def test_vtotal_pb(file_path):
"""
Test VTOTAL parser for Lead
"""
vtotal_path = file_path("/Pb/VTOTAL")
vtotal_pb = Vtotal.from_file(vtotal_path)
assert len(vtotal_pb.radius) == len(vtotal_pb.down_potential)
assert np.isclose(0.38023005e-6, vtotal_pb.radius[0])
assert np.isclose(119.197347174, vtotal_pb.radius[-1])
assert np.isclose(-163.966204585, vtotal_pb.down_potential[0])
assert np.isclose(-0.423502617e-1, vtotal_pb.down_potential[-1])
def test_vtotal_ti(file_path):
"""
Test VTOTAL parser for Titanium
"""
vtotal_path = file_path("/Ti/VTOTAL")
vtotal_ti = Vtotal.from_file(vtotal_path)
assert len(vtotal_ti.radius) == len(vtotal_ti.down_potential)
assert np.isclose(0.141722e-05, vtotal_ti.radius[0])
assert np.isclose(119.576532343, vtotal_ti.radius[-1])
assert np.isclose(-43.9675322335, vtotal_ti.down_potential[0])
assert np.isclose(-0.4248498e-01, vtotal_ti.down_potential[-1])
def test_vtotal_i(file_path):
"""
Test VTOTAL parser for Iodine
"""
vtotal_path = file_path("/I/VTOTAL")
vtotal_i = Vtotal.from_file(vtotal_path)
assert len(vtotal_i.radius) == len(vtotal_i.down_potential)
assert np.isclose(0.5882804e-6, vtotal_i.radius[0])
assert np.isclose(119.069540176, vtotal_i.radius[-1])
assert np.isclose(-105.966477381, vtotal_i.down_potential[0])
assert np.isclose(-0.4230485e-1, vtotal_i.down_potential[-1])
def test_vtotal_rb(file_path):
"""
Test VTOTAL parser for Rubidium
"""
vtotal_path = file_path("/Rb/VTOTAL")
vtotal_rb = Vtotal.from_file(vtotal_path)
assert len(vtotal_rb.radius) == len(vtotal_rb.down_potential)
assert np.isclose(0.842672003e-6, vtotal_rb.radius[0])
assert np.isclose(118.697889692, vtotal_rb.radius[-1])
assert np.isclose(-73.9667917002, vtotal_rb.down_potential[0])
assert np.isclose(-0.42172806e-1, vtotal_rb.down_potential[-1])
def test_vtotal_ni(file_path):
"""
Test VTOTAL parser for Nickel
"""
vtotal_path = file_path("/Ni/VTOTAL")
vtotal_ni = Vtotal.from_file(vtotal_path)
assert len(vtotal_ni.radius) == len(vtotal_ni.down_potential)
assert np.isclose(0.111353e-5, vtotal_ni.radius[0])
assert np.isclose(119.139460842, vtotal_ni.radius[-1])
assert np.isclose(-55.9671391768, vtotal_ni.down_potential[0])
assert np.isclose(-0.42329694e-1, vtotal_ni.down_potential[-1])
def test_vtotal_s(file_path):
"""
Test VTOTAL parser for Sulfur
"""
vtotal_path = file_path("/S/VTOTAL")
vtotal_s = Vtotal.from_file(vtotal_path)
assert len(vtotal_s.radius) == len(vtotal_s.down_potential)
assert np.isclose(0.19486790e-5, vtotal_s.radius[0])
assert np.isclose(118.796265787, vtotal_s.radius[-1])
assert np.isclose(-31.9681713318, vtotal_s.down_potential[0])
assert np.isclose(-0.42207759e-1, vtotal_s.down_potential[-1])
def test_vtotal_cs(file_path):
"""
Test VTOTAL parser for Cesium
"""
vtotal_path = file_path("/Cs/VTOTAL")
vtotal_cs = Vtotal.from_file(vtotal_path)
assert len(vtotal_cs.radius) == len(vtotal_cs.down_potential)
assert np.isclose(0.5668884e-6, vtotal_cs.radius[0])
assert np.isclose(119.124174998, vtotal_cs.radius[-1])
assert np.isclose(-109.966452133, vtotal_cs.down_potential[0])
assert np.isclose(-0.423242639e-1, vtotal_cs.down_potential[-1])
def test_vtotal_cl(file_path):
"""
Test VTOTAL parser for Cloro
"""
vtotal_path = file_path("/Cl/VTOTAL")
vtotal_cl = Vtotal.from_file(vtotal_path)
assert len(vtotal_cl.radius) == len(vtotal_cl.down_potential)
assert np.isclose(0.1834e-5, vtotal_cl.radius[0])
assert np.isclose(119.019272152, vtotal_cl.radius[-1])
assert np.isclose(-33.9680314505, vtotal_cl.down_potential[0])
assert np.isclose(-0.422869e-01, vtotal_cl.down_potential[-1])
def test_vtotal_h(file_path):
"""
Test VTOTAL parser for Hydrogen
"""
vtotal_path = file_path("/H/VTOTAL")
vtotal_h = Vtotal.from_file(vtotal_path)
assert len(vtotal_h.radius) == len(vtotal_h.down_potential)
assert np.isclose(0.31178864e-4, vtotal_h.radius[0])
assert np.isclose(119.998512118, vtotal_h.radius[-1])
assert np.isclose(-1.99796354987, vtotal_h.down_potential[0])
assert np.isclose(-0.4263491e-1, vtotal_h.down_potential[-1])
def test_vtotal_cu(file_path):
"""
Test VTOTAL parser for Cooper
"""
vtotal_path = file_path("/Cu/VTOTAL")
vtotal_cu = Vtotal.from_file(vtotal_path)
assert len(vtotal_cu.radius) == len(vtotal_cu.down_potential)
assert np.isclose(0.107513324e-5, vtotal_cu.radius[0])
assert np.isclose(119.426778853, vtotal_cu.radius[-1])
assert np.isclose(-57.9670822880, vtotal_cu.down_potential[0])
assert np.isclose(-0.42431777e-1, vtotal_cu.down_potential[-1])
def test_vtotal_n(file_path):
"""
Test VTOTAL parser for Nitrogen
"""
vtotal_path = file_path("/N/VTOTAL")
vtotal_n = Vtotal.from_file(vtotal_path)
assert len(vtotal_n.radius) == len(vtotal_n.down_potential)
assert np.isclose(0.445412344e-05, vtotal_n.radius[0])
assert np.isclose(118.995642542, vtotal_n.radius[-1])
assert np.isclose(-13.9711782037, vtotal_n.down_potential[0])
assert np.isclose(-0.42278597e-1, vtotal_n.down_potential[-1])
def test_vtotal_mn(file_path):
"""
Test VTOTAL parser for Manganese
"""
vtotal_path = file_path("/Mn/VTOTAL")
vtotal_mn = Vtotal.from_file(vtotal_path)
assert len(vtotal_mn.radius) == len(vtotal_mn.down_potential)
assert np.isclose(0.12471545e-5, vtotal_mn.radius[0])
assert np.isclose(119.238220332, vtotal_mn.radius[-1])
assert np.isclose(-49.9673154957, vtotal_mn.down_potential[0])
assert np.isclose(-0.423647837e-1, vtotal_mn.down_potential[-1])
def test_vtotal_po(file_path):
"""
Test VTOTAL parser for Polonium
"""
vtotal_path = file_path("/Po/VTOTAL")
vtotal_po = Vtotal.from_file(vtotal_path)
assert len(vtotal_po.radius) == len(vtotal_po.down_potential)
assert np.isclose(0.3711769e-6, vtotal_po.radius[0])
assert np.isclose(119.304965932, vtotal_po.radius[-1])
assert np.isclose(-167.966193113, vtotal_po.down_potential[0])
assert np.isclose(-0.4238849e-1, vtotal_po.down_potential[-1])
def test_vtotal_p(file_path):
"""
Test VTOTAL parser for Phosphor
"""
vtotal_path = file_path("/P/VTOTAL")
vtotal_p = Vtotal.from_file(vtotal_path)
assert len(vtotal_p.radius) == len(vtotal_p.down_potential)
assert np.isclose(0.20785e-5, vtotal_p.radius[0])
assert np.isclose(119.038671474, vtotal_p.radius[-1])
assert np.isclose(-29.9683278539, vtotal_p.down_potential[0])
assert np.isclose(-0.4229388e-01, vtotal_p.down_potential[-1])
def test_vtotal_zn(file_path):
"""
Test VTOTAL parser for Zinco
"""
vtotal_path = file_path("/Zn/VTOTAL")
vtotal_zn = Vtotal.from_file(vtotal_path)
assert len(vtotal_zn.radius) == len(vtotal_zn.down_potential)
assert np.isclose(0.10392e-5, vtotal_zn.radius[0])
assert np.isclose(119.857307249, vtotal_zn.radius[-1])
assert np.isclose(-59.9670386149, vtotal_zn.down_potential[0])
assert np.isclose(-0.425847e-01, vtotal_zn.down_potential[-1])
def test_vtotal_c(file_path):
"""
Test VTOTAL parser for Carbon
"""
vtotal_path = file_path("/C/VTOTAL")
vtotal_c = Vtotal.from_file(vtotal_path)
assert len(vtotal_c.radius) == len(vtotal_c.down_potential)
assert np.isclose(0.5196477e-5, vtotal_c.radius[0])
assert np.isclose(119.490524267, vtotal_c.radius[-1])
assert np.isclose(-11.9720173404, vtotal_c.down_potential[0])
assert np.isclose(-0.4245442e-01, vtotal_c.down_potential[-1])
def test_vtotal_sb(file_path):
"""
Test VTOTAL parser for Antimony
"""
vtotal_path = file_path("/Sb/VTOTAL")
vtotal_sb = Vtotal.from_file(vtotal_path)
assert len(vtotal_sb.radius) == len(vtotal_sb.down_potential)
assert np.isclose(0.61135027e-6, vtotal_sb.radius[0])
assert np.isclose(119.184648607, vtotal_sb.radius[-1])
assert np.isclose(-101.966505327, vtotal_sb.down_potential[0])
assert np.isclose(-0.42345749e-1, vtotal_sb.down_potential[-1])
def test_vtotal_bi(file_path):
"""
Test VTOTAL parser for Bismuth
"""
vtotal_path = file_path("/Bi/VTOTAL")
vtotal_bi = Vtotal.from_file(vtotal_path)
assert len(vtotal_bi.radius) == len(vtotal_bi.down_potential)
assert np.isclose(0.375648e-6, vtotal_bi.radius[0])
assert np.isclose(119.242488916, vtotal_bi.radius[-1])
assert np.isclose(-165.966198780, vtotal_bi.down_potential[0])
assert np.isclose(-0.42366300e-01, vtotal_bi.down_potential[-1])
def test_vtotal_tm(file_path):
"""
Test VTOTAL parser for Thulium
"""
vtotal_path = file_path("/Tm/VTOTAL")
vtotal_tm = Vtotal.from_file(vtotal_path)
assert len(vtotal_tm.radius) == len(vtotal_tm.down_potential)
assert np.isclose(0.45186759e-6, vtotal_tm.radius[0])
assert np.isclose(118.913126048, vtotal_tm.radius[-1])
assert np.isclose(-137.966300055, vtotal_tm.down_potential[0])
assert np.isclose(-0.4224927929e-1, vtotal_tm.down_potential[-1])
def test_vtotal_k(file_path):
"""
Test VTOTAL parser for Potassium
"""
vtotal_path = file_path("/K/VTOTAL")
vtotal_k = Vtotal.from_file(vtotal_path)
assert len(vtotal_k.radius) == len(vtotal_k.down_potential)
assert np.isclose(0.16409928e-5, vtotal_k.radius[0])
assert np.isclose(119.171058353, vtotal_k.radius[-1])
assert np.isclose(-37.9677993761, vtotal_k.down_potential[0])
assert np.isclose(-0.423409214e-1, vtotal_k.down_potential[-1])
def _get_atom_potential_class(self, base_path: str,
symbol: str) -> AtomicPotential:
"""
Creates atom_potential class
Args:
symbol (str): Atom symbol
base_path (str): Path to mkpotcar{symbol}
"""
pseudopotential_folder = os.path.join(base_path, "pseudopotential")
vtotal_path = os.path.join(pseudopotential_folder, "VTOTAL.ae")
vtotal_occ_path = os.path.join(pseudopotential_folder, "VTOTAL_OCC")
vtotal = Vtotal.from_file(vtotal_path)
vtotal_occ = Vtotal.from_file(vtotal_occ_path)
potential_filename = "{}.{}".format(self.potential_filename.upper(),
symbol.lower())
potential_class = self.software_factory.get_potential_class(
potential_filename, self.corrected_potfiles_folder)
return AtomicPotential(vtotal, vtotal_occ, potential_class)
def correct_potfile(
quiet: bool,
base_potfile_path: str,
vtotal_path: str,
vtotal_occupied_path: str,
software: str,
correction: str,
cut: str,
amplitude: float,
) -> None:
"""Generate the occupied atomic potential file used for ab initio calculations.
Requires:
VTOTAL.ae: potential of the atom with all electrons
VTOTAL_OCC: potential of the occupied atom
INP_OCC: Input file for the run-atomic command of the occupied atom
The command also needs the potential files used by the chosen software:
VASP: POTCAR (This name can't be changed)
Generates:
POTFILEcut${CUT_VALUE} (If amplitude is equal to 1.0)
POTFILEcut${CUT_VALUE}A${AMPLITUDE_VALUE} (If amplitude is different from 1.0)
"""
welcome_message("minushalf")
if quiet:
logger.remove()
logger.add(sys.stdout, level="ERROR")
softwares = {"VASP": Vasp()}
factory = softwares[software.upper()]
vtotal = Vtotal.from_file(vtotal_path)
vtotal_occ = Vtotal.from_file(vtotal_occupied_path)
potential_file = factory.get_potential_class(base_path=base_potfile_path)
atomic_potential = AtomicPotential(vtotal, vtotal_occ, potential_file)
cut_numbers = parse_cut(cut)
is_conduction = False
if correction.upper() == "CONDUCTION":
is_conduction = True
for new_cut in cut_numbers:
logger.info("Correcting POTFILE for cut = {:.2f} a.u".format(new_cut))
new_potential = atomic_potential.correct_potential(
new_cut, amplitude, is_conduction)
atomic_potential.correct_file(new_potential, new_cut, amplitude,
is_conduction)
end_message()