def fill_LJ(self):
"""
Fills the LJ_radius, LJ_depth arrays and LJ_types dictionary with data
from LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF sections of the prmtop
files, by undoing the canonical combining rules.
"""
AmberParm.fill_LJ(self)
acoef = self.parm_data['LENNARD_JONES_14_ACOEF']
bcoef = self.parm_data['LENNARD_JONES_14_BCOEF']
ntypes = self.pointers['NTYPES']
self.LJ_14_radius = [] # empty LJ_radii so it can be re-filled
self.LJ_14_depth = [] # empty LJ_depths so it can be re-filled
one_sixth = 1.0 / 6.0 # we need to raise some numbers to the 1/6th power
for i in range(ntypes):
lj_index = self.parm_data["NONBONDED_PARM_INDEX"][ntypes * i +
i] - 1
if acoef[lj_index] < 1.0e-6:
self.LJ_14_radius.append(0)
self.LJ_14_depth.append(0)
else:
factor = 2 * acoef[lj_index] / bcoef[lj_index]
self.LJ_14_radius.append(pow(factor, one_sixth) * 0.5)
self.LJ_14_depth.append(bcoef[lj_index] / 2 / factor)
def fill_LJ(self):
"""
Fills the LJ_radius, LJ_depth arrays and LJ_types dictionary with data
from LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF sections of the prmtop
files, by undoing the canonical combining rules.
"""
AmberParm.fill_LJ(self)
acoef = self.parm_data['LENNARD_JONES_14_ACOEF']
bcoef = self.parm_data['LENNARD_JONES_14_BCOEF']
ntypes = self.pointers['NTYPES']
self.LJ_14_radius = [] # empty LJ_radii so it can be re-filled
self.LJ_14_depth = [] # empty LJ_depths so it can be re-filled
one_sixth = 1.0 / 6.0 # we need to raise some numbers to the 1/6th power
for i in range(ntypes):
lj_index = self.parm_data["NONBONDED_PARM_INDEX"][ntypes*i+i] - 1
if acoef[lj_index] < 1.0e-6:
self.LJ_14_radius.append(0)
self.LJ_14_depth.append(0)
else:
factor = 2 * acoef[lj_index] / bcoef[lj_index]
self.LJ_14_radius.append(pow(factor, one_sixth) * 0.5)
self.LJ_14_depth.append(bcoef[lj_index] / 2 / factor)
