def correction(self, it, pair):
# Compute force table based on current iteration.
rdf = distribution.iteration_rdf_files(it, pair)
# Appends new force, energy, distance, table.
self.compute(distribution.average_rdf(rdf))
# Computes the correction to the force.
df = self.force[-1] - self.force[0]
self.force[-1] = self.force[-2] - df
# Need to reintegrate energy
rr = self.distance[-1]
ff = self.force[-1]
ff = smooth_force(rr, ff, len(self.force))[0]
self.energy[-1] = -simpson_integrate(rr[::-1], ff[::-1])[::-1]
self.energy[-1] -= self.energy[-1][-1]
def __init__(self, md_temp, md_rdf):
# Sets the temperature of the all-atom simulation.
self.temperature = md_temp
# Sets the smallest distance in the pair table.
# If LAMMPS simulations crash with pair cutoff error, this needs to be smaller.
self.min_distance = 0.00001
self.npts = 1000
# Pair force correct per unit pressure.
self.pfactor = 1.0/5000.0
self.last_p_error = 0.0
# Computes the average distribution functions for the all-atom case.
self.all_atom_rdf = distribution.average_rdf(distribution.md_rdf_files())
# Initializes the pair tables as empty lists.
self.distance = []
self.force = []
self.energy = []
# Computes the initial potential with the all-atom data.
self.allatomcompute(self.all_atom_rdf)