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 = []