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Description:

pfcutil 0.4.12

PFC simulation in python
created by michael in 2022/04
pfc_util is a python package for PFC (phase field crystal) simulations.

Documentation
Documentation is available on https://pfc-util.readthedocs.io .

Dependencies

numpy
scipy
matplotlib
pyfftw
torusgrid
rich

Installation
Install via pip:
pip install pfc-util

Modules
pfc_util.core - Core module; definitions of PFC free energy functional, state functions, as well as minimizers
pfc_util.extra - Extensions to vanilla PFC. Currently includes pfc6, which is a 6th-order generalization to the PFC functional
pfc_util.toolkit - Static preminimized solid/liquid profiles & utility functions.

Minimizers
The package provides three main means of minimizing/evolving a PFC system:

Constant chemical potential - The grand potential Ω≡F−μ∫drψ is minimized with fixed μ
Stress relaxer - The grand potential density ω≡Ω/V is minimized with respect to the density field and system size with fixed μ
Conserved dynamics - The free energy F is minimized with fixed ψ¯

Example Code Snippet
The following code snippet will retrieve a preminimized solid unit cell, evolve
it under ϵ=0.05 and μ=0.08 until ψ¯ barely changes, and save the newly minimized
unit cell to solid_eps0.05_mu0.08.field
import pfc_util as pfc
import torusgrid as tg

'''Get a preminimized solid profile at epsilon = 0.1'''
solid = pfc.toolkit.get_unit_cell(eps='0.1')

'''Minimize this profile at epsilon = 0.05 and mu = 0.08'''
pfc.ConstantMuMinimizer(solid, dt=0.001, eps=0.05, mu=0.08).run(
n_steps=31, # n_steps means the number of evolution steps between hook calls
# hooks are invoked to update display, monitor values, etc
hooks= (
tg.dynamics.Display() # add display capability
+ tg.dynamics.Panel() # add a panel to live display
+ tg.dynamics.MonitorValues(
{'psibar': lambda e: e.field.psi.mean()},
period=8
) # tell the minimizer that psi.mean() should be monitored and stored as "psibar"
# here e refers to the minimizer instance
# period = 8 means that the values are logged every 8 hook calls
# so in this case we would be calculating the values every 31*8 = 248 time steps
+ tg.dynamics.Text('psibar={psibar:.8f}')
+ tg.dynamics.DetectSlow(
'psibar', rtol=1e-9, atol=0, period=8, patience=200
) # make the minimizer stop if psibar varies sufficiently slowly
)
)

tg.save(solid, './solid_eps0.05_mu0.08.field') # save the minimized field