def parse_psp(files: typ.Dict[str, str], dftcode: str) -> str:
"""
Returns simplified string representation of the pseudopotnetial used in a
DFT calculation
"""
if dftcode == 'vasp':
return '{}' #ideally we parse the potcar to reconstruct setups dictionary
elif dftcode == 'gpaw':
log = files.get('log', '')
pspth = parse_line(log, 'setups', 0).split(': ')[-1].strip()
elif dftcode == 'quantumespresso':
pwinp = files.get('pwinp', '')
pspth = parse_line(pwinp, 'pseudo_dir', 0).split("='")[1][:-2]
else:
raise NotImplementedError("new dftcode? ", dftcode)
if 'gbrv' in pspth: return 'gbrv15pbe'
elif 'dacapo' in pspth: return 'dacapo'
elif 'sg15' in pspth: return 'sg15'
elif 'paw' in pspth:
if 'gpaw-setups-0.6.6300' in log: return 'oldpaw'
else: return 'paw'
else:
raise NotImplementedError('New psp? path = ', pspth)
def parse_xc(files: typ.Dict[str, str], dftcode: str) -> str:
"""
Finds the exchange correlation functional
"""
log = files.get('log')
pwinp = files.get('pwinp')
incar = files.get('incar')
if dftcode == 'gpaw':
xc = parse_line(log, 'xc:', 0).split(':')[-1].strip()
elif dftcode == 'quantumespresso':
xc = parse_line(pwinp, 'input_dft',
0).split('=')[-1].replace(',', '').replace("'",
'').strip()
elif dftcode == 'vasp':
if parse_line(incar, 'GGA', 0).split('=')[-1].strip() == 'PE':
if True: #if not BEEF?
xc = 'PBE'
else:
raise NotImplementedError('New functional in vasp?')
else:
raise NotImplementedError('New DFT code? ' + dftcode)
if xc.lower() == 'pbe':
return 'PBE'
elif xc.lower() in ['beef', 'beef-vdw']:
return 'BEEF'
elif xc.lower() == 'rpbe':
return 'RPBE'
elif xc.lower() == 'mbeef':
return 'mBEEF'
else:
raise ValueError("weird xc: ", xc)
def get_sigma(dftcode : str
,files : typ.Dict[str,str]
) -> typ.Optional[float]:
"""
Helpful docstring
"""
if dftcode == 'gpaw':
log = files['log']
parsed = parse_line(log,'Fermi-Dirac',0)
raw = parsed.split('=')[1].split()[0]
return float(raw)
elif dftcode == 'quantumespresso':
pwinp = files['pwinp']
parsed = parse_line(pwinp,'degauss',0)
raw = parsed.split('=')[1][:7]
return round(13.60569 * float(raw),3)
elif dftcode == 'vasp':
incar = files['incar']
parsed = parse_line(incar,'SIGMA',0)
raw = parsed.split('=')[-1]
return float(raw)
else:
raise NotImplementedError
def get_econv(dftcode: str, files: typ.Dict[str, str]) -> typ.Optional[float]:
"""
Docstring
"""
if dftcode == 'gpaw':
log = files['log']
parsed = parse_line(log, 'convergence:', 0)
raw = parsed.split('energy:')[-1]
pure = raw.replace('}', '')
return float(pure)
elif dftcode == 'quantumespresso':
pwinp = files['pwinp']
try:
line = parse_line(pwinp, 'conv_thr', -1)
except IndexError:
raise ValueError('Problem with parse line')
raw = line.split('=')[1][:-1]
return round(13.60569 * float(raw), 6)
elif dftcode == 'vasp':
incar = files['incar']
parsed = parse_line(incar, 'EDIFF', 0)
raw = parsed.split('=')[-1]
return float(raw)
else:
raise NotImplementedError("Unknown dft code?")
def get_vasp_key(dftcode : str
,files : typ.Dict[str,str]
,key : str
,dtype : str
) -> typ.Optional[typ.Union[int,str,float]]:
"""
common form of extracting VASP input info
"""
assert dtype in cast_maybe.keys(), 'bad dtype argument for get_vasp_key: '+dtype
if dftcode =='vasp':
incar = files['incar']
try:
parsed = parse_line(incar,key,0).split('=')[-1].strip()
except IndexError:
parsed = None # type: ignore
return cast_maybe[dtype](parsed) # type: ignore
else:
return None
def get_kpts(dftcode: str, files: typ.Dict[str,
str]) -> typ.Tuple[int, int, int]:
"""
docstring
"""
if dftcode == 'gpaw':
log = files['log']
parsed = parse_line(log, 'kpts')
raw = parsed.split(': ')[-1].split()
pure = ','.join(raw)
return tuple(ast.literal_eval(pure)) #type: ignore
elif dftcode == 'quantumespresso':
pwinp = files['pwinp']
line = pwinp.split('\n')[-2]
raw = line.split()[:3]
return tuple([int(x) for x in raw]) #type: ignore
elif dftcode == 'vasp':
kptcar = files['kptcar']
line = kptcar.split('\n')[-2]
raw = [int(x) for x in line.split()]
return tuple(raw) #type: ignore
else:
raise NotImplementedError('new dftcode? ', dftcode)
def get_nmix(dftcode: str, files: typ.Dict[str, str]) -> typ.Optional[float]:
"""
Docstring
"""
if dftcode == 'gpaw':
log = files['log']
parsed = parse_line(log, 'nmaxold', 0)
raw = parsed.split(':')[1].replace(',', '')
return float(raw)
elif dftcode == 'quantumespresso':
pwinp = files['pwinp']
parsed = parse_line(pwinp, 'mixing_ndim', 0)
raw = parsed.split("=")[1][:-1]
return round(float(raw), 3)
else:
return None
def get_dw(dftcode: str, files: typ.Dict[str, str]) -> typ.Optional[int]:
"""
Docstring
"""
if dftcode == 'quantumespresso':
pwinp = files['pwinp']
parsed = parse_line(pwinp, 'ecutrho', 0)
raw = parsed.split('=')[1][:7]
return round(13.60569 * float(raw))
else:
return None
def get_mixtype(dftcode: str, files: typ.Dict[str, str]) -> typ.Optional[str]:
"""
Helpful docstring
"""
if dftcode == 'quantumespresso':
log = files['log']
parsed = parse_line(log, 'number of iterations used', 0)
return parsed.split()[6]
else:
return None
def get_fmax(dftcode: str, paramsdict: str,
files: typ.Dict[str, str]) -> typ.Optional[float]:
"""
docstring
"""
if dftcode == 'vasp':
incar = files['incar']
return -float(parse_line(incar, 'EDIFFG', 0).split('=')[-1])
else:
params = json.loads(paramsdict)
return params.get(
'fmax') # no conceivable way of getting this from log
def get_diag(dftcode: str, files: typ.Dict[str, str]) -> typ.Optional[float]:
"""
Docstring
"""
if dftcode == 'gpaw':
log = files['log']
parsed = parse_line(log, 'eigensolver', 0)
eigenline = parsed.split(': ')[-1]
if 'dav' in eigenline:
return 'david'
else:
return eigenline
elif dftcode == 'quantumespresso':
pwinp = files['pwinp']
parsed = parse_line(pwinp, 'diagonalization', 0)
return parsed.split("='")[1][:-2]
else:
return None
def get_nbands(dftcode : str
,paramsdict : str
,files : typ.Dict[str,str]
) -> typ.Optional[float]:
"""
docstring
"""
if dftcode == 'vasp':
outcar = files['outcar']
return int(parse_line(outcar,'NBANDS',0).split('=')[-1])
else:
params = json.loads(paramsdict)
return params.get('fmax') # no conceivable way of getting this from log
def get_maxstep(dftcode : str
,files : typ.Dict[str,str]
) -> int :
"""
Helpful docstring
"""
if dftcode == 'gpaw':
log = files['log']
parsed = parse_line(log,'maxiter',0)
return int(parsed.split(':')[-1])
elif dftcode == 'quantumespresso':
pwinp = files['pwinp']
parsed = parse_line(pwinp,'electron_maxstep',0)
return int(parsed.split('=')[1][:-1])
elif dftcode == 'vasp':
incar = files['incar']
parsed = parse_line(incar,'NELM',0)
return int(parsed.split('=')[-1])
else:
raise NotImplementedError
def parse_pw(files: typ.Dict[str, str], dftcode: str) -> int:
"""
Using "dftcode" as a switch, choose an appropriate file from a directory
and parse it for the planewave cutoff (in eV).
files - a dictionary mapping file names to file content
dftcode - must be one of {gpaw,vasp,quantumespresso}
parse_line
- args are: haystack,needle,n
- returns: the Nth line of a haystack that contains the needle
"""
# Constants
#----------
RYDBERG_TO_EV = 13.60569
# Parsing
#-------
if dftcode == 'gpaw':
log = files.get('log')
parsed = parse_line(log, 'ecut', 0)
raw_num = parsed.split()[-1].replace(',', '')
elif dftcode == 'quantumespresso':
pwinp = files.get('pwinp')
parsed = parse_line(pwinp, 'ecutwfc', 0)
raw_rydberg = parsed.split('=')[1][:7]
raw_num = RYDBERG_TO_EV * float(raw_rydberg)
elif dftcode == 'vasp':
incar = files.get('incar')
parsed = parse_line(incar, 'ENCUT', 0)
raw_num = parsed.split('=')[-1]
else:
raise ValueError('new dftcode? ', dftcode)
return int(round(float(raw_num)))
def get_dipol(dftcode: str, files: typ.Dict[str, str]) -> typ.Optional[str]:
"""
Docstring
"""
if dftcode == 'vasp':
incar = files['incar']
for l in incar.split('\n'):
if 'DIPOL' in l and 'LDIPOL' not in l:
line = parse_line(incar, '\nDIPOL', 0)
raw = line.split('=')[-1].split()
output = [float(x) for x in raw]
return json.dumps(output)
return None
else:
return None
def get_dipole(dftcode: str, files: typ.Dict[str, str]) -> int:
"""
Docstring
"""
if dftcode == 'gpaw':
return 0
elif dftcode == 'quantumespresso':
pwinp = files['pwinp']
return int('dipfield=.true.' in pwinp)
elif dftcode == 'vasp':
incar = files['incar']
parsed = parse_line(incar, 'LDIPOL', 0)
return int('TRUE' in parsed)
else:
raise NotImplementedError
def getENG_QE(log: str) -> float:
e = float(parse_line(log, 'total energy', -2).split()[-2])
ts = float(parse_line(log, 'smearing contrib.', -1).split()[-2])
return (e - ts / 2) * 13.6057
def getENG_GPAW(log: str) -> float:
return float(parse_line(log, 'Extrapolated:', -1).split()[-1])
def getENG_VASP(log: str) -> float:
return float(parse_line(log, 'energy(sigma->0)', -1).split()[-1])