def test_hex_contact_3D_order2_onFace(self):
file="hex_contact_3D_order2_onFace.msh"
ms1=Brick(1,1,1,2,l2=0.5,useElementsOnFace=True)
ms2=Brick(1,1,1,2,l2=0.5,useElementsOnFace=True)
ms2.setX(ms2.getX()+[0,0,0.5])
my_dom=JoinFaces([ms1,ms2],optimize=False)
self.checker(my_dom,file)
def test_brickconstr(self):
self.assertRaises(ValueError, Brick, 4,4, diracPoints=[(0,0,0)])
self.assertRaises(ValueError, Brick, 4,4, diracPoints=[(0,0,0), (1,1,1)], diracTags=[40])
self.assertRaises(ValueError, Brick, 4,4, diracPoints=[(0,0,0), (1,1,1)], diracTags=[40])
self.assertRaises(ValueError, Brick, 4,4, diracPoints=[(0,0,0), (1,1,1)], diracTags=["cows"])
self.assertRaises(ValueError, Brick, 4,4, diracPoints=[(0,0)], diracTags=["test"])
z=Brick(4,4, diracPoints=[(0,0,0), (0.25,0.25, 0.25)], diracTags=[40,51])
z=Brick(4,4, diracPoints=[(0.125,0.625,0), (0.5,1,0), (0.75, 0.25, 0.51), (0.89, 0.875,1)], diracTags=["A", "B", "A", "C"])
v=interpolate(z.getX(), DiracDeltaFunctions(z))
if mpisize==1:
self.assertEqual(v.toListOfTuples(),[(0.0, 0.5, 0.0), (0.5, 1.0, 0.0), (0.75, 0.25, 1), (1.0, 0.75, 1.0)])
self.assertEqual(v.getNumberOfDataPoints(), 4)
self.assertEqual(inf(v[0]), 0)
self.assertEqual(inf(v[1]), 0.25)
self.assertEqual(Lsup(v[0]), 1)
self.assertEqual(Lsup(v[1]), 1)
v.setTaggedValue("A",(-10,0.5,-500))
if mpisize==1:
self.assertEqual(inf(v[0]), -10)
self.assertEqual(inf(v[1]), 0.5)
self.assertEqual(inf(v[2]),-500)
v.setTaggedValue(500,(-100,-100, -100)) # non-existant tag
if mpisize==1:
self.assertEqual(inf(v[0]), -10)
self.assertEqual(inf(v[1]), 0.5)
self.assertEqual(z.showTagNames(), 'A, B, C, back, bottom, front, left, right, top')
self.assertEqual(z.getTag("C"), 42)
def test_data_dump_to_NetCDF_brick(self):
mydomain1 = Brick(n0=NE0, n1=NE1, n2=NE2, order=2, l0=1., l1=1., l2=1., optimize=False)
d1=Data(mydomain1.getMPIRank(), Function(mydomain1))
d1.expand()
dumpfile=os.path.join(FINLEY_WORKDIR, "tempfile.dump.nc")
d1.dump(dumpfile)
d2=load(dumpfile, mydomain1)
self.assertTrue(Lsup(abs(d1-d2)) <= REL_TOL, "data objects differ")
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 test_hex_3D_order2(self):
file = "hex_3D_order1_macro.msh"
my_dom = Brick(1, 1, 1, -1, useElementsOnFace=0)
self.checker(my_dom, file)
def test_hex3D_order1_integorder10(self):
NE = getMPIRankWorld()
my_dom = Brick(NE, NE, NE, integrationOrder=10)
self.__test_3DQ(my_dom, 10)
def setUp(self):
self.order = 1
self.domain = Brick(n0=NE, n1=NE, n2=NE, order=-1, useElementsOnFace=0)
def setUp(self):
self.domain = Brick(NE0, NE1, NE2, 2, optimize=OPTIMIZE)
self.package = SolverOptions.PASO
self.method = SolverOptions.BICGSTAB
self.preconditioner = SolverOptions.JACOBI
def getDomain():
"""
this defines a dom as a brick of length and width l and hight h
"""
global netotal
v_p = {}
for tag in sorted(rho_tab.keys()):
v_p[tag] = sqrt((2 * mu_tab[tag] + lmbd_tab[tag]) / rho_tab[tag])
v_p_ref = min(v_p.values())
print(
"velocities: bedrock = %s, sand = %s, water =%s, absorber =%s, reference =%s"
% (v_p[bedrock], v_p[sand], v_p[water], v_p[absorber], v_p_ref))
sections = {}
sections["x"] = [
d_absorber, x_sand, l_sand, l_x_water, l_sand,
l - x_sand - 2 * l_sand - l_x_water, d_absorber
]
sections["y"] = [
d_absorber, y_sand, l_sand, l_y_water, l_sand,
l - y_sand - 2 * l_sand - l_y_water, d_absorber
]
sections["z"] = [d_absorber, h - h_water - h_sand, h_sand, h_water]
if output:
print("sections x = ", sections["x"])
print("sections y = ", sections["y"])
print("sections z = ", sections["z"])
mats = [[
[absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber]
],
[[
absorber, absorber, absorber, absorber, absorber, absorber,
absorber
],
[absorber, bedrock, bedrock, bedrock, bedrock, bedrock, absorber],
[absorber, bedrock, bedrock, bedrock, bedrock, bedrock, absorber],
[absorber, bedrock, bedrock, bedrock, bedrock, bedrock, absorber],
[absorber, bedrock, bedrock, bedrock, bedrock, bedrock, absorber],
[absorber, bedrock, bedrock, bedrock, bedrock, bedrock, absorber],
[
absorber, absorber, absorber, absorber, absorber, absorber,
absorber
]],
[[
absorber, absorber, absorber, absorber, absorber, absorber,
absorber
],
[absorber, bedrock, bedrock, bedrock, bedrock, bedrock, absorber],
[absorber, bedrock, sand, sand, sand, bedrock, absorber],
[absorber, bedrock, sand, sand, sand, bedrock, absorber],
[absorber, bedrock, sand, sand, sand, bedrock, absorber],
[absorber, bedrock, bedrock, bedrock, bedrock, bedrock, absorber],
[
absorber, absorber, absorber, absorber, absorber, absorber,
absorber
]],
[[
absorber, absorber, absorber, absorber, absorber, absorber,
absorber
],
[absorber, bedrock, bedrock, bedrock, bedrock, bedrock, absorber],
[absorber, bedrock, sand, sand, sand, bedrock, absorber],
[absorber, bedrock, sand, water, sand, bedrock, absorber],
[absorber, bedrock, sand, sand, sand, bedrock, absorber],
[absorber, bedrock, bedrock, bedrock, bedrock, bedrock, absorber],
[
absorber, absorber, absorber, absorber, absorber, absorber,
absorber
]]]
num_elem = {}
for d in sections:
num_elem[d] = []
for i in range(len(sections[d])):
if d == "x":
v_p_min = v_p[mats[0][0][i]]
for q in range(len(sections["y"])):
for r in range(len(sections["z"])):
v_p_min = min(v_p[mats[r][q][i]], v_p_min)
elif d == "y":
v_p_min = v_p[mats[0][i][0]]
for q in range(len(sections["x"])):
for r in range(len(sections["z"])):
v_p_min = min(v_p[mats[r][i][q]], v_p_min)
elif d == "z":
v_p_min = v_p[mats[i][0][0]]
for q in range(len(sections["x"])):
for r in range(len(sections["y"])):
v_p_min = min(v_p[mats[i][r][q]], v_p_min)
num_elem[d].append(
max(1,
int(sections[d][i] * v_p_ref / v_p_min / resolution +
0.5)))
ne_x = sum(num_elem["x"])
ne_y = sum(num_elem["y"])
ne_z = sum(num_elem["z"])
netotal = ne_x * ne_y * ne_z
if output:
print("grid : %s x %s x %s (%s elements)" %
(ne_x, ne_y, ne_z, netotal))
dom = Brick(ne_x,
ne_y,
ne_z,
l0=o * ne_x,
l1=o * ne_y,
l2=o * ne_z,
order=o)
x_old = dom.getX()
x_new = 0
for d in sections:
if d == "x":
i = 0
f = [1, 0, 0]
if d == "y":
i = 1
f = [0, 1, 0]
if d == "z":
i = 2
f = [0, 0, 1]
x = x_old[i]
p = origin[d]
ne = 0
s = 0.
for i in range(len(sections[d]) - 1):
msk = whereNonPositive(x - o * ne + 0.5)
s = s * msk + (sections[d][i] / (o * num_elem[d][i]) *
(x - o * ne) + p) * (1. - msk)
ne += num_elem[d][i]
p += sections[d][i]
x_new = x_new + s * f
dom.setX(x_new)
fs = Function(dom)
x = Function(dom).getX()
x0 = x[0]
x1 = x[1]
x2 = x[2]
p_z = origin["z"]
for i in range(len(mats)):
f_z = wherePositive(x2 - p_z) * wherePositive(x2 - p_z +
sections["z"][i])
p_y = origin["y"]
for j in range(len(mats[i])):
f_y = wherePositive(x1 - p_y) * wherePositive(x1 - p_z +
sections["y"][j])
p_x = origin["x"]
for k in range(len(mats[i][j])):
f_x = wherePositive(x0 - p_x) * wherePositive(x0 - p_x +
sections["x"][k])
fs.setTags(mats[i][j][k], f_x * f_y * f_z)
p_x += sections["x"][k]
p_y += sections["y"][j]
p_z += sections["z"][i]
return dom
def setUp(self):
self.domain = Brick(NE0, NE1, NE2, 1, optimize=OPTIMIZE)
self.package = SolverOptions.TRILINOS
self.method = SolverOptions.MINRES
self.preconditioner = SolverOptions.JACOBI
except ImportError:
print("Finley module required but not available")
HAVE_FINLEY = False
if HAVE_FINLEY:
#... set some parameters ...
lam=1.
mu=0.1
alpha=1.e-6
xc=[0.3,0.3,1.]
beta=8.
T_ref=0.
T_0=1.
#... generate domain ...
mydomain = Brick(l0=1.,l1=1., l2=1.,n0=10, n1=10, n2=10)
x=mydomain.getX()
#... set temperature ...
T=T_0*exp(-beta*length(x-xc))
#... open symmetric PDE ...
mypde=LinearPDE(mydomain)
mypde.setSymmetryOn()
#... set coefficients ...
C=Tensor4(0.,Function(mydomain))
for i in range(mydomain.getDim()):
for j in range(mydomain.getDim()):
C[i,i,j,j]+=lam
C[i,j,i,j]+=mu
C[i,j,j,i]+=mu
msk=whereZero(x[0])*[1.,0.,0.] \
+whereZero(x[1])*[0.,1.,0.] \
def test_getPotentialPolDip(self):
structured = False
totalApparentRes = 130.
if structured:
extents = [100, 100, 100]
dom = Brick(25,
25,
25,
l0=extents[0],
l1=extents[1],
l2=-extents[2])
else:
if not HAVE_GMSH:
raise unittest.SkipTest("gmsh required for test")
extents = [100, 100, 100]
electrodes = []
tags = []
tags.append("e0")
tags.append("e1")
tags.append("e2")
tags.append("e3")
tags.append("e4")
tags.append("e5")
tags.append("e6")
tags.append("e7")
tags.append("e8")
tags.append("e9")
tags.append("e10")
tags.append("e11")
electrodes.append([-22.0, 0.0, 0])
electrodes.append([-18.0, 0.0, 0])
electrodes.append([-14.0, 0.0, 0])
electrodes.append([-10.0, 0.0, 0])
electrodes.append([-6.0, 0.0, 0])
electrodes.append([-2.0, 0.0, 0])
electrodes.append([2.0, 0.0, 0])
electrodes.append([6.0, 0.0, 0])
electrodes.append([10.0, 0.0, 0])
electrodes.append([14.0, 0.0, 0])
electrodes.append([18.0, 0.0, 0])
electrodes.append([22.0, 0.0, 0])
filename = os.path.join(TEST_DATA_ROOT, "dip.geo")
meshname = os.path.join(TEST_DATA_ROOT, "dcRespoldip10-1.msh")
verbosity = 3
gmshGeo2Msh(filename, meshname, 3, 1, verbosity)
dom = ReadGmsh(meshname, 3, diracTags=tags, diracPoints=electrodes)
if mpirank == 0:
os.unlink(meshname)
n = 5
totalApparentResVal = 130.
primaryConductivity = Scalar(1 / 100., ContinuousFunction(dom))
secondaryConductivity = Scalar(1 / 130., ContinuousFunction(dom))
current = 1000.
numElectrodes = 12
# a=(.8*extents[0])/numElectrodes
a = 4
midPoint = [0, 0]
directionVector = [1., 0.]
poldips = PoleDipoleSurvey(dom, primaryConductivity,
secondaryConductivity, current, a, n,
midPoint, directionVector, numElectrodes)
poldips.getPotential()
primaryApparentRes = poldips.getApparentResistivityPrimary()
SecondaryApparentRes = poldips.getApparentResistivitySecondary()
totalApparentRes = poldips.getApparentResistivityTotal()
for i in totalApparentRes:
for j in i:
res_a = abs(j - totalApparentResVal)
res_b = 0.1 * totalApparentResVal
self.assertLess(
res_a, res_b, "result of %g greater than tolerance of %g" %
(res_a, res_b))
def test_mesh_dump_to_NetCDF_brick(self):
mydomain1 = Brick(n0=NE0, n1=NE1, n2=NE2, order=2, l0=1., l1=1., l2=1., optimize=False)
dumpfile=os.path.join(FINLEY_WORKDIR, "tempfile.mesh.nc")
mydomain1.dump(dumpfile)
mydomain2=LoadMesh(dumpfile)
self.domainsEqual(mydomain1, mydomain2)
def generate(self):
(numGridPts1, numGridPts2) = self.getGridPointsPerDim()
periodic0 = True
if (self.getDim() == 2):
mesh1 = \
Rectangle(
numGridPts1[0],
numGridPts1[1],
order=1,
l0=self.bBox1.getSize()[0],
l1=self.bBox1.getSize()[1],
periodic0=periodic0
)
mesh2 = \
Rectangle(
numGridPts2[0],
numGridPts2[1],
order=1,
l0=self.bBox2.getSize()[0],
l1=self.bBox2.getSize()[1],
periodic0=periodic0
)
else:
mesh1 = \
Brick(
numGridPts1[0],
numGridPts1[1],
numGridPts1[2],
order=1,
l0=self.bBox1.getSize()[0],
l1=self.bBox1.getSize()[1],
l2=self.bBox1.getSize()[2],
periodic0=periodic0
)
mesh2 = \
Brick(
numGridPts2[0],
numGridPts2[1],
numGridPts2[2],
order=1,
l0=self.bBox2.getSize()[0],
l1=self.bBox2.getSize()[1],
l2=self.bBox2.getSize()[2],
periodic0=periodic0
)
x1 = mesh1.getX()
x2 = mesh2.getX()
#
# To get the same identical tags on the particle boundary elements
# of both meshes, reflect about the y-axis.
#
x2[1] = -x2[1]
x2[1] += abs(inf(x2[1]))
#
# Now translate the meshes so they correspond to the
# specified bounding boxes.
#
for d in range(0, self.getDim()):
x1[d] += self.bBox1.getMinPt()[d]
x2[d] += self.bBox2.getMinPt()[d]
mesh1.setX(x1)
mesh2.setX(x2)
self.mesh = Merge([mesh1, mesh2])
ndx = 15 # mesh steps in x direction
ndy = 15 # mesh steps in y direction - one dimension means one element
ndz = 10
#PDE related
rho=100.0
rholoc=[0,0,-0]
G=6.67300*10E-11
################################################ESTABLISHING PARAMETERS
#the folder to put our outputs in, leave blank "" for script path
save_path= os.path.join("data","example10")
#ensure the dir exists
mkDir(save_path)
####################################################DOMAIN CONSTRUCTION
domain = Brick(l0=mx,l1=my,n0=ndx, n1=ndy,l2=mz,n2=ndz)
x=Solution(domain).getX()
x=x-[mx/2,my/2,mz/2]
domain.setX(interpolate(x, ContinuousFunction(domain)))
mask=wherePositive(100-length(x-rholoc))
rho=rho*mask
kro=kronecker(domain)
mass=rho*vol(domain)
ipot=FunctionOnBoundary(domain)
xb=ipot.getX()
q=whereZero(x[2]-inf(x[2]))
###############################################ESCRIPT PDE CONSTRUCTION
mypde=LinearPDE(domain)
NEz = 200 # number of nodes in the z direction
H0 = 600 # height [m] of transect above bottom of domain (will be locked to grid)
b_hx = 45000.0 # background magnetic field in nT x direction
b_hz = 0.0 # background magnetic field in nT y direction
b_hy = 0.0 # background magnetic field in nT z direction
ksi = 0.015 # assumed susceptibility
Lx = dx*NEx
Ly = dx*NEy
Lz = dx*NEz
print("domain dimensions = [%dm x %dm x %dm]"%(Lx,Ly,Lz))
print("grid = [%d x %d x %d]"%(NEx, NEy, NEz))
# Create domain
domain=Brick(n0=NEx, n1=NEy, n2=NEz, l0=Lx, l1=Ly, l2=Lz)
# Define model using class MagneticModel3D
# Assumes zero Dirichlet BC at bottom left front corner
model=MagneticModel3D(domain)
# Define susceptibility
Z0=100 # vertical position of circle below transect [m]
c=[Lx/2.,Ly/2., H0-Z0] # circle center
R=20. # radius
x=domain.getX()
d=length(x-c)
kC=ksi*whereNegative(d-R) # 0 for d>R and 1 for d<R
model.setSusceptibility(kC)
print("file ", filename, " is generated")
if d == 2:
m = [[11., 12.], [21., 22.]]
else:
m = [[11., 12., 13.], [21., 22., 23.], [31., 32., 33.]]
try:
eval("(x*m).save%s(\"%s\")" % (format.upper(), filename))
except Exception as msg:
print("%% failed because of ", msg)
for format in ["vtk", "dx"]:
for d in [2, 3]:
for order in [1, 2]:
if (d == 2):
mesh = Rectangle(ne, ne, order, l0=order * ne, l1=order * ne)
elif (d == 3):
mesh = Brick(ne,
ne,
ne,
order,
l0=order * ne,
l1=order * ne,
l2=order * ne)
for fs in [
"ContinuousFunction", "Function", "FunctionOnBoundary",
"Solution", "ReducedSolution", "FunctionOnContact"
]:
filetype = "%s.o%d.d%d" % (fs, order, d)
writeInFormat(eval("%s(mesh)" % fs), format, filetype)
def setUp(self):
self.domain = Brick(NE,NE,NE,-1,useElementsOnFace=0)
self.order = 1
import errno
try:
os.mkdir('./result/')
os.mkdir('./result/gauss')
os.mkdir('./result/vtk')
os.mkdir('./result/packing')
except OSError as exc:
if exc.errno != errno.EEXIST:
raise
pass
vel = -0.0001; confining=-1.e5;
lx = 0.05; ly = 0.05; lz = 0.1; # sample dimension
nx = 8; ny = 8; nz = 16; # discretization
mydomain = Brick(l0=lx,l1=ly,l2=lz,n0=nx,n1=ny,n2=nz,order=2,integrationOrder=2) # 20-noded,8-Gauss hexahedral element
dim = 3; k = kronecker(mydomain)
numg = 8*nx*ny*nz; # number of Gauss points
packNo=list(range(0,numg,8))
prob = MultiScale(domain=mydomain,ng=numg,useMPI=True,rtol=1e-2) # mpi is activated
disp = Vector(0.,Solution(mydomain))
t=0
stress = prob.getCurrentStress()
proj = Projector(mydomain)
sig = proj(stress)
sig_bounda = interpolate(sig,FunctionOnBoundary(mydomain))
traction = matrix_mult(sig_bounda,mydomain.getNormal()) # traction on boundary
x = mydomain.getX()
def setUp(self):
self.domain = Brick(NE0, NE1, NE2, 2, optimize=OPTIMIZE)
self.package = SolverOptions.TRILINOS
self.method = SolverOptions.DIRECT
def setUp(self):
self.domain = Brick(NE0, NE1, NE2, 2, optimize=OPTIMIZE)
self.package = SolverOptions.TRILINOS
self.method = SolverOptions.PCG
self.preconditioner = SolverOptions.ILUT
def setUp(self):
NE = 29 # warning: smaller NE may case a failure for VarioF tests due to discretization errors.
self.dom = Brick(NE, NE, NE)
self.rescaleDomain()
T_END = 0.05 # set T_END=(2*pi)/OMEGA to run a full simulation
n = 0
if DIM == 2:
mydomain = Rectangle(int(ceil(L * NE / H)),
NE,
l0=L,
l1=H,
order=1,
useFullElementOrder=True,
optimize=True)
else:
mydomain = Brick(int(ceil(L * NE / H)),
int(ceil(L * NE / H)),
NE,
l0=L,
l1=L,
l2=H,
order=1,
useFullElementOrder=True,
optimize=True)
x = mydomain.getX()
v = Vector(0.0, Solution(mydomain))
if DIM == 2:
a0 = 1
n0 = 1
n1 = 0.5
a1 = -(a0 * n0) / n1
v[0] = a0 * sin(pi * n0 * x[0]) * cos(pi * n1 * x[1])
v[1] = a1 * cos(pi * n0 * x[0]) * sin(pi * n1 * x[1])
else:
c = integrate(u_h, Function(dom)) - 1.
x0 = getCenter(t)
x0h = integrate(x * u_h, Function(dom))
d = length(x0 - x0h)
sigma_h2 = sqrt(integrate(length(x - x0h)**2 * u_h, Function(dom)))
if DIM == 3: sigma_h2 *= sqrt(2. / 3.)
e = sigma_h2 / sqrt(4 * E * t) - 1
# return a,b,c,e,1./(4*pi*E*t)**(DIM/2.)
return d, e
# return a,b,c,d,e
if DIM == 2:
dom = Rectangle(NE, NE)
else:
dom = Brick(NE, NE, NE)
dom.setX(2 * dom.getX() - 1)
# set initial value
x = dom.getX()
u0 = 1 / (4. * pi * E * T0)**(DIM / 2.) * exp(
-length(dom.getX() - getCenter(T0))**2 / (4. * E * T0))
print("QUALITY ", QUALITY(T0, u0))
x = Function(dom).getX()
if DIM == 2:
V = OMEGA0 * (x[0] * [0, -1] + x[1] * [1, 0])
else:
V = OMEGA0 * (x[0] * [0, cos(ALPHA), 0] + x[1] *
[-cos(ALPHA), 0, sin(ALPHA)] + x[2] * [0., -sin(ALPHA), 0.])
def setUp(self):
self.domain = Brick(NE0, NE1, NE2, 2, optimize=OPTIMIZE)
self.package = SolverOptions.PASO
self.method = SolverOptions.TFQMR
self.preconditioner = SolverOptions.GAUSS_SEIDEL
def setUp(self):
self.domain = Brick(NE0, NE1, NE2, 2, optimize=OPTIMIZE)
self.package = SolverOptions.TRILINOS
self.method = SolverOptions.BICGSTAB
self.preconditioner = SolverOptions.GAUSS_SEIDEL
def getMesh(NE_X, NE_Y, t, d, o, fullOrder, r, l_X):
if t == "Hex":
if d == 2:
dom = Rectangle(n0=NE_X,
n1=NE_Y,
l0=l_X,
order=o,
useFullElementOrder=fullOrder,
useElementsOnFace=r,
optimize=True)
else:
Brick()
dom = Brick(n0=NE_X,
n1=NE_Y,
n2=NE_Y,
l0=l_X,
order=o,
useFullElementOrder=fullOrder,
useElementsOnFace=r,
optimize=True)
else:
des = Design(dim=d,
order=o,
element_size=min(l_X / max(3, NE_X), 1. / max(3, NE_Y)),
keep_files=True)
des.setScriptFileName("tester.geo")
if d == 2:
p0 = Point(0., 0.)
p1 = Point(l_X, 0.)
p2 = Point(l_X, 1.)
p3 = Point(0., 1.)
l01 = Line(p0, p1)
l12 = Line(p1, p2)
l23 = Line(p2, p3)
l30 = Line(p3, p0)
s = PlaneSurface(CurveLoop(l01, l12, l23, l30))
des.addItems(s, l01, l12, l23, l30)
else:
p000 = Point(0., 0., 0.)
p100 = Point(l_X, 0., 0.)
p010 = Point(0., 1., 0.)
p110 = Point(l_X, 1., 0.)
p001 = Point(0., 0., 1.)
p101 = Point(l_X, 0., 1.)
p011 = Point(0., 1., 1.)
p111 = Point(l_X, 1., 1.)
l10 = Line(p000, p100)
l20 = Line(p100, p110)
l30 = Line(p110, p010)
l40 = Line(p010, p000)
l11 = Line(p000, p001)
l21 = Line(p100, p101)
l31 = Line(p110, p111)
l41 = Line(p010, p011)
l12 = Line(p001, p101)
l22 = Line(p101, p111)
l32 = Line(p111, p011)
l42 = Line(p011, p001)
bottom = PlaneSurface(-CurveLoop(l10, l20, l30, l40))
top = PlaneSurface(CurveLoop(l12, l22, l32, l42))
front = PlaneSurface(CurveLoop(l10, l21, -l12, -l11))
back = PlaneSurface(CurveLoop(l30, l41, -l32, -l31))
left = PlaneSurface(CurveLoop(l11, -l42, -l41, l40))
right = PlaneSurface(CurveLoop(-l21, l20, l31, -l22))
vol = Volume(SurfaceLoop(bottom, top, front, back, left, right))
des.addItems(vol)
dom = MakeDomain(des)
return dom
ndx = 15 # mesh steps in x direction
ndy = 15 # mesh steps in y direction - one dimension means one element
ndz = 10
#PDE related
rho=100.0
rholoc=[0,0,-0]
G=6.67300*10E-11
################################################ESTABLISHING PARAMETERS
#the folder to put our outputs in, leave blank "" for script path
save_path= os.path.join("data","example10")
#ensure the dir exists
mkDir(save_path)
####################################################DOMAIN CONSTRUCTION
domain = Brick(l0=mx,l1=my,n0=ndx, n1=ndy,l2=mz,n2=ndz)
x=Solution(domain).getX()
x=x-[mx/2,my/2,mz/2]
domain.setX(interpolate(x, ContinuousFunction(domain)))
mask=wherePositive(100-length(x-rholoc))
rho=rho*mask
kro=kronecker(domain)
mass=rho*vol(domain)
ipot=FunctionOnBoundary(domain)
xb=ipot.getX()
q=whereZero(x[2]-inf(x[2]))
###############################################ESCRIPT PDE CONSTRUCTION
mypde=LinearPDE(domain)
import time
vel = -0.0001
confining = -1.e5
lx = 0.05
ly = 0.05
lz = 0.1
# sample dimension
nx = 8
ny = 8
nz = 16
# discretization
mydomain = Brick(l0=lx,
l1=ly,
l2=lz,
n0=nx,
n1=ny,
n2=nz,
order=2,
integrationOrder=2) # 20-noded,8-Gauss hexahedral element
dim = 3
k = kronecker(mydomain)
numg = 8 * nx * ny * nz
# number of Gauss points
packNo = range(0, numg, 8)
prob = MultiScale(domain=mydomain, ng=numg, useMPI=True,
rtol=1e-2) # mpi is activated
disp = Vector(0., Solution(mydomain))
t = 0
def setUp(self):
self.domain = Brick(NE, NE, NE, 2)
self.order = 2
def setUp(self):
self.domain = Brick(NE0, NE1, NE2, 1, optimize=OPTIMIZE)
self.package = SolverOptions.UMFPACK
self.method = SolverOptions.DIRECT
def setUp(self):
self.domain = Brick(NE0, NE1, NE2, 2, optimize=OPTIMIZE)
self.package = SolverOptions.PASO
self.method = SolverOptions.MINRES
self.preconditioner = SolverOptions.RILU
#diagnostics_file=FileWriter(DIAGNOSTICS_FN,append=True)
print(("<%s> Restart at time step %d (t=%e) completed." %
(time.asctime(), n, t)))
else:
if DIM == 2:
dom = Rectangle(int(ceil(L * NE / H)),
NE,
l0=L / H,
l1=1,
order=-1,
optimize=True)
else:
dom = Brick(int(ceil(L * NE / H)),
int(ceil(L * NE / H)),
NE,
l0=L / H,
l1=L / H,
l2=1,
order=-1,
optimize=True)
x = dom.getX()
T = Scalar(1, Solution(dom))
for d in range(DIM):
if d == DIM - 1:
T *= sin(x[d] / H * pi)
else:
T *= cos(x[d] / L * pi)
T = (1. - x[DIM - 1]) + PERT * T
v = Vector(0, Solution(dom))
stress = Tensor(0, Function(dom))
x2 = ReducedSolution(dom).getX()
def test_hex_3D_order2(self):
file = "hex_3D_order2.msh"
my_dom = Brick(1, 1, 1, 2)
self.checker(my_dom, file)
def XXX(dim, tend, dt, s, h, b, c, d, c_dir="x", d_dir="x", a=1., CN=True):
"""
dim - sparial dimension
s - width of initial profile
h - mesh size
"""
v_c = c / a * getDirection(dim, c_dir)
v_d = d / a * getDirection(dim, d_dir)
v = (v_c + v_d)
E = b / a
if VERBOSITY:
print("=" * 100)
print(
"XX Start test dim = %d , h=%e, b=%e, c=%e, d=%e, c_dir=%s, d_dir=%s, a=%e, s=%e"
% (dim, h, b, c, d, c_dir, d_dir, a, s))
print("=" * 100)
print("initial width s = ", s)
print("diffusion = ", E)
print("total velocity = ", v)
print("tend = ", tend)
print("tolerance = ", TOL)
print("number of elements over s =", s / h)
b0 = sqrt(-log(TAU) * 4 * (s**2 + E * tend))
b1 = sqrt(-log(TAU)) * 2 * s
X0_0 = max(b1, -v[0] * tend + b0)
X0_1 = max(b1, -v[1] * tend + b0)
l_0 = X0_0 + max(v[0] * tend + b0, b1)
l_1 = X0_1 + max(v[1] * tend + b0, b1)
NE_0 = max(int(l_0 / h + 0.5), 1)
NE_1 = max(int(l_1 / h + 0.5), 1)
if dim == 2:
if VERBOSITY:
print("%d x %d grid over %e x %e with element size %e." %
(NE_0, NE_1, l_0, l_1, h))
if NE_0 * NE_1 > NE_MAX:
raise ValueError("too many elements %s." % (NE_0 * NE_1, ))
dom = Rectangle(n0=NE_0, n1=NE_1, l0=l_0, l1=l_1)
x0 = [X0_0, X0_1]
else:
X0_2 = max(b1, -v[2] * tend + b0)
l_2 = X0_2 + max(v[2] * tend + b0, b1)
NE_2 = max(int(l_2 / h + 0.5), 1)
if VERBOSITY:
print(
"%d x %d x %d grid over %e x %e x %e with element size %e." %
(NE_0, NE_1, NE_2, l_0, l_1, l_2, h))
if NE_0 * NE_1 * NE_2 > NE_MAX:
raise ValueError("too many elements %s." % (NE_0 * NE_1 * NE_2, ))
dom = Brick(n0=NE_0, n1=NE_1, ne2=NE_2, l0=l_0, l1=l_1, l2=l_2)
x0 = [X0_0, X0_1, X0_2]
if VERBOSITY:
print("initial location = ", x0)
print("XX", interpolate(uRef(dom, 0., E, s, v, x0),
FunctionOnBoundary(dom)))
fc_BE = TransportPDE(dom, numEquations=1)
fc_BE.setValue(M=a, A=-b * kronecker(dom), B=-v_d * a, C=-v_c * a)
fc_BE.getSolverOptions().setVerbosity(VERBOSITY)
fc_BE.getSolverOptions().setTolerance(TOL)
#
fc_BE.getSolverOptions().setPreconditioner(
fc_BE.getSolverOptions().GAUSS_SEIDEL)
fc_BE.getSolverOptions().setNumSweeps(5)
if VERBOSITY: print("Backward Euler Transport created")
fc_CN = TransportPDE(dom, numEquations=1)
fc_CN.setValue(M=a, A=-b * kronecker(dom), B=-v_d * a, C=-v_c * a)
fc_CN.getSolverOptions().setVerbosity(VERBOSITY)
fc_CN.getSolverOptions().setTolerance(TOL)
#fc_CN.getSolverOptions().setPreconditioner(fc_CN.getSolverOptions().GAUSS_SEIDEL)
fc_CN.getSolverOptions().setNumSweeps(2)
if VERBOSITY: print("Crank Nicolson Transport created")
dt_CN = fc_CN.getSafeTimeStepSize()
if VERBOSITY: print("time step size by Crank Nicolson=", dt_CN)
U0 = uRef(dom, 0, E, s, v, x0)
U0_e = uRef(dom, 0, E, s, v, x0, True)
fc_CN.setInitialSolution(U0)
fc_BE.setInitialSolution(U0)
initial_error_L2 = sqrt(integrate((U0 - U0_e)**2))
if VERBOSITY:
print("initial Lsup = ", Lsup(U0), Lsup(U0_e))
print("initial integral = ", integrate(U0_e))
print("initial error = ", initial_error_L2)
print("used time step size =", dt)
if not CN:
n = int(ceil(tend / dt))
if VERBOSITY:
print("Solve Backward Euler:")
print("substeps : ", n)
t0 = clock()
for i in range(n):
u = fc_BE.getSolution(dt)
t0 = clock() - t0
else:
if VERBOSITY: print("Solve Crank Nicolson:")
dt = dt_CN
t0 = clock()
u = fc_CN.getSolution(tend)
t0 = clock() - t0
out = QUALITY(u, uRef(dom, tend, E, s, v, x0, True))
print("XX",
interpolate(uRef(dom, tend, E, s, v, x0), FunctionOnBoundary(dom)))
out['time'] = t0
out['tend'] = tend
out['dt'] = dt
out['dx'] = h
if abs(b) > 0:
out["peclet"] = length(v) * s / b
else:
out["peclet"] = 9999999.
# saveVTK("bb.vtu",u0=U0,u_CN=u_CN, uRef=uRef(dom,dt2,E,s,v,X0) )
return out
def test_hex_3D_order2_onFace(self):
file = "hex_3D_order2_onFace.msh"
my_dom = Brick(1, 1, 1, 2, useElementsOnFace=1)
self.checker(my_dom, file)
def setUp(self):
self.domain = Brick(NE0, NE1, NE2, 2, optimize=OPTIMIZE)
self.package = SolverOptions.TRILINOS
self.method = SolverOptions.BICGSTAB
self.preconditioner = SolverOptions.JACOBI
self.REL_TOL = 5.e-6
def test_hex3D_order2_integorder6(self):
NE = getMPIRankWorld()
my_dom = Brick(NE, NE, NE, order=2, integrationOrder=6)
self.__test_3DQ(my_dom, 6)
def getDomain():
"""
this defines a dom as a brick of length and width l and hight h
"""
global netotal
v_p={}
for tag in sorted(rho_tab.keys()):
v_p[tag]=sqrt((2*mu_tab[tag]+lmbd_tab[tag])/rho_tab[tag])
v_p_ref=min(v_p.values())
print("velocities: bedrock = %s, sand = %s, water =%s, absorber =%s, reference =%s"%(v_p[bedrock],v_p[sand],v_p[water],v_p[absorber],v_p_ref))
sections={}
sections["x"]=[d_absorber, x_sand, l_sand, l_x_water, l_sand, l-x_sand-2*l_sand-l_x_water, d_absorber]
sections["y"]=[d_absorber, y_sand, l_sand, l_y_water, l_sand, l-y_sand-2*l_sand-l_y_water, d_absorber]
sections["z"]=[d_absorber,h-h_water-h_sand,h_sand,h_water]
if output:
print("sections x = ",sections["x"])
print("sections y = ",sections["y"])
print("sections z = ",sections["z"])
mats= [
[ [absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber] ],
[ [absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, bedrock , bedrock , bedrock , bedrock , bedrock , absorber],
[absorber, bedrock , bedrock , bedrock , bedrock , bedrock , absorber],
[absorber, bedrock , bedrock , bedrock , bedrock , bedrock , absorber],
[absorber, bedrock , bedrock , bedrock , bedrock , bedrock , absorber],
[absorber, bedrock , bedrock , bedrock , bedrock , bedrock , absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber] ],
[ [absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, bedrock , bedrock , bedrock , bedrock , bedrock , absorber],
[absorber, bedrock , sand , sand , sand , bedrock , absorber],
[absorber, bedrock , sand , sand , sand , bedrock , absorber],
[absorber, bedrock , sand , sand , sand , bedrock , absorber],
[absorber, bedrock , bedrock , bedrock , bedrock , bedrock , absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber] ],
[ [absorber, absorber, absorber, absorber, absorber, absorber, absorber],
[absorber, bedrock , bedrock , bedrock , bedrock , bedrock , absorber],
[absorber, bedrock , sand , sand , sand , bedrock , absorber],
[absorber, bedrock , sand , water , sand , bedrock , absorber],
[absorber, bedrock , sand , sand , sand , bedrock , absorber],
[absorber, bedrock , bedrock , bedrock , bedrock , bedrock , absorber],
[absorber, absorber, absorber, absorber, absorber, absorber, absorber] ] ]
num_elem={}
for d in sections:
num_elem[d]=[]
for i in range(len(sections[d])):
if d=="x":
v_p_min=v_p[mats[0][0][i]]
for q in range(len(sections["y"])):
for r in range(len(sections["z"])):
v_p_min=min(v_p[mats[r][q][i]],v_p_min)
elif d=="y":
v_p_min=v_p[mats[0][i][0]]
for q in range(len(sections["x"])):
for r in range(len(sections["z"])):
v_p_min=min(v_p[mats[r][i][q]],v_p_min)
elif d=="z":
v_p_min=v_p[mats[i][0][0]]
for q in range(len(sections["x"])):
for r in range(len(sections["y"])):
v_p_min=min(v_p[mats[i][r][q]],v_p_min)
num_elem[d].append(max(1,int(sections[d][i] * v_p_ref/v_p_min /resolution+0.5)))
ne_x=sum(num_elem["x"])
ne_y=sum(num_elem["y"])
ne_z=sum(num_elem["z"])
netotal=ne_x*ne_y*ne_z
if output: print("grid : %s x %s x %s (%s elements)"%(ne_x,ne_y,ne_z,netotal))
dom=Brick(ne_x,ne_y,ne_z,l0=o*ne_x,l1=o*ne_y,l2=o*ne_z,order=o)
x_old=dom.getX()
x_new=0
for d in sections:
if d=="x":
i=0
f=[1,0,0]
if d=="y":
i=1
f=[0,1,0]
if d=="z":
i=2
f=[0,0,1]
x=x_old[i]
p=origin[d]
ne=0
s=0.
for i in range(len(sections[d])-1):
msk=whereNonPositive(x-o*ne+0.5)
s=s*msk + (sections[d][i]/(o*num_elem[d][i])*(x-o*ne)+p)*(1.-msk)
ne+=num_elem[d][i]
p+=sections[d][i]
x_new=x_new + s * f
dom.setX(x_new)
fs=Function(dom)
x=Function(dom).getX()
x0=x[0]
x1=x[1]
x2=x[2]
p_z=origin["z"]
for i in range(len(mats)):
f_z=wherePositive(x2-p_z)*wherePositive(x2-p_z+sections["z"][i])
p_y=origin["y"]
for j in range(len(mats[i])):
f_y=wherePositive(x1-p_y)*wherePositive(x1-p_z+sections["y"][j])
p_x=origin["x"]
for k in range(len(mats[i][j])):
f_x=wherePositive(x0-p_x)*wherePositive(x0-p_x+sections["x"][k])
fs.setTags(mats[i][j][k],f_x*f_y*f_z)
p_x+=sections["x"][k]
p_y+=sections["y"][j]
p_z+=sections["z"][i]
return dom