class PotcarSettings:
def __init__(self, species=None, functionals=None):
if species and functionals:
self._potcar = Potcar(species, functionals)
self._species = species
self._functionals = functionals
else:
self._potcar = None
self._species = None
self._functionals = None
self._file_path = None
def from_file(self, file_path):
#add exception handeling
self._file_path = file_path
self._potcar = Potcar().from_file(file_path)
self._species = self._potcar.symbols
self._functionals = self._potcar.FUNCTIONAL_CHOICES
def write_file(self, path):
if self._potcar:
self._potcar.write_file(path)
else:
pass
def update_pot_by_symbols(InputSet, write_file=True):
"""
Update POTCAR by symbols considering the MAGMOM difference
Parameter
---------
InputSet: VaspInputSet
The input set defined by pymatgen, e.g. MPRelaxSet
write_file: bool
Write POSCAR (True) or not (False)
Return
------
potcar: Potcar (in pymatgen)
The Potcar type defined in pymatgen
"""
symbol, natom = check_symbol(InputSet)
potcar_symbols = []
settings = InputSet._config_dict["POTCAR"]
if isinstance(settings[symbol[-1]], dict):
for el in symbol:
potcar_symbols.append(settings[el]["symbol"] if el in
settings else el)
else:
for el in symbol:
potcar_symbols.append(settings.get(el, el))
potcar = Potcar(symbols=potcar_symbols,
functional=InputSet.potcar_functional)
if write_file:
potcar.write_file(filename="POTCAR")
return potcar
def generate_files(args):
from pymatgen.io.vasp.inputs import Potcar
if args.symbols:
try:
p = Potcar(args.symbols, functional=args.functional)
p.write_file("POTCAR")
except Exception as ex:
print("An error has occurred: {}".format(str(ex)))
else:
print("No valid options selected.")
def generate_potcar(struct,dirname='.'):
avail_pot =" ".join(Potcar.FUNCTIONAL_CHOICES)
tip="""
Available Pseudo-potentials are:
"""
tip+=avail_pot+'\n'
warn_tip(1,tip)
print('your choice ?')
wait_sep()
in_str=""
while in_str=="":
in_str=input().strip()
assert in_str.upper() in avail_pot
potcar=Potcar([el.value for el in struct.types_of_specie],functional=in_str)
potcar.write_file(os.path.join(dirname, "POTCAR"))
def generate_potcar(struct, dirname='.'):
"""
Generate POTCAR according to input structure via pymatgen's POTCAR module
"""
avail_pot = " ".join(Potcar.FUNCTIONAL_CHOICES)
tip = """
Available Pseudo-potentials are:
"""
tip += avail_pot + '\n'
warn_tip(1, tip)
print('your choice ?')
wait_sep()
in_str = wait()
assert in_str.upper() in avail_pot
potcar = Potcar([el.value for el in struct.types_of_specie],
functional=in_str)
potcar.write_file(os.path.join(dirname, "POTCAR"))
potcar_symbols.sort()
POTCAR = Potcar(potcar_symbols)
f.writelines(['\tPOTCAR_symbols: ',str(potcar_symbols), '\n'])
potcar_symbols.remove('H')
else:
f.writelines('\tLDAUL: %s\t LDAUU: %s\tLDAUJ: %s\n' % (INCAR['LDAUL'], INCAR['LDAUU'], INCAR['LDAUJ']))
POTCAR = Potcar(potcar_symbols)
f.writelines(['\tPOTCAR_symbols: ',str(potcar_symbols), '\n'])
view(slab_sorted)
write_vasp(file_path + '%s/POSCAR' % (adsorbate_names[ads_idx]), slab_sorted) # Put AFM, def in the path if requried
INCAR.write_file(file_path + '%s/INCAR' % (adsorbate_names[ads_idx])) # Put AFM, def in the path if requried
KPOINTS.write_file(file_path + '%s/KPOINTS' % (adsorbate_names[ads_idx])) # Put AFM, def in the path if requried
POTCAR.write_file(file_path + '%s/POTCAR' % (adsorbate_names[ads_idx])) # Put AFM, def in the path if requried
# jobscript copy
for n, line in enumerate(fileinput.FileInput('jobscript_vasp.sh')):
if '#PBS -N' in line:
n_line = n
elif '#PBS -q' in line:
q_line = n
PBS_N = '#PBS -N %03d_%s\n' % (idx + 1.0, adsorbate_names[ads_idx])
replace_line('jobscript_vasp.sh', n_line, PBS_N)
queue = 'normal' # Change queue name if required
PBS_q = '#PBS -q %s\n' % (queue)
replace_line('jobscript_vasp.sh', q_line, PBS_q)
def run_job(mat=None,incar=None,kpoints=None,jobname='',copy_file=[]):
"""
Generic function to run a VASP job, error correction implemented using
custodian package
A jobname+.json file is produced after successful completion of the job
A first_cust.py file is generated which is invoked using python command
Args:
mat: Poscar object with structure information
incar: Incar object with control information
kpoints: Kpoints object with mesh information
jobname: a uniq name for a job-type, say MAIN-ELAST for elastic properties
copy_file: copy file from previous runs, say CHGCAR for Non-SCF bandstructure calculations
Returns:
f_energy: final energy
contcar: path to final relaxed structure
"""
#hostname=str(socket.gethostname())
poscar_list=[(mat)]
cwd=str(os.getcwd())
job_name=str(mat.comment)
job_dir=str(jobname)
run_file = str(os.getcwd())+str('/')+str(jobname)+str('.json')
run_dir = str(os.getcwd())+str('/')+str(jobname)
if mat.comment.startswith('Surf'):
[a,b,c]=kpoints.kpts[0]
kpoints.kpts=[[a,b,1]]
try:
pol=check_polar(mat.structure)
if pol==True:
ase_atoms = AseAtomsAdaptor().get_atoms(mat.structure)
COM=ase_atoms.get_center_of_mass(scaled=True)
print ("COM=",COM)
print ('Found polar surface, will be setting dipole corrections')
incar.update({"LDIPOL": '.TRUE.',"IDIPOL":3,"ISYM": 0,"DIPOL":str(COM[0])+str(" ")+str(COM[2])+str(" ")+str(COM[2])})
print ("Polar surface encountered in run_job",mat.comment)
except:
pass
wait=False
json_file=str(jobname)+str('.json')
print ('json should be here=',str(os.getcwd())+str('/')+str(json_file))
#print ('json should be=',json_file,run_file,os.getcwd())
if os.path.exists(str(os.getcwd())+str('/')+str(json_file)):
try:
data_cal=loadfn(str(os.getcwd())+str('/')+str(json_file),cls=MontyDecoder)
tmp_outcar=str(os.getcwd())+str('/')+str(json_file.split('.json')[0])+str('/OUTCAR')
print ('outcar is',tmp_outcar)
wait=main_outcar(tmp_outcar) #True
print ('outcar status',wait)
if wait==True:
f_energy=data_cal[0]['final_energy']
contcar=str(os.getcwd())+str('/')+str(json_file.split('.json')[0])+str('/CONTCAR')
return f_energy,contcar
except:
pass
while wait==False:
print ("Setting up POTCAR")
with open(pot_yaml, 'r') as f:
doc = yaml.load(f)
pots=doc['POTCAR']
new_symb=[]
for el in mat.site_symbols:
new_symb.append(pots[el])
#potcar = Potcar(symbols=new_symb,functional=functional)
try:
potcar = Potcar(symbols=new_symb,functional=functional)
except:
print ('JARVIS-ERROR: Could not set POTCAR, check POTCAR yaml file and VASP_PSP_DIR')
pass
if not os.path.exists(run_dir):
print ('Starting new job')
os.makedirs(run_dir)
os.chdir(run_dir)
incar.write_file("INCAR")
potcar.write_file("POTCAR")
kpoints.write_file("KPOINTS")
mat.write_file("POSCAR")
for i in copy_file:
print ('copying',i)
shutil.copy2(i,'./')
#f=open('job.out','w')
cmd=str('python first_cust.py >out_dat')+'\n'
cust_file=open("first_cust.py","w")
cline=str('from pymatgen.io.vasp.inputs import Incar, Poscar, VaspInput,Potcar, Kpoints')+'\n'
cust_file.write(cline)
cline=str('import os,shutil')+'\n'
cust_file.write(cline)
cline=str('from custodian.vasp.jobs import VaspJob')+'\n'
cust_file.write(cline)
cline=str('from custodian.vasp.handlers import VaspErrorHandler, UnconvergedErrorHandler,MeshSymmetryErrorHandler, NonConvergingErrorHandler, PotimErrorHandler')+'\n'
cust_file.write(cline)
cline=str('from custodian.vasp.validators import VaspFilesValidator,VasprunXMLValidator')+'\n'
cust_file.write(cline)
cline=str('from custodian.custodian import Custodian')+'\n'
cust_file.write(cline)
cline=str('inc=Incar.from_file("INCAR")')+'\n'
cust_file.write(cline)
cline=str('pot=Potcar.from_file("POTCAR")')+'\n'
cust_file.write(cline)
cline=str('pos=Poscar.from_file("POSCAR")')+'\n'
cust_file.write(cline)
cline=str('kp=Kpoints.from_file("KPOINTS")')+'\n'
cust_file.write(cline)
cline=str("shutil.copy2('")+vdw_dat+str("','./')")+'\n'
cust_file.write(cline)
cline=str('vinput = VaspInput.from_directory(".")')+'\n'
cust_file.write(cline)
cline=str("job=VaspJob(['mpirun', '")+str(main_exe)+str("'], final=False, backup=False)")+'\n'
if mat.comment.startswith('Surf'):
cline=str("job=VaspJob(['mpirun', '")+str(surf_exe)+str("'], final=False, backup=False)")+'\n'
if 'SOC' in jobname:
cline=str("job=VaspJob(['mpirun', '")+str(soc_exe)+str("'], final=False, backup=False)")+'\n'
cust_file.write(cline)
cline=str('handlers = [VaspErrorHandler(), MeshSymmetryErrorHandler(),UnconvergedErrorHandler(), NonConvergingErrorHandler(),PotimErrorHandler()]')+'\n'
cust_file.write(cline)
cline=str('validators = [VasprunXMLValidator()]')+'\n'
#cline=str('validators = [VaspFilesValidator()]')+'\n'
cust_file.write(cline)
cline=str('c = Custodian(handlers, [job],max_errors=5,validators=validators)')+'\n'
cust_file.write(cline)
cline=str('c.run()')+'\n'
cust_file.write(cline)
cust_file.close()
print ("I AM HERE 2")
os.system(cmd)
if os.path.isfile('OUTCAR'):
try:
wait=main_outcar('OUTCAR') #Vasprun("vasprun.xml").converged
except:
pass
print ("End of the first loop",os.getcwd(),wait)
else :
print ('Jobs seens to have started before')
os.chdir(run_dir)
wait=False
if os.path.isfile('OUTCAR'):
try:
wait=main_outcar('OUTCAR') #Vasprun("vasprun.xml").converged
#wait=Vasprun("vasprun.xml").converged
except:
pass
print ("Tried to find OUTCAR, wait is=",wait)
if wait==False:
incar.write_file("INCAR")
kpoints.write_file("KPOINTS")
mat.write_file("POSCAR")
try:
potcar.write_file("POTCAR")
print ('FOUND OLD CONTCAR in', os.getcwd())
old_contcar=Poscar.from_file('CONTCAR')
#old_contcar.write_file('POSCAR')
copy_cmd=str('cp CONTCAR POSCAR')
print ('copy_cmd=',copy_cmd)
if 'ELAST' not in jobname:
#Because in ELASTIC calculations structures are deformed
os.system(copy_cmd)
#time.sleep(3)
except:
pass
for i in copy_file:
print ('copying',i)
shutil.copy2(i,'./')
cmd=str('python first_cust.py >out_dat')+'\n'
cust_file=open("first_cust.py","w")
cline=str('from pymatgen.io.vasp.inputs import Incar, Poscar, VaspInput,Potcar, Kpoints')+'\n'
cust_file.write(cline)
cline=str('import os,shutil')+'\n'
cust_file.write(cline)
cline=str('from custodian.vasp.jobs import VaspJob')+'\n'
cust_file.write(cline)
cline=str('from custodian.vasp.handlers import VaspErrorHandler, UnconvergedErrorHandler,MeshSymmetryErrorHandler, NonConvergingErrorHandler, PotimErrorHandler')+'\n'
cust_file.write(cline)
cline=str('from custodian.vasp.validators import VaspFilesValidator,VasprunXMLValidator')+'\n'
cust_file.write(cline)
cline=str('from custodian.custodian import Custodian')+'\n'
cust_file.write(cline)
cline=str('inc=Incar.from_file("INCAR")')+'\n'
cust_file.write(cline)
cline=str('pot=Potcar.from_file("POTCAR")')+'\n'
cust_file.write(cline)
cline=str('pos=Poscar.from_file("POSCAR")')+'\n'
cust_file.write(cline)
cline=str('kp=Kpoints.from_file("KPOINTS")')+'\n'
cust_file.write(cline)
cline=str("shutil.copy2('")+vdw_dat+str("','./')")+'\n'
cust_file.write(cline)
cline=str('vinput = VaspInput.from_directory(".")')+'\n'
cust_file.write(cline)
cline=str("job=VaspJob(['mpirun', '")+str(main_exe)+str("'], final=False, backup=False)")+'\n'
if mat.comment.startswith('Surf'):
cline=str("job=VaspJob(['mpirun', '")+str(surf_exe)+str("'], final=False, backup=False)")+'\n'
if 'SOC' in jobname:
cline=str("job=VaspJob(['mpirun', '")+str(soc_exe)+str("'], final=False, backup=False)")+'\n'
cust_file.write(cline)
cline=str('handlers = [VaspErrorHandler(), MeshSymmetryErrorHandler(),UnconvergedErrorHandler(), NonConvergingErrorHandler(),PotimErrorHandler()]')+'\n'
cust_file.write(cline)
#cline=str('validators = [VaspFilesValidator()]')+'\n'
cline=str('validators = [VasprunXMLValidator()]')+'\n'
cust_file.write(cline)
cline=str('c = Custodian(handlers, [job],max_errors=5,validators=validators)')+'\n'
cust_file.write(cline)
cline=str('c.run()')+'\n'
cust_file.write(cline)
cust_file.close()
os.system(cmd)
if os.path.isfile('OUTCAR'):
try:
wait=main_outcar('OUTCAR') #Vasprun("vasprun.xml").converged
#wait=Vasprun("vasprun.xml").converged
except:
pass
f_energy='na'
enp='na'
contcar=str(os.getcwd())+str('/')+str('CONTCAR')
final_str=Structure.from_file(contcar)
try:
oszicar = Oszicar("OSZICAR")
f_energy=float(oszicar.final_energy)
enp=float(oszicar.final_energy)/float(final_str.composition.num_atoms)
except:
print ('Error in OSZICAR file during re-run jpb')
pass
natoms=final_str.composition.num_atoms
os.chdir('../')
if wait==True:
data_cal=[]
data_cal.append({'jobname':jobname,'poscar_initial':mat.as_dict(),'poscar_final':final_str.as_dict(),'incar':incar.as_dict(),'kpoints':kpoints.as_dict(),'final_energy':(f_energy),'contcar':final_str.as_dict()})
json_file=str(jobname)+str('.json')
f_json=open(json_file,'w')
f_json.write(json.dumps(data_cal,indent=4,cls=MontyEncoder))
f_json.close()
print ('Wrote json file',contcar)
return f_energy,contcar
INCAR['LDAUL'] = [2, -1]
INCAR['LDAUU'] = [U_dict[TM], 0.0]
INCAR['LDAUJ'] = [0.0, 0.0]
else:
INCAR['LDAU'] = '.FALSE.'
INCAR['LDAUL'] = [-1, -1]
INCAR['LDAUU'] = [0.0, 0.0]
INCAR['LDAUJ'] = [0.0, 0.0]
INCAR.write_file('%02d_%s/INCAR' % (idx + 1.0, formula))
KPOINTS.write_file('%02d_%s/KPOINTS' % (idx + 1.0, formula))
# Potcar setup
POTCAR = Potcar([PP_dict[TM], PP_dict['O']])
POTCAR.write_file('%02d_%s/POTCAR' % (idx + 1.0, formula))
# jobscript copy
for n, line in enumerate(fileinput.FileInput('jobscript_vasp.sh')):
if '#PBS -N' in line:
n_line = n
PBS_N = '#PBS -N %02d_%s_np\n' % (idx + 1.0, formula)
replace_line('jobscript_vasp.sh', n_line, PBS_N)
destination = '%02d_%s/' % (idx + 1.0, formula)
job_file = os.getcwd() + '/jobscript_vasp.sh'
shutil.copy(job_file, destination)
end_time = time.time()
print('Execution time for script (sec) : %5.1f\n' %
(end_time - start_time))
f.writelines([
'\t', 'LDAUL: ',
str(INCAR['LDAUL']), '\t', 'LDAUU: ',
str(INCAR['LDAUU']), '\t', 'LDAUJ: ',
str(INCAR['LDAUJ']), '\n'
])
f.writelines(['\t', 'MAGMOM: ', str(magm), '\n'])
"""
Write files
"""
write_vasp(file_path + 'surface/POSCAR', slab_sorted)
INCAR.write_file(file_path + 'surface/INCAR')
KPOINTS.write_file(file_path + 'surface/KPOINTS')
POTCAR.write_file(file_path + 'surface/POTCAR')
# jobscript copy
for n, line in enumerate(fileinput.FileInput('jobscript_vasp.sh')):
if '#PBS -N' in line:
n_line = n
elif '#PBS -q' in line:
q_line = n
PBS_N = '#PBS -N %03d_%s\n' % (idx + 1.0, formula)
replace_line('jobscript_vasp.sh', n_line, PBS_N)
queue = 'flat' # Change queue name if required
PBS_q = '#PBS -q %s\n' % (queue)
replace_line('jobscript_vasp.sh', q_line, PBS_q)
destination = file_path + 'surface/'
f.writelines(['\t', 'POTCAR_symbols: ', str(potcar_symbols), '\n'])
f.writelines([
'\t', 'LDAUL: ',
str(INCAR['LDAUL']), '\t', 'LDAUU: ',
str(INCAR['LDAUU']), '\t', 'LDAUJ: ',
str(INCAR['LDAUJ']), '\n'
])
f.writelines(['\t', 'MAGMOM: ', str(magm), '\n'])
"""
Write files
"""
write_vasp('%03d_%s/2nd/surface/POSCAR' % (idx + 1.0, formula),
slab_sorted)
INCAR.write_file('%03d_%s/2nd/surface/INCAR' % (idx + 1.0, formula))
KPOINTS.write_file('%03d_%s/2nd/surface/KPOINTS' %
(idx + 1.0, formula))
POTCAR.write_file('%03d_%s/2nd/surface/POTCAR' % (idx + 1.0, formula))
# jobscript copy
destination = '%03d_%s/2nd/surface/' % (idx + 1.0, formula)
job_file = os.getcwd() + '/jobscript_vasp.sh'
shutil.copy(job_file, destination)
f.writelines(['#' * 80, '\n'])
end_time = time.time()
f.writelines('Execution time for script (sec) : %6.1f\n' %
(end_time - start_time))
from pymatgen.io.vasp.inputs import Incar, Poscar
from pymatgen.io.vasp.inputs import Potcar
import yaml
import os
os.environ["VASP_PSP_DIR"] = "/home/knc6/Software/VASP-POTENTIAL"
with open('/home/knc6/bin/Special_POTCAR.yaml', 'r') as f:
doc = yaml.load(f)
pots = doc['POTCAR']
mat = Poscar.from_file('POSCAR')
new_symb = []
for el in mat.site_symbols:
new_symb.append(pots[el])
potcar = Potcar(symbols=new_symb, functional="PBE")
potcar.write_file("POTCAR")
INCAR['LDAUU'][index] = U_dict[element]
INCAR.write_file('%03d_%s/INCAR' % (idx + 1.0, formula))
KPOINTS.write_file('%03d_%s/KPOINTS' % (idx + 1.0, formula))
# Potcar setup
mp_calc = mpr.get_entry_by_material_id({'material_id': mp_id})
mp_potcar_symbols = mp_calc.parameters['potcar_symbols']
for i in range(len(mp_potcar_symbols)):
mp_potcar_symbols[i] = mp_potcar_symbols[i].replace("PBE ", "")
if 'W_pv' in mp_potcar_symbols:
mp_potcar_symbols[1] = 'W_sv'
POTCAR = Potcar(mp_potcar_symbols)
POTCAR.write_file(file_path + 'POTCAR')
print('%02d' % (idx + 1.0), " ", formula, " ", conv_struc.formula, " ",
len(conv_struc), " %4.3f %4.3f %4.3f" % (conv_struc.lattice.abc),
" ", mp_potcar_symbols, " ", INCAR['LDAUU'],
" %s" % INCAR['MAGMOM'])
f.writelines([
'%02d' % (idx + 1.0), " ", formula, " ", conv_struc.formula, " ",
str(len(conv_struc)),
" %4.3f %4.3f %4.3f" % (conv_struc.lattice.abc),
" %s" % mp_potcar_symbols,
" %s" % INCAR['LDAUU'],
" %s\n" % INCAR['MAGMOM']
])
# jobscript copy
KPOINTS.write_file('%03d_%s/KPOINTS' % (i + 1.0, formula))
# Potcar setup
mp_calc = mpr.get_entry_by_material_id({'material_id': mp_id})
mp_potcar_symbols = mp_calc.parameters['potcar_symbols']
for idx in range(len(mp_potcar_symbols)):
mp_potcar_symbols[idx] = mp_potcar_symbols[idx].replace("PBE ", "")
if 'W_pv' in mp_potcar_symbols:
mp_potcar_symbols[1] = 'W_sv'
# ordering for exception_list
if mp_potcar_symbols[-1] != 'O':
# print(i," ", formula," ",mp_potcar_symbols)
mp_potcar_symbols.reverse()
POTCAR = Potcar(mp_potcar_symbols)
print('%d\t%s\t%s\t%s' %
(i + 1, formula, mp_potcar_symbols, INCAR['LDAUU']))
f.writelines('%d\t%s\t%s\t%s\n' %
(i + 1, formula, mp_potcar_symbols, INCAR['LDAUU']))
POTCAR.write_file('%03d_%s/POTCAR' % (i + 1.0, formula))
# jobscript copy
destination = '%03d_%s/' % (i + 1.0, formula)
job_file = os.getcwd() + '/jobscript_vasp.sh'
shutil.copy(job_file, destination)
end_time = time.time()
f.writelines('Execution time for script (sec) : %6.1f\n' %
(end_time - start_time))
f.writelines(['\t', 'LDAUL: ',str(INCAR['LDAUL']),'\t',
'LDAUU: ',str(INCAR['LDAUU']),'\t',
'LDAUJ: ',str(INCAR['LDAUJ']),'\n'])
f.writelines(['\t','MAGMOM: ',str(magm),'\n'])
print(sorted(elements)," ",INCAR['LDAUU']," ",magm," ",potcar_symbols)
"""
Write files
"""
write_vasp(file_path + 'slab_100/POSCAR', slab_sorted)
INCAR.write_file(file_path + 'slab_100/INCAR')
KPOINTS.write_file(file_path + 'slab_100/KPOINTS')
POTCAR.write_file(file_path + 'slab_100/POTCAR')
# view(slab_sorted)
# jobscript copy
for n, line in enumerate(fileinput.FileInput('jobscript_vasp.sh')):
if '#PBS -N' in line:
n_line = n
elif '#PBS -q' in line:
q_line = n
elif '#PBS -l' in line:
w_line = n
PBS_N = '#PBS -N %02d_%s\n' % (idx + 1.0, formula)
replace_line('jobscript_vasp.sh', n_line, PBS_N)
if idx < 15:
queue = 'normal' # Change queue name if required
INCAR['LDAUU'] = [LDAUU_dic[x] for x in sorted(elements)]
INCAR['LDAUJ'] = [LDAUJ_dic[x] for x in sorted(elements)]
f.writelines('\tLDAUL: %s\t LDAUU: %s\tLDAUJ: %s\n' % (INCAR['LDAUL'], INCAR['LDAUU'], INCAR['LDAUJ']))
potcar_symbols.append('H')
potcar_symbols.sort()
POTCAR = Potcar(potcar_symbols)
f.writelines(['\tPOTCAR_symbols: ',str(potcar_symbols), '\n'])
potcar_symbols.remove('H')
else:
f.writelines('\tLDAUL: %s\t LDAUU: %s\tLDAUJ: %s\n' % (INCAR['LDAUL'], INCAR['LDAUU'], INCAR['LDAUJ']))
POTCAR = Potcar(potcar_symbols)
f.writelines(['\tPOTCAR_symbols: ',str(potcar_symbols), '\n'])
# view(slab_sorted)
write_vasp(file_path + '%s/POSCAR' % (adsorbate_names[ads_idx]), slab_sorted)
INCAR.write_file(file_path + '%s/INCAR' % (adsorbate_names[ads_idx]))
KPOINTS.write_file(file_path + '%s/KPOINTS' % (adsorbate_names[ads_idx]))
POTCAR.write_file(file_path + '%s/POTCAR' % (adsorbate_names[ads_idx]))
# jobscript copy
destination = file_path + adsorbate_names[ads_idx] + '/'
job_file = os.getcwd() + '/jobscript_vasp.sh'
shutil.copy(job_file, destination)
f.writelines(['#'*80,'\n'])
end_time = time.time()
f.writelines('Execution time for script (sec) : %6.1f\n' % (end_time - start_time))
