def get_KPPRA(self):
# Open up the OUTCAR
with open(self.outcar) as fp:
#store the number of atoms and number of irreducible K-points
for line in fp:
if "number of ions NIONS =" in line:
words = line.split()
NI = int(words[11])
elif "k-points NKPTS =" in line:
words = line.split()
NIRK = float(words[3])
#check if the number of k-points was reduced by VASP if so, sum all the k-points weight
if "irreducible" in open(self.outcar).read():
fp.seek(0)
for line in fp:
#sum all the k-points weight
if "Coordinates Weight" in line:
NK = 0
counter = 0
for line in fp:
if counter == NIRK:
break
NK += float(line.split()[3])
counter += 1
return Value(scalars=[Scalar(value=NI * NK)])
#if k-points were not reduced KPPRA equals the number of atoms * number of irreducible k-points
else:
return Value(scalars=[Scalar(value=NI * NIRK)])
def get_KPPRA(self):
# Open up the OUTCAR
with open(os.path.join(self._directory, 'OUTCAR')) as fp:
#store the number of atoms and number of irreducible K-points
for line in fp:
if "NIONS" in line:
words = line.split()
NI = int(words[11])
elif "NKPTS" in line:
words = line.split()
NIRK = float(words[3])
#check if the number of k-points was reduced by VASP if so, sum all the k-points weight
if "irreducible" in open(os.path.join(self._directory,
'OUTCAR')).read():
fp.seek(0)
for line in fp:
#sum all the k-points weight
if "Coordinates Weight" in line:
NK = 0
counter = 0
for line in fp:
if counter == NIRK:
break
NK += float(line.split()[3])
counter += 1
return Value(scalars=[Scalar(value=NI * NK)])
#if k-points were not reduced KPPRA equals the number of atoms * number of irreducible k-points
else:
return Value(scalars=[Scalar(value=NI * NIRK)])
# Error handling: NKPTS or NIONS not found
raise Exception('NIONS, irredicuble or Coordinates not found')
def get_dos(self):
file_path = os.path.join(self._directory, 'DOSCAR')
if not os.path.isfile(file_path):
return None
#open DOSCAR
with open(os.path.join(self._directory, 'DOSCAR')) as fp:
for i in range(6):
l = fp.readline()
n_step = int(l.split()[2])
energy = []
dos = []
for i in range(n_step):
l = fp.readline().split()
e = float(l.pop(0))
energy.append(Scalar(value=e))
dens = 0
for j in range(int(len(l) / 2)):
dens += float(l[j])
dos.append(Scalar(value=dens))
# Convert to property
return Property(scalars=dos,
units='number of states per unit cell',
conditions=Value(name='energy',
scalars=energy,
units='eV'))
def get_xc_functional(self):
# Open up the OUTCAR
with open(self.outcar) as fp:
# Look for TITEL
for line in fp:
if "TITEL" in line:
words = line.split()
return Value(scalars=[Scalar(value=words[2])])
def get_xc_functional(self):
# Open up the OUTCAR
with open(os.path.join(self._directory, 'OUTCAR')) as fp:
# Look for TITEL
for line in fp:
if "TITEL" in line:
words = line.split()
return Value(scalars=[Scalar(value=words[2])])
break
def get_forces(self):
self.atoms = read_vasp_out(os.path.join(self._directory, 'OUTCAR'))
forces_raw = self.atoms.get_calculator().results['forces'].tolist()
forces_wrapped = [[Scalar(value=x) for x in y] for y in forces_raw]
positions_raw = self.atoms.positions.tolist()
positions_wrapped = [[Scalar(value=x) for x in y]
for y in positions_raw]
return Property(vectors=forces_wrapped,
conditions=Value(name="positions",
vectors=positions_wrapped))
def test_condition_elevation():
"""Test that read views elevate conditions"""
condition = Value(name="spam", scalars=[Scalar(value="eggs")])
pif = System(properties=[
Property(
name="foo", scalars=[Scalar(value="bar")], conditions=[condition])
])
r = ReadView(pif)
assert r["foo"].scalars[0].value == "bar", "Didn't elevate property key"
assert r["spam"].scalars[0].value == "eggs", "Didn't elevate condition key"
def get_cutoff_energy(self):
# Open up the OUTCAR
with open(os.path.join(self._directory, 'OUTCAR'), 'r') as fp:
# Look for ENCUT
for line in fp:
if "ENCUT" in line:
words = line.split()
return Value(scalars=[Scalar(value=float(words[2]))],
units=words[3])
# Error handling: ENCUT not found
raise Exception('ENCUT not found')
def get_pp_name(self):
# Open up the OUTCAR
with open(self.outcar) as fp:
#initialize empty list to store pseudopotentials
pp = []
# Look for TITEL
for line in fp:
if "TITEL" in line:
words = line.split()
pp.append(words[3])
return Value(vectors=[[Scalar(value=x) for x in pp]])
def get_pp_name(self):
# Open up the OUTCAR
with open(os.path.join(self._directory, 'OUTCAR')) as fp:
#initialize empty list to store pseudopotentials
pp = []
# Look for TITEL
for line in fp:
if "TITEL" in line:
words = line.split()
pp.append(words[3])
return Value(vectors=[[Scalar(value=x) for x in pp]])
# Error handling: TITEL not found
raise Exception('TITEL not found')
def get_U_settings(self):
#Open up the OUTCAR
with open(os.path.join(self._directory, 'OUTCAR')) as fp:
#Check if U is used
if "LDAU" in open(os.path.join(self._directory, 'OUTCAR')).read():
U_param = {}
atoms = []
#get the list of pseupotential used
for line in fp:
if "TITEL" in line:
atoms.append(line.split()[3])
#Get the U type used
if "LDAUTYPE" in line:
U_param['Type'] = int(line.split()[-1])
atoms.reverse()
fp.seek(0)
#Get the L value
U_param['Values'] = {}
for line in fp:
for atom, i in zip(atoms, range(len(atoms))):
if "LDAUL" in line:
U_param['Values'][atom] = {
'L': int(line.split()[-1 - i])
}
fp.seek(0)
#Get the U value
for line in fp:
for atom, i in zip(atoms, range(len(atoms))):
if "LDAUU" in line:
U_param['Values'][atom]['U'] = float(
line.split()[-1 - i])
fp.seek(0)
#Get the J value
for line in fp:
for atom, i in zip(atoms, range(len(atoms))):
if "LDAUJ" in line:
U_param['Values'][atom]['J'] = float(
line.split()[-1 - i])
return Value(**U_param)
#if U is not used, return None
else:
return None
def get_vdW_settings(self):
#define the name of the vdW methods in function of their keyword
vdW_dict = {
'BO': 'optPBE-vdW',
'MK': 'optB88-vdW',
'ML': 'optB86b-vdW',
'RE': 'vdW-DF',
'OR': 'Klimes-Bowler-Michaelides'
}
#Open up the OUTCAR
with open(self.outcar) as fp:
#Check if vdW is used
if "LUSE_VDW" in open(self.outcar).read():
#if vdW is used, get its keyword
for line in fp:
if "GGA =" in line:
words = line.split()
return Value(
scalars=[Scalar(value=vdW_dict[words[2]])])
#if vdW is not used, return None
else:
return None
from pypif_sdk.func import replace_by_key, copy
from pypif_sdk.accessor import get_property_by_name
from pypif.obj import System, Property, Scalar, Value, FileReference
test_pif = System(names=["methane"],
properties=[
Property(name="foo", scalars=[Scalar(value="bar")]),
Property(name="spam",
units="eV",
scalars=[Scalar(value=2.7)],
conditions=[
Value(name="tomato",
units="eV",
scalars=[Scalar(value=1.0)])
]),
Property(
name="image",
files=[FileReference(relative_path="/tmp/file.png")])
])
def test_simple_replace():
"""Test replace a single field with default arguments"""
prop = get_property_by_name(copy(test_pif), "image")
assert prop.files[
0].relative_path == "/tmp/file.png", "Didn't shorten file name"
new_pif = replace_by_key(test_pif, "relative_path",
{"/tmp/file.png": "file.png"})
prop = get_property_by_name(new_pif, "image")
assert prop.files[
0].relative_path == "file.png", "Didn't shorten file name"
def get_poscar(self):
raw_path = os.path.join(self._directory, 'POSCAR')
if raw_path[0:2] == "./":
raw_path = raw_path[2:]
return Value(files=[FileReference(relative_path=raw_path)])
def get_poscar(self):
if self.poscar is None: return None
raw_path = self.poscar
if raw_path[0:2] == "./":
raw_path = raw_path[2:]
return Value(files=[FileReference(relative_path=raw_path)])