def PCV4(r : VecR, ro : VecR, v : VecR, a : VecR, a1 : VecR, a2 : VecR, \
wv : float, cv : float, deltaT : float) -> None:
v.x = (r.x - ro.x) / deltaT + wv * (cv[0] * a.x + cv[1] * a1.x +
cv[2] * a2.x)
v.y = (r.y - ro.y) / deltaT + wv * (cv[0] * a.y + cv[1] * a1.y +
cv[2] * a2.y)
v.z = (r.z - ro.z) / deltaT + wv * (cv[0] * a.z + cv[1] * a1.z +
cv[2] * a2.z)
def PCR4(r : VecR, ro : VecR, v : VecR, a : VecR, a1 : VecR, a2 : VecR, \
wr : float, cr : float, deltaT : float) -> None:
r.x = ro.x + deltaT * v.x + wr * (cr[0] * a.x + cr[1] * a1.x +
cr[2] * a2.x)
r.y = ro.y + deltaT * v.y + wr * (cr[0] * a.y + cr[1] * a1.y +
cr[2] * a2.y)
r.z = ro.z + deltaT * v.z + wr * (cr[0] * a.z + cr[1] * a1.z +
cr[2] * a2.z)
def vecr_copy(a_to: VecR, b_from: VecR) -> None:
"""Copy VecR objects component-wise.
Parameters
----------
a_to : VecR, molecule to copy to.
b_from : VecR, molecule to copy from.
"""
a_to.x = b_from.x
a_to.y = b_from.y
a_to.z = b_from.z
def _VCell_wrap_all(vc: VecI, cells: VecI, rs: VecR, region: VecR):
# Wrap the x-coordinate
if vc.x >= cells.x:
vc.x = 0
rs.x = region.x
elif vc.x < 0:
vc.x = cells.x - 1
rs.x = -region.x
# Wrap the y-coordinate
if vc.y >= cells.y:
vc.y = 0
rs.y = region.y
elif vc.y < 0:
vc.y = cells.y - 1
rs.y = -region.y
# Wrap the z-coordinate
if vc.z >= cells.z:
vc.z = 0
rs.z = region.z
elif vc.z < 0:
vc.z = cells.z - 1
rs.z = -region.z