MD module needs to be updated

[ark245]

KT does not run MD yet.

if mode == 'md':
		md(atoms)

def md(atoms,dir_name='md',**kwargs):
	total_zeolite_atoms = analyze_zeolite_structure(atoms)
	atoms = assign_calculator(atoms,my_encut=300) # Using ASE calculator
	atoms = initialize_magmoms(atoms,total_zeolite_atoms)
	atoms.calc.set(ibrion=0,potim=0.5,tebeg=298, nsw=100000, isif=2, smass=0, **kwargs)
	cwd = os.getcwd()
	encut_for_dir = atoms.calc.float_params['encut']
	directory = dir_name + '_' + str(encut_for_dir)
	if not os.path.exists(directory):
		os.makedirs(directory)
	os.chdir(directory)
	energy = atoms.get_potential_energy() # Run vasp here
	#change back
	os.chdir(cwd)
	return(atoms)