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 axialstrainrate_genmaxwell_soln import AnalyticalSoln
soln = AnalyticalSoln()
disp = soln.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("axialstrainrate_genmaxwell_disp.spatialdb")
io.write(data)
io = createWriter("axialstrainrate_genmaxwell_bc.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 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': "initial_amplitude_x",
'units': "m",
'data': numpy.ravel(disp[0, :, 0])
}, {
'name': "initial_amplitude_y",
'units': "m",
'data': numpy.ravel(disp[0, :, 1])
}]
}
from spatialdata.spatialdb.SimpleIOAscii import createWriter
io = createWriter("axialdisp_bc.spatialdb")
io.write(data)
data["values"][0]["name"] = "displacement_x"
data["values"][1]["name"] = "displacement_y"
io = createWriter("axialdisp_ic.spatialdb")
io.write(data)
return
def main(self, *args, **kwds):
"""
Application driver.
"""
from spatialdata.spatialdb.SimpleIOAscii import createWriter
self._info.log("Reading geometry.")
self.geometry.read()
points = self.geometry.vertices
coordsys = self.geometry.coordsys
data = {
'points': points,
'coordsys': coordsys,
'data_dim': self.geometry.dataDim,
'values': [],
}
for value in self.values.components():
self._info.log("Creating value '%s'" % value.name)
data['values'].append({
'name': value.vname,
'units': value.units,
'data': value.calculate(points, coordsys),
})
self._info.log("Writing database.")
writer = createWriter(self.filename)
writer.write(data)
def generate(sim, fileRoot, materials):
from coordsys import cs_mesh
for material in materials:
filenameH5 = "../output/%s-%s.h5" % (sim, material)
filenameDB = "%s-%s.spatialdb" % (fileRoot, 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)
# Get stresses from final time step.
stress = h5['cell_fields/stress'][-1, :, :]
h5.close()
# Compute coordinates of quadrature points.
quadCoords = getCellCenters(vertices, cells)
# Create writer for spatial database file
values = [
{
'name': "stress-xx",
'units': "Pa",
'data': stress[:, 0]
},
{
'name': "stress-yy",
'units': "Pa",
'data': stress[:, 1]
},
{
'name': "stress-zz",
'units': "Pa",
'data': stress[:, 2]
},
{
'name': "stress-xy",
'units': "Pa",
'data': stress[:, 3]
},
{
'name': "stress-yz",
'units': "Pa",
'data': stress[:, 4]
},
{
'name': "stress-xz",
'units': "Pa",
'data': stress[:, 5]
},
]
writer = createWriter(filenameDB)
writer.write({
'points': quadCoords,
'coordsys': cs_mesh(),
'data_dim': 3,
'values': values
})
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
# 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
cs = CSCart()
cs._configure()
cs.setSpaceDim(2)
# Create writer for spatial database file
writer = createWriter("afterslip_tractions.spatialdb")
writer.write({
'points':
vertices,
'coordsys':
cs,
'data_dim':
1,
'values': [{
'name': "initial_amplitude_tangential",
'units': "Pa",
'data': tractions_shear
}, {
'name': "initial_amplitude_normal",
'units': "Pa",
'data': tractions_normal
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