def EvalProps():
"""Evaluate thermodynamic properties
"""
density = _mdsim_globals['density']
deltaT = _mdsim_globals['deltaT']
mol = _mdsim_globals['mol']
nMol = _mdsim_globals['nMol']
uSum = _mdsim_globals['uSum']
virSum = _mdsim_globals['virSum']
vSum = VecR()
vvMax : float = 0.
vvSum : float = 0.
for m in mol:
rv_add(vSum, m)
vv = rv_dot(m, m)
vvSum += vv
vvMax = max([vvMax, vv])
_mdsim_globals['dispHi'] += math.sqrt(vvMax) * deltaT
if _mdsim_globals['dispHi'] > 0.5 * _mdsim_globals['rNebrShell']:
_mdsim_globals['nebrNow'] = True
_mdsim_globals['vSum'] = vSum
_mdsim_globals['kinEnergy'].val = 0.5 * vvSum / nMol
_mdsim_globals['totEnergy'].val = \
_mdsim_globals['kinEnergy'].val + uSum / nMol
_mdsim_globals['pressure'].val = density * (vvSum + virSum) / (nMol * NDIM)
def InitVels():
"""Initialize the molecular velocities
"""
mol = _mdsim_globals['mol']
nMol = _mdsim_globals['nMol']
velMag = _mdsim_globals['velMag']
vSum = VecR(x=0., y=0., z=0.)
for m in mol:
m.rv = VecR()
rv_rand(m)
rv_scale(m, velMag)
rv_add(vSum, m)
_mdsim_globals['vSum'] = vSum
# Scale molecular velocities
for m in mol:
rv_sadd(m, -1. / nMol, vSum)
def EvalProps():
"""Evaluate thermodynamic properties
"""
density= _mdsim_globals['density']
mol = _mdsim_globals['mol']
nMol = _mdsim_globals['nMol']
uSum = _mdsim_globals['uSum']
virSum = _mdsim_globals['virSum']
vSum = VecR()
vvSum : float = 0.
for m in mol:
rv_add(vSum, m)
vvSum += rv_dot(m, m)
_mdsim_globals['vSum'] = vSum
_mdsim_globals['kinEnergy'].val = 0.5 * vvSum / nMol
_mdsim_globals['totEnergy'].val = \
_mdsim_globals['kinEnergy'].val + uSum / nMol
_mdsim_globals['pressure'].val = density * (vvSum + virSum) / (nMol * NDIM)