os.system('grep PotEng log.lammps | awk {\'print $3\'} > PotEng.md')
energies = sp.loadtxt('PotEng.md')
energies *= units.kcal / units.mol
# write kinetic energies to file
os.system('grep KinEng log.lammps | awk {\'print $6\'} > KinEng.md')
kinengs = sp.loadtxt('KinEng.md')
kinengs *= units.kcal / units.mol
# now extract CVs from positions
colvars = []
print("Converting positions into collective variables...")
for positions in data:
atoms = Atoms(['H']*n_atoms, positions)
colvars.append(atoms.colvars().flatten())
colvars = sp.asarray(colvars)
phipsi_pot = sp.hstack((colvars,energies[:,None], kinengs[:,None]))
print("Saving data...")
sp.savetxt('phi_psi_pot_md300.csv', phipsi_potkin)
else:
data = sp.loadtxt('phi_psi_pot_md300.csv')
colvars = data[:,:2]
energies = data[:,2]
kinengs = data[:,3]
colvars_r = round_vector(colvars)
energies_r = {}
kinengs_r = {}
