def calc(self, phi=None):
"""Calculate torsion angle and energy
Args:
phi (float, optional): define the angle instead of calculating it
from the structure
Returns tuple (E [kcal/mol], phi [degrees])
"""
if phi == None:
ac1, ac2, ac3, ac4 = [a.struct.coordinates for a in self.atoms]
phi = qpotential.torsion_angle(ac1, ac2, ac3, ac4)
energy = 0
for fc, multiplicity, phase, npaths in self.prm.get_prms():
energy += qpotential.torsion_energy(phi, fc, multiplicity, npaths,
phase)
return (energy, phi)
nprm[bati_name] = 0
data[bati_name] = []
for bati in getattr(qtop, bati_name):
if bati_name == "bonds":
e0 = 0
v0 = bati.prm.r0
elif bati_name == "angles":
e0 = 0
v0 = bati.prm.theta0
elif bati_name == "torsions":
# get the torsion minimum
energy_profile = []
for phi in range(0, 181, 30):
energy = 0
for fc, multiplicity, phase, npaths in bati.prm.get_prms():
energy += torsion_energy(phi, fc, multiplicity,
npaths, phase)
energy_profile.append((energy, phi))
energy_profile.sort()
e0, v0 = min(energy_profile)
elif bati_name == "improper":
e0 = 0
v0 = bati.prm.phi0
e, v = bati.calc()
de = e - e0
data[bati_name].append((bati, de, v, v0))
total_e[bati_name] += de
if de > max_e[bati_name]:
max_e[bati_name] = de
nprm[bati_name] += 1