energy_all = np.zeros((nsteps,3)) # store energy
pos_par_0 = np.zeros((nsteps,3)) # the postions of particle 0
veloc_t0 = np.zeros((num_atoms,3)) #init velocity for all the particles
veloc_t = np.zeros((num_atoms,3)) # store vel. for particles at t
vv_a = np.zeros(nsteps) # store velocity products at tj steps
Inst_T_all = np.zeros(nsteps) # store instananeous time
seed = 3 # change seed to initial velocity
r_num = 50 # the pieces of g(r) is cut into
maxk = 5 #max value of k vector component
firstcutoff = 50 # the start of equillibrium
g_r_ave = np.zeros(r_num)
s_r_ave = np.zeros(num_k_mag(maxk,3))
vv_0 = np.zeros(num_atoms)
# create and initialize a set of particles
pset = ParticleSet(num_atoms,mass)
#pset._alloc_pos_vel_accel()
pset.init_pos_cubic(box_length)
pset.init_vel(temperature,seed)
# molecular dynamics simulation loop
for istep in range(nsteps):
# calculate properties of the particles
Ene_all = compute_energy(pset,box_length)
print(istep, Ene_all[0],Ene_all[1],Ene_all[2])
#record the initial velocity and vv_0 for all the particles
if istep == 0:
veloc_t0 = pset.all_vel()
return (tot_kinetic, tot_potential, tot_energy)
# end def compute_energy
if __name__ == '__main__':
num_atoms = 64
mass = 48.0
temperature = 0.728
box_length = 4.2323167
nsteps = 10
dt = 0.01
# create and initialize a set of particles
pset = ParticleSet(num_atoms, mass)
pset.init_pos_cubic(box_length)
pset.init_vel(temperature)
# molecular dynamics simulation loop
for istep in range(nsteps):
# calculate properties of the particles
print(istep, compute_energy(pset, box_length))
# update positions
for iat in range(num_atoms):
my_next_pos = verlet_next_pos(pset.pos(iat), pset.vel(iat),
pset.accel(iat), dt)
new_pos = pos_in_box(my_next_pos, box_length)
pset.change_pos(iat, new_pos)
veloc_t0 = np.zeros((num_atoms,3)) #init velocity for all the particles
veloc_t = np.zeros((num_atoms,3)) # store vel. for particles at t
#vv_a = np.zeros(nsteps) # store velocity products at tj steps
#Inst_T_all = np.zeros(nsteps) # store instananeous time
seed = 3 # change seed to initial velocity
r_num = 50 # the pieces of g(r) is cut into
maxk = 5 #max value of k vector component
firstcutoff = 1000 # the start of equillibrium
g_r_sum = np.zeros(r_num)
s_r_sum = np.zeros(num_k_mag(maxk,3))
sigma = 0.04 # the std dev for position update
beta = 1.0/temperature
poten = [] #store pot. after equillibrium
# create and initialize a set of particles
pset = ParticleSet(num_atoms,mass)
#pset._alloc_pos_vel_accel()
pset.init_pos_cubic(box_length)
pset.init_vel(temperature,seed)
# Monte Carlo simulation main loop
for istep in range(nsteps):
old_pot = compute_potential(pset,box_length)
pot_all[istep] = old_pot
print('*'*60)
print(istep,pot_all[istep])
# update positions
for iat in range(num_atoms):
return (tot_kinetic, tot_potential, tot_energy)
# end def compute_energy
if __name__ == '__main__':
num_atoms = 64
mass = 48.0
temperature = 0.728
box_length = 4.2323167
nsteps = 1000
dt = 0.01
# create and initialize a set of particles
pset = ParticleSet(num_atoms, mass)
pset.init_pos_cubic(box_length)
pset.init_vel(temperature)
# molecular dynamics simulation loop
for istep in range(nsteps):
# update accelerations/forces
for iat in range(num_atoms):
iaccel = internal_force(iat, pset, box_length)
for idim in range(pset.ndim()):
iaccel[idim] /= mass
pset.change_accel(iat, iaccel)
# end for iat
# calculate properties of the particles
if __name__ == '__main__':
num_atoms = 64
mass = 48.0
temperature = 0.728
box_length = 4.2323167
nsteps = 1000 # total step for simulation
energy_all = np.zeros((nsteps, 3)) # used to store energy
pos_par_0 = np.zeros(
(nsteps, 3)) # used to store the postions of particle 0
dt = 0.01 #time step
seed = 20 # change seed to initial velocity
# create and initialize a set of particles
pset = ParticleSet(num_atoms, mass)
pset._alloc_pos_vel_accel()
pset.init_pos_cubic(box_length)
pset.init_vel(temperature, seed)
# molecular dynamics simulation loop
for istep in range(nsteps):
# calculate properties of the particles
Ene_all = compute_energy(pset, box_length)
print(istep, Ene_all[0], Ene_all[1], Ene_all[2])
energy_all[istep][0] = Ene_all[0]
energy_all[istep][1] = Ene_all[1]
energy_all[istep][2] = Ene_all[2]
# update positions
for iat in range(num_atoms):