def mesh_statistics(in_file):
""" Compute mesh statistics for a .msh mesh realization
Parameters
----------
in_file : Path
Path to a .msh file
Returns
-------
"""
in_file = Path(in_file)
assert in_file.suffix == ".msh"
assert in_file.is_file()
import gmsh
gmsh.initialize()
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(in_file)
gmsh.finalize()
def mesh_bar_gmshapi(
name, Lx, Ly, lc, tdim, order=1, msh_file=None, comm=MPI.COMM_WORLD
):
"""
Create mesh of 3d tensile test specimen according to ISO 6892-1:2019 using the Python API of Gmsh.
"""
# Perform Gmsh work only on rank = 0
if comm.rank == 0:
import gmsh
# Initialise gmsh and set options
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 1)
# gmsh.option.setNumber("Mesh.Algorithm", 6)
gmsh.option.setNumber("Mesh.Algorithm", 5)
gmsh.model.mesh.optimize("Netgen")
model = gmsh.model()
model.add("Rectangle")
model.setCurrent("Rectangle")
p0 = model.geo.addPoint(0.0, 0.0, 0, lc, tag=0)
p1 = model.geo.addPoint(Lx, 0.0, 0, lc, tag=1)
p2 = model.geo.addPoint(Lx, Ly, 0.0, lc, tag=2)
p3 = model.geo.addPoint(0, Ly, 0, lc, tag=3)
# points = [p0, p1, p2, p3]
bottom = model.geo.addLine(p0, p1)
right = model.geo.addLine(p1, p2)
top = model.geo.addLine(p2, p3)
left = model.geo.addLine(p3, p0)
cloop1 = model.geo.addCurveLoop([bottom, right, top, left])
# surface_1 =
model.geo.addPlaneSurface([cloop1])
model.geo.synchronize()
surface_entities = [model[1] for model in model.getEntities(tdim)]
model.addPhysicalGroup(tdim, surface_entities, tag=5)
model.setPhysicalName(tdim, 5, "Rectangle surface")
# Set geometric order of mesh cells
gmsh.model.mesh.setOrder(order)
gmsh.model.addPhysicalGroup(tdim - 1, [3, 0], tag=6)
gmsh.model.setPhysicalName(tdim - 1, 6, "left")
gmsh.model.addPhysicalGroup(tdim - 1, [1, 2], tag=7)
gmsh.model.setPhysicalName(tdim - 1, 7, "right")
gmsh.model.addPhysicalGroup(tdim - 1, [2, 3], tag=8)
gmsh.model.setPhysicalName(tdim - 1, 8, "top")
gmsh.model.addPhysicalGroup(tdim - 1, [0, 1], tag=9)
gmsh.model.setPhysicalName(tdim - 1, 9, "bottom")
model.mesh.generate(tdim)
# Optional: Write msh file
if msh_file is not None:
os.makedirs(os.path.dirname(msh_file), exist_ok=True)
gmsh.write(msh_file)
return gmsh.model if comm.rank == 0 else None, tdim
def convertMEDfile(med_file):
"""
This function opens an MED file by means of gmsh
and saves it in .msh2 format.
:param str med_file: has to end with .med
"""
filename, ext = os.path.splitext(med_file)
if ext != ".med":
print("You must provide a med file!")
sys.exit(0)
# initialize gmsh
gmsh.initialize()
# gmsh writes out messages
gmsh.option.setNumber("General.Terminal", 1)
# add a new model
gmsh.model.add("new_model")
# open med file
gmsh.open(med_file)
# need dirty hack to write in correct format
gmsh.write(filename + ".msh2")
gmsh.finalize()
with open(filename + ".msh2", 'r') as mesh_file:
mesh = mesh_file.read()
with open(filename + ".msh2", 'w') as mesh_file:
mesh_file.write(mesh.replace(',', '.'))
return
def create_model(res_points, outer_points, cntr, name):
model = gmsh.model
factory = model.geo
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 1)
model.add("rotor")
lc = 1e-2
factory.addPoint(cntr[0], cntr[1], 0, lc, 1)
for i in range(4):
factory.addPoint(outer_points[i][0], outer_points[i][1], 0, lc, i + 2)
factory.addLine(2, 3, 1)
factory.addCircleArc(3, 1, 4, 2)
factory.addLine(4, 5, 3)
factory.addCircleArc(5, 1, 2, 4)
point_cnt = 5
for i in range(len(res_points)):
for j in range(len(res_points[i])):
point_cnt += 1
factory.addPoint(res_points[i][j][0], res_points[i][j][1], 0, lc,
point_cnt)
start = point_cnt - len(res_points[i]) + 1
for j in range(len(res_points[i]) - 1):
factory.addLine(start + j, start + j + 1)
factory.addLine(point_cnt, start)
factory.synchronize()
model.mesh.generate(2)
gmsh.write(name)
gmsh.finalize()
def woofersSLA(maxElementSize=0.01):
r = 0.0635 # Effective membrane radius of Eminence Alpha 6a (computed from Sd as per spec sheet)
zOffset = 0.0
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 1)
gmsh.model.add("disk")
gmsh.model.geo.addPoint(0.0, 0.0, zOffset, maxElementSize, 1)
gmsh.model.geo.addPoint(r, 0.0, zOffset, maxElementSize, 2)
gmsh.model.geo.addPoint(0.0, r, zOffset, maxElementSize, 3)
gmsh.model.geo.addPoint(-r, 0.0, zOffset, maxElementSize, 4)
gmsh.model.geo.addPoint(0.0, -r, zOffset, maxElementSize, 5)
gmsh.model.geo.addCircleArc(2, 1, 3, 1)
gmsh.model.geo.addCircleArc(3, 1, 4, 2)
gmsh.model.geo.addCircleArc(4, 1, 5, 3)
gmsh.model.geo.addCircleArc(5, 1, 2, 4)
gmsh.model.geo.addCurveLoop([1, 2, 3, 4], 1)
gmsh.model.geo.addPlaneSurface([1], 1)
gmsh.model.geo.translate([(2, 1)], 0.0, r + 0.005, 0.0)
w2 = gmsh.model.geo.copy([(2, 1)])
gmsh.model.geo.translate(w2, 0.0, 2.0 * r + 0.01, 0.0)
w3 = gmsh.model.geo.copy([(2, 1)])
gmsh.model.geo.translate(w3, 0.0, -(2 * r + 0.01), 0.0)
w4 = gmsh.model.geo.copy([(2, 1)])
gmsh.model.geo.translate(w4, 0.0, -(4.0 * r + 0.02), 0.0)
gmsh.model.addPhysicalGroup(2, [1, w2[0][1], w3[0][1], w4[0][1]], 1)
gmsh.model.setPhysicalName(2, 1, "Woofers")
gmsh.model.geo.synchronize()
oMesh = getTriangleMesh("WoofersSLA")
gmsh.finalize()
return oMesh
def disk(r=0.1, z_offset=1.0, name="Disk", max_element_size=0.01):
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 1)
gmsh.model.add("disk")
gmsh.model.geo.addPoint(0.0, 0.0, z_offset, max_element_size, 1)
gmsh.model.geo.addPoint(r, 0.0, z_offset, max_element_size, 2)
gmsh.model.geo.addPoint(0.0, r, z_offset, max_element_size, 3)
gmsh.model.geo.addPoint(-r, 0.0, z_offset, max_element_size, 4)
gmsh.model.geo.addPoint(0.0, -r, z_offset, max_element_size, 5)
gmsh.model.geo.addCircleArc(2, 1, 3, 1)
gmsh.model.geo.addCircleArc(3, 1, 4, 2)
gmsh.model.geo.addCircleArc(4, 1, 5, 3)
gmsh.model.geo.addCircleArc(5, 1, 2, 4)
gmsh.model.geo.addCurveLoop([1, 2, 3, 4], 1)
gmsh.model.geo.addPlaneSurface([1], 1)
gmsh.model.addPhysicalGroup(2, [1], 1)
gmsh.model.setPhysicalName(2, 1, name)
gmsh.model.geo.synchronize()
mesh = get_triangle_mesh(name)
gmsh.finalize()
return mesh
def read_from_msh(filename: str, cell_data=False, facet_data=False, gdim=None):
"""
Reads a mesh from a msh-file and returns the dolfin-x mesh.
Input:
filename: Name of msh file
cell_data: Boolean, True of a mesh tag for cell data should be returned
(Default: False)
facet_data: Boolean, True if a mesh tag for facet data should be
returned (Default: False)
gdim: Geometrical dimension of problem (Default: 3)
"""
if MPI.COMM_WORLD.rank == 0:
# Check if gmsh is already initialized
try:
current_model = gmsh.model.getCurrent()
except ValueError:
current_model = None
gmsh.initialize()
gmsh.model.add("Mesh from file")
gmsh.merge(filename)
output = gmsh_model_to_mesh(gmsh.model, cell_data=cell_data,
facet_data=facet_data, gdim=gdim)
if MPI.COMM_WORLD.rank == 0:
if current_model is None:
gmsh.finalize()
else:
gmsh.model.setCurrent(current_model)
return output
def test_nx_ny_21_with_material(self):
"""Test nx, ny with 2 levels of 1 division and a material."""
ref_groups = groups_21_with_material
ref_centroids = centroids_21
mocmg.initialize()
gmsh.initialize()
rectangular_grid(bb_44, nx=[2, 2], ny=[2, 2], material="material_UO2")
group_nums = gmsh.model.getPhysicalGroups()
names = [gmsh.model.getPhysicalName(*grp) for grp in group_nums]
ref_names = list(ref_groups.keys())
# Check correct names/entities
for i, name in enumerate(ref_names):
self.assertEqual(name, names[i])
index = names.index(name)
group_ents = list(
gmsh.model.getEntitiesForPhysicalGroup(*group_nums[index]))
ref_group_ents = ref_groups[name]
self.assertEqual(group_ents, ref_group_ents)
# Check correct area/centroid
for ent in gmsh.model.getEntities(2):
tag = ent[1]
mass = gmsh.model.occ.getMass(2, tag)
self.assertAlmostEqual(1.0,
mass,
places=5,
msg="1 width, 1 height, 1 area")
x, y, z = gmsh.model.occ.getCenterOfMass(2, tag)
centroid = (x, y, z)
for i in range(3):
self.assertAlmostEqual(centroid[i], ref_centroids[tag][i])
# Check materials
gmsh.clear()
gmsh.finalize()
def grupos_fisicos(archivo, dim=-1):
''' Lee un archivo de texto con extensión .msh que contiene los datos de
una malla generada en GMSH.
Si se especifica el argumento dim, solo se reportan los grupos físicos
de tal dimensión, si no, se reportan todos.
Retorna:
- Un diccionario en el cual las claves son las ETIQUETAS de los
grupos físicos y los valores son tuplas con la DIMENSIÓN y el
NOMBRE asociados a cada etiqueta.
- Un diccionario en el cual las claves son las etiquetas de los
grupos físicos y los valores son listas con los nodos asociados
a cada grupo físico.
'''
if archivo[-4:] != '.msh':
raise ValueError('Solo se admite un archivo de extensión .msh')
gmsh.initialize()
gmsh.open(archivo)
grupos = gmsh.model.getPhysicalGroups(dim)
dims = [d[0] for d in grupos]
tags = [d[1] for d in grupos]
nombres = [(dim, gmsh.model.getPhysicalName(dim, tag))
for dim, tag in grupos]
dict1 = dict(zip(tags, nombres)) # Primer diccionario a reportar
nodos = [gmsh.model.mesh.getNodesForPhysicalGroup(dims[i], tags[i])[0]
for i in range(len(dims))]
dict2 = dict(zip(tags, nodos)) # Segundo diccionario a reportar
gmsh.finalize()
return dict1, dict2
def test_nx_y_11(self):
"""Test nx, y with 1 division."""
ref_groups = groups_11
ref_centroids = centroids_11
mocmg.initialize()
gmsh.initialize()
rectangular_grid(bb_44, nx=[2], y=[[2.0]])
group_nums = gmsh.model.getPhysicalGroups()
names = [gmsh.model.getPhysicalName(*grp) for grp in group_nums]
ref_names = list(ref_groups.keys())
# Check correct names/entities
for i, name in enumerate(ref_names):
self.assertEqual(name, names[i])
index = names.index(name)
group_ents = list(
gmsh.model.getEntitiesForPhysicalGroup(*group_nums[index]))
ref_group_ents = ref_groups[name]
self.assertEqual(group_ents, ref_group_ents)
# Check correct area/centroid
for ent in gmsh.model.getEntities(2):
tag = ent[1]
mass = gmsh.model.occ.getMass(2, tag)
self.assertAlmostEqual(4.0,
mass,
places=5,
msg="2 width, 2 height, 4 area")
x, y, z = gmsh.model.occ.getCenterOfMass(2, tag)
centroid = (x, y, z)
for i in range(3):
self.assertAlmostEqual(centroid[i], ref_centroids[tag][i])
gmsh.clear()
gmsh.finalize()
def test_x_y_nonuniform_2(self):
"""Test x, y with nonuniform grid with 2 levels."""
ref_groups = groups_nu2
ref_centroids = centroids_nu2
ref_areas = areas_nu2
mocmg.initialize()
gmsh.initialize()
rectangular_grid(bb_12_4,
x=[[0.0, 12.0], [2.0, 10.0]],
y=[[2.0], [1.0, 3.0]])
group_nums = gmsh.model.getPhysicalGroups()
names = [gmsh.model.getPhysicalName(*grp) for grp in group_nums]
ref_names = list(ref_groups.keys())
# Check correct names/entities
for i, name in enumerate(ref_names):
self.assertEqual(name, names[i])
index = names.index(name)
group_ents = list(
gmsh.model.getEntitiesForPhysicalGroup(*group_nums[index]))
ref_group_ents = ref_groups[name]
self.assertEqual(group_ents, ref_group_ents)
# Check correct area/centroid
for ent in gmsh.model.getEntities(2):
tag = ent[1]
mass = gmsh.model.occ.getMass(2, tag)
self.assertAlmostEqual(ref_areas[tag], mass, places=5)
x, y, z = gmsh.model.occ.getCenterOfMass(2, tag)
centroid = (x, y, z)
for i in range(3):
self.assertAlmostEqual(centroid[i], ref_centroids[tag][i])
gmsh.clear()
gmsh.finalize()
def test_gmsh_primitives(self):
shapes = [
Box(np.array([0, 0, 0]), np.array([1, 1, 1])),
Sphere(np.array([0, 0, 0]), 1),
Cylinder(np.array([0, 0, 0]), np.array([1, 1, 1]), 1),
Cone(np.array([0, 0, 0]), np.array([1, 1, 1]), 1, 2)
]
gmsh.initialize()
model = gmsh.model
factory = model.occ
for i, shape in enumerate(shapes):
model.add(str(i))
tag = shape.as_gmsh(model)
factory.synchronize()
x = model.occ.getCenterOfMass(3, tag)
y = shape.center_of_mass
self.assertTrue(np.linalg.norm(x - y) < 1E-13)
model.mesh.generate(3)
vtx_order, vtices, _ = model.mesh.getNodes()
self.assertTrue(len(vtx_order))
model.remove()
gmsh.finalize()
def wrapper(*args, **kwargs):
gmsh.initialize()
logging.info('Gmsh initialized')
out = f(*args, **kwargs) if f is not None else None
gmsh.finalize()
logging.info('Gmsh finalized')
return out
def test_inf(type='gap'):
global gap, mur, mus, ref, TEST, PRINT, PRINTF
TEST = True
[PRINT, PRINTF] = 2 * [False]
gmsh.initialize(sys.argv)
# gmsh.write("ndt.unv")
gmsh.option.setNumber("General.Terminal", 1)
gmsh.option.setNumber("View[0].IntervalsType", 3)
gmsh.option.setNumber("View[0].NbIso", 20)
if type == 'all' or type == 'gap':
for gap in np.arange(0.0001, 0.005, 0.0005):
# MIN GAP : 0.1 cm
# MAX GAP : 2.0 cm
create_geometry()
model.mesh.generate(2)
solve()
# gmsh.fltk.run()
ALL = np.zeros((3, len(xgap)))
ALL[0] = np.array(xgap)
ALL[1] = np.array(ymin)
ALL[2] = np.array(ymax)
np.save('influences/numpy/gap', ALL)
if type == 'all' or type == 'ref':
for ref in range(1, 6):
print('REF ======= %d' % ref)
create_geometry()
model.mesh.generate(2)
solve()
# gmsh.fltk.run()
ALL = np.zeros((3, len(xref)))
ALL[0] = np.array(xref)
ALL[1] = np.array(ymin)
ALL[2] = np.array(ymax)
np.save('influences/numpy/ref', ALL)
if type == 'all' or type == 'perm':
gap = 0.2 * cm
for mur in range(1, 300):
create_geometry()
model.mesh.generate(2)
solve()
# gmsh.fltk.run()
ALL = np.zeros((3, len(xgap)))
ALL[0] = np.arange(1, 300)
ALL[1] = np.array(ymin)
ALL[2] = np.array(ymax)
np.save('influences/numpy/perm', ALL)
if type == 'all' or type == 'experm':
gap = 0.2 * cm
for (mur, mat) in mus.items():
create_geometry()
model.mesh.generate(2)
solve()
# gmsh.fltk.run()
ALL = np.zeros((3, len(xgap)))
ALL[0] = np.array(list(mus.keys()))
ALL[1] = np.array(ymin)
ALL[2] = np.array(ymax)
np.save('influences/numpy/experm', ALL)
def get_mesh():
gmsh.initialize()
air_tag, pec_tags, isrc_tag = g03.make_geom()
gmsh.model.occ.synchronize()
isrc, pec, air = g03.assign_physicals(air_tag, pec_tags, isrc_tag)
#gmsh.model.mesh.setSize(gmsh.model.getEntities(0), 3)
gmsh.model.mesh.setSize(gmsh.model.getEntities(0), 0.7)
gmsh.option.setNumber("Mesh.Algorithm", 8)
nodes, elems = g03.gen_mesh()
gmsh.finalize()
ret_elems = []
for e in elems:
attr = ()
if e[0] == isrc:
ptype = 'e'
x = e[3][0].reshape(-1, 2) - 1
attr = ([0, 0, 1], )
elif e[0] == pec:
ptype = 'b'
x = e[3][0].reshape(-1, 3) - 1
elif e[0] == air:
ptype = 'v'
x = e[3][0].reshape(-1, 4) - 1
attr = (0, p04.e0, p04.u0)
x.sort()
ret_elems.append((ptype, attr, x))
return nodes[1].reshape(-1, 3), ret_elems
def create_fluid():
dx = 1
gmsh.initialize()
gmsh.open('t.msh')
# Launch the GUI to see the results:
# if '-nopopup' not in sys.argv:
# gmsh.fltk.run()
nodeTags, nodesCoord, parametricCoord = gmsh.model.mesh.getNodes()
liquid_x = nodesCoord[0::3]
liquid_y = nodesCoord[2::3]
liquid_z = nodesCoord[1::3]
liquid_y = liquid_y + abs(min(liquid_y))
liquid_x = liquid_x + abs(min(liquid_x))
liquid_x = liquid_x[0::3]
liquid_y = liquid_y[0::3]
liquid_z = liquid_z[0::3]
# x, y, z = np.meshgrid(liquid_x, liquid_y, liquid_z)
# x = x.ravel()
# y = y.ravel()
# z = z.ravel()
# return x * 1e-3, y * 1e-3, z * 1e-3
return liquid_x * 1e-3, liquid_y * 1e-3, liquid_z * 1e-3
def mesh_bar_gmshapi(name, msh_file=None, comm=MPI.COMM_WORLD):
"""
Create mesh.
"""
# http://jsdokken.com/converted_files/tutorial_gmsh.html
# https://moorejustinmusic.com/trending/how-do-i-use-gmsh-in-python/
# https://stackoverflow.com/questions/54951925/questions-about-the-gmsh-python-api
# Perform Gmsh work only on rank = 0
if comm.rank == 0:
import gmsh
import warnings
warnings.filterwarnings("ignore")
# Initialise gmsh and set options
gmsh.initialize()
# gmsh.option.setNumber("General.Terminal", 1)
# gmsh.option.setNumber("Mesh.Algorithm", 6)
# model = gmsh.model()
gmsh.model.add("Bool 2D")
L, H, r = 1., 1., .1
hole = gmsh.model.occ.addCircle(L / 2, L / 2, 0., r, tag=1)
domain = gmsh.model.occ.addRectangle(0,
0,
0.,
L,
H,
tag=2,
roundedRadius=.1)
boolean = gmsh.model.occ.cut([(2, hole)], [(2, domain)], tag=3)
def make_geometry():
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 0)
# cube
box = gmsh.model.occ.addBox(-1000, -1000, -1000, 2000, 2000, 2000)
# two "wells" extending above and bellow
left_hole = gmsh.model.occ.addBox(-500, 0, -1200, 30, 30, 2400)
right_hole = gmsh.model.occ.addBox(500, 0, -1200, 30, 30, 2400)
gmsh.model.occ.synchronize()
box = (3, box)
b_box = gmsh.model.getBoundary([box], oriented=False)
l_hole = (3, left_hole)
r_hole = (3, right_hole)
b_lhole = gmsh.model.getBoundary([l_hole], oriented=False)
b_rhole = gmsh.model.getBoundary([r_hole], oriented=False)
box_names = ["left", "right", "front", "back", "bottom", "top"]
b_box_names = dict(zip(b_box, box_names))
b_lhole_names = dict(zip(b_lhole, ["lhole_" + n for n in box_names]))
b_rhole_names = dict(zip(b_rhole, ["rhole_" + n for n in box_names]))
names = b_box_names
names.update(b_lhole_names)
names.update(b_rhole_names)
holes = [l_hole, r_hole]
b_holes = b_lhole + b_rhole
return b_box, holes, b_holes, names
def main():
args = docopt(__doc__)
qc_surf = args['<qc_surf>']
C = np.load(args['<C>'])
R = np.load(args['<R>'])
b = np.load(args['<bounds>'])
out = args['<out>']
# Construct parameteric surface coordinates
X, Y = np.meshgrid(np.linspace(b[0, 0] + 1, b[0, 1] - 1),
np.linspace(b[1, 0] + 1, b[1, 1] - 1))
XX = X.flatten()
YY = Y.flatten()
poly_arr = np.c_[np.ones(XX.shape[0]), XX, YY, XX * YY, XX * XX, YY * YY]
Z = np.dot(poly_arr, C)
poly_coords = np.matmul(R, np.c_[XX, YY, Z].T).T
# Load in mesh
gmsh.initialize()
gmsh.open(qc_surf)
entity = gmsh.model.getEntities()[0]
n_tag, n_coord, params = gmsh.model.mesh.getNodes(entity[0], entity[1])
samp_surf_coords = poly_coords.flatten(order='C')
samp_surf_nodes = np.arange(max(n_tag), max(n_tag) + poly_coords.shape[0])
grid = samp_surf_nodes.reshape((50, 50))
n = grid.shape[0]
# Construct mesh
trig_list = np.zeros((6 * (n - 1)**2), dtype=np.int64)
for j in np.arange(0, grid.shape[0] - 1):
for i in np.arange(0, grid.shape[1] - 1):
# Upper triangular
trig_list[6 * i + 6 * (n - 1) * j] = grid[(j, i)]
trig_list[6 * i + 1 + 6 * (n - 1) * j] = grid[(j, i + 1)]
trig_list[6 * i + 2 + 6 * (n - 1) * j] = grid[(j + 1, i + 1)]
# Lower triangular
trig_list[6 * i + 3 + 6 * (n - 1) * j] = grid[(j + 1, i)]
trig_list[6 * i + 4 + 6 * (n - 1) * j] = grid[(j, i)]
trig_list[6 * i + 5 + 6 * (n - 1) * j] = grid[(j + 1, i + 1)]
gmsh.initialize()
gmsh.model.add('sampling_surf')
tag = gmsh.model.addDiscreteEntity(2, 3002)
gmsh.model.mesh.setNodes(2,
tag,
nodeTags=samp_surf_nodes,
coord=samp_surf_coords)
gmsh.model.mesh.setElements(
2,
tag, [2],
elementTags=[range(1,
len(trig_list) // 3 + 1)],
nodeTags=[trig_list])
gmsh.write(out)
gmsh.finalize()
def _write_stl(self, target_path):
target_geo = os.path.join(target_path, 'new_surface.geo')
target_stl = os.path.join(target_path, 'new_surface.stl')
gmsh.initialize()
gmsh.open(target_geo)
gmsh.model.mesh.generate(3)
gmsh.write(target_stl)
gmsh.finalize()
def embed_mesh1d(mesh1d, bounding_shape, how, gmsh_args, **kwargs):
'''
Embed 1d in Xd mesh Xd padded hypercube. Embedding can be as
points / lines (these are gmsh options).
Returns: LineMeshEmbedding
'''
assert mesh1d.topology().dim() == 1
assert mesh1d.geometry().dim() > 1
# Some convenience API where we expand
if isinstance(bounding_shape, str):
bounding_shape = STLShape(bounding_shape)
return embed_mesh1d(mesh1d, bounding_shape, how, gmsh_args, **kwargs)
# int -> padded
if is_number(bounding_shape):
bounding_shape = (bounding_shape, ) * mesh1d.geometry().dim()
return embed_mesh1d(mesh1d, bounding_shape, how, gmsh_args, **kwargs)
# Padded to relative box
if isinstance(bounding_shape, (tuple, list, np.ndarray)):
bounding_shape = BoundingBox(bounding_shape)
return embed_mesh1d(mesh1d, bounding_shape, how, gmsh_args, **kwargs)
kwargs = configure_options(**kwargs)
etime = Timer(
'Emebdding %d vertices and %d edges in R^%d' %
(mesh1d.num_vertices(), mesh1d.num_cells(), mesh1d.geometry().dim()))
# At this point the type of bounding shape must check out
assert isinstance(bounding_shape, BoundingShape)
# FIXME: we should have that all 1d points are <= bounding shape
# later ... compute intersects for points on surface
# skip all for now
model = gmsh.model
gmsh.initialize(list(gmsh_args))
gmsh.option.setNumber("General.Terminal", 1)
if bounding_shape.is_inside(mesh1d, mesh1d.coordinates()):
if how.lower() == 'as_lines':
out = line.line_embed_mesh1d(model, mesh1d, bounding_shape,
**kwargs)
else:
assert how.lower() == 'as_points'
out = point.point_embed_mesh1d(model, mesh1d, bounding_shape,
**kwargs)
gmsh.finalize()
etime.done()
return out
# FIXME: Doing points on manifolds is more involved in gmsh
# because the surface needs to be broken apart (manually?)
raise NotImplementedError
def __init__(self, Meangen, IN):
# Storing Meangen class.
self.M = Meangen
# Reading mesh parameters from input file.
self.wedge = IN["WEDGE"][0] # Importing mesh wedge angle
self.n_sec = int(IN["SECTIONS_PER_DEGREE"][0]) * self.wedge # Calculating number of tangential nodes
self.n_point = int(IN["AXIAL_POINTS"][0]) # Importing axial node count
self.inlet_fac = IN["INLET_FACTOR"][0] # Importing inlet cell size factor
self.outlet_fac = IN["OUTLET_FACTOR"][0] # Importing outlet cell size factor
self.rot_axis = IN["Rotation_axis"]
self.Coords = type('', (), {})()
# Initiating Gmesh.
self.model = gmsh.model
self.factory = self.model.geo
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 1)
self.model.add("3DBFM")
# Creating all the mesh points.
self.makePoints()
# Connecting the mesh points to create lines.
self.makeLines()
# Making periodic plane.
self.makePlane()
# Revolving plane around rotation axis to create 3D wedge.
self.revolve()
# Setting names to boundaries.
self.nameBoundaries()
# Creating 3D mesh.
gmsh.model.geo.synchronize()
# Applying mesh refinement along the lines in the mesh
self.refineLines()
# Generate the 3D mesh geometry
gmsh.model.mesh.generate(3)
# Saving mesh as su2 file
gmsh.write(self.fileName)
# Transforming mesh to periodic mesh.
print("Building periodic mesh...")
self.makePerio()
print("Done!")
# In case of selection of mesh visualization option, the gmesh GUI will display the 3D BFM mesh.
if IN["PLOT_MESH"] == 'YES':
self.plotmesh()
gmsh.finalize()
def __init__(self, Meangen):
self.M = Meangen
self.model = gmsh.model
self.factory = self.model.geo
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 1)
self.model.add("3DBFM")
def create_mesh(vol, F):
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 0)
f = 0.01 * F
a = (vol / (1 / 8 * 4 / 3 * math.pi * f**3 + 3 * 1 / 4 * math.pi * f**2 *
(1 - f) + 3 * f * (1 - f)**2 + (1 - f)**3))**(1.0 / 3.0)
internal = []
gmsh.model.add("cubesphere")
if (F < 1):
# a cube
gmsh.model.occ.addBox(0, 0, 0, a, a, a, 1)
internal = [1, 3, 5]
external = [2, 4, 6]
elif (F > 99):
# a sphere
gmsh.model.occ.addSphere(0, 0, 0, a, 1, 0, math.pi / 2, math.pi / 2)
internal = [2, 3, 4]
external = [1]
else:
gmsh.model.occ.addBox(0, 0, 0, a, a, a, 1)
gmsh.model.occ.fillet([1], [12, 7, 6], [f * a], True)
internal = [1, 4, 6]
external = [2, 3, 5, 7, 8, 9, 10]
gmsh.model.occ.synchronize()
gmsh.model.addPhysicalGroup(3, [1], 1)
gmsh.model.setPhysicalName(3, 1, "fuel")
gmsh.model.addPhysicalGroup(2, internal, 2)
gmsh.model.setPhysicalName(2, 2, "internal")
gmsh.model.addPhysicalGroup(2, external, 3)
gmsh.model.setPhysicalName(2, 3, "external")
gmsh.model.occ.synchronize()
gmsh.option.setNumber("Mesh.ElementOrder", 2)
gmsh.option.setNumber("Mesh.Optimize", 1)
gmsh.option.setNumber("Mesh.OptimizeNetgen", 1)
gmsh.option.setNumber("Mesh.HighOrderOptimize", 1)
gmsh.option.setNumber("Mesh.CharacteristicLengthMin", a / 10)
gmsh.option.setNumber("Mesh.CharacteristicLengthMax", a / 10)
gmsh.model.mesh.generate(3)
gmsh.write("cubesphere-%g.msh" % (F))
gmsh.model.remove()
#gmsh.fltk.run()
gmsh.finalize()
return
def define_geometry(self) -> None:
"""Feed the geometry specified in self._data to gmsh."""
gmsh.initialize()
gmsh.option.setNumber("General.Verbosity", 3)
# All geometries need their points
self._point_tags = self._add_points()
# The boundary, and the domain, must be specified prior to the
# co-dimension 1 objects (fractures) so that the latter can be
# embedded in the domain. This requires some specialized treatment
# in 2d and 3d, since the boundary and fractures are made of up
# different geometric objects in the two:
if self._dim == 1:
# This should not be difficult, but has not been prioritized.
raise NotImplementedError("1d geometries are not implemented")
elif self._dim == 2:
# First add the domain. This will add the lines that form the domain
# boundary, but not the fracture lines.
self._domain_tag = self._add_domain_2d()
# Next add the fractures (and constraints). This adds additional lines,
# and embeds them in the domain.
self._add_fractures_2d()
else:
# In 3d, we can first add lines to the description, they are only used
# to define surfaces later.
# Make a index list covering all the lines
inds = np.arange(self._data.lines.shape[1])
# The function to write lines assumes that the lines are formed by
# point indices (first two rows), tags (third) and line index (fourth)
# Add the latter, essentially saying that each line is a separate line.
if self._data.lines.shape[0] < 4:
self._data.lines = np.vstack((self._data.lines, inds))
# Now we can write the lines
# The lines are not directly embedded in the domain.
# NOTE: If we ever get around to do a 1d-3d model (say a well), this may
# be a place to do that.
self._line_tags = self._add_lines(inds, embed_in_domain=False)
# Next add the domain. This adds the boundary surfaces, embeds lines in
# the relevant boundary surfaces, and constructs a 3d volume from the
# surfaces
self._domain_tag = self._add_domain_3d()
# Finally, we can add the fractures and constraints and embed them in
# the domain
self._add_fractures_3d()
gmsh.model.geo.synchronize()
def __init__(self, name):
gmsh.initialize()
gmsh.clear()
gmsh.model.add(name)
self.name = name
self.model = gmsh.model
self.fac = self.model.occ
self.pos = gmsh.view
self.vertices = np.array([])
self.tetra = np.array([])
def __init__(self, settings, BoundaryNames, Polylines):
self._boundary_name = BoundaryNames
self.contour_polylines = Polylines
self.mesh_size = settings["mesh_size"].GetDouble()
self.user_2d_output = settings["output_gmsh_2d"].GetBool()
self.gmsh_format = ".vtk"
self.file_name_user = settings["file_name"].GetString()
self.gmsh_kratos_format = settings["output_gmsh_2d_format"].GetString()
gmsh.initialize(sys.argv)
gmsh.model.add("Volumemesh")
def __init__(self,
name: Optional[str] = None,
verbose: bool = False) -> None:
gmsh.initialize(sys.argv)
gmsh.model.add(name or f'{self.__class__.__name__}')
self._verbose = False
self.verbose = verbose
self.model = gmsh.model
self.mesh = gmsh.model.mesh
self.occ = gmsh.model.occ
def volume_with_fracture():
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 1)
gmsh.model.add("volume-with-fracture")
gmsh.logger.start()
kernel = gmsh.model.occ
# Add outer box
dx = dy = dz = 1
outer_box = kernel.addBox(0, 0, 0, dx, dy, dz)
# Add inner box
cx = cy = cz = dx / 2 # Center # Set to dx/2 in production
sx = sy = sz = 0.2 # Radius
corner = (cx - sx, cy - sy, cz - sz)
size = (2 * sx, 2 * sy, 2 * sz)
inner_box = kernel.addBox(*corner, *size)
kernel.synchronize()
# Add fracture
xmin, ymin, zmin, xmax, ymax, zmax = gmsh.model.getBoundingBox(
3, inner_box)
dx = xmax - xmin
dy = ymax - ymin
dz = zmax - zmin
angle = -math.pi / 6
lx = dx / math.cos(angle)
# Through-going fracture
frac = kernel.addRectangle(xmin, ymin, zmin, lx, dy)
# Rotate
f = [(2, frac)]
kernel.rotate([f[0]], xmin, ymin, zmin, 0, 1, 0, angle)
# Insert the fracture to the domain
f_out, f_m = kernel.fragment([(3, inner_box)], [f[0]])
kernel.synchronize()
# Partition domain
box_dim = 3
out, m = kernel.fragment(
[(box_dim, outer_box)],
f_out,
)
kernel.synchronize()
# Mesh the domain
gmsh.option.setNumber("Mesh.CharacteristicLengthMin", 0.05)
gmsh.option.setNumber("Mesh.CharacteristicLengthMax", 0.05)
gmsh.model.mesh.generate(3)
gmsh.fltk.run()
gmsh.finalize()
def test_gmsh_input_3d(order, cell_type):
try:
import gmsh
except ImportError:
pytest.skip()
if cell_type == CellType.hexahedron and order > 2:
pytest.xfail("GMSH permutation for order > 2 hexahedra not implemented in DOLFINx.")
res = 0.2
gmsh.initialize()
if cell_type == CellType.hexahedron:
gmsh.option.setNumber("Mesh.RecombinationAlgorithm", 2)
gmsh.option.setNumber("Mesh.RecombineAll", 2)
gmsh.option.setNumber("Mesh.CharacteristicLengthMin", res)
gmsh.option.setNumber("Mesh.CharacteristicLengthMax", res)
circle = gmsh.model.occ.addDisk(0, 0, 0, 1, 1)
if cell_type == CellType.hexahedron:
gmsh.model.occ.extrude([(2, circle)], 0, 0, 1, numElements=[5], recombine=True)
else:
gmsh.model.occ.extrude([(2, circle)], 0, 0, 1, numElements=[5])
gmsh.model.occ.synchronize()
gmsh.model.mesh.generate(3)
gmsh.model.mesh.setOrder(order)
idx, points, _ = gmsh.model.mesh.getNodes()
points = points.reshape(-1, 3)
idx -= 1
srt = np.argsort(idx)
assert np.all(idx[srt] == np.arange(len(idx)))
x = points[srt]
element_types, element_tags, node_tags = gmsh.model.mesh.getElements(dim=3)
name, dim, order, num_nodes, local_coords, num_first_order_nodes = gmsh.model.mesh.getElementProperties(
element_types[0])
cells = node_tags[0].reshape(-1, num_nodes) - 1
if cell_type == CellType.tetrahedron:
gmsh_cell_id = MPI.COMM_WORLD.bcast(gmsh.model.mesh.getElementType("tetrahedron", order), root=0)
elif cell_type == CellType.hexahedron:
gmsh_cell_id = MPI.COMM_WORLD.bcast(gmsh.model.mesh.getElementType("hexahedron", order), root=0)
gmsh.finalize()
# Permute the mesh topology from GMSH ordering to DOLFINx ordering
domain = ufl_mesh_from_gmsh(gmsh_cell_id, 3)
cells = cells[:, perm_gmsh(cell_type, cells.shape[1])]
mesh = create_mesh(MPI.COMM_WORLD, cells, x, domain)
volume = assemble_scalar(form(1 * dx(mesh)))
assert mesh.comm.allreduce(volume, op=MPI.SUM) == pytest.approx(np.pi, rel=10 ** (-1 - order))
def __init__(self, filename):
if not _gmsh_found: raise _gmsh_exeption
# suppress loggin
if not os.path.isfile(filename):
raise IOError("No such file or directory: '%s'" % filename)
gmsh.initialize()
gmsh.open(filename)
self._model = gmsh.model
self._physical_cell_ids = None
self._physical_face_ids = None
import gmsh
import math
model = gmsh.model
factory = model.occ
gmsh.initialize()
gmsh.option.setNumber("General.Terminal", 1)
model.add("spline")
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)
import gmsh
import sys
gmsh.initialize(sys.argv)
gmsh.option.setNumber("General.Terminal", 1)
print(gmsh.option.getNumber("Mesh.Algorithm"))
gmsh.open("square.msh")
model = gmsh.model
model.add("square")
factory = model.geo
factory.addPoint(0,0,0,0.1,1)
factory.addPoint(1,0,0,0.1,2)
factory.addPoint(1,1,0,0.1,3)
factory.addPoint(0,1,0,0.1,4)
factory.addLine(1,2,1)
factory.addLine(2,3,2)
factory.addLine(3,4,3)
line4 = factory.addLine(4,1)
print("line4 received tag ", line4)
factory.addCurveLoop([1,2,3,line4],1)
factory.addPlaneSurface([1],6)
factory.synchronize()
ptag = model.addPhysicalGroup(1,[1,2,3,4])
ent = model.getEntitiesForPhysicalGroup(1,ptag)
print("new physical group ",ptag,":",ent, type(ent))
model.addPhysicalGroup(2,[6])