[cig-commits] r15078 - in short/3D/PyLith/trunk: . pylith/perf tests/1d tests/1d/line2 tests/1d/line3
brad at geodynamics.org
brad at geodynamics.org
Thu May 28 14:22:26 PDT 2009
Author: brad
Date: 2009-05-28 14:22:24 -0700 (Thu, 28 May 2009)
New Revision: 15078
Added:
short/3D/PyLith/trunk/tests/1d/line3/TestLine3.py
short/3D/PyLith/trunk/tests/1d/line3/finalslip.spatialdb
short/3D/PyLith/trunk/tests/1d/line3/sliptime.spatialdb
Removed:
short/3D/PyLith/trunk/tests/1d/line3/dislocation_disp.spatialdb
short/3D/PyLith/trunk/tests/1d/line3/dislocation_slip.spatialdb
short/3D/PyLith/trunk/tests/1d/line3/dislocation_sliprate.spatialdb
short/3D/PyLith/trunk/tests/1d/line3/dislocation_sliptime.spatialdb
Modified:
short/3D/PyLith/trunk/TODO
short/3D/PyLith/trunk/configure.ac
short/3D/PyLith/trunk/pylith/perf/Mesh.py
short/3D/PyLith/trunk/tests/1d/Makefile.am
short/3D/PyLith/trunk/tests/1d/line2/Makefile.am
short/3D/PyLith/trunk/tests/1d/line2/TestLine2.py
short/3D/PyLith/trunk/tests/1d/line2/axialextension.cfg
short/3D/PyLith/trunk/tests/1d/line2/dislocation.cfg
short/3D/PyLith/trunk/tests/1d/line3/Makefile.am
short/3D/PyLith/trunk/tests/1d/line3/TestAxial.py
short/3D/PyLith/trunk/tests/1d/line3/TestDislocation.py
short/3D/PyLith/trunk/tests/1d/line3/axialextension.cfg
short/3D/PyLith/trunk/tests/1d/line3/bar.mesh
short/3D/PyLith/trunk/tests/1d/line3/dislocation.cfg
short/3D/PyLith/trunk/tests/1d/line3/matprops.spatialdb
short/3D/PyLith/trunk/tests/1d/line3/testpylith.py
Log:
Added line3 full-scale tests.
Modified: short/3D/PyLith/trunk/TODO
===================================================================
--- short/3D/PyLith/trunk/TODO 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/TODO 2009-05-28 21:22:24 UTC (rev 15078)
@@ -8,7 +8,7 @@
Brad
Questions for Matt:
- How to set symmetric matrix flag?
+ How to use symmetric matrix (updateOperator)?
cleanup
full-scale testing
test uniform refinement
Modified: short/3D/PyLith/trunk/configure.ac
===================================================================
--- short/3D/PyLith/trunk/configure.ac 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/configure.ac 2009-05-28 21:22:24 UTC (rev 15078)
@@ -267,6 +267,7 @@
tests/petsc/Makefile
tests/1d/Makefile
tests/1d/line2/Makefile
+ tests/1d/line3/Makefile
tests/2d/Makefile
tests/2d/tri3/Makefile
tests/2d/quad4/Makefile
Modified: short/3D/PyLith/trunk/pylith/perf/Mesh.py
===================================================================
--- short/3D/PyLith/trunk/pylith/perf/Mesh.py 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/pylith/perf/Mesh.py 2009-05-28 21:22:24 UTC (rev 15078)
@@ -4,6 +4,7 @@
class Mesh(Memory):
cellTypes = {(1,2): 'line2',
+ (1,3): 'line3',
(2,3): 'tri3',
(2,4): 'quad4',
(3,4): 'tet4',
Modified: short/3D/PyLith/trunk/tests/1d/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/tests/1d/Makefile.am 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/Makefile.am 2009-05-28 21:22:24 UTC (rev 15078)
@@ -11,7 +11,8 @@
#
SUBDIRS = \
- line2
+ line2 \
+ line3
# End of file
Modified: short/3D/PyLith/trunk/tests/1d/line2/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line2/Makefile.am 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line2/Makefile.am 2009-05-28 21:22:24 UTC (rev 15078)
@@ -14,12 +14,12 @@
check_SCRIPTS = testpylith.py
-noinst_PYTHON = \
+dist_noinst_PYTHON = \
TestLine2.py \
TestAxial.py \
TestDislocation.py
-noinst_DATA = \
+dist_noinst_DATA = \
bar.mesh \
matprops.spatialdb \
axialextension.cfg \
@@ -30,12 +30,12 @@
noinst_TMP = \
axialextension_t0000000.vtk \
- axialextension-statevars-elastic_info.vtk \
- axialextension-statevars-elastic_t0000000.vtk \
+ axialextension-elastic_info.vtk \
+ axialextension-elastic_t0000000.vtk \
dislocation-fault_info.vtk \
dislocation-fault_t0000000.vtk \
- dislocation-statevars-elastic_info.vtk \
- dislocation-statevars-elastic_t0000000.vtk \
+ dislocation-elastic_info.vtk \
+ dislocation-elastic_t0000000.vtk \
dislocation_t0000000.vtk
TESTS_ENVIRONMENT = $(PYTHON)
@@ -43,15 +43,14 @@
# 'export' the input files by performing a mock install
export_datadir = $(top_builddir)/tests/1d/line2
-export-data: $(noinst_PYTHON) $(noinst_DATA)
- for f in $(noinst_PYTHON) $(noinst_DATA); do $(install_sh_DATA) $(srcdir)/$$f $(export_datadir); done
+export-data: $(dist_noinst_PYTHON) $(dist_noinst_DATA)
+ for f in $(dist_noinst_PYTHON) $(dist_noinst_DATA); do $(install_sh_DATA) $(srcdir)/$$f $(export_datadir); done
+clean-data:
+ if [ "X$(top_srcdir)" != "X$(top_builddir)" ]; then for f in $(dist_noinst_PYTHON) $(dist_noinst_DATA) $(noinst_TMP); do $(RM) $(RM_FLAGS) $(export_datadir)/$$f; done; fi
+
BUILT_SOURCES = export-data
+clean-local: clean-data
-CLEANFILES = \
- $(export_datadir)/$(noinst_PYTHON) \
- $(export_datadir)/$(noinst_DATA) \
- $(export_datadir)/$(noinst_TMP)
-
# End of file
Modified: short/3D/PyLith/trunk/tests/1d/line2/TestLine2.py
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line2/TestLine2.py 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line2/TestLine2.py 2009-05-28 21:22:24 UTC (rev 15078)
@@ -46,7 +46,7 @@
ncells= self.mesh['ncells']
- filename = "%s-statevars-elastic_info.vtk" % self.outputRoot
+ filename = "%s-elastic_info.vtk" % self.outputRoot
m = self.density*self.vs**2
l = self.density*self.vp**2 - 2*m
@@ -85,7 +85,7 @@
if self.reader is None:
return
- filename = "%s-statevars-elastic_t0000000.vtk" % self.outputRoot
+ filename = "%s-elastic_t0000000.vtk" % self.outputRoot
from pylith.tests.StateVariables import check_state_variables
stateVars = ["total_strain", "stress"]
Modified: short/3D/PyLith/trunk/tests/1d/line2/axialextension.cfg
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line2/axialextension.cfg 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line2/axialextension.cfg 2009-05-28 21:22:24 UTC (rev 15078)
@@ -1,8 +1,8 @@
# -*- Python -*-
[axialextension]
-[axialextension.launcher]
-command = mpiexec -n ${nodes}
+[axialextension.launcher] # WARNING: THIS IS NOT PORTABLE
+command = mpirun -np ${nodes}
# ----------------------------------------------------------------------
# journal
@@ -85,4 +85,4 @@
[axialextension.timedependent.materials.elastic.output]
cell_filter = pylith.meshio.CellFilterAvgMesh
-writer.filename = axialextension-statevars-elastic.vtk
+writer.filename = axialextension-elastic.vtk
Modified: short/3D/PyLith/trunk/tests/1d/line2/dislocation.cfg
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line2/dislocation.cfg 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line2/dislocation.cfg 2009-05-28 21:22:24 UTC (rev 15078)
@@ -1,8 +1,8 @@
# -*- Python -*-
[dislocation]
-[dislocation.launcher]
-command = mpiexec -n ${nodes}
+[dislocation.launcher] # WARNING: THIS IS NOT PORTABLE
+command = mpirun -np ${nodes}
# ----------------------------------------------------------------------
# journal
@@ -12,10 +12,11 @@
#implicit = 1
#petsc = 1
#solverlinear = 1
-#meshiocubit = 1
+#meshioascii = 1
#implicitelasticity = 1
#quadrature = 1
#fiatsimplex = 1
+#faultcohesivekin = 1
# ----------------------------------------------------------------------
# mesh_generator
@@ -67,11 +68,8 @@
# faults
# ----------------------------------------------------------------------
[dislocation.timedependent.interfaces]
-# Set the type of fault interface condition.
fault = pylith.faults.FaultCohesiveKin
-# Set the parameters for the fault interface condition.
-
[dislocation.timedependent.interfaces.fault]
label = fault
quadrature.cell.shape = point
@@ -104,7 +102,7 @@
[dislocation.timedependent.materials.elastic.output]
cell_filter = pylith.meshio.CellFilterAvgMesh
-writer.filename = dislocation-statevars-elastic.vtk
+writer.filename = dislocation-elastic.vtk
[dislocation.timedependent.interfaces.fault.output.writer]
filename = dislocation-fault.vtk
Modified: short/3D/PyLith/trunk/tests/1d/line3/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/Makefile.am 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line3/Makefile.am 2009-05-28 21:22:24 UTC (rev 15078)
@@ -14,26 +14,29 @@
check_SCRIPTS = testpylith.py
-noinst_PYTHON = \
+dist_noinst_PYTHON = \
+ TestLine3.py \
TestAxial.py \
TestDislocation.py
-noinst_DATA = \
+dist_noinst_DATA = \
bar.mesh \
+ matprops.spatialdb \
axialextension.cfg \
axialextension_disp.spatialdb \
dislocation.cfg \
- dislocation_disp.spatialdb \
- dislocation_slip.spatialdb \
- dislocation_sliprate.spatialdb \
- dislocation_sliptime.spatialdb \
- matprops.spatialdb
+ finalslip.spatialdb \
+ sliptime.spatialdb
noinst_TMP = \
- axialextension_t0.vtk \
- axialextension_t1.vtk \
- dislocation_t0.vtk \
- dislocation_t1.vtk
+ axialextension_t0000000.vtk \
+ axialextension-elastic_info.vtk \
+ axialextension-elastic_t0000000.vtk \
+ dislocation-fault_info.vtk \
+ dislocation-fault_t0000000.vtk \
+ dislocation-elastic_info.vtk \
+ dislocation-elastic_t0000000.vtk \
+ dislocation_t0000000.vtk
TESTS_ENVIRONMENT = $(PYTHON)
@@ -41,14 +44,14 @@
# 'export' the input files by performing a mock install
export_datadir = $(top_builddir)/tests/1d/line3
-export-data: $(noinst_DATA)
- for f in $(noinst_DATA); do $(install_sh_DATA) $(srcdir)/$$f $(export_datadir); done
+export-data: $(dist_noinst_PYTHON) $(dist_noinst_DATA)
+ for f in $(dist_noinst_PYTHON) $(dist_noinst_DATA); do $(install_sh_DATA) $(srcdir)/$$f $(export_datadir); done
+clean-data:
+ if [ "X$(top_srcdir)" != "X$(top_builddir)" ]; then for f in $(dist_noinst_PYTHON) $(dist_noinst_DATA) $(noinst_TMP); do $(RM) $(RM_FLAGS) $(export_datadir)/$$f; done; fi
+
BUILT_SOURCES = export-data
+clean-local: clean-data
-CLEANFILES = \
- $(export_datadir)/$(noinst_DATA) \
- $(export_datadir)/$(noinst_TMP)
-
# End of file
Modified: short/3D/PyLith/trunk/tests/1d/line3/TestAxial.py
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/TestAxial.py 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line3/TestAxial.py 2009-05-28 21:22:24 UTC (rev 15078)
@@ -14,23 +14,33 @@
##
## @brief Test suite for testing pylith with 1-D axial extension.
-import unittest
import numpy
-import tables
+from TestLine3 import TestLine3
+from pylith.utils.VTKDataReader import has_vtk
+from pylith.utils.VTKDataReader import VTKDataReader
+
+# Local version of PyLithApp
+from pylith.apps.PyLithApp import PyLithApp
+class AxialApp(PyLithApp):
+ def __init__(self):
+ PyLithApp.__init__(self, name="axialextension")
+ return
+
+
+# Helper function to run PyLith
def run_pylith():
"""
Run pylith.
"""
if not "done" in dir(run_pylith):
- from pylith.PyLithApp import PyLithApp
- app = PyLithApp("axialextension")
+ app = AxialApp()
app.run()
run_pylith.done = True
return
-class TestAxial(unittest.TestCase):
+class TestAxial(TestLine3):
"""
Test suite for testing pylith with 1-D axial extension.
"""
@@ -39,15 +49,48 @@
"""
Setup for test.
"""
+ TestLine3.setUp(self)
run_pylith()
+ self.outputRoot = "axialextension"
+ if has_vtk():
+ self.reader = VTKDataReader()
+ else:
+ self.reader = None
return
- def test_disp(self):
+ def calcDisplacements(self, vertices):
"""
- Check displacement field.
+ Calculate displacement field given coordinates of vertices.
"""
- return
+ nvertices = self.mesh['nvertices']
+ spaceDim = self.mesh['spaceDim']
+ disp = numpy.zeros( (nvertices, spaceDim), dtype=numpy.float64)
+ disp[:,0] = -0.2 + 0.1 * vertices[:,0]
+ return disp
+
+ def calcStateVar(self, name, vertices, cells):
+ """
+ Calculate state variable.
+ """
+ exx = 0.1
+
+ ncells = self.mesh['ncells']
+ tensorSize = self.mesh['tensorSize']
+
+ if name == "total_strain":
+ stateVar = exx*numpy.ones( (ncells, tensorSize), dtype=numpy.float64)
+
+ elif name == "stress":
+ lp2m = self.density*self.vp**2
+ stateVar = lp2m*exx * numpy.ones( (ncells, tensorSize),
+ dtype=numpy.float64)
+ else:
+ raise ValueError("Unknown state variable '%s'." % name)
+
+ return stateVar
+
+
# End of file
Modified: short/3D/PyLith/trunk/tests/1d/line3/TestDislocation.py
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/TestDislocation.py 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line3/TestDislocation.py 2009-05-28 21:22:24 UTC (rev 15078)
@@ -12,42 +12,169 @@
## @file tests/1d/line3/TestDislocation.py
##
-## @brief Test suite for testing pylith with dislocation in 1-D mesh.
+## @brief Test suite for testing pylith with 1-D axial extension.
-import unittest
import numpy
-import tables
+from TestLine3 import TestLine3
+from pylith.utils.VTKDataReader import has_vtk
+from pylith.utils.VTKDataReader import VTKDataReader
+from pylith.tests.Fault import check_vertex_fields
+# Local version of PyLithApp
+from pylith.apps.PyLithApp import PyLithApp
+class DislocationApp(PyLithApp):
+ def __init__(self):
+ PyLithApp.__init__(self, name="dislocation")
+ return
+
+
+# Helper function to run PyLith
def run_pylith():
"""
Run pylith.
"""
if not "done" in dir(run_pylith):
- from pylith.PyLithApp import PyLithApp
- app = PyLithApp("dislocationextension")
+ app = DislocationApp()
app.run()
run_pylith.done = True
return
-class TestDislocation(unittest.TestCase):
+class TestDislocation(TestLine3):
"""
- Test suite for testing pylith with dislocation in 1-D mesh.
+ Test suite for testing pylith with 1-D axial extension.
"""
def setUp(self):
"""
Setup for test.
"""
+ TestLine3.setUp(self)
+ self.mesh['nvertices'] = 6
+ self.nverticesO = 5
+
+ self.faultMesh = {'nvertices': 1,
+ 'spaceDim': 3,
+ 'ncells': 1,
+ 'ncorners': 1}
+
run_pylith()
+ self.outputRoot = "dislocation"
+ if has_vtk():
+ self.reader = VTKDataReader()
+ else:
+ self.reader = None
return
- def test_disp(self):
+ def test_fault_info(self):
"""
- Check displacement field.
+ Check fault information.
"""
+ if self.reader is None:
+ return
+
+ filename = "%s-fault_info.vtk" % self.outputRoot
+ fields = ["normal_dir", "final_slip", "slip_time"]
+ check_vertex_fields(self, filename, self.faultMesh, fields)
+
return
+ def test_fault_data(self):
+ """
+ Check fault information.
+ """
+ if self.reader is None:
+ return
+
+ filename = "%s-fault_t0000000.vtk" % self.outputRoot
+ fields = ["cumulative_slip", "traction_change"]
+ check_vertex_fields(self, filename, self.faultMesh, fields)
+
+ return
+
+
+ def calcDisplacements(self, vertices):
+ """
+ Calculate displacement field given coordinates of vertices.
+ """
+ nvertices = self.mesh['nvertices']
+ spaceDim = self.mesh['spaceDim']
+ nverticesO = self.nverticesO
+
+ disp = numpy.zeros( (nvertices, spaceDim), dtype=numpy.float64)
+ maskP = vertices[:,0] >= 2.0
+ maskP[nverticesO:nvertices] = False
+ maskN = numpy.bitwise_and(vertices[:,0] <= 2.0, ~maskP)
+ disp[:,0] = \
+ maskN*(-0.20 - 0.025*vertices[:,0]) + \
+ maskP*(+0.30 - 0.025*vertices[:,0])
+
+ return disp
+
+
+ def calcStateVar(self, name, vertices, cells):
+ """
+ Calculate state variable.
+ """
+ exx = -0.025
+
+ ncells = self.mesh['ncells']
+ tensorSize = self.mesh['tensorSize']
+
+ if name == "total_strain":
+ stateVar = exx*numpy.ones( (ncells, tensorSize), dtype=numpy.float64)
+
+ elif name == "stress":
+ lp2m = self.density*self.vp**2
+ stateVar = lp2m*exx * numpy.ones( (ncells, tensorSize),
+ dtype=numpy.float64)
+ else:
+ raise ValueError("Unknown state variable '%s'." % name)
+
+ return stateVar
+
+
+ def calcFaultField(self, name, vertices):
+ """
+ Calculate fault info.
+ """
+
+ normalDir = 1.0
+ finalSlip = -0.5
+ slipTime = 0.0
+
+ slip = 1.0
+ exx = -0.025
+ lp2m = self.density*self.vp**2
+ traction = -exx*lp2m
+
+ nvertices = self.faultMesh['nvertices']
+
+ if name == "normal_dir":
+ field = numpy.zeros( (nvertices, 3), dtype=numpy.float64)
+ field[:,0] = normalDir
+
+ elif name == "final_slip":
+ field = numpy.zeros( (nvertices, 3), dtype=numpy.float64)
+ field[:,0] = finalSlip
+
+ elif name == "slip_time":
+ field = slipTime*numpy.ones( (nvertices, 1), dtype=numpy.float64)
+
+ elif name == "cumulative_slip":
+ field = numpy.zeros( (nvertices, 3), dtype=numpy.float64)
+ field[:,0] = finalSlip
+
+ elif name == "traction_change":
+ field = numpy.zeros( (nvertices, 3), dtype=numpy.float64)
+ field[:,0] = traction
+
+ else:
+ raise ValueError("Unknown fault field '%s'." % name)
+
+ return field
+
+
# End of file
Added: short/3D/PyLith/trunk/tests/1d/line3/TestLine3.py
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/TestLine3.py (rev 0)
+++ short/3D/PyLith/trunk/tests/1d/line3/TestLine3.py 2009-05-28 21:22:24 UTC (rev 15078)
@@ -0,0 +1,97 @@
+#!/usr/bin/env python
+#
+# ----------------------------------------------------------------------
+#
+# Brad T. Aagaard
+# U.S. Geological Survey
+#
+# <LicenseText>
+#
+# ----------------------------------------------------------------------
+#
+
+## @file tests/1d/line2/TestLine3.py
+##
+## @brief Generic tests for problems using 1-D bar mesh.
+
+import unittest
+import numpy
+
+class TestLine3(unittest.TestCase):
+ """
+ Generic tests for problems using 1-D bar mesh.
+ """
+
+ def setUp(self):
+ """
+ Setup for tests.
+ """
+ self.mesh = {'ncells': 2,
+ 'ncorners': 3,
+ 'nvertices': 5,
+ 'spaceDim': 3,
+ 'tensorSize': 1}
+ self.vs = 3000.0
+ self.vp = 5291.502622129181
+ self.density = 2500.0
+ return
+
+
+ def test_elastic_info(self):
+ """
+ Check elastic info.
+ """
+ if self.reader is None:
+ return
+
+ ncells= self.mesh['ncells']
+
+ filename = "%s-elastic_info.vtk" % self.outputRoot
+ m = self.density*self.vs**2
+ l = self.density*self.vp**2 - 2*m
+
+ propMu = m*numpy.ones( (ncells, 1), dtype=numpy.float64)
+ propLambda = l*numpy.ones( (ncells, 1), dtype=numpy.float64)
+ propDensity = self.density*numpy.ones( (ncells, 2), dtype=numpy.float64)
+
+ properties = {'mu': propMu,
+ 'lambda': propLambda,
+ 'density': propDensity}
+
+ from pylith.tests.PhysicalProperties import check_properties
+ check_properties(self, filename, self.mesh, properties)
+
+ return
+
+
+ def test_soln(self):
+ """
+ Check solution (displacement) field.
+ """
+ if self.reader is None:
+ return
+
+ filename = "%s_t0000000.vtk" % self.outputRoot
+ from pylith.tests.Solution import check_displacements
+ check_displacements(self, filename, self.mesh)
+
+ return
+
+
+ def test_elastic_statevars(self):
+ """
+ Check elastic state variables.
+ """
+ if self.reader is None:
+ return
+
+ filename = "%s-elastic_t0000000.vtk" % self.outputRoot
+
+ from pylith.tests.StateVariables import check_state_variables
+ stateVars = ["total_strain", "stress"]
+ check_state_variables(self, filename, self.mesh, stateVars)
+
+ return
+
+
+# End of file
Modified: short/3D/PyLith/trunk/tests/1d/line3/axialextension.cfg
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/axialextension.cfg 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line3/axialextension.cfg 2009-05-28 21:22:24 UTC (rev 15078)
@@ -1,73 +1,89 @@
# -*- Python -*-
-[pylithapp]
+[axialextension]
+[axialextension.launcher] # WARNING: THIS IS NOT PORTABLE
+command = mpirun -np ${nodes}
+
# ----------------------------------------------------------------------
# journal
# ----------------------------------------------------------------------
-[pylithapp.journal.info]
-timedependent = 1
-explicit = 1
-implicit = 1
-petsc = 1
-solverlinear = 1
-meshioascii = 1
-homogeneous = 1
-explicitelasticity = 1
-quadrature1d = 1
-fiatsimplex = 1
+[axialextension.journal.info]
+#timedependent = 1
+#explicit = 1
+#implicit = 1
+#petsc = 1
+#solverlinear = 1
+#meshioascii = 1
+#homogeneous = 1
+#explicitelasticity = 1
+#quadrature1d = 1
+#fiatsimplex = 1
# ----------------------------------------------------------------------
# mesh_generator
# ----------------------------------------------------------------------
-[pylithapp.mesh_generator]
+[axialextension.mesh_generator]
debug = 1
-[pylithapp.mesh_generator.importer]
+[axialextension.mesh_generator.reader]
filename = bar.mesh
coordsys.space_dim = 1
# ----------------------------------------------------------------------
# problem
# ----------------------------------------------------------------------
-[pylithapp.timedependent]
-total_time = 0.0*s
-default_dt = 1.0*s
+[axialextension.timedependent]
dimension = 1
-formulation = pylith.problems.Implicit
-bc = pylith.bc.BCSingle
+bc = [bc]
+[axialextension.timedependent.formulation.time_step]
+total_time = 0.0*s
+
# ----------------------------------------------------------------------
# materials
# ----------------------------------------------------------------------
-[pylithapp.timedependent.materials]
-material = pylith.materials.ElasticStrain1D
+[axialextension.timedependent]
+materials = [elastic]
+materials.elastic = pylith.materials.ElasticStrain1D
-[pylithapp.timedependent.materials.material]
-label = elastic material
+[axialextension.timedependent.materials.elastic]
+label = Elastic material
id = 1
-db.iohandler.filename = matprops.spatialdb
-quadrature = pylith.feassemble.quadrature.Quadrature1D
+properties_db.iohandler.filename = matprops.spatialdb
quadrature.cell.shape = line
quadrature.cell.degree = 2
# ----------------------------------------------------------------------
# boundary conditions
# ----------------------------------------------------------------------
-[pylithapp.timedependent.bc.bc]
+[axialextension.timedependent.bc.bc]
fixed_dof = [0]
-id = 10
label = end points
+db = spatialdata.spatialdb.SimpleDB
db.label = Dirichlet BC
db.iohandler.filename = axialextension_disp.spatialdb
# ----------------------------------------------------------------------
# PETSc
# ----------------------------------------------------------------------
-[pylithapp.petsc]
-pc_type = jacobi
+[axialextension.petsc]
+ksp_rtol = 1.0e-8
+pc_type = asm
+ksp_max_it = 100
+ksp_gmres_restart = 50
+#ksp_monitor = true
+#ksp_view = true
+#log_summary = true
+#start_in_debugger = true
+#snes_monitor = true
+#snes_view = true
# ----------------------------------------------------------------------
# output
# ----------------------------------------------------------------------
-[pylithapp.problem.formulation.output.output.writer]
+[axialextension.problem.formulation.output.output.writer]
filename = axialextension.vtk
+
+[axialextension.timedependent.materials.elastic.output]
+cell_filter = pylith.meshio.CellFilterAvgMesh
+writer.filename = axialextension-elastic.vtk
Modified: short/3D/PyLith/trunk/tests/1d/line3/bar.mesh
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/bar.mesh 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line3/bar.mesh 2009-05-28 21:22:24 UTC (rev 15078)
@@ -2,19 +2,21 @@
dimension = 1
vertices = {
dimension = 1
- count = 3
+ count = 5
coordinates = {
0 0.0
- 1 2.0
- 2 4.0
+ 1 1.0
+ 2 2.0
+ 3 3.0
+ 4 4.0
}
}
cells = {
- num-corners = 2
+ num-corners = 3
count = 2
simplices = {
- 0 0 1
- 1 1 2
+ 0 0 2 1
+ 1 2 4 3
}
material-ids = {
0 1
@@ -27,7 +29,7 @@
count = 2
indices = {
0
- 2
+ 4
}
}
group = {
@@ -35,7 +37,7 @@
type = vertices
count = 1
indices = {
- 1
+ 2
}
}
}
Modified: short/3D/PyLith/trunk/tests/1d/line3/dislocation.cfg
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/dislocation.cfg 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line3/dislocation.cfg 2009-05-28 21:22:24 UTC (rev 15078)
@@ -1,93 +1,106 @@
# -*- Python -*-
-[pylithapp]
+[dislocation]
+[dislocation.launcher] # WARNING: THIS IS NOT PORTABLE
+command = mpirun -np ${nodes}
+
# ----------------------------------------------------------------------
# journal
# ----------------------------------------------------------------------
-[pylithapp.journal.info]
-timedependent = 1
-explicit = 1
-implicit = 1
-petsc = 1
-solverlinear = 1
-meshioascii = 1
-homogeneous = 1
-implicitelasticity = 1
-quadrature1d = 1
-fiatsimplex = 1
-faultcohesivekin = 1
+[dislocation.journal.info]
+#timedependent = 1
+#implicit = 1
+#petsc = 1
+#solverlinear = 1
+#meshioascii = 1
+#implicitelasticity = 1
+#quadrature = 1
+#fiatsimplex = 1
+#faultcohesivekin = 1
# ----------------------------------------------------------------------
# mesh_generator
# ----------------------------------------------------------------------
-[pylithapp.mesh_generator]
-debug = 1
+[dislocation.mesh_generator]
+#debug = 1
-[pylithapp.mesh_generator.importer]
+[dislocation.mesh_generator.reader]
filename = bar.mesh
coordsys.space_dim = 1
# ----------------------------------------------------------------------
# problem
# ----------------------------------------------------------------------
-[pylithapp.timedependent]
-total_time = 0.0*s
-default_dt = 1.0*s
+[dislocation.timedependent]
dimension = 1
-formulation = pylith.problems.Implicit
-bc = pylith.bc.BCSingle
-interfaces = pylith.faults.SingleFault
+bc = [bc]
+interfaces = [fault]
+[dislocation.timedependent.formulation.time_step]
+total_time = 0.0*s
+
# ----------------------------------------------------------------------
# materials
# ----------------------------------------------------------------------
-[pylithapp.timedependent.materials]
-material = pylith.materials.ElasticStrain1D
+[dislocation.timedependent]
+materials = [elastic]
+materials.elastic = pylith.materials.ElasticStrain1D
-[pylithapp.timedependent.materials.material]
-label = elastic material
+[dislocation.timedependent.materials.elastic]
+label = Elastic material
id = 1
-db.iohandler.filename = matprops.spatialdb
-quadrature = pylith.feassemble.quadrature.Quadrature1D
+properties_db.iohandler.filename = matprops.spatialdb
quadrature.cell.shape = line
quadrature.cell.degree = 2
# ----------------------------------------------------------------------
# boundary conditions
# ----------------------------------------------------------------------
-[pylithapp.timedependent.bc.bc]
+[dislocation.timedependent.bc.bc]
fixed_dof = [0]
-id = 10
label = end points
+db = spatialdata.spatialdb.SimpleDB
db.label = Dirichlet BC
-db.iohandler.filename = dislocation_disp.spatialdb
+db.iohandler.filename = axialextension_disp.spatialdb
# ----------------------------------------------------------------------
# faults
# ----------------------------------------------------------------------
-[pylithapp.timedependent.interfaces]
+[dislocation.timedependent.interfaces]
fault = pylith.faults.FaultCohesiveKin
-[pylithapp.timedependent.interfaces.fault]
-id = 20
+[dislocation.timedependent.interfaces.fault]
label = fault
-quadrature = pylith.feassemble.quadrature.Quadrature0D
quadrature.cell.shape = point
-[pylithapp.timedependent.interfaces.fault.eq_src.slip_function]
-slip.iohandler.filename = dislocation_slip.spatialdb
-slip_rate.iohandler.filename = dislocation_sliprate.spatialdb
-slip_time.iohandler.filename = dislocation_sliptime.spatialdb
+[dislocation.timedependent.interfaces.fault.eq_srcs.rupture.slip_function]
+slip.iohandler.filename = finalslip.spatialdb
+slip_time.iohandler.filename = sliptime.spatialdb
-
# ----------------------------------------------------------------------
# PETSc
# ----------------------------------------------------------------------
-[pylithapp.petsc]
-pc_type = jacobi
+[dislocation.petsc]
+ksp_rtol = 1.0e-8
+pc_type = asm
+ksp_max_it = 100
+ksp_gmres_restart = 50
+#ksp_monitor = true
+#ksp_view = true
+#log_summary = true
+#start_in_debugger = true
+#snes_monitor = true
+#snes_view = true
# ----------------------------------------------------------------------
# output
# ----------------------------------------------------------------------
-[pylithapp.problem.formulation.output.output.writer]
+[dislocation.problem.formulation.output.output.writer]
filename = dislocation.vtk
+
+[dislocation.timedependent.materials.elastic.output]
+cell_filter = pylith.meshio.CellFilterAvgMesh
+writer.filename = dislocation-elastic.vtk
+
+[dislocation.timedependent.interfaces.fault.output.writer]
+filename = dislocation-fault.vtk
Deleted: short/3D/PyLith/trunk/tests/1d/line3/dislocation_disp.spatialdb
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/dislocation_disp.spatialdb 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line3/dislocation_disp.spatialdb 2009-05-28 21:22:24 UTC (rev 15078)
@@ -1,14 +0,0 @@
-#SPATIAL.ascii 1
-SimpleDB {
- num-values = 1
- value-names = dof-0
- value-units = m
- num-locs = 1
- data-dim = 0
- space-dim = 1
- cs-data = cartesian {
- to-meters = 1.0
- space-dim = 1
- }
-}
-0.0 0.0
Deleted: short/3D/PyLith/trunk/tests/1d/line3/dislocation_slip.spatialdb
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/dislocation_slip.spatialdb 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line3/dislocation_slip.spatialdb 2009-05-28 21:22:24 UTC (rev 15078)
@@ -1,14 +0,0 @@
-#SPATIAL.ascii 1
-SimpleDB {
- num-values = 1
- value-names = fault-opening
- value-units = m
- num-locs = 1
- data-dim = 0
- space-dim = 1
- cs-data = cartesian {
- to-meters = 1.0
- space-dim = 1
- }
-}
-0.0 1.0
Deleted: short/3D/PyLith/trunk/tests/1d/line3/dislocation_sliprate.spatialdb
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/dislocation_sliprate.spatialdb 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line3/dislocation_sliprate.spatialdb 2009-05-28 21:22:24 UTC (rev 15078)
@@ -1,14 +0,0 @@
-#SPATIAL.ascii 1
-SimpleDB {
- num-values = 1
- value-names = slip-rate
- value-units = m/s
- num-locs = 1
- data-dim = 0
- space-dim = 1
- cs-data = cartesian {
- to-meters = 1.0
- space-dim = 1
- }
-}
-0.0 1.0e+6
Deleted: short/3D/PyLith/trunk/tests/1d/line3/dislocation_sliptime.spatialdb
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/dislocation_sliptime.spatialdb 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line3/dislocation_sliptime.spatialdb 2009-05-28 21:22:24 UTC (rev 15078)
@@ -1,14 +0,0 @@
-#SPATIAL.ascii 1
-SimpleDB {
- num-values = 1
- value-names = slip-time
- value-units = s
- num-locs = 1
- data-dim = 0
- space-dim = 1
- cs-data = cartesian {
- to-meters = 1.0
- space-dim = 1
- }
-}
-0.0 -1.0
Added: short/3D/PyLith/trunk/tests/1d/line3/finalslip.spatialdb
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/finalslip.spatialdb (rev 0)
+++ short/3D/PyLith/trunk/tests/1d/line3/finalslip.spatialdb 2009-05-28 21:22:24 UTC (rev 15078)
@@ -0,0 +1,15 @@
+// -*- C++ -*-
+#SPATIAL.ascii 1
+SimpleDB {
+ num-values = 1
+ value-names = fault-opening
+ value-units = m
+ num-locs = 1
+ data-dim = 0
+ space-dim = 1
+ cs-data = cartesian {
+ to-meters = 1.0
+ space-dim = 1
+ }
+}
+0.0 -0.50
Modified: short/3D/PyLith/trunk/tests/1d/line3/matprops.spatialdb
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/matprops.spatialdb 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line3/matprops.spatialdb 2009-05-28 21:22:24 UTC (rev 15078)
@@ -2,7 +2,7 @@
SimpleDB {
num-values = 3
value-names = density vs vp
- value-units = kg/m^3 m/s m/s
+ value-units = kg/m**3 m/s m/s
num-locs = 1
data-dim = 0
space-dim = 1
Added: short/3D/PyLith/trunk/tests/1d/line3/sliptime.spatialdb
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/sliptime.spatialdb (rev 0)
+++ short/3D/PyLith/trunk/tests/1d/line3/sliptime.spatialdb 2009-05-28 21:22:24 UTC (rev 15078)
@@ -0,0 +1,15 @@
+// -*- C++ -*-
+#SPATIAL.ascii 1
+SimpleDB {
+ num-values = 1
+ value-names = slip-time
+ value-units = s
+ num-locs = 1
+ data-dim = 0
+ space-dim = 1
+ cs-data = cartesian {
+ to-meters = 1.0
+ space-dim = 1
+ }
+}
+0.0 0.0
Modified: short/3D/PyLith/trunk/tests/1d/line3/testpylith.py
===================================================================
--- short/3D/PyLith/trunk/tests/1d/line3/testpylith.py 2009-05-28 20:39:35 UTC (rev 15077)
+++ short/3D/PyLith/trunk/tests/1d/line3/testpylith.py 2009-05-28 21:22:24 UTC (rev 15078)
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env nemesis
#
# ======================================================================
#
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