def accept(s, q_old, q_new, w_old=1.0, w_new=1.0):
"""Returns accept/reject decision based on supplied entropy table."""
import numpy as np
from maths_module import metropolis
# This routine is essentially the Metropolis-Hastings formula, generalized
# to use a specified tabulated function of the energy in the exponent
# For NVT MC, s(q) is just E(q)/kT = -q/kT since energy is -q
# For Wang-Landau, s(q) is the entropy function, which is updated through the run
# In either case, weights (real, but taking positive integer values here) may optionally appear
w_tol = np.float_(0.5)
# Check that we are within bounds for the entropy table
assert q_new >= 0 and q_new < s.size, 'q_new out of bounds'
assert q_old >= 0 and q_old < s.size, 'q_old out of bounds'
# Check values of weights
assert w_old > w_tol, 'Impossible weight error'
if w_new < w_tol: # Should really have been detected before
return False
delta = s[q_new] - s[q_old] # Change in entropy function
# Equivalent to exp(-delta) -> (w_new/w_old)*exp(-delta)
delta = delta - np.log(w_new / w_old)
result = metropolis(delta)
return result
for k in range(p): # Loop over ring polymer indices
rkj = np.delete(r[k, :, :], i,
0) # Array of all other atoms for this k
partial_old = partial_old + potential_1(
r[k, i, :], box, r_cut, rkj,
p) # Old atom classical potential etc
rki = r[k, i, :] + dc
rki = rki - np.rint(rki)
partial_new = partial_new + potential_1(
rki, box, r_cut, rkj,
p) # New atom classical potential etc
assert not partial_old.ovr, 'Overlap in current configuration'
if not partial_new.ovr: # Test for non-overlapping configuration
delta = partial_new.pot - partial_old.pot # Change in classical cut (but not shifted) potential
delta = delta / temperature
if metropolis(delta): # Accept Metropolis test
total = total + partial_new - partial_old # Update total values
r[:, i, :] = r[:, i, :] + dc # Update positions
r[:, i, :] = r[:, i, :] - np.rint(
r[:, i, :]) # Periodic boundary conditions
c_moves = c_moves + 1 # Increment move counter
# Individual atom moves
for k in range(p): # Loop over ring polymer indices
rkj = np.delete(r[k, :, :], i,
0) # Array of all the other atoms
partial_old = potential_1(
r[k, i, :], box, r_cut, rkj,
p) # Old atom classical potential etc
assert not partial_old.ovr, 'Overlap in current configuration'
rj = np.delete(r, i, 0) # Array of all the other atoms
partial_old = potential_1(r[i, :], box, r_cut,
rj) # Old atom potential, virial etc
assert not partial_old.ovr, 'Overlap in current configuration'
ri = random_translate_vector(
dr_max / box,
r[i, :]) # Trial move to new position (in box=1 units)
ri = ri - np.rint(ri) # Periodic boundary correction
partial_new = potential_1(ri, box, r_cut,
rj) # New atom potential, virial etc
if not partial_new.ovr: # Test for non-overlapping configuration
delta = partial_new.pot - partial_old.pot # Use cut (but not shifted) potential
delta = delta / temperature
if metropolis(delta): # Accept Metropolis test
total = total + partial_new - partial_old # Update total values
r[i, :] = ri # Update position
moves = moves + 1 # Increment move counter
m_ratio = moves / n
x_ratio = 0.0
for updown in range(2): # Loop to look one way then the other
if m % 2 == updown: # Look up, partner is m+1
if m + 1 < nproc: # Ensure partner exists
other_beta = every_beta[
m + 1] # We already know the other beta
other_pot = comm.recv(
source=m + 1,
tag=msg1_id) # Receive pot from other process