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Update py_nve.py

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Richard Berger
2021-05-10 18:23:39 -04:00
parent 85acf0b067
commit e1b2235d36
1 changed files with 4 additions and 12 deletions
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16
examples/python/py_nve.py
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@ -1,7 +1,5 @@
from __future__ import print_function from __future__ import print_function
from lammps import lammps, LAMMPS_INT, LAMMPS_DOUBLE from lammps import lammps
import ctypes
import traceback
import numpy as np import numpy as np
class LAMMPSFix(object): class LAMMPSFix(object):
@ -80,36 +78,30 @@ class NVE_Opt(LAMMPSFixMove):
self.ntypes = self.lmp.extract_global("ntypes") self.ntypes = self.lmp.extract_global("ntypes")
self.dtv = dt self.dtv = dt
self.dtf = 0.5 * dt * ftm2v self.dtf = 0.5 * dt * ftm2v
self.mass = self.lmp.numpy.extract_atom("mass")
def initial_integrate(self, vflag): def initial_integrate(self, vflag):
nlocal = self.lmp.extract_global("nlocal") mass = self.lmp.numpy.extract_atom("mass")
atype = self.lmp.numpy.extract_atom("type") atype = self.lmp.numpy.extract_atom("type")
x = self.lmp.numpy.extract_atom("x") x = self.lmp.numpy.extract_atom("x")
v = self.lmp.numpy.extract_atom("v") v = self.lmp.numpy.extract_atom("v")
f = self.lmp.numpy.extract_atom("f") f = self.lmp.numpy.extract_atom("f")
dtf = self.dtf dtf = self.dtf
dtv = self.dtv dtv = self.dtv
mass = self.mass
dtfm = dtf / np.take(mass, atype) dtfm = dtf / np.take(mass, atype)
dtfm.reshape((nlocal, 1))
for d in range(x.shape[1]): for d in range(x.shape[1]):
v[:,d] += dtfm[:,0] * f[:,d] v[:,d] += dtfm * f[:,d]
x[:,d] += dtv * v[:,d] x[:,d] += dtv * v[:,d]
def final_integrate(self): def final_integrate(self):
nlocal = self.lmp.extract_global("nlocal")
mass = self.lmp.numpy.extract_atom("mass") mass = self.lmp.numpy.extract_atom("mass")
atype = self.lmp.numpy.extract_atom("type") atype = self.lmp.numpy.extract_atom("type")
v = self.lmp.numpy.extract_atom("v") v = self.lmp.numpy.extract_atom("v")
f = self.lmp.numpy.extract_atom("f") f = self.lmp.numpy.extract_atom("f")
dtf = self.dtf dtf = self.dtf
mass = self.mass
dtfm = dtf / np.take(mass, atype) dtfm = dtf / np.take(mass, atype)
dtfm.reshape((nlocal, 1))
for d in range(v.shape[1]): for d in range(v.shape[1]):
v[:,d] += dtfm[:,0] * f[:,d] v[:,d] += dtfm * f[:,d]