def generate_mesh(fractures_data, max_el_size, file_name, verbose=0):
r""" Create mesh and write it to a file.
Parameters
----------
fractures_data : list of FractureData
Array of objects defining fractures.
max_el_size : double
Maximal size of mesh element.
file_name : str
File name to write mesh into.
verbose : {0, 1}
If set to 1, messages during mesh generation will be printed.
"""
model = gmsh.model
factory = model.occ
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", verbose)
model.add("test_api")
# set options
gmsh.option.setNumber("Geometry.Tolerance", 0)
gmsh.option.setNumber("Geometry.ToleranceBoolean", 0)
gmsh.option.setNumber("Geometry.MatchMeshTolerance", 0)
gmsh.option.setNumber("Mesh.ToleranceInitialDelaunay", 1e-12)
# Compute mesh element sizes from values given at geometry points, default value: 1
gmsh.option.setNumber("Mesh.CharacteristicLengthFromPoints", 1)
# Automatically compute mesh element sizes from curvature, respects surface curvature, default value: 0
gmsh.option.setNumber("Mesh.CharacteristicLengthFromCurvature", 0)
gmsh.option.setNumber("Mesh.CharacteristicLengthExtendFromBoundary", 0)
# Element size constraint options
# gmsh.option.setNumber("Mesh.CharacteristicLengthMin", max_el_size*0.01)
# gmsh.option.setNumber("Mesh.CharacteristicLengthMax", max_el_size)
# gmsh.option.setNumber("Mesh.MinimumCurvePoints", 5)
# create fractures (currently we ignore r2 and create circular disks)
disks = []
tags = []
for f in fractures_data:
pc = factory.addPoint(f.centre[0], f.centre[1], f.centre[2], f.r1)
axis, angle = f.get_rotation_axis_angle()
p0 = factory.addPoint(f.centre[0] + f.r1, f.centre[1], f.centre[2],
f.r1)
p1 = factory.addPoint(f.centre[0] + f.r1 * cos(pi * 2 / 3),
f.centre[1] + f.r1 * sin(pi * 2 / 3),
f.centre[2], f.r1)
p2 = factory.addPoint(f.centre[0] + f.r1 * cos(pi * 4 / 3),
f.centre[1] + f.r1 * sin(pi * 4 / 3),
f.centre[2], f.r1)
factory.rotate([(0, p0), (0, p1), (0, p2)], f.centre[0], f.centre[1],
f.centre[2], axis[0], axis[1], axis[2], angle)
c1 = factory.addCircleArc(p0, pc, p1)
c2 = factory.addCircleArc(p1, pc, p2)
c3 = factory.addCircleArc(p2, pc, p0)
cl = factory.addCurveLoop([c1, c2, c3])
d = factory.addPlaneSurface([cl])
disks.append((2, d))
tags.append(f.tag)
# fragment fractures
fractures, fractures_map = factory.fragment(disks, [])
print('disks = ', disks)
# List of fracture tuples (dim, tag)
print('fractures = ', fractures)
# List of lists of tuples, each sublist contains fragments (dim, tag) from particular fracture
print('fractures_map = ', fractures_map)
assert len(fractures_map) == len(disks)
# set physical id and name of fractures
fractures_phys_id = model.addPhysicalGroup(2,
[id for dim, id in fractures])
model.setPhysicalName(2, fractures_phys_id, "fractures")
# define 3d volume and embed fractures into it
box = factory.addBox(0, 0, 0, 1, 1, 1)
factory.synchronize()
# Embed the model entities of dimension 'dim', and tags 'tag' in the other model entity which is given by
# dimension (3) and tag (box)
model.mesh.embed(2, [tag for dim, tag in fractures], 3, box)
# define physical id of volume and its boundaries
box_phys_id = model.addPhysicalGroup(3, [box], -1)
model.setPhysicalName(3, box_phys_id, "box")
# box_bdry = model.getBoundary([(3,box)], True)
# box_bdry_left_phys_id = model.addPhysicalGroup(2, [box_bdry[0][1]], -1)
# box_bdry_right_phys_id = model.addPhysicalGroup(2, [box_bdry[1][1]], -1)
# model.setPhysicalName(2, box_bdry_left_phys_id, ".left")
# model.setPhysicalName(2, box_bdry_right_phys_id, ".right")
# Define fields for mesh refinement
# Compute the distance from curves, each curve is replaced by NNodesByEdge equidistant nodes
# and the distance from those nodes is computed.
model.mesh.field.add("Distance", 1)
model.mesh.field.setNumber(1, "NNodesByEdge", 100)
frac_bdry = model.getBoundary(fractures, False, False, False)
# Set the numerical list option "EdgesList" to list of "frac_bdry" tags for field tag 1.
model.mesh.field.setNumbers(1, "EdgesList",
[tag for dm, tag in frac_bdry if dm == 1])
# Threshold
# F = LCMin if Field[IField] <= DistMin,
# F = LCMax if Field[IField] >= DistMax,
# F = interpolation between LcMin and LcMax if DistMin < Field[IField] < DistMax
model.mesh.field.add("Threshold", 2)
# Index of the field to evaluate (in this case 1 is "Distance")
model.mesh.field.setNumber(2, "IField", 1)
# Element size inside DistMin
model.mesh.field.setNumber(2, "LcMin", max_el_size * 0.03)
# Element size outside DistMax
model.mesh.field.setNumber(2, "LcMax", max_el_size)
# Distance from entity up to which element size will be LcMin, it should depend on particular model
model.mesh.field.setNumber(2, "DistMin", 0.001)
# Distance from entity after which element size will be LcMax, it should depend on particular model
model.mesh.field.setNumber(2, "DistMax", 0.5)
# Set threshold as the background mesh size field.
model.mesh.field.setAsBackgroundMesh(2)
# generate mesh, write to file and output number of entities that produced error
factory.synchronize()
gmsh.write(file_name + '.brep')
model.mesh.generate(3)
bad_entities = model.mesh.getLastEntityError()
gmsh.write(file_name)
gmsh.finalize()
return len(bad_entities)
def test_extrude_polygon():
"""
Test extrusion of an polygon.
BUG: Currently failing:
- in this setting (set mesh step directly to nodes of polygon) it generates elements but writes empty mesh
- when setting mesh step by getting boundary inside make_mesh, it fails
"""
gmsh.initialize()
file_name = "extrude_polygon"
gmsh.model.add(file_name)
# plane directional vectors vector
u = np.array([1, 1, 0])
u = u / np.linalg.norm(u)
v = np.array([0, 1, 1])
v = v / np.linalg.norm(v)
#normal
n = np.cross(u, v)
n = n / np.linalg.norm(n)
# add some points in the plane
points = []
points.append(u)
points.append(2 * u + 1 * v)
points.append(5 * u + -2 * v)
points.append(5 * u + 3 * v)
points.append(4 * u + 5 * v)
points.append(-2 * u + 3 * v)
points.append(v)
point_tags = [gmsh.model.occ.addPoint(*p) for p in points]
# point_tags = [gmsh.model.occ.addPoint(*p, meshSize=0.2) for p in points]
lines = [
gmsh.model.occ.addLine(point_tags[i - 1], point_tags[i])
for i in range(len(points))
]
cl = gmsh.model.occ.addCurveLoop(lines)
pol = gmsh.model.occ.addPlaneSurface([cl])
ext_dimtags = gmsh.model.occ.extrude([(2, pol)], *(3 * n))
tube_dimtags = [ext_dimtags[1]]
gmsh.model.occ.synchronize()
nodes = gmsh.model.getBoundary(tube_dimtags,
combined=False,
oriented=False,
recursive=True)
print(nodes)
p_dimtags = [(0, tag) for tag in point_tags]
gmsh.model.occ.mesh.setSize(p_dimtags, size=0.2)
gmsh.model.occ.synchronize()
# generate mesh, write to file and output number of entities that produced error
# gmsh.option.setNumber("Mesh.CharacteristicLengthFromPoints", 0.2)
# gmsh.option.setNumber("Mesh.CharacteristicLengthFromCurvature", 0)
# gmsh.option.setNumber("Mesh.CharacteristicLengthExtendFromBoundary", 1)
# gmsh.option.setNumber("Mesh.CharacteristicLengthMin", 0.1)
# gmsh.option.setNumber("Mesh.CharacteristicLengthMax", 1.0)
gmsh.model.mesh.generate(3)
gmsh.model.mesh.removeDuplicateNodes()
bad_entities = gmsh.model.mesh.getLastEntityError()
print(bad_entities)
# gmsh.fltk.run()
gmsh.write(sandbox_fname(file_name, "msh2"))
gmsh.finalize()
def generate_mesh():
gmsh.initialize()
file_name = "box_wells"
gmsh.model.add(file_name)
box = gmsh.model.occ.addBox(-1000, -1000, -1000, 2000, 2000, 2000)
rec1 = gmsh.model.occ.addRectangle(-800, -800, 0, 1600, 1600)
rec2 = gmsh.model.occ.addRectangle(-1200, -1200, 0, 2400, 2400)
rec1_dt = (2, rec1)
rec2_dt = (2, rec2)
gmsh.model.occ.rotate([rec2_dt], 0, 0, 0, 0, 1, 0, np.pi / 2)
rectangle, map = gmsh.model.occ.fragment([rec1_dt, rec2_dt], [])
box = [(3, box)]
box_copy = gmsh.model.occ.copy(box)
dim_tags, map = gmsh.model.occ.intersect(rectangle, box_copy)
gmsh.model.occ.synchronize()
dim_tags_copy = gmsh.model.occ.copy(dim_tags)
box_copy = gmsh.model.occ.copy(box)
box_cut, map = gmsh.model.occ.fragment(box_copy, dim_tags_copy)
gmsh.model.occ.removeAllDuplicates()
gmsh.model.occ.synchronize()
b = gmsh.model.addPhysicalGroup(3, [tag for dim, tag in box_cut])
gmsh.model.setPhysicalName(3, b, "box")
rect = gmsh.model.addPhysicalGroup(2, [tag for dim, tag in dim_tags])
gmsh.model.setPhysicalName(2, rect, "rectangle")
bc_tags = gmsh.model.getBoundary(dim_tags, combined=False, oriented=False)
bc_nodes = gmsh.model.getBoundary(dim_tags,
combined=False,
oriented=False,
recursive=True)
bc_box_nodes = gmsh.model.getBoundary(box_cut,
combined=False,
oriented=False,
recursive=True)
bc_rect = gmsh.model.addPhysicalGroup(1, [tag for dim, tag in bc_tags])
gmsh.model.setPhysicalName(1, bc_rect, ".rectangle")
gmsh.model.occ.setMeshSize(bc_nodes, 50)
#gmsh.model.mesh.embed(2, [tag for dim, tag in dim_tags], 3, box_copy[0][1])
#factory.synchronize()
model = gmsh.model
# generate mesh, write to file and output number of entities that produced error
gmsh.option.setNumber("Mesh.CharacteristicLengthFromPoints", 1)
gmsh.option.setNumber("Mesh.CharacteristicLengthFromCurvature", 0)
gmsh.option.setNumber("Mesh.CharacteristicLengthExtendFromBoundary", 1)
#gmsh.option.setNumber("Mesh.CharacteristicLengthMin", 100)
gmsh.option.setNumber("Mesh.CharacteristicLengthMax", 300)
gmsh.write(file_name + '.brep')
gmsh.write(file_name + '.geo')
model.mesh.generate(3)
gmsh.model.mesh.removeDuplicateNodes()
bad_entities = model.mesh.getLastEntityError()
print(bad_entities)
gmsh.write(file_name + ".msh")
gmsh.fltk.run()
gmsh.finalize()
return len(bad_entities)
def draw_GMSH(
output,
sym,
is_antiper=False,
is_remove_vent=False,
is_remove_slotS=False,
is_remove_slotR=False,
is_lam_only_S=False,
is_lam_only_R=False,
kgeo_fineness=1,
kmesh_fineness=1,
user_mesh_dict={},
path_save="GMSH_model.msh",
is_sliding_band=True,
transform_list=[],
):
"""Draws a machine mesh in GMSH format
Parameters
----------
output : Output
Output object
is_remove_vent : bool
True to remove the ventilation ducts (Default value = False)
is_remove_slotS : bool
True to solve without slot effect on the Stator (Default value = False)
is_remove_slotR : bool
True to solve without slot effect on the Rotor (Default value = False)
kgeo_fineness : float
global coefficient to adjust geometry fineness
kmesh_fineness : float
global coefficient to adjust mesh fineness
sym : int
the symmetry applied on the stator and the rotor (take into account antiperiodicity)
is_antiper: bool
To apply antiperiodicity boundary conditions
is_lam_only_S: bool
Draw only stator lamination
is_lam_only_R: bool
Draw only rotor lamination
Returns
-------
GMSH_dict : dict
Dictionnary containing the main parameters of GMSH File
"""
# check some input parameter
if is_lam_only_S and is_lam_only_R:
raise InputError(
"Only 'is_lam_only_S' or 'is_lam_only_R' can be True at the same time"
)
# get machine
machine = output.simu.machine
mesh_dict = {}
tol = 1e-6
# For readibility
model = gmsh.model
factory = model.geo
# Start a new model
gmsh.initialize(sys.argv)
gmsh.option.setNumber("General.Terminal", int(True))
gmsh.option.setNumber("Geometry.CopyMeshingMethod", 1)
gmsh.option.setNumber("Geometry.PointNumbers", 0)
gmsh.option.setNumber("Geometry.LineNumbers", 0)
model.add("Pyleecan")
rotor_list = list()
rotor_list.extend(machine.shaft.build_geometry(sym=sym))
rotor_list.extend(machine.rotor.build_geometry(sym=sym))
stator_list = list()
stator_list.extend(machine.stator.build_geometry(sym=sym))
oo = factory.addPoint(0, 0, 0, 0, tag=-1)
gmsh_dict = {
0: {
"tag": 0,
"label": "origin",
"with_holes": False,
1: {
"tag": 0,
"n_elements": 1,
"bc_name": None,
"begin": {
"tag": oo,
"coord": complex(0.0, 0.0)
},
"end": {
"tag": None,
"coord": None
},
"cent": {
"tag": None,
"coord": None
},
"arc_angle": None,
"line_angle": None,
},
}
}
# Default rotor mesh element size
mesh_size = machine.rotor.Rext / 25.0
nsurf = 0 # number of surfaces
if not is_lam_only_S:
for surf in rotor_list:
nsurf += 1
gmsh_dict.update({nsurf: {"tag": None, "label": surf.label}})
if surf.label.find("Lamination_Rotor") != -1:
gmsh_dict[nsurf]["with_holes"] = True
lam_rotor_surf_id = nsurf
else:
gmsh_dict[nsurf]["with_holes"] = False
if user_mesh_dict is not None:
mesh_dict = surf.comp_mesh_dict(element_size=mesh_size)
mesh_dict.update(user_mesh_dict)
for line in surf.get_lines():
# When symmetry is 1 the shaft surface is substrtacted from Rotor Lam instead
if sym == 1 and line.label == "Lamination_Rotor_Yoke_Radius_Int":
continue
n_elem = mesh_dict.get(line.label)
n_elem = n_elem if n_elem is not None else 0
bc_name = get_boundary_condition(line)
# Gmsh built-in engine does not allow arcs larger than 180deg
# so arcs are split into two
if (isinstance(line, Arc)
and abs(line.get_angle() * 180.0 / cmath.pi) >= 180.0):
rot_dir = 1 if line.is_trigo_direction == True else -1
arc1 = Arc2(
begin=line.get_begin(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
arc2 = Arc2(
begin=arc1.get_end(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
for arc in [arc1, arc2]:
_add_line_to_dict(
geo=factory,
line=arc,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
n_elements=n_elem,
bc=bc_name,
)
elif isinstance(line, Arc) and (abs(
line.get_angle() * 180.0 / cmath.pi) <= tol):
# Don't draw anything, this is a circle and usually is repeated ?
pass
else:
_add_line_to_dict(
geo=factory,
line=line,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
n_elements=n_elem,
bc=bc_name,
)
lam_and_holes = list()
ext_lam_loop = None
for s_id, s_data in gmsh_dict.items():
lloop = []
if s_id == 0:
continue
for lvalues in s_data.values():
if type(lvalues) is not dict:
continue
lloop.extend([lvalues["tag"]])
cloop = factory.addCurveLoop(lloop)
# search for the holes to substract from rotor lam
if s_data["label"].find("Lamination_Rotor") != -1:
ext_lam_loop = cloop
else:
# MachineSIPSM does not have holes in rotor lam
# only shaft is taken out if symmetry is one
if isinstance(machine, MachineSIPMSM):
if sym == 1 and s_data["label"] == "Shaft":
lam_and_holes.extend([cloop])
else:
if sym == 1:
lam_and_holes.extend([cloop])
elif s_data["label"] != "Shaft":
lam_and_holes.extend([cloop])
else:
pass
# Shaft, magnets and magnet pocket surfaces are created
if not is_lam_only_R:
s_data["tag"] = factory.addPlaneSurface([cloop], tag=-1)
pg = model.addPhysicalGroup(2, [s_data["tag"]])
model.setPhysicalName(2, pg, s_data["label"])
# Finally rotor lamination is built
if ext_lam_loop is not None:
lam_and_holes.insert(0, ext_lam_loop)
gmsh_dict[lam_rotor_surf_id]["tag"] = factory.addPlaneSurface(
lam_and_holes, tag=-1)
pg = model.addPhysicalGroup(2, [gmsh_dict[lam_rotor_surf_id]["tag"]])
model.setPhysicalName(2, pg, gmsh_dict[lam_rotor_surf_id]["label"])
# rotor_cloops = lam_and_holes
# store rotor dict
rotor_dict = gmsh_dict.copy()
# init new dict for stator
gmsh_dict = {
0: {
"tag": 0,
"label": "origin",
"with_holes": False,
1: {
"tag": 0,
"n_elements": 1,
"bc_name": None,
"begin": {
"tag": oo,
"coord": complex(0.0, 0.0)
},
"end": {
"tag": None,
"coord": None
},
"cent": {
"tag": None,
"coord": None
},
},
}
}
# Default stator mesh element size
mesh_size = machine.stator.Rext / 100.0
# nsurf = 0
if not is_lam_only_R:
stator_cloops = []
for surf in stator_list:
nsurf += 1
gmsh_dict.update({nsurf: {"tag": None, "label": surf.label}})
if surf.label.find("Lamination_Stator") != -1:
gmsh_dict[nsurf]["with_holes"] = True
else:
gmsh_dict[nsurf]["with_holes"] = False
if user_mesh_dict is not None:
mesh_dict = surf.comp_mesh_dict(element_size=mesh_size)
mesh_dict.update(user_mesh_dict)
for line in surf.get_lines():
n_elem = mesh_dict.get(line.label)
n_elem = n_elem if n_elem is not None else 0
bc_name = get_boundary_condition(line)
# Gmsh built-in engine does not allow arcs larger than 180deg
# so arcs are split into two
if (isinstance(line, Arc)
and abs(line.get_angle() * 180.0 / cmath.pi) >= 180.0):
rot_dir = 1 if line.is_trigo_direction == True else -1
arc1 = Arc2(
begin=line.get_begin(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
arc2 = Arc2(
begin=arc1.get_end(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
for arc in [arc1, arc2]:
_add_line_to_dict(
geo=factory,
line=arc,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
n_elements=n_elem,
bc=bc_name,
)
else:
_add_line_to_dict(
geo=factory,
line=line,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
n_elements=n_elem,
bc=bc_name,
)
for s_id, s_data in gmsh_dict.items():
lloop = []
if s_id == 0:
continue
for lvalues in s_data.values():
if type(lvalues) is not dict:
continue
lloop.extend([lvalues["tag"]])
cloop = factory.addCurveLoop(lloop)
stator_cloops.append(cloop)
# Winding surfaces are created
if (s_data["label"].find("Lamination_Stator") !=
-1) or (not is_lam_only_S):
s_data["tag"] = factory.addPlaneSurface([cloop], tag=-1)
pg = model.addPhysicalGroup(2, [s_data["tag"]])
model.setPhysicalName(2, pg, s_data["label"])
# stator_dict = gmsh_dict.copy()
gmsh_dict.update(rotor_dict)
if is_sliding_band and (not is_lam_only_R) and (not is_lam_only_S):
sb_list = get_sliding_band(sym=sym, machine=machine)
else:
sb_list = []
# Default sliding mesh element size
mesh_size = 2.0 * cmath.pi * machine.rotor.Rext / 360.0
# nsurf = 0
for surf in sb_list:
nsurf += 1
gmsh_dict.update({nsurf: {"tag": None, "label": surf.label}})
for line in surf.get_lines():
n_elem = mesh_dict.get(line.label)
n_elem = n_elem if n_elem is not None else 0
bc_name = get_boundary_condition(line)
# Gmsh built-in engine does not allow arcs larger than 180deg
# so arcs are split into two
if (isinstance(line, Arc)
and abs(line.get_angle() * 180.0 / cmath.pi) >= 180.0):
rot_dir = 1 if line.is_trigo_direction == True else -1
arc1 = Arc2(
begin=line.get_begin(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
arc2 = Arc2(
begin=arc1.get_end(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
for arc in [arc1, arc2]:
_add_agline_to_dict(
geo=factory,
line=arc,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
n_elements=n_elem,
bc=bc_name,
)
else:
_add_agline_to_dict(
geo=factory,
line=line,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
n_elements=n_elem,
bc=bc_name,
)
for s_id, s_data in gmsh_dict.items():
lloop = []
if s_id == 0:
continue
for lvalues in s_data.values():
if (s_data["label"].find("Airgap") != -1
or s_data["label"].find("SlidingBand") != -1):
if type(lvalues) is not dict:
continue
lloop.extend([lvalues["tag"]])
else:
continue
if lloop:
cloop = factory.addCurveLoop(lloop)
s_data["tag"] = factory.addPlaneSurface([cloop], tag=-1)
pg = model.addPhysicalGroup(2, [s_data["tag"]])
model.setPhysicalName(2, pg, s_data["label"])
# Set boundary conditions in gmsh lines
bc_master_stator_id = []
bc_slave_stator_id = []
bc_master_rotor_id = []
bc_slave_rotor_id = []
for propname in boundary_list:
# propname = boundary_prop[bound_label]
bc_id = []
for s_id, s_data in gmsh_dict.items():
for lid, lvalues in s_data.items():
if type(lvalues) is not dict:
continue
if lvalues["bc_name"] == propname:
if propname == "MASTER_SLAVE_STATOR_BOUNDARY":
line_angle = lvalues.get("line_angle", None)
print(propname, lvalues["tag"], line_angle)
# Assumes Master coincides with x-Axis
if line_angle is not None and abs(line_angle) < tol:
bc_master_stator_id.extend([abs(lvalues["tag"])])
else:
bc_slave_stator_id.extend([abs(lvalues["tag"])])
elif propname == "MASTER_SLAVE_ROTOR_BOUNDARY":
line_angle = lvalues.get("line_angle", None)
print(propname, lvalues["tag"], line_angle)
# Assumes Master coincides with x-Axis
if line_angle is not None and abs(line_angle) < tol:
bc_master_rotor_id.extend([abs(lvalues["tag"])])
else:
bc_slave_rotor_id.extend([abs(lvalues["tag"])])
else:
bc_id.extend([abs(lvalues["tag"])])
if bc_id:
pg = model.addPhysicalGroup(1, bc_id)
model.setPhysicalName(1, pg, propname)
if bc_master_stator_id:
pg = model.addPhysicalGroup(1, bc_master_stator_id)
model.setPhysicalName(1, pg, "MASTER_SATOR_BOUNDARY")
print("MASTER_STATOR_BOUNDARY", bc_master_stator_id)
if bc_slave_stator_id:
pg = model.addPhysicalGroup(1, bc_slave_stator_id)
model.setPhysicalName(1, pg, "SLAVE_SATOR_BOUNDARY")
print("SLAVE_STATOR_BOUNDARY", bc_slave_stator_id)
if bc_master_rotor_id:
pg = model.addPhysicalGroup(1, bc_master_rotor_id)
model.setPhysicalName(1, pg, "MASTER_ROTOR_BOUNDARY")
print("MASTER_ROTOR_BOUNDARY", bc_master_rotor_id)
if bc_slave_rotor_id:
pg = model.addPhysicalGroup(1, bc_slave_rotor_id)
model.setPhysicalName(1, pg, "SLAVE_ROTOR_BOUNDARY")
print("SLAVE_ROTOR_BOUNDARY", bc_slave_rotor_id)
factory.synchronize()
gmsh.model.mesh.generate(2)
# Save and close
gmsh.write(path_save)
# gmsh.fltk.run() # Uncomment to launch Gmsh GUI
gmsh.finalize()
return gmsh_dict
def _finalize_gmsh():
gmsh.finalize()
# Origin, width, inside, outside sizes
fid = 1
field = model.mesh.field
# Refine close to left
field.add('Box', fid)
field.setNumber(fid, 'XMin', 0)
field.setNumber(fid, 'XMax', 0.1 * geometry_parameters['X'])
field.setNumber(fid, 'YMin', 0)
field.setNumber(fid, 'YMax', geometry_parameters['Y'])
field.setNumber(fid, 'VIn', 0.05)
field.setNumber(fid, 'VOut', 0.2)
field.setAsBackgroundMesh(fid)
model.occ.synchronize()
# gmsh.fltk.initialize()
# gmsh.fltk.run()
h5_filename = './test/square_domain.h5'
mesh_model2d(model, tags, h5_filename)
mesh, markers, lookup = load_mesh2d(h5_filename)
cell_f, facet_f = markers
gmsh.finalize()
df.File('./test/square_cells.pvd') << cell_f
df.File('./test/square_facets.pvd') << facet_f
def draw_GMSH(
output,
sym,
is_antiper=False,
is_remove_vent=False,
is_remove_slotS=False,
is_remove_slotR=False,
is_lam_only_S=False,
is_lam_only_R=False,
kgeo_fineness=1,
kmesh_fineness=1,
user_mesh_dict={},
path_save="GMSH_model.msh",
is_sliding_band=True,
transform_list=[],
):
"""Draws a machine mesh in GMSH format
Parameters
----------
output : Output
Output object
is_remove_vent : bool
True to remove the ventilation ducts (Default value = False)
is_remove_slotS : bool
True to solve without slot effect on the Stator (Default value = False)
is_remove_slotR : bool
True to solve without slot effect on the Rotor (Default value = False)
kgeo_fineness : float
global coefficient to adjust geometry fineness
kmesh_fineness : float
global coefficient to adjust mesh fineness
sym : int
the symmetry applied on the stator and the rotor (take into account antiperiodicity)
is_antiper: bool
To apply antiperiodicity boundary conditions
is_lam_only_S: bool
Draw only stator lamination
is_lam_only_R: bool
Draw only rotor lamination
Returns
-------
GMSH_dict : dict
Dictionnary containing the main parameters of GMSH File
"""
machine = output.simu.machine
mesh_dict = {}
tol = 1e-6
# For readibility
model = gmsh.model
factory = model.geo
# Start a new model
gmsh.initialize(sys.argv)
gmsh.option.setNumber("General.Terminal", int(True))
gmsh.option.setNumber("Geometry.CopyMeshingMethod", 1)
gmsh.option.setNumber("Geometry.PointNumbers", 0)
gmsh.option.setNumber("Geometry.LineNumbers", 0)
model.add("Pyleecan")
rotor_list = list()
rotor_list.extend(machine.shaft.build_geometry(sym=sym))
rotor_list.extend(machine.rotor.build_geometry(sym=sym))
stator_list = list()
stator_list.extend(machine.stator.build_geometry(sym=sym))
oo = factory.addPoint(0, 0, 0, 0, tag=-1)
gmsh_dict = {
0: {
"tag": 0,
"label": "origin",
"with_holes": False,
1: {
"tag": 0,
"n_elements": 1,
"begin": {
"tag": oo,
"coord": complex(0.0, 0.0)
},
"end": {
"tag": None,
"coord": None
},
"cent": {
"tag": None,
"coord": None
},
},
}
}
# Default rotor mesh element size
mesh_size = machine.rotor.Rext / 25.0
nsurf = 0
for surf in rotor_list:
nsurf += 1
gmsh_dict.update({nsurf: {"tag": None, "label": surf.label}})
if surf.label.find("Lamination_Rotor") != -1:
gmsh_dict[nsurf]["with_holes"] = True
lam_rotor_surf_id = nsurf
else:
gmsh_dict[nsurf]["with_holes"] = False
if user_mesh_dict is not None:
mesh_dict = surf.comp_mesh_dict(element_size=mesh_size)
mesh_dict.update(user_mesh_dict)
for line in surf.get_lines():
# When symmetry is 1 the shaft surface is substrtacted from Rotor Lam instead
if sym == 1 and line.label == "Lamination_Rotor_Yoke_Radius_Int":
continue
n_elem = mesh_dict.get(line.label)
if (isinstance(line, Arc)
and abs(line.get_angle() * 180.0 / cmath.pi) >= 180.0):
if line.is_trigo_direction == True:
arc1 = Arc2(
begin=line.get_begin(),
center=line.get_center(),
angle=cmath.pi / 2.0,
label=line.label,
)
arc2 = Arc2(
begin=arc1.get_end(),
center=line.get_center(),
angle=cmath.pi / 2.0,
label=line.label,
)
else:
arc1 = Arc2(
begin=line.get_begin(),
center=line.get_center(),
angle=-cmath.pi / 2.0,
label=line.label,
)
arc2 = Arc2(
begin=arc1.get_end(),
center=line.get_center(),
angle=-cmath.pi / 2.0,
label=line.label,
)
if n_elem is not None:
_add_line_to_dict(
geo=factory,
line=arc1,
d=gmsh_dict,
idx=nsurf,
n_elements=n_elem,
)
_add_line_to_dict(
geo=factory,
line=arc2,
d=gmsh_dict,
idx=nsurf,
n_elements=n_elem,
)
else:
_add_line_to_dict(
geo=factory,
line=arc1,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
)
_add_line_to_dict(
geo=factory,
line=arc2,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
)
elif isinstance(
line,
Arc) and (abs(line.get_angle() * 180.0 / cmath.pi) <= tol):
# Don't draw anything, this is a circle and usually is repeated ?
pass
else:
if n_elem is not None:
_add_line_to_dict(
geo=factory,
line=line,
d=gmsh_dict,
idx=nsurf,
n_elements=n_elem,
)
else:
_add_line_to_dict(
geo=factory,
line=line,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
)
lam_and_holes = list()
ext_lam_loop = None
for s_id, s_data in gmsh_dict.items():
lloop = []
if s_id == 0:
continue
for lid, lvalues in s_data.items():
if type(lvalues) is not dict:
continue
lloop.extend([lvalues["tag"]])
cloop = factory.addCurveLoop(lloop)
# search for the holes to substract from rotor lam
if s_data["label"].find("Lamination_Rotor") != -1:
ext_lam_loop = cloop
else:
# MachineSIPSM does not have holes in rotor lam
# only shaft is taken out if symmetry is one
if isinstance(machine, MachineSIPMSM):
if sym == 1 and s_data["label"] == "Shaft":
lam_and_holes.extend([cloop])
else:
if sym == 1:
lam_and_holes.extend([cloop])
elif s_data["label"] != "Shaft":
lam_and_holes.extend([cloop])
else:
pass
# Shaft, magnets and magnet pocket surfaces are created
if not is_lam_only_R:
s_data["tag"] = factory.addPlaneSurface([cloop], tag=-1)
pg = model.addPhysicalGroup(2, [s_data["tag"]])
model.setPhysicalName(2, pg, s_data["label"])
# Finally rotor lamination is built
if ext_lam_loop is not None:
lam_and_holes.insert(0, ext_lam_loop)
gmsh_dict[lam_rotor_surf_id]["tag"] = factory.addPlaneSurface(
lam_and_holes, tag=-1)
pg = model.addPhysicalGroup(2, [gmsh_dict[lam_rotor_surf_id]["tag"]])
model.setPhysicalName(2, pg, gmsh_dict[lam_rotor_surf_id]["label"])
# Default rotor mesh element size
mesh_size = machine.stator.Rext / 100.0
nsurf = 0
for surf in stator_list:
nsurf += 1
gmsh_dict.update({nsurf: {"tag": None, "label": surf.label}})
if surf.label.find("Lamination_Stator") != -1:
gmsh_dict[nsurf]["with_holes"] = True
else:
gmsh_dict[nsurf]["with_holes"] = False
if user_mesh_dict is not None:
mesh_dict = surf.comp_mesh_dict(element_size=mesh_size)
mesh_dict.update(user_mesh_dict)
for line in surf.get_lines():
n_elem = mesh_dict.get(line.label)
# Gmsh built-in engine does not allow arcs larger than 180deg
# so arcs are split into two
if (isinstance(line, Arc)
and abs(line.get_angle() * 180.0 / cmath.pi) == 180.0):
if line.is_trigo_direction == True:
arc1 = Arc2(
begin=line.get_begin(),
center=line.get_center(),
angle=cmath.pi / 2.0,
label=line.label,
)
arc2 = Arc2(
begin=arc1.get_end(),
center=line.get_center(),
angle=cmath.pi / 2.0,
label=line.label,
)
else:
arc1 = Arc2(
begin=line.get_begin(),
center=line.get_center(),
angle=-cmath.pi / 2.0,
label=line.label,
)
arc2 = Arc2(
begin=arc1.get_end(),
center=line.get_center(),
angle=-cmath.pi / 2.0,
label=line.label,
)
if n_elem is not None:
_add_line_to_dict(
geo=factory,
line=arc1,
d=gmsh_dict,
idx=nsurf,
n_elements=n_elem,
)
_add_line_to_dict(
geo=factory,
line=arc2,
d=gmsh_dict,
idx=nsurf,
n_elements=n_elem,
)
else:
_add_line_to_dict(
geo=factory,
line=arc1,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
)
_add_line_to_dict(
geo=factory,
line=arc2,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
)
else:
if n_elem is not None:
_add_line_to_dict(
geo=factory,
line=line,
d=gmsh_dict,
idx=nsurf,
n_elements=n_elem,
)
else:
_add_line_to_dict(
geo=factory,
line=line,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
)
for s_id, s_data in gmsh_dict.items():
lloop = []
if s_id == 0:
continue
for lid, lvalues in s_data.items():
if type(lvalues) is not dict:
continue
lloop.extend([lvalues["tag"]])
cloop = factory.addCurveLoop(lloop)
# Winding surfaces are created
if s_data["label"].find("Lamination_Stator") != -1:
s_data["tag"] = factory.addPlaneSurface([cloop], tag=-1)
pg = model.addPhysicalGroup(2, [s_data["tag"]])
model.setPhysicalName(2, pg, s_data["label"])
else:
# Stator lamination is built
if not is_lam_only_S:
s_data["tag"] = factory.addPlaneSurface([cloop], tag=-1)
pg = model.addPhysicalGroup(2, [s_data["tag"]])
model.setPhysicalName(2, pg, s_data["label"])
factory.synchronize()
gmsh.model.mesh.generate(2)
# Save and close
gmsh.write(path_save)
# gmsh.fltk.run() # Uncomment to launch Gmsh GUI
gmsh.finalize()
return gmsh_dict
def create_mesh(r, w, l1, l2, n):
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 0)
gmsh.model.add("fork")
lc = 0
gmsh.model.occ.addPoint(0, 0, 0, lc, 1)
gmsh.model.occ.addPoint(-r, 0, 0, lc, 2)
gmsh.model.occ.addPoint(-(r + w), 0, 0, lc, 3)
gmsh.model.occ.addPoint(+r, 0, 0, lc, 4)
gmsh.model.occ.addPoint(+(r + w), 0, 0, lc, 5)
gmsh.model.occ.addPoint(-(r + w), +l1, 0, lc, 6)
gmsh.model.occ.addPoint(+(r + w), +l1, 0, lc, 7)
gmsh.model.occ.addPoint(-r, +l1, 0, lc, 8)
gmsh.model.occ.addPoint(+r, +l1, 0, lc, 9)
x1 = w / 2
y1 = math.sqrt((r + w) * (r + w) - (w / 2) * (w / 2))
a = x1 / y1
y2 = math.sqrt(r * r / (1 + a * a))
x2 = a * y2
gmsh.model.occ.addPoint(-x1, -y1, lc, 10)
gmsh.model.occ.addPoint(-x2, -y2, lc, 11)
gmsh.model.occ.addPoint(+x1, -y1, lc, 12)
gmsh.model.occ.addPoint(+x2, -y2, lc, 13)
gmsh.model.occ.addPoint(-w / 2, -l2, lc, 14)
gmsh.model.occ.addPoint(+w / 2, -l2, lc, 15)
gmsh.model.occ.addLine(14, 10, 1)
gmsh.model.occ.addLine(10, 11, 2)
gmsh.model.occ.addLine(14, 15, 3)
gmsh.model.occ.addLine(15, 12, 4)
gmsh.model.occ.addLine(12, 13, 5)
gmsh.model.occ.addLine(3, 6, 6)
gmsh.model.occ.addLine(6, 8, 7)
gmsh.model.occ.addLine(8, 2, 8)
gmsh.model.occ.addLine(2, 3, 9)
gmsh.model.occ.addLine(4, 9, 10)
gmsh.model.occ.addLine(9, 7, 11)
gmsh.model.occ.addLine(7, 5, 12)
gmsh.model.occ.addLine(5, 4, 13)
gmsh.model.occ.addCircleArc(2, 1, 11, 14)
gmsh.model.occ.addCircleArc(11, 1, 13, 15)
gmsh.model.occ.addCircleArc(13, 1, 4, 16)
gmsh.model.occ.addCircleArc(3, 1, 10, 17)
gmsh.model.occ.addCircleArc(10, 1, 12, 18)
gmsh.model.occ.addCircleArc(12, 1, 5, 19)
gmsh.model.occ.addCurveLoop([3, 4, -18, -1], 1)
gmsh.model.occ.addCurveLoop([18, 5, -15, -2], 2)
gmsh.model.occ.addCurveLoop([19, 13, -16, -5], 3)
gmsh.model.occ.addCurveLoop([14, -2, -17, -9], 4)
gmsh.model.occ.addCurveLoop([13, 10, 11, 12], 5)
gmsh.model.occ.addCurveLoop([8, 9, 6, 7], 6)
gmsh.model.occ.addPlaneSurface([1], 1)
gmsh.model.occ.addPlaneSurface([2], 2)
gmsh.model.occ.addPlaneSurface([3], 3)
gmsh.model.occ.addPlaneSurface([4], 4)
gmsh.model.occ.addPlaneSurface([5], 5)
gmsh.model.occ.addPlaneSurface([6], 6)
gmsh.model.occ.synchronize()
gmsh.model.mesh.setTransfiniteCurve(3, n + 1)
gmsh.model.mesh.setTransfiniteCurve(18, n + 1)
gmsh.model.mesh.setTransfiniteCurve(15, n + 1)
gmsh.model.mesh.setTransfiniteCurve(5, n + 1)
gmsh.model.mesh.setTransfiniteCurve(2, n + 1)
gmsh.model.mesh.setTransfiniteCurve(9, n + 1)
gmsh.model.mesh.setTransfiniteCurve(13, n + 1)
gmsh.model.mesh.setTransfiniteCurve(11, n + 1)
gmsh.model.mesh.setTransfiniteCurve(7, n + 1)
gmsh.model.mesh.setTransfiniteCurve(6, 12 * n + 1)
gmsh.model.mesh.setTransfiniteCurve(8, 12 * n + 1)
gmsh.model.mesh.setTransfiniteCurve(10, 12 * n + 1)
gmsh.model.mesh.setTransfiniteCurve(12, 12 * n + 1)
gmsh.model.mesh.setTransfiniteCurve(14, 3 * n + 1)
gmsh.model.mesh.setTransfiniteCurve(17, 3 * n + 1)
gmsh.model.mesh.setTransfiniteCurve(16, 3 * n + 1)
gmsh.model.mesh.setTransfiniteCurve(19, 3 * n + 1)
gmsh.model.mesh.setTransfiniteCurve(1, 8 * n + 1)
gmsh.model.mesh.setTransfiniteCurve(4, 8 * n + 1)
gmsh.model.mesh.setTransfiniteSurface(1)
gmsh.model.mesh.setTransfiniteSurface(2)
gmsh.model.mesh.setTransfiniteSurface(3)
gmsh.model.mesh.setTransfiniteSurface(4)
gmsh.model.mesh.setTransfiniteSurface(5)
gmsh.model.mesh.setTransfiniteSurface(6)
gmsh.model.occ.extrude([(2, 1), (2, 2), (2, 3), (2, 4), (2, 5), (2, 6)], 0,
0, w, [int(n)], [], True)
gmsh.model.occ.synchronize()
gmsh.model.addPhysicalGroup(3, [1, 2, 3, 4, 5, 6], 1)
gmsh.model.setPhysicalName(3, 1, "bulk")
gmsh.model.addPhysicalGroup(2, [7], 2)
gmsh.model.setPhysicalName(2, 2, "base")
gmsh.model.occ.synchronize()
gmsh.option.setNumber("Mesh.RecombineAll", 1)
gmsh.option.setNumber("Mesh.ElementOrder", 2)
gmsh.model.mesh.generate(3)
nodes, coord, parametric_coord = gmsh.model.mesh.getNodes()
gmsh.write("fork.msh")
gmsh.model.remove()
#gmsh.fltk.run()
gmsh.finalize()
return len(nodes)
def optimize_mesh(in_file,
out_file=None,
method="",
force=False,
dim_tags=[],
dim=3):
""" Optimize a mesh using an optimizer
See: https://gitlab.onelab.info/gmsh/gmsh/-/blob/master/api/gmsh.py#L1444
Parameters
----------
in_file : Path or str
path to .geo file to be optimized
Note: You are unable to optimize .msh-files.
Therefore, only .geo files can be passed.
out_file : Path or str
output file. By default, in_file+"optimized"
method : str
name of optimizer.
Default: '' (gmsh default tetrahedral optimizer)
Other options:
'Netgen': Netgen optimizer
'HighOrder': direct high-order mesh optimizer
'HighOrderElastic': high-order elastic smoother
'HighOrderFastCurving': fast curving algorithm
'Laplace2D': Laplace smoothing
'Relocate2D': Node relocation, 2d
'Relocate3D': Node relocation, 3d
force : bool
If set, apply the optimization also to discrete entities
dim_tags : List
If supplied, only apply the optimizer to the given entities
dim : int
Which dimension to mesh. Defaults to 3D.
"""
# Check in- and out-file paths
in_file = Path(in_file)
out_file = Path(out_file)
assert in_file.is_file()
assert in_file.suffix == ".geo"
out_file.parent.mkdir(exist_ok=True, parents=True)
out_file.with_suffix(".msh")
print(out_file)
# Optimize the mesh.
import gmsh
gmsh.initialize()
# Mesh Statistics
gmsh.option.setNumber("General.Terminal", 1)
# gmsh.option.setNumber("Print.PostGamma", 1)
# gmsh.option.setNumber("Print.PostEta", 1)
# gmsh.option.setNumber("Print.PostSICN", 1)
# gmsh.option.setNumber("Print.PostSIGE", 1)
gmsh.open(str(in_file))
gmsh.model.mesh.generate(dim=dim)
gmsh.model.mesh.optimize(method=method, force=force, dimTags=dim_tags)
# Write to .msh and close gmsh
gmsh.write(str(out_file))
gmsh.finalize()
def _finalize_gmsh(self):
gmsh.finalize()
def __exit__(self, *a):
# TODO remove once gmsh 4.7.0 is out
# <https://gitlab.onelab.info/gmsh/gmsh/-/issues/1001>
gmsh.option.setNumber("Mesh.CharacteristicLengthMin", 0.0)
gmsh.option.setNumber("Mesh.CharacteristicLengthMax", 1.0e22)
gmsh.finalize()
def __exit__(self, *a):
gmsh.finalize()
def PVSbrain_simulation(args):
""" Test case for simple diffusion from PVS to the brain.
Outputs :
- a logfile with information about the simulation
- .pvd files at specified args.toutput time period with the u, p and c fields in stokes domain and u, p , q, phi and c fields in Biot domain
- .csv files of u, p, c 1D array of the u, p, c fields on the middle line of the PVS
- .csv files of the total mass in the domain, mass flux from the brain to sas, brain to PVS, PVS to SAS
"""
# output folder name
outputfolder = args.output_folder + '/' + args.job_name + '/'
if not os.path.exists(outputfolder):
os.makedirs(outputfolder)
if not os.path.exists(outputfolder + '/fields'):
os.makedirs(outputfolder + '/fields')
# Create output files
#pvd files
c_out = File(outputfolder + 'fields' + '/c.pvd')
facets_out_fluid = File(outputfolder + 'fields' + '/facets_fluid.pvd')
facets_out_solid = File(outputfolder + 'fields' + '/facets_solid.pvd')
# Create logger
logger = logging.getLogger()
logger.setLevel(logging.INFO)
# log to a file
now = datetime.now().strftime("%Y%m%d_%H%M%S")
filename = os.path.join(outputfolder + '/', 'PVSBrain_info.log')
file_handler = logging.FileHandler(filename, mode='w')
file_handler.setLevel(logging.INFO)
#formatter = logging.Formatter("%(asctime)s %(filename)s, %(lineno)d, %(funcName)s: %(message)s")
#file_handler.setFormatter(formatter)
logger.addHandler(file_handler)
# log to the console
console_handler = logging.StreamHandler()
level = logging.INFO
console_handler.setLevel(level)
logger.addHandler(console_handler)
# initialise logging
logging.info(
title1(
"Test case of simple diffusion from PVS to the brain using the diffusion-advection solver"
))
logging.info("Date and time:" +
datetime.now().strftime("%m/%d/%Y, %H:%M:%S"))
logging.info('Job name : ' + args.job_name)
logging.debug('logging initialized')
# Set parameters
logging.info(title1("Parameters"))
# Geometry params
logging.info('\n * Geometry')
Rv = args.radius_vessel # centimeters
Rpvs = args.radius_pvs # centimeters
Rbrain = args.radius_brain # centimeters
L = args.length # centimeters
logging.info('Vessel radius : %e cm' % Rv)
logging.info('PVS radius : %e cm' % Rpvs)
logging.info('Brain radius : %e cm' % Rbrain)
logging.info('length : %e cm' % L)
#Mesh
logging.info('\n * Mesh')
#number of cells in the radial direction fluid domain
Nr = args.N_radial_fluid
#number of cells in the radial direction biot domain
Nr_biot = args.N_radial_biot
s_biot = args.biot_progression
DR = (Rpvs - Rv) / Nr
#number of cells in the axial direction
if args.N_axial:
Nl = args.N_axial
else:
Nl = round(L / DR)
DY = L / Nl
logging.info('N axial: %i' % Nl)
logging.info('N radial PVS: %e' % Nr)
logging.info('N radial Biot: %e' % Nr_biot)
logging.info('progression parameter in biot: %e' % s_biot)
#time parameters
logging.info('\n * Time')
toutput = args.toutput
tfinal = args.tend
dt = args.time_step
logging.info('final time: %e s' % tfinal)
logging.info('output period : %e s' % toutput)
logging.info('time step : %e s' % dt)
dt_advdiff = dt
logging.info('\n* Tracer properties')
D = args.diffusion_coef
sigma_gauss = args.sigma
logging.info('Free diffusion coef: %e cm2/s' % D)
logging.info('STD of initial gaussian profile: %e ' % sigma_gauss)
xi_gauss = args.initial_pos
logging.info('Initial position: %e cm2' % xi_gauss)
logging.info('\n * Porous medium properties')
porosity_0 = args.biot_porosity
tortuosity = args.biot_tortuosity
dt_solid = dt
logging.info('initial porosity: %e ' % porosity_0)
logging.info('tortuosity: %e ' % tortuosity)
## The tracer is solver in the full domain, so it has two subdomains
# 1 for solid
# 0 for fluid
tracer_parameters = {
'kappa_0': D,
'kappa_1': D * tortuosity,
'dt': dt_advdiff,
'nsteps': 1
}
# Mesh
logging.info(title1('Meshing'))
meshing = args.mesh_method
##### Meshing method : regular
if meshing == 'regular':
# Create a mesh using Rectangle mesh : all the cells are regulars but this means a lot of cells
logging.info('cell size : %e cm' % (np.sqrt(DR**2 + DY**2)))
# Create a rectangle mesh with Nr + Nsolid cells in the radias direction and Nl cells in the axial direction
# the geometrical progression for the solid mesh is s
#Creation of the uniform mesh
Rext = 1 + Nr_biot / Nr
mesh = RectangleMesh(Point(0, 0), Point(L, Rext), Nl, Nr + Nr_biot)
x = mesh.coordinates()[:, 0]
y = mesh.coordinates()[:, 1]
#Deformation of the mesh
def deform_mesh(x, y):
transform_fluid = Rv + (Rpvs - Rv) * y
transform_solid = Rpvs + (Rbrain - Rpvs) * ((y - 1) /
(Rext - 1))**s_biot
yp = np.where(y <= 1, transform_fluid, transform_solid)
return [x, yp]
x_bar, y_bar = deform_mesh(x, y)
xy_bar_coor = np.array([x_bar, y_bar]).transpose()
mesh.coordinates()[:] = xy_bar_coor
mesh.bounding_box_tree().build(mesh)
else:
##### Meshing method : gmsh with box for refinement
from sleep.mesh import mesh_model2d, load_mesh2d, set_mesh_size
import sys
gmsh.initialize(['', '-format', 'msh2'])
model = gmsh.model
import math
Apvs0 = math.pi * Rpvs**2
Av0 = math.pi * Rv**2
A0 = Apvs0 - Av0
# progressive mesh
factory = model.occ
a = factory.addPoint(0, Rv, 0)
b = factory.addPoint(L, Rv, 0)
c = factory.addPoint(L, Rpvs, 0)
d = factory.addPoint(0, Rpvs, 0)
e = factory.addPoint(L, Rbrain, 0)
f = factory.addPoint(0, Rbrain, 0)
fluid_lines = [
factory.addLine(*p) for p in ((a, b), (b, c), (c, d), (d, a))
]
named_lines = dict(
zip(('bottom', 'pvs_right', 'interface', 'pvs_left'), fluid_lines))
fluid_loop = factory.addCurveLoop(fluid_lines)
fluid = factory.addPlaneSurface([fluid_loop])
solid_lines = [
factory.addLine(*p) for p in ((d, c), (c, e), (e, f), (f, d))
]
named_lines.update(
dict(
zip(('interface', 'brain_right', 'brain_top', 'brain_left'),
solid_lines)))
solid_loop = factory.addCurveLoop(solid_lines)
solid = factory.addPlaneSurface([solid_loop])
factory.synchronize()
tags = {'cell': {'F': 1, 'S': 2}, 'facet': {}}
model.addPhysicalGroup(2, [fluid], 1)
model.addPhysicalGroup(2, [solid], 2)
for name in named_lines:
tag = named_lines[name]
model.addPhysicalGroup(1, [tag], tag)
# boxes for mesh refinement
cell_size = DR * (Rpvs - Rv) / (Rpvs - Rv)
boxes = []
# add box on the PVS for mesh
field = model.mesh.field
fid = 1
field.add('Box', fid)
field.setNumber(fid, 'XMin', 0)
field.setNumber(fid, 'XMax', L)
field.setNumber(fid, 'YMin', Rv)
field.setNumber(fid, 'YMax', Rpvs)
field.setNumber(fid, 'VIn', cell_size * 2)
field.setNumber(fid, 'VOut', DR * 50)
field.setNumber(fid, 'Thickness', (Rpvs - Rv) / 4)
boxes.append(fid)
# Combine
field.add('Min', fid + 1)
field.setNumbers(fid + 1, 'FieldsList', boxes)
field.setAsBackgroundMesh(fid + 1)
model.occ.synchronize()
h5_filename = outputfolder + '/mesh.h5'
mesh_model2d(model, tags, h5_filename)
mesh, markers, lookup = load_mesh2d(h5_filename)
from IPython import embed
embed()
gmsh.finalize()
## Define subdomains
x = mesh.coordinates()[:, 0]
y = mesh.coordinates()[:, 1]
tol = 1e-7
class Omega_0(SubDomain):
def inside(self, x, on_boundary):
return x[1] < Rpvs + tol
class Omega_1(SubDomain):
def inside(self, x, on_boundary):
return x[1] > Rpvs - tol
subdomains = MeshFunction("size_t", mesh, mesh.topology().dim(), 0)
subdomain_0 = Omega_0()
subdomain_1 = Omega_1()
subdomain_0.mark(subdomains, 0)
subdomain_1.mark(subdomains, 1)
mesh_f = EmbeddedMesh(subdomains, 0)
mesh_s = EmbeddedMesh(subdomains, 1)
## Define boundaries
solid_bdries = MeshFunction("size_t", mesh_s,
mesh_s.topology().dim() - 1, 0)
fluid_bdries = MeshFunction("size_t", mesh_f,
mesh_f.topology().dim() - 1, 0)
full_bdries = MeshFunction("size_t", mesh, mesh.topology().dim() - 1, 0)
# Label facets
class Boundary_left_fluid(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and near(x[0], 0, tol) and (x[1] <= Rpvs + tol
) #left fluid
class Boundary_right_fluid(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and near(x[0], L, tol) and (x[1] <= Rpvs + tol
) # right fluid
class Boundary_left_solid(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and near(x[0], 0, tol) and (x[1] >= Rpvs - tol
) #left solid
class Boundary_right_solid(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and near(x[0], L, tol) and (x[1] >= Rpvs - tol
) # right solid
class Boundary_bottom(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and near(x[1], Rv, tol) #bottom
class Boundary_top(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and near(x[1], Rbrain, tol) #top
class Boundary_interface(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and near(x[1], Rpvs, tol) #interface
#todo : keep separate F and S for right and left in the full bdries
btop = Boundary_top()
bbottom = Boundary_bottom()
bleft_fluid = Boundary_left_fluid()
bright_fluid = Boundary_right_fluid()
bleft_solid = Boundary_left_solid()
bright_solid = Boundary_right_solid()
binterface = Boundary_interface()
bbottom.mark(fluid_bdries, 2)
binterface.mark(fluid_bdries, 4)
bleft_fluid.mark(fluid_bdries, 1)
bright_fluid.mark(fluid_bdries, 3)
binterface.mark(solid_bdries, 4)
bright_solid.mark(solid_bdries, 5)
btop.mark(solid_bdries, 6)
bleft_solid.mark(solid_bdries, 7)
bleft_fluid.mark(full_bdries, 1)
bleft_solid.mark(full_bdries, 7)
bbottom.mark(full_bdries, 2)
bright_fluid.mark(full_bdries, 3)
bright_solid.mark(full_bdries, 5)
btop.mark(full_bdries, 6)
facet_lookup = {
'F_left': 1,
'F_bottom': 2,
'F_right': 3,
'Interface': 4,
'S_left': 7,
'S_top': 6,
'S_right': 5
}
facets_out_fluid << fluid_bdries
facets_out_solid << solid_bdries
# define the domain specific parameters for the tracer
# NOTE: Here we do P0 projection
dx = Measure('dx', domain=mesh, subdomain_data=subdomains)
CoefSpace = FunctionSpace(mesh, 'DG', 0)
q = TestFunction(CoefSpace)
# Remove
coef = 'kappa'
fluid_coef = tracer_parameters.pop('%s_0' % coef)
solid_coef = tracer_parameters.pop('%s_1' % coef)
form = ((1 / CellVolume(mesh)) * fluid_coef * q * dx(0) +
(1 / CellVolume(mesh)) * solid_coef * q * dx(1))
tracer_parameters[coef] = Function(CoefSpace, assemble(form))
#FEM space
logging.info(title1("Set FEM spaces"))
logging.info('\n * Tracer')
#### Todo : I would like to be able to have discontinuous concentration when we will have the membrane
#### Beter to solve in two domains or one domain with discontinuous lagrange element ?
Ct_elm = FiniteElement('Lagrange', triangle, 1)
Ct = FunctionSpace(mesh, Ct_elm)
logging.info('Concentration : "Lagrange", triangle, 1')
#Advection velocity
FS_advvel = VectorFunctionSpace(mesh, 'CG', 2)
# Setup of boundary conditions
logging.info(title1("Boundary conditions"))
## to do : allow zero concentration if fluid BC is free on the right
logging.info('\n * Tracer concentration')
bcs_tracer = {
'concentration': [(facet_lookup['S_top'], Constant(0))],
'flux': [
(facet_lookup['S_left'], Constant(0)),
(facet_lookup['S_right'], Constant(0)),
(facet_lookup['F_right'], Constant(0)),
(facet_lookup['F_left'], Constant(0)),
(facet_lookup['F_bottom'], Constant(0)),
]
}
# Initialisation :
# 1 in the PVS
cf_0 = Expression('x[1]<= Rpvs ? 1 : 0 ',
degree=2,
a=1 / 2 / sigma_gauss**2,
b=xi_gauss,
Rv=Rv,
Rpvs=Rpvs)
c_n = project(cf_0, Ct) #
File('initial_reg.pvd') << c_n
exit()
#Initial deformation of the fluid domain
# We start at a time shift
tshift = 0 #
c_n.rename("c", "tmp")
c_out << (c_n, 0)
############# RUN ############3
logging.info(title1("Run"))
# Time loop
time = tshift
timestep = 0
# Here I dont know if there will be several dt for advdiff and fluid solver
while time < tfinal + tshift:
time += dt
timestep += 1
print('time', time - tshift)
# Solve tracer problem
tracer_parameters["T0"] = time
advection_velocity = project(Constant((0, 0)), FS_advvel)
c_, T0 = solve_adv_diff(Ct,
velocity=advection_velocity,
phi=Constant(0.2),
f=Constant(0),
c_0=c_n,
phi_0=Constant(0.2),
bdries=full_bdries,
bcs=bcs_tracer,
parameters=tracer_parameters)
# Update current solution
c_n.assign(c_)
# Save output
if (timestep % int(toutput / dt) == 0):
logging.info("\n*** save output time %e s" % (time - tshift))
logging.info("number of time steps %i" % timestep)
# may report Courant number or other important values that indicate how is doing the run
c_n.rename("c", "tmp")
c_out << (c_n, time - tshift)
advection_velocity.rename("adv_vel", "tmp")
File(outputfolder + 'fields' +
'/adv_vel.pvd') << (advection_velocity, time - tshift)
def draw_GMSH(
output,
sym,
boundary_prop,
boundary_list,
surface_label,
is_antiper=False,
is_remove_vent=False,
is_remove_slotS=False,
is_remove_slotR=False,
is_lam_only_S=False,
is_lam_only_R=False,
kgeo_fineness=1,
kmesh_fineness=1,
user_mesh_dict={},
path_save="GMSH_model.msh",
is_sliding_band=False,
is_airbox=False,
transform_list=[],
is_set_labels=False,
):
"""Draws a machine mesh in GMSH format
Parameters
----------
output : Output
Output object
sym : int
the symmetry applied on the stator and the rotor (take into account antiperiodicity)
boundary_prop : dict
dictionary to match FEA boundary conditions (dict values) with line labels (dict keys) that are set in the build_geometry methods
boundary_list : list
list of boundary condition names
surface_label : dict
dict for the translation of the actual surface labels into FEA software compatible labels
is_remove_vent : bool
True to remove the ventilation ducts (Default value = False)
is_remove_slotS : bool
True to solve without slot effect on the Stator (Default value = False)
is_remove_slotR : bool
True to solve without slot effect on the Rotor (Default value = False)
kgeo_fineness : float
global coefficient to adjust geometry fineness
kmesh_fineness : float
global coefficient to adjust mesh fineness
is_antiper: bool
To apply antiperiodicity boundary conditions
is_lam_only_S: bool
Draw only stator lamination
is_lam_only_R: bool
Draw only rotor lamination
Returns
-------
GMSH_dict : dict
dictionary containing the main parameters of GMSH File
"""
# check some input parameter
if is_lam_only_S and is_lam_only_R:
raise InputError(
"Only 'is_lam_only_S' or 'is_lam_only_R' can be True at the same time"
)
# get machine
machine = output.simu.machine
mesh_dict = {}
tol = 1e-6
# Default stator mesh element size
mesh_size_S = machine.stator.Rext / 100.0
mesh_size_R = machine.rotor.Rext / 25.0
# For readibility
model = gmsh.model
factory = model.geo
# Start a new model
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", int(False))
gmsh.option.setNumber("Geometry.CopyMeshingMethod", 1)
gmsh.option.setNumber("Geometry.PointNumbers", 0)
gmsh.option.setNumber("Geometry.LineNumbers", 0)
gmsh.option.setNumber("Mesh.CharacteristicLengthMin",
min(mesh_size_S, mesh_size_R))
gmsh.option.setNumber("Mesh.CharacteristicLengthMax",
max(mesh_size_S, mesh_size_R))
model.add("Pyleecan")
# build geometry
alpha = 0
rotor_list = list()
rotor_list.extend(machine.shaft.build_geometry(sym=sym, alpha=alpha))
rotor_list.extend(machine.rotor.build_geometry(sym=sym, alpha=alpha))
stator_list = list()
stator_list.extend(machine.stator.build_geometry(sym=sym, alpha=alpha))
# set origin
oo = factory.addPoint(0, 0, 0, 0, tag=-1)
gmsh_dict = {
0: {
"tag": 0,
"label": "origin",
"with_holes": False,
1: {
"tag": 0,
"n_elements": 1,
"bc_name": None,
"begin": {
"tag": oo,
"coord": complex(0.0, 0.0)
},
"end": {
"tag": None,
"coord": None
},
"cent": {
"tag": None,
"coord": None
},
"arc_angle": None,
"line_angle": None,
},
}
}
nsurf = 0 # number of surfaces
if not is_lam_only_S:
for surf in rotor_list:
nsurf += 1
# print(surf.label)
gmsh_dict.update({
nsurf: {
"tag": None,
"label": surface_label.get(surf.label, "UNKNOWN"),
}
})
if "Lamination_Rotor" in surf.label:
gmsh_dict[nsurf]["with_holes"] = True
lam_rotor_surf_id = nsurf
else:
gmsh_dict[nsurf]["with_holes"] = False
# comp. number of elements on the lines & override by user values in case
mesh_dict = surf.comp_mesh_dict(element_size=mesh_size_R)
if user_mesh_dict: # check if dict is not None nor empty
mesh_dict.update(user_mesh_dict)
# add all lines of the current surface to the gmsh_dict
for line in surf.get_lines():
# When symmetry is 1 the shaft surface is substrtacted from Rotor Lam instead
if sym == 1 and line.label == "Lamination_Rotor_Yoke_Radius_Int":
continue
n_elem = mesh_dict.get(line.label)
n_elem = n_elem if n_elem is not None else 0
bc_name = get_boundary_condition(line, boundary_prop)
# Gmsh built-in engine does not allow arcs larger than 180deg
# so arcs are split into two
if (isinstance(line, Arc)
and abs(line.get_angle() * 180.0 / cmath.pi) >= 180.0):
rot_dir = 1 if line.is_trigo_direction == True else -1
arc1 = Arc2(
begin=line.get_begin(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
arc2 = Arc2(
begin=arc1.get_end(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
for arc in [arc1, arc2]:
_add_line_to_dict(
geo=factory,
line=arc,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size_R,
n_elements=n_elem,
bc=bc_name,
)
elif isinstance(line, Arc) and (abs(
line.get_angle() * 180.0 / cmath.pi) <= tol):
# Don't draw anything, this is a circle and usually is repeated ?
pass
else:
_add_line_to_dict(
geo=factory,
line=line,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size_R,
n_elements=n_elem,
bc=bc_name,
)
lam_and_holes = list()
ext_lam_loop = None
rotor_cloops = list()
# loop though all (surface) entries of the rotor lamination
for s_data in gmsh_dict.values():
lloop = []
# skip this surface dataset if it is the origin
if s_data["label"] == "origin":
continue
# build a lineloop of the surfaces lines
for lvalues in s_data.values():
if type(lvalues) is not dict:
continue
lloop.extend([lvalues["tag"]])
cloop = factory.addCurveLoop(lloop)
if "MAGNET" in s_data["label"]:
rotor_cloops.extend([cloop])
# search for the holes to substract from rotor lam
if "ROTOR_LAM" in s_data["label"]:
ext_lam_loop = cloop
else:
# MachineSIPSM does not have holes in rotor lam
# only shaft is taken out if symmetry is one
if isinstance(machine, MachineSIPMSM):
if sym == 1 and s_data["label"] == "SHAFT":
lam_and_holes.extend([cloop])
else:
if sym == 1:
lam_and_holes.extend([cloop])
elif s_data["label"] != "SHAFT":
lam_and_holes.extend([cloop])
else:
pass
# Shaft, magnets and magnet pocket surfaces are created
if not is_lam_only_R:
s_data["tag"] = factory.addPlaneSurface([cloop], tag=-1)
pg = model.addPhysicalGroup(2, [s_data["tag"]])
model.setPhysicalName(2, pg, s_data["label"])
# Finally rotor lamination is built
if ext_lam_loop is not None:
lam_and_holes.insert(0, ext_lam_loop)
if len(lam_and_holes) > 0:
gmsh_dict[lam_rotor_surf_id]["tag"] = factory.addPlaneSurface(
lam_and_holes, tag=-1)
pg = model.addPhysicalGroup(2, [gmsh_dict[lam_rotor_surf_id]["tag"]])
model.setPhysicalName(2, pg, gmsh_dict[lam_rotor_surf_id]["label"])
# rotor_cloops = lam_and_holes
# store rotor dict
rotor_dict = gmsh_dict.copy()
# init new dict for stator
gmsh_dict = {
0: {
"tag": 0,
"label": "origin",
"with_holes": False,
1: {
"tag": 0,
"n_elements": 1,
"bc_name": None,
"begin": {
"tag": oo,
"coord": complex(0.0, 0.0)
},
"end": {
"tag": None,
"coord": None
},
"cent": {
"tag": None,
"coord": None
},
},
}
}
# nsurf = 0
if not is_lam_only_R:
stator_cloops = []
for surf in stator_list:
nsurf += 1
gmsh_dict.update({
nsurf: {
"tag": None,
"label": surface_label.get(surf.label, "UNKNOWN"),
}
})
if surf.label.find("Lamination_Stator") != -1:
gmsh_dict[nsurf]["with_holes"] = True
else:
gmsh_dict[nsurf]["with_holes"] = False
# comp. number of elements on the lines & override by user values in case
mesh_dict = surf.comp_mesh_dict(element_size=mesh_size_S)
if user_mesh_dict: # check if dict is not None nor empty
mesh_dict.update(user_mesh_dict)
# add all lines of the current surface to the gmsh_dict
for line in surf.get_lines():
n_elem = mesh_dict.get(line.label)
n_elem = n_elem if n_elem is not None else 0
bc_name = get_boundary_condition(line, boundary_prop)
# Gmsh built-in engine does not allow arcs larger than 180deg
# so arcs are split into two
if (isinstance(line, Arc)
and abs(line.get_angle() * 180.0 / cmath.pi) >= 180.0):
rot_dir = 1 if line.is_trigo_direction == True else -1
arc1 = Arc2(
begin=line.get_begin(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
arc2 = Arc2(
begin=arc1.get_end(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
for arc in [arc1, arc2]:
_add_line_to_dict(
geo=factory,
line=arc,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size_S,
n_elements=n_elem,
bc=bc_name,
)
else:
_add_line_to_dict(
geo=factory,
line=line,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size_S,
n_elements=n_elem,
bc=bc_name,
)
for s_data in gmsh_dict.values():
lloop = []
# skip this surface dataset if it is the origin
if s_data["label"] == "origin":
continue
# build a lineloop of the surfaces lines
for lvalues in s_data.values():
if type(lvalues) is not dict:
continue
lloop.extend([lvalues["tag"]])
cloop = factory.addCurveLoop(lloop)
stator_cloops.append(cloop)
# Winding surfaces are created
if (s_data["label"].find("STATOR_LAM") !=
-1) or (not is_lam_only_S):
s_data["tag"] = factory.addPlaneSurface([cloop], tag=-1)
pg = model.addPhysicalGroup(2, [s_data["tag"]])
model.setPhysicalName(2, pg, s_data["label"])
# stator_dict = gmsh_dict.copy()
gmsh_dict.update(rotor_dict)
if is_sliding_band and (not is_lam_only_R) and (not is_lam_only_S):
sb_list = get_sliding_band(sym=sym, machine=machine)
else:
sb_list = []
# Default sliding mesh element size
mesh_size = 2.0 * cmath.pi * machine.rotor.Rext / 360.0
# nsurf = 0
for surf in sb_list:
nsurf += 1
gmsh_dict.update({
nsurf: {
"tag": None,
"label": surface_label.get(surf.label, "UNKNOWN"),
}
})
for line in surf.get_lines():
n_elem = mesh_dict.get(line.label)
n_elem = n_elem if n_elem is not None else 0
bc_name = get_boundary_condition(line, boundary_prop)
# Gmsh built-in engine does not allow arcs larger than 180deg
# so arcs are split into two
if (isinstance(line, Arc)
and abs(line.get_angle() * 180.0 / cmath.pi) >= 180.0):
rot_dir = 1 if line.is_trigo_direction == True else -1
arc1 = Arc2(
begin=line.get_begin(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
arc2 = Arc2(
begin=arc1.get_end(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
for arc in [arc1, arc2]:
_add_agline_to_dict(
geo=factory,
line=arc,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
n_elements=n_elem,
bc=bc_name,
)
else:
_add_agline_to_dict(
geo=factory,
line=line,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
n_elements=n_elem,
bc=bc_name,
)
for s_data in gmsh_dict.values():
lloop = []
# skip this surface dataset if it is the origin
if s_data["label"] == "origin" or not ("AG_" in s_data["label"]
or "SB_" in s_data["label"]):
continue
# build a lineloop of the surfaces lines
for lvalues in s_data.values():
if type(lvalues) is not dict:
continue
lloop.extend([lvalues["tag"]])
if lloop:
cloop = factory.addCurveLoop(lloop)
if "AG_INT" in s_data["label"] and isinstance(
machine, MachineSIPMSM):
s_data["tag"] = factory.addPlaneSurface([cloop] + rotor_cloops,
tag=-1)
else:
s_data["tag"] = factory.addPlaneSurface([cloop], tag=-1)
pg = model.addPhysicalGroup(2, [s_data["tag"]])
model.setPhysicalName(2, pg, s_data["label"])
if is_airbox and (not is_lam_only_R) and (not is_lam_only_S):
ab_list = get_air_box(sym=sym, machine=machine)
else:
ab_list = []
# Default airbox mesh element size
mesh_size = machine.stator.Rext / 50.0
for surf in ab_list:
nsurf += 1
gmsh_dict.update({
nsurf: {
"tag": None,
"label": surface_label.get(surf.label, "UNKNOWN"),
}
})
for line in surf.get_lines():
n_elem = mesh_dict.get(line.label)
n_elem = n_elem if n_elem is not None else 0
bc_name = get_boundary_condition(line, boundary_prop)
# Gmsh built-in engine does not allow arcs larger than 180deg
# so arcs are split into two
if (isinstance(line, Arc)
and abs(line.get_angle() * 180.0 / cmath.pi) >= 180.0):
rot_dir = 1 if line.get_angle() > 0 else -1
arc1 = Arc2(
begin=line.get_begin(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
arc2 = Arc2(
begin=arc1.get_end(),
center=line.get_center(),
angle=rot_dir * cmath.pi / 2.0,
label=line.label,
)
for arc in [arc1, arc2]:
_add_line_to_dict(
geo=factory,
line=arc,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
n_elements=n_elem,
bc=bc_name,
)
else:
_add_line_to_dict(
geo=factory,
line=line,
d=gmsh_dict,
idx=nsurf,
mesh_size=mesh_size,
n_elements=n_elem,
bc=bc_name,
)
for s_id, s_data in gmsh_dict.items():
lloop = []
if s_id == 0:
continue
for lvalues in s_data.values():
if s_data["label"].find("AIRBOX") != -1:
if type(lvalues) is not dict:
continue
lloop.extend([lvalues["tag"]])
else:
continue
if lloop:
cloop = factory.addCurveLoop(lloop)
s_data["tag"] = factory.addPlaneSurface([cloop], tag=-1)
pg = model.addPhysicalGroup(2, [s_data["tag"]])
model.setPhysicalName(2, pg, s_data["label"])
# Set boundary conditions in gmsh lines
for propname in boundary_list:
bc_id = []
for s_data in gmsh_dict.values():
for lvalues in s_data.values():
if type(lvalues) is not dict:
continue
if lvalues["bc_name"] == propname:
bc_id.extend([abs(lvalues["tag"])])
if bc_id:
pg = model.addPhysicalGroup(1, bc_id)
model.setPhysicalName(1, pg, propname)
# Set all line labels as physical groups
if is_set_labels:
groups = {}
for s_data in gmsh_dict.values():
for lvalues in s_data.values():
if (type(lvalues) is not dict or "label" not in lvalues
or not lvalues["label"]):
continue
if lvalues["label"] not in groups.keys():
groups[lvalues["label"]] = []
groups[lvalues["label"]].append(abs(lvalues["tag"]))
for label, tags in groups.items():
pg = model.addPhysicalGroup(1, tags)
model.setPhysicalName(1, pg, label)
factory.synchronize()
# save mesh or geo file depending on file extension
filename, file_extension = splitext(path_save)
if file_extension == ".geo":
gmsh.write(filename + ".geo_unrolled")
replace(filename + ".geo_unrolled", filename + file_extension)
else:
gmsh.model.mesh.generate(2)
gmsh.write(path_save)
# gmsh.fltk.run() # Uncomment to launch Gmsh GUI
gmsh.finalize()
return gmsh_dict
def chain(self, maxElementSize=None):
"""Get a polygonal chain representing the speaker membrane."""
# check if cached polygonal chain is still good
if not (maxElementSize is None
or maxElementSize == self.maxElementSize):
self.maxElementSize = maxElementSize
self.aVertex = None
self.aSegment = None
self.nOpenElements = -1
if self.aVertex is None or self.aSegment is None or self.nOpenElements == -1:
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 1)
gmsh.model.add("Cone Speaker")
gmsh.model.geo.addPoint(0.0, 0.0, 0.0, self.maxElementSize, 1)
gmsh.model.geo.addPoint(*self.coneEdge(), self.maxElementSize, 2)
gmsh.model.geo.addPoint(*self.capEdge(), self.maxElementSize, 3)
gmsh.model.geo.addPoint(*self.capSphereCenter(),
self.maxElementSize, 4)
gmsh.model.geo.addPoint(*self.capCenter(), self.maxElementSize, 5)
gmsh.model.geo.addLine(1, 2, 1)
gmsh.model.addPhysicalGroup(1, [1], 1)
gmsh.model.setPhysicalName(1, 1, "Interface")
gmsh.model.geo.addLine(2, 3, 2)
gmsh.model.geo.addCircleArc(3, 4, 5, 3)
gmsh.model.addPhysicalGroup(1, [2, 3], 2)
gmsh.model.setPhysicalName(1, 2, "Speaker Cone")
gmsh.model.geo.synchronize()
gmsh.model.mesh.generate(1)
nodeTags, coord, parametricCoord = gmsh.model.mesh.getNodes(
1, -1, True)
self.aVertex = np.asarray(coord, dtype=np.float32).reshape(
len(nodeTags), 3)
# build reordering dictionary
nodeTagToIdx = dict()
for i, t in enumerate(nodeTags):
nodeTagToIdx[t] = i
aNodeTags = []
# extract "open elements" or "Interface" first
elementTypes, elementTags, nodeTags = gmsh.model.mesh.getElements(
1, 1)
assert len(elementTypes
) == 1 and elementTypes[0] == 1 # only line segments
assert len(elementTags) == 1
assert len(nodeTags) == 1 and len(
nodeTags[0]) == len(elementTags[0]) * 2
aNodeTags.extend(nodeTags[0]) # extract line segment node tags
self.nOpenElements = len(elementTags[0])
# extract speaker elements
elementTypes, elementTags, nodeTags = gmsh.model.mesh.getElements(
1, 2)
assert len(elementTypes
) == 1 and elementTypes[0] == 1 # only line segments
assert len(elementTags) == 1
assert len(nodeTags) == 1 and len(
nodeTags[0]) == len(elementTags[0]) * 2
aNodeTags.extend(nodeTags[0]) # extract line segment node tags
elementTypes, elementTags, nodeTags = gmsh.model.mesh.getElements(
1, 3)
assert len(elementTypes
) == 1 and elementTypes[0] == 1 # only line segments
assert len(elementTags) == 1
assert len(nodeTags) == 1 and len(
nodeTags[0]) == len(elementTags[0]) * 2
aNodeTags.extend(nodeTags[0]) # extract line segment node tags
# relabel node tags with index into vertex array
aTempNodeTags = np.empty(len(aNodeTags), dtype=np.int32)
for i, t in enumerate(aNodeTags):
aTempNodeTags[i] = nodeTagToIdx[t]
self.aSegment = aTempNodeTags.reshape(len(aNodeTags) // 2, 2)
gmsh.finalize()
self.oGeometry = Chain(self.aVertex.shape[0],
self.aSegment.shape[0])
self.oGeometry.aVertex = self.aVertex[:, 1:3]
self.oGeometry.aEdge = self.aSegment
self.oGeometry.namedPartition['interface'] = (0,
self.nOpenElements)
self.oGeometry.namedPartition['cavity'] = (self.nOpenElements,
self.aSegment.shape[0])
return self.oGeometry
def create_plate_mesh(plate,
geom_repr="solid",
max_size=0.1,
order=1,
algo=8,
tol=1e-3,
fem=None,
interactive=False,
gmsh_session=None):
"""
:param plate:
:param gmsh_session:
:param geom_repr:
:param max_size:
:param order:
:param algo: Mesh algorithm
:param tol: Maximum geometry tolerance
:param fem:
:param interactive:
:type plate: ada.Plate
:type fem: ada.fem.FEM
:type gmsh_session: gmsh
"""
temp_dir = _Settings.temp_dir
if gmsh_session is None:
gmsh_session = _init_gmsh_session()
option = gmsh_session.option
model = gmsh_session.model
option.setNumber("Mesh.Algorithm", algo)
option.setNumber("Mesh.MeshSizeFromCurvature", True)
option.setNumber("Mesh.MinimumElementsPerTwoPi", 12)
option.setNumber("Mesh.MeshSizeMax", max_size)
option.setNumber("Mesh.ElementOrder", order)
option.setNumber("Mesh.SecondOrderIncomplete", 1)
option.setNumber("Mesh.Smoothing", 3)
option.setNumber("Geometry.Tolerance", tol)
option.setNumber("Geometry.OCCImportLabels", 1) # import colors from STEP
if geom_repr == "solid":
option.setNumber("Geometry.OCCMakeSolids", 1)
name = f"temp_{create_guid()}"
plate.to_stp(temp_dir / name, geom_repr=geom_repr)
gmsh_session.merge(str(temp_dir / f"{name}.stp"))
factory = model.geo
factory.synchronize()
model.mesh.setRecombine(2, 1)
model.mesh.generate(3)
model.mesh.removeDuplicateNodes()
if interactive:
gmsh_session.fltk.run()
if fem is None:
gmsh_session.write(str(temp_dir / f"{name}.msh"))
m = meshio.read(str(temp_dir / f"{name}.msh"))
m.write(temp_dir / f"{name}.xdmf")
gmsh.finalize()
return None
fem_set_name = f"{plate.name}_all"
get_nodes_and_elements(gmsh_session, fem, fem_set_name=fem_set_name)
femset = fem.elsets[fem_set_name]
if geom_repr == "solid":
fem_sec = FemSection(
f"{plate.name}_sec",
"solid",
femset,
plate.material,
)
else: # geom_repr == "shell":
fem_sec = FemSection(f"{plate.name}_sec",
"shell",
femset,
plate.material,
local_z=plate.n,
thickness=plate.t,
int_points=5)
fem.add_section(fem_sec)
def discretize(self, g, data):
# Get the dictionaries for storage of data and discretization matrices
parameter_dictionary = data[pp.PARAMETERS][self.keyword]
matrix_dictionary = data[pp.DISCRETIZATION_MATRICES][self.keyword]
# The the local mesh arguments
local_mesh_args = data.get("local_mesh_args", None)
micro_network = parameter_dictionary[self.network_keyword]
num_processes = parameter_dictionary.get("num_processes", 1)
discr_ig = partial(
self._discretize_interaction_region,
g,
micro_network,
parameter_dictionary,
local_mesh_args,
)
if num_processes == 1:
# run the code in serial, useful also for debug
out = []
for reg in self._interaction_regions(g):
out.append(discr_ig(reg))
else:
# run the code in parallel
with mp.Pool(processes=num_processes) as p:
out = p.map(discr_ig, list(self._interaction_regions(g)))
# Finalize gmsh now that we're done with the discretization.
gmsh.finalize()
# Also inform the Gmsh writer we have finalized gmsh.
pp.fracs.gmsh_interface.GmshWriter.gmsh_initialized = False
# Data structures to build up the flux discretization as a sparse coo-matrix
rows_flux, cols_flux, data_flux = [], [], []
# Data structures for the discretization of boundary conditions
rows_bound, cols_bound, data_bound = [], [], []
# data structures for discretization of pressure trace operator on macro boundaries
rows_cell_trace, cols_cell_trace, data_cell_trace = [], [], []
rows_face_trace, cols_face_trace, data_face_trace = [], [], []
# unpack all the values
for reg_values in out:
cell, bound, cell_trace, face_trace = reg_values
cols_flux += cell[0]
rows_flux += cell[1]
data_flux += cell[2]
cols_bound += bound[0]
rows_bound += bound[1]
data_bound += bound[2]
cols_cell_trace += cell_trace[0]
rows_cell_trace += cell_trace[1]
data_cell_trace += cell_trace[2]
cols_face_trace += face_trace[0]
rows_face_trace += face_trace[1]
data_face_trace += face_trace[2]
# Construct the global matrix
flux = sps.coo_matrix((data_flux, (rows_flux, cols_flux)),
shape=(g.num_faces, g.num_cells)).tocsr()
# Construct the global flux matrix
bound_flux = sps.coo_matrix((data_bound, (rows_bound, cols_bound)),
shape=(g.num_faces, g.num_faces)).tocsr()
bound_pressure_cell = sps.coo_matrix(
(data_cell_trace, (rows_cell_trace, cols_cell_trace)),
shape=(g.num_faces, g.num_cells),
).tocsr()
bound_pressure_face = sps.coo_matrix(
(data_face_trace, (rows_face_trace, cols_face_trace)),
shape=(g.num_faces, g.num_faces),
).tocsr()
# For Neumann boundaries, we should not use the flux discretization (the flux
# is known). The boundary discretization is modified to simply reuse the flux.
bc = parameter_dictionary["bc"]
neumann_faces = np.where(bc.is_neu)[0]
pp.fvutils.zero_out_sparse_rows(flux, neumann_faces)
# Set sign of Neumann faces according to the divergence operator. This will
# counteract minus signs in the divergence during assembly.
sgn, _ = g.signs_and_cells_of_boundary_faces(neumann_faces)
# Here we also zero out non-diagonal terms, but these should be zero anyhow
# (by construction of the coarse problems), but better safe than sorry
bound_flux = pp.fvutils.zero_out_sparse_rows(bound_flux,
neumann_faces,
diag=sgn)
matrix_dictionary[self.flux_matrix_key] = flux
matrix_dictionary[self.bound_flux_matrix_key] = bound_flux
matrix_dictionary[
self.bound_pressure_cell_matrix_key] = bound_pressure_cell
matrix_dictionary[
self.bound_pressure_face_matrix_key] = bound_pressure_face
# Empty discretization of vector sources - we will not provide this for the
# foreseeable future.
matrix_dictionary[self.vector_source_matrix_key] = sps.csc_matrix(
(g.num_faces, g.num_cells * g.dim))
matrix_dictionary[
self.bound_pressure_vector_source_matrix_key] = sps.csc_matrix(
(g.num_faces, g.num_cells * g.dim))
def generalized_mesher(elements,
fem,
geom_repr="solid",
max_size=0.1,
order=1,
algo=8,
tol=1e-3,
interactive=False,
gmsh_session=None):
"""
:param elements:
:param gmsh_session:
:param geom_repr:
:param max_size:
:param order:
:param algo: Mesh algorithm
:param tol: Maximum geometry tolerance
:param interactive:
:type elements: list
:type fem: ada.fem.FEM
:type gmsh_session: gmsh
"""
from ada import Beam
if gmsh_session is None:
gmsh_session = _init_gmsh_session()
temp_dir = _Settings.temp_dir
name = fem.parent.name.replace("/", "") + f"_{create_guid()}"
option = gmsh_session.option
model = gmsh_session.model
option.setNumber("Mesh.Algorithm", algo)
option.setNumber("Mesh.MeshSizeFromCurvature", True)
option.setNumber("Mesh.MinimumElementsPerTwoPi", 12)
option.setNumber("Mesh.MeshSizeMax", max_size)
option.setNumber("Mesh.ElementOrder", order)
option.setNumber("Mesh.SecondOrderIncomplete", 1)
option.setNumber("Mesh.Smoothing", 3)
option.setNumber("Geometry.Tolerance", tol)
option.setNumber("Geometry.OCCImportLabels", 1) # import colors from STEP
if geom_repr == "solid":
option.setNumber("Geometry.OCCMakeSolids", 1)
model.add(name)
p = Part("DummyPart") / elements
if geom_repr in ["shell", "solid"]:
p.to_stp(temp_dir / name, geom_repr=geom_repr)
gmsh_session.open(str(temp_dir / f"{name}.stp"))
else: # beam
for el in elements:
if type(el) is Beam:
p1, p2 = el.n1.p, el.n2.p
s = get_point(p1, gmsh_session)
e = get_point(p2, gmsh_session)
if len(s) == 0:
s = [(0, model.geo.addPoint(*p1.tolist(), max_size))]
if len(e) == 0:
e = [(0, model.geo.addPoint(*p2.tolist(), max_size))]
# line = model.geo.addLine(s[0][1], e[0][1])
model.geo.synchronize()
model.mesh.setRecombine(3, 1)
model.mesh.generate(3)
model.mesh.removeDuplicateNodes()
if interactive:
gmsh_session.fltk.run()
get_nodes_and_elements(gmsh_session, fem, name)
if fem is None:
gmsh_session.write(str(temp_dir / f"{name}.msh"))
m = meshio.read(str(temp_dir / f"{name}.msh"))
m.write(temp_dir / f"{name}.xdmf")
gmsh.finalize()
return None
# TODO: Identify which part of cross section the entities belong to and add physical group to assign section props
# Alternatively it might be more simple to just build the geometries from scratch.
# p1, p2 = beam.n1.p, beam.n2.p
if geom_repr == "solid":
NotImplementedError("")
elif geom_repr == "shell":
# Get element section properties
ents = gmsh.model.occ.getEntities(2)
for dim, ent in ents:
r = model.occ.getCenterOfMass(2, ent)
for el in elements:
if type(el) is Beam:
elname = el.name.replace("/", "")
t, n, c = eval_thick_normal_from_cog_of_beam_plate(el, r)
name = model.getEntityName(dim, ent)
tags, coord, param = model.mesh.getNodes(2, ent, True)
# get surface normal on all nodes, i.e. including on the geometrical
# singularities (edges/points)
# normals = gmsh.model.getNormal(ent, param)
# curv = gmsh.model.getCurvature(2, ent, param)
# print(ent, r)
elemTypes, elemTags, elemNodeTags = model.mesh.getElements(
2, ent)
femset = FemSet(f"{elname}_ent{ent}", [
fem.elements.from_id(x)
for x in chain.from_iterable(elemTags)
], "elset")
fem.add_set(femset)
fem_sec = FemSection(
f"{elname}_{c}_{ent}",
"shell",
femset,
el.material,
local_z=n,
thickness=t,
int_points=5,
)
fem.add_section(fem_sec)
else: # geom_repr == "beam":
raise NotImplementedError()
gmsh.finalize()
for i in range(1, 11):
factory.addPoint(i, math.sin(i/9.*2.*math.pi), 0, 0.1, i)
factory.addSpline(range(1, 11), 1)
factory.addBSpline(range(1, 11), 2)
factory.addBezier(range(1, 11), 3)
factory.addPoint(0.2,-1.6,0,0.1, 101)
factory.addPoint(1.2,-1.6,0,0.1, 102)
factory.addPoint(1.2,-1.1,0,0.1, 103)
factory.addPoint(0.3,-1.1,0,0.1, 104)
factory.addPoint(0.7,-1,0,0.1, 105)
# periodic bspline through the control points
factory.addSpline([103,102,101,104,105,103], 100)
# periodic bspline from given control points and default parameters - will
# create a new vertex
factory.addBSpline([103,102,101,104,105,103], 101)
# general bspline with explicit degree, knots and multiplicities
factory.addPoint(0,-2,0,0.1,201)
factory.addPoint(1,-2,0,0.1,202)
factory.addPoint(1,-3,0,0.1,203)
factory.addPoint(0,-3,0,0.1,204)
factory.addBSpline([201,202,203,204], 200, 2, [], [0,0.5,1], [3,1,3])
factory.synchronize()
gmsh.fltk.run()
gmsh.finalize()
def mesh_w_tube(mesh_params, mesh_name):
filename_stem = __file__.split(".")[0]
case_stem = f"{filename_stem}_{mesh_name}"
gmsh.initialize()
model.add(case_stem)
inner_radius = physical_params.r - physical_params.thickness
outer_radius = physical_params.r
# 1
origin = -physical_params.R, 0.0, 0.0
axis_dir = 0.0, 1.0, 0.0
center_of_rot = 0.0, 0.0, 0.0
rot_normal = 0.0, 0.0, -1.0
make_elbow(origin, axis_dir, inner_radius, outer_radius, center_of_rot,
rot_normal, mesh_params.n_rings, mesh_params.n_sectors,
mesh_params.n_axial)
# 2
origin = physical_params.R, -physical_params.l1, 0.0
axis_dir = 0.0, 1.0, 0.0
height = physical_params.l1
make_tube(origin, axis_dir, inner_radius, outer_radius, height,
mesh_params.n_rings, mesh_params.n_sectors,
mesh_params.n_layers_2_3)
# 3
origin = -physical_params.R, -physical_params.l1, 0.0
axis_dir = 0.0, 1.0, 0.0
height = physical_params.l1
make_tube(origin, axis_dir, inner_radius, outer_radius, height,
mesh_params.n_rings, mesh_params.n_sectors,
mesh_params.n_layers_2_3)
# 4
origin = -3.0 * physical_params.R, -physical_params.l1, 0.0
axis_dir = 0.0, 1.0, 0.0
center_of_rot = -2.0 * physical_params.R, -physical_params.l1, 0.0
rot_normal = 0.0, 0.0, 1.0
make_elbow(origin, axis_dir, inner_radius, outer_radius, center_of_rot,
rot_normal, mesh_params.n_rings, mesh_params.n_sectors,
mesh_params.n_axial)
# 5
origin = 3.0 * physical_params.R, -physical_params.l1, 0.0
axis_dir = 0.0, 1.0, 0.0
center_of_rot = 2.0 * physical_params.R, -physical_params.l1, 0.0
rot_normal = 0.0, 0.0, -1.0
make_elbow(origin, axis_dir, inner_radius, outer_radius, center_of_rot,
rot_normal, mesh_params.n_rings, mesh_params.n_sectors,
mesh_params.n_axial)
# 6
origin = 3.0 * physical_params.R, physical_params.l2, 0.0
axis_dir = 0.0, -1.0, 0.0
height = physical_params.l1 + physical_params.l2
make_tube(origin, axis_dir, inner_radius, outer_radius, height,
mesh_params.n_rings, mesh_params.n_sectors,
mesh_params.n_layers_6_7)
# 7
origin = -3.0 * physical_params.R, physical_params.l2, 0.0
axis_dir = 0.0, -1.0, 0.0
height = physical_params.l1 + physical_params.l2
make_tube(origin, axis_dir, inner_radius, outer_radius, height,
mesh_params.n_rings, mesh_params.n_sectors,
mesh_params.n_layers_6_7)
model.geo.synchronize()
model.mesh.generate(3)
gmsh.write(f"{case_stem}.msh")
gmsh.finalize()