def de_df(nsolatoms, optatoms, optlist, epsilon, sigma, charge, n, x, y, z, atomtype, conv):
delist = np.zeros((n, 3 * len(optatoms)))
dflist = np.zeros((n, 3 * len(optatoms), len(optlist), 3))
for i in xrange(n):
for j in xrange(len(optlist)):
h = optlist[j]
g = -1
for u in xrange(len(optatoms)):
if atomtype[i][h] == optatoms[u]:
g = u
break
else:
print "Something terrible has happened."
sys.exit()
for k in xrange(nsolatoms, len(x[i])):
ep1 = epsilon[atomtype[i][h]]
ep2 = epsilon[atomtype[i][k]]
sig1 = sigma[atomtype[i][h]]
sig2 = sigma[atomtype[i][k]]
r = np.array([x[i][h] - x[i][k], y[i][h] - y[i][k], z[i][h] - z[i][k]])
q1 = charge[atomtype[i][h]]
q2 = charge[atomtype[i][k]]
if ep1 != 0 and ep2 != 0:
(delist[i][3 * g], delist[i][3 * g + 1], dflist[i][3 * g][j], dflist[i][3 * g + 1][j]) = map(
operator.add,
(delist[i][3 * g], delist[i][3 * g + 1], dflist[i][3 * g][j], dflist[i][3 * g + 1][j]),
analyze.dedf_lj(ep1, ep2, sig1, sig2, r),
)
if q1 != 0 and q2 != 0:
(delist[i][3 * g + 2], dflist[i][3 * g + 2][j]) = map(
operator.add,
(delist[i][3 * g + 2], dflist[i][3 * g + 2][j]),
analyze.dedf_coul(conv, q1, q2, r),
)
return delist, dflist
def de_df_chcomp(nsolatoms, chcomptype, epsilon, sigma, charge, n, x, y, z, atomtype, conv):
delist = []
dflist = []
for i in xrange(n):
de = 0
df = []
for j in xrange(nsolatoms):
if atomtype[i][j] == chcomptype:
dfi = np.zeros(3)
for k in xrange(nsolatoms, len(x[i])):
r = np.array([x[i][j] - x[i][k], y[i][j] - y[i][k], z[i][j] - z[i][k]])
q1 = charge[atomtype[i][j]]
q2 = charge[atomtype[i][k]]
if q1 != 0 and q2 != 0:
(de, dfi) = map(operator.add, (de, dfi), analyze.dedf_coul(conv, q1, q2, r))
df.append(dfi)
else:
df.append(np.zeros(3))
delist.append(de)
dflist.append(df)
return np.array(delist), np.array(dflist)