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from __future__ import print_function
from lammps import lammps
class LAMMPSFix(object):
def __init__(self, ptr, group_name="all"):
self.lmp = lammps(ptr=ptr)
self.group_name = group_name
class LAMMPSFixMove(LAMMPSFix):
def __init__(self, ptr, group_name="all"):
super(LAMMPSFixMove, self).__init__(ptr, group_name)
def init(self):
pass
def initial_integrate(self, vflag):
pass
def final_integrate(self):
pass
def initial_integrate_respa(self, vflag, ilevel, iloop):
pass
def final_integrate_respa(self, ilevel, iloop):
pass
def reset_dt(self):
pass
class NVE(LAMMPSFixMove):
""" Python implementation of fix/nve """
def __init__(self, ptr, group_name="all"):
super(NVE, self).__init__(ptr)
assert(self.group_name == "all")
self._step_respa = None
def init(self):
dt = self.lmp.extract_global("dt")
ftm2v = self.lmp.extract_global("ftm2v")
self.ntypes = self.lmp.extract_global("ntypes")
self.dtv = dt
self.dtf = 0.5 * dt * ftm2v
@property
def step_respa(self):
if not self._step_respa:
self._step_respa = self.lmp.extract_global("respa_dt")
return self._step_respa
def initial_integrate(self, vflag):
nlocal = self.lmp.extract_global("nlocal")
mass = self.lmp.extract_atom("mass")
atype = self.lmp.extract_atom("type")
x = self.lmp.extract_atom("x")
v = self.lmp.extract_atom("v")
f = self.lmp.extract_atom("f")
for i in range(nlocal):
dtfm = self.dtf / mass[int(atype[i])]
v[i][0] += dtfm * f[i][0]
v[i][1] += dtfm * f[i][1]
v[i][2] += dtfm * f[i][2]
x[i][0] += self.dtv * v[i][0]
x[i][1] += self.dtv * v[i][1]
x[i][2] += self.dtv * v[i][2]
def final_integrate(self):
nlocal = self.lmp.extract_global("nlocal")
mass = self.lmp.extract_atom("mass")
atype = self.lmp.extract_atom("type")
v = self.lmp.extract_atom("v")
f = self.lmp.extract_atom("f")
for i in range(nlocal):
dtfm = self.dtf / mass[int(atype[i])]
v[i][0] += dtfm * f[i][0]
v[i][1] += dtfm * f[i][1]
v[i][2] += dtfm * f[i][2]
def initial_integrate_respa(self, vflag, ilevel, iloop):
ftm2v = self.lmp.extract_global("ftm2v")
self.dtv = self.step_respa[ilevel]
self.dtf = 0.5 * self.step_respa[ilevel] * ftm2v
# innermost level - NVE update of v and x
# all other levels - NVE update of v
if ilevel == 0:
self.initial_integrate(vflag)
else:
self.final_integrate()
def final_integrate_respa(self, ilevel, iloop):
ftm2v = self.lmp.extract_global("ftm2v")
self.dtf = 0.5 * self.step_respa[ilevel] * ftm2v
self.final_integrate()
def reset_dt(self):
dt = self.lmp.extract_global("dt")
ftm2v = self.lmp.extract_global("ftm2v")
self.dtv = dt;
self.dtf = 0.5 * dt * ftm2v;
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