def AdjustInitTemp():
mol = _mdsim_globals['mol']
_mdsim_globals['kinEnInitSum'] += _mdsim_globals['kinEnergy'].val
if _mdsim_globals['stepCount'] % _mdsim_globals['stepInitlzTemp'] == 0:
_mdsim_globals['kinEnInitSum'] /= _mdsim_globals['stepInitlzTemp']
vFac = \
_mdsim_globals['velMag'] / math.sqrt(2. * _mdsim_globals['kinEnInitSum'])
for m in mol:
rv_scale(m, vFac)
_mdsim_globals['kinEnInitSum'] = 0.0
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)