diff --git a/phasefield/analytical.py b/phasefield/analytical.py
index 4d0f9c8d954c8376dc40aaf128fcde879fbc02a1..d91600c751c3d81b42c9f2c4cea29185c1a9c34f 100644
--- a/phasefield/analytical.py
+++ b/phasefield/analytical.py
@@ -170,26 +170,28 @@ def separate_into_bulk_and_interface(free_energy):
def analytic_interface_profile(x, interface_width=interface_width_symbol):
- """Analytic expression for a 1D interface normal to x with given interface width
+ """Analytic expression for a 1D interface normal to x with given interface width.
The following doctest shows that the returned analytical solution is indeed a solution of the ODE that we
get from the condition :math:`\mu_0 = 0` (thermodynamic equilibrium) for a situation with only a single order
parameter, i.e. at a transition between two phases.
- >>> numPhases = 4
- >>> x, phi = sp.Symbol("x"), symbolic_order_parameters(numPhases-1)
- >>> F = free_energy_functional_n_phases(order_parameters=phi)
- >>> mu = chemical_potentials_from_free_energy(F)
- >>> mu0 = mu[0].subs({p: 0 for p in phi[1:]}) # mu[0] as function of one order parameter only
- >>> solution = analytic_interface_profile(x)
- >>> solutionSubstitution = {phi[0]: solution, Diff(Diff(phi[0])): sp.diff(solution, x, x) }
- >>> sp.expand(mu0.subs(solutionSubstitution)) # inserting solution should solve the mu_0=0 equation
- 0
+
+ Examples:
+ >>> numPhases = 4
+ >>> x, phi = sp.Symbol("x"), symbolic_order_parameters(numPhases-1)
+ >>> F = free_energy_functional_n_phases(order_parameters=phi)
+ >>> mu = chemical_potentials_from_free_energy(F)
+ >>> mu0 = mu[0].subs({p: 0 for p in phi[1:]}) # mu[0] as function of one order parameter only
+ >>> solution = analytic_interface_profile(x)
+ >>> solutionSubstitution = {phi[0]: solution, Diff(Diff(phi[0])): sp.diff(solution, x, x) }
+ >>> sp.expand(mu0.subs(solutionSubstitution)) # inserting solution should solve the mu_0=0 equation
+ 0
"""
return (1 + sp.tanh(x / (2 * interface_width))) / 2
def chemical_potentials_from_free_energy(free_energy, order_parameters=None):
- """Computes chemical potentials as functional derivative of free energy"""
+ """Computes chemical potentials as functional derivative of free energy."""
symbols = free_energy.atoms(sp.Symbol)
if order_parameters is None:
order_parameters = [s for s in symbols if s.name.startswith(orderParameterSymbolName)]
diff --git a/phasefield/experiments1D.py b/phasefield/experiments1D.py
index b2360cc270f81d108050aa1db1b35734f88758ab..110bb8cadb0bed3b0acbf4dfd76d8d723456c1c9 100644
--- a/phasefield/experiments1D.py
+++ b/phasefield/experiments1D.py
@@ -13,26 +13,26 @@ def plot_status(phase_field_step, from_x=None, to_x=None):
dh = phase_field_step.data_handling
- num_phases = phase_field_step.numOrderParameters
+ num_phases = phase_field_step.num_order_parameters
plt.subplot(1, 3, 1)
plt.title('φ')
- phi_name = phase_field_step.phiFieldName
+ phi_name = phase_field_step.phi_field_name
for i in range(num_phases):
plt.plot(dh.gather_array(phi_name, make_slice[from_x:to_x, 0, i]), marker='x', label='φ_%d' % (i,))
plt.legend()
plt.subplot(1, 3, 2)
plt.title("μ")
- mu_name = phase_field_step.muFieldName
+ mu_name = phase_field_step.mu_field_name
for i in range(num_phases):
plt.plot(dh.gather_array(mu_name, make_slice[from_x:to_x, 0, i]), marker='x', label='μ_%d' % (i,))
plt.legend()
plt.subplot(1, 3, 3)
plt.title("Force and Velocity")
- plt.plot(dh.gather_array(phase_field_step.forceFieldName, make_slice[from_x:to_x, 0, 0]), label='F', marker='x')
- plt.plot(dh.gather_array(phase_field_step.velFieldName, make_slice[from_x:to_x, 0, 0]), label='u', marker='v')
+ plt.plot(dh.gather_array(phase_field_step.force_field_name, make_slice[from_x:to_x, 0, 0]), label='F', marker='x')
+ plt.plot(dh.gather_array(phase_field_step.vel_field_name, make_slice[from_x:to_x, 0, 0]), label='u', marker='v')
plt.legend()
@@ -59,14 +59,14 @@ def init_sharp_interface(pf_step, phase_idx, x1=None, x2=None, inverse=False):
if x2 is None:
x2 = 3 * x1
- if phase_idx >= pf_step.numOrderParameters:
+ if phase_idx >= pf_step.num_order_parameters:
return
for b in pf_step.data_handling.iterate():
x = b.cell_index_arrays[0]
mid = np.logical_and(x1 < x, x < x2)
- phi = b[pf_step.phiFieldName]
+ phi = b[pf_step.phi_field_name]
val1, val2 = (1, 0) if inverse else (0, 1)
phi[..., phase_idx].fill(val1)
@@ -94,7 +94,7 @@ def tanh_test(pf_step, phase0, phase1, expected_interface_width=1, time_steps=10
domain_size = pf_step.data_handling.shape
pf_step.reset()
- pf_step.data_handling.fill(pf_step.phiFieldName, 0)
+ pf_step.data_handling.fill(pf_step.phi_field_name, 0)
init_sharp_interface(pf_step, phase_idx=phase0, inverse=False)
init_sharp_interface(pf_step, phase_idx=phase1, inverse=True)
pf_step.set_pdf_fields_from_macroscopic_values()
@@ -140,14 +140,14 @@ def galilean_invariance_test(pf_step, velocity=0.05, rounds=3, phase0=0, phase1=
print("Velocity:", velocity, " Time steps for round:", round_time_steps)
pf_step.reset()
- pf_step.data_handling.fill(pf_step.phiFieldName, 0)
+ pf_step.data_handling.fill(pf_step.phi_field_name, 0)
init_sharp_interface(pf_step, phase_idx=phase0, inverse=False)
init_sharp_interface(pf_step, phase_idx=phase1, inverse=True)
pf_step.set_pdf_fields_from_macroscopic_values()
print("Running", init_time_steps, "initial time steps")
pf_step.run(init_time_steps)
- pf_step.data_handling.fill(pf_step.velFieldName, velocity, value_idx=0)
+ pf_step.data_handling.fill(pf_step.vel_field_name, velocity, value_idx=0)
pf_step.set_pdf_fields_from_macroscopic_values()
step_location = domain_size[0] // 4
diff --git a/phasefield/phasefieldstep.py b/phasefield/phasefieldstep.py
index a787062a4c999db3eaca708d8a877b00d634ede0..b32c70e4df4d4d48c76710d06e0c223a8e427010 100644
--- a/phasefield/phasefieldstep.py
+++ b/phasefield/phasefieldstep.py
@@ -30,11 +30,11 @@ class PhaseFieldStep:
if data_handling is None:
data_handling = SerialDataHandling(domain_size, periodicity=True)
- self.freeEnergy = free_energy
- self.concentrationToOrderParameter = concentration_to_order_parameters
- self.orderParametersToConcentrations = order_parameters_to_concentrations
+ self.free_energy = free_energy
+ self.concentration_to_order_parameter = concentration_to_order_parameters
+ self.order_parameters_to_concentrations = order_parameters_to_concentrations
- self.chemicalPotentials = chemical_potentials_from_free_energy(free_energy, order_parameters)
+ self.chemical_potentials = chemical_potentials_from_free_energy(free_energy, order_parameters)
# ------------------ Adding arrays ---------------------
gpu = target == 'gpu'
@@ -61,7 +61,7 @@ class PhaseFieldStep:
# ------------------ Creating kernels ------------------
phi = tuple(self.phi_field(i) for i in range(len(order_parameters)))
- F = self.freeEnergy.subs({old: new for old, new in zip(order_parameters, phi)})
+ F = self.free_energy.subs({old: new for old, new in zip(order_parameters, phi)})
if homogeneous_neumann_boundaries:
def apply_neumann_boundaries(eqs):
@@ -77,7 +77,7 @@ class PhaseFieldStep:
# μ and pressure tensor update
self.phiSync = data_handling.synchronization_function([self.phi_field_name], target=target)
self.muEqs = mu_kernel(F, phi, self.phi_field, self.mu_field, dx)
- self.pressureTensorEqs = pressure_tensor_kernel(self.freeEnergy, order_parameters,
+ self.pressureTensorEqs = pressure_tensor_kernel(self.free_energy, order_parameters,
self.phi_field, self.pressure_tensor_field, dx)
mu_and_pressure_tensor_eqs = self.muEqs + self.pressureTensorEqs
mu_and_pressure_tensor_eqs = apply_neumann_boundaries(mu_and_pressure_tensor_eqs)
@@ -225,8 +225,8 @@ class PhaseFieldStep:
return self.hydroLbmStep.boundary_handling
def set_concentration(self, slice_obj, concentration):
- if self.concentrationToOrderParameter is not None:
- phi = self.concentrationToOrderParameter(concentration)
+ if self.concentration_to_order_parameter is not None:
+ phi = self.concentration_to_order_parameter(concentration)
else:
phi = np.array(concentration)
@@ -255,7 +255,7 @@ class PhaseFieldStep:
def concentration_slice(self, slice_obj=None):
phi = self.phi_slice(slice_obj)
- return phi if self.orderParametersToConcentrations is None else self.orderParametersToConcentrations(phi)
+ return phi if self.order_parameters_to_concentrations is None else self.order_parameters_to_concentrations(phi)
def mu_slice(self, slice_obj=None):
return self._get_slice(self.mu_field_name, slice_obj)