def test_2DmultiRegion(verbose=0):
"""Test for loading gmsh mesh through PUMI with multiple-regions"""
testDir = os.path.dirname(os.path.abspath(__file__))
Model = testDir + '/TwoQuads.dmg'
Mesh = testDir + '/TwoQuads.smb'
domain = Domain.PUMIDomain(
dim=2, manager=MeshAdapt.AdaptManager()) #initialize the domain
domain.AdaptManager.reconstructedFlag = 0 #this is used to indicate that no mesh reconstruction is being done.
domain.AdaptManager.PUMIAdapter.loadModelAndMesh(bytes(Model, 'utf-8'),
bytes(Mesh, 'utf-8'))
domain.faceList = [[14], [12], [11], [13], [15], [16]]
domain.boundaryLabels = [1, 2, 3, 4, 5, 6]
domain.regList = [[41], [42]]
mesh = MeshTools.TriangularMesh()
mesh.cmesh = cmeshTools.CMesh()
comm = Comm.init()
mesh.convertFromPUMI(domain,
domain.AdaptManager.PUMIAdapter,
domain.faceList,
domain.regList,
parallel=comm.size() > 1,
dim=domain.nd)
ok(mesh.elementMaterialTypes[0] == 1)
ok(mesh.elementMaterialTypes[-1] == 2)
def testCalculate_init(self):
from proteus import Domain
from proteus.mprans import SpatialTools as mst
from proteus.mprans.BodyDynamics import PaddleBody
domain2D = Domain.PlanarStraightLineGraphDomain()
pos = np.array([2.0, 0.1 , 0.0])
dim = (0.3, 1.)
paddle = mst.Rectangle(domain=domain2D, dim=dim, coords=[pos[0], pos[1]])
PB=PaddleBody(paddle,substeps=20)
PB.calculate_init()
npt.assert_equal(PB.position,[pos[0],0.,0.])
npt.assert_equal(PB.last_position,[pos[0],0.,0.])
npt.assert_equal(PB.rotation,np.eye(3))
npt.assert_equal(PB.last_rotation,np.eye(3))
from proteus.mprans.BodyDynamics import getEulerAngles
npt.assert_equal(PB.rotation_euler,getEulerAngles(PB.rotation))
npt.assert_equal(PB.last_rotation_euler,getEulerAngles(PB.last_rotation))
npt.assert_equal(PB.cV_init,np.array([(1.85,-0.4),
(2.15,-0.4),
(2.15,0.6),
(1.85,0.6)]))
npt.assert_equal(PB.cV,np.array([(1.85,-0.4),
(2.15,-0.4),
(2.15,0.6),
(1.85,0.6)]))
npt.assert_equal(PB.cV_last,np.array([(1.85,-0.4),
(2.15,-0.4),
(2.15,0.6),
(1.85,0.6)]))
def testPaddleMotion(self):
from proteus import Domain
from proteus.mprans import SpatialTools as mst
from proteus.mprans.BodyDynamics import PaddleBody
domain2D = Domain.PlanarStraightLineGraphDomain()
pos = np.array([2.0, 0.1 , 0.0])
dim = (0.3, 1.)
paddle = mst.Rectangle(domain=domain2D, dim=dim, coords=[pos[0], pos[1]])
PB=PaddleBody(paddle,substeps=20)
PB.calculate_init()
At = [1.,0.,0.]
Ar = [0.1,0.,0.]
Tt = Tr = [0.5,0.,0.]
rampS = 0.1
rampE = 0.1
Tend = 2.
PB.inputMotion(InputMotion=True, pivot=None,
At=At, Tt=Tt,
Ar=Ar, Tr=Tr,
rampStart=rampS, rampEnd =rampE, Tend = Tend)
# tersting initial ramp
times= [0.04, 0.95 ,1.93]
for tt in times:
ramp = min(1.,tt/rampS,(Tend-tt)/rampE)
getVars = PB.imposeSinusoidalMotion(tt=tt)
disp = ramp*np.array(At)*np.sin(2*np.pi/Tt[0]*tt)
rot = ramp*np.array(Ar)*np.sin(2*np.pi/Tt[0]*tt)
disp = disp - (PB.last_position - PB.init_barycenter)
npt.assert_equal(disp,getVars[0])
npt.assert_equal(rot,getVars[1])
def test_adaptIBM_adaptMesh(self):
currentPath = os.path.dirname(os.path.abspath(__file__))
runCommand = "cd " + currentPath + "; parun -l5 cylinder_so.py -C 'T=0.01 onlySaveFinalSolution=True genMesh=False usePUMI=True';"
subprocess.check_call(runCommand, shell=True)
#load initial mesh and extract element count
domain = Domain.PUMIDomain(
manager=MeshAdapt.AdaptManager()) #initialize the domain
filePath = bytes(currentPath + '/', 'utf-8')
domain.AdaptManager.PUMIAdapter.loadModelAndMesh(
filePath + b"Reconstructed.dmg", filePath + b"Reconstructed.smb")
mesh = MeshTools.TetrahedralMesh()
mesh.convertFromPUMI(domain,
domain.AdaptManager.PUMIAdapter, [1], [1],
parallel=comm.size() > 1,
dim=2)
nElements_initial = mesh.nElements_global
#load final mesh and extract element count
domain.AdaptManager.PUMIAdapter.loadModelAndMesh(
filePath + b"Reconstructed.dmg", filePath + b"finalMesh.smb")
mesh2 = MeshTools.TetrahedralMesh()
mesh2.convertFromPUMI(domain,
domain.AdaptManager.PUMIAdapter, [1], [1],
parallel=comm.size() > 1,
dim=2)
nElements_final = mesh2.nElements_global
#adapted mesh should have less elements
assert (nElements_final < nElements_initial)
def tank2d(L=[1.0, 1.0, 1.0], fileprefix=None):
boundaries = [
'left', 'right', 'bottom', 'top', 'front', 'back', 'obstacle'
]
boundaryTags = dict([(key, i + 1) for (i, key) in enumerate(boundaries)])
vertices = [
[0.0, 0.0], #0
[L[0], 0.0], #1
[L[0], L[1]], #2
[0.0, L[1]]
] #3
vertexFlags = [
boundaryTags['left'], boundaryTags['right'], boundaryTags['right'],
boundaryTags['left']
]
segments = [[0, 1], [1, 2], [2, 3], [3, 0]]
segmentFlags = [
boundaryTags['front'], boundaryTags['right'], boundaryTags['back'],
boundaryTags['left']
]
regions = [[0.5 * L[0], 0.5 * L[1]]]
regionFlags = [1.0]
domain = Domain.PlanarStraightLineGraphDomain(fileprefix=fileprefix,
vertices=vertices,
vertexFlags=vertexFlags,
segments=segments,
segmentFlags=segmentFlags,
regions=regions,
regionFlags=regionFlags)
#go ahead and add a boundary tags member
domain.boundaryTags = boundaryTags
return domain
def test_gmsh_generation_3D(self):
domain = Domain.PiecewiseLinearComplexDomain()
cube = st.Cuboid(domain, dim=[2., 2., 2.])
st.assembleDomain(domain)
domain.writeGeo('gmsh_mesh_test_3D', he_max=0.1)
gmsh_cmd = "gmsh {0:s} -v 10 -3 -o {1:s} -format msh".format(
domain.geofile + ".geo", domain.geofile + ".msh")
check_call(gmsh_cmd, shell=True)
MeshTools.msh2simplex(domain.geofile, nd=3)
# cek disabling exact tests due to cross-platform non-reproducibility
# with open('gmsh_mesh_test_3D.node', 'r') as nodefile:
# npt.assert_equal(nodefile.readline(), '7674 3 0 1\n')
# with open('gmsh_mesh_test_3D.edge', 'r') as edgefile:
# npt.assert_equal(edgefile.readline(), '9384 1\n')
# with open('gmsh_mesh_test_3D.face', 'r') as facefile:
# npt.assert_equal(facefile.readline(), '6256 3 1\n')
# with open('gmsh_mesh_test_3D.ele', 'r') as elefile:
# npt.assert_equal(elefile.readline(), '37473 4 1\n')
with open('gmsh_mesh_test_3D.node', 'r') as nodefile:
assert (abs(int(nodefile.readline().split()[0]) - 7674) / 7674.0 <
.02)
with open('gmsh_mesh_test_3D.edge', 'r') as edgefile:
assert (abs(int(edgefile.readline().split()[0]) - 9384) / 9384.0 <
.02)
with open('gmsh_mesh_test_3D.face', 'r') as facefile:
assert (abs(int(facefile.readline().split()[0]) - 6256) / 6256.0 <
.02)
with open('gmsh_mesh_test_3D.ele', 'r') as elefile:
assert (abs(int(elefile.readline().split()[0]) - 37473) / 37473.0 <
.02)
def testGetInertia(self):
from proteus import Domain
from proteus import SpatialTools as st
from proteus.mprans import SpatialTools as mst
from proteus.mprans import BodyDynamics as bd
# parameters
domain2D = Domain.PlanarStraightLineGraphDomain()
pos = np.array([1.0, 1.0, 0.0])
dim = (0.3, 0.385)
dt, substeps = 0.001, 20
caisson = mst.Rectangle(domain=domain2D, dim=dim, coords=[pos[0], pos[1]])
caisson2D = bd.CaissonBody(shape=caisson, substeps=substeps)
mst.assembleDomain(domain2D)
c2d = caisson2D
c2d.nd = 2
mass = c2d.mass = 50.0
pivot = np.array([(caisson.vertices[0][0]+caisson.vertices[1][0])*0.5, caisson.vertices[0][1], 0.0])
d = dx, dy, dz = pivot - caisson.barycenter
# inertia transformation with different pivot
Ix = (old_div((dim[0]**2),12.)) + dy**2
Iy = (old_div((dim[1]**2),12.)) + dx**2
It = Ix + Iy
I = It*mass
I1 = c2d.getInertia(vec=(0.,0.,1.), pivot=pivot)
npt.assert_equal(I, I1)
def testOverturningModule(self):
from proteus import Domain
from proteus import SpatialTools as st
from proteus.mprans import SpatialTools as mst
from proteus.mprans import BodyDynamics as bd
# parameters
domain2D = Domain.PlanarStraightLineGraphDomain()
pos = np.array([1.0, 1.0, 0.0])
dim = (0.3, 0.385)
dt, substeps = 0.001, 20
caisson = mst.Rectangle(domain=domain2D, dim=dim, coords=[pos[0], pos[1]])
caisson2D = bd.CaissonBody(shape=caisson, substeps=substeps)
mst.assembleDomain(domain2D)
c2d = caisson2D
c2d.nd = 2
dt_sub = c2d.dt_sub = float(old_div(dt,substeps))
Krot = 200000.
Crot = 2000.
c2d.Krot, c2d.Crot = Krot, Crot
c2d.substeps, c2d.dt, c2d.ang_acc = substeps, dt, c2d.getAngularAcceleration()
c2d.setFriction(friction=True, m_static=0.0, m_dynamic=0.0, tolerance=0.000001, grainSize=0.02)
rotation, last_rotation = c2d.Shape.coords_system, c2d.Shape.coords_system
ang_vel, last_ang_vel = np.array([0., 0., 0.]), np.array([0., 0., 0.])
F = Fx, Fy, Fz = np.array([200., -300., 0.0])
M = np.array([0., 0., 10.0])
init_barycenter, last_position = pos, pos
c2d.F, c2d.M, c2d.init_barycenter, c2d.last_position = F, M, init_barycenter, last_position
eps = 10.**-30
mass = c2d.mass = 50.0
# moment and inertia transformations
pivot = c2d.pivot_friction = np.array([(caisson.vertices[0][0]+caisson.vertices[1][0])*0.5, caisson.vertices[0][1], 0.0])
barycenter = caisson.barycenter
distance = dx, dy, dz = pivot - barycenter
Mpivot = np.array([0., 0., dx*Fy-dy*Fx]) # Moment calculated in pivot
Mp = M - Mpivot # Moment transformation through the new pivot
Ix = (old_div((dim[0]**2),12.)) + dy**2
Iy = (old_div((dim[1]**2),12.)) + dx**2
It = Ix + Iy
I = It*mass
c2d.springs = True
# runge-kutta calculation
c2d.scheme = 'Runge_Kutta'
rz0, vrz0 = atan2(last_rotation[0,1], last_rotation[0,0]), last_ang_vel[2]
arz0 = old_div((Mp[2] - Crot*vrz0 - Krot*rz0), I)
rz, vrz, arz = bd.runge_kutta(rz0, vrz0, arz0, dt_sub, substeps, Mp[2], Krot, Crot, I, False)
# calculation with bodydynamics mopdule
c2d.cV_init = c2d.cV = c2d.cV_last = caisson.vertices
c2d.inertia = c2d.getInertia(pivot=pivot)
c2d.overturning_module(dt)
# test
ang_disp = rz - rz0
npt.assert_equal(c2d.ang_disp[2], ang_disp)
npt.assert_equal(c2d.ang_vel[2], vrz)
npt.assert_equal(c2d.ang_acc[2], arz)
def get_domain_one_box(x0=(0.0, 0.0, 0.0), L=(1.0, 1.0, 1.0), he=0.001):
boundaries = ['left', 'right', 'bottom', 'top', 'front', 'back']
boundaryTags = dict([(key, i + 1) for (i, key) in enumerate(boundaries)])
x1 = (x0[0] + L[0], x0[1] + L[1], x0[2] + L[2])
vertices = [(x0[0], x0[1], x0[2]), (x1[0], x0[1], x0[2]),
(x1[0], x1[1], x0[2]), (x0[0], x1[1], x0[2]),
(x0[0], x0[1], x1[2]), (x1[0], x0[1], x1[2]),
(x1[0], x1[1], x1[2]), (x0[0], x1[1], x1[2])]
vertexFlags = [
boundaryTags['bottom'],
boundaryTags['bottom'],
boundaryTags['top'],
boundaryTags['top'],
boundaryTags['bottom'],
boundaryTags['bottom'],
boundaryTags['top'],
boundaryTags['top'],
]
planes = []
planeFlags = []
planeHolds = []
planes.extend([[
[0, 1, 2, 3],
], [
[4, 5, 6, 7],
], [[0, 3, 7, 4]], [[1, 2, 6, 5]], [[0, 1, 5, 4]], [[2, 3, 7, 6]]])
planeFlags.extend([
boundaryTags['back'],
boundaryTags['front'],
boundaryTags['left'],
boundaryTags['right'],
boundaryTags['bottom'],
boundaryTags['top'],
])
planeHolds.extend([[], [], [], [], [], []])
regions = [
[0.5 * (x0[0] + x1[0]), 0.5 * (x0[1] + x1[1]), 0.5 * (x0[2] + x1[2])],
]
regionFlags = [
1,
]
regionConstraints = [0.5 * he**2]
domain = Domain.PiecewiseLinearComplexDomain(
vertices=vertices,
facets=planes,
facetFlags=planeFlags,
facetHoles=planeHolds,
regions=regions,
regionFlags=regionFlags,
regionConstraints=regionConstraints)
return domain, boundaryTags, x0, x1
def boxInTank3d(L=[1.0, 1.0, 1.0], box_xy=[0.25, 0.25], box_L=[0.5, 0.5, 0.5]):
boundaries = [
'left', 'right', 'bottom', 'top', 'front', 'back', 'obstacle'
]
boundaryTags = dict([(key, i + 1) for (i, key) in enumerate(boundaries)])
holes = [[
0.5 * box_L[0] + box_xy[0], 0.5 * box_L[1] + box_xy[1], 0.5 * box_L[2]
]]
vertices = [
[0.0, 0.0, 0.0], #0
[L[0], 0.0, 0.0], #1
[L[0], L[1], 0.0], #2
[0.0, L[1], 0.0], #3
[0.0, 0.0, L[2]], #4
[L[0], 0.0, L[2]], #5
[L[0], L[1], L[2]], #6
[0.0, L[1], L[2]], #7
[box_xy[0], box_xy[1], 0.0], #8
[box_xy[0] + box_L[0], box_xy[1], 0.0], #9
[box_xy[0] + box_L[0], box_xy[1] + box_L[1], 0.0], #10
[box_xy[0], box_xy[1] + box_L[1], 0.0], #11
[box_xy[0], box_xy[1], box_L[2]], #12
[box_xy[0] + box_L[0], box_xy[1], box_L[2]], #13
[box_xy[0] + box_L[0], box_xy[1] + box_L[1], box_L[2]], #14
[box_xy[0], box_xy[1] + box_L[1], box_L[2]]
] #15
vertexFlags = [
boundaryTags['left'], boundaryTags['right'], boundaryTags['right'],
boundaryTags['left'], boundaryTags['left'], boundaryTags['right'],
boundaryTags['right'], boundaryTags['left'], boundaryTags['obstacle'],
boundaryTags['obstacle'], boundaryTags['obstacle'],
boundaryTags['obstacle'], boundaryTags['obstacle'],
boundaryTags['obstacle'], boundaryTags['obstacle'],
boundaryTags['obstacle']
]
facets = [[[0, 1, 2, 3], [8, 9, 10, 11]], [[0, 1, 5, 4]], [[1, 2, 6, 5]],
[[2, 3, 7, 6]], [[3, 0, 4, 7]], [[4, 5, 6, 7]], [[8, 9, 13, 12]],
[[9, 10, 14, 13]], [[10, 11, 15, 14]], [[11, 8, 12, 15]],
[[12, 13, 14, 15]]]
facetFlags = [
boundaryTags['bottom'], boundaryTags['front'], boundaryTags['right'],
boundaryTags['back'], boundaryTags['left'], boundaryTags['top'],
boundaryTags['obstacle'], boundaryTags['obstacle'],
boundaryTags['obstacle'], boundaryTags['obstacle'],
boundaryTags['obstacle']
]
domain = Domain.PiecewiseLinearComplexDomain(vertices=vertices,
vertexFlags=vertexFlags,
facets=facets,
facetFlags=facetFlags,
holes=holes)
#go ahead and add a boundary tags member
domain.boundaryTags = boundaryTags
return domain
def cylinder2d(height=1.0,
length=1.0,
radius=0.25,
center=[0.5, 0.5],
n_points_on_obstacle=10,
cross_section=circular_cross_section):
#enumerate the boundaries so we can supply integer flags for vertices and segments
boundaries = ['upstream', 'downstream', 'bottom', 'top', 'obstacle']
boundaryTags = dict([(key, i + 1) for (i, key) in enumerate(boundaries)])
#now work around the domain from (0.0,0.0) going counterclockwise building vertices and segments (and flags)
vertices = [[0.0, 0.0], [length, 0.0], [length, height], [0.0, height]]
vertexFlags = [
boundaryTags['bottom'], boundaryTags['bottom'], boundaryTags['top'],
boundaryTags['top']
]
segments = [[0, 1], [1, 2], [2, 3], [3, 0]]
segmentFlags = [
boundaryTags['bottom'], boundaryTags['downstream'],
boundaryTags['top'], boundaryTags['upstream']
]
#now do the vertices and segments on the cylinder
theta = 0.0
pb = cross_section(center, radius, theta)
vertices.append([pb[0], pb[1]])
vertexFlags.append(boundaryTags['obstacle'])
for gb in range(1, n_points_on_obstacle):
theta = float(gb) / float(n_points_on_obstacle) * 2.0 * math.pi
pb = cross_section(center, radius, theta)
vertices.append([pb[0], pb[1]])
vertexFlags.append(boundaryTags['obstacle'])
nv = len(vertices)
segments.append((nv - 2, nv - 1))
segmentFlags.append(boundaryTags['obstacle'])
segments.append((nv - 1, nv - n_points_on_obstacle))
segmentFlags.append(boundaryTags['obstacle'])
#done with vertices and segments
#holes
holes = [center]
#regions (just pick a point inside to indicate the flow region)
regions = [[
vertices[0][0] + length * 1.0e-8, vertices[0][1] + length * 1.0e-8
]]
regionFlags = [1]
#construct domain object
domain = Domain.PlanarStraightLineGraphDomain(vertices=vertices,
vertexFlags=vertexFlags,
segments=segments,
segmentFlags=segmentFlags,
holes=holes,
regions=regions,
regionFlags=regionFlags)
#go ahead and add a boundary tags member
domain.boundaryTags = boundaryTags
return domain
def testStoreLastValues(self):
from proteus import Domain
from proteus.mprans import SpatialTools as st
from proteus.mprans import BodyDynamics as bd
domain = Domain.PlanarStraightLineGraphDomain()
pos = np.array([1.0, 1.0, 0.0])
rot = np.array([ [1.,0.,0.], [0.,1.,0.], [0.,0.,1.] ])
dim=(0.3, 0.385)
caisson = st.Rectangle(domain, dim=dim, coords=[pos[0], pos[1]])
caisson2D = bd.RigidBody(shape=caisson)
st.assembleDomain(domain)
c2d = caisson2D
nd = 2
anglez = radians(5.0)
rotz = np.array([ [ cos(anglez), sin(anglez), 0.0 ],
[ -sin(anglez), cos(anglez), 0.0 ],
[ 0.0, 0.0, 1.0 ] ])
c2d.calculate_init()
# Imposing values on rigid body's parameters
c2d.position = np.array([2.0, 3.0, 0.0])
c2d.velocity = np.array([0.5, -0.3, 0.0])
c2d.acceleration = np.array([0.1, 0.2, 0.0])
c2d.rotation = rotz
c2d.rotation_euler = bd.getEulerAngles(rotz)
c2d.ang_disp = np.array([0.0, 0.0, 0.001])
c2d.ang_vel = np.array([0.0, 0.0, -0.003])
c2d.ang_acc = np.array([0.0, 0.0, 0.005])
c2d.F = np.array([100.0, -300.0, 0.0])
c2d.M = np.array([0.0, 0.0, 50.0])
c2d.pivot = c2d.barycenter
c2d.ux = 0.5
c2d.uy = 0.05
c2d.uz = 0.0
c2d._store_last_values()
npt.assert_equal(c2d.position, c2d.last_position)
npt.assert_equal(c2d.velocity, c2d.last_velocity)
npt.assert_equal(c2d.acceleration, c2d.last_acceleration)
npt.assert_equal(c2d.rotation, c2d.last_rotation)
npt.assert_equal(c2d.rotation_euler, c2d.last_rotation_euler)
npt.assert_equal(c2d.ang_disp, c2d.last_ang_disp)
npt.assert_equal(c2d.ang_vel, c2d.last_ang_vel)
npt.assert_equal(c2d.ang_acc, c2d.last_ang_acc)
npt.assert_equal(c2d.F, c2d.last_F)
npt.assert_equal(c2d.M, c2d.last_M)
npt.assert_equal(c2d.pivot, c2d.last_pivot)
npt.assert_equal(c2d.ux, c2d.last_ux)
npt.assert_equal(c2d.uy, c2d.last_uy)
npt.assert_equal(c2d.uz, c2d.last_uz)
def gl_5_3d(width, h):
"""
A 3d levee profile for the sacramento levee modeling
"""
boundaryLegend = {
'left': 1,
'right': 2,
'front': 3,
'back': 4,
'bottom': 5,
'top': 6
}
vertices_front = [
[0.0, 0.0, 0.0], #0
[0.0, 0.0, h], #1
[1.2 * h, 0.0, h], #2
[3.2 * h, 0.0, 0.0]
] #3
vertexFlags_front = [
boundaryLegend['left'], boundaryLegend['left'], boundaryLegend['top'],
boundaryLegend['top']
]
vertices_back = [[v[0], width, v[2]] for v in vertices_front]
vertexFlags_back = vertexFlags_front
vertices = vertices_front + vertices_back
vertexFlags = vertexFlags_front + vertexFlags_back
facets = [
[[0, 1, 2, 3]], #front
[[4, 5, 6, 7]], #back
[[0, 1, 5, 4]], #left
[[3, 2, 6, 7]], #right
[[0, 4, 7, 3]], #bottom
[[1, 5, 6, 2]]
] #top
facetFlags = [
boundaryLegend['front'], boundaryLegend['back'],
boundaryLegend['left'], boundaryLegend['top'],
boundaryLegend['bottom'], boundaryLegend['top']
]
regions = [[h, width / 2.0, h]]
regionFlags = [1]
print vertices, vertexFlags, facets, facetFlags, regions, regionFlags
domain = Domain.PiecewiseLinearComplexDomain(vertices=vertices,
vertexFlags=vertexFlags,
facets=facets,
facetFlags=facetFlags,
regions=regions,
regionFlags=regionFlags)
domain.boundaryFlags = boundaryLegend
domain.regionLegend = {'levee': 1, 'default': 0}
return domain
def build_PSLG():
"""
build PlanarStraightLineGraph and return
"""
from proteus import Domain
v, s, vf, sf, btags = build_vertices_and_segments()
domain = Domain.PlanarStraightLineGraphDomain(vertices=v,
segments=s,
vertexFlags=vf,
segmentFlags=sf)
domain.boundaryTags = btags
return domain
def testStep(self):
from proteus import Domain
from proteus import SpatialTools as st
from proteus.mprans import SpatialTools as mst
from proteus.mprans import BodyDynamics as bd
# parameters
domain2D = Domain.PlanarStraightLineGraphDomain()
pos = np.array([1.0, 1.0, 0.0])
dim = (0.3, 0.385)
caisson = mst.Rectangle(domain=domain2D,
dim=dim,
coords=[pos[0], pos[1]])
caisson2D = bd.RigidBody(shape=caisson)
mst.assembleDomain(domain2D)
c2d = caisson2D
nd = c2d.nd = 2
Ix = ((dim[0]**2) / 12.)
Iy = ((dim[1]**2) / 12.)
It = Ix + Iy
mass = 50.0
I = mass * It
c2d.mass, c2d.It = mass, It
init_barycenter, last_position, last_velocity, last_rotation, last_ang_vel = pos, pos * 2.0, np.array(
[0.05, 0.07,
0.0]), np.array([0.0, 0.0, 0.0001]), np.array([0., 0., 0.0000002])
c2d.init_barycenter, c2d.last_position, c2d.last_velocity, c2d.last_rotation, c2d.last_ang_vel = init_barycenter, last_position, last_velocity, last_rotation, last_ang_vel
F = Fx, Fy, Fz = np.array([200., 300., 0.0])
M = Mx, My, Mz = np.array([0., 0., 50.0])
dt, substeps = 0.001, 20
dt_sub = c2d.dt_sub = float(dt / substeps)
c2d.F, c2d.substeps, c2d.dt, c2d.acceleration = F, substeps, dt, c2d.getAcceleration(
)
c2d.InputMotion = False
c2d.scheme = 'Forward_Euler'
h, tra_velocity = bd.forward_euler(last_position, last_velocity,
F / mass, dt)
rot, rot_velocity = bd.forward_euler(last_rotation, last_ang_vel,
M / I, dt)
if rot[2] < 0.0: rot[2] = -rot[2]
# 2d calculation
caisson.translate(h[:nd]), caisson.rotate(rot[2])
posTra1, rot1 = caisson.barycenter, caisson.coords_system
# 2d from bodydynamics
caisson.translate(-h[:nd]), caisson.rotate(-rot[2])
c2d.step(dt)
posTra2, rot2 = c2d.position, c2d.rotation[:nd, :nd]
npt.assert_allclose(posTra1, posTra2, atol=1e-10)
npt.assert_allclose(rot1, rot2, atol=1e-10)
def testGetDisplacement(self):
from proteus import Domain
from proteus import SpatialTools as st
from proteus.mprans import SpatialTools as mst
from proteus.mprans import BodyDynamics as bd
# parameters
domain2D = Domain.PlanarStraightLineGraphDomain()
pos = np.array([1.0, 1.0, 0.0])
dim = (0.3, 0.385)
caisson = mst.Rectangle(domain=domain2D,
dim=dim,
coords=[pos[0], pos[1]])
caisson2D = bd.RigidBody(shape=caisson)
mst.assembleDomain(domain2D)
c2d = caisson2D
c2d.nd = 2
Ix = ((dim[0]**2) / 12.)
Iy = ((dim[1]**2) / 12.)
It = Ix + Iy
mass = 50.0
c2d.mass, c2d.It = mass, It
Kx, Ky, Kz = K = [200000., 250000., 0.0]
Cx, Cy, Cz = C = [2000., 4000., 0.0]
c2d.Kx, c2d.Ky, c2d.Kz, c2d.Cx, c2d.Cy, c2d.Cz = Kx, Ky, Kz, Cx, Cy, Cz
init_barycenter, last_position, last_velocity = pos, pos * 2.0, np.array(
[0.05, 0.07, 0.0])
c2d.init_barycenter, c2d.last_position, c2d.last_velocity = init_barycenter, last_position, last_velocity
Fx, Fy, Fz = F = np.array([200., 300., 0.0])
dt, substeps = 0.001, 50
dt_sub = c2d.dt_sub = float(dt / substeps)
c2d.F, c2d.substeps, c2d.dt, c2d.acceleration = F, substeps, dt, c2d.getAcceleration(
)
# runge-kutta calculation
c2d.scheme = 'Runge_Kutta'
u0 = ux0, uy0, uz0 = last_position - init_barycenter
v0 = vx0, vy0, vz0 = last_velocity
a0 = ax0, ay0, az0 = (F - C * v0 - K * u0) / mass
for ii in range(substeps):
ux, vx, ax = bd.runge_kutta(ux0, vx0, ax0, dt_sub, substeps, Fx,
Kx, Cx, mass, False)
uy, vy, ay = bd.runge_kutta(uy0, vy0, ay0, dt_sub, substeps, Fy,
Ky, Cy, mass, False)
uz, vz, az = bd.runge_kutta(uz0, vz0, az0, dt_sub, substeps, Fz,
Kz, Cz, mass, False)
h = hx, hy, hz = [ux - ux0, uy - uy0, uz - uz0]
c2d.h = c2d.getDisplacement(dt)
npt.assert_equal(c2d.h, h)
def test_gmsh_generation_2D(self):
domain = Domain.PlanarStraightLineGraphDomain()
domain.vertices = [[0., 0., 0.], [5., 0., 0.], [5., 5., 0.],
[0., 5., 0.]]
domain.segments = [[0, 1], [1, 2], [2, 3], [3, 0]]
domain.facets = [[[0, 1, 2, 3]]]
domain.writeGeo('gmsh_mesh_test_2D', he_max=0.1)
gmsh_cmd = "gmsh {0:s} -v 10 -2 -o {1:s} -format msh".format(
domain.geofile + ".geo", domain.geofile + ".msh")
check_call(gmsh_cmd, shell=True)
MeshTools.msh2simplex(domain.geofile, nd=2)
with open('gmsh_mesh_test_2D.node', 'r') as nodefile:
npt.assert_equal(nodefile.readline(), '3425 2 0 1\n')
with open('gmsh_mesh_test_2D.edge', 'r') as edgefile:
npt.assert_equal(edgefile.readline(), '10072 1\n')
with open('gmsh_mesh_test_2D.ele', 'r') as elefile:
npt.assert_equal(elefile.readline(), '6648 3 1\n')
def test_parallelLoadPUMI(verbose=0):
"""Test to load parallel PUMI model and mesh"""
comm = Comm.init()
eq(comm.size(),2)
testDir=os.path.dirname(os.path.abspath(__file__))
domain = Domain.PUMIDomain()
Model=testDir+ '/Prism.dmg'
Mesh=testDir + '/Prism.smb'
domain.PUMIMesh=MeshAdaptPUMI.MeshAdaptPUMI()
domain.PUMIMesh.loadModelAndMesh(Model, Mesh)
mesh = MeshTools.TetrahedralMesh()
mesh.cmesh = cmeshTools.CMesh()
mesh.convertFromPUMI(domain.PUMIMesh, domain.faceList, parallel = comm.size() > 1, dim = domain.nd)
eq(mesh.nElements_global,8148)
eq(mesh.nNodes_global,1880)
eq(mesh.nEdges_global,11001)
eq(mesh.nElementBoundaries_global,17270)
def beachBakhtyar3d(L=[8.5, 1.0, 0.8], Lb=3.5):
boundaries = [
'left', 'right', 'bottom', 'top', 'front', 'back', 'obstacle'
]
boundaryTags = dict([(key, i + 1) for (i, key) in enumerate(boundaries)])
vertices = [
[0.0, 0.0, 0.0], #0
[Lb, 0.0, 0.0], #1
[L[0], 0.0, 0.5], #2
[L[0], 0.0, L[2]], #3
[0.0, 0.0, L[2]], #4
[0.0, L[1], 0.0], #5
[Lb, L[1], 0.0], #6
[L[0], L[1], 0.5], #7
[L[0], L[1], L[2]], #8
[0.0, L[1], L[2]]
] #9
vertexFlags = [
boundaryTags['left'], #0
boundaryTags['bottom'], #1
boundaryTags['right'], #2
boundaryTags['right'], #3
boundaryTags['left'], #4
boundaryTags['left'], #5
boundaryTags['bottom'], #6
boundaryTags['right'], #7
boundaryTags['right'], #8
boundaryTags['left']
] #9
facets = [[[0, 1, 2, 3, 4]], [[0, 4, 9, 5]], [[2, 3, 8, 7]], [[3, 4, 9,
8]],
[[0, 1, 6, 5]], [[1, 2, 7, 6]], [[5, 6, 7, 8, 9]]]
facetFlags = [
boundaryTags['front'], boundaryTags['left'], boundaryTags['right'],
boundaryTags['top'], boundaryTags['bottom'], boundaryTags['bottom'],
boundaryTags['back']
]
domain = Domain.PiecewiseLinearComplexDomain(vertices=vertices,
vertexFlags=vertexFlags,
facets=facets,
facetFlags=facetFlags)
#go ahead and add a boundary tags member
domain.boundaryTags = boundaryTags
return domain
def gauge_setup(nd, total_nodes=None):
comm = Comm.get()
#Simplified Physics
p.name = "test_gauges"
p.nd = nd
class LinearSolution(object):
def uOfXT(self, x, t):
return (x[0] + 10 * x[1] + 100 * x[2]) * (t + 1.0)
p.initialConditions = {0: LinearSolution()}
p.dirichletConditions = {0: lambda x, flag: None}
p.domain = Domain.RectangularDomain(name="test_gauges_domain")
p.coefficients = TransportCoefficients.PoissonEquationCoefficients(
aOfX=[lambda x: np.eye(p.nd, p.nd)], fOfX=[lambda x: 0], nc=1, nd=p.nd)
#Simplified and Incomplete Numerics
n.femSpaces = {0: FemTools.C0_AffineLinearOnSimplexWithNodalBasis}
n.elementQuadrature = Quadrature.SimplexGaussQuadrature(p.nd, 3)
n.elementBoundaryQuadrature = Quadrature.SimplexGaussQuadrature(
p.nd - 1, 3)
n.numericalFluxType = NumericalFlux.NoFlux
n.cfluxtag = None
n.conservativeFlux = None
if total_nodes is None:
total_nodes = 2 * comm.size()
if p.nd == 1:
mlMesh = build1DMesh(p, total_nodes + 1)
elif p.nd == 2:
nnx = nny = int(ceil(sqrt(total_nodes))) + 1
mlMesh = build2DMesh(p, nnx, nny)
elif p.nd == 3:
nnx = nny = nnz = int(ceil(pow(total_nodes, old_div(1.0, 3.0)))) + 1
mlMesh = build3DMesh(p, nnx, nny, nnz)
model = Transport.MultilevelTransport(p, n, mlMesh)
return model, p.initialConditions
def test_2DparallelLoadPUMI(verbose=0):
"""Test to load 2D parallel PUMI model and mesh"""
comm = Comm.init()
eq(comm.size(), 2)
testDir = os.path.dirname(os.path.abspath(__file__))
domain = Domain.PUMIDomain(dim=2)
Model = testDir + '/Rectangle.dmg'
Mesh = testDir + '/Rectangle.smb'
domain.PUMIMesh = MeshAdaptPUMI.MeshAdaptPUMI()
domain.PUMIMesh.loadModelAndMesh(Model, Mesh)
mesh = MeshTools.TriangularMesh()
mesh.cmesh = cmeshTools.CMesh()
mesh.convertFromPUMI(domain.PUMIMesh,
domain.faceList,
domain.regList,
parallel=comm.size() > 1,
dim=domain.nd)
eq(mesh.nElements_global, 8)
eq(mesh.nNodes_global, 10)
eq(mesh.nEdges_global, 17)
eq(mesh.nElementBoundaries_global, 17)
def testGetAngularAcceleration(self):
from proteus import Domain
from proteus.mprans import SpatialTools as st
from proteus.mprans import BodyDynamics as bd
domain = Domain.PlanarStraightLineGraphDomain()
pos = np.array([1.0, 1.0, 0.0])
rot = np.array([ [1.,0.,0.], [0.,1.,0.], [0.,0.,1.] ])
dim=(0.3, 0.385)
caisson = st.Rectangle(domain, dim=dim, coords=[pos[0], pos[1]])
caisson2D = bd.RigidBody(shape=caisson)
st.assembleDomain(domain)
c2d = caisson2D
F = np.array([100.0, -200.0, 10.0])
mass = 150.0
acceleration = old_div(F,mass)
c2d.F = F
c2d.mass = mass
c2d.acceleration = c2d.getAcceleration()
npt.assert_equal(c2d.acceleration, acceleration)
def test_2DmultiRegion(verbose=0):
"""Test for loading gmsh mesh through PUMI with multiple-regions"""
testDir = os.path.dirname(os.path.abspath(__file__))
Model = testDir + '/TwoQuads.dmg'
Mesh = testDir + '/TwoQuads.smb'
domain = Domain.PUMIDomain(dim=2) #initialize the domain
domain.PUMIMesh = MeshAdaptPUMI.MeshAdaptPUMI()
domain.PUMIMesh.loadModelAndMesh(Model, Mesh)
domain.faceList = [[14], [12], [11], [13], [15], [16]]
domain.regList = [[41], [42]]
mesh = MeshTools.TriangularMesh()
mesh.cmesh = cmeshTools.CMesh()
comm = Comm.init()
mesh.convertFromPUMI(domain.PUMIMesh,
domain.faceList,
domain.regList,
parallel=comm.size() > 1,
dim=domain.nd)
ok(mesh.elementMaterialTypes[0] == 1)
ok(mesh.elementMaterialTypes[-1] == 2)
def testCalculateInit(self):
from proteus import Domain
from proteus.mprans import SpatialTools as st
from proteus.mprans import BodyDynamics as bd
domain = Domain.PlanarStraightLineGraphDomain()
pos = np.array([1.0, 1.0, 0.0])
rot = np.array([ [1.,0.,0.], [0.,1.,0.], [0.,0.,1.] ])
dim=(0.3, 0.385)
caisson = st.Rectangle(domain, dim=dim, coords=[pos[0], pos[1]])
caisson2D = bd.RigidBody(shape=caisson)
st.assembleDomain(domain)
c2d = caisson2D
nd = 2
angle = bd.getEulerAngles(rot)
c2d.calculate_init()
npt.assert_equal(c2d.position, pos)
npt.assert_equal(c2d.last_position, pos)
npt.assert_equal(c2d.rotation, rot)
npt.assert_equal(c2d.last_rotation, rot)
npt.assert_equal(c2d.rotation_euler, angle)
npt.assert_equal(c2d.last_rotation_euler, angle)
def tank3d(L=[1.0, 1.0, 1.0]):
boundaries = [
'left', 'right', 'bottom', 'top', 'front', 'back', 'obstacle'
]
boundaryTags = dict([(key, i + 1) for (i, key) in enumerate(boundaries)])
vertices = [
[0.0, 0.0, 0.0], #0
[L[0], 0.0, 0.0], #1
[L[0], L[1], 0.0], #2
[0.0, L[1], 0.0], #3
[0.0, 0.0, L[2]], #4
[L[0], 0.0, L[2]], #5
[L[0], L[1], L[2]], #6
[0.0, L[1], L[2]]
] #7
vertexFlags = [
boundaryTags['left'], boundaryTags['right'], boundaryTags['right'],
boundaryTags['left'], boundaryTags['left'], boundaryTags['right'],
boundaryTags['right'], boundaryTags['left']
]
facets = [[[0, 1, 2, 3]], [[0, 1, 5, 4]], [[1, 2, 6, 5]], [[2, 3, 7, 6]],
[[3, 0, 4, 7]], [[4, 5, 6, 7]]]
facetFlags = [
boundaryTags['bottom'], boundaryTags['front'], boundaryTags['right'],
boundaryTags['back'], boundaryTags['left'], boundaryTags['top']
]
regions = [[0.5 * L[0], 0.5 * L[1], 0.5 * L[2]]]
regionFlags = [1.0]
domain = Domain.PiecewiseLinearComplexDomain(vertices=vertices,
vertexFlags=vertexFlags,
facets=facets,
facetFlags=facetFlags,
regions=regions,
regionFlags=regionFlags)
#go ahead and add a boundary tags member
domain.boundaryTags = boundaryTags
return domain
def test_poiseuilleError(verbose=0):
"""Test for loading gmsh mesh through PUMI, estimating error for
a Poiseuille flow case. The estimated error should be larger than the
exact error in the seminorm"""
testDir = os.path.dirname(os.path.abspath(__file__))
Model = testDir + '/Couette.null'
Mesh = testDir + '/Couette.msh'
domain = Domain.PUMIDomain() #initialize the domain
domain.PUMIMesh = MeshAdaptPUMI.MeshAdaptPUMI(hmax=0.01,
hmin=0.008,
numIter=1,
sfConfig='ERM',
maType='isotropic',
logType='off')
domain.PUMIMesh.loadModelAndMesh(Model, Mesh)
domain.faceList = [[80], [76], [42], [24], [82], [78]]
mesh = MeshTools.TetrahedralMesh()
mesh.cmesh = cmeshTools.CMesh()
comm = Comm.init()
nElements_initial = mesh.nElements_global
mesh.convertFromPUMI(domain.PUMIMesh,
domain.faceList,
domain.regList,
parallel=comm.size() > 1,
dim=domain.nd)
domain.PUMIMesh.transferFieldToPUMI("coordinates", mesh.nodeArray)
rho = numpy.array([998.2, 998.2])
nu = numpy.array([1.004e-6, 1.004e-6])
g = numpy.asarray([0.0, 0.0, 0.0])
deltaT = 1.0 #dummy number
domain.PUMIMesh.transferPropertiesToPUMI(rho, nu, g, deltaT)
#Poiseuille Flow
Ly = 0.2
Lz = 0.05
Re = 100
Umax = Re * nu[0] / Lz
def vOfX(x):
return 4 * Umax / (Lz**2) * (x[2]) * (Lz - x[2])
def dvOfXdz(x):
return 4 * Umax / (Lz**2) * (Lz - 2 * x[2])
#hard code solution
vector = numpy.zeros((mesh.nNodes_global, 3), 'd')
dummy = numpy.zeros(mesh.nNodes_global)
vector[:, 0] = dummy
vector[:, 1] = 4 * Umax / (Lz**2) * (mesh.nodeArray[:, 2]) * (
Lz - mesh.nodeArray[:, 2]) #v-velocity
vector[:, 2] = dummy
domain.PUMIMesh.transferFieldToPUMI("velocity", vector)
scalar = numpy.zeros((mesh.nNodes_global, 1), 'd')
domain.PUMIMesh.transferFieldToPUMI("p", scalar)
scalar[:, 0] = mesh.nodeArray[:, 2]
domain.PUMIMesh.transferFieldToPUMI("phi", scalar)
del scalar
scalar = numpy.zeros((mesh.nNodes_global, 1), 'd') + 1.0
domain.PUMIMesh.transferFieldToPUMI("vof", scalar)
errorTotal = domain.PUMIMesh.get_local_error()
# load the femspace with linear basis and get the quadrature points on a reference element
elementQuadrature = Quadrature.SimplexGaussQuadrature(domain.nd, 3)
ok(mesh.nNodes_element == 4) #confirm all of the elements have 4 nodes
#hard code computation for H1 seminorm; ideally will be reformatted using the classes within proteus
derivativeArrayRef = [[1, 0, 0], [0, 1, 0], [0, 0, 1], [-1, -1, -1]]
error = 0
for eID in range(mesh.nElements_global):
nodes = mesh.elementNodesArray[eID]
coords = []
for i in range(mesh.nNodes_element):
coords.append(mesh.nodeArray[nodes[i]])
J = numpy.matrix([[
coords[0][0] - coords[3][0], coords[1][0] - coords[3][0],
coords[2][0] - coords[3][0]
],
[
coords[0][1] - coords[3][1],
coords[1][1] - coords[3][1],
coords[2][1] - coords[3][1]
],
[
coords[0][2] - coords[3][2],
coords[1][2] - coords[3][2],
coords[2][2] - coords[3][2]
]])
invJ = J.I
detJ = numpy.linalg.det(J)
gradPhi_h = 0
for k in range(len(elementQuadrature.points)):
tempQpt = 0
zCoord = elementQuadrature.points[k][0]*coords[0][2] \
+elementQuadrature.points[k][1]*coords[1][2] \
+elementQuadrature.points[k][2]*coords[2][2] \
+(1-elementQuadrature.points[k][0]-elementQuadrature.points[k][1]-elementQuadrature.points[k][2])*coords[3][2]
for i in range(mesh.nNodes_element):
temp = 0
for j in range(domain.nd):
temp = temp + derivativeArrayRef[i][j] * invJ[j, 2]
tempQpt = tempQpt + vector[nodes[i]][1] * temp
exactgradPhi = dvOfXdz([0, 0, zCoord])
gradPhi_h = gradPhi_h + tempQpt
error = error + (exactgradPhi - gradPhi_h
)**2 * elementQuadrature.weights[k] * abs(detJ)
error = sqrt(error)
ok(error < errorTotal)
parallelPartitioningType = proteus.MeshTools.MeshParallelPartitioningTypes.node
nLayersOfOverlapForParallel = 0
use_petsc4py=True#False
if useHex:
hex=True
comm=Comm.get()
if comm.isMaster():
size = numpy.array([[0.520,0.510 ,0.520],
[0.330,0.335833,0.330],
[0.320,0.325 ,0.000]])/float(Refinement)
numpy.savetxt('size.mesh', size)
failed = os.system("../../scripts/marinHexMesh")
domain = Domain.MeshHexDomain("marinHex")
else:
L = [3.22,1.0,1.0]
box_L = [0.161,0.403,0.161]
box_xy = [2.3955,0.2985]
#he = L[0]/float(6.5*Refinement)
he = L[0]/64.0
he*=0.5#256
boundaries=['left','right','bottom','top','front','back','box_left','box_right','box_top','box_front','box_back',]
boundaryTags=dict([(key,i+1) for (i,key) in enumerate(boundaries)])
bt = boundaryTags
holes = [[0.5*box_L[0]+box_xy[0],0.5*box_L[1]+box_xy[1],0.5*box_L[2]]]
vertices=[[0.0,0.0,0.0],#0
[L[0],0.0,0.0],#1
[L[0],L[1],0.0],#2
[0.0,L[1],0.0],#3
rho_0 = 998.2
nu_0 = 1.004e-6
# Air
rho_1 = 1.205
nu_1 = 1.500e-5
g = [0., -9.81, 0.]
# ****************** #
# ***** GAUGES ***** #
# ****************** #
# *************************** #
# ***** DOMAIN AND MESH ***** #
# ****************** #******* #
domain = Domain.PlanarStraightLineGraphDomain()
# ----- TANK ----- #
boundaryOrientations = {
'y-': np.array([0., -1., 0.]),
'x+': np.array([+1., 0., 0.]),
'y+': np.array([0., +1., 0.]),
'x-': np.array([-1., 0., 0.]),
'airvent': np.array([-1., 0., 0.]),
}
boundaryTags = {
'y-': 1,
'x+': 2,
'y+': 3,
'x-': 4,
'airvent': 5,
he = L[0]/float(4*Refinement-1)
#he*=0.5
#he*=0.5
#he*=0.5
#he*=0.5
weak_bc_penalty_constant = 100.0
nLevels = 1
#parallelPartitioningType = proteus.MeshTools.MeshParallelPartitioningTypes.element
parallelPartitioningType = proteus.MeshTools.MeshParallelPartitioningTypes.node
nLayersOfOverlapForParallel = 0
structured=False
if useHex:
nnx=4*Refinement+1
nny=2*Refinement+1
hex=True
domain = Domain.RectangularDomain(L)
else:
boundaries=['left','right','bottom','top','front','back']
boundaryTags=dict([(key,i+1) for (i,key) in enumerate(boundaries)])
if structured:
nnx=4*Refinement
nny=2*Refinement
else:
vertices=[[0.0,0.0],#0
[L[0],0.0],#1
[L[0],L[1]],#2
[0.0,L[1]]]#3
vertexFlags=[boundaryTags['bottom'],
boundaryTags['bottom'],
boundaryTags['top'],
boundaryTags['top']]
def test_2DgmshLoadAndAdapt(verbose=0):
"""Test for loading gmsh mesh through PUMI, estimating error and adapting for
a 2D Couette flow case"""
testDir=os.path.dirname(os.path.abspath(__file__))
Model=testDir + '/Couette2D.null'
Mesh=testDir + '/Couette2D.msh'
domain = Domain.PUMIDomain(dim=2) #initialize the domain
domain.PUMIMesh=MeshAdaptPUMI.MeshAdaptPUMI(hmax=0.01, hmin=0.008, numIter=1,sfConfig=b'ERM',maType=b'isotropic',targetError=1)
domain.PUMIMesh.loadModelAndMesh(bytes(Model,'utf-8'), bytes(Mesh,'utf-8'))
domain.faceList=[[14],[12],[11],[13]]
domain.boundaryLabels=[1,2,3,4]
mesh = MeshTools.TriangularMesh()
mesh.cmesh = cmeshTools.CMesh()
comm = Comm.init()
nElements_initial = mesh.nElements_global
mesh.convertFromPUMI(domain,domain.PUMIMesh, domain.faceList,domain.regList, parallel = comm.size() > 1, dim = domain.nd)
domain.PUMIMesh.transferFieldToPUMI(b"coordinates",mesh.nodeArray)
rho = numpy.array([998.2,998.2])
nu = numpy.array([1.004e-6, 1.004e-6])
g = numpy.asarray([0.0,0.0])
deltaT = 1.0 #dummy number
epsFact = 1.0 #dummy number
domain.PUMIMesh.transferPropertiesToPUMI(rho,nu,g,deltaT,epsFact)
#Couette Flow
Lz = 0.05
Uinf = 2e-3
#hard code solution
vector=numpy.zeros((mesh.nNodes_global,3),'d')
dummy = numpy.zeros(mesh.nNodes_global);
vector[:,0] = Uinf*mesh.nodeArray[:,1]/Lz #v-velocity
vector[:,1] = dummy
vector[:,2] = dummy
domain.PUMIMesh.transferFieldToPUMI(b"velocity", vector)
del vector
del dummy
scalar=numpy.zeros((mesh.nNodes_global,1),'d')
domain.PUMIMesh.transferFieldToPUMI(b"p", scalar)
scalar[:,0] = mesh.nodeArray[:,1]
domain.PUMIMesh.transferFieldToPUMI(b"phi", scalar)
del scalar
scalar = numpy.zeros((mesh.nNodes_global,1),'d')+1.0
domain.PUMIMesh.transferFieldToPUMI(b"vof", scalar)
errorTotal=domain.PUMIMesh.get_local_error()
ok(errorTotal<1e-14)
#ok(domain.PUMIMesh.willAdapt(),1)
domain.PUMIMesh.adaptPUMIMesh()
mesh = MeshTools.TriangularMesh()
mesh.convertFromPUMI(domain,domain.PUMIMesh,
domain.faceList,
domain.regList,
parallel = comm.size() > 1,
dim = domain.nd)
nElements_final = mesh.nElements_global
ok(nElements_final>nElements_initial)
