def step_vv(x, v, f, dt, xup):
global rcut, skin, fmax
# 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:
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, fmax)
# we assume that m=1 for all particles
# second half update of the velocity
v += 0.5 * f * dt
return x, v, f, xup
def step_vv(x, v, f, dt, xup):
global rcut, skin, fmax
# 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:
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, fmax) + force_ld(v)
# we assume that m=1 for all particles
# second half update of the velocity
v += 0.5 * f * dt
return x, v, f, xup
# variables to cumulate data
traj = np.empty((steps, 3, N))
ts = np.empty(steps)
Es = np.empty(steps)
Epots = np.empty(steps)
Ekins = np.empty(steps)
Ts = np.empty(steps)
Ps = np.empty(steps)
# ==== CALCULATION ====
print "Simulating until tmax=%s..." % (t + tadd)
set_globals(L, N, rcut, shift)
rebuild_neighbor_lists(x, rcut + skin)
xup = x.copy()
f = compute_forces(x, fmax)
# calculate or load the data from the time before the current run will start
if os.path.exists(datafilename):
ts_old, Es_old, Epots_old, Ekins_old, Ts_old, Ps_old, traj_old = np.load(
datafilename)
else:
a, b, c = compute_energy(x, v)
d = compute_temperature(c)
e = compute_pressure(x, v)
ts_old = np.array([t])
Es_old = np.array([a])
Epots_old = np.array([b])
Ekins_old = np.array([c])
Ts_old = np.array([d])
Ps_old = np.array([e])
# variables to cumulate data
traj = np.empty((steps, 3, N))
ts = np.empty(steps)
Es = np.empty(steps)
Epots = np.empty(steps)
Ekins = np.empty(steps)
Ts = np.empty(steps)
Ps = np.empty(steps)
# ==== CALCULATION ====
print "Simulating until tmax=%s..." % (t + tadd)
set_globals(L, N, rcut, shift)
rebuild_neighbor_lists(x, rcut + skin)
xup = x.copy()
f = compute_forces(x, fmax) + force_ld(v)
# calculate or load the data from the time before the current run will start
if os.path.exists(datafilename):
ts_old, Es_old, Epots_old, Ekins_old, Ts_old, Ps_old, traj_old = np.load(datafilename)
else:
a, b, c = compute_energy(x, v)
d = compute_temperature(c)
e = compute_pressure(x, v)
ts_old = np.array([t])
Es_old = np.array([a])
Epots_old = np.array([b])
Ekins_old = np.array([c])
Ts_old = np.array([d])
Ps_old = np.array([e])
traj_old = np.array([x])
# variables to cumulate data
traj = np.empty((steps,3,N))
ts = np.empty(steps)
Es = np.empty(steps)
Epots = np.empty(steps)
Ekins = np.empty(steps)
Ts = np.empty(steps)
Ps = np.empty(steps)
# ==== CALCULATION ====
print "Simulating until tmax=%s..." % (t + tadd)
set_globals(L, N, rcut, shift)
rebuild_neighbor_lists(x, rcut+skin)
xup = x.copy()
f = compute_forces(x,fmax)
# calculate or load the data from the time before the current run will start
if os.path.exists(datafilename):
ts_old, Es_old, Epots_old, Ekins_old, Ts_old, Ps_old, traj_old = np.load(datafilename)
else:
a,b,c = compute_energy(x, v)
d = compute_temperature(c)
e = compute_pressure(x,v)
ts_old = np.array([t])
Es_old = np.array([a])
Epots_old = np.array([b])
Ekins_old = np.array([c])
Ts_old = np.array([d])
Ps_old = np.array([e])
traj_old = np.array([x])
# variables to cumulate data
traj = np.empty((steps, 3, N))
ts = np.empty(steps)
Es = np.empty(steps)
Epots = np.empty(steps)
Ekins = np.empty(steps)
Ts = np.empty(steps)
Ps = np.empty(steps)
# ==== CALCULATION ====
print "Simulating until tmax=%s..." % (t + tadd)
set_globals(L, N, rcut, shift)
rebuild_neighbor_lists(x, rcut + skin)
xup = x.copy()
f = compute_forces(x, fmax) + force_ld(v)
# calculate or load the data from the time before the current run will start
if os.path.exists(datafilename):
ts_old, Es_old, Epots_old, Ekins_old, Ts_old, Ps_old, traj_old = np.load(
datafilename)
else:
a, b, c = compute_energy(x, v)
d = compute_temperature(c)
e = compute_pressure(x, v)
ts_old = np.array([t])
Es_old = np.array([a])
Epots_old = np.array([b])
Ekins_old = np.array([c])
Ts_old = np.array([d])
Ps_old = np.array([e])