if vec_sepm <= rcutoff:
pe_mod = Particle3D.Lj_pot(particles[j], vec_sepm)
f_mod = Particle3D.Lj_force(particles[j], vec_sep,
vec_sepm)
force = force + f_mod
pe = pe + pe_mod
#position update using the velocity verlet algorithim is done
p1 = j + 1
particles[j].leapPos2nd(dt, force)
particles[j].position = Particle3D.PBC(particles[j], boxSize)
#As the particle position is calcualted the mean square displacement is calculated and put into a array to be plotted, data calcualted every 100 timesteps
if i % 100 == 0:
bb = 0
for aa in range(len(particles)):
seppy = Particle3D.MsD(particles[aa], particles1[bb])
sum_seppy = seppy + seppy
bb = bb + 1
#data is written and outputted for the vmd program and is formated and outputted
outfile1_0.write(
str(p1) + " " + str(particles[j].position[0]) + " " +
str(particles[j].position[1]) + " " +
str(particles[j].position[2]) + "\n")
if i % 100 == 0:
MsD = (1 / nAt) * sum_seppy
tvalue.append(gg)
gg = gg + 1
MSSD.append(MsD)
#count = copy.deepcopy(RDF(particles,n,maxr,dr,count,rho))
#print count
p1 = j+1
particles[j].leapPos2nd(dt,force)
particles[j].position = Particle3D.PBC(particles[j],boxSize)
#As the particle position is calcualted the mean square displacement is calculated and put into a array to be plotted, data calcualted every 100 timesteps
if i%20 == 0:
#data is written and outputted for the vmd program and is formated and outputted
outfile1_0.write(str(p1) + " " + str(particles[j].position[0]) + " " + str(particles[j].position[1]) + " " + str(particles[j].position[2]) + "\n")
for r in range(len(particles)):
if r != 0:
dist = Particle3D.vec_sep(particles[0],particles[r],boxSize)
vec_sepr = np.linalg.norm(dist)
rdf.append(vec_sepr)
if i%20 == 0:
for aa in range(len(particles)):
seppy = Particle3D.MsD(particles[aa],particles1[aa],boxSize)
sum_seppy = seppy + seppy
MsD = (1/nAt)*sum_seppy
tValueM.append(gg*20)
tValue.append(gg*20)
gg = gg + 1
MSSD.append(MsD)
if i%100 == 0:
print(str((i/10000.0)*100.0)+ '%' )
#count = copy.deepcopy(RDF(particles,n,maxr,dr,count,rho))
#print count