def _runTest(self, filenameIn, filenameOut, filenameOutE, faultGroup=None):
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
io = MeshIOAscii()
io.inventory.filename = filenameIn
io.inventory.coordsys = cs
io._configure()
mesh = io.read(debug=False, interpolate=True)
if not faultGroup is None:
from pylith.faults.FaultCohesiveKin import FaultCohesiveKin
fault = FaultCohesiveKin()
fault.inventory.matId = 10
fault.inventory.faultLabel = faultGroup
fault._configure()
nvertices = fault.numVerticesNoMesh(mesh)
firstFaultVertex = 0
firstLagrangeVertex = nvertices
firstFaultCell = 2*nvertices
fault.adjustTopology(mesh,
firstFaultVertex,
firstLagrangeVertex,
firstFaultCell)
from pylith.topology.RefineUniform import RefineUniform
refiner = RefineUniform()
meshRefined = refiner.refine(mesh)
return
def setUp(self):
"""
Setup mesh and associated field.
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
self.mesh = importer.read(debug=False, interpolate=False)
self.field = Field(self.mesh)
self.field.allocate()
return
def test_readwrite(self):
"""
Test write() and read().
"""
filenameIn = "data/mesh2Din3D.txt"
filenameOut = "data/mesh2Din3D_test.txt"
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs._configure()
io = MeshIOAscii()
io.inventory.filename = filenameIn
io.inventory.coordsys = cs
io._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
mesh = io.read(debug=False, interpolate=True)
io.filename(filenameOut)
io.write(mesh)
fileE = open(filenameIn, "r")
linesE = fileE.readlines()
fileE.close()
fileT = open(filenameOut, "r")
linesT = fileT.readlines()
fileT.close()
self.assertEqual(len(linesE), len(linesT))
for (lineE, lineT) in zip(linesE, linesT):
self.assertEqual(lineE, lineT)
return
def test_databasemulti(self):
locs = numpy.array([[2.3, -0.1, 1.8], [2.0, 0.4, -2.0]], numpy.float64)
cs = CSCart()
cs._configure()
queryVals = ["two", "one"]
dataE = numpy.array([[0.0207, 1.17], [0.0209, 1.15]], numpy.float64)
errE = numpy.array([0, 0], numpy.int32)
db = self._db
db.open()
db.queryVals(queryVals)
data = numpy.zeros(dataE.shape, dtype=numpy.float64)
err = numpy.zeros(errE.shape, dtype=numpy.int32)
db.multiquery(data, err, locs, cs)
db.close()
self.assertEqual(len(errE), len(err))
for vE, v in zip(errE, err):
self.assertEqual(vE, v)
self.assertEqual(len(dataE.shape), len(data.shape))
for dE, d in zip(dataE.shape, data.shape):
self.assertEqual(dE, d)
for vE, v in zip(numpy.reshape(dataE, -1), numpy.reshape(data, -1)):
self.assertAlmostEqual(vE, v, 6)
return
def setUp(self):
"""
Setup mesh and associated field.
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
self.mesh = importer.read(debug=False, interpolate=False)
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(self.mesh)
fields.add("disp t+dt", "displacement")
fields.solutionName("disp t+dt")
solution = fields.solution()
solution.newSection(solution.VERTICES_FIELD, self.mesh.dimension())
solution.allocate()
solution.zero()
self.fields = fields
self.jacobian = Jacobian(solution)
return
def getCellSizeDB(points):
from spatialdata.geocoords.CSCart import CSCart
from spatialdata.spatialdb.SimpleDB import SimpleDB
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
# Coordinate system for mesh (must match coordsys in ExodusII file)
cs = CSCart()
cs._configure()
cs.initialize()
# Spatial database with physical properties (Vs)
dbIO = SimpleIOAscii()
dbIO.inventory.filename = filenameDB
dbIO._configure()
db = SimpleDB()
db.inventory.iohandler = dbIO
db.inventory.label = "Physical properties"
db.inventory.queryType = "linear"
db._configure()
(npoints, spacedim) = points.shape
# Query database
db.open()
db.queryVals(["vs"])
data = numpy.zeros((npoints, 1), dtype=numpy.float64)
err = numpy.zeros((npoints,), dtype=numpy.int32)
db.multiquery(data, err, points, cs)
db.close()
vs = data[:,0]
cellSize = minPeriod*vs / 10.0
return cellSize
def test_database(self):
locs = numpy.array([[3.5, 0.1, 0.8], [8.0, -0.4, 1.8]], numpy.float64)
cs = CSCart()
cs._configure()
queryVals = ["two", "one"]
dataE = numpy.array([[0.0220, 1.04], [0.0222, 1.02]], numpy.float64)
errE = [0, 0]
db = self._db
db.open()
db.queryVals(queryVals)
data = numpy.zeros(dataE.shape, dtype=numpy.float64)
err = []
nlocs = locs.shape[0]
for i in xrange(nlocs):
e = db.query(data[i, :], locs[i, :], cs)
err.append(e)
db.close()
self.assertEqual(len(errE), len(err))
for vE, v in zip(errE, err):
self.assertEqual(vE, v)
self.assertEqual(len(dataE.shape), len(data.shape))
for dE, d in zip(dataE.shape, data.shape):
self.assertEqual(dE, d)
for vE, v in zip(numpy.reshape(dataE, -1), numpy.reshape(data, -1)):
self.assertAlmostEqual(vE, v, 6)
return
def test_preinitialize(self):
"""
Test preinitialize().
WARNING: This is not a rigorous test of initialize() because we
don't verify the results.
"""
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 2
cell.inventory.order = 1
cell.inventory.degree = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature.inventory.minJacobian = 1.0e-4
quadrature._configure()
from spatialdata.spatialdb.SimpleDB import SimpleDB
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
iohandler = SimpleIOAscii()
iohandler.inventory.filename = "data/matinitialize.spatialdb"
iohandler._configure()
db = SimpleDB()
db.inventory.label = "material properties"
db.inventory.iohandler = iohandler
db._configure()
from pylith.materials.ElasticPlaneStrain import ElasticPlaneStrain
material = ElasticPlaneStrain()
material.inventory.quadrature = quadrature
material.inventory.dbProperties = db
material.inventory.label = "my material"
material.inventory.id = 54
material._configure()
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/twoelems.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
material.preinitialize(mesh)
# No test of result.
return
def _preinitialize(self):
"""
Setup mesh and integrator and preinitialize integrator.
"""
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
# Setup mesh
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
# Setup material
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 2
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
from spatialdata.spatialdb.SimpleDB import SimpleDB
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
iohandler = SimpleIOAscii()
iohandler.inventory.filename = "data/elasticplanestrain.spatialdb"
iohandler._configure()
db = SimpleDB()
db.inventory.label = "elastic plane strain"
db.inventory.iohandler = iohandler
db._configure()
from pylith.materials.ElasticPlaneStrain import ElasticPlaneStrain
material = ElasticPlaneStrain()
material.inventory.label = "elastic plane strain"
material.inventory.id = 0
material.inventory.dbProperties = db
material.inventory.quadrature = quadrature
material._configure()
from pylith.meshio.OutputMatElastic import OutputMatElastic
material.output = OutputMatElastic()
material.output._configure()
material.output.writer._configure()
# Setup integrator
integrator = ElasticityImplicitLgDeform()
integrator.preinitialize(mesh, material)
return (mesh, integrator)
def test(self):
"""
Test GenSimpleDBApp with 1-D data in 2-D space.
"""
from spatialdata.spatialdb.generator.GenSimpleDBApp import GenSimpleDBApp
from spatialdata.geocoords.CSCart import CSCart
from spatialdata.spatialdb.SimpleDB import SimpleDB
app = GenSimpleDBApp()
app.run()
# Test write using query
db = SimpleDB()
db.inventory.iohandler.inventory.filename = \
"data/gen1Din2D.spatialdb"
db.inventory.iohandler._configure()
db.inventory.label = "test"
db.inventory.queryType = "nearest"
db._configure()
qlocs = numpy.array( [[-2.0, 2.0],
[ 3.0, -4.0],
[ 0.0, 0.7]],
numpy.float64)
dataE = numpy.array( [[-0.15, 3.45],
[2.4, 6.4],
[-0.6, 3.45]], numpy.float64)
errE = [0, 0, 0]
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
db.open()
db.queryVals(["two", "one"])
data = numpy.zeros(dataE.shape, dtype=numpy.float64)
err = []
nlocs = qlocs.shape[0]
for i in xrange(nlocs):
e = db.query(data[i,:], qlocs[i,:], cs)
err.append(e)
db.close()
self.assertEqual(len(errE), len(err))
for vE, v in zip(errE, err):
self.assertEqual(vE, v)
self.assertEqual(len(dataE.shape), len(data.shape))
for dE, d in zip(dataE.shape, data.shape):
self.assertEqual(dE, d)
for vE, v in zip(numpy.reshape(dataE, -1), numpy.reshape(data, -1)):
self.assertAlmostEqual(vE, v, 6)
return
def test_initialize(self):
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.units = "km"
cs.inventory.spaceDim = 2
cs._configure()
cs.initialize()
self.assertEqual(1.0e+3, cs.toMeters())
self.assertEqual(2, cs.spaceDim())
return
def _initialize(self):
"""
Initialize DirichletBoundary boundary condition.
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
from spatialdata.spatialdb.SimpleDB import SimpleDB
db = SimpleDB()
db.inventory.label = "TestDirichletBoundary tri3"
db.inventory.iohandler.inventory.filename = "data/tri3_disp.spatialdb"
db.inventory.iohandler._configure()
db._configure()
from spatialdata.spatialdb.SimpleDB import SimpleDB
dbRate = SimpleDB()
dbRate.inventory.label = "TestDirichletBoundary tri3"
dbRate.inventory.iohandler.inventory.filename = "data/tri3_vel.spatialdb"
dbRate.inventory.iohandler._configure()
dbRate._configure()
from pylith.bc.DirichletBoundary import DirichletBoundary
bc = DirichletBoundary()
bc.inventory.output._configure()
bc.inventory.output.writer._configure()
bc.inventory.label = "bc"
bc.inventory.bcDOF = [1]
bc.inventory.dbInitial = db
bc.inventory.dbRate = dbRate
bc._configure()
bc.preinitialize(mesh)
bc.initialize(totalTime=0.0, numTimeSteps=1, normalizer=normalizer)
# Setup field
from pylith.topology.Field import Field
field = Field(mesh)
field.newSection(field.VERTICES_FIELD, cs.spaceDim())
return (mesh, bc, field)
def test_coordsys(self):
"""
Test coordsys().
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
mesh = Mesh()
mesh.coordsys(cs)
self.assertEqual(cs.spaceDim(), mesh.coordsys().spaceDim())
return
def run(self):
"""
Generate the database.
"""
# Domain
x = numpy.arange(-4000.0, 4000.1, 500.0)
y = numpy.arange(-4000.0, 4000.1, 500.0)
z = numpy.arange(-6000.0, 0.1, 500.0)
nxpts = x.shape[0]
nypts = y.shape[0]
nzpts = z.shape[0]
xx = numpy.tile(x, (1,nypts*nzpts))
yy = numpy.tile(y, (nxpts,nzpts)).transpose()
zz = numpy.tile(z, (nxpts*nypts,1)).transpose()
xyz = numpy.zeros( (nxpts*nypts*nzpts, 3), dtype=numpy.float64)
xyz[:,0] = numpy.ravel(xx)
xyz[:,1] = numpy.ravel(yy)
xyz[:,2] = numpy.ravel(zz)
from axialdisp_soln import AnalyticalSoln
soln = AnalyticalSoln()
disp = soln.displacement(xyz)
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 3
cs._configure()
data = {'points': xyz,
'coordsys': cs,
'data_dim': 3,
'values': [{'name': "displacement-x",
'units': "m",
'data': numpy.ravel(disp[:,0])},
{'name': "displacement-y",
'units': "m",
'data': numpy.ravel(disp[:,1])},
{'name': "displacement-z",
'units': "m",
'data': numpy.ravel(disp[:,2])}]}
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
io = SimpleIOAscii()
io.inventory.filename = "axial_disp.spatialdb"
io._configure()
io.write(data)
return
def run(self):
"""
Generate the database.
"""
# Domain
x = numpy.arange(-4000.0, 4000.1, 1000.0)
y = numpy.arange(-4000.0, 4000.1, 1000.0)
z = numpy.arange(-6000.0, 0000.1, 1000.0)
nptsX = x.shape[0]
nptsY = y.shape[0]
nptsZ = z.shape[0]
xx = x * numpy.ones( (nptsY*nptsZ, 1), dtype=numpy.float64)
yy0 = y * numpy.ones( (nptsZ, 1), dtype=numpy.float64)
yy = yy0.ravel() * numpy.ones( (nptsX, 1), dtype=numpy.float64)
zz = z * numpy.ones( (nptsX*nptsY, 1), dtype=numpy.float64)
xyz = numpy.zeros( (nptsX*nptsY*nptsZ, 3), dtype=numpy.float64)
xyz[:,0] = numpy.ravel(xx)
xyz[:,1] = numpy.ravel(numpy.transpose(yy))
xyz[:,2] = numpy.ravel(numpy.transpose(zz))
from rigidbody_soln import AnalyticalSoln
soln = AnalyticalSoln()
disp = soln.displacement(xyz)
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 3
cs._configure()
data = {'locs': xyz,
'coordsys': cs,
'data_dim': 2,
'values': [{'name': "displacement-x",
'units': "m",
'data': numpy.ravel(disp[:,0])},
{'name': "displacement-y",
'units': "m",
'data': numpy.ravel(disp[:,1])},
{'name': "displacement-z",
'units': "m",
'data': numpy.ravel(disp[:,2])}]}
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
io = SimpleIOAscii()
io.inventory.filename = "rigidbody_disp.spatialdb"
io._configure()
io.write(data)
return
def run(self):
"""
Generate the database.
"""
from sheardisp_soln import AnalyticalSoln
soln = AnalyticalSoln()
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 3
cs._configure()
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
io = SimpleIOAscii()
for component in ["x","y","z"]:
if component == "y":
xyz = numpy.array([[-40.0e+3, 0.0, 0.0],
[+40.0e+3, 0.0, 0.0]], dtype=numpy.float64)
ic = 1
elif component == "x":
xyz = numpy.array([[0.0, -40.0e+3, 0.0],
[0.0, +40.0e+3, 0.0]], dtype=numpy.float64)
ic = 0
elif component == "z":
xyz = numpy.array([[0.0, 0.0, -40.0e+3],
[0.0, 0.0, 0.0]], dtype=numpy.float64)
ic = 2
disp = soln.displacement(xyz)
io.inventory.filename = "shear_disp%s.spatialdb" % component
io._configure()
data = {'points': xyz,
'coordsys': cs,
'data_dim': 1,
'values': [{'name': "displacement-%s" % component,
'units': "m",
'data': numpy.ravel(disp[0,:,ic])},
]}
io.write(data)
return
def run(self):
"""
Generate the database.
"""
# Domain
x = numpy.arange(-4000.0, 4000.1, 1000.0)
y = numpy.arange(-4000.0, 4000.1, 1000.0)
npts = x.shape[0]
xx = x * numpy.ones((npts, 1), dtype=numpy.float64)
yy = y * numpy.ones((npts, 1), dtype=numpy.float64)
xy = numpy.zeros((npts ** 2, 2), dtype=numpy.float64)
xy[:, 0] = numpy.ravel(xx)
xy[:, 1] = numpy.ravel(numpy.transpose(yy))
from sheardisp_soln import AnalyticalSoln
soln = AnalyticalSoln()
disp = soln.displacement(xy)
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
data = {
"points": xy,
"coordsys": cs,
"data_dim": 2,
"values": [
{"name": "displacement-x", "units": "m", "data": numpy.ravel(disp[0, :, 0])},
{"name": "displacement-y", "units": "m", "data": numpy.ravel(disp[0, :, 1])},
],
}
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
io = SimpleIOAscii()
io.inventory.filename = "shear_disp.spatialdb"
io._configure()
io.write(data)
return
def test_readwrite(self):
"""
Test read().
"""
filenameGmvIn = "data/cube2_ascii.gmv"
filenamePsetIn = "data/cube2_ascii.pset"
filenameOut = "data/cube2_test.txt"
filenameE = "data/cube2.txt"
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs._configure()
# For now, we only test reading the file. We would like to write
# the file and compare against the original.
io = MeshIOLagrit()
io.inventory.filenameGmv = filenameGmvIn
io.inventory.filenamePset = filenamePsetIn
io._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
mesh = io.read(debug=False, interpolate=True)
testhandler = MeshIOAscii()
testhandler.filename(filenameOut)
testhandler.coordsys = cs
testhandler.write(mesh)
fileE = open(filenameE, "r")
linesE = fileE.readlines()
fileE.close()
fileT = open(filenameOut, "r")
linesT = fileT.readlines()
fileT.close()
self.assertEqual(len(linesE), len(linesT))
for (lineE, lineT) in zip(linesE, linesT):
self.assertEqual(lineE, lineT)
return
def test_readwrite(self):
"""
Test read().
"""
filenameIn = "data/twohex8.exo"
filenameOut = "data/twohex8_test.txt"
filenameE = "data/twohex8.txt"
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs._configure()
# For now, we only test reading the file.
io = MeshIOCubit()
io.inventory.filename = filenameIn
io.inventory.useNames = False
io._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
mesh = io.read(debug=False, interpolate=False)
testhandler = MeshIOAscii()
testhandler.filename(filenameOut)
testhandler.coordsys = cs
testhandler.write(mesh)
fileE = open(filenameE, "r")
linesE = fileE.readlines()
fileE.close()
fileT = open(filenameOut, "r")
linesT = fileT.readlines()
fileT.close()
self.assertEqual(len(linesE), len(linesT))
for (lineE, lineT) in zip(linesE, linesT):
self.assertEqual(lineE, lineT)
return
def run(self):
"""
Generate the database.
"""
# Domain
dx = 200.0
x = numpy.arange(-1000.0, 1000.1, dx)
y = numpy.arange(-1000.0, 0.1, dx)
nptsx = x.shape[0]
nptsy = y.shape[0]
xx = x * numpy.ones( (nptsy, 1), dtype=numpy.float64)
yy = y * numpy.ones( (nptsx, 1), dtype=numpy.float64)
xy = numpy.zeros( (nptsx*nptsy, 2), dtype=numpy.float64)
xy[:,0] = numpy.ravel(xx)
xy[:,1] = numpy.ravel(numpy.transpose(yy))
from compressrotate_soln import AnalyticalSoln
soln = AnalyticalSoln()
disp = soln.displacement(xy)
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
data = {'points': xy,
'coordsys': cs,
'data_dim': 2,
'values': [{'name': "displacement-x",
'units': "m",
'data': numpy.ravel(disp[0,:,0])},
{'name': "displacement-y",
'units': "m",
'data': numpy.ravel(disp[0,:,1])}]}
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
io = SimpleIOAscii()
io.inventory.filename = "compressrotate_disp.spatialdb"
io._configure()
io.write(data)
return
def _getMesh(self):
"""
Get mesh from file.
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
return mesh
def run(self):
"""
Generate the database.
"""
# Domain
x = numpy.arange(-4000.0, 4000.1, 1000.0)
y = numpy.arange(-4000.0, 4000.1, 1000.0)
npts = x.shape[0]
xx = x * numpy.ones( (npts, 1), dtype=numpy.float64)
yy = y * numpy.ones( (npts, 1), dtype=numpy.float64)
xy = numpy.zeros( (npts**2, 2), dtype=numpy.float64)
xy[:,0] = numpy.ravel(xx)
xy[:,1] = numpy.ravel(numpy.transpose(yy))
from axialdisp_soln import AnalyticalSoln
soln = AnalyticalSoln()
disp = soln.displacement(xy)
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
data = {'points': xy,
'coordsys': cs,
'data_dim': 2,
'values': [{'name': "displacement-x",
'units': "m",
'data': numpy.ravel(disp[0,:,0])},
{'name': "displacement-y",
'units': "m",
'data': numpy.ravel(disp[0,:,1])}]}
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
io = SimpleIOAscii()
io.inventory.filename = "axial_disp.spatialdb"
io._configure()
io.write(data)
return
def test_readwrite(self):
"""
Test read().
"""
filenameIn = "data/twohex8.exo"
filenameOut = "data/twohex8_test.txt"
filenameE = "data/twohex8.txt"
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs._configure()
# For now, we only test reading the file.
io = MeshIOCubit()
io.inventory.filename = filenameIn
io.inventory.useNames = False
io._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
mesh = io.read(debug=False, interpolate=True)
testhandler = MeshIOAscii()
testhandler.filename(filenameOut)
testhandler.coordsys = cs
testhandler.write(mesh)
fileE = open(filenameE, "r")
linesE = fileE.readlines()
fileE.close()
fileT = open(filenameOut, "r")
linesT = fileT.readlines()
fileT.close()
self.assertEqual(len(linesE), len(linesT))
for (lineE, lineT) in zip(linesE, linesT):
self.assertEqual(lineE, lineT)
return
def setUp(self):
"""
Setup mesh and associated field.
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
self.mesh = importer.read(debug=False, interpolate=False)
self.fields = Fields(self.mesh)
return
def test_adjustTopology(self):
"""
Test adjustTopology().
WARNING: This is not a rigorous test of adjustTopology() because we
neither set the input fields or verify the results.
"""
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
fault = FaultCohesiveKin()
fault.inventory.matId = 10
fault.inventory.faultLabel = "fault"
fault.inventory.faultEdge = "fault_edge"
fault._configure()
nvertices = fault.numVerticesNoMesh(mesh)
firstFaultVertex = 0
firstLagrangeVertex = nvertices
firstFaultCell = 2*nvertices
fault.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex,
firstFaultCell)
# We should really add something here to check to make sure things
# actually initialized correctly
return
def test_adjustTopology(self):
"""
Test adjustTopology().
WARNING: This is not a rigorous test of adjustTopology() because we
neither set the input fields or verify the results.
"""
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
fault = FaultCohesiveKin()
fault.inventory.matId = 10
fault.inventory.faultLabel = "fault"
fault.inventory.faultEdge = "fault_edge"
fault._configure()
nvertices = fault.numVerticesNoMesh(mesh)
firstFaultVertex = 0
firstLagrangeVertex = nvertices
firstFaultCell = 2*nvertices
fault.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex,
firstFaultCell)
# We should really add something here to check to make sure things
# actually initialized correctly
return
def run(self):
"""
Generate the database.
"""
# Domain
x = numpy.arange(-4000.0, 4000.1, 500.0)
y = numpy.arange(-4000.0, 4000.1, 500.0)
npts = x.shape[0]
xx = x * numpy.ones( (npts, 1), dtype=numpy.float64)
yy = y * numpy.ones( (npts, 1), dtype=numpy.float64)
xy = numpy.zeros( (npts**2, 2), dtype=numpy.float64)
xy[:,0] = numpy.ravel(xx)
xy[:,1] = numpy.ravel(numpy.transpose(yy))
disp = self.soln.displacement(xy)
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
data = {'points': xy,
'coordsys': cs,
'data_dim': 2,
'values': [{'name': "displacement-x",
'units': "m",
'data': numpy.ravel(disp[0,:,0])},
{'name': "displacement-y",
'units': "m",
'data': numpy.ravel(disp[0,:,1])}]}
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
io = SimpleIOAscii()
io.inventory.filename = self.filename
io._configure()
io.write(data)
return
def _initialize(self):
"""
Initialize fault.
"""
dt = 2.4
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
# Setup mesh
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
# Setup quadrature
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 1
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
# Setup earthquake source
from spatialdata.spatialdb.SimpleDB import SimpleDB
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
ioFinalSlip = SimpleIOAscii()
ioFinalSlip.inventory.filename = "data/tri3_finalslip.spatialdb"
ioFinalSlip._configure()
dbFinalSlip = SimpleDB()
dbFinalSlip.inventory.iohandler = ioFinalSlip
dbFinalSlip.inventory.label = "final slip"
dbFinalSlip._configure()
ioSlipTime = SimpleIOAscii()
ioSlipTime.inventory.filename = "data/tri3_sliptime.spatialdb"
ioSlipTime._configure()
dbSlipTime = SimpleDB()
dbSlipTime.inventory.iohandler = ioSlipTime
dbSlipTime.inventory.label = "slip time"
dbSlipTime._configure()
from pylith.faults.StepSlipFn import StepSlipFn
slipfn = StepSlipFn()
slipfn.inventory.dbSlip = dbFinalSlip
slipfn.inventory.dbSlipTime = dbSlipTime
slipfn._configure()
# Setup fault
fault = FaultCohesiveKin()
fault.inventory.output.inventory.writer._configure()
fault.inventory.output._configure()
fault.inventory.matId = 10
fault.inventory.faultLabel = "fault"
fault.inventory.upDir = [0, 0, 1]
fault.inventory.faultQuadrature = quadrature
fault._configure()
eqsrc = fault.eqsrcs.components()[0]
eqsrc.inventory.originTime = 1.23*second
eqsrc.inventory.slipfn = slipfn
eqsrc._configure()
nvertices = fault.numVerticesNoMesh(mesh)
firstFaultVertex = 0
firstLagrangeVertex = nvertices
firstFaultCell = 2*nvertices
fault.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex,
firstFaultCell)
fault.preinitialize(mesh)
fault.timeStep(dt)
fault.verifyConfiguration()
from pyre.units.time import s
fault.initialize(totalTime=0.0*s, numTimeSteps=1, normalizer=normalizer)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("dispIncr(t->t+dt)", "displacement_increment")
fields.add("disp(t)", "displacement")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
residual.subfieldAdd("displacement", cs.spaceDim(), residual.VECTOR)
residual.subfieldAdd("lagrange_multiplier", cs.spaceDim(), residual.VECTOR)
residual.subfieldsSetup()
residual.setupSolnChart()
residual.setupSolnDof(cs.spaceDim())
fault.setupSolnDof(residual)
residual.allocate()
residual.zero()
fields.copyLayout("residual")
return (mesh, fault, fields)
def run(self):
"""Generate the database.
"""
# Domain
x1 = numpy.arange(-0.1, 10.1, 0.1)
y1 = numpy.arange(-0.1, 1.01, 0.1)
x, y = numpy.meshgrid(x1, y1)
xy = numpy.zeros((len(x1) * len(y1), 2), dtype=numpy.float64)
xy[:, 0] = x.ravel()
xy[:, 1] = y.ravel()
from mandel_soln import AnalyticalSoln
soln = AnalyticalSoln()
disp = soln.initial_displacement(xy)
pres = soln.initial_pressure(xy)
trace_strain = soln.initial_trace_strain(xy)
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
data = {
'x':
x1,
'y':
y1,
'points':
xy,
'coordsys':
cs,
'data_dim':
2,
'values': [{
'name': "initial_amplitude_x",
'units': "m",
'data': numpy.ravel(disp[0, :, 0])
}, {
'name': "initial_amplitude_y",
'units': "m",
'data': numpy.ravel(disp[0, :, 1])
}, {
'name': "initial_pressure",
'units': "Pa",
'data': numpy.ravel(pres[0, :])
}, {
'name': "initial_trace_strain",
'units': "none",
'data': numpy.ravel(trace_strain[0, :])
}]
}
from spatialdata.spatialdb.SimpleGridAscii import SimpleGridAscii
io = SimpleGridAscii()
io.inventory.filename = "mandel_bc.spatialdb"
io._configure()
io.write(data)
data["values"] = [{
'name': "displacement_x",
'units': "m",
'data': numpy.ravel(disp[0, :, 0])
}, {
'name': "displacement_y",
'units': "m",
'data': numpy.ravel(disp[0, :, 1])
}, {
'name': "pressure",
'units': "Pa",
'data': numpy.ravel(pres[0, :])
}, {
'name': "trace_strain",
'units': "none",
'data': numpy.ravel(trace_strain[0, :])
}]
io.inventory.filename = "mandel_ic.spatialdb"
io._configure()
io.write(data)
return
def run(self):
"""Generate the database.
"""
# Domain
x = numpy.arange(-1.0e+4, 1.01e+4, 5.0e+3)
y = numpy.arange(-1.0e+4, 1.01e+4, 5.0e+3)
z = numpy.array([0])
x3, y3, z3 = numpy.meshgrid(x, y, z)
nptsX = x.shape[0]
nptsY = y.shape[0]
nptsZ = z.shape[0]
xyz = numpy.zeros((nptsX * nptsY * nptsZ, 3), dtype=numpy.float64)
xyz[:, 0] = x3.ravel()
xyz[:, 1] = y3.ravel()
xyz[:, 2] = z3.ravel()
from sheartraction_rate_soln import AnalyticalSoln
soln = AnalyticalSoln()
disp = soln.bc_initial_displacement(xyz)
velocity_time = soln.bc_rate_time(xyz) / year.value
velocity = soln.bc_velocity(xyz) * year.value
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 3
cs._configure()
data = {
"x":
x,
"y":
y,
"z":
z,
'points':
xyz,
'coordsys':
cs,
'data_dim':
2,
'values': [
{
'name': "initial_amplitude_x",
'units': "m",
'data': disp[0, :, 0].ravel()
},
{
'name': "initial_amplitude_y",
'units': "m",
'data': disp[0, :, 1].ravel()
},
{
'name': "initial_amplitude_z",
'units': "m",
'data': disp[0, :, 2].ravel()
},
{
'name': "rate_amplitude_x",
'units': "m/year",
'data': velocity[0, :, 0].ravel()
},
{
'name': "rate_amplitude_y",
'units': "m/year",
'data': velocity[0, :, 1].ravel()
},
{
'name': "rate_amplitude_z",
'units': "m/year",
'data': velocity[0, :, 2].ravel()
},
{
'name': "rate_start_time",
'units': "year",
'data': velocity_time[0, :, 0].ravel()
},
]
}
from spatialdata.spatialdb.SimpleGridAscii import SimpleGridAscii
io = SimpleGridAscii()
io.inventory.filename = "sheartraction_rate_disp.spatialdb"
io._configure()
io.write(data)
return
def run(self):
"""Generate the database.
"""
# Domain
x = numpy.arange(-6000.0, 6000.1, 2000.0)
y = numpy.arange(-6000.0, 6000.1, 2000.0)
z = numpy.arange(-10000.0, 2000.1, 2000.0)
(x3, y3, z3) = numpy.meshgrid(x, y, z)
nptsX = x.shape[0]
nptsY = y.shape[0]
nptsZ = z.shape[0]
xyz = numpy.zeros((nptsX * nptsY * nptsZ, 3), dtype=numpy.float64)
xyz[:, 0] = x3.ravel()
xyz[:, 1] = y3.ravel()
xyz[:, 2] = z3.ravel()
from axialstrainrate_genmaxwell_soln import AnalyticalSoln
soln = AnalyticalSoln()
disp = soln.initial_displacement(xyz)
velocity_time = soln.bc_rate_time(xyz) / year.value
velocity = soln.bc_velocity(xyz) * year.value
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 3
cs._configure()
data = {
'x':
x,
'y':
y,
'z':
z,
'points':
xyz,
'coordsys':
cs,
'data_dim':
3,
'values': [{
'name': "initial_amplitude_x",
'units': "m",
'data': disp[0, :, 0].ravel()
}, {
'name': "initial_amplitude_y",
'units': "m",
'data': disp[0, :, 1].ravel()
}, {
'name': "initial_amplitude_z",
'units': "m",
'data': disp[0, :, 2].ravel()
}, {
'name': "rate_amplitude_x",
'units': "m/year",
'data': velocity[0, :, 0].ravel()
}, {
'name': "rate_amplitude_y",
'units': "m/year",
'data': velocity[0, :, 1].ravel()
}, {
'name': "rate_amplitude_z",
'units': "m/year",
'data': velocity[0, :, 2].ravel()
}, {
'name': "rate_start_time",
'units': "year",
'data': velocity_time[0, :, 0].ravel()
}]
}
from spatialdata.spatialdb.SimpleGridAscii import SimpleGridAscii
io = SimpleGridAscii()
io.inventory.filename = "axialstrainrate_genmaxwell_bc.spatialdb"
io._configure()
io.write(data)
return
def _initialize(self):
"""
Initialize AbsorbingDampers boundary condition.
"""
from spatialdata.spatialdb.SimpleDB import SimpleDB
db = SimpleDB()
db.inventory.label = "TestAbsorbingDampers tri3"
db.inventory.iohandler.inventory.filename = \
"data/elasticplanestrain.spatialdb"
db.inventory.iohandler._configure()
db._configure()
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 1
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
from pylith.bc.AbsorbingDampers import AbsorbingDampers
bc = AbsorbingDampers()
bc.inventory.quadrature = quadrature
bc.inventory.db = db
bc.inventory.id = 0
bc.inventory.label = "bc"
bc._configure()
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
bc.preinitialize(mesh)
bc.initialize(totalTime=0.0, numTimeSteps=1, normalizer=normalizer)
bc.timeStep(0.01)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("dispIncr(t->t+dt)", "displacement")
fields.add("disp(t)", "displacement")
fields.add("disp(t-dt)", "displacement")
fields.add("velocity(t)", "velocity")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
residual.newSection(residual.VERTICES_FIELD, cs.spaceDim())
residual.allocate()
residual.zero()
fields.copyLayout("residual")
return (mesh, bc, fields)
def run(self):
"""Generate the database.
"""
# Domain
z = numpy.arange(-9000.0, 0.1, 9000.0)
x = numpy.zeros(z.shape)
y = numpy.zeros(z.shape)
npts = z.shape[0]
xyz = numpy.vstack((x, y, z)).transpose()
from gravity_refstate_soln import AnalyticalSoln
from gravity_refstate_soln import p_density, p_vs, p_vp
soln = AnalyticalSoln()
stress = soln.stress(xyz)
strain = soln.strain(xyz)
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 3
cs._configure()
data = {
'points': xyz,
'coordsys': cs,
'data_dim': 1,
'values': [
{
'name': "density",
'units': "kg/m**3",
'data': p_density * numpy.ones((npts,)),
}, {
'name': "vs",
'units': "m/s",
'data': p_vs * numpy.ones((npts,)),
}, {
'name': "vp",
'units': "m/s",
'data': p_vp * numpy.ones((npts,)),
}, {
'name': "reference_stress_xx",
'units': "Pa",
'data': numpy.ravel(stress[0, :, 0]),
}, {
'name': "reference_stress_yy",
'units': "Pa",
'data': numpy.ravel(stress[0, :, 1]),
}, {
'name': "reference_stress_zz",
'units': "Pa",
'data': numpy.ravel(stress[0, :, 2]),
}, {
'name': "reference_stress_yz",
'units': "Pa",
'data': numpy.ravel(stress[0, :, 4]),
}, {
'name': "reference_stress_xz",
'units': "Pa",
'data': numpy.ravel(stress[0, :, 5]),
}, {
'name': "reference_stress_xy",
'units': "Pa",
'data': numpy.ravel(stress[0, :, 3]),
}, {
'name': "reference_strain_xx",
'units': "none",
'data': numpy.ravel(strain[0, :, 0]),
}, {
'name': "reference_strain_yy",
'units': "none",
'data': numpy.ravel(strain[0, :, 1]),
}, {
'name': "reference_strain_zz",
'units': "none",
'data': numpy.ravel(strain[0, :, 2]),
}, {
'name': "reference_strain_xy",
'units': "none",
'data': numpy.ravel(strain[0, :, 3]),
}, {
'name': "reference_strain_yz",
'units': "none",
'data': numpy.ravel(strain[0, :, 4]),
}, {
'name': "reference_strain_xz",
'units': "none",
'data': numpy.ravel(strain[0, :, 5]),
}
]
}
from spatialdata.spatialdb.SimpleIOAscii import createWriter
io = createWriter("gravity_refstate_matfields.spatialdb")
io.write(data)
return
def run(self):
"""Generate the database.
"""
# Domain
x = numpy.arange(-4000.0, 4000.1, 1000.0)
y = numpy.arange(-4000.0, 4000.1, 1000.0)
npts = x.shape[0]
xx = x * numpy.ones((npts, 1), dtype=numpy.float64)
yy = y * numpy.ones((npts, 1), dtype=numpy.float64)
xy = numpy.zeros((npts**2, 2), dtype=numpy.float64)
xy[:, 0] = numpy.ravel(xx)
xy[:, 1] = numpy.ravel(numpy.transpose(yy))
from sheartraction_rate_soln import AnalyticalSoln
soln = AnalyticalSoln()
disp = soln.bc_initial_displacement(xy)
velocity_time = soln.bc_rate_time(xy) / year.value
velocity = soln.bc_velocity(xy) * year.value
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
data = {
'points':
xy,
'coordsys':
cs,
'data_dim':
2,
'values': [
{
'name': "initial_amplitude_x",
'units': "m",
'data': disp[0, :, 0].ravel()
},
{
'name': "initial_amplitude_y",
'units': "m",
'data': disp[0, :, 1].ravel()
},
{
'name': "rate_amplitude_x",
'units': "m/year",
'data': velocity[0, :, 0].ravel()
},
{
'name': "rate_amplitude_y",
'units': "m/year",
'data': velocity[0, :, 1].ravel()
},
{
'name': "rate_start_time",
'units': "year",
'data': velocity_time[0, :, 0].ravel()
},
]
}
from spatialdata.spatialdb.SimpleIOAscii import createWriter
io = createWriter("sheartraction_rate_disp.spatialdb")
io.write(data)
return
def _initialize(self):
"""
Initialize fault.
"""
dt = 2.4
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
# Setup mesh
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
# Setup quadrature
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 1
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
# Setup impulses
from spatialdata.spatialdb.SimpleDB import SimpleDB
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
ioImpulseAmp = SimpleIOAscii()
ioImpulseAmp.inventory.filename = "data/tri3_impulses.spatialdb"
ioImpulseAmp._configure()
dbImpulseAmp = SimpleDB()
dbImpulseAmp.inventory.iohandler = ioImpulseAmp
dbImpulseAmp.inventory.label = "impulse amplitude"
dbImpulseAmp._configure()
# Setup fault
fault = FaultCohesiveImpulses()
fault.inventory.output.inventory.writer._configure()
fault.inventory.output._configure()
fault.inventory.matId = 10
fault.inventory.faultLabel = "fault"
fault.inventory.upDir = [0, 0, 1]
fault.inventory.faultQuadrature = quadrature
fault.inventory.dbImpulseAmp = dbImpulseAmp
fault._configure()
nvertices = fault.numVerticesNoMesh(mesh)
firstFaultVertex = 0
firstLagrangeVertex = nvertices
firstFaultCell = 2*nvertices
fault.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex,
firstFaultCell)
fault.preinitialize(mesh)
fault.timeStep(dt)
fault.verifyConfiguration()
from pyre.units.time import s
fault.initialize(totalTime=0.0*s, numTimeSteps=1, normalizer=normalizer)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("dispIncr(t->t+dt)", "displacement_increment")
fields.add("disp(t)", "displacement")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
residual.subfieldAdd("displacement", cs.spaceDim(), residual.VECTOR)
residual.subfieldAdd("lagrange_multiplier", cs.spaceDim(), residual.VECTOR)
residual.subfieldsSetup()
residual.setupSolnChart()
residual.setupSolnDof(cs.spaceDim())
fault.setupSolnDof(residual)
residual.allocate()
residual.zero()
fields.copyLayout("residual")
return (mesh, fault, fields)
def test_write(self):
"""
Test write().
"""
# Database info
cs = CSCart()
cs._configure()
filename = "data/test.spatialdb"
data = {
'points':
numpy.array([[1.0, 2.0, 3.0], [0.5, 3.0, -3.0]], numpy.float64),
'coordsys':
cs,
'data_dim':
1,
'values': [{
'name': "One",
'units': "m",
'data': numpy.array([2.0, 8.0], numpy.float64)
}, {
'name': "Two",
'units': "m",
'data': numpy.array([-2.0, 3.0], numpy.float64)
}]
}
dataDim = 1
qlocs = numpy.array(
[[0.875, 2.25, 1.5], [0.6, 2.8, -1.8], [1.0, 2.0, 3.0]],
numpy.float64)
valsE = numpy.array([[-0.75, 3.5], [2.0, 6.8], [-2.0, 2.0]],
numpy.float64)
errE = [0, 0, 0]
# Write database
from spatialdata.spatialdb.SimpleIOAscii import createWriter
writer = createWriter(filename)
writer.write(data)
# Test write using query
from spatialdata.spatialdb.SimpleDB import SimpleDB
db = SimpleDB()
db.inventory.label = "test"
db.inventory.queryType = "linear"
db.inventory.iohandler.inventory.filename = filename
db.inventory.iohandler._configure()
db._configure()
db.open()
db.setQueryValues(["two", "one"])
vals = numpy.zeros(valsE.shape, dtype=numpy.float64)
err = []
nlocs = qlocs.shape[0]
for i in range(nlocs):
e = db.query(vals[i, :], qlocs[i, :], cs)
err.append(e)
db.close()
self.assertEqual(len(valsE.shape), len(vals.shape))
for dE, d in zip(valsE.shape, vals.shape):
self.assertEqual(dE, d)
for vE, v in zip(numpy.reshape(valsE, -1), numpy.reshape(vals, -1)):
self.assertAlmostEqual(vE, v, 6)
return
def test_io_3d(self):
from spatialdata.spatialdb.SimpleGridAscii import SimpleGridAscii
filename = "data/gridio3d.spatialdb"
x = numpy.array([-2.0, 0.0, 3.0], dtype=numpy.float64)
y = numpy.array([0.0, 1.0], dtype=numpy.float64)
z = numpy.array([-2.0, -1.0, 2.0], dtype=numpy.float64)
points = numpy.array(
[
[-2.0, 0.0, -2.0],
[-2.0, 1.0, -2.0],
[-2.0, 0.0, -1.0],
[-2.0, 1.0, -1.0],
[-2.0, 0.0, 2.0],
[-2.0, 1.0, 2.0],
[0.0, 0.0, -2.0],
[0.0, 1.0, -2.0], # query (5.7, 8.2)
[0.0, 0.0, -1.0],
[0.0, 1.0, -1.0],
[0.0, 0.0, 2.0],
[0.0, 1.0, 2.0],
[3.0, 0.0, -2.0],
[3.0, 1.0, -2.0],
[3.0, 0.0, -1.0],
[3.0, 1.0, -1.0],
[3.0, 0.0, 2.0],
[3.0, 1.0, 2.0],
],
dtype=numpy.float64)
one = numpy.array([
6.6, 5.5, 2.3, 5.7, 6.3, 3.4, 7.2, 5.7, 3.4, 5.7, 9.4, 7.2, 4.8,
9.2, 5.8, 4.7, 7.8, 2.9
],
dtype=numpy.float64)
two = numpy.array([
3.4, 6.7, 4.1, 2.0, 6.7, 6.4, 6.8, 8.2, 9.8, 2.3, 8.5, 9.3, 7.5,
8.3, 8.5, 8.9, 6.2, 8.3
],
dtype=numpy.float64)
cs = CSCart()
cs.initialize()
writer = SimpleGridAscii()
writer.inventory.filename = filename
writer._configure()
writer.write({
'points':
points,
'x':
x,
'y':
y,
'z':
z,
'coordsys':
cs,
'data_dim':
3,
'values': [
{
'name': "one",
'units': "m",
'data': one
},
{
'name': "two",
'units': "m",
'data': two
},
]
})
db = SimpleGridDB()
db.inventory.label = "test"
db.inventory.queryType = "nearest"
db.inventory.filename = filename
db._configure()
self._db = db
locs = numpy.array([[0.1, 0.95, -1.8]], numpy.float64)
cs = CSCart()
cs._configure()
queryVals = ["two", "one"]
dataE = numpy.array([[8.2, 5.7]], numpy.float64)
errE = [0]
db = self._db
db.open()
db.queryVals(queryVals)
data = numpy.zeros(dataE.shape, dtype=numpy.float64)
err = []
nlocs = locs.shape[0]
for i in xrange(nlocs):
e = db.query(data[i, :], locs[i, :], cs)
err.append(e)
db.close()
self.assertEqual(len(errE), len(err))
for vE, v in zip(errE, err):
self.assertEqual(vE, v)
self.assertEqual(len(dataE.shape), len(data.shape))
for dE, d in zip(dataE.shape, data.shape):
self.assertEqual(dE, d)
for vE, v in zip(numpy.reshape(dataE, -1), numpy.reshape(data, -1)):
self.assertAlmostEqual(vE, v, 6)
return
def _initialize(self):
"""
Initialize fault.
"""
dt = 2.4
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
# Setup mesh
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
# Setup quadrature
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 1
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
# Setup impulses
from spatialdata.spatialdb.SimpleDB import SimpleDB
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
ioImpulseAmp = SimpleIOAscii()
ioImpulseAmp.inventory.filename = "data/tri3_impulses.spatialdb"
ioImpulseAmp._configure()
dbImpulseAmp = SimpleDB()
dbImpulseAmp.inventory.iohandler = ioImpulseAmp
dbImpulseAmp.inventory.label = "impulse amplitude"
dbImpulseAmp._configure()
# Setup fault
fault = FaultCohesiveImpulses()
fault.inventory.output.inventory.writer._configure()
fault.inventory.output._configure()
fault.inventory.matId = 10
fault.inventory.faultLabel = "fault"
fault.inventory.upDir = [0, 0, 1]
fault.inventory.faultQuadrature = quadrature
fault.inventory.dbImpulseAmp = dbImpulseAmp
fault._configure()
nvertices = fault.numVerticesNoMesh(mesh)
firstFaultVertex = 0
firstLagrangeVertex = nvertices
firstFaultCell = 2*nvertices
fault.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex,
firstFaultCell)
fault.preinitialize(mesh)
fault.timeStep(dt)
fault.verifyConfiguration()
from pyre.units.time import s
fault.initialize(totalTime=0.0*s, numTimeSteps=1, normalizer=normalizer)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("dispIncr(t->t+dt)", "displacement_increment")
fields.add("disp(t)", "displacement")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
residual.newSection(residual.VERTICES_FIELD, cs.spaceDim())
residual.allocate()
residual.zero()
fields.copyLayout("residual")
return (mesh, fault, fields)
def test_constructor(self):
cs = CSCart()
cs._configure()
self.assertEqual(3, cs.getSpaceDim())
def _initialize(self):
"""
Initialize fault.
"""
dt = 2.4
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
# Setup mesh
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
# Setup quadrature
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 1
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
# Setup rupture info
from spatialdata.spatialdb.SimpleDB import SimpleDB
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
ioTractions = SimpleIOAscii()
ioTractions.inventory.filename = "data/tri3_initialtractions.spatialdb"
ioTractions._configure()
dbTractions = SimpleDB()
dbTractions.inventory.iohandler = ioTractions
dbTractions.inventory.label = "initial tractions"
dbTractions._configure()
from pylith.faults.TractPerturbation import TractPerturbation
tract = TractPerturbation()
tract.inventory.dbInitial = dbTractions
tract._configure()
ioFriction = SimpleIOAscii()
ioFriction.inventory.filename = "data/tri3_staticfriction.spatialdb"
ioFriction._configure()
dbFriction = SimpleDB()
dbFriction.inventory.iohandler = ioFriction
dbFriction.inventory.label = "friction"
dbFriction._configure()
from pylith.friction.StaticFriction import StaticFriction
friction = StaticFriction()
friction.inventory.label = "Static friction"
friction.inventory.dbProperties = dbFriction
friction._configure()
# Setup fault
fault = FaultCohesiveDyn()
fault.inventory.output.inventory.writer._configure()
fault.inventory.output._configure()
fault.inventory.matId = 10
fault.inventory.faultLabel = "fault"
fault.inventory.upDir = [0, 0, 1]
fault.inventory.faultQuadrature = quadrature
fault.inventory.tract = tract
fault.inventory.friction = friction
fault._configure()
nvertices = fault.numVerticesNoMesh(mesh)
firstFaultVertex = 0
firstLagrangeVertex = nvertices
firstFaultCell = 2*nvertices
fault.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex,
firstFaultCell)
from pylith.topology.topology import MeshOps_nondimensionalize
MeshOps_nondimensionalize(mesh, normalizer)
fault.preinitialize(mesh)
fault.timeStep(dt)
fault.verifyConfiguration()
from pyre.units.time import s
fault.initialize(totalTime=0.0*s, numTimeSteps=1, normalizer=normalizer)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("dispIncr(t->t+dt)", "displacement_increment")
fields.add("disp(t)", "displacement")
fields.add("velocity(t)", "velocity")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
residual.subfieldAdd("displacement", cs.spaceDim(), residual.VECTOR)
residual.subfieldAdd("lagrange_multiplier", cs.spaceDim(), residual.VECTOR)
residual.subfieldsSetup()
residual.setupSolnChart()
residual.setupSolnDof(cs.spaceDim())
fault.setupSolnDof(residual)
residual.allocate()
residual.zero()
fields.copyLayout("residual")
return (mesh, fault, fields)
#!/usr/bin/env python """ This script creates a spatial database for the initial stress and state variables for a Maxwell plane strain material. """ material = "maxps" import numpy import h5py from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii from spatialdata.geocoords.CSCart import CSCart cs = CSCart() cs._configure() cs.setSpaceDim(2) filenameH5 = "output/grav_static_%s-visco.h5" % material filenameDB = "grav_statevars-%s.spatialdb" % material # Open HDF5 file and get coordinates, cells, and stress. h5 = h5py.File(filenameH5, "r") vertices = h5['geometry/vertices'][:] cells = numpy.array(h5['topology/cells'][:], dtype=numpy.int) stress = h5['cell_fields/stress'][0,:,:] strain = h5['cell_fields/total_strain'][0,:,:] strainViscous = h5['cell_fields/viscous_strain'][0,:,:] h5.close() # Get cell centers for output. cellCoords = vertices[cells,:]
def test_io_2d(self):
from spatialdata.spatialdb.SimpleGridAscii import SimpleGridAscii
filename = "data/gridio2d.spatialdb"
x = numpy.array([-2.0, 0.0, 3.0], dtype=numpy.float64)
y = numpy.array([0.0, 1.0], dtype=numpy.float64)
points = numpy.array([
[-2.0, 0.0],
[-2.0, 1.0],
[ 0.0, 0.0],
[ 0.0, 1.0], # query (5.7, 8.2)
[ 3.0, 0.0],
[ 3.0, 1.0],
], dtype=numpy.float64)
one = numpy.array([6.6, 5.5, 7.2, 5.7, 4.8, 9.2], dtype=numpy.float64)
two = numpy.array([3.4, 6.7, 6.8, 8.2, 7.5, 8.3], dtype=numpy.float64)
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
cs.initialize()
writer = SimpleGridAscii()
writer.inventory.filename = filename
writer._configure()
writer.write({'points': points,
'x': x,
'y': y,
'coordsys': cs,
'data_dim': 2,
'values': [{'name': "one",
'units': "m",
'data': one},
{'name': "two",
'units': "m",
'data': two},
]})
db = SimpleGridDB()
db.inventory.label = "test"
db.inventory.queryType = "nearest"
db.inventory.filename = filename
db._configure()
self._db = db
locs = numpy.array( [[0.1, 0.95]], numpy.float64)
queryVals = ["two", "one"]
dataE = numpy.array( [[8.2, 5.7]], numpy.float64)
errE = [0]
db = self._db
db.open()
db.queryVals(queryVals)
data = numpy.zeros(dataE.shape, dtype=numpy.float64)
err = []
nlocs = locs.shape[0]
for i in xrange(nlocs):
e = db.query(data[i,:], locs[i,:], cs)
err.append(e)
db.close()
self.assertEqual(len(errE), len(err))
for vE, v in zip(errE, err):
self.assertEqual(vE, v)
self.assertEqual(len(dataE.shape), len(data.shape))
for dE, d in zip(dataE.shape, data.shape):
self.assertEqual(dE, d)
for vE, v in zip(numpy.reshape(dataE, -1), numpy.reshape(data, -1)):
self.assertAlmostEqual(vE, v, 6)
return
def _initialize(self):
"""
Initialize AbsorbingDampers boundary condition.
"""
from spatialdata.spatialdb.SimpleDB import SimpleDB
db = SimpleDB()
db.inventory.label = "TestAbsorbingDampers tri3"
db.inventory.iohandler.inventory.filename = \
"data/elasticplanestrain.spatialdb"
db.inventory.iohandler._configure()
db._configure()
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 1
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
from pylith.bc.AbsorbingDampers import AbsorbingDampers
bc = AbsorbingDampers()
bc.inventory.quadrature = quadrature
bc.inventory.db = db
bc.inventory.id = 0
bc.inventory.label = "bc"
bc._configure()
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
bc.preinitialize(mesh)
bc.initialize(totalTime=0.0, numTimeSteps=1, normalizer=normalizer)
bc.timeStep(0.01)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("dispIncr(t->t+dt)", "displacement")
fields.add("disp(t)", "displacement")
fields.add("disp(t-dt)", "displacement")
fields.add("velocity(t)", "velocity")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
residual.newSection(residual.VERTICES_FIELD, cs.spaceDim())
residual.allocate()
residual.zero()
fields.copyLayout("residual")
return (mesh, bc, fields)
def test_io(self):
from spatialdata.spatialdb.SimpleGridAscii import SimpleGridAscii
filename = "data/gridio.spatialdb"
x = numpy.array([-2.0, 0.0, 3.0], dtype=numpy.float64)
y = numpy.array([0.0, 1.0], dtype=numpy.float64)
z = numpy.array([-2.0, -1.0, 2.0], dtype=numpy.float64)
points = numpy.array(
[
[-2.0, 0.0, -2.0],
[-2.0, 1.0, -2.0],
[-2.0, 0.0, -1.0],
[-2.0, 1.0, -1.0],
[-2.0, 0.0, 2.0],
[-2.0, 1.0, 2.0],
[0.0, 0.0, -2.0],
[0.0, 1.0, -2.0], # query (5.7, 8.2)
[0.0, 0.0, -1.0],
[0.0, 1.0, -1.0],
[0.0, 0.0, 2.0],
[0.0, 1.0, 2.0],
[3.0, 0.0, -2.0],
[3.0, 1.0, -2.0],
[3.0, 0.0, -1.0],
[3.0, 1.0, -1.0],
[3.0, 0.0, 2.0],
[3.0, 1.0, 2.0],
],
dtype=numpy.float64,
)
one = numpy.array(
[6.6, 5.5, 2.3, 5.7, 6.3, 3.4, 7.2, 5.7, 3.4, 5.7, 9.4, 7.2, 4.8, 9.2, 5.8, 4.7, 7.8, 2.9],
dtype=numpy.float64,
)
two = numpy.array(
[3.4, 6.7, 4.1, 2.0, 6.7, 6.4, 6.8, 8.2, 9.8, 2.3, 8.5, 9.3, 7.5, 8.3, 8.5, 8.9, 6.2, 8.3],
dtype=numpy.float64,
)
cs = CSCart()
cs.initialize()
writer = SimpleGridAscii()
writer.inventory.filename = filename
writer._configure()
writer.write(
{
"points": points,
"x": x,
"y": y,
"z": z,
"coordsys": cs,
"data_dim": 3,
"values": [{"name": "one", "units": "m", "data": one}, {"name": "two", "units": "m", "data": two}],
}
)
db = SimpleGridDB()
db.inventory.label = "test"
db.inventory.queryType = "nearest"
db.inventory.filename = filename
db._configure()
self._db = db
locs = numpy.array([[0.1, 0.95, -1.8]], numpy.float64)
cs = CSCart()
cs._configure()
queryVals = ["two", "one"]
dataE = numpy.array([[8.2, 5.7]], numpy.float64)
errE = [0]
db = self._db
db.open()
db.queryVals(queryVals)
data = numpy.zeros(dataE.shape, dtype=numpy.float64)
err = []
nlocs = locs.shape[0]
for i in xrange(nlocs):
e = db.query(data[i, :], locs[i, :], cs)
err.append(e)
db.close()
self.assertEqual(len(errE), len(err))
for vE, v in zip(errE, err):
self.assertEqual(vE, v)
self.assertEqual(len(dataE.shape), len(data.shape))
for dE, d in zip(dataE.shape, data.shape):
self.assertEqual(dE, d)
for vE, v in zip(numpy.reshape(dataE, -1), numpy.reshape(data, -1)):
self.assertAlmostEqual(vE, v, 6)
return
# Background normal tractions are overburden and compressive
# (negative, y is negative)
tractions_bg_normal = density*gacc*(vertices[:,1])
# Background shear tractions are reverse (in 2-D right-lateral is negative)
# because the normal tractions are negative.
tractions_bg_shear = coef_friction*tractions_bg_normal
# Combine traction changes and background tractions
tractions_shear = tractions_bg_shear + tractions_change[:,0]
tractions_normal = tractions_bg_normal + tractions_change[:,1]
# Create coordinate system for spatial database
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs._configure()
cs.setSpaceDim(2)
# Create writer for spatial database file
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
writer = SimpleIOAscii()
writer.inventory.filename = "afterslip_tractions.spatialdb"
writer._configure()
writer.write({'points': vertices,
'coordsys': cs,
'data_dim': 1,
'values': [{'name': "traction-shear",
'units': "Pa",
'data': tractions_shear},
{'name': "traction-normal",
'units': "Pa",
def run(self):
"""Generate the database.
"""
# Domain
x = numpy.arange(-4.0e+3, 4.01e+3, 1.0e+3)
y = numpy.arange(-4.0e+3, 4.01e+3, 1.0e+3)
z = numpy.arange(-8.0e+3, 0.01e+3, 1.0e+3)
x3, y3, z3 = numpy.meshgrid(x, y, z)
nptsX = x.shape[0]
nptsY = y.shape[0]
nptsZ = z.shape[0]
xyz = numpy.zeros((nptsX * nptsY * nptsZ, 3), dtype=numpy.float64)
xyz[:, 0] = x3.ravel()
xyz[:, 1] = y3.ravel()
xyz[:, 2] = z3.ravel()
from axialdisp_soln import AnalyticalSoln
soln = AnalyticalSoln()
disp = soln.displacement(xyz)
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 3
cs._configure()
data = {
"x":
x,
"y":
y,
"z":
z,
"points":
xyz,
"coordsys":
cs,
"data_dim":
3,
"values": [
{
"name": "initial_amplitude_x",
"units": "m",
"data": numpy.ravel(disp[0, :, 0])
},
{
"name": "initial_amplitude_y",
"units": "m",
"data": numpy.ravel(disp[0, :, 1])
},
{
"name": "initial_amplitude_z",
"units": "m",
"data": numpy.ravel(disp[0, :, 2])
},
]
}
from spatialdata.spatialdb.SimpleGridAscii import SimpleGridAscii
io = SimpleGridAscii()
io.inventory.filename = "axialdisp_bc.spatialdb"
io._configure()
io.write(data)
return
