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py_pot.py
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Wed, Nov 13, 03:50

py_pot.py
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from __future__ import print_function
class LJCutMelt(object):
def __init__(self):
self.pmap=dict()
# set coeffs: eps, sig, 48*eps*sig**12, 24*eps*sig**6,
# 4*eps*sig**12, 4*eps*sig**6
self.coeff = {'lj' : {'lj' : (1.0,1.0,48.0,24.0,4.0,4.0),
'NULL': (0.0,1.0, 0.0, 0.0,0.0,0.0)},
'NULL': {'lj' : (0.0,1.0, 0.0, 0.0,0.0,0.0),
'NULL': (0.0,1.0, 0.0, 0.0,0.0,0.0)}}
def map_coeff(self,name,type):
if name in self.coeff:
self.pmap[type] = name
else:
raise Exception("cannot match atom type %s" % name)
def compute_force(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
r2inv = 1.0/rsq
r6inv = r2inv*r2inv*r2inv
lj1 = coeff[2]
lj2 = coeff[3]
return (r6inv * (lj1*r6inv - lj2))
def compute_energy(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
r2inv = 1.0/rsq
r6inv = r2inv*r2inv*r2inv
lj3 = coeff[4]
lj4 = coeff[5]
return (r6inv * (lj3*r6inv - lj4))
class LJCutSPCE(object):
def __init__(self):
self.pmap=dict()
# SPCE oxygen in real units
eps=0.15535
sig=3.166
# set coeffs: eps, sig, 48*eps*sig**12, 24*eps*sig**6,
# 4*eps*sig**12, 4*eps*sig**6
self.coeff = {'OW' : {'OW' : (1.0,1.0,
48.0*eps*sig**12,24.0*eps*sig**6,
4.0*eps*sig**12, 4.0*eps*sig**6),
'NULL': (0.0,1.0, 0.0, 0.0,0.0,0.0)},
'NULL': {'OW' : (0.0,1.0, 0.0, 0.0,0.0,0.0),
'NULL': (0.0,1.0, 0.0, 0.0,0.0,0.0)}}
def map_coeff(self,name,type):
if name in self.coeff:
self.pmap[type] = name
else:
raise Exception("cannot match atom type %s" % name)
def compute_force(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
r2inv = 1.0/rsq
r6inv = r2inv*r2inv*r2inv
lj1 = coeff[2]
lj2 = coeff[3]
return (r6inv * (lj1*r6inv - lj2))
def compute_energy(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
r2inv = 1.0/rsq
r6inv = r2inv*r2inv*r2inv
lj3 = coeff[4]
lj4 = coeff[5]
return (r6inv * (lj3*r6inv - lj4))

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