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completed lj parameter set and compute functions for melt example

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Axel Kohlmeyer
2017-05-15 00:14:36 -04:00
parent 86283c6309
commit f484ab6dfb
1 changed files with 20 additions and 13 deletions
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33
examples/python/lj-melt-potential.py
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@ -4,25 +4,32 @@ class LAMMPSLJCutPotential(object):
def __init__(self): def __init__(self):
self.pmap=dict() self.pmap=dict()
# coefficients: epsilon, sigma # set coeffs: eps, sig, 48*eps*sig**12, 24*eps*sig**6,
self.coeff = {'lj' : {'lj' : (1.0,1.0), # 4*eps*sig**12, 4*eps*sig**6
'NULL': (0.0,1.0)}, self.coeff = {'lj' : {'lj' : (1.0,1.0,48.0,24.0,4.0,4.0),
'NULL': {'lj' : (0.0,1.0), 'NULL': (0.0,1.0, 0.0, 0.0,0.0,0.0)},
'NULL': (0.0,1.0)}} '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,type,name): def map_coeff(self,name,type):
if self.coeff.has_key(name): if self.coeff.has_key(name):
print("map type %d to name %s" % (type,name))
self.pmap[type] = name self.pmap[type] = name
else: else:
print("cannot match atom type",name) raise Exception("cannot match atom type %s" % name)
def compute_force(self,r,itype,jtype,factor_lj): def compute_force(self,rsq,itype,jtype):
return 0.0 r2inv = 1.0/rsq
r6inv = r2inv*r2inv*r2inv
lj1 = self.coeff[self.pmap[itype]][self.pmap[jtype]][2]
lj2 = self.coeff[self.pmap[itype]][self.pmap[jtype]][3]
return (r6inv * (lj1*r6inv - lj2))
def compute_energy(self,r,itype,jtype,factor_lj): def compute_energy(self,rsq,itype,jtype):
return 0.0 r2inv = 1.0/rsq
r6inv = r2inv*r2inv*r2inv
lj3 = self.coeff[self.pmap[itype]][self.pmap[jtype]][4]
lj4 = self.coeff[self.pmap[itype]][self.pmap[jtype]][5]
return (r6inv * (lj3*r6inv - lj4))
lammps_pair_style = LAMMPSLJCutPotential() lammps_pair_style = LAMMPSLJCutPotential()
print ("lj-melt potential file loaded")