def test_sharp_field_dg0():
sim = Simulation()
sim.input.read_yaml(yaml_string=INP)
mesh = dolfin.UnitCubeMesh(2, 2, 2)
sim.set_mesh(mesh)
# Sharp jump at the cell boundaries
field_inp = sim.input.get_value('fields/0', required_type='Input')
f = SharpField(sim, field_inp).get_variable('rho')
check_vector_value_histogram(f.vector(), {1: 24, 1000: 24}, round_digits=6)
# Sharp jump in the middle of the cells
field_inp['z'] = 0.25
f = SharpField(sim, field_inp).get_variable('rho')
hist = get_vector_value_histogram(f.vector())
assert len(hist) == 4
for k, v in hist.items():
if round(k, 6) != 1:
assert v == 8
else:
assert v == 24
# Non-projected sharp jump between cells
field_inp['local_projection'] = False
field_inp['z'] = 0.50
f = SharpField(sim, field_inp).get_variable('rho')
check_vector_value_histogram(f.vector(), {1: 24, 1000: 24}, round_digits=6)
# Non-projected sharp jump the middle of the cells
field_inp['z'] = 0.25
f = SharpField(sim, field_inp).get_variable('rho')
hist = get_vector_value_histogram(f.vector())
check_vector_value_histogram(f.vector(), {1: 40, 1000: 8}, round_digits=6)
def test_get_dof_region_marks():
sim = Simulation()
sim.input.read_yaml(yaml_string=BASE_INPUT)
setup_simulation(sim)
Vp = sim.data['Vp']
dofs_x = Vp.tabulate_dof_coordinates().reshape((-1, 2))
drm = get_dof_region_marks(sim, Vp)
num_in_region = [0, 0]
ok = True
for dof, marks in drm.items():
x, y = dofs_x[dof]
if not (x == 0 or x == 1 or y == 0 or y == 1):
mpi_print('Got unexpected dof coords', x, y)
ok = False
if (0 in marks) != (x == 1 or y == 0 or y == 1):
mpi_print('Got unexpected dof coords in region 0', x, y)
ok = False
if (1 in marks) != (x == 0):
mpi_print('Got unexpected dof coords in region 0', x, y)
ok = False
for mark in marks:
num_in_region[mark] += 1
assert all_ok(ok)
assert mpi_int_sum(num_in_region[0]) == 30 + 29 * 2
assert mpi_int_sum(num_in_region[1]) == 30
def test_user_constants():
sim = Simulation()
sim.input.read_yaml(yaml_string=INPUT_USER_CONSTANTS)
success = setup_simulation(sim)
assert success
assert sim.input.get_value('ref') == 42.0
def test_bdm_identity_transform(gdim):
N = 5
k = 2
# Create mesh and define a divergence free field
if gdim == 2:
mesh = dolfin.UnitSquareMesh(N, N)
field = ['-sin(pi*x[1])*cos(pi*x[0])', 'sin(pi*x[0])*cos(pi*x[1])']
elif gdim == 3:
mesh = dolfin.UnitCubeMesh(N, N, N)
field = [
'-sin(pi*x[0])*cos(pi*x[1])*sin(pi*x[2])',
'sin(pi*x[0])*cos(pi*x[1])*sin(pi*x[2])',
'-cos(pi*x[2])*cos(pi*(x[0]-x[1]))',
]
V = dolfin.FunctionSpace(mesh, 'DG', k)
u = dolfin.as_vector([dolfin.Function(V) for _ in range(gdim)])
a = dolfin.as_vector([dolfin.Function(V) for _ in range(gdim)])
# Make a divergence free field
for i, cpp in enumerate(field):
ei = dolfin.Expression(cpp, degree=k)
u[i].interpolate(ei)
a[i].assign(u[i])
# Run the projection into BDM and then assign this to u
bdm = VelocityBDMProjection(simulation=Simulation(), w=u, use_bcs=False)
bdm.run()
# Check the changes made
for ui, ai in zip(u, a):
error = dolfin.errornorm(ai, ui, degree_rise=0)
assert error < 1e-15
def test_dirichlet_bcs_scalar_constant_value(method):
"Test inhomogenous Dirichlet BCs using a Poisson solver"
sim = Simulation()
sim.input.read_yaml(yaml_string=BASE_INPUT)
sim.input.set_value('boundary_conditions', [{}])
sim.input.set_value('boundary_conditions/0/name', 'all walls')
sim.input.set_value('boundary_conditions/0/selector', 'code')
sim.input.set_value('boundary_conditions/0/inside_code', 'on_boundary')
if method == 'const':
sim.input.set_value('boundary_conditions/0/phi/type', 'ConstantValue')
sim.input.set_value('boundary_conditions/0/phi/value', 1.0)
elif method == 'py_eval':
sim.input.set_value('boundary_conditions/0/phi/type', 'CodedValue')
sim.input.set_value('boundary_conditions/0/phi/code', '1.0')
elif method == 'py_exec':
sim.input.set_value('boundary_conditions/0/phi/type', 'CodedValue')
sim.input.set_value('boundary_conditions/0/phi/code', 'value[0] = 1.0')
elif method == 'cpp':
sim.input.set_value('boundary_conditions/0/phi/type', 'CppCodedValue')
sim.input.set_value('boundary_conditions/0/phi/cpp_code', '1.0')
setup_simulation(sim)
run_simulation(sim)
p = sim.data['phi'].vector().get_local()
assert numpy.linalg.norm(p - 1.0) < 1e-8
def test_has_path():
fn = get_test_file_name('base.inp')
sim = Simulation()
sim.input.read_yaml(fn)
assert sim.input.has_path('ocellaris') is True
assert sim.input.has_path('ocellaris/type') is True
assert sim.input.has_path('ocellaris222') is False
assert sim.input.has_path('ocellaris222/type') is False
assert sim.input.has_path('ocellaris/type222') is False
def test_use_code():
dummy_mod = '__DUMMY__'
assert dummy_mod not in sys.modules
sim = Simulation()
sim.input.read_yaml(yaml_string=INPUT_USER_CODE)
success = setup_simulation(sim)
assert success
assert dummy_mod in sys.modules
sys.modules.pop(dummy_mod)
def test_child_input():
fn = get_test_file_name('child.inp')
sim = Simulation()
sim.input.read_yaml(fn)
gv = lambda k, t: sim.input.get_value(k, required_type=t)
assert gv('metadata/author', 'string') == 'Tormod Landet'
# assert gv('metadata/date', 'date') == '2018-04-03'
assert gv('metadata/description', 'string') == 'ThisIsTheDescription'
assert gv('some_vals/computed', 'float') == 2.0
assert gv('test_py_val/C', 'float') == 8.0
def test_base_input():
fn = get_test_file_name('base.inp')
sim = Simulation()
sim.input.read_yaml(fn)
gv = lambda k, t: sim.input.get_value(k, required_type=t)
assert gv('metadata/author', 'string') == 'Tormod Landet'
assert gv('metadata/description', 'string') == 'NoDescription'
assert tuple(gv('some_vals/bools', 'list(int)')) == (1, 1, 0, 0)
assert tuple(gv('some_vals/floats', 'list(float)')) == (1.1, 2, 3.0e3)
assert gv('some_vals/computed', 'float') == 2.0
def mk_scheme(N, Vname, Vorder, cpp_expr, expr_args, convection_inp, dim=2, comm=None):
if comm is None:
comm = MPI.comm_world
parameters['ghost_mode'] = 'shared_vertex'
if dim == 2:
mesh = UnitSquareMesh(comm, N, N)
else:
mesh = UnitCubeMesh(comm, N, N, N)
V = FunctionSpace(mesh, Vname, Vorder)
C = Function(V)
e = Expression(cpp_expr, element=V.ufl_element(), **expr_args)
C.interpolate(e)
D = Function(V)
D.assign(C)
sim = Simulation()
sim.set_mesh(mesh)
sim.data['constrained_domain'] = None
sim.data['C'] = C
for key, value in convection_inp.items():
sim.input.set_value('convection/C/%s' % key, value)
scheme_name = convection_inp['convection_scheme']
return get_convection_scheme(scheme_name)(sim, 'C')
def test_vector_field():
sim = Simulation()
sim.input.read_yaml(yaml_string=INP)
mesh = dolfin.UnitCubeMesh(2, 2, 2)
sim.set_mesh(mesh)
field_inp = sim.input.get_value('fields/0', required_type='Input')
field = VectorField(sim, field_inp)
def verify(f, t, A):
print(t, A)
check_vector_value_histogram(f[0].vector(), {t + A: 125})
check_vector_value_histogram(f[1].vector(), {t * A: 125})
check_vector_value_histogram(f[2].vector(), {t * A + A: 125})
# t = 0
t, A = 0, 1
f = field.get_variable('u')
verify(f, t, A)
# t = 1
t, A = 1, 1
sim.time = t
sim.input.set_value('user_code/constants/A', A)
field.update(1, t, 1.0)
verify(f, t, A)
# t = 2
t, A = 2, 10
sim.time = t
sim.input.set_value('user_code/constants/A', A)
field.update(2, t, 1.0)
verify(f, t, A)
def test_scalar_field():
sim = Simulation()
sim.input.read_yaml(yaml_string=INP)
mesh = dolfin.UnitCubeMesh(2, 2, 2)
sim.set_mesh(mesh)
field_inp = sim.input.get_value('fields/1', required_type='Input')
field = ScalarField(sim, field_inp)
# t = 0
t, A = 0, 1
f = field.get_variable('rho')
check_vector_value_histogram(f.vector(), {t * A + A: 125})
# t = 1
t, A = 1, 1
sim.time = t
field.update(1, t, 1.0)
check_vector_value_histogram(f.vector(), {t * A + A: 125})
# t = 2
t, A = 2, 10
sim.time = t
sim.input.set_value('user_code/constants/A', A)
field.update(2, t, 1.0)
check_vector_value_histogram(f.vector(), {t * A + A: 125})
def test_restart_file_io(tmpdir_factory):
dir_name = mpi_tmpdir(tmpdir_factory, 'test_restart_file_io')
prefix = os.path.join(dir_name, 'ocellaris')
sim = Simulation()
sim.input.read_yaml(yaml_string=BASE_INPUT_PHI)
sim.input.set_value('output/prefix', prefix)
sim.input.set_value('time/tstart', 42.0)
sim.input.set_value('time/dt', 1.0)
setup_simulation(sim)
# Fill in the phi function
phi = sim.data['phi']
phi_arr = phi.vector().get_local()
phi_arr[:] = numpy.random.rand(*phi_arr.shape)
phi.vector().set_local(phi_arr)
phi.vector().apply('insert')
# Save restart file
file_name = sim.io.write_restart_file()
assert file_name.startswith(prefix)
# Load input from restart file
sim2 = Simulation()
sim2.io.load_restart_file_input(file_name)
assert sim2.input.get_value('time/tstart') == 42.0
assert str(sim.input) == str(sim2.input)
# Load phi from restart file
setup_simulation(sim2)
sim2.io.load_restart_file_results(file_name)
phi2 = sim2.data['phi']
phi2_arr = phi2.vector().get_local()
# FIXME: make tests work in parallel
if sim2.data['mesh'].mpi_comm().size == 1:
assert all(phi_arr == phi2_arr)
assert sim.data['mesh'].hash() == sim2.data['mesh'].hash()
def mk_limiter(degree, dim, use_cpp, comm_self=False):
dolfin.parameters['ghost_mode'] = 'shared_vertex'
sim = Simulation()
sim.input.read_yaml(yaml_string=BASE_INPUT)
if dim == 2:
sim.input.set_value('mesh/type', 'Rectangle')
sim.input.set_value('mesh/Nx', 10)
sim.input.set_value('mesh/Ny', 10)
cpp = 'A + A*sin(B*pi*x[0])*sin(B*pi*x[1])'
else:
sim.input.set_value('mesh/type', 'Box')
sim.input.set_value('mesh/Nx', 5)
sim.input.set_value('mesh/Ny', 5)
sim.input.set_value('mesh/Nz', 5)
cpp = 'A + A*sin(B*pi*x[0])*sin(B*pi*x[1])*sin(B*pi*x[2])'
# Create simulation with mesh and the phi function
sim.input.set_value('mesh/mpi_comm', 'SELF' if comm_self else 'WORLD')
sim.input.set_value('solver/polynomial_degree', degree)
sim.input.set_value('output/stdout_enabled', False)
setup_simulation(sim)
phi = sim.data['phi']
V = phi.function_space()
# Create a phi field with some jumps
e = dolfin.Expression(cpp, element=V.ufl_element(), A=0.5, B=2.0)
phi.interpolate(e)
arr = phi.vector().get_local()
arr[arr > 0.8] = 2 * 0.8 - arr[arr > 0.8]
arr[arr < 0.2] = 0.5
phi.vector().set_local(arr)
phi.vector().apply('insert')
# Create slope limiter
sim.input.set_value('slope_limiter/phi/method', 'HierarchicalTaylor')
sim.input.set_value('slope_limiter/phi/use_cpp', use_cpp)
sim.input.set_value('slope_limiter/phi/skip_boundaries', [])
lim = SlopeLimiter(sim, 'phi', phi)
if True:
from matplotlib import pyplot
pyplot.figure()
patches = dolfin.plot(phi)
pyplot.colorbar(patches)
pyplot.savefig('ht_lim_phi.png')
return phi, lim
def test_ensure_path():
fn = get_test_file_name('base.inp')
sim = Simulation()
sim.input.read_yaml(fn)
a = sim.input.ensure_path('user_code/constants')
assert 'A' in a
b = sim.input.ensure_path('does_not_exist')
assert len(b) == 0
assert 'does_not_exist' in sim.input
c = sim.input.ensure_path('does_not_exist/c')
assert len(c) == 0
assert len(sim.input.get_value('does_not_exist')) == 1
def test_import_module():
# A randomly selected script that does nothing at import time
dummy_mod = 'plot_reports'
assert dummy_mod not in sys.modules
# Account for current working directory
inp = INPUT_MODULE_IMPORT % os.path.join(TEST_DIR, '..')
sim = Simulation()
sim.input.read_yaml(yaml_string=inp)
success = setup_simulation(sim)
assert success
assert dummy_mod in sys.modules
sys.modules.pop(dummy_mod)
def test_isoline_circle(degree):
sim = Simulation()
sim.input.read_yaml(yaml_string=ISO_INPUT)
sim.input.set_value('multiphase_solver/polynomial_degree_colour', degree)
sim.input.set_value('mesh/Nx', 10)
sim.input.set_value('mesh/Ny', 10)
sim.input.set_value(
'initial_conditions/cp/cpp_code', '1.1*pow(pow(x[0] - 0.5, 2) + pow(x[1] - 0.5, 2), 0.5)'
)
setup_simulation(sim)
sim.data['c'].assign(sim.data['cp'])
probe = sim.probes['free_surface']
lines = probe.run(force_active=True)
if False:
from matplotlib import pyplot
c = dolfin.plot(sim.data['c'])
pyplot.colorbar(c)
for x, y in lines:
pyplot.plot(x, y)
pyplot.savefig('test_isoline_circle_%d.png' % degree)
pyplot.close()
print(probe.name, probe.field_name, probe.value)
print(len(lines))
for x, y in lines:
# Check that the radius is constant
r = ((x - 0.5) ** 2 + (y - 0.5) ** 2) ** 0.5
print('x', x)
print('y', y)
print('dr', r - 0.5 / 1.1)
assert all(abs(r - 0.5 / 1.1) < 5e-3)
# Check that the line is clockwise or counter clockwise
# for all segments, no going back and forth
theta = numpy.arctan2(y - 0.5, x - 0.5) * 180 / numpy.pi
theta[theta < 0] += 360
tdt = numpy.diff(theta)
tdt2 = tdt[abs(tdt) < 340]
print('dt', tdt)
assert all(tdt2 > 0) or all(tdt2 < 0)
if sim.ncpu == 1:
# The iso surface code is not written for full parallel support
assert len(lines) == 1
assert x[0] == x[-1] and y[0] == y[-1], "The loop should be closed"
def test_plot_io_3D(iotype, tmpdir_factory):
dir_name = mpi_tmpdir(tmpdir_factory, 'test_plot_io_3D')
prefix = os.path.join(dir_name, 'ocellaris')
N = 4
sim = Simulation()
sim.input.read_yaml(yaml_string=BASE_INPUT_VELPRES)
sim.input.set_value('output/prefix', prefix)
sim.input.set_value('user_code/constants/N', N)
setup_simulation(sim)
sim.io.setup() # Normally called in sim._at_start_of_simulation()
for d in range(3):
sim.data['u%d' % d].assign(sim.data['up%d' % d])
ncell = N**3 * 6
npoint = ncell * 10
if iotype == 'vtk':
file_name = sim.io.lvtk.write()
assert file_name.startswith(prefix)
assert file_name.endswith('.vtk')
assert os.path.isfile(file_name)
with open(file_name, 'rt') as f:
for line in f:
if line.startswith('POINTS'):
pline = line
elif line.startswith('CELLS'):
cline = line
elif line.startswith('CELL_TYPES'):
tline = line
elif line.startswith('POINT_DATA'):
dline = line
assert pline.strip() == 'POINTS %d float' % npoint
assert cline.strip() == 'CELLS %d %d' % (ncell, ncell * 11)
assert tline.strip() == 'CELL_TYPES %d' % ncell
assert dline.strip() == 'POINT_DATA %d' % (ncell * 10)
elif iotype == 'xdmf':
file_name = sim.io.xdmf.write()
assert file_name.startswith(prefix)
assert file_name.endswith('.xdmf')
assert os.path.isfile(file_name)
def test_mark_cell_layers():
sim = Simulation()
sim.input.read_yaml(yaml_string=BASE_INPUT)
setup_simulation(sim)
mesh = sim.data['mesh']
Vp = sim.data['Vp']
# No named == all
cells = mark_cell_layers(sim, Vp)
for cid in cells:
cell = dolfin.Cell(mesh, cid)
mp = cell.midpoint()[:]
assert mp[0] < 0.1 or mp[0] > 0.9 or mp[1] < 0.1 or mp[1] > 0.9
assert mpi_int_sum(len(cells)) == 20 * 2 + 16 * 2
# Test all
cells = mark_cell_layers(sim, Vp, named_boundaries=['all'])
for cid in cells:
cell = dolfin.Cell(mesh, cid)
mp = cell.midpoint()[:]
assert mp[0] < 0.1 or mp[0] > 0.9 or mp[1] < 0.1 or mp[1] > 0.9
assert mpi_int_sum(len(cells)) * 2 + 16 * 2
# Test only left side
cells = mark_cell_layers(sim, Vp, named_boundaries=['left'])
for cid in cells:
cell = dolfin.Cell(mesh, cid)
mp = cell.midpoint()[:]
assert mp[0] < 0.1
assert mpi_int_sum(len(cells)) == 20
cells = mark_cell_layers(sim, Vp, named_boundaries=['not left'])
for cid in cells:
cell = dolfin.Cell(mesh, cid)
mp = cell.midpoint()[:]
assert mp[0] > 0.9 or mp[1] < 0.1 or mp[1] > 0.9
assert mpi_int_sum(len(cells)) == 20 * 1 + 18 * 2
cells = mark_cell_layers(sim, Vp, named_boundaries=['left', 'not left'])
assert mpi_int_sum(len(cells)) == 20 * 2 + 16 * 2
def test_dirichlet_bcs_scalar_mms(method):
"Test inhomogenous coded Dirichlet BCs using a Poisson solver"
sim = Simulation()
sim.input.read_yaml(yaml_string=BASE_INPUT)
sim.input.set_value('boundary_conditions', [{}])
sim.input.set_value('boundary_conditions/0/name', 'all walls')
sim.input.set_value('boundary_conditions/0/selector', 'code')
sim.input.set_value('boundary_conditions/0/inside_code', 'on_boundary')
# Get analytical expressions
cphi, _, _, cf = mms_case()
sim.input.set_value('solver/source', cf)
# Setup the boundary conditions to test
if method == 'py_eval':
sim.input.set_value('boundary_conditions/0/phi/type', 'CodedValue')
sim.input.set_value('boundary_conditions/0/phi/code', cphi)
elif method == 'py_exec':
sim.input.set_value('boundary_conditions/0/phi/type', 'CodedValue')
sim.input.set_value('boundary_conditions/0/phi/code', 'value[0] = ' + cphi)
elif method == 'cpp':
sim.input.set_value('boundary_conditions/0/phi/type', 'CppCodedValue')
sim.input.set_value('boundary_conditions/0/phi/cpp_code', cphi)
# Run Ocellaris
setup_simulation(sim)
run_simulation(sim)
# The numeric (phih) and analytic (phia) solution functions
Vphi = sim.data['Vphi']
phi = dolfin.Expression(cphi, degree=5)
phih = sim.data['phi']
phia = dolfin.interpolate(phi, Vphi)
# Compute relative error and check that it is reasonable
phidiff = dolfin.errornorm(phi, phih)
analytical = dolfin.norm(phia)
relative_error = phidiff / analytical
print('RELATIVE ERROR IS %.3f' % relative_error)
assert relative_error < 0.074
def test_isoline_horizontal(degree):
sim = Simulation()
sim.input.read_yaml(yaml_string=ISO_INPUT)
sim.input.set_value('multiphase_solver/polynomial_degree_colour', degree)
setup_simulation(sim)
probe = sim.probes['free_surface']
# Initial value with sharp interface at x[1] == 0.5
Vc = sim.data['Vc']
c = sim.data['c']
dm = Vc.dofmap()
arr = c.vector().get_local()
for cell in dolfin.cells(sim.data['mesh']):
cell_value = 1 if cell.midpoint().y() < 0.5 else 0
for dof in dm.cell_dofs(cell.index()):
arr[dof] = cell_value
c.vector().set_local(arr)
c.vector().apply('insert')
lines = probe.run(force_active=True)
print('\nDegree:', degree, 'Vcdim:', Vc.dim())
print(probe.name, probe.field_name, probe.value)
print(len(lines))
if sim.ncpu > 1:
raise pytest.skip()
for x, y in lines:
print('x', x, '\ny', y)
assert all(abs(y - 0.5) < 1e-12)
# Results should be in sorted order
xdx = numpy.diff(x)
assert all(xdx > 0) or all(xdx < 0)
assert len(lines) == 1
def run_and_calculate_error(N, dt, tmax, polydeg_rho, last=False):
"""
Run Ocellaris and return L2 & H1 errors in the last time step
"""
say(N, dt, tmax, polydeg_rho)
# Setup and run simulation
sim = Simulation()
sim.input.read_yaml('transport.inp')
mesh_type = sim.input.get_value('mesh/type')
if mesh_type == 'XML':
# Create unstructured mesh with gmsh
cmd1 = [
'gmsh', '-string',
'lc = %f;' % (3.14 / N), '-o',
'disc_%d.msh' % N, '-2',
'../convergence-variable-density-disk/disc.geo'
]
cmd2 = ['dolfin-convert', 'disc_%d.msh' % N, 'disc.xml']
with open('/dev/null', 'w') as devnull:
for cmd in (cmd1, cmd2):
say(' '.join(cmd))
if ISROOT:
subprocess.call(cmd, stdout=devnull, stderr=devnull)
elif mesh_type == 'UnitDisc':
sim.input.set_value('mesh/N', N // 2)
else:
sim.input.set_value('mesh/Nx', N)
sim.input.set_value('mesh/Ny', N)
sim.input.set_value('time/dt', dt)
sim.input.set_value('time/tmax', tmax)
sim.input.set_value('multiphase_solver/polynomial_degree_rho', polydeg_rho)
sim.input.set_value('output/stdout_enabled', False)
say('Running with multiphase solver %s ...' %
(sim.input.get_value('multiphase_solver/type')))
t1 = time.time()
setup_simulation(sim)
run_simulation(sim)
duration = time.time() - t1
say('DONE')
# Interpolate the analytical solution to the same function space
Vu = sim.data['Vu']
Vp = sim.data['Vp']
Vr = sim.data['Vrho']
polydeg_r = Vr.ufl_element().degree()
vals = dict(t=sim.time, dt=sim.dt)
rho_e = dolfin.Expression(
sim.input.get_value('initial_conditions/rho_p/cpp_code'),
degree=polydeg_r,
**vals)
rho_a = dolfin.project(rho_e, Vr)
rho_e.t = 0
rho_0 = dolfin.project(rho_e, Vr)
# Calculate L2 errors
err_rho = calc_err(sim.data['rho'], rho_a)
# Calculate H1 errors
err_rho_H1 = calc_err(sim.data['rho'], rho_a, 'H1')
mesh = sim.data['mesh']
n = dolfin.FacetNormal(mesh)
reports = sim.reporting.timestep_xy_reports
say('Num time steps:', sim.timestep)
say('Num cells:', mesh.num_cells())
say('Co_max:', numpy.max(reports['Co']))
say('rho_min went from %r to %r' %
(reports['min(rho)'][0], reports['min(rho)'][-1]))
say('rho_max went from %r to %r' %
(reports['max(rho)'][0], reports['max(rho)'][-1]))
m0, m1 = reports['mass'][0], reports['mass'][-1]
say('mass error %.3e (%.3e)' % (m1 - m0, (m1 - m0) / m0))
say('vel compat error %.3e' %
dolfin.assemble(dolfin.dot(sim.data['u'], n) * dolfin.ds))
int_p = dolfin.assemble(sim.data['p'] * dolfin.dx)
say('p*dx', int_p)
div_u_Vp = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vp).vector().get_local()).max()
say('div(u)|Vp', div_u_Vp)
div_u_Vu = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vu).vector().get_local()).max()
say('div(u)|Vu', div_u_Vu)
Vdg0 = dolfin.FunctionSpace(mesh, "DG", 0)
div_u_DG0 = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vdg0).vector().get_local()).max()
say('div(u)|DG0', div_u_DG0)
Vdg1 = dolfin.FunctionSpace(mesh, "DG", 1)
div_u_DG1 = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vdg1).vector().get_local()).max()
say('div(u)|DG1', div_u_DG1)
isoparam = mesh.ufl_coordinate_element().degree() > 1
if last and (not isoparam
or sim.input.get_value('mesh/type') == 'UnitDisc'):
# Plot the results
for fa, name in ((rho_a, 'rho'), ):
fh = sim.data[name]
if isoparam:
# Bug in matplotlib plotting for isoparametric elements
mesh2 = dolfin.UnitDiscMesh(dolfin.MPI.comm_world, N // 2, 1,
2)
ue = fa.function_space().ufl_element()
V2 = dolfin.FunctionSpace(mesh2, ue.family(), ue.degree())
fa2, fh2 = dolfin.Function(V2), dolfin.Function(V2)
fa2.vector().set_local(fa.vector().get_local())
fh2.vector().set_local(fh.vector().get_local())
fa, fh = fa2, fh2
plot(fh - fa, name + ' diff', '%g_%g_%s_diff' % (N, dt, name))
plot(fa, name + ' analytical',
'%g_%g_%s_analytical' % (N, dt, name))
plot(fh, name + ' numerical', '%g_%g_%s_numerical' % (N, dt, name))
plot(rho_0, name + ' initial', '%g_%g_%s_initial' % (N, dt, name))
hmin = mesh.hmin()
return err_rho, err_rho_H1, hmin, dt, duration
def plot_backward_facing_step(res):
u = df.as_vector([res['u0'], res['u1']])
V = u[0].function_space()
mesh = V.mesh()
############################################################################
# Get some meta data
sim = Simulation()
sim.input.read_yaml(yaml_string=res['input'])
Re = sim.input.get_value('user_code/constants/Re', required_type='float')
time = res['time']
############################################################################
# Find the length X1 of primary recirculating bubble
x1_ypos = -0.99 * H2
xf, _, _, f = get_probe_values(u[0], [0, x1_ypos, 0], [L2, x1_ypos, 0], 200)
x1_c0 = get_zero_crossings(xf, f)
print(x1_c0)
############################################################################
# Find the inflow profile
x_inflow = -1.5 * H1
_, y_inflow, _, u0_inflow = get_probe_values(
u[0], [x_inflow, 0, 0], [x_inflow, H1, 0], 20
)
############################################################################
# Refine the mesh and get a triangluated stream function
for _ in range(2):
old = mesh, V
mesh = df.refine(mesh)
V = df.FunctionSpace(mesh, V.ufl_element())
df.parameters['allow_extrapolation'] = True
try:
u0 = df.interpolate(u[0], V)
u1 = df.interpolate(u[1], V)
u = df.as_vector([u0, u1])
except Exception:
mesh, V = old
u0, u1 = u[0], u[1]
print('Refining failed ------------------------------')
break
df.parameters['allow_extrapolation'] = False
sf = StreamFunction(u, degree=V.ufl_element().degree())
sf.compute()
levels = get_probe_values(
sf.psi, [1.5 * H2, -0.5 * H2, 0], [H2, H1 * 0.99, 0], N_levels
)[-1]
levels2 = []
for xi, _idx, _upcrossing in x1_c0:
# Add stream function values at upcrossing locations
if xi - 0.3 > 0:
levels2.append(get_probe_value(sf.psi, (xi - 0.3, x1_ypos, 0)))
if xi + 0.1 < L2:
levels2.append(get_probe_value(sf.psi, (xi + 0.1, x1_ypos, 0)))
if levels2:
levels = numpy.concatenate((levels, levels2))
levels.sort()
coords = mesh.coordinates()
triangles = []
for cell in df.cells(mesh):
cell_vertices = cell.entities(0)
triangles.append(cell_vertices)
triangulation = Triangulation(coords[:, 0], coords[:, 1], triangles)
Z = sf.psi.compute_vertex_values()
############################################################################
# Plot streamlines and velocity distributions
fig = pyplot.figure(figsize=(15, 2.5))
ax = fig.add_subplot(111)
ax.plot([-L1, -L1, 0, 0, L2, L2, -L1], [H1, 0, 0, -H2, -H2, H1, H1], 'k')
# ax.triplot(triangulation, color='#000000', alpha=0.5, lw=0.25)
ax.tricontour(
triangulation, Z, levels, linestyles='solid', colors='#0000AA', linewidths=0.5
)
ax.plot(x_inflow + u0_inflow, y_inflow, 'm')
ax.plot(x_inflow - 6 * (y_inflow - 1) * y_inflow, y_inflow, 'k.', ms=4)
# ax2 = fig.add_subplot(212)
# ax2.plot(xf, f)
# ax2.set_xlim(-L1, L2)
for xi, _idx, _upcrossing in x1_c0:
ax.plot(xi, x1_ypos, 'rx')
# ax.text(xi, x1_ypos+0.1, 'X1=%.3f' % x1, backgroundcolor='white')
ax.set_title(
'Re = %g, t = %g, xi = %s' % (Re, time, ', '.join('%.3f' % e[0] for e in x1_c0))
)
fig.tight_layout()
def test_robin_bcs_scalar_mms(bcs, b):
"""
Test Robin BCs using a Poisson solver to solve
-∇⋅∇φ = f
where φ = 1 + x and hence f = 0. We use Neumann
BCs n⋅∇φ = 0 on the horizontal walls and Robin
BCs on the vertical walls
"""
sim = Simulation()
sim.input.read_yaml(yaml_string=BASE_INPUT)
# Create boundary regions
sim.input.set_value('boundary_conditions', [{}, {}, {}])
sim.input.set_value('boundary_conditions/0/name', 'vertical wall x=0')
sim.input.set_value('boundary_conditions/0/selector', 'code')
sim.input.set_value(
'boundary_conditions/0/inside_code', 'on_boundary and (x[0] < 1e-6 or x[0] > 1 - 1e-6)'
)
sim.input.set_value('boundary_conditions/1/name', 'vertical walls x=1')
sim.input.set_value('boundary_conditions/1/selector', 'code')
sim.input.set_value('boundary_conditions/1/inside_code', 'on_boundary and x[0] > 1 - 1e-6')
sim.input.set_value('boundary_conditions/2/name', 'horizontal walls')
sim.input.set_value('boundary_conditions/2/selector', 'code')
sim.input.set_value(
'boundary_conditions/2/inside_code', 'on_boundary and (x[1] < 1e-6 or x[1] > 1 - 1e-6)'
)
# Setup the boundary conditions to test
if bcs == 'robin':
sim.input.set_value('boundary_conditions/0/phi/type', 'ConstantRobin')
sim.input.set_value('boundary_conditions/0/phi/blend', b)
sim.input.set_value('boundary_conditions/0/phi/dval', 1.0)
sim.input.set_value('boundary_conditions/0/phi/nval', -1.0)
sim.input.set_value('boundary_conditions/1/phi/type', 'ConstantRobin')
sim.input.set_value('boundary_conditions/1/phi/blend', b)
sim.input.set_value('boundary_conditions/1/phi/dval', 2.0)
sim.input.set_value('boundary_conditions/1/phi/nval', 1.0)
sim.input.set_value('boundary_conditions/2/phi/type', 'ConstantGradient')
sim.input.set_value('boundary_conditions/2/phi/value', 0.0)
elif bcs == 'neumann':
sim.input.set_value('boundary_conditions/0/phi/type', 'ConstantGradient')
sim.input.set_value('boundary_conditions/0/phi/value', -1.0)
sim.input.set_value('boundary_conditions/1/phi/type', 'ConstantGradient')
sim.input.set_value('boundary_conditions/1/phi/value', 1.0)
# RHS
sim.input.set_value('solver/source', '2*pi*pi*(pow(sin(x[0]*pi), 2) - pow(cos(x[0]*pi), 2))')
# Run Ocellaris
setup_simulation(sim)
run_simulation(sim)
# The numeric (phih) and analytic (phia) solution functions
cphi = '1.0 + x[0] + pow(sin(x[0]*pi), 2)'
Vphi = sim.data['Vphi']
phi = dolfin.Expression(cphi, degree=5)
phih = sim.data['phi']
phia = dolfin.interpolate(phi, Vphi)
# Correct the constant offset due to how the null space is handledFalse
if bcs == 'neumann':
correct_constant_offset(sim, phih, phia)
# Plot to file for debugging
# debug_phi_plot(phia, phih, 'test_robin_bcs_scalar_mms_%s.png' % bcs)
# Compute relative error and check that it is reasonable
phidiff = dolfin.errornorm(phi, phih)
analytical = dolfin.norm(phia)
relative_error = phidiff / analytical
print('RELATIVE ERROR IS %.3f' % relative_error)
assert relative_error < 0.015 # Expect 0.0139 with Robin
def run_and_calculate_error(N, dt, tmax, polydeg_u, polydeg_p, modifier=None):
"""
Run Ocellaris and return L2 & H1 errors in the last time step
"""
say(N, dt, tmax, polydeg_u, polydeg_p)
# Setup and run simulation
sim = Simulation()
sim.input.read_yaml('kovasznay.inp')
sim.input.set_value('mesh/Nx', N)
sim.input.set_value('mesh/Ny', N)
sim.input.set_value('time/dt', dt)
sim.input.set_value('time/tmax', tmax)
sim.input.set_value('solver/polynomial_degree_velocity', polydeg_u)
sim.input.set_value('solver/polynomial_degree_pressure', polydeg_p)
sim.input.set_value('output/stdout_enabled', False)
if modifier:
modifier(sim) # Running regression tests, modify some input params
say('Running ...')
try:
t1 = time.time()
setup_simulation(sim)
run_simulation(sim)
duration = time.time() - t1
except KeyboardInterrupt:
raise
except BaseException as e:
raise
import traceback
traceback.print_exc()
return [1e10] * 6 + [1, dt, time.time() - t1]
say('DONE')
tmax_warning = ' <------ NON CONVERGENCE!!' if sim.time > tmax - dt / 2 else ''
# Interpolate the analytical solution to the same function space
Vu = sim.data['Vu']
Vp = sim.data['Vp']
lambda_ = sim.input.get_value('user_code/constants/LAMBDA',
required_type='float')
u0e = dolfin.Expression(
sim.input.get_value('boundary_conditions/0/u/cpp_code/0'),
LAMBDA=lambda_,
degree=polydeg_u)
u1e = dolfin.Expression(
sim.input.get_value('boundary_conditions/0/u/cpp_code/1'),
LAMBDA=lambda_,
degree=polydeg_u)
pe = dolfin.Expression(
'-0.5*exp(LAMBDA*2*x[0]) + 1/(4*LAMBDA)*(exp(2*LAMBDA) - 1.0)',
LAMBDA=lambda_,
degree=polydeg_p,
)
u0a = dolfin.project(u0e, Vu)
u1a = dolfin.project(u1e, Vu)
pa = dolfin.project(pe, Vp)
# Correct pa (we want to be spot on, not close)
int_pa = dolfin.assemble(pa * dolfin.dx)
vol = dolfin.assemble(dolfin.Constant(1.0) * dolfin.dx(domain=Vp.mesh()))
pa.vector()[:] -= int_pa / vol
# Calculate L2 errors
err_u0 = calc_err(sim.data['u0'], u0a)
err_u1 = calc_err(sim.data['u1'], u1a)
err_p = calc_err(sim.data['p'], pa)
# Calculate H1 errors
err_u0_H1 = calc_err(sim.data['u0'], u0a, 'H1')
err_u1_H1 = calc_err(sim.data['u1'], u1a, 'H1')
err_p_H1 = calc_err(sim.data['p'], pa, 'H1')
say('Number of time steps:', sim.timestep, tmax_warning)
loglines = sim.log.get_full_log().split('\n')
say('Num inner iterations:',
sum(1 if 'Inner iteration' in line else 0 for line in loglines))
say('max(ui_new-ui_prev)',
sim.reporting.get_report('max(ui_new-ui_prev)')[1][-1])
int_p = dolfin.assemble(sim.data['p'] * dolfin.dx)
say('p*dx', int_p)
say('pa*dx', dolfin.assemble(pa * dolfin.dx(domain=Vp.mesh())))
div_u_Vp = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vp).vector().get_local()).max()
say('div(u)|Vp', div_u_Vp)
div_u_Vu = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vu).vector().get_local()).max()
say('div(u)|Vu', div_u_Vu)
Vdg0 = dolfin.FunctionSpace(sim.data['mesh'], "DG", 0)
div_u_DG0 = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vdg0).vector().get_local()).max()
say('div(u)|DG0', div_u_DG0)
Vdg1 = dolfin.FunctionSpace(sim.data['mesh'], "DG", 1)
div_u_DG1 = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vdg1).vector().get_local()).max()
say('div(u)|DG1', div_u_DG1)
if False:
# Plot the results
for fa, name in ((u0a, 'u0'), (u1a, 'u1'), (pa, 'p')):
p1 = dolfin.plot(sim.data[name] - fa,
title='%s_diff' % name,
key='%s_diff' % name)
p2 = dolfin.plot(fa, title=name + ' analytical', key=name)
p1.write_png('%g_%g_%s_diff' % (N, dt, name))
p2.write_png('%g_%g_%s' % (N, dt, name))
dolfin.interactive()
from numpy import argmax
for d in range(2):
up = sim.data['up%d' % d]
upp = sim.data['upp%d' % d]
V = up.function_space()
coords = V.tabulate_dof_coordinates().reshape((-1, 2))
up.vector()[:] -= upp.vector()
diff = abs(up.vector().get_local())
i = argmax(diff)
say('Max difference in %d direction is %.4e at %r' %
(d, diff[i], coords[i]))
if 'uppp%d' % d in sim.data:
uppp = sim.data['uppp%d' % d]
upp.vector()[:] -= uppp.vector()
diffp = abs(upp.vector().get_local())
ip = argmax(diffp)
say('Prev max diff. in %d direction is %.4e at %r' %
(d, diffp[ip], coords[ip]))
if False and N == 24:
# dolfin.plot(sim.data['u0'], title='u0')
# dolfin.plot(sim.data['u1'], title='u1')
# dolfin.plot(sim.data['p'], title='p')
# dolfin.plot(u0a, title='u0a')
# dolfin.plot(u1a, title='u1a')
# dolfin.plot(pa, title='pa')
plot_err(sim.data['u0'], u0a, title='u0a - u0')
plot_err(sim.data['u1'], u1a, title='u1a - u1')
plot_err(sim.data['p'], pa, 'pa - p')
# plot_err(sim.data['u0'], u0a, title='u0a - u0')
dolfin.plot(sim.data['up0'], title='up0 - upp0')
dolfin.plot(sim.data['upp0'], title='upp0 - uppp0')
# plot_err(sim.data['u1'], u1a, title='u1a - u1')
dolfin.plot(sim.data['up1'], title='up1 - upp1')
# dolfin.plot(sim.data['upp1'], title='upp1 - uppp1')
hmin = sim.data['mesh'].hmin()
return err_u0, err_u1, err_p, err_u0_H1, err_u1_H1, err_p_H1, hmin, dt, duration
def test_slip_length_robin_bcs_scalar_mms(slip_length, method):
"""
Test slip length Robin BCs using a Poisson solver to solve
-∇⋅∇φ = f
where φ = (-6x² + 6x + 6𝛿)/(6𝛿 - 1) and hence f = 12/(6𝛿 - 1).
We use Neumann BCs n⋅∇φ = 0 on the horizontal walls and Navier's
slip length boundary condition on the vertical walls. The selected
analytical solution is such that for any slip length 𝛿 the average
value of φ is 1.0
This mimics a flow profile going vertically in a 1.0 wide channel
"""
sim = Simulation()
sim.input.read_yaml(yaml_string=BASE_INPUT)
# Create boundary regions
sim.input.set_value('boundary_conditions', [{}, {}])
sim.input.set_value('boundary_conditions/0/name', 'vertical walls')
sim.input.set_value('boundary_conditions/0/selector', 'code')
sim.input.set_value(
'boundary_conditions/0/inside_code', 'on_boundary and (x[0] < 1e-6 or x[0] > 1 - 1e-6)'
)
sim.input.set_value('boundary_conditions/1/name', 'horizontal walls')
sim.input.set_value('boundary_conditions/1/selector', 'code')
sim.input.set_value(
'boundary_conditions/1/inside_code', 'on_boundary and (x[1] < 1e-6 or x[1] > 1 - 1e-6)'
)
# Vertical wall BCs
if method == 'Constant':
sim.input.set_value('boundary_conditions/0/phi/type', 'SlipLength')
sim.input.set_value('boundary_conditions/0/phi/slip_length', slip_length)
elif method == 'C++':
sim.input.set_value('boundary_conditions/0/phi/type', 'SlipLength')
sim.input.set_value('boundary_conditions/0/phi/slip_length', repr(slip_length))
else:
sim.input.set_value('boundary_conditions/0/phi/type', 'InterfaceSlipLength')
sim.input.set_value('boundary_conditions/0/phi/slip_length', slip_length)
sim.input.set_value('boundary_conditions/0/phi/slip_factor_function', 'fs_zone/phi')
sim.input.set_value('fields', [{}])
sim.input.set_value('fields/0/name', 'fs_zone')
sim.input.set_value('fields/0/type', 'FreeSurfaceZone')
sim.input.set_value('fields/0/radius', 0.5)
# Create dummy scalar field
sim.input.set_value('multiphase_solver/type', 'BlendedAlgebraicVOF')
sim.input.set_value('multiphase_solver/function_space_colour', 'DG')
sim.input.set_value('multiphase_solver/polynomial_degree_colour', 0)
sim.input.set_value('initial_conditions/cp/cpp_code', 'x[1] < 0.5 ? 1.0 : 0.0')
sim.input.set_value('physical_properties/rho0', 1.0)
sim.input.set_value('physical_properties/rho1', 1.0)
sim.input.set_value('physical_properties/nu0', 1.0)
sim.input.set_value('physical_properties/nu1', 1.0)
sim.input.set_value('multiphase_solver/project_uconv_dgt0', False)
sim.data['u_conv'] = dolfin.as_vector([0, 0])
sim.data['dt'] = dolfin.Constant(1.0)
# Horizontal wall BCs
sim.input.set_value('boundary_conditions/1/phi/type', 'ConstantGradient')
sim.input.set_value('boundary_conditions/1/phi/value', 0.0)
# RHS
sim.input.set_value('solver/source', '12/(6*𝛿 - 1.0)'.replace('𝛿', repr(slip_length)))
# Run Ocellaris
setup_simulation(sim)
run_simulation(sim)
# The numeric (phih) and analytic (phia) solution functions
cphi = '(-6*x[0]*x[0] + 6*x[0] + 6*𝛿)/(6*𝛿 - 1.0)'.replace('𝛿', repr(slip_length))
Vphi = sim.data['Vphi']
phi = dolfin.Expression(cphi, degree=5)
phih = sim.data['phi']
phia = dolfin.interpolate(phi, Vphi)
# Plot to file for debugging
# debug_phi_plot(phi, phia, phih, 'test_slip_length_bcs_scalar_mms_%g.png' % slip_length)
# Compute relative error and check that it is reasonable
phidiff = dolfin.errornorm(phi, phih)
analytical = dolfin.norm(phia)
relative_error = phidiff / analytical
print('RELATIVE ERROR IS %.4f for 𝛿=%r' % (relative_error, slip_length))
if method == 'Interface' and False:
from matplotlib import pyplot
fig = pyplot.figure(figsize=(8, 15))
fig.add_subplot(311)
c = dolfin.plot(sim.data['c'])
pyplot.colorbar(c)
fig.add_subplot(312)
c = dolfin.plot(sim.data['ls_c_0_5'])
pyplot.colorbar(c)
fig.add_subplot(313)
c = dolfin.plot(sim.fields['fs_zone'].get_variable('phi'))
pyplot.colorbar(c)
fig.tight_layout()
fig.savefig('AAAAAAAAAAAaaaa.png')
assert relative_error < 0.0099 # Expect 0.0097 for 𝛿=0.001
def main(inputfile, input_override):
"""
Run Ocellaris
"""
if os.environ.get('OCELLARIS_SUPER_DEBUG', False):
print('FOUND OCELLARIS_SUPER_DEBUG in environment')
from ocellaris.utils.debug import enable_super_debug
enable_super_debug()
sim = Simulation()
# Read input
if sim.io.is_restart_file(inputfile):
sim.io.load_restart_file_input(inputfile)
else:
sim.input.read_yaml(inputfile)
# Alter input by values given on the command line
override_input_variables(sim, input_override)
# Setup logging before we start printing anything
sim.log.setup()
# Print banner with Ocellaris version number
version = get_detailed_version()
location = os.path.split(os.path.abspath(__file__))[0]
sim.log.info('=' * 80)
sim.log.info(' Ocellaris %s' % version)
sim.log.info('=' * 80)
sim.log.info('Installed at:')
sim.log.info(' %s' % location)
sim.log.info(' host: %s' % platform.node())
sim.log.info()
# Print some version information
sim.log.info('Running on Python %s' % sys.version)
sim.log.info(' Using dolfin %s' % dolfin.__version__)
sim.log.info(' Using mpi4py %s' % mpi4py.__version__)
sim.log.info(' Using h5py %s' % h5py.__version__)
sim.log.info(' Using meshio %s' % meshio.__version__)
sim.log.info(' Using PyYAML %s' % yaml.__version__)
sim.log.info(' Using petsc4py %s' % petsc4py_version)
sim.log.info(' Using PETSc %d.%d.%d\n' % PETSc.Sys.getVersion())
# Setup the Ocellaris simulation
ok = setup_simulation(sim, setup_logging=False, catch_exceptions=True)
if not ok:
sim.log.error('Setup did not suceed, exiting')
sys.exit(1)
if sim.restarted:
# Load previous results
sim.io.load_restart_file_results(inputfile)
# Run the Ocellaris simulation time loop
run_simulation(sim, catch_exceptions=True)
sim.log.info('=' * 80)
if sim.success:
sim.log.info('Ocellaris finished successfully')
else:
sim.log.info('Ocellaris finished with errors')
def run_and_calculate_error(N, dt, tmax, polydeg_u, polydeg_p, nu, last=False):
"""
Run Ocellaris and return L2 & H1 errors in the last time step
"""
say(N, dt, tmax, polydeg_u, polydeg_p)
# Setup and run simulation
timingtypes = [
dolfin.TimingType.user, dolfin.TimingType.system,
dolfin.TimingType.wall
]
dolfin.timings(dolfin.TimingClear_clear, timingtypes)
sim = Simulation()
sim.input.read_yaml('disc.inp')
mesh_type = sim.input.get_value('mesh/type')
if mesh_type == 'XML':
# Create unstructured mesh with gmsh
cmd1 = [
'gmsh', '-string',
'lc = %f;' % (3.14 / N), '-o',
'disc_%d.msh' % N, '-2', 'disc.geo'
]
cmd2 = ['dolfin-convert', 'disc_%d.msh' % N, 'disc.xml']
with open('/dev/null', 'w') as devnull:
for cmd in (cmd1, cmd2):
say(' '.join(cmd))
subprocess.call(cmd, stdout=devnull, stderr=devnull)
elif mesh_type == 'UnitDisc':
sim.input.set_value('mesh/N', N // 2)
else:
sim.input.set_value('mesh/Nx', N)
sim.input.set_value('mesh/Ny', N)
sim.input.set_value('time/dt', dt)
sim.input.set_value('time/tmax', tmax)
sim.input.set_value('solver/polynomial_degree_velocity', polydeg_u)
sim.input.set_value('solver/polynomial_degree_pressure', polydeg_p)
sim.input.set_value('physical_properties/nu', nu)
sim.input.set_value('output/stdout_enabled', False)
say('Running with %s %s solver ...' %
(sim.input.get_value('solver/type'),
sim.input.get_value('solver/function_space_velocity')))
t1 = time.time()
setup_simulation(sim)
run_simulation(sim)
duration = time.time() - t1
say('DONE')
# Interpolate the analytical solution to the same function space
Vu = sim.data['Vu']
Vp = sim.data['Vp']
Vr = sim.data['Vrho']
polydeg_r = Vr.ufl_element().degree()
vals = dict(t=sim.time,
dt=sim.dt,
Q=sim.input.get_value('user_code/constants/Q'))
rho_e = dolfin.Expression(
sim.input.get_value('initial_conditions/rho_p/cpp_code'),
degree=polydeg_r,
**vals)
u0e = dolfin.Expression(
sim.input.get_value('initial_conditions/up0/cpp_code'),
degree=polydeg_u,
**vals)
u1e = dolfin.Expression(
sim.input.get_value('initial_conditions/up1/cpp_code'),
degree=polydeg_u,
**vals)
pe = dolfin.Expression(
sim.input.get_value('initial_conditions/p/cpp_code'),
degree=polydeg_p,
**vals)
rho_a = dolfin.project(rho_e, Vr)
u0a = dolfin.project(u0e, Vu)
u1a = dolfin.project(u1e, Vu)
pa = dolfin.project(pe, Vp)
mesh = sim.data['mesh']
n = dolfin.FacetNormal(mesh)
# Correct for possible non-zero average p
int_p = dolfin.assemble(sim.data['p'] * dolfin.dx)
int_pa = dolfin.assemble(pa * dolfin.dx)
vol = dolfin.assemble(dolfin.Constant(1.0) * dolfin.dx(domain=mesh))
pa_avg = int_pa / vol
sim.data['p'].vector()[:] += pa_avg
# Calculate L2 errors
err_rho = calc_err(sim.data['rho'], rho_a)
err_u0 = calc_err(sim.data['u0'], u0a)
err_u1 = calc_err(sim.data['u1'], u1a)
err_p = calc_err(sim.data['p'], pa)
# Calculate H1 errors
err_rho_H1 = calc_err(sim.data['rho'], rho_a, 'H1')
err_u0_H1 = calc_err(sim.data['u0'], u0a, 'H1')
err_u1_H1 = calc_err(sim.data['u1'], u1a, 'H1')
err_p_H1 = calc_err(sim.data['p'], pa, 'H1')
reports = sim.reporting.timestep_xy_reports
say('Num time steps:', sim.timestep)
say('Num cells:', mesh.num_cells())
Co_max, Pe_max = numpy.max(reports['Co']), numpy.max(reports['Pe'])
say('Co_max:', Co_max)
say('Pe_max:', Pe_max)
say('rho_min went from %r to %r' %
(reports['min(rho)'][0], reports['min(rho)'][-1]))
say('rho_max went from %r to %r' %
(reports['max(rho)'][0], reports['max(rho)'][-1]))
m0, m1 = reports['mass'][0], reports['mass'][-1]
say('mass error %.3e (%.3e)' % (m1 - m0, (m1 - m0) / m0))
say('vel repr error %.3e' %
dolfin.assemble(dolfin.dot(sim.data['u'], n) * dolfin.ds))
say('p*dx', int_p)
div_u_Vp = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vp).vector().get_local()).max()
say('div(u)|Vp', div_u_Vp)
div_u_Vu = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vu).vector().get_local()).max()
say('div(u)|Vu', div_u_Vu)
Vdg0 = dolfin.FunctionSpace(mesh, "DG", 0)
div_u_DG0 = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vdg0).vector().get_local()).max()
say('div(u)|DG0', div_u_DG0)
Vdg1 = dolfin.FunctionSpace(mesh, "DG", 1)
div_u_DG1 = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vdg1).vector().get_local()).max()
say('div(u)|DG1', div_u_DG1)
isoparam = mesh.ufl_coordinate_element().degree() > 1
allways_plot = True
if (last or allways_plot) and (
not isoparam or sim.input.get_value('mesh/type') == 'UnitDisc'):
# Plot the results
for fa, name in ((u0a, 'u0'), (u1a, 'u1'), (pa, 'p'), (rho_a, 'rho')):
fh = sim.data[name]
if isoparam:
# Bug in matplotlib plotting for isoparametric elements
mesh2 = dolfin.UnitDiscMesh(dolfin.MPI.comm_world, N // 2, 1,
2)
ue = fa.function_space().ufl_element()
V2 = dolfin.FunctionSpace(mesh2, ue.family(), ue.degree())
fa2, fh2 = dolfin.Function(V2), dolfin.Function(V2)
fa2.vector().set_local(fa.vector().get_local())
fh2.vector().set_local(fh.vector().get_local())
fa, fh = fa2, fh2
discr = '' # '%g_%g_' % (N, dt)
plot(fa, name + ' analytical', '%s%s_1analytical' % (discr, name))
plot(fh, name + ' numerical', '%s%s_2numerical' % (discr, name))
plot(fh - fa, name + ' diff', '%s%s_3diff' % (discr, name))
hmin = mesh.hmin()
return err_rho, err_u0, err_u1, err_p, err_rho_H1, err_u0_H1, err_u1_H1, err_p_H1, hmin, dt, Co_max, Pe_max, duration
def mk_vof_sim(case_name, modifier=None):
sim = Simulation()
sim.input.read_yaml(yaml_string=BASE_INPUT)
cases = {
'DG0_2D_y': (2, 0, 'y'),
'DG0_3D_z': (3, 0, 'z'),
'DG0_2D_x': (2, 0, 'x')
}
dim, vof_deg, surf_normal = cases[case_name]
if dim == 3:
sim.input.set_value('mesh/type', 'Box')
sim.input.set_value('mesh/Nz', 2)
sim.test_name = case_name
if surf_normal == 'x':
sim.input.set_value('initial_conditions/cp/cpp_code',
'x[0] < 0.5 ? 0.0 : 1.0')
sim.test_surf_normal = [1, 0, 0]
sim.test_coord_index = 0
elif surf_normal == 'y':
sim.input.set_value('initial_conditions/cp/cpp_code',
'x[1] < 0.5 ? 1.0 : 0.0')
sim.test_surf_normal = [0, -1, 0]
sim.test_coord_index = 1
elif surf_normal == 'z':
sim.input.set_value('initial_conditions/cp/cpp_code',
'x[2] < 0.5 ? 1.0 : 0.0')
sim.test_surf_normal = [0, 0, -1]
sim.test_coord_index = 2
sim.input.set_value('multiphase_solver/polynomial_degree_colour', vof_deg)
# Run any custom code
if modifier is not None:
modifier(sim)
sim.log.setup()
sim.setup()
sim.data['c'].assign(sim.data['cp'])
return sim
def run_and_calculate_error(N, dt, tmax, polydeg_u, polydeg_p, modifier=None):
"""
Run Ocellaris and return L2 & H1 errors in the last time step
"""
say(N, dt, tmax, polydeg_u, polydeg_p)
# Setup and run simulation
sim = Simulation()
sim.input.read_yaml('taylor-green.inp')
if sim.input.get_value('mesh/type') == 'Rectangle':
# Use structured mesh
sim.input.set_value('mesh/Nx', N)
sim.input.set_value('mesh/Ny', N)
else:
# Create unstructured mesh with gmsh
cmd1 = [
'gmsh',
'-string',
'lc = %f;' % (2.0 / N),
'-o',
'taylor-green_%d.msh' % N,
'-2',
'taylor-green.geo',
]
cmd2 = [
'dolfin-convert',
'taylor-green_%d.msh' % N, 'taylor-green.xml'
]
with open('/dev/null', 'w') as devnull:
for cmd in (cmd1, cmd2):
say(' '.join(cmd))
subprocess.call(cmd, stdout=devnull, stderr=devnull)
sim.input.set_value('time/dt', dt)
sim.input.set_value('time/tmax', tmax)
sim.input.set_value('solver/polynomial_degree_velocity', polydeg_u)
sim.input.set_value('solver/polynomial_degree_pressure', polydeg_p)
sim.input.set_value('output/stdout_enabled', False)
if sim.input.get_value('solver/timestepping_method', 'BDF') == 'CN':
sim.input.set_value(
'initial_conditions/p/cpp_code',
'-(cos(2*pi*x[0]) + cos(2*pi*x[1])) * exp(-4*pi*pi*nu*(t+dt/2))/4',
)
# Turn off BDM
# sim.input.set_value('solver/velocity_postprocessing', 'None')
if modifier:
modifier(sim) # Running regression tests, modify some input params
say('Running with %s %s solver ...' % (
sim.input.get_value('solver/type'),
sim.input.get_value('solver/function_space_velocity', 'DG'),
))
t1 = time.time()
setup_simulation(sim)
if 'Vcoupled' in sim.data:
say('Num unknowns', sim.data['Vcoupled'].dim())
run_simulation(sim)
duration = time.time() - t1
say('DONE')
# Interpolate the analytical solution to the same function space
Vu = sim.data['Vu']
Vp = sim.data['Vp']
vals = dict(
t=sim.time,
dt=sim.dt,
nu=sim.input['physical_properties']['nu'],
rho=sim.input['physical_properties']['rho'],
)
u0e = dolfin.Expression(
sim.input.get_value('initial_conditions/up0/cpp_code'),
degree=polydeg_u + 3,
**vals)
u1e = dolfin.Expression(
sim.input.get_value('initial_conditions/up1/cpp_code'),
degree=polydeg_u + 3,
**vals)
if sim.input.get_value('solver/timestepping_method', 'BDF') == 'CN':
vals['t'] = sim.time - sim.dt
pe = dolfin.Expression(
sim.input.get_value('initial_conditions/p/cpp_code'),
degree=polydeg_p + 3,
**vals)
u0a = dolfin.project(u0e, Vu)
u1a = dolfin.project(u1e, Vu)
pa = dolfin.project(pe, Vp)
# Calculate L2 errors
err_u0 = calc_err(sim.data['u0'], u0a)
err_u1 = calc_err(sim.data['u1'], u1a)
err_p = calc_err(sim.data['p'], pa)
# Calculate H1 errors
err_u0_H1 = calc_err(sim.data['u0'], u0a, 'H1')
err_u1_H1 = calc_err(sim.data['u1'], u1a, 'H1')
err_p_H1 = calc_err(sim.data['p'], pa, 'H1')
say('Number of time steps:', sim.timestep)
loglines = sim.log.get_full_log().split('\n')
say('Num inner iterations:',
sum(1 if 'iteration' in line else 0 for line in loglines))
int_p = dolfin.assemble(sim.data['p'] * dolfin.dx)
say('Number of mesh cells:', sim.data['mesh'].num_cells())
say('p*dx', int_p)
div_u_Vp = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vp).vector().get_local()).max()
say('div(u)|Vp', div_u_Vp)
div_u_Vu = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vu).vector().get_local()).max()
say('div(u)|Vu', div_u_Vu)
Vdg0 = dolfin.FunctionSpace(sim.data['mesh'], "DG", 0)
div_u_DG0 = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vdg0).vector().get_local()).max()
say('div(u)|DG0', div_u_DG0)
Vdg1 = dolfin.FunctionSpace(sim.data['mesh'], "DG", 1)
div_u_DG1 = abs(
dolfin.project(dolfin.div(sim.data['u']),
Vdg1).vector().get_local()).max()
say('div(u)|DG1', div_u_DG1)
if 'u_mesh' in sim.data:
Vmesh = sim.data['Vmesh']
div_u_mesh_Vmesh = abs(
dolfin.project(dolfin.div(sim.data['u_mesh']),
Vmesh).vector().get_local()).max()
say('div(u_mesh)|V_mesh', div_u_mesh_Vmesh)
div_u_mesh_DG0 = abs(
dolfin.project(dolfin.div(sim.data['u_mesh']),
Vdg0).vector().get_local()).max()
say('div(u_mesh)|DG0', div_u_mesh_DG0)
div_u_mesh_DG1 = abs(
dolfin.project(dolfin.div(sim.data['u_mesh']),
Vdg1).vector().get_local()).max()
say('div(u_mesh)|DG1', div_u_mesh_DG1)
if False:
# Plot the results
for fa, name in ((u0a, 'u0'), (u1a, 'u1'), (pa, 'p')):
p1 = dolfin.plot(sim.data[name] - fa,
title='%s_diff' % name,
key='%s_diff' % name)
p2 = dolfin.plot(fa, title=name + ' analytical', key=name)
p1.write_png('%g_%g_%s_diff' % (N, dt, name))
p2.write_png('%g_%g_%s' % (N, dt, name))
dolfin.interactive()
if N == 40 and False:
dolfin.plot(sim.data['u0'], title='u0')
dolfin.plot(sim.data['u1'], title='u1')
dolfin.plot(sim.data['p'], title='p')
dolfin.plot(u0a, title='u0a')
dolfin.plot(u1a, title='u1a')
dolfin.plot(pa, title='pa')
plot_err(sim.data['u0'], u0a, 'u0a - u0')
plot_err(sim.data['u1'], u1a, 'u1a - u1')
plot_err(sim.data['p'], pa, 'pa - p')
hmin = sim.data['mesh'].hmin()
return err_u0, err_u1, err_p, err_u0_H1, err_u1_H1, err_p_H1, hmin, dt, duration