# Call function to read initial positions
num, pos, types = md.readXYZ(infile, nondim) #non dimensional lj units
del infile #clean up variables
# Call function to initialize velocities (trivial here)
vels = md.vInit(pos, dist, val, nondim) #get initial velocites
# Call function to initialize forces
fij, vij, vTot = md.fLJ(pos, num, nondim, elem)
###############################################################
md.tic()
print('\nRunning MD simulation!\n')
for k in range(steps): #run the MD simulation
if (k + 1) % 1000 == 0:
print('\n\tNow on step:\t' + str(k + 1) + ' out of ' + str(steps))
pos, vels, fij, vTot = md.vVerlet(num, pos, vels, fij, dt, nondim, elem)
try:
dump
except NameError:
dump = 'no'
if type(dump) == int and (k + 1) % dump == 0:
md.dump(k, dump, num, pos, types)
try:
thermo
except NameError:
thermo = 'no'
if type(thermo) == int and (k + 1) % thermo == 0:
md.thermo(k, thermo, vels, vTot, nondim, elem)
num, pos, types = md.readXYZ(infile) #non dimensional lj units
del infile #clean up variables
# Call function to initialize velocities (trivial here)
vels = md.vInit(pos, dist, val) #get initial velocites
# Call function to initialize forces
fij, vij, vTot = md.fLJ(pos, num)
###############################################################
md.tic()
print('\nRunning MD simulation!\n')
for k in range(steps): #run the MD simulation
if (k + 1) % 500 == 0:
print('\tNow on step:\t' + str(k + 1) + ' out of ' + str(steps))
pos, vels, fij, vTot = md.vVerlet(num, pos, vels, fij, dt)
try:
dump
except NameError:
dump = 'no'
if type(dump) == int and (k + 1) % dump == 0:
md.dump(k, dump, num, pos, types)
try:
thermo
except NameError:
thermo = 'no'
if type(thermo) == int and (k + 1) % thermo == 0:
md.thermo(k, thermo, vels, vTot)