def setUp(self):
self.domain = Brick(l0=1.,
l1=1.,
l2=1.,
n0=10,
n1=10 * getMPISizeWorld() - 1,
n2=10,
d1=getMPISizeWorld())
def write(self, filename):
"""
writes to segy file
:param filename: file name
:note: the function uses the `obspy` module.
"""
if not OBSPY_AVAILABLE:
raise RuntimeError("This feature (SimpleSEGYWriter.write())"+\
" depends on obspy, which is not installed, see "+\
"https://github.com/obspy/obspy for install guide")
if escript.getMPISizeWorld() > 1:
raise RuntimeError("Writing segy files with multiple ranks is"+\
" not yet supported.")
stream = Stream()
for i in range(len(self.__receiver_group)):
trace = Trace(data=np.array(self.__trace[i], dtype='float32'))
# Attributes in trace.stats will overwrite everything in
# trace.stats.segy.trace_header (in Hz)
trace.stats.sampling_rate = 1. / self.getSamplingInterval()
#trace.stats.starttime = UTCDateTime(2011,11,11,0,0,0)
if not hasattr(trace.stats, 'segy.trace_header'):
trace.stats.segy = {}
trace.stats.segy.trace_header = SEGYTraceHeader()
trace.stats.segy.trace_header.trace_identification_code = 1
trace.stats.segy.trace_header.trace_sequence_number_within_line = i + 1
trace.stats.segy.trace_header.scalar_to_be_applied_to_all_coordinates = -int(
self.COORDINATE_SCALE)
trace.stats.segy.trace_header.coordinate_units = 1
trace.stats.segy.trace_header.source_coordinate_x = int(
self.__source[0] * self.COORDINATE_SCALE)
trace.stats.segy.trace_header.source_coordinate_y = int(
self.__source[1] * self.COORDINATE_SCALE)
trace.stats.segy.trace_header.group_coordinate_x = int(
self.__receiver_group[i][0] * self.COORDINATE_SCALE)
trace.stats.segy.trace_header.group_coordinate_y = int(
self.__receiver_group[i][1] * self.COORDINATE_SCALE)
# Add trace to stream
stream.append(trace)
# A SEGY file has file wide headers. This can be attached to the stream
# object. If these are not set, they will be autocreated with default
# values.
stream.stats = AttribDict()
stream.stats.textual_file_header = 'C.. ' + self.__text + '\nC.. with esys.escript.downunder r%s\nC.. %s' % (
escript.getVersion(), time.asctime())
stream.stats.binary_file_header = SEGYBinaryFileHeader()
if escript.getMPIRankWorld() < 1:
stream.write(filename,
format="SEGY",
data_encoding=1,
byteorder=sys.byteorder)
def setUp(self):
self.order = 2
d1 = Brick(n0=NE // 2, n1=NE, n2=NE, l0=0.5, order=2, useElementsOnFace=True)
d2 = Brick(n0=NE // 2 + 1, n1=NE, n2=NE, l0=0.5, order=2, useElementsOnFace=True)
d2.setX(d2.getX() + [0.5, 0.0, 0.0])
if getMPISizeWorld() > 1:
with self.assertRaises(NotImplementedError) as pkg:
self.domain = JoinFaces([d1, d2], optimize=False)
e = pkg.exception
if FINLEY_MERGE_ERROR not in str(e):
raise e
raise unittest.SkipTest(FINLEY_MERGE_ERROR)
else:
self.domain = JoinFaces([d1, d2], optimize=False)
def setUp(self):
self.order = 2
d1 = Rectangle(n0=NE // 2, n1=NE, l0=0.5, order=2, useElementsOnFace=0)
d2 = Rectangle(n0=NE // 2, n1=NE, l0=0.5, order=2, useElementsOnFace=0)
d2.setX(d2.getX() + [0.5, 0.])
if getMPISizeWorld() > 1:
with self.assertRaises(NotImplementedError) as pkg:
self.domain = JoinFaces([d1, d2], optimize=False)
e = pkg.exception
if FINLEY_MERGE_ERROR not in str(e):
raise e
raise unittest.SkipTest(FINLEY_MERGE_ERROR)
else:
self.domain = JoinFaces([d1, d2], optimize=False)
def test_geodetic_domain(self):
COORDINATES = WGS84ReferenceSystem()
db = DomainBuilder(reference_system=COORDINATES)
source1a = NetCdfData(DataSource.GRAVITY,
NC_DATA1,
scale_factor=1.,
reference_system=COORDINATES)
db.addSource(source1a)
db.setVerticalExtents(depth=20000., air_layer=30000., num_cells=10)
dom = db.getDomain()
x = dom.getX()
self.assertAlmostEqual(inf(x[0]),
120.2,
delta=0.001,
msg="phi range wrong")
self.assertAlmostEqual(inf(x[1]),
-29.2,
delta=0.0001,
msg="lambda range wrong")
self.assertAlmostEqual(inf(x[2]),
-0.2,
msg="h range wrong" + str(x[2]))
# Cannot check upper bounds of coordinates with more than 1 rank
# because ripley may adjust internally.
if getMPISizeWorld() == 1:
self.assertAlmostEqual(sup(x[0]),
120.3,
delta=0.001,
msg="phi range wrong")
self.assertAlmostEqual(sup(x[1]),
-29.1,
delta=0.0001,
msg="lambda range wrong")
self.assertAlmostEqual(sup(x[2]),
0.3,
msg="h range wrong: " + str(x[2]))
# mesh for illustration purposes only.
#
#######################################################EXTERNAL MODULES
from esys.pycad import * #domain constructor
from esys.pycad.extras import layer_cake
from esys.pycad.gmsh import Design #Finite Element meshing package
from esys.escript import mkDir, getMPISizeWorld
import os
try:
from esys.finley import MakeDomain
HAVE_FINLEY = True
except ImportError:
print("Finley module not available")
HAVE_FINLEY = False
########################################################MPI WORLD CHECK
if getMPISizeWorld() > 1:
import sys
print("This example will not run in an MPI world.")
sys.exit(0)
if HAVE_FINLEY:
# make sure path exists
save_path = os.path.join("data", "example11")
mkDir(save_path)
################################################ESTABLISHING PARAMETERS
#Model Parameters
xwidth = 500.0 #x width of model
ywidth = 500.0 #y width of model
depth = 250.0 #depth of model
element_size = 5.0
from test_simplesolve import SimpleSolveTestCase
import esys.escriptcore.utestselect as unittest
from esys.escriptcore.testing import *
from esys.escript import getMPISizeWorld, hasFeature, sqrt
from esys.ripley import Rectangle, Brick
from esys.escript.linearPDEs import SolverOptions
HAVE_PASO = hasFeature('paso')
# number of elements in the spatial directions
NE0=12
NE1=12
NE2=8
mpiSize=getMPISizeWorld()
for x in [int(sqrt(mpiSize)),2,3,5,7,1]:
NX=x
NY=mpiSize//x
if NX*NY == mpiSize:
break
for x in [(int(mpiSize**(1/3.)),int(mpiSize**(1/3.))),(2,3),(2,2),(1,2),(1,1)]:
NXb=x[0]
NYb=x[1]
NZb=mpiSize//(x[0]*x[1])
if NXb*NYb*NZb == mpiSize:
break
@unittest.skipIf(not HAVE_PASO, "PASO not available")
class SimpleSolveOnPaso(SimpleSolveTestCase):
from esys.downunder.domainbuilder import DomainBuilder
from esys.downunder.coordinates import WGS84ReferenceSystem
HAVE_RIPLEY = True
try:
from esys.ripley import Rectangle
except ImportError as e:
HAVE_RIPLEY = False
try:
import pyproj
haveProj=True
except ImportError:
haveProj=False
mpisize = getMPISizeWorld()
# this is mainly to avoid warning messages
logging.basicConfig(format='%(name)s: %(message)s', level=logging.INFO)
try:
TEST_DATA_ROOT=os.environ['DOWNUNDER_TEST_DATA_ROOT']
except KeyError:
TEST_DATA_ROOT='ref_data'
try:
WORKDIR=os.environ['DOWNUNDER_WORKDIR']
except KeyError:
WORKDIR='.'
ERS32_DATA = os.path.join(TEST_DATA_ROOT, 'ermapper32_test.ers')
# reference model origin (west, south, bottom)
MODEL_ORIGIN = [originX, originY, -thickness]
# we are using geodetic coordinates
COORDINATES=WGS84ReferenceSystem()
h_unit = COORDINATES.getHeightUnit()
dom_origin = [originX, originY, -thickness/h_unit]
#dom_origin = [1e-5*np.floor(oi*1e5) for oi in dom_origin]
spacing = [resolution, resolution, np.floor((thickness+l_air)/n_cells_v)/h_unit]
l0 = (dom_origin[0], dom_origin[0]+spacing[0]*NX)
l1 = (dom_origin[1], dom_origin[1]+spacing[1]*NY)
l2 = (dom_origin[2], dom_origin[2]+spacing[2]*n_cells_v)
# ensure ripley does not add additional elements in horizontal direction
d0,d1,d2=1,1,getMPISizeWorld()
mpifactors=list(factor(d2))
while len(mpifactors)>0:
f=mpifactors.pop()
if d1>=d0:
if (NX+1)%(d0*f) == 0:
d0 = d0 * f
d2 = d2 / f
elif (NY+1)%(d1*f) == 0:
d1 = d1 * f
d2 = d2 / f
else:
if (NY+1)%(d1*f) == 0:
d1 = d1 * f
d2 = d2 / f
elif (NX+1)%(d0*f) == 0:
#
#######################################################EXTERNAL MODULES
from esys.escript import mkDir, getMPISizeWorld, hasFeature
from esys.pycad import * #domain constructor
from esys.pycad.extras import layer_cake
from esys.pycad.gmsh import Design #Finite Element meshing package
try:
from esys.finley import MakeDomain
HAVE_FINLEY = True
except ImportError:
print("Finley module not available")
HAVE_FINLEY = False
########################################################MPI WORLD CHECK
if getMPISizeWorld() > 1 or (hasFeature('mpi') and hasFeature('gmsh_mpi')):
print("This example will not run in an MPI world!")
elif HAVE_FINLEY:
import os
import subprocess as sp
# make sure path exists
save_path = os.path.join("data","example10m")
mkDir(save_path)
################################################BIG DOMAIN
#ESTABLISHING PARAMETERS
width=10000. #width of model
depth=10000. #depth of model
bele_size=500. #big element size
#DOMAIN CONSTRUCTION
p0=Point(0.0, 0.0)
#
#######################################################EXTERNAL MODULES
from esys.escript import mkDir, getMPISizeWorld, hasFeature
from esys.pycad import * #domain constructor
from esys.pycad.extras import layer_cake
from esys.pycad.gmsh import Design #Finite Element meshing package
try:
from esys.finley import MakeDomain
HAVE_FINLEY = True
except ImportError:
print("Finley module not available")
HAVE_FINLEY = False
########################################################MPI WORLD CHECK
if getMPISizeWorld() > 1 or (hasFeature('mpi') and hasFeature('gmsh_mpi')):
print("This example will not run in an MPI world!")
elif HAVE_FINLEY:
import os
import subprocess as sp
# make sure path exists
save_path = os.path.join("data", "example10m")
mkDir(save_path)
################################################BIG DOMAIN
#ESTABLISHING PARAMETERS
width = 10000. #width of model
depth = 10000. #depth of model
bele_size = 500. #big element size
#DOMAIN CONSTRUCTION
p0 = Point(0.0, 0.0)
def setUp(self):
self.domain = Rectangle(l0=1.,
l1=1.,
n0=10,
n1=10 * getMPISizeWorld() - 1,
d1=getMPISizeWorld())
def setUp(self):
self.domain = Rectangle(l0=1.,l1=1., n0=10, n1=10*getMPISizeWorld()-1, d1=getMPISizeWorld())
from test_simplesolve import SimpleSolveTestCase
import esys.escriptcore.utestselect as unittest
from esys.escriptcore.testing import *
from esys.escript import getMPISizeWorld, hasFeature, sqrt
from esys.ripley import Rectangle, Brick
from esys.escript.linearPDEs import SolverOptions
SOLVER = "mkl"
HAVE_REQUESTED_SOLVER = hasFeature(SOLVER)
# number of elements in the spatial directions
NE0 = 12
NE1 = 12
NE2 = 8
mpiSize = getMPISizeWorld()
for x in [int(sqrt(mpiSize)), 2, 3, 5, 7, 1]:
NX = x
NY = mpiSize // x
if NX * NY == mpiSize:
break
for x in [(int(mpiSize**(1 / 3.)), int(mpiSize**(1 / 3.))), (2, 3), (2, 2),
(1, 2), (1, 1)]:
NXb = x[0]
NYb = x[1]
NZb = mpiSize // (x[0] * x[1])
if NXb * NYb * NZb == mpiSize:
break
rho_1d = {"left": rho_1d_left, "right": rho_1d_rght}
# ---
# Run MT_2D
# ---
# Class options:
mt2d.MT_2D._solver = "DIRECT"
mt2d.MT_2D._debug = False
if mt2d.MT_2D._solver == "DIRECT" and not escript.hasFeature('paso'):
print(
"Trilinos direct solvers cannot currently handle PDE systems. Please compile with Paso."
)
elif mt2d.MT_2D._solver == "DIRECT" and not HAVE_DIRECT:
if escript.getMPISizeWorld() > 1:
print(
"Direct solvers and multiple MPI processes are not currently supported."
)
else:
print(
"escript was not built with support for direct solvers, aborting."
)
elif not escript.hasFeature('gmsh'):
print("This example requires gmsh, aborting.")
else:
# Instantiate an MT_2D object with required & optional parameters:
obj_mt2d = mt2d.MT_2D(domain,
mode,
freq_def,
tags,
# Save in dictionary with layer interfaces and resistivities left and right:
ifc_1d = {"left":ifc_1d_left , "right":ifc_1d_rght}
rho_1d = {"left":rho_1d_left , "right":rho_1d_rght}
# ---
# Run MT_2D
# ---
# Class options:
mt2d.MT_2D._solver = "DIRECT"
mt2d.MT_2D._debug = False
if mt2d.MT_2D._solver == "DIRECT" and not escript.hasFeature('paso'):
print("Trilinos direct solvers cannot currently handle PDE systems. Please compile with Paso.")
elif mt2d.MT_2D._solver == "DIRECT" and not HAVE_DIRECT:
if escript.getMPISizeWorld() > 1:
print("Direct solvers and multiple MPI processes are not currently supported.")
else:
print("escript was not built with support for direct solvers, aborting.")
elif not escript.hasFeature('gmsh'):
print("This example requires gmsh, aborting.")
else:
# Instantiate an MT_2D object with required & optional parameters:
obj_mt2d = mt2d.MT_2D(domain, mode, freq_def, tags, rho, rho_1d, ifc_1d,
xstep=xstep ,zstep=zstep, maps=None, plot=True)
# Solve for fields, apparent resistivity and phase:
mt2d_fields, arho_2d, aphi_2d = obj_mt2d.pdeSolve()
#
print(datetime.datetime.now()-startTime)
def setUp(self):
self.domain = Brick(l0=1.,l1=1.,l2=1., n0=10, n1=10*getMPISizeWorld()-1, n2=10, d1=getMPISizeWorld())
#
#######################################################EXTERNAL MODULES
from esys.pycad import * #domain constructor
from esys.pycad.gmsh import Design #Finite Element meshing package
from esys.escript import mkDir, getMPISizeWorld
import os
import math
try:
# This imports the rectangle domain function
from esys.finley import MakeDomain
HAVE_FINLEY = True
except ImportError:
print("Finley module not available")
HAVE_FINLEY = False
########################################################MPI WORLD CHECK
if getMPISizeWorld() > 1:
import sys
print("This example will not run in an MPI world.")
sys.exit(0)
if HAVE_FINLEY:
# make sure path exists
save_path= os.path.join("data","example09c")
mkDir(save_path)
################################################ESTABLISHING PARAMETERS
#Model Parameters
origin=[0,0] #orign of model
xwidth=300.0 #width of model
depth=-100.0 #depth of model
nintf=3 #number of the interfaces
try:
from esys.ripley import Rectangle
except ImportError as e:
HAVE_RIPLEY = False
if hasFeature('netcdf'):
HAVE_NETCDF = True
else:
HAVE_NETCDF = False
try:
import pyproj
haveProj = True
except ImportError:
haveProj = False
mpisize = getMPISizeWorld()
# this is mainly to avoid warning messages
logging.basicConfig(format='%(name)s: %(message)s', level=logging.INFO)
try:
TEST_DATA_ROOT = os.environ['DOWNUNDER_TEST_DATA_ROOT']
except KeyError:
TEST_DATA_ROOT = 'ref_data'
try:
WORKDIR = os.environ['DOWNUNDER_WORKDIR']
except KeyError:
WORKDIR = '.'
ERS32_DATA = os.path.join(TEST_DATA_ROOT, 'ermapper32_test.ers')
