def method(ts,
show=False,
save=True,
dt=None,
fps=25,
skip=0,
delete_after=True,
plot_u=False,
inverse_phase=False,
**kwargs):
""" Make fancy gif animation. """
info_cyan("Making a fancy gif animation.")
anim_name = "animation"
ts.compute_charge()
steps = get_steps(ts, dt)[::(skip + 1)]
for step in steps[rank::size]:
info("Step " + str(step) + " of " + str(len(ts)))
if "phi" in ts:
phi = ts["phi", step][:, 0]
else:
phi = np.zeros(len(ts.nodes)) - 1.
if inverse_phase:
phi = -phi
charge = ts["charge", step][:, 0]
charge_max = max(ts.max("charge"), -ts.min("charge"))
charge_max = max(charge_max, 1e-8) # Remove numerical noise
if plot_u and "u" in ts:
u = ts["u", step]
else:
u = None
if save:
save_file = os.path.join(ts.tmp_folder,
anim_name + "_{:06d}.png".format(step))
else:
save_file = None
plot_fancy(ts.nodes,
ts.elems,
phi,
charge,
charge_max=charge_max,
show=show,
u=u,
save=save_file)
comm.Barrier()
if save and rank == 0:
tmp_files = os.path.join(ts.tmp_folder, anim_name + "_*.png")
anim_file = os.path.join(ts.plots_folder, anim_name + ".gif")
os.system(("convert -delay {delay} {tmp_files} -trim +repage"
" -loop 0 {anim_file}").format(tmp_files=tmp_files,
anim_file=anim_file,
delay=int(100. / fps)))
if delete_after:
os.system("rm {tmp_files}".format(tmp_files=tmp_files))
def method(ts, dt=0, extra_boundaries="", **kwargs):
""" Plot value in time. """
info_cyan("Plot value at boundary in time.")
params = ts.get_parameters()
steps = get_steps(ts, dt)
problem = params["problem"]
info("Problem: {}".format(problem))
boundary_to_mark, ds = fetch_boundaries(ts, problem, params,
extra_boundaries)
x_ = ts.functions()
fields = dict()
for field, f in x_.items():
if field == "u":
fields["u_x"] = f[0]
fields["u_y"] = f[1]
else:
fields[field] = f
t = np.zeros(len(steps))
data = dict()
for boundary_name in boundary_to_mark:
data[boundary_name] = dict()
for field in fields:
data[boundary_name][field] = np.zeros(len(steps))
for i, step in enumerate(steps):
info("Step {} of {}".format(step, len(ts)))
for field in x_:
ts.update(x_[field], field, step)
for boundary_name, (mark, k) in boundary_to_mark.items():
for field, f in fields.items():
data[boundary_name][field][i] = df.assemble(f * ds[k](mark))
t[i] = ts.times[step]
savedata = dict()
field_keys = sorted(fields.keys())
for boundary_name in boundary_to_mark:
savedata[boundary_name] = np.array(
list(
zip(steps, t,
*[data[boundary_name][field] for field in field_keys])))
if rank == 0:
header = "Step\tTime\t" + "\t".join(field_keys)
for boundary_name in boundary_to_mark:
with open(
os.path.join(ts.analysis_folder,
"value_in_time_{}.dat".format(boundary_name)),
"w") as outfile:
np.savetxt(outfile, savedata[boundary_name], header=header)
def method(ts, dt=0, **kwargs):
""" Analyze geometry in time."""
info_cyan("Analyzing the evolution of the geometry through time.")
if not ts.get_parameter("enable_PF"):
print "Phase field not enabled."
return False
f_mask = df.Function(ts.function_space)
f_mask_x = []
f_mask_u = []
for d in range(ts.dim):
f_mask_x.append(df.Function(ts.function_space))
f_mask_u.append(df.Function(ts.function_space))
length = np.zeros(len(ts))
area = np.zeros(len(ts))
com = np.zeros((len(ts), ts.dim))
u = np.zeros((len(ts), ts.dim))
makedirs_safe(os.path.join(ts.analysis_folder, "contour"))
steps = get_steps(ts, dt)
for step in steps:
info("Step " + str(step) + " of " + str(len(ts)))
phi = ts["phi", step][:, 0]
mask = 0.5 * (1. - phi) # 0.5*(1.-np.sign(phi))
ts.set_val(f_mask, mask)
for d in range(ts.dim):
ts.set_val(f_mask_x[d], mask * ts.nodes[:, d])
ts.set_val(f_mask_u[d], mask * ts["u", step][:, d])
contour_file = os.path.join(ts.analysis_folder, "contour",
"contour_{:06d}.dat".format(step))
paths = zero_level_set(ts.nodes, ts.elems, phi, save_file=contour_file)
length[step] = path_length(paths)
area[step] = df.assemble(f_mask * df.dx)
for d in range(ts.dim):
com[step, d] = df.assemble(f_mask_x[d] * df.dx)
u[step, d] = df.assemble(f_mask_u[d] * df.dx)
for d in range(ts.dim):
com[:, d] /= area
u[:, d] /= area
if rank == 0:
np.savetxt(os.path.join(ts.analysis_folder, "time_data.dat"),
np.array(
zip(np.arange(len(ts)), ts.times, length, area,
com[:, 0], com[:, 1], u[:, 0], u[:, 1])),
header=("Timestep\tTime\tLength\tArea\t"
"CoM_x\tCoM_y\tU_x\tU_y"))
def method(ts, dt=0, **kwargs):
""" Plot mean field values in time. """
info_cyan("Plot mean field values in time.")
params = ts.get_parameters()
steps = get_steps(ts, dt)
problem = params["problem"]
info("Problem: {}".format(problem))
t = np.zeros(len(steps))
x_ = ts.functions()
fields = dict()
for field, f in x_.items():
if field == "u":
fields["u_x"] = f[0]
fields["u_y"] = f[1]
else:
fields[field] = f
data = dict()
for field in fields:
data[field] = np.zeros(len(steps))
for i, step in enumerate(steps):
info("Step {} of {}".format(step, len(ts)))
for field in x_.keys():
ts.update(x_[field], field, step)
for field, f in fields.items():
data[field][i] = df.assemble(f * df.dx)
t[i] = ts.times[step]
field_keys = sorted(fields.keys())
savedata = np.array(
list(zip(steps, t, *[data[field] for field in field_keys])))
if rank == 0:
header = "Step\tTime\t" + "\t".join(field_keys)
with open(os.path.join(ts.analysis_folder, "value_in_time.dat"),
"w") as outfile:
np.savetxt(outfile, savedata, header=header)
def method(ts, dt=0, **kwargs):
""" Plot energy in time. """
info_cyan("Plot energy in time.")
params = ts.get_parameters()
steps = get_steps(ts, dt)
problem = params["problem"]
info("Problem: {}".format(problem))
solver = params["solver"]
info("Solver: {}".format(solver))
exec("from solvers.{} import discrete_energy".format(solver))
t = np.zeros(len(steps))
x_ = ts.functions()
F_keys = discrete_energy(None, **params)
F = []
for i in range(len(F_keys)):
F.append(np.zeros(len(steps)))
for i, step in enumerate(steps):
info("Step {} of {}".format(step, len(ts)))
for field in x_:
ts.update(x_[field], field, step)
fs = discrete_energy(x_, **params)
for j in range(len(F_keys)):
F[j][i] = df.assemble(fs[j] * df.dx)
t[i] = ts.times[step]
data = np.array(zip(steps, t, *F))
if rank == 0:
filename = os.path.join(ts.analysis_folder, "energy_in_time.dat")
np.savetxt(filename, data, header="Step\tTime\t" + "\t".join(F_keys))
def method(ts,
dx=0.1,
line="[0.,0.]--[1.,1.]",
time=None,
dt=None,
skip=0,
**kwargs):
""" Probe along a line. """
info_cyan("Probe along a line.")
try:
x_a, x_b = [tuple(eval(pt)) for pt in line.split("--")]
assert (len(x_a) == ts.dim)
assert (len(x_b) == ts.dim)
assert (all([
bool(isinstance(xd, float) or isinstance(xd, int))
for xd in list(x_a) + list(x_b)
]))
except:
info_on_red("Faulty line format. Use 'line=[x1,y1]--[x2,y2]'.")
exit()
x = np.array(line_points(x_a, x_b, dx))
info("Probes {num} points from {a} to {b}".format(num=len(x), a=x_a,
b=x_b))
if rank == 0:
plot_probes(ts.nodes, ts.elems, x, colorbar=False, title="Probes")
f = ts.functions()
probes = dict()
from fenicstools import Probes
for field, func in f.iteritems():
probes[field] = Probes(x.flatten(), func.function_space())
steps = get_steps(ts, dt, time)
for step in steps:
info("Step " + str(step) + " of " + str(len(ts)))
ts.update_all(f, step)
for field, probe in probes.iteritems():
probe(f[field])
probe_arr = dict()
for field, probe in probes.iteritems():
probe_arr[field] = probe.array()
if rank == 0:
for i, step in enumerate(steps):
chunks = [x]
header_list = [index2letter(d) for d in range(ts.dim)]
for field, chunk in probe_arr.iteritems():
if chunk.ndim == 1:
header_list.append(field)
chunk = chunk[:].reshape(-1, 1)
elif chunk.ndim == 2:
header_list.append(field)
chunk = chunk[:, i].reshape(-1, 1)
elif chunk.ndim > 2:
header_list.extend(
[field + "_" + index2letter(d) for d in range(ts.dim)])
chunk = chunk[:, :, i]
chunks.append(chunk)
data = np.hstack(chunks)
header = "\t".join(header_list)
makedirs_safe(os.path.join(ts.analysis_folder, "probes"))
np.savetxt(os.path.join(ts.analysis_folder, "probes",
"probes_{:06d}.dat".format(step)),
data,
header=header)
def method(ts, dt=0, extra_boundaries="", **kwargs):
""" Plot flux in time. """
info_cyan("Plot flux in time.")
params = ts.get_parameters()
steps = get_steps(ts, dt)
problem = params["problem"]
info("Problem: {}".format(problem))
boundary_to_mark, ds = fetch_boundaries(ts, problem, params,
extra_boundaries)
x_ = ts.functions()
if params["enable_NS"]:
u = x_["u"]
else:
u = df.Constant(0.)
if params["enable_PF"]:
phi = x_["phi"]
g = x_["g"]
exec("from problems.{} import pf_mobility".format(problem))
M = pf_mobility(phi, params["pf_mobility_coeff"])
else:
phi = 1.
g = df.Constant(0.)
M = df.Constant(0.)
solutes = params["solutes"]
c = []
c_grad_g_c = []
if params["enable_EC"]:
V = x_["V"]
else:
V = df.Constant(0.)
dbeta = [] # Diff. in beta
z = [] # Charge z[species]
K = [] # Diffusivity K[species]
beta = [] # Conc. jump func. beta[species]
for solute in solutes:
ci = x_[solute[0]]
dbetai = dramp([solute[4], solute[5]])
c.append(ci)
z.append(solute[1])
K.append(ramp(phi, [solute[2], solute[3]]))
beta.append(ramp(phi, [solute[4], solute[5]]))
dbeta.append(dbetai)
# THIS HAS NOT BEEN GENERALIZED!
c_grad_g_ci = df.grad(ci) + solute[1] * ci * df.grad(V)
if params["enable_PF"]:
c_grad_g_ci += dbetai * df.grad(phi)
c_grad_g_c.append(c_grad_g_ci)
nu = ramp(phi, params["viscosity"])
veps = ramp(phi, params["permittivity"])
rho = ramp(phi, params["density"])
dveps = dramp(params["permittivity"])
drho = dramp(params["density"])
t = np.zeros(len(steps))
# Define the fluxes
fluxes = dict()
fluxes["Velocity"] = u
fluxes["Phase"] = phi * u
fluxes["Mass"] = rho * x_["u"]
if params["enable_PF"]:
fluxes["Phase"] += -M * df.grad(g)
fluxes["Mass"] += -drho * M * df.grad(g)
if params["enable_EC"]:
for i, solute in enumerate(solutes):
fluxes["Solute {}".format(solute[0])] = K[i] * c_grad_g_c[i]
fluxes["E-field"] = -df.grad(V)
data = dict()
for boundary_name in boundary_to_mark:
data[boundary_name] = dict()
for flux_name in fluxes:
data[boundary_name][flux_name] = np.zeros(len(steps))
n = df.FacetNormal(ts.mesh)
for i, step in enumerate(steps):
info("Step {} of {}".format(step, len(ts)))
for field in x_:
ts.update(x_[field], field, step)
for boundary_name, (mark, k) in boundary_to_mark.items():
for flux_name, flux in fluxes.items():
data[boundary_name][flux_name][i] = df.assemble(
df.dot(flux, n) * ds[k](mark))
t[i] = ts.times[step]
savedata = dict()
flux_keys = sorted(fluxes.keys())
for boundary_name in boundary_to_mark:
savedata[boundary_name] = np.array(
list(
zip(
steps, t, *[
data[boundary_name][flux_name]
for flux_name in flux_keys
])))
if rank == 0:
header = "Step\tTime\t" + "\t".join(flux_keys)
for boundary_name in boundary_to_mark:
with open(
os.path.join(ts.analysis_folder,
"flux_in_time_{}.dat".format(boundary_name)),
"w") as outfile:
np.savetxt(outfile, savedata[boundary_name], header=header)