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Step1.py
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Tue, Dec 3, 03:18

Step1.py
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import matplotlib.pyplot as plt
from MD import *
import sys
# Step 1.1
# Create a crystalline fcc structure
#############################################################
Ncells = 6 # Number of unit cells along each axis
lat_par = 1.7048 # Lattice parameter
L = lat_par*Ncells # Size of the simulation box
N = 4*Ncells**3 # Number of atoms in the simulation box
# Generate fcc structure
pos, vel = crystal(Ncells, lat_par)
# Write positions and velocities into a file
dump_pos_vel('sample10.dat', pos, vel, N, L)
# Step 1.2
# Run a test simulation
#############################################################
nsteps = 200 # Number of steps
dt = 0.003 # Integration step
# Read crystal shape, positions and velocities from a file
N, L, pos, vel = read_pos_vel('sample10.dat')
# Perform simulation and collect the output into a dictionary
output = run_NVE(pos, vel, L, nsteps, N, dt)
# Write positions and velocities into a file
dump_pos_vel('sample11.dat', output['pos'], output['vel'], N, L)
# Step 1.3
# Compute velocities
#############################################################
nsteps = 200
dt = 0.0046
# Perform simulation starting from the output of a previous run
output = run_NVE(output['pos'], output['vel'], L, nsteps, N, dt)
# Step 1.4
# Change T
#############################################################
nsteps = 200
dt = 0.0046
T = 0.7867 # requested temperature
# Change T
output = run_NVE(output['pos'], output['vel'], L, nsteps, N, dt, T)
# Track energy
NVT_Energy = output['EnKin'] + output['EnPot']
NVT_steps = output['nsteps']
# Plot temperature vs step
plt.figure()
plt.plot(output['nsteps'],output['EnKin']*2/3)
plt.ylabel(r'$T$ [L.J.]')
plt.xlabel(r'$t$')
#plt.show()
# Equilibrate
#############################################################
nsteps = 800
dt = 0.0046
# Equilibrate
output = run_NVE(output['pos'], output['vel'], L, nsteps, N, dt)
# Write positions and velocities into a file
dump_pos_vel('sampleT94.4.dat', output['pos'], output['vel'], N, L)
# Plot total energy vs step
plt.figure()
plt.plot(output['nsteps'],output['EnKin']+output['EnPot'], label= 'Equilibrate')
plt.plot(NVT_steps, NVT_Energy, label='Fixed temperature')
plt.ylabel('Total energy [L.J.]')
plt.xlabel(r'$t$')
plt.legend()
plt.show()

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