def get_latlon_mesh(mesh):
"""Build 2D projected mesh of spherical mesh"""
crds_orig = mesh.coordinates
mesh_dg_fs = VectorFunctionSpace(mesh, "DG", 1)
crds_dg = Function(mesh_dg_fs)
crds_latlon = Function(mesh_dg_fs)
par_loop(
"""
for (int i=0; i<3; i++) {
for (int j=0; j<3; j++) {
dg[i][j] = cg[i][j];
}
}
""", dx, {
'dg': (crds_dg, WRITE),
'cg': (crds_orig, READ)
})
# lat-lon 'x' = atan2(y, x)
crds_latlon.dat.data[:, 0] = arctan2(crds_dg.dat.data[:, 1],
crds_dg.dat.data[:, 0])
# lat-lon 'y' = asin(z/sqrt(x^2 + y^2 + z^2))
crds_latlon.dat.data[:, 1] = (arcsin(
crds_dg.dat.data[:, 2] /
np_sqrt(crds_dg.dat.data[:, 0]**2 + crds_dg.dat.data[:, 1]**2 +
crds_dg.dat.data[:, 2]**2)))
crds_latlon.dat.data[:, 2] = 0.0
kernel = op2.Kernel(
"""
#define PI 3.141592653589793
#define TWO_PI 6.283185307179586
void splat_coords(double **coords) {
double diff0 = (coords[0][0] - coords[1][0]);
double diff1 = (coords[0][0] - coords[2][0]);
double diff2 = (coords[1][0] - coords[2][0]);
if (fabs(diff0) > PI || fabs(diff1) > PI || fabs(diff2) > PI) {
const int sign0 = coords[0][0] < 0 ? -1 : 1;
const int sign1 = coords[1][0] < 0 ? -1 : 1;
const int sign2 = coords[2][0] < 0 ? -1 : 1;
if (sign0 < 0) {
coords[0][0] += TWO_PI;
}
if (sign1 < 0) {
coords[1][0] += TWO_PI;
}
if (sign2 < 0) {
coords[2][0] += TWO_PI;
}
}
}
""", "splat_coords")
op2.par_loop(kernel, crds_latlon.cell_set,
crds_latlon.dat(op2.RW, crds_latlon.cell_node_map()))
return Mesh(crds_latlon)
def test_2D_dirichlet_regions():
# Can't do mesh refinement because MeshHierarchy ruins the domain tags
mesh = Mesh("./2D_mesh.msh")
dim = mesh.geometric_dimension()
x = SpatialCoordinate(mesh)
S = VectorFunctionSpace(mesh, "CG", 1)
beta = 1.0
reg_solver = RegularizationSolver(
S, mesh, beta=beta, gamma=0.0, dx=dx, design_domain=0
)
# Exact solution with free Neumann boundary conditions for this domain
u_exact = Function(S)
u_exact_component = (-cos(x[0] * pi * 2) + 1) * (-cos(x[1] * pi * 2) + 1)
u_exact.interpolate(
as_vector(tuple(u_exact_component for _ in range(dim)))
)
f = Function(S)
f_component = (
-beta
* (
4.0 * pi * pi * cos(2 * pi * x[0]) * (-cos(2 * pi * x[1]) + 1)
+ 4.0 * pi * pi * cos(2 * pi * x[1]) * (-cos(2 * pi * x[0]) + 1)
)
+ u_exact_component
)
f.interpolate(as_vector(tuple(f_component for _ in range(dim))))
theta = TestFunction(S)
rhs_form = inner(f, theta) * dx
velocity = Function(S)
rhs = assemble(rhs_form)
reg_solver.solve(velocity, rhs)
assert norm(project(domainify(u_exact, x) - velocity, S)) < 1e-3
def to_2nd_order(mesh, circle_bdy_id=None, rad=1.0):
# make new coordinates function
V = VectorFunctionSpace(mesh, 'CG', 2)
new_coordinates = project(mesh.coordinates, V)
# If we have a circle, move any nodes on the circle bdy
# onto the circle. Note circle MUST be centered at origin
if circle_bdy_id is not None:
nodes_on_circle = V.boundary_nodes(circle_bdy_id, 'geometric')
#Force all cell nodes to have given radius :arg:`rad`
for node in nodes_on_circle:
scale = rad / la.norm(new_coordinates.dat.data[node])
new_coordinates.dat.data[node] *= scale
# Make a new mesh with given coordinates
return Mesh(new_coordinates)
def mesh_from_gmsh_code(geo_code, clscale=1.0, dim=2, comm=COMM_WORLD,
name="/tmp/tmp", smooth=0, delete_files=True):
if comm.rank == 0:
with open("%s.geo" % name, "w") as text_file:
text_file.write(geo_code)
comm.Barrier()
generateGmsh("%s.geo" % name, "%s.msh" % name, dim, clscale,
comm=comm, smooth=smooth)
mesh = Mesh("%s.msh" % name)
if delete_files:
try:
os.remove("%s.geo" % name)
except OSError:
pass
try:
os.remove("%s.msh" % name)
except OSError:
pass
return mesh
def max_mesh_dimension(mesh: fd.Mesh):
coords = mesh.coordinates
MAXSP = fd.FunctionSpace(mesh, "R", 0)
max_y = fd.Function(MAXSP)
min_y = fd.Function(MAXSP)
max_x = fd.Function(MAXSP)
min_x = fd.Function(MAXSP)
domain = "{[i, j] : 0 <= i < u.dofs}"
def extract_comp(mode, comp, result):
instruction = f"""
component[0] = abs(u[i, {comp}])
"""
fd.par_loop(
(domain, instruction),
fd.dx,
{
"u": (coords, fd.READ),
"component": (result, mode)
},
is_loopy_kernel=True,
)
return result
max_y_comp = extract_comp(fd.MAX, 1, max_y).dat.data[0]
min_y_comp = extract_comp(fd.MIN, 1, min_y).dat.data[0]
max_x_comp = extract_comp(fd.MAX, 0, max_x).dat.data[0]
min_x_comp = extract_comp(fd.MIN, 0, min_x).dat.data[0]
max_dim_x = abs(max_x_comp - min_x_comp)
max_dim_y = abs(max_y_comp - min_y_comp)
max_dim = max(max_dim_x, max_dim_y)
if mesh.geometric_dimension() == 3:
max_z = fd.Function(MAXSP)
min_z = fd.Function(MAXSP)
max_z_comp = extract_comp(fd.MAX, 2, max_z).dat.data[0]
min_z_comp = extract_comp(fd.MIN, 2, min_z).dat.data[0]
max_dim_z = abs(max_z_comp - min_z_comp)
max_dim = max(max_dim, max_dim_z)
return max_dim
xc = L/2.
x, z = SpatialCoordinate(ext_mesh)
hm = 1.
zs = hm*a**2/((x-xc)**2 + a**2)
smooth_z = True
dirname = 'nh_mountain'
if smooth_z:
dirname += '_smootherz'
zh = 5000.
xexpr = as_vector([x, conditional(z < zh, z + cos(0.5*pi*z/zh)**6*zs, z)])
else:
xexpr = as_vector([x, z + ((H-z)/H)*zs])
new_coords = Function(Vc).interpolate(xexpr)
mesh = Mesh(new_coords)
# sponge function
W_DG = FunctionSpace(mesh, "DG", 2)
x, z = SpatialCoordinate(mesh)
zc = H-10000.
mubar = 0.15/dt
mu_top = conditional(z <= zc, 0.0, mubar*sin((pi/2.)*(z-zc)/(H-zc))**2)
mu = Function(W_DG).interpolate(mu_top)
fieldlist = ['u', 'rho', 'theta']
timestepping = TimesteppingParameters(dt=dt)
output = OutputParameters(dirname=dirname,
dumpfreq=18,
dumplist=['u'],
perturbation_fields=['theta', 'rho'],
def test_3D_dirichlet_regions():
# Can't do mesh refinement because MeshHierarchy ruins the domain tags
mesh = Mesh("./3D_mesh.msh")
dim = mesh.geometric_dimension()
x = SpatialCoordinate(mesh)
solver_parameters_amg = {
"ksp_type": "cg",
"ksp_converged_reason": None,
"ksp_rtol": 1e-7,
"pc_type": "hypre",
"pc_hypre_type": "boomeramg",
"pc_hypre_boomeramg_max_iter": 5,
"pc_hypre_boomeramg_coarsen_type": "PMIS",
"pc_hypre_boomeramg_agg_nl": 2,
"pc_hypre_boomeramg_strong_threshold": 0.95,
"pc_hypre_boomeramg_interp_type": "ext+i",
"pc_hypre_boomeramg_P_max": 2,
"pc_hypre_boomeramg_relax_type_all": "sequential-Gauss-Seidel",
"pc_hypre_boomeramg_grid_sweeps_all": 1,
"pc_hypre_boomeramg_truncfactor": 0.3,
"pc_hypre_boomeramg_max_levels": 6,
}
S = VectorFunctionSpace(mesh, "CG", 1)
beta = 1.0
reg_solver = RegularizationSolver(
S,
mesh,
beta=beta,
gamma=0.0,
dx=dx,
design_domain=0,
solver_parameters=solver_parameters_amg,
)
# Exact solution with free Neumann boundary conditions for this domain
u_exact = Function(S)
u_exact_component = (
(-cos(x[0] * pi * 2) + 1)
* (-cos(x[1] * pi * 2) + 1)
* (-cos(x[2] * pi * 2) + 1)
)
u_exact.interpolate(
as_vector(tuple(u_exact_component for _ in range(dim)))
)
f = Function(S)
f_component = (
-beta
* (
4.0
* pi
* pi
* cos(2 * pi * x[0])
* (-cos(2 * pi * x[1]) + 1)
* (-cos(2 * pi * x[2]) + 1)
+ 4.0
* pi
* pi
* cos(2 * pi * x[1])
* (-cos(2 * pi * x[0]) + 1)
* (-cos(2 * pi * x[2]) + 1)
+ 4.0
* pi
* pi
* cos(2 * pi * x[2])
* (-cos(2 * pi * x[1]) + 1)
* (-cos(2 * pi * x[0]) + 1)
)
+ u_exact_component
)
f.interpolate(as_vector(tuple(f_component for _ in range(dim))))
theta = TestFunction(S)
rhs_form = inner(f, theta) * dx
velocity = Function(S)
rhs = assemble(rhs_form)
reg_solver.solve(velocity, rhs)
error = norm(
project(
domainify(u_exact, x) - velocity,
S,
solver_parameters=solver_parameters_amg,
)
)
assert error < 5e-2
def get_latlon_mesh(mesh):
coords_orig = mesh.coordinates
coords_fs = coords_orig.function_space()
if coords_fs.extruded:
cell = mesh._base_mesh.ufl_cell().cellname()
DG1_hori_elt = FiniteElement("DG", cell, 1, variant="equispaced")
DG1_vert_elt = FiniteElement("DG", interval, 1, variant="equispaced")
DG1_elt = TensorProductElement(DG1_hori_elt, DG1_vert_elt)
else:
cell = mesh.ufl_cell().cellname()
DG1_elt = FiniteElement("DG", cell, 1, variant="equispaced")
vec_DG1 = VectorFunctionSpace(mesh, DG1_elt)
coords_dg = Function(vec_DG1).interpolate(coords_orig)
coords_latlon = Function(vec_DG1)
shapes = {"nDOFs": vec_DG1.finat_element.space_dimension(), 'dim': 3}
radius = np.min(
np.sqrt(coords_dg.dat.data[:, 0]**2 + coords_dg.dat.data[:, 1]**2 +
coords_dg.dat.data[:, 2]**2))
# lat-lon 'x' = atan2(y, x)
coords_latlon.dat.data[:, 0] = np.arctan2(coords_dg.dat.data[:, 1],
coords_dg.dat.data[:, 0])
# lat-lon 'y' = asin(z/sqrt(x^2 + y^2 + z^2))
coords_latlon.dat.data[:, 1] = np.arcsin(
coords_dg.dat.data[:, 2] /
np.sqrt(coords_dg.dat.data[:, 0]**2 + coords_dg.dat.data[:, 1]**2 +
coords_dg.dat.data[:, 2]**2))
# our vertical coordinate is radius - the minimum radius
coords_latlon.dat.data[:,
2] = np.sqrt(coords_dg.dat.data[:, 0]**2 +
coords_dg.dat.data[:, 1]**2 +
coords_dg.dat.data[:, 2]**2) - radius
# We need to ensure that all points in a cell are on the same side of the branch cut in longitude coords
# This kernel amends the longitude coords so that all longitudes in one cell are close together
kernel = op2.Kernel(
"""
#define PI 3.141592653589793
#define TWO_PI 6.283185307179586
void splat_coords(double *coords) {{
double max_diff = 0.0;
double diff = 0.0;
for (int i=0; i<{nDOFs}; i++) {{
for (int j=0; j<{nDOFs}; j++) {{
diff = coords[i*{dim}] - coords[j*{dim}];
if (fabs(diff) > max_diff) {{
max_diff = diff;
}}
}}
}}
if (max_diff > PI) {{
for (int i=0; i<{nDOFs}; i++) {{
if (coords[i*{dim}] < 0) {{
coords[i*{dim}] += TWO_PI;
}}
}}
}}
}}
""".format(**shapes), "splat_coords")
op2.par_loop(kernel, coords_latlon.cell_set,
coords_latlon.dat(op2.RW, coords_latlon.cell_node_map()))
return Mesh(coords_latlon)
def run_trial(trial_id):
"""
(key, output), or *None* if use_cache is *True*
and already have this result stored
"""
# {{{ Get indexes into lists
mesh_ndx = trial_id % len(mesh_names)
trial_id //= len(mesh_names)
mesh_name = mesh_names[mesh_ndx]
# If new mesh, delete old mesh and read in new one
global current_mesh_name, mesh
if current_mesh_name != mesh_name:
del mesh
mesh = Mesh(mesh_name)
if use_2nd_order:
mesh = to_2nd_order(mesh)
current_mesh_name = mesh_name
mesh_h = mesh_h_vals[mesh_ndx]
degree_ndx = trial_id % len(degree_list)
trial_id //= len(degree_list)
degree = degree_list[degree_ndx]
kappa_ndx = trial_id % len(kappa_list)
trial_id //= len(kappa_list)
kappa = kappa_list[kappa_ndx]
method_ndx = trial_id % len(method_list)
trial_id //= len(method_list)
method = method_list[method_ndx]
solver_params = method_to_kwargs[method]['solver_parameters']
# Make sure this is a valid iteration index
assert trial_id == 0
# }}}
kwargs = method_to_kwargs[method]
# {{{ Create key holding data of this trial run:
setup_info['h'] = str(mesh_h)
setup_info['degree'] = str(degree)
setup_info['kappa'] = str(kappa)
setup_info['method'] = str(method)
setup_info['pc_type'] = str(solver_params['pc_type'])
if solver_params['ksp_type'] == 'preonly':
setup_info['ksp_rtol'] = ''
setup_info['ksp_atol'] = ''
else:
setup_info['ksp_rtol'] = str(solver_params['ksp_rtol'])
setup_info['ksp_atol'] = str(solver_params['ksp_atol'])
if method == 'nonlocal':
fmm_order = get_fmm_order(kappa, mesh_h)
setup_info['FMM Order'] = str(fmm_order)
kwargs['FMM Order'] = fmm_order
else:
setup_info['FMM Order'] = ''
# Add gamma/beta to setup_info if there, else make sure
# it's recorded as absent in special_key
for special_key in ['gamma', 'beta']:
if special_key in solver_params:
setup_info[special_key] = solver_params[special_key]
else:
setup_info[special_key] = ''
key = frozenset(setup_info.items())
if key in cache and use_cache:
return None
trial = {
'mesh': mesh,
'degree': degree,
'true_sol_expr': get_true_sol_expr(SpatialCoordinate(mesh), kappa)
}
# {{{ Solve problem and evaluate error
output = {}
true_sol, comp_sol, snes_or_ksp = \
run_method.run_method(trial, method, kappa,
comp_sol_name=method + " Computed Solution", **kwargs)
if isinstance(snes_or_ksp, PETSc.SNES):
ksp = snes_or_ksp.getKSP()
elif isinstance(snes_or_ksp, PETSc.KSP):
ksp = snes_or_ksp
else:
raise ValueError("snes_or_ksp must be of type PETSc.SNES or"
" PETSc.KSP")
l2_err = norms.l2_norm(true_sol - comp_sol, region=inner_region)
h1_err = norms.h1_norm(true_sol - comp_sol, region=inner_region)
# }}}
# Store err in output and return
output['L2 Error'] = l2_err
output['H1 Error'] = h1_err
ndofs = true_sol.dat.data.shape[0]
output['ndofs'] = str(ndofs)
if solver_params['ksp_type'] != 'preonly':
output['Iteration Number'] = ksp.getIterationNumber()
output['Residual Norm'] = ksp.getResidualNorm()
output['Converged Reason'] = KSPReasons[ksp.getConvergedReason()]
if solver_params['ksp_type'] == 'gmres':
emin, emax = ksp.computeExtremeSingularValues()
output['Min Extreme Singular Value'] = emin
output['Max Extreme Singular Value'] = emax
if visualize:
plot(comp_sol)
plot(true_sol)
plt.show()
if print_trials:
for name, val in sorted(key):
if val != '':
print('{0: <9}: {1}'.format(name, val))
for name, val in sorted(output.items()):
print('{0: <18}: {1}'.format(name, val))
return key, output
str(solver_params[new_special_key])
# Gets computed solution, prints and caches
key = frozenset(setup_info.items())
new_result = not use_cache or key not in cache
if new_result:
# Build mesh if not done so already
if mesh is None:
logger.info(
"Reading Mesh %s with element size %s " +
" and mesh order %s...", mesh_file_name, cell_size,
order)
# read in using open-cascade with 0 refinements, this allows
# for order 2 meshes
mesh = Mesh(join('meshes/', mesh_file_name))
if order == 2:
if mesh_name not in [
'circle_in_square', 'ball_in_cube',
'circle_in_square_no_pml'
]:
raise NotImplementedError(
"2nd order mesh only avaiilbale" +
" for circle_in_square, circle_in_square_no_pml, or ball_in_cube. "
+ " Not available for '%s'" % mesh_name)
mesh = to_2nd_order(mesh, inner_bdy_id,
mesh_options['radius'])
logger.info("Mesh read in")
if visualize:
from firedrake import triplot
if options_prefix[-1] != '_':
options_prefix += '_'
new_special_key = options_prefix + special_key
# FIXME: CHECK FROM COMMAND LINE
if new_special_key in solver_params:
setup_info[special_key] = str(
solver_params[new_special_key])
# Gets computed solution, prints and caches
key = frozenset(setup_info.items())
if not use_cache or key not in cache:
# {{{ Read in mesh if haven't already
if mesh is None:
print("\nReading Mesh...")
mesh = Mesh(mesh_name)
if use_2nd_order:
mesh = to_2nd_order(mesh,
circle_bdy_id=inner_bdy_id)
spatial_coord = SpatialCoordinate(mesh)
trial['mesh'] = mesh
print("Mesh Read in.\n")
if true_sol_expr is None:
true_sol_expr = get_true_sol_expr(spatial_coord)
trial['true_sol_expr'] = true_sol_expr
# }}}
kwargs = method_to_kwargs[method]
true_sol, comp_sol, snes_or_ksp = run_method.run_method(
N = mesh.num_vertices()
ground_truth = np.zeros((N))
period = 2 * np.pi / 0.3 * 2
for i in range(N):
ground_truth[i] = 2 * np.sin(geodesics.get(i) * period + 0.3)
return ground_truth
if __name__ == '__main__':
parser = argument_parser()
args = parser.parse_args()
mesh = Mesh('resources/meshes/dragon_connected.msh', dim=3)
num_eigenpairs = args.num_eigenpairs
print('Constructing ground truth. It may take a while')
ground_truth = construct_ground_truth(mesh)
mayavi_installed = False
if args.mayavi:
try:
import manifold_matern.plotting
mayavi_installed = True
except ImportError:
import warnings
warnings.warn(
'Mayavi does not seem to be installed.\n'
'No mayavi-based plotting will occur.', RuntimeWarning)
if mesh_dim == 3:
x, y, z = spatial_coord
norm = sqrt(x**2 + y**2 + z**2)
return Constant(1j / (4 * pi)) / norm * exp(1j * wave_number * norm)
elif mesh_dim == 2:
x, y = spatial_coord
return Constant(1j / 4) * hankel_function(
wave_number * sqrt(x**2 + y**2), n=80)
raise ValueError("Only meshes of dimension 2, 3 supported")
# Get the mesh and appropriate boundary tags
mesh_file_name = 'meshes/circle_in_square/max0%25.msh'
h = mesh_file_name[mesh_file_name.find('%') - 1:mesh_file_name.find('.')]
mesh = Mesh(mesh_file_name)
if mesh.geometric_dimension() == 2:
scatterer_bdy_id = 1
outer_bdy_id = 2
else:
scatterer_bdy_id = 1
outer_bdy_id = 3
# build fspace and bilinear forms
fspace = FunctionSpace(mesh, 'CG', 1)
u = TrialFunction(fspace)
v = TestFunction(fspace)
wave_number = 0.1 # one of [0.1, 1.0, 5.0, 10.0]
true_sol = get_true_sol_expr(SpatialCoordinate(mesh), wave_number)
