def simulation(n_atoms, n_steps, rho, T_want, eps, dt):
dist = []
t_together = 0.0
t_apart = 0.0
N_a = 2 * n_atoms
R, V, F, box_width = md.initialize_particles(n_atoms, T_want, rho, eps)
KinE = []
PotE = []
TotE = []
Temp = []
for i in range(n_steps):
Rnew = R + V*dt + 0.5*dt**2*F
if i%1000 ==0:
video.add_frame(R[0],R[1], i)
if i%100000 == 0:
print i
energy_potential, Fnew = md.lennard_jones(Rnew, box_width, eps)
V = scale_temp(V, T_want, N_a)
ke = (1.0/2.0) * np.sum(V*V)
d = dister(0,1,R, box_width)
dist.append(d)
if d < 1.52:
t_together += 1.0
if d > 1.52:
t_apart += 1.0
KinE.append(ke)
PotE.append(energy_potential)
TotE.append(ke + energy_potential)
Temp.append(2 * ke / (N_a))
Vnew = V + 0.5*dt*(F + Fnew)
V = Vnew.copy()
R = Rnew.copy()
video.save("colorparticle", periodic_boundary=True)
return PotE, KinE, TotE, Temp, dist, t_together/t_apart
if abs(positions_x[i]) > box_width:
velocities_x[i] = -velocities_x[i]
positions_x[i] = positions_x[i] + velocities_x[i]*dt
if abs(positions_y[i]) > box_width:
velocities_y[i] = -velocities_y[i]
positions_y[i] = positions_y[i] + velocities_y[i]*dt
# save a 'frame' for the video every 10 step
if n % 10 == 0:
video.add_frame(positions_x, positions_y)
if n % 100 == 0:
print 'step', n
# Plot the x- and y- coordinates
plt.clf() # clear figure
plt.plot(positions_x, positions_y, 'ro')
plt.axis((-box_width, box_width, -box_width, box_width))
plt.savefig("coordinates_end.png")
plt.clf()
# Save video
video.save('video1')
plt.savefig('start.png')
## Create file for saving energy
f = open('simulation_energy', 'w')
## Take simulation steps
for n in range(n_steps):
X, Y, Vx, Vy, Fx, Fy, energy = velo_verlet(X, Y, Vx, Vy, Fx, Fy, box_width, n_particles, dt)
if n % 5 == 0:
# calculate kinetic energy
energy_kinetic = kinetic(Vx, Vy)
line = str(n) + "," + str(energy) + ',' + str(energy_kinetic)
f.write(line)
f.write('\n')
if n % 30 == 0:
video.add_frame(X, Y)
if n % 100 == 0:
print "step", n, "of", n_steps
# Save video
video.save("video3", box_width)
def simulation(n_atoms, n_steps, rho, temperature, dt,
eps = [],
save_freq=60,
video_filename='',
constant_temperature=False):
n_eq = 200*save_freq
if video_filename != '':
save_video = True
if len(eps) == 0:
eps = np.ones((n_atoms, n_atoms))
else:
# set particle 1 and 2 to other color
colors = ['#4daf4a' for _ in range(n_atoms)]
colors[0] = "#377eb8"
colors[1] = "#377eb8"
video.add_color(colors)
# Initialize simulation
R, V, F, box_width = md.initialize_particles(n_atoms, temperature, rho, eps)
print 'Initialized'
# # Calculate the tail correction
# p_tail = 16.0/3.0 * np.pi * rho * (2.0/3.0 * (2.5**-9) - (2.5**-3))
# Storage arrays
ek_list = [] # Kinetic energy
ep_list = [] # Potential energy
et_list = [] # Total energy
# pr_list = [] # Pressure
te_list = [] # Temperature
r_list = [] # distance list
# Run simulation for n_steps
for n in range(n_steps + 1):
# Step 1: Calculate new positions
R += V*dt + 0.5*F*dt*dt
# Step 2: Calculate new forces
F0 = copy.copy(F)
potential_energy, F = md.lennard_jones(R, box_width, eps)
# Step 3: Calculate new velocities
V += 0.5*(F + F0)*dt
# if temperture is set to constant, then scale the velocities
if constant_temperature:
V = md.scale_temp(V, temperature)
# for every save_freq steps
if n % save_freq == 0 and n > n_eq:
print "step:", n
# Calculate properties
kinetic_energy = calc_kinetic(V)
total_energy = kinetic_energy + potential_energy
temperature = calc_temperature(V)
# pressure = rho*temperature + 1.0/(3.0*box_width**3)*vir + p_tail
ek_list.append(kinetic_energy)
ep_list.append(potential_energy)
et_list.append(total_energy)
# pr_list.append(pressure)
te_list.append(temperature)
# calculate the distance between 0 and 1
X = R[0, 0] - R[0, 1]
Y = R[1, 0] - R[1, 1]
# Periodic boundary condition
X -= box_width * np.rint(X/box_width)
Y -= box_width * np.rint(Y/box_width)
d = np.sqrt(X**2 + Y**2)
r_list.append(d)
# Add frame to video
if save_video:
video.add_frame(R[0], R[1])
# Remember not to save a video for large n_steps
if save_video:
video.save(video_filename, box_width, periodic_boundary=True)
return ek_list, ep_list, et_list, te_list, r_list
def simulation(n_atoms, n_steps, rho, temperature, dt,
eps = [],
save_freq=60,
video_filename='',
constant_temperature=False):
n_eq = 200*save_freq
if video_filename != '':
save_video = True
if len(eps) == 0:
eps = np.ones((n_atoms, n_atoms))
else:
# set particle 1 and 2 to other color
colors = ['#4daf4a' for _ in range(n_atoms)]
colors[0] = "#377eb8"
colors[1] = "#377eb8"
video.add_color(colors)
# Initialize simulation
R, V, F, box_width = md.initialize_particles(n_atoms, temperature, rho, eps)
print 'Initialized'
# # Calculate the tail correction
# p_tail = 16.0/3.0 * np.pi * rho * (2.0/3.0 * (2.5**-9) - (2.5**-3))
# Storage arrays
ek_list = [] # Kinetic energy
ep_list = [] # Potential energy
et_list = [] # Total energy
# pr_list = [] # Pressure
te_list = [] # Temperature
r_list = [] # distance list
# Run simulation for n_steps
for n in range(n_steps + 1):
# Step 1: Calculate new positions
R += V*dt + 0.5*F*dt*dt
# Step 2: Calculate new forces
F0 = copy.copy(F)
potential_energy, F = md.lennard_jones(R, box_width, eps)
# Step 3: Calculate new velocities
V += 0.5*(F + F0)*dt
# if temperture is set to constant, then scale the velocities
if constant_temperature:
V = md.scaletemp(V, temperature)
# for every save_freq steps
if n % save_freq == 0 and n > n_eq:
print "step:", n
# Calculate properties
kinetic_energy = calc_kinetic(V)
total_energy = kinetic_energy + potential_energy
temperature = calc_temperature(V)
# pressure = rho*temperature + 1.0/(3.0*box_width**3)*vir + p_tail
ek_list.append(kinetic_energy)
ep_list.append(potential_energy)
et_list.append(total_energy)
# pr_list.append(pressure)
te_list.append(temperature)
# calculate the distance between 0 and 1
X = R[0, 0] - R[0, 1]
Y = R[1, 0] - R[1, 1]
# Periodic boundary condition
X -= box_width * np.rint(X/box_width)
Y -= box_width * np.rint(Y/box_width)
d = np.sqrt(X**2 + Y**2)
r_list.append(d)
# Add frame to video
if save_video:
video.add_frame(R[0], R[1])
# Remember not to save a video for large n_steps
if save_video:
video.save(video_filename, box_width, periodic_boundary=True)
return ek_list, ep_list, et_list, te_list, r_list
if n % 200 == 0:
print "Step {0:6d}".format(n)
# Save frame for video every 10th step
if n % 10 == 0:
video.add_frame(X, Y)
# Count the particles in the right part of the box
if n % 5 == 0:
no_part = 0
for i in range(n_particles):
# No need to check for x_positions > 10 or y_positions since we are ALWAYS
# within the box.
if X[i] > 0.0:
no_part += 1
partdist.append(
no_part) # Save number of particles in right half of box
if n > n_step / 2.0: # Only save number of particles for the last half of the simulation
partdisteq.append(no_part)
write_list('test_list', partdist)
write_list('test_list_eq', partdisteq)
# plot particles in the end of the simulation
# plot_particles(X, Y, 'coordinates_end.png')
video.save('video2')
# Count the particles in the right part of the box
if n % 5 == 0:
no_part = 0
for i in range(n_particles):
# No need to check for x_positions > 10 or y_positions since we are ALWAYS
# within the box.
if X[i] > 0.0:
no_part += 1
partdist.append(no_part) # Save number of particles in right half of box
if n > n_step / 2.0: # Only save number of particles for the last half of the simulation
partdisteq.append(no_part)
write_list('test_list', partdist)
write_list('test_list_eq', partdisteq)
# plot particles in the end of the simulation
# plot_particles(X, Y, 'coordinates_end.png')
video.save('video2')
