def random_positions(n):
"""Returns n random 3-d vectors in a numpy array (n,3).
d_min, d_max, npos should be in global scope"""
import numpy as np
from maths_module import random_vector
import sys
r = np.zeros((n, 3), dtype=np.float_)
# atom 0 is always at the origin, now place the others randomly
for i in range(1, r.shape[0]):
for pos_try in range(npos):
zeta = np.random.rand()
d = d_min + (d_max - d_min) * zeta # Magnitude of r
r[i, :] = random_vector() * d # In random direction
ok = True
for j in range(1, i): # Check intermediate atoms if any
d = np.sqrt(np.sum((r[i, :] - r[j, :])**2))
ok = ok and (d >= d_min) and (d <= d_max)
if ok:
break
else:
print('Exceeded maximum number of tries in random_positions')
sys.exit()
return r
def random_orientations(n):
"""Returns n random 3-d vectors in a numpy array (n,3)."""
import numpy as np
from maths_module import random_vector
e = np.empty((n, 3), dtype=np.float_)
for i in range(e.shape[0]):
e[i, :] = random_vector()
return e
def chain_positions(n, bond, soft):
"""Chooses chain positions randomly, at desired bond length, avoiding overlap."""
import numpy as np
from maths_module import random_vector
tol = 1.0e-9
iter_max = 500
print("{:40}{:15.6f}".format('Chain, randomly oriented bonds = ', bond))
r = np.empty((n, 3), dtype=np.float_)
r[0, :] = [0.0, 0.0, 0.0] # First atom at origin
r[1, :] = bond * random_vector(
) # Second atom at random position (bond length away)
for i in range(2, n): # Loop over atom indices
iter = 0
while True: # Loop until non-overlapping position found
r[i, :] = r[i - 1, :] + bond * random_vector(
) # Subsequent atoms randomly placed (bond length away)
if soft: # No overlap test
break
# Overlap test on all so far except bonded neighbour
if not chain_overlap(r[i, :], r[:i - 1, :]):
break
iter = iter + 1
assert iter <= iter_max, 'Too many iterations'
r_cm = np.sum(r, axis=0) / n # Compute centre of mass
r = r - r_cm # Shift centre of mass to origin
for i in range(n - 1):
diff_sq = np.sum((r[i, :] - r[i + 1, :])**2) - bond**2
if np.fabs(diff_sq) > tol:
print("{}{:5d}{:5d}{:15.8f}".format('Bond length warning', i,
i + 1, diff_sq))
return r
def ran_positions(n, box, length, soft, quaternions):
"""Places atoms at random positions."""
import numpy as np
from maths_module import random_quaternion, random_vector
# Unlikely to be useful, unless the interaction potential is soft
# or the density rather low
# For atoms, for which length=0.0, the e-coordinates will be ignored
iter_max = 10000 # Max random placement iterations
print('Random positions')
r = np.empty((n, 3), dtype=np.float_)
if quaternions:
e = np.empty((n, 4), dtype=np.float_)
else:
e = np.empty((n, 3), dtype=np.float_)
for i in range(n):
iter = 0
while True: # Loop until non-overlapping position found
r[i, :] = (np.random.rand(3) - 0.5) * box # In range -box/2..box/2
if quaternions:
e[i, :] = random_quaternion()
else:
e[i, :] = random_vector()
if soft:
break
if not overlap(r[i, :], e[i, :], r[:i, :], e[:i, :], box, length):
break
iter = iter + 1
assert iter <= iter_max, "Too many iterations"
return r, e
"quad1_mag"] # Quadrupole moment of molecule 1
quad2_mag = nml["quad2_mag"] if "quad2_mag" in nml else defaults[
"quad2_mag"] # Quadrupole moment of molecule 2
# Write out parameters
print("{:40}{:15.6f}".format('Min separation d_min', d_min))
print("{:40}{:15.6f}".format('Max separation d_max', d_max))
print("{:40}{:15.6f}".format('Dipole moment of molecule 1', mu1_mag))
print("{:40}{:15.6f}".format('Dipole moment of molecule 2', mu2_mag))
print("{:40}{:15.6f}".format('Quadrupole moment of molecule 1', quad1_mag))
print("{:40}{:15.6f}".format('Quadrupole moment of molecule 2', quad2_mag))
np.random.seed()
# Choose orientations at random
e1 = random_vector()
e2 = random_vector()
# Place atom 2 at origin and atom 1 in a random direction within desired distance range
r12_hat = random_vector()
r12_mag = np.random.rand()
r12_mag = d_min + (d_max - d_min) * r12_mag # Magnitude of r12
r12 = r12_hat * r12_mag # Within desired range of origin
c1 = np.dot(e1, r12_hat) # Cosine of angle between e1 and r12
c2 = np.dot(e2, r12_hat) # Cosine of angle between e2 and r12
c12 = np.dot(e1, e2) # Cosine of angle between e1 and e2
print("{:40}{:10.6f}{:10.6f}{:10.6f}".format('Displacement r12', *r12))
print("{:40}{:10.6f}{:10.6f}{:10.6f}".format('Orientation e1', *e1))
print("{:40}{:10.6f}{:10.6f}{:10.6f}".format('Orientation e2', *e2))
def regrow(temperature, m_max, k_max, bond, k_spring, r):
"""Carries out single regrowth move, returning new r and indicator of success."""
# A short sequence of m atoms (m<=m_max) is deleted and regrown in the CBMC manner
# We randomly select which end of the chain to apply each of these operations to
# At each stage, k_max different atom positions are tried
# Function random_bond selects bond lengths according to the internal (harmonic) potential
# Rosenbluth weights are computed using the external (nonbonded) potential
# Acceptance/rejection is determined using these weights
# r_old and r_new are used as working arrays
import numpy as np
from maths_module import random_vector
w_tol = 1.e-10 # Min weight tolerance
n, d = r.shape
assert d == 3, 'Dimension error in regrow'
r_try = np.empty((k_max, 3), dtype=np.float_)
w = np.empty(k_max, dtype=np.float_)
std = np.sqrt(temperature / k_spring) # Spring bond standard deviation
d_max = 3.0 * std # Impose a limit on variation, say 3*std
assert d_max < 0.75 * bond, 'Spring bond strength error'
d_max = d_max + bond # This is the actual max d allowed
r_old = np.copy(r) # Store copy of r
m = 1 + np.random.randint(m_max) # Number of atoms to regrow
c = np.random.randint(4) # Growth option
# PART 1: CONSTRUCT NEW CONFIGURATION WITH NEW WEIGHT
if c == 0: # Remove from end and add to end
r[:n - m, :] = r_old[:n - m, :] # Copy first n-m atoms
elif c == 1: # Remove from end and add to start
r[:n - m, :] = r_old[n - m -
1::-1, :] # Copy and reverse first n-m atoms
elif c == 2: # Remove from start and add to start
r[:n - m, :] = r_old[:m - 1:-1, :] # Copy and reverse last n-m atoms
else: # Remove from start and add to end
r[:n - m, :] = r_old[m:, :] # Copy last n-m atoms
# Take the opportunity to place atom 0 at the origin
r0 = np.copy(r[0, :])
r[:n - m, :] = r[:n - m, :] - r0
w_new = 1.0
for i in range(n - m,
n): # Loop to regrow last m atoms, computing new weight
for k in range(k_max): # Loop over k_max tries
d = random_bond(bond, std,
d_max) # Generate random bond length around d=bond
r_try[k, :] = r[i - 1, :] + d * random_vector(
) # Trial position in random direction from i-1
partial = potential_1(
r_try[k, :],
r[:i -
1, :]) # Nonbonded interactions with earlier atoms (not i-1)
w[k] = 0.0 if partial.ovr else np.exp(
-partial.pot / temperature) # Weight for this try
w_sum = np.sum(w)
if w_sum < w_tol: # Early exit if this happens at any stage
return r_old, False
w = w / w_sum
k = np.random.choice(k_max,
p=w) # Pick winning try according to weights
r[i, :] = r_try[k, :] # Store winning position
w_new = w_new * w_sum # Accumulate total weight
if w_new < w_tol: # Exit if this happens
return r_old, False
r_new = np.copy(r) # Store new configuration
# END OF PART 1: NEW CONFIGURATION AND WEIGHT ARE COMPLETE
# PART 2: RECONSTRUCT OLD CONFIGURATION WITH OLD WEIGHT
if c == 0 or c == 1: # Remove and hence reconstruct at end
r[:, :] = r_old[:, :] # Copy all n atoms
else: # Remove and reconstruct at start
r[:, :] = r_old[::-1, :] # Copy and reverse all n atoms
w_old = 1.0
for i in range(n - m, n):
# Old position and weight are stored as try 0
r_try[0, :] = r[i, :]
partial = potential_1(
r_try[0, :],
r[:i - 1, :]) # Nonbonded energy with earlier atoms (not i-1)
w[0] = 0.0 if partial.ovr else np.exp(
-partial.pot / temperature) # Weight for this try
# Remaining tries only required to compute weight
for k in range(1, k_max): # Loop over k_max-1 other tries
d = random_bond(bond, std,
d_max) # Generate random bond length around d=bond
r_try[k, :] = r[i - 1, :] + d * random_vector(
) # Trial position in random direction from i-1
partial = potential_1(
r_try[k, :],
r[:i -
1, :]) # Nonbonded interactions with earlier atoms (not i-1)
w[k] = 0.0 if partial.ovr else np.exp(
-partial.pot / temperature) # Weight for this try
w_sum = np.sum(w)
r[i, :] = r_try[
0, :] # Restore winning position (always the original one)
w_old = w_old * w_sum # Accumulate total weight
assert w_old > w_tol, 'Old weight error'
# END OF PART 2: OLD CONFIGURATION AND WEIGHT ARE COMPLETE
# Choose either old or new configuration according to weight
# All non-bonded Boltzmann factors are incorporated into the weights
# All spring-bond Boltzmann factors are included in the selection of d
zeta = np.random.rand()
if zeta < (w_new / w_old):
return r_new, True
else:
return r_old, False
def regrow(s, m_max, k_max, bond, q_range, r, q):
"""Carries out single regrowth move, returning new r, q and indicator of success."""
# A short sequence of m atoms (m<=m_max) is deleted and regrown in the CBMC manner
# We randomly select which end of the chain to apply each of these operations to
# At each stage, k_max different atom positions are tried
# The bond length is fixed throughout
# Weights used in the regrowth are athermal, computed only on the basis of the
# hard-core overlap part of the non-bonded interactions: essentially they count non-overlaps
# Hence they are suitable for use in both NVT and Wang-Landau simulations
# r_old and r_new are used as working arrays
import numpy as np
from maths_module import random_vector
w_tol = 1.e-10 # Min weight tolerance
n, d = r.shape
assert d == 3, 'Dimension error in regrow'
r_try = np.empty((k_max, 3), dtype=np.float_)
w = np.empty(k_max, dtype=np.float_)
r_old = np.copy(r) # Store copy of r
q_old = q # Store old q
if m_max <= 0:
return r_old, q_old, False
m = 1 + np.random.randint(m_max) # Number of atoms to regrow
c = np.random.randint(4) # Growth option
# PART 1: CONSTRUCT NEW CONFIGURATION WITH NEW WEIGHT
if c == 0: # Remove from end and add to end
r[:n - m, :] = r_old[:n - m, :] # Copy first n-m atoms
elif c == 1: # Remove from end and add to start
r[:n - m, :] = r_old[n - m -
1::-1, :] # Copy and reverse first n-m atoms
elif c == 2: # Remove from start and add to start
r[:n - m, :] = r_old[:m - 1:-1, :] # Copy and reverse last n-m atoms
else: # Remove from start and add to end
r[:n - m, :] = r_old[m:, :] # Copy last n-m atoms
# Take the opportunity to place atom 0 at the origin
r0 = np.copy(r[0, :])
r[:n - m, :] = r[:n - m, :] - r0
w_new = np.float_(1.0)
for i in range(n - m,
n): # Loop to regrow last m atoms, computing new weight
for k in range(k_max): # Loop over k_max tries
r_try[k, :] = r[i - 1, :] + bond * random_vector(
) # Trial position in random direction from i-1
w[k] = weight_1(r_try[k, :],
r[:i - 1, :]) # Store overlap weight for this try
w_sum = np.sum(w)
if w_sum < w_tol: # Early exit if this happens at any stage
return r_old, q_old, False
w = w / w_sum
k = np.random.choice(k_max,
p=w) # Pick winning try according to weights
r[i, :] = r_try[k, :] # Store winning position
w_new = w_new * w_sum # Accumulate total weight
if w_new < w_tol: # Exit if this happens
return r_old, q_old, False
q_new = qcount(r, q_range) # Compute full new nonbonded energy
r_new = np.copy(r) # Store new configuration
# END OF PART 1: NEW CONFIGURATION AND WEIGHT ARE COMPLETE
# PART 2: RECONSTRUCT OLD CONFIGURATION WITH OLD WEIGHT
if c == 0 or c == 1: # Remove and hence reconstruct at end
r[:, :] = r_old[:, :] # Copy all n atoms
else: # Remove and reconstruct at start
r[:, :] = r_old[::-1, :] # Copy and reverse all n atoms
w_old = np.float_(1.0)
for i in range(n - m, n):
# Old position and weight are stored as try 0
r_try[0, :] = r[i, :]
w[0] = 1 # Current weight must be 1
# Remaining tries only required to compute weight
for k in range(1, k_max): # Loop over k_max-1 other tries
r_try[k, :] = r[i - 1, :] + bond * random_vector(
) # Trial position in random direction from i-1
w[k] = weight_1(r_try[k, :],
r[:i - 1, :]) # Store overlap weight for this try
w_sum = np.sum(w)
r[i, :] = r_try[
0, :] # Restore winning position (always the original one)
w_old = w_old * w_sum # Accumulate total weight
assert w_old > w_tol, 'Old weight error'
# END OF PART 2: OLD CONFIGURATION AND WEIGHT ARE COMPLETE
# Choose either old or new configuration
if accept(s, q_old, q_new, w_old, w_new):
return r_new, q_new, True
else:
return r_old, q_old, False
def pivot(s, phi_max, q_range, r, q):
"""Carries out a pivot move, returning new r, q and indicator of success."""
# An atom is picked at random, and the part of the chain lying to one side of it
# is rotated as a whole, by a random angle, about a randomly oriented axis
# There are no weights to take into account in the acceptance/rejection decision
# (the function weight_1 is used simply to indicate overlap / no overlap)
# r_old and r_new are used as working arrays
import numpy as np
from maths_module import random_vector, rotate_vector
n, d = r.shape
assert d == 3, 'Dimension error in regrow'
if n < 3:
return r, q, False # Makes no sense to pivot such a short chain
r_old = np.copy(r) # Store copy of r
q_old = q # Store old q
c = np.random.randint(2) # Which part to pivot (actually redundant here)
if c == 0: # Copy atoms
r[:, :] = r_old[:, :]
else: # Copy and reverse atoms
r[:, :] = r_old[::-1, :]
# Take the opportunity to place atom 0 at the origin
r0 = np.copy(r[0, :])
r = r - r0
j = np.random.randint(1, n - 1) # Pivot position (not at either end)
rj = r[j, :] # Pivot point
for i in range(1, j +
1): # Loop over static atoms, redundant but for roundoff
if weight_1(r[i, :], r[:i - 1, :]) == 0: # Check for overlaps
return r_old, q_old, False
# Pivot, and check for overlap in new configuration
# NB include overlap checks within rotated segment, because of roundoff
axis = random_vector() # Pivot rotation axis
phi = phi_max * (2.0 * np.random.rand() - 1.0
) # Pivot rotation angle in desired range
for i in range(j + 1, n): # Loop over moving atoms
rij = r[i, :] - rj # Relative vector of atom
rij = rotate_vector(phi, axis, rij) # Rotate relative vector
r[i, :] = rj + rij # New absolute position
if weight_1(r[i, :], r[:i - 1, :]) == 0: # Check for overlaps
return r_old, q_old, False
q_new = qcount(r, q_range) # Compute full new nonbonded energy
r_new = np.copy(r) # Store new configuration
# Choose either old or new configuration
if accept(s, q_old, q_new):
return r_new, q_new, True
else:
return r_old, q_old, False