for j, i in zip(a, c):
b.write(
str(j.symbol) + ' ' + str(i[0]) + ' ' + str(i[1]) + ' ' +
str(i[2]) + '\n')
dyn.attach(printenergy, interval=50)
#dyn.attach(MDLogger(dyn, bz, 'bz_md_NVT_10ps_1fs.log', header=True, stress=False,
# peratom=False, mode="w"), interval=50)
#traj = Trajectory('killerapp.traj', 'w', atoms=bz)
#dyn.attach(traj.write, interval=100)
printenergy()
dyn.set_temperature(300.0 * units.kB)
start_time2 = time.time()
dyn.run(20000) # Do 5ps of MD
end_time2 = time.time()
print('Post-heat Total Time:', end_time2 - start_time2)
#dyn = LBFGS(bz)
#dyn.run(fmax=0.0001)
#dyn = BFGS(bz)
#dyn.run(fmax=0.1)
#print('[ANI Total time:', time.time() - start_time, 'seconds]')
# Write visualization of molecule
#f = open("optmol_final.xyz",'w')
#f.write('\n' + str(len(bz)) + '\n')
#for i in bz:
#print('Step %i - Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
# 'Etot = %.3feV' % (d.get_number_of_steps(),epot, ekin, ekin / (1.5 * units.kB), epot + ekin))
t.write(
str(d.get_number_of_steps()) + ' ' + str(d.get_time()) + ' ' +
str(ekin / (1.5 * units.kB)) + ' ' + str(epot) + ' ' + str(ekin) +
' ' + str(epot + ekin) + '\n')
b.write('\n' + str(len(a)) + '\n')
c = a.get_positions(wrap=True)
for j, i in zip(a, c):
b.write(
str(j.symbol) + ' ' + str(i[0]) + ' ' + str(i[1]) + ' ' +
str(i[2]) + '\n')
dyn.attach(printenergy, interval=50)
dyn.set_temperature(T * units.kB)
start_time2 = time.time()
# get the chemical symbols
spc = mol.get_chemical_symbols()
#xo = open(stdir + 'data/md-peptide-cvnms.xyz', 'w')
f = open(stdir + 'md-peptide-cv.dat', 'w')
l_sigma = []
for i in range(10000):
dyn.run(100) # Do 100 steps of MD
xyz = np.array(mol.get_positions(), dtype=np.float32).reshape(len(spc), 3)
energies = np.zeros((5), dtype=np.float64)
forces = []