def mcmove(npart, part_pos_array, dr, beta, en, vir, attempt, nacc, box_length, rc2, sigma2, epsilon4, epsilon48, shift_pot, ecut):
attempt += 1
jb = 0
# select a particle at random
o = int(npart*np.random.random()) # +1
# calculate energy old configuration
eno, viro = cener.eneri(npart, part_pos_array, o, jb, box_length, rc2, sigma2, epsilon4, epsilon48, shift_pot, ecut)
# give particle a random displacement and store previous position
xo = part_pos_array[o, 0]
yo = part_pos_array[o, 1]
zo = part_pos_array[o, 2]
part_pos_array[o, 0] += (np.random.random()-0.5)*dr
part_pos_array[o, 1] += (np.random.random()-0.5)*dr
part_pos_array[o, 2] += (np.random.random()-0.5)*dr
# calculate energy new configuration:
enn, virn = cener.eneri(npart, part_pos_array, o, jb, box_length, rc2, sigma2, epsilon4, epsilon48, shift_pot, ecut)
# acceptance test
if np.random.random() < min(1, np.exp(-beta*(enn-eno))):
# accepted
nacc += 1
en = en + (enn-eno)
vir = vir + (virn-viro)
# put particle in simulation box
if part_pos_array[o, 0] < 0:
part_pos_array[o, 0] += box_length
if part_pos_array[o, 0] > box_length:
part_pos_array[o, 0] -= box_length
if part_pos_array[o, 1] < 0:
part_pos_array[o, 1] += box_length
if part_pos_array[o, 1] > box_length:
part_pos_array[o, 1] -= box_length
if part_pos_array[o, 2] < 0:
part_pos_array[o, 2] += box_length
if part_pos_array[o, 2] > box_length:
part_pos_array[o, 2] -= box_length
else: # if move is rejected return to previous coordinates
part_pos_array[o, 0] = xo
part_pos_array[o, 1] = yo
part_pos_array[o, 2] = zo
return en, vir, nacc, attempt, part_pos_array
def mcexch(npart, part_pos_array, beta, en, vir, attempt, nacc, box_length, rc,
rc2, sigma, sigma2, epsilon4, epsilon48, shift_pot, tail_corr, ecut,
zz, av_cav, n_cavs, n_nodes, use_cavity_bias):
attempt += 1
vol = box_length**3
rhoo = npart / vol
# select to add or delete a particle
if np.random.random() < 0.5:
# random insertion
if len(av_cav) == 0 or not use_cavity_bias:
# add a particle at a random position
xn = np.random.random() * box_length
yn = np.random.random() * box_length
zn = np.random.random() * box_length
pc = 1
else:
# cavity biased insertion
if len(av_cav) > 1:
cav_index = np.random.randint(0, len(av_cav) - 1)
else:
cav_index = 0
xn = av_cav[cav_index, 0]
yn = av_cav[cav_index, 1]
zn = av_cav[cav_index, 2]
pc = float(n_cavs) / float(n_nodes)
o = npart
jb = 0
part_pos_array = np.append(part_pos_array, [[xn, yn, zn]], axis=0)
# determine energy of this particle
enn, virn = cener.eneri(npart, part_pos_array, o, jb, box_length, rc2,
sigma2, epsilon4, epsilon48, shift_pot, ecut)
# tail correction
if tail_corr:
rhon = (npart + 1) / vol
enn += ((npart + 1) * ccor.coru(rc, rhon, sigma, epsilon4) -
npart * ccor.coru(rc, rhoo, sigma, epsilon4))
# acceptance test:
arg = zz * vol * pc * np.exp(-beta * enn) / (npart + 1)
if np.random.random() < min(1, arg):
# accepted
nacc += 1
en += enn
vir += virn
npart += 1
else:
part_pos_array = np.delete(part_pos_array, o, 0)
else:
if np.random.random() < (
1 - (float(n_cavs) - 1) / float(n_nodes))**n_nodes:
pc = 1
else:
pc = (float(n_cavs) - 1) / float(n_nodes)
# delete a randomly selected particle
o = int(npart * np.random.random())
jb = 0
eno, viro = cener.eneri(npart, part_pos_array, o, jb, box_length, rc2,
sigma2, epsilon4, epsilon48, shift_pot, ecut)
# particle is removed, so new energy
enn = -eno
virn = -viro
# tail correction
if tail_corr:
rhon = (npart - 1) / vol
enn += ((npart - 1) * ccor.coru(rc, rhon, sigma, epsilon4) -
npart * ccor.coru(rc, rhoo, sigma, epsilon4))
# acceptance test:
arg = npart * np.exp(-beta * enn) / (zz * pc * vol)
if np.random.random() < min(1, arg):
# accepted
nacc += 1
en += enn
vir += virn
npart -= 1
part_pos_array = np.delete(part_pos_array, o, 0)
return en, vir, nacc, attempt, part_pos_array, npart
def mcexch(npart, part_pos_array, beta, en, vir, attempt,
nacc, box_length, rc, rc2, sigma, sigma2, epsilon4,
epsilon48, shift_pot, tail_corr, ecut, zz, av_cav, n_cavs, n_nodes, use_cavity_bias):
attempt += 1
vol = box_length**3
rhoo = npart/vol
# select to add or delete a particle
if np.random.random() < 0.5:
# random insertion
if len(av_cav) == 0 or not use_cavity_bias:
# add a particle at a random position
xn = np.random.random()*box_length
yn = np.random.random()*box_length
zn = np.random.random()*box_length
pc = 1
else:
# cavity biased insertion
if len(av_cav) > 1:
cav_index = np.random.randint(0, len(av_cav) - 1)
else:
cav_index = 0
xn = av_cav[cav_index, 0]
yn = av_cav[cav_index, 1]
zn = av_cav[cav_index, 2]
pc = float(n_cavs)/float(n_nodes)
o = npart
jb = 0
part_pos_array = np.append(part_pos_array, [[xn, yn, zn]], axis=0)
# determine energy of this particle
enn, virn = cener.eneri(npart, part_pos_array, o, jb, box_length, rc2, sigma2, epsilon4, epsilon48, shift_pot, ecut)
# tail correction
if tail_corr:
rhon = (npart+1)/vol
enn += ((npart+1)*ccor.coru(rc, rhon, sigma, epsilon4)-npart*ccor.coru(rc, rhoo, sigma, epsilon4))
# acceptance test:
arg = zz*vol*pc*np.exp(-beta*enn)/(npart+1)
if np.random.random() < min(1, arg):
# accepted
nacc += 1
en += enn
vir += virn
npart += 1
else:
part_pos_array = np.delete(part_pos_array, o, 0)
else:
if np.random.random() < (1 - (float(n_cavs) - 1) / float(n_nodes))**n_nodes:
pc = 1
else:
pc = (float(n_cavs) - 1) / float(n_nodes)
# delete a randomly selected particle
o = int(npart*np.random.random())
jb = 0
eno, viro = cener.eneri(npart, part_pos_array, o, jb, box_length, rc2, sigma2, epsilon4, epsilon48, shift_pot, ecut)
# particle is removed, so new energy
enn = -eno
virn = -viro
# tail correction
if tail_corr:
rhon = (npart-1)/vol
enn += ((npart-1)*ccor.coru(rc, rhon, sigma, epsilon4)-npart*ccor.coru(rc, rhoo, sigma, epsilon4))
# acceptance test:
arg = npart*np.exp(-beta*enn)/(zz*pc*vol)
if np.random.random() < min(1, arg):
# accepted
nacc += 1
en += enn
vir += virn
npart -= 1
part_pos_array = np.delete(part_pos_array, o, 0)
return en, vir, nacc, attempt, part_pos_array, npart