def _initialize_velocities(self):
vrand_1 = BoxMueller(SEED_2)
vrand_2 = BoxMueller(SEED_3)
for particle in self.particles:
tmp = vrand_1.generate()
particle.set_velocity(tmp[0], tmp[1], vrand_2.generate()[0])
def __init__(self, filename="LJ_108_1.txt", metal="gold"):
self.system_potential_energy, self.system_kinetic_energy, self.system_total_energy, self.current_temperature = (
0.0,
0.0,
0.0,
0.0,
)
self.time, self.system_average_energy_per_particle = 0.0, 0.0
self.particles = []
self.normal_dist = BoxMueller(SEED)
self.N = 108
self.tau = 0.001 # Bussi thermostat variable
if metal == "silver":
self.target_temp = SILVER_TEMP
self.density = SILVER_DENSITY
self.n = SILVER_N
self.m = SILVER_M
self.c = SILVER_C
else:
self.target_temp = GOLD_TEMP
self.density = GOLD_DENSITY
self.n = GOLD_N
self.m = GOLD_M
self.c = GOLD_C
# actually half of the box's boundary
self.cube_boundary = ((self.N / self.density) ** (1.0 / 3.0)) / 2.0
# initialize particles, positions, and velocities
r_file = open(filename, "r")
r_line = r_file.readline()
temp_sqrt = sqrt(self.target_temp)
while r_line != "":
r = map(float, r_line.strip().replace(",", " ").split())
tmp = Particle(r[0], r[1], r[2], self.cube_boundary)
tmp.add_velocity(
temp_sqrt * self.normal_dist.generate()[0],
temp_sqrt * self.normal_dist.generate()[0],
temp_sqrt * self.normal_dist.generate()[0],
)
self.particles.append(tmp)
r_line = r_file.readline()
r_file.close()
# initialize rho and forces
self.update_forces_and_energies()
self.update_observables()
# for finding best global minimum energy and associated configuration
self.best_config = []
for p in self.particles:
self.best_config.append(p.position())
self.best_potential_energy = self.system_potential_energy
self.best_total_energy = 0.0
def __init__(self, filename="LJ_108_1.txt", metal="gold"):
self.system_potential_energy, self.system_kinetic_energy, self.system_total_energy, self.current_temperature = 0.0, 0.0, 0.0, 0.0
self.time, self.system_average_energy_per_particle = 0.0, 0.0
self.particles = []
self.normal_dist = BoxMueller(SEED)
self.N = 108
self.tau = 0.001 # Bussi thermostat variable
if metal == "silver":
self.target_temp = SILVER_TEMP
self.density = SILVER_DENSITY
self.n = SILVER_N
self.m = SILVER_M
self.c = SILVER_C
else:
self.target_temp = GOLD_TEMP
self.density = GOLD_DENSITY
self.n = GOLD_N
self.m = GOLD_M
self.c = GOLD_C
# initialize particles, positions, and velocities
r_file = open(filename, 'r')
r_line = r_file.readline()
temp_sqrt = sqrt(self.target_temp)
while r_line != '':
r = map(float, r_line.strip().replace(',', ' ').split())
tmp = Particle(r[0], r[1], r[2])
tmp.add_velocity(temp_sqrt*self.normal_dist.generate()[0], temp_sqrt*self.normal_dist.generate()[0], temp_sqrt*self.normal_dist.generate()[0])
self.particles.append(tmp)
r_line = r_file.readline()
r_file.close()
# initialize rho and forces
self.update_forces_and_energies()
self.update_observables()
class SCCluster:
def __init__(self, filename="LJ_108_1.txt", metal="gold"):
self.system_potential_energy, self.system_kinetic_energy, self.system_total_energy, self.current_temperature = 0.0, 0.0, 0.0, 0.0
self.time, self.system_average_energy_per_particle = 0.0, 0.0
self.particles = []
self.normal_dist = BoxMueller(SEED)
self.N = 108
self.tau = 0.001 # Bussi thermostat variable
if metal == "silver":
self.target_temp = SILVER_TEMP
self.density = SILVER_DENSITY
self.n = SILVER_N
self.m = SILVER_M
self.c = SILVER_C
else:
self.target_temp = GOLD_TEMP
self.density = GOLD_DENSITY
self.n = GOLD_N
self.m = GOLD_M
self.c = GOLD_C
# initialize particles, positions, and velocities
r_file = open(filename, 'r')
r_line = r_file.readline()
temp_sqrt = sqrt(self.target_temp)
while r_line != '':
r = map(float, r_line.strip().replace(',', ' ').split())
tmp = Particle(r[0], r[1], r[2])
tmp.add_velocity(temp_sqrt*self.normal_dist.generate()[0], temp_sqrt*self.normal_dist.generate()[0], temp_sqrt*self.normal_dist.generate()[0])
self.particles.append(tmp)
r_line = r_file.readline()
r_file.close()
# initialize rho and forces
self.update_forces_and_energies()
self.update_observables()
def update_observables(self):
self.update_system_kinetic_energy()
self.current_temperature = (2 * self.system_kinetic_energy) / (3*self.N - 3)
self.system_total_energy = self.system_potential_energy + self.system_kinetic_energy
self.average_energy_per_particle = self.system_total_energy / len(self.particles)
def calculate_rho_for_particle(self, i):
rho = 0.0;
for j in range(self.N):
if j != i:
dx, dy, dz = self.particles[j].x-self.particles[i].x, self.particles[j].y-self.particles[i].y, self.particles[j].z-self.particles[i].z
rho += (1 / sqrt((dx**2.0)+(dy**2.0)+(dz**2.0))) ** self.m;
return rho;
def Bussi_Thermostat(self):
cc = exp(-DT/self.tau)
d = (1-cc)*(self.target_temp/self.current_temperature)/(self.N+1)
r = self.normal_dist.generate()[0]
s = 0
for i in range(self.N-1):
si = self.normal_dist.generate()[0]
s += si**2
scale = sqrt( cc+(s+r*r)*d + 2.0*r*sqrt(cc*d) )
if r + sqrt(cc/d) < 0.0:
scale = -scale
# rescale velocities
for particle in self.particles:
particle.vx *= scale
particle.vy *= scale
particle.vz *= scale
def update_system_kinetic_energy(self):
self.system_kinetic_energy = 0.0
for first in self.particles:
self.system_kinetic_energy += (first.m*(first.vx**2.0)) + (first.m*(first.vy**2.0)) + (first.m*(first.vz**2.0))
self.system_kinetic_energy /= 2.0
def update_forces_and_energies(self):
self.system_potential_energy = 0.0
# Clear forces from previous calculations
# Use the same loop to calculate rho's for each and all particles
for i in range(self.N):
self.particles[i].fx, self.particles[i].fy, self.particles[i].fz = 0.0, 0.0, 0.0
self.particles[i].rho = self.calculate_rho_for_particle(i)
# calculate forces and energies
for i in range(self.N):
for j in range(self.N):
if j != i:
dx, dy, dz = self.particles[j].x-self.particles[i].x, self.particles[j].y-self.particles[i].y, self.particles[j].z-self.particles[i].z
r2 = (dx**2.0)+(dy**2.0)+(dz**2.0)
# Do calculation
r_i = 1 / sqrt(r2)
self.system_potential_energy += r_i**self.n
tmp_f = ( self.n*(r_i**self.n) - (self.c/2.0)*self.m*(self.particles[i].rho**-0.5 + self.particles[j].rho**-0.5)*(r_i**self.m) ) / r2
self.particles[i].fx += dx * tmp_f
self.particles[i].fy += dy * tmp_f
self.particles[i].fz += dz * tmp_f
#self.system_potential_energy /= 2
#self.system_potential_energy -= self.c * sqrt(self.particles[i].rho)
'''
def calculate_diffusitivity(self):
diffusitivity = 0.0
for i in range(self.N):
dx = self.particles[i].x - self.particles[i].x0
dy = self.particles[i].y - self.particles[i].y0
dz = self.particles[i].z - self.particles[i].z0
diffusitivity += dx**2 + dy**2 + dz**2
#(dx, dy, dz) = self.mirror_convention(self.particles[j].x-self.particles[i].x, self.particles[j].y-self.particles[i].y, self.particles[j].z-self.particles[i].z)
# average it and divide by 6*deltaT*step (also 6*total_time)
diffusitivity /= (6*self.N*self.time)
return diffusitivity
'''
def MD_step(self):
self.time += DT
for first in self.particles:
# second terms of Taylor expansion, for less computing in next 2 steps
sx = first.fx/(2.0*first.m)
sy = first.fy/(2.0*first.m)
sz = first.fz/(2.0*first.m)
# update position
dx = (first.vx*DT) + (sx*DTT)
dy = (first.vy*DT) + (sy*DTT)
dz = (first.vz*DT) + (sz*DTT)
first.add_position(dx, dy, dz)
# update velocity at half step with current forces
dvx = sx*DT
dvy = sy*DT
dvz = sz*DT
first.add_velocity(dvx, dvy, dvz)
self.update_forces_and_energies()
# update velocity at second half step with new forces
for first in self.particles:
dvx = (first.fx*DT)/(2*first.m)
dvy = (first.fy*DT)/(2*first.m)
dvz = (first.fz*DT)/(2*first.m)
first.add_velocity(dvx, dvy, dvz)
#self.update_observables()
self.Bussi_Thermostat()
