class CalculationSettingsTest(unittest.TestCase):
def setUp(self):
self.calc_directory = "data/calculations_pto"
self.incar = IncarSettings()
self.incar.from_file("data/incar_pto")
self.poscar = PoscarSettings()
self.poscar.from_file("data/poscar_pto.vasp")
self.potcar = PotcarSettings()
self.potcar.from_file("data/potcar_pto")
runscript_file_path = "data/run_cl.sh"
run_settings = {
"job_name": "scf_cl",
"qos": "regular",
"nodes": 1,
"constraint": "knl",
"time": "24:00:00"
}
modules = ["vasp/20181030-knl"]
exports = ["OMP_NUM_THREADS=4"]
execute = "vasp_std"
self.runscript = RunscriptSettings(runscript_file_path, run_settings,
modules, exports, execute)
self.kpoints = KpointsSettings()
self.kpoints.from_file("data/kpoints_pto")
def test_makecalc(self):
calc = Calculation(self.incar, self.kpoints, self.poscar, self.potcar,
self.runscript)
calc.make_calculation("data/scf_calc_workdir")
def __init__(self, encut):
"""
Sets default input parameters for scf ground state energy calculation
**Args:
encut (float): planewave energy cutoff for calculation
name (str): name for scf setting [default="scf_settings"]
"""
IncarSettings.__init__(self, name=name)
self.update_settings(setting_type="electronic", "encut", encut)
def test_write_file(self):
out_path = "data/incar_pto_out"
incar_1 = IncarSettings(self.settings)
incar_1.write_file(out_path)
incar_2 = IncarSettings()
incar_2.from_file(out_path)
for key in self.settings:
self.assertEqual(incar_1._settings[key], incar_2._settings[key])
def __init__(self, spinaxis, encut, ldaul, Uparam, Jparam):
"""
Sets default input parameters for scf spin non-collinear calculation
encut (flt): planewave energy cutoff for calculation
spinaxis (ndarray): spinaxis for calculation
ldaul (list): list of orbital types for each species
Uparam (list): list of U parameters for each species
Jparam (list): list of J paramters for each species
name (str): name for magnetic noncolinear calculation setting [default="DFTNCL_settings"]
"""
ncl_settings = {"ispin": 2, "magmom": None, "saxis": spinaxis, "lsorbit": ".TRUE.", "lnoncollinear": ".TRUE."}
dftu_settings = {"ldau": ".TRUE.", "ldauu": Uparam, "ldatype": 2, "ldaul": ldaul, "ldauj": Jparam , "lmaxmix": 4}
IncarSettings.__init__(self, magnetic_settings=ncl_settings, hubbard_settings=dftu_settings)
self.update_electronic_settings("encut", encut)
def __init__(self, encut, ldaul, Uparam, Jparam):
"""
Sets default input parameters for scf ground state energy calculation with +U correction
encut (float): planewave energy cutoff for calculation
ldaul (list): list of orbital types for each species
Uparam (list): list of U parameters for each species
Jparam (list): list of J paramters for each species
name (str): name for scf+U setting [default="DFTU_settings"]
"""
dftu_settings = {"ldau": ".TRUE." , "ldauu": Uparam, "ldatype": 2, "ldaul": ldaul, "ldauj": Jparam , "lmaxmix": 4}
IncarSettings.__init__(self, hubbard_settings=dftu_settings)
self.update_settings(setting_type="electronic", "encut", encut)
def setUp(self):
##runscript paramaters
# run_settings = {"job_name": "scf", "qos": "regular", "nodes": 1, "constraint": "knl", "time": "12:00:00"}
# modules = ["vasp/20181030-knl"]
# exports = ["OMP_NUM_THREADS=4"]
# links = ["ln -l ../scf_cl/WAVECAR .", "ln -l ../scf_cl/CHARGCAR ."]
# runscript_cl = RunscriptSettings(run_settings=run_settings,modules=modules,exports=exports, execute="vasp_std")
# self.runscript_ncl = RunscriptSettings(run_settings=run_settings,modules=modules,exports=exports, execute="vasp_ncl",links=links)
##cl_calculation settings
incar = IncarSettings()
incar.from_file("data/incar_pto")
poscar = PoscarSettings()
poscar.from_file("data/poscar_pto.vasp")
potcar = PotcarSettings()
potcar.from_file("data/potcar_pto")
kpoints = KpointsSettings()
kpoints.from_file("data/kpoints_pto")
self.calc_cl = Calculation(incar=incar,
kpoints=kpoints,
poscar=poscar,
potcar=potcar)
def __init__(self,
npoints,
work_dir,
cl_calculation=None,
cl_dir=None,
symm_reduce=False,
angle_range=None):
#insert excpetion handeling for inputs
self._work_dir = work_dir
self._npoints = npoints
os.mkdir(self._work_dir)
#new_cl_dir = self._work_dir + "/scf_cl"
if cl_calculation:
#cl_calculation.make_calculation(new_cl_dir)
self._cl_calculation = cl_calculation
# If directory for calculation provided
elif cl_dir:
new_cl_dir = self._work_dir + "/scf_cl"
copy(cl_dir, new_cl_dir)
incar_cl = IncarSettings()
incar_cl.from_file(cl_dir + "/INCAR")
poscar = PoscarSettings()
poscar.from_file(cl_dir + "/POSCAR")
potcar = PotcarSettings()
potcar.from_file(cl_dir + "/POTCAR")
kpts = KPointsSettings()
kpts.from_file(cl_dir + "/KPOINTS")
#runscript = RunscriptSettings()
#runscript.from_file(cl_dir+"/run.sh")
self._cl_calculation = Calculation(incar_cl, kpt, poscar, potcar)
else:
pass
self._cl_calculation.make_calculation(
os.path.join(self._work_dir, "scf_cl"))
struct = self._cl_calculation._poscar._structure
space_group = SpacegroupAnalyzer(struct).get_space_group_number()
if angle_range:
spins = SpinVectors(npoints=npoints, angle_range=angle_range)
elif symm_reduce is True:
spins = SpinVectors(npoints=npoints, space_group=space_group)
else:
spins = SpinVectors(npoints=npoints)
self._spins = spins._spin_axes.T
def setup_ncl_calc(work_dir, spins, incar_cl, poscar, potcar, kpoints):
ncl_calcs = []
incar_ncl = incar_cl
incar_ncl.remove_settings("MAGMOM")
incar_ncl.update_settings("ISPIN", 1)
incar_ncl.update_settings("LSORBIT", ".TRUE.")
incar_ncl.update_settings("LNONCOLLINEAR", ".TRUE.")
incar_ncl.update_settings("LPLANE", ".FALSE.")
#incar_ncl.update_settings("NBANDS", str(2*nbands))
ncl_dir = os.path.join(work_dir, "scf_ncl")
os.mkdir(ncl_dir)
itr = 0
for spin in spins:
itr += 1
incar_ncl.update_settings("SAXIS", [spin[0], spin[1], spin[2]])
calc = Calculation(incar_ncl, kpoints, poscar, potcar)
calc.make_calculation(os.path.join(ncl_dir, "ncl_" + str(itr)))
setup_ncl_calc(self._work_dir, self._spins,
self._cl_calculation._incar,
self._cl_calculation._poscar,
self._cl_calculation._potcar,
self._cl_calculation._kpoints)
def test_update_method(self):
## add update method for magmom
incar = IncarSettings(self.settings)
incar.update_settings("KPAR", 8)
self.assertEqual(incar._settings["KPAR"], 8)
def test_get_method(self):
##add get method for magmom (and maybe also U paramaters)
incar = IncarSettings(self.settings)
out = incar.get_settings("KPAR")
self.assertEqual(out, 4)
def test_from_file(self):
incar_infile_sett = IncarSettings()
incar_infile_sett.from_file(self.incar_file_path)
incar_sett = incar_infile_sett._settings
for key in self.settings:
self.assertEqual(self.settings[key], incar_sett[key])