Loading examples/python/in.pair_python_hybrid +1 −1 Original line number Diff line number Diff line Loading @@ -12,7 +12,7 @@ mass * 1.0 velocity all create 3.0 87287 pair_style hybrid lj/cut 2.5 python 2.5 pair_coeff * * python potentials.LAMMPSLJCutPotential lj NULL pair_coeff * * python potentials.LJCutMelt lj NULL pair_coeff * 2 lj/cut 1.0 1.0 neighbor 0.3 bin Loading examples/python/in.pair_python_melt +1 −1 Original line number Diff line number Diff line Loading @@ -12,7 +12,7 @@ mass * 1.0 velocity all create 3.0 87287 pair_style python 2.5 pair_coeff * * potentials.LAMMPSLJCutPotential lj pair_coeff * * potentials.LJCutMelt lj neighbor 0.3 bin neigh_modify every 20 delay 0 check no Loading examples/python/in.pair_python_spce 0 → 100644 +28 −0 Original line number Diff line number Diff line units real atom_style full read_data data.spce pair_style hybrid/overlay python 12.0 coul/long 12.0 kspace_style pppm 1.0e-6 pair_coeff * * coul/long pair_coeff * * python potentials.LJCutSPCE OW NULL bond_style harmonic angle_style harmonic dihedral_style none improper_style none bond_coeff 1 1000.00 1.000 angle_coeff 1 100.0 109.47 special_bonds lj/coul 0.0 0.0 1.0 neighbor 2.0 bin fix 1 all shake 0.0001 20 0 b 1 a 1 fix 2 all nvt temp 300.0 300.0 100.0 thermo 10 run 100 examples/python/potentials.py +40 −1 Original line number Diff line number Diff line from __future__ import print_function class LAMMPSLJCutPotential(object): class LJCutMelt(object): def __init__(self): self.pmap=dict() Loading Loading @@ -32,3 +32,42 @@ class LAMMPSLJCutPotential(object): 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)) Loading
examples/python/in.pair_python_hybrid +1 −1 Original line number Diff line number Diff line Loading @@ -12,7 +12,7 @@ mass * 1.0 velocity all create 3.0 87287 pair_style hybrid lj/cut 2.5 python 2.5 pair_coeff * * python potentials.LAMMPSLJCutPotential lj NULL pair_coeff * * python potentials.LJCutMelt lj NULL pair_coeff * 2 lj/cut 1.0 1.0 neighbor 0.3 bin Loading
examples/python/in.pair_python_melt +1 −1 Original line number Diff line number Diff line Loading @@ -12,7 +12,7 @@ mass * 1.0 velocity all create 3.0 87287 pair_style python 2.5 pair_coeff * * potentials.LAMMPSLJCutPotential lj pair_coeff * * potentials.LJCutMelt lj neighbor 0.3 bin neigh_modify every 20 delay 0 check no Loading
examples/python/in.pair_python_spce 0 → 100644 +28 −0 Original line number Diff line number Diff line units real atom_style full read_data data.spce pair_style hybrid/overlay python 12.0 coul/long 12.0 kspace_style pppm 1.0e-6 pair_coeff * * coul/long pair_coeff * * python potentials.LJCutSPCE OW NULL bond_style harmonic angle_style harmonic dihedral_style none improper_style none bond_coeff 1 1000.00 1.000 angle_coeff 1 100.0 109.47 special_bonds lj/coul 0.0 0.0 1.0 neighbor 2.0 bin fix 1 all shake 0.0001 20 0 b 1 a 1 fix 2 all nvt temp 300.0 300.0 100.0 thermo 10 run 100
examples/python/potentials.py +40 −1 Original line number Diff line number Diff line from __future__ import print_function class LAMMPSLJCutPotential(object): class LJCutMelt(object): def __init__(self): self.pmap=dict() Loading Loading @@ -32,3 +32,42 @@ class LAMMPSLJCutPotential(object): 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))
