def res_aloal(mc, sim, n, a1, a2):
# @note: this is hard coded.
nres_prev = 0
nres_now = 0
cutoff = 3.6
grp = mc.swap_grp2_atms[n]
for i in range(len(grp)):
if grp[i] == a2:
pass
else:
r = get_dist(sim.atoms[a2].x, sim.atoms[grp[i]].x, sim.pbc)
#print r, a2, grp[i]
if r < cutoff:
nres_prev += 1
for i in range(len(grp)):
if grp[i] == a2:
pass
else:
r = get_dist(sim.atoms[a1].x, sim.atoms[grp[i]].x, sim.pbc)
#print r, a2, grp[i]
if r < cutoff:
nres_now += 1
return nres_now - nres_prev
def res_aloal(mc, sim, n, a1, a2):
# @note: this is hard coded.
nres_prev = 0
nres_now = 0
cutoff = 3.6
grp = mc.swap_grp2_atms[n]
for i in range(len(grp)):
if grp[i] == a2:
pass
else:
r = get_dist(sim.atoms[a2].x, sim.atoms[grp[i]].x, sim.pbc)
#print r, a2, grp[i]
if r < cutoff:
nres_prev += 1
for i in range(len(grp)):
if grp[i] == a2:
pass
else:
r = get_dist(sim.atoms[a1].x, sim.atoms[grp[i]].x, sim.pbc)
#print r, a2, grp[i]
if r < cutoff:
nres_now += 1
return nres_now - nres_prev
def getBondDist(self, a1, a2):
"""Get the distance
"""
x1 = self.atoms[a1 - 1].x
x2 = self.atoms[a2 - 1].x
dist = get_dist(x1, x2)
return dist
def getBondDist(self, a1, a2):
"""Get the distance
"""
x1 = self.atoms[a1-1].x
x2 = self.atoms[a2-1].x
dist = get_dist(x1, x2)
return dist
def sphere_cut(control, b, grp):
"""Cut the sphere and balance the charge.
Here, we use the ratio from input as criteria. We eliminate the extra
atoms according to the distances to the center. (So we first sort the
atoms according to distance).
"""
# coarse cut (only according to radius
print " Cutting the sphere ..."
natoms = [0]*len(control.atoms)
ndx1 = [] # coarse cut
ndx2 = [] # refine cut
ndx3 = [] # final atoms
for i in range(len(control.atoms)):
ndx1.append([])
ndx2.append([])
ndx3.append([])
# should be useful for Li3PS4 case
"""
for i in range(len(grp.subgroups)):
nc = int(control.grpatomscenter[i]) - 1
counter = 0
for j in grp.subgroups[i]:
at = b.atoms[j[nc]]
dist = get_dist(at.x, control.center)
if dist < control.radius:
natoms[i] += 1
ndx1[i].append("%09d_%08d"%(dist*1000, counter))
counter += 1
"""
counter = 0
for i in b.atoms:
dist = get_dist(i.x, control.center)
if dist < control.radius:
n = control.atoms.index(i.name)
natoms[n] += 1
ndx1[n].append("%09d_%08d"%(dist*1000, counter))
counter += 1
# print information of coarse cut
print " After Coarse cut we get:"
for i in range(len(control.atoms)):
print " %-6s = %8d"%(control.atoms[i], len(ndx1[i]))
# sort the atoms
for i in ndx1:
i.sort()
nmin = MAX_ATOMS
for i in range(len(control.natoms)):
n = int(natoms[i]/control.natoms[i])
if n < nmin:
nmin = n
for i in range(len(control.atoms)):
n = nmin * control.natoms[i]
for j in range(n):
ndx2[i].append(int(ndx1[i][j].split("_")[-1]))
print " After balancing charge we get:"
for i in range(len(control.atoms)):
print " %-6s = %8d"%(control.atoms[i], len(ndx2[i]))
return ndx2
