Skip to content

Commit

Permalink
Playing with the Diablo mesh
Browse files Browse the repository at this point in the history
  • Loading branch information
@lmoresi
lmoresi committed Oct 27, 2024
1 parent 9e2c2a8 commit d39f76d
Show file tree
Hide file tree
Showing 3 changed files with 135 additions and 149 deletions.
Binary file modified Notebooks/Examples-Meshing/Batmesh_number_one.h5
View file
Binary file not shown.
175 changes: 132 additions & 43 deletions Notebooks/Examples-Meshing/Convection-AdaptedMesh.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -39,12 +39,14 @@ class bd(Enum):
batmesh.dm.view()

# %%
Rayleigh_number = uw.function.expression(r"\textrm{Ra}", sympy.sympify(10)**6, "Rayleigh number")
Rayleigh_number = uw.function.expression(r"\textrm{Ra}", sympy.sympify(10000000), "Rayleigh number")

# %%
v_soln = uw.discretisation.MeshVariable("U", batmesh, batmesh.dim, degree=2, continuous=True)
p_soln = uw.discretisation.MeshVariable("P", batmesh, 1, degree=1, continuous=True)
t_soln = uw.discretisation.MeshVariable("T", batmesh, 1, degree=2)
v_soln = uw.discretisation.MeshVariable("U", batmesh, batmesh.dim, degree=2, continuous=True)
v_soln1 = uw.discretisation.MeshVariable("U1", batmesh, batmesh.dim, degree=2, continuous=True)
p_soln = uw.discretisation.MeshVariable("P", batmesh, 1, degree=1, continuous=True)
t_soln = uw.discretisation.MeshVariable("T", batmesh, 1, degree=2, varsymbol=r"T_0")
t_soln1 = uw.discretisation.MeshVariable("T1", batmesh, 1, degree=2, varsymbol=r"T_1")
cell_properties = uw.discretisation.MeshVariable("Bat", batmesh, 1, degree=0)


Expand All @@ -68,18 +70,24 @@ class bd(Enum):

stokes.constitutive_model = uw.constitutive_models.ViscousFlowModel
stokes.constitutive_model.Parameters.shear_viscosity_0 = 1
stokes.tolerance = 1.0e-3
stokes.tolerance = 1.0e-5

unit_r_vec = batmesh.CoordinateSystem.unit_e_0
unit_y_vec = batmesh.CoordinateSystem.unit_j

# free slip.
# note with petsc we always need to provide a vector of correct cardinality.

stokes.add_natural_bc(10000 * unit_r_vec.dot(v_soln.sym) * unit_r_vec, "Upper")
stokes.bodyforce = Rayleigh_number * unit_r_vec * t_soln.sym[0]
stokes.add_essential_bc([0,0], "Upper")
# stokes.add_natural_bc(1e6 * Rayleigh_number * unit_r_vec.dot(v_soln.sym) * unit_r_vec, "Upper")

# Make the bat stagnant
# stokes.bodyforce -= 10000 * (1-cell_properties.sym[0]) * v_soln.sym
stokes.bodyforce = Rayleigh_number * unit_y_vec * t_soln.sym[0] + \
Rayleigh_number * unit_y_vec * t_soln1.sym[0]


stokes.petsc_options.setValue("ksp_monitor", None)
stokes.petsc_options.setValue("snes_monitor", None)
stokes.petsc_options.setValue("snes_min_it", 1)

stokes.view()

Expand All @@ -92,48 +100,65 @@ class bd(Enum):

adv_diff.constitutive_model = uw.constitutive_models.DiffusionModel
adv_diff.constitutive_model.Parameters.diffusivity = 1
adv_diff.f = 10 * (1-cell_properties.sym[0])

adv_diff.add_dirichlet_bc(0.0, "Upper")


adv_diff1 = uw.systems.AdvDiffusionSLCN(
batmesh,
u_Field=t_soln1,
V_fn=v_soln1,
)

adv_diff1.constitutive_model = uw.constitutive_models.DiffusionModel
adv_diff1.constitutive_model.Parameters.diffusivity = 1
adv_diff1.add_dirichlet_bc(0.0, "Upper")

t_init = 1-cell_properties.sym[0]

with batmesh.access(t_soln):
with batmesh.access(t_soln, t_soln1):
t_soln.data[:,0] = uw.function.evalf(t_init, t_soln.coords)
t_soln1.data[:,0] = uw.function.evalf(t_init, t_soln1.coords)


# %%
stokes.solve(zero_init_guess=True)

# %%
v_soln.view()
stokes.solve(zero_init_guess=True, picard=0, verbose=False)
with batmesh.access(v_soln1):
v_soln1.data[...] = -v_soln.data[...]

# %%

t_step = 0

# %%

for step in range(0, 50):
for step in range(0, 250):
stokes.solve(zero_init_guess=False)
delta_t = 2.0 * stokes.estimate_dt()
adv_diff.solve(timestep=delta_t, zero_init_guess=False)
with batmesh.access(v_soln1):
v_soln1.data[...] = -v_soln.data[...]


delta_t = 5.0 * stokes.estimate_dt()
adv_diff.solve(timestep=delta_t, zero_init_guess=True)
adv_diff1.solve(timestep=delta_t, zero_init_guess=True)

# stats then loop
tstats = t_soln.stats()

if uw.mpi.rank == 0:
print("Timestep {}, dt {}".format(step, delta_t))

batmesh.write_timestep(
"Batmesh",
meshUpdates=True,
meshVars=[p_soln, v_soln, t_soln],
outputPath="output",
index=t_step,
)
if t_step%1==0:
batmesh.write_timestep(
"Batmesh",
meshUpdates=True,
meshVars=[p_soln, v_soln, t_soln, t_soln1],
outputPath="output",
index=t_step,
)

with batmesh.access(t_soln):
t_soln.data[:,0] = np.maximum(t_soln.data[:,0], uw.function.evalf(t_init, t_soln.coords))
# with batmesh.access(t_soln):
# t_soln.data[:,0] = np.maximum(t_soln.data[:,0], uw.function.evalf(t_init, t_soln.coords))

t_step += 1

Expand All @@ -146,69 +171,133 @@ class bd(Enum):

pvmesh = vis.mesh_to_pv_mesh(batmesh)
pvmesh.point_data["T"] = vis.scalar_fn_to_pv_points(pvmesh, t_soln.sym[0])
pvmesh.point_data["R"] = vis.scalar_fn_to_pv_points(pvmesh, batmesh.CoordinateSystem.R[0])
pvmesh.point_data["T1"] = vis.scalar_fn_to_pv_points(pvmesh, t_soln1.sym[0])
pvmesh.point_data["V"] = vis.vector_fn_to_pv_points(pvmesh, v_soln.sym)
pvmesh.point_data["L"] = vis.scalar_fn_to_pv_points(pvmesh, cell_properties.sym[0])

pvmesh_t = vis.meshVariable_to_pv_mesh_object(t_soln)
pvmesh_t.point_data["T"] = vis.scalar_fn_to_pv_points(pvmesh_t, t_soln.sym[0])
pvmesh_t.point_data["T1"] = vis.scalar_fn_to_pv_points(pvmesh_t, t_soln1.sym[0])

pvmesh_t.point_data["To"] = (pvmesh_t.point_data["T"] > 0.25).astype(float)
pvmesh_t.point_data["T1o"] = (pvmesh_t.point_data["T1"] > 0.25).astype(float)
pvmesh_t.point_data["TD"] = pvmesh_t.point_data["T"] - pvmesh_t.point_data["T1"]


pl = pv.Plotter(window_size=(750, 750))
pl.enable_depth_peeling()

doughnut = pvmesh.clip_scalar(scalars="R",
value=0.3,
invert=False)

pvstream = pvmesh.streamlines_from_source(
pvmesh.cell_centers(),
pv.PointSet(doughnut.cell_centers().points[::5]),
vectors="V",
integrator_type=45,
surface_streamlines=True,
max_steps=1000,
max_time=0.25,
)


# pl.add_mesh(pvmesh,
# style="wireframe",
# color="#FEFEF0",
# opacity=0.1)

pl.add_mesh(pvstream,
cmap=["orange", "white", "green"],
show_scalar_bar=False,
opacity=0.1
)


pl.add_mesh(
pvmesh,
pvmesh_t,
cmap="Oranges",
scalars="T",
opacity="sigmoid",
edge_color="Grey",
show_edges=False,
use_transparency=False,
opacity=1.0,
show_scalar_bar=True,
clim=[0,1]
show_scalar_bar=False,
)

pl.add_mesh(
pvmesh,
scalars="L",
cmap="Greys_r",
edge_color="Black",
opacity="L",
pvmesh_t,
copy_mesh=True,
cmap="Blues",
scalars="T1",
opacity="sigmoid",
edge_color="Grey",
show_edges=False,
use_transparency=True,
use_transparency=False,
show_scalar_bar=False,

# clim=[0,2]
)

# pl.add_mesh(pvstream, cmap="jet", show_scalar_bar=False)



# pl.add_mesh(
# pvmesh,
# scalars="L",
# cmap="Greys_r",
# edge_color="Black",
# opacity="L",
# show_edges=False,
# use_transparency=True,
# show_scalar_bar=False,
# )


# pl.add_arrows(pvmesh.points, pvmesh.point_data["V"],
# mag=float(20.0/Rayleigh_number.sym),
# mag=float(0.2/Rayleigh_number.sym),
# show_scalar_bar=False)


pl.show(jupyter_backend='html')

# %%
0/0

# %%

# %%
## Check the results saved to file

expt_name = "Batmesh"
output_path="output"
step = 20
step = 50

v_soln.read_timestep(expt_name, "U", step, outputPath=output_path)
p_soln.read_timestep(expt_name, "P", step, outputPath=output_path)
t_soln.read_timestep(expt_name, "T", step, outputPath=output_path)
t_soln1.read_timestep(expt_name, "T1", step, outputPath=output_path)



# %%
t_soln.stats()

# %%
t_soln1.stats()

# %%
adv_diff

# %%
adv_diff1

# %%
adv_diff1.DuDt.bdf(1)

# %%
adv_diff.DuDt.bdf(1)

# %%
batmesh.dm.view()

# %% [markdown]
# #
Loading

0 comments on commit d39f76d

Please sign in to comment.