**2)**0.5
+ slipRateMag = (slipRate[itime,:,0]**2 + slipRate[itime,:,1]**2)**0.5
# Set rupture time at locations where threshold is exceeded
- tmpTime[slipRateMag > threshold] = t
+ mask = slipRateMag > threshold
+ tmpTime[:] = maxTime
+ tmpTime[mask] = t
- #print "slipRateMag \n", slipRateMag
- #print "slipRateMag > threshold \n ", slipRateMag > threshold
-
- #print "tmpTime \n", tmpTime[1:50]
- #print "time", t
-
- # Get indicates where current time is less than current rupture
- # time (this is only the locations that just started slipping)
- #indices = numpy.where((tmpTime < rupTime) and (rupTime < 0.00001))[0]
- #indices = ((tmpTime < rupTime) & (rupTime < testarr))
- indices = numpy.where((tmpTime < rupTime) & (tmpTime > 0.00001))[0]
-
- #print "indices \n", indices[1:200]
-
-
+ indices = numpy.where(tmpTime < rupTime)[0]
rupTime[indices] = t
- #print "rupTime \n", rupTime[1:200]
-
itime += 1
-# print "rupTime \n", rupTime
-# rupTime[rupTime < 0.00001] = 1.0e+9
-
# Write data
headerA = \
"# problem = TPV205\n" + \
- "# author = Surendra N. Somala\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 + \
"# Contour data in 3 columns of E14.6:\n" + \
"# Column #1 = Distance along strike from hypocenter (m)\n" + \
@@ -102,12 +75,8 @@
"#\n"
-lengthScale = 1000.0
-timeScale = 1000.0
distDip = -vertices[:,2]
-distStrike = vertices[:,0]
-time = timestamps / timeScale
-print "time", time
+distStrike = vertices[:,1]
filename = "%sruptime.dat" % (outdir)
fout = open(filename, "w")
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tet4_200m.cfg
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tet4_200m.cfg 2011-10-28 23:48:01 UTC (rev 19125)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tet4_200m.cfg 2011-10-28 23:49:25 UTC (rev 19126)
@@ -11,7 +11,7 @@
# problem
# ----------------------------------------------------------------------
[pylithapp.timedependent.formulation.time_step]
-dt = 0.01666666666666666666666667*s
+dt = 0.0125*s
# ----------------------------------------------------------------------
# output
Modified: short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tractions.spatialdb
===================================================================
--- short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tractions.spatialdb 2011-10-28 23:48:01 UTC (rev 19125)
+++ short/3D/PyLith/benchmarks/trunk/dynamic/scecdynrup/tpv205/tractions.spatialdb 2011-10-28 23:49:25 UTC (rev 19126)
@@ -3,7 +3,7 @@
num-values = 3
value-names = traction-shear-leftlateral traction-shear-updip traction-normal
value-units = MPa MPa MPa
- num-locs = 48
+ num-locs = 108
data-dim = 2
space-dim = 3
cs-data = cartesian {
@@ -11,54 +11,116 @@
space-dim = 3
}
}
-0.0 -9.0001 -5.9999 -70.0 0.0 -120.0
-0.0 -9.0 -5.9999 -70.0 0.0 -120.0
-0.0 -6.0 -5.9999 -70.0 0.0 -120.0
-0.0 -5.9999 -5.9999 -70.0 0.0 -120.0
-0.0 -1.5001 -5.9999 -70.0 0.0 -120.0
-0.0 -1.5 -5.9999 -70.0 0.0 -120.0
-0.0 +1.5 -5.9999 -70.0 0.0 -120.0
-0.0 +1.5001 -5.9999 -70.0 0.0 -120.0
-0.0 +5.9999 -5.9999 -70.0 0.0 -120.0
-0.0 +6.0 -5.9999 -70.0 0.0 -120.0
-0.0 +9.0 -5.9999 -70.0 0.0 -120.0
-0.0 +9.0001 -5.9999 -70.0 0.0 -120.0
+0.0 -9.001 -5.999 -70.0 0.0 -120.0
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+0.0 -6.001 -5.999 -70.0 0.0 -120.0
+0.0 -6.0 -5.999 -70.0 0.0 -120.0
+0.0 -5.999 -5.999 -70.0 0.0 -120.0
+0.0 -1.501 -5.999 -70.0 0.0 -120.0
+0.0 -1.5 -5.999 -70.0 0.0 -120.0
+0.0 -1.499 -5.999 -70.0 0.0 -120.0
+0.0 +1.499 -5.999 -70.0 0.0 -120.0
+0.0 +1.5 -5.999 -70.0 0.0 -120.0
+0.0 +1.501 -5.999 -70.0 0.0 -120.0
+0.0 +5.999 -5.999 -70.0 0.0 -120.0
+0.0 +6.0 -5.999 -70.0 0.0 -120.0
+0.0 +6.001 -5.999 -70.0 0.0 -120.0
+0.0 +8.999 -5.999 -70.0 0.0 -120.0
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+0.0 +9.001 -5.999 -70.0 0.0 -120.0
-0.0 -9.0001 -6.0 -70.0 0.0 -120.0
-0.0 -9.0 -6.0 -78.0 0.0 -120.0
-0.0 -6.0 -6.0 -78.0 0.0 -120.0
-0.0 -5.9999 -6.0 -70.0 0.0 -120.0
-0.0 -1.5001 -6.0 -70.0 0.0 -120.0
-0.0 -1.5 -6.0 -81.6 0.0 -120.0
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-0.0 +1.5001 -6.0 -70.0 0.0 -120.0
-0.0 +5.9999 -6.0 -70.0 0.0 -120.0
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