def step_vv(x, v, f, dt, xup):
global rcut, skin
# update positions
x += v*dt + 0.5*f * dt*dt
# compute maximal position update
# vectorial
dx = x - xup
# square
dx *= dx
# sum up
dx = dx.sum(axis=0)
# test whether the neighbor list needs to be rebuilt
if max(dx) > (0.5*skin)**2:
lj.rebuild_neighbor_lists(x, rcut+skin)
xup = x.copy()
# half update of the velocity
v += 0.5*f * dt
# compute new forces
f = compute_forces(x)
# second half update of the velocity
v += 0.5*f * dt
return x, v, f, xup
vtffile = open(vtffilename, 'a')
# write the structure of the system into the file:
# N particles ("atoms") with a radius of 0.5
vtffile.write('atom 0:{} radius 0.5\n'.format(N-1))
vtffile.write('pbc {} {} {}\n'.format(L, L, L))
# write out that a new timestep starts
vtffile.write('timestep\n')
# write out the coordinates of the particles
for i in range(N):
vtffile.write("{} {} {}\n".format(x[0,i], x[1,i], x[2,i]))
# main loop
lj.set_globals(L, N, rcut, shift)
lj.rebuild_neighbor_lists(x, rcut+skin)
xup = x.copy()
f = compute_forces(x)
tmax = t+trun
if warmup_on:
print("Warmup simulation...")
warmup_finished = False
else:
print("Simulating until tmax={}...".format(tmax))
while (not warmup_on and t < tmax) or (warmup_on and not warmup_finished):
x, v, f, xup = step_vv(x, v, f, dt, xup)
t += dt
step += 1
if warmup_on:
Tm = compute_temperature(v)