def _check_incar_ele_temp(testCase, idx, ele_temp):
fp_path = os.path.join('iter.%06d' % idx, '02.fp')
tasks = glob.glob(os.path.join(fp_path, 'task.*'))
cwd = os.getcwd()
for ii in tasks:
os.chdir(ii)
bname = os.path.basename(ii)
sidx = int(bname.split('.')[1])
tidx = int(bname.split('.')[2])
with open('INCAR') as fp:
incar = fp.read()
incar0 = Incar.from_string(incar)
# make_fake_md: the frames in a system shares the same ele_temp
incar1 = Incar.from_string(
vasp_incar_ele_temp_ref %
(ele_temp[sidx][0] * pc.Boltzmann / pc.electron_volt))
for ii in incar0.keys():
# skip checking nbands...
if ii == 'NBANDS':
continue
testCase.assertAlmostEqual(incar0[ii],
incar1[ii],
msg='key %s differ' % (ii),
places=5)
os.chdir(cwd)
def make_vasp_kpoints_from_incar(work_dir, jdata):
cwd = os.getcwd()
fp_aniso_kspacing = jdata.get('fp_aniso_kspacing')
os.chdir(work_dir)
# get kspacing and kgamma from incar
assert (os.path.exists('INCAR'))
with open('INCAR') as fp:
incar = fp.read()
standard_incar = incar_upper(Incar.from_string(incar))
if fp_aniso_kspacing is None:
try:
kspacing = standard_incar['KSPACING']
except KeyError:
raise RuntimeError("KSPACING must be given in INCAR")
else:
kspacing = fp_aniso_kspacing
try:
gamma = standard_incar['KGAMMA']
if isinstance(gamma, bool):
pass
else:
if gamma[0].upper() == "T":
gamma = True
else:
gamma = False
except KeyError:
raise RuntimeError("KGAMMA must be given in INCAR")
# check poscar
assert (os.path.exists('POSCAR'))
# make kpoints
ret = make_kspacing_kpoints('POSCAR', kspacing, gamma)
kp = Kpoints.from_string(ret)
kp.write_file("KPOINTS")
os.chdir(cwd)
def test_get_defect_charge_state(tmpdir):
tmpdir.chdir()
structure = Structure(Lattice.cubic(10), ["H", "He"],
[[0.0] * 3, [0.5] * 3])
fake_potcar_str = """ PAW_PBE H 15Jun2001
1.00000000000000
parameters from PSCTR are:
VRHFIN =H: ultrasoft test
LEXCH = PE
TITEL = PAW_PBE H 15Jun2001
POMASS = 1.000; ZVAL = 1.000 mass and valenz
ENMAX = 250.000; ENMIN = 200.000 eV
END of PSCTR-controll parameters
End of Dataset
PAW_PBE He_pv 15Jun2001
1.00000000000000
parameters from PSCTR are:
VRHFIN =He: ultrasoft test
LEXCH = PE
TITEL = PAW_PBE He_pv 15Jun2001
POMASS = 1.000; ZVAL = 1.000 mass and valenz
ENMAX = 250.000; ENMIN = 200.000 eV
END of PSCTR-controll parameters
End of Dataset
"""
Path("POTCAR").write_text(fake_potcar_str)
potcar = Potcar.from_file("POTCAR")
incar = Incar.from_string("NELECT = 1")
assert get_defect_charge_state(Poscar(structure), potcar, incar) == 2 - 1
structure = Structure(Lattice.cubic(10), ["H", "He", "H", "H"],
[[0.0] * 3, [0.2] * 3, [0.4] * 3, [0.6] * 3])
with pytest.raises(ValueError):
get_defect_charge_state(Poscar(structure), potcar, incar)
incar = Incar.from_string("")
assert get_defect_charge_state(Poscar(structure), potcar, incar) == 0