def test_enabled_complex_nlep(vasp, structure, Specie):
from numpy import all, abs, array
from pylada.vasp.specie import U, nlep
import pylada
pylada.vasp_has_nlep = True
vasp.species = {
'A': Specie([U(2, 0, 0.5)]),
'B': Specie([U(2, 0, -0.5), nlep(2, 2, -1.0, -3.0)]),
'X': Specie([])
}
vasp.ldau = True
map = vasp.output_map(vasp=vasp, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(
abs(array(map['LDUL1'].split(), dtype='float64') - [0, 0, -1]) < 1e-8)
assert all(
abs(array(map['LDUU1'].split(), dtype='float64') -
[0.5, -0.5, 0]) < 1e-8)
assert all(
abs(array(map['LDUJ1'].split(), dtype='float64') - [0, 0, 0]) < 1e-8)
assert all(
abs(array(map['LDUO1'].split(), dtype='float64') - [1, 1, 1]) < 1e-8)
assert all(
abs(array(map['LDUL2'].split(), dtype='float64') - [-1, 2, -1]) < 1e-8)
assert all(
abs(array(map['LDUU2'].split(), dtype='float64') -
[0, -1.0, 0]) < 1e-8)
assert all(
abs(array(map['LDUJ2'].split(), dtype='float64') -
[0, -3.0, 0]) < 1e-8)
assert all(
abs(array(map['LDUO2'].split(), dtype='float64') - [1, 3, 1]) < 1e-8)
def test_enabled_complex_U(vasp, Specie, structure):
from numpy import all, abs, array
from pylada.vasp.specie import U
import pylada
pylada.vasp_has_nlep = False
vasp.species = {'A': Specie([U(2, 0, 0.5)]), 'B': Specie([U(2, 1, 0.6)]), 'X': Specie([])}
vasp.ldau = True
map = vasp.output_map(vasp=vasp, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(abs(array(map['LDUJ'].split(), dtype='float64')) < 1e-8)
assert all(abs(array(map['LDUU'].split(), dtype='float64') - [0.5, 0.6, 0]) < 1e-8)
assert all(abs(array(map['LDUL'].split(), dtype='float64') - [0, 1, -1]) < 1e-8)
def test_disabled_nlep(vasp, Specie, structure):
from numpy import all, abs, array
from pylada.vasp.specie import U, nlep
import pylada
pylada.vasp_has_nlep = True
vasp.species = {
'A': Specie([U(2, 0, 0.5)]),
'B': Specie([U(2, 0, -0.5), nlep(2, 1, -1.0)]),
'X': Specie([])
}
vasp.ldau = False
assert vasp.ldau == False
assert vasp.output_map(vasp=vasp) is None
def test_U_disabled(vasp, structure, Specie):
from pylada.vasp.specie import U
import pylada
pylada.vasp_has_nlep = False
vasp.ldau = False
vasp.species = {'A': Specie([U(2, 0, 0.5)]), 'B': Specie([]), 'X': Specie([])}
assert vasp.ldau == False
assert vasp.output_map(vasp=vasp) is None
def test_U():
""" Test U translation. """
from pylada.vasp.specie import U
a = U("liechtenstein", 's', -1e0, 1e0)
assert a['type'] == 1 and a['l'] == 0 and abs(a['U'] + 1e0) < 1e-8 \
and abs(a['J'] - 1e0) < 1e-8 and a['func'] == 'U'
a = U("dudarev", 'p', -0.5, 5e0)
assert a['type'] == 2 and a['l'] == 1 and abs(a['U'] + 0.5) < 1e-8 \
and abs(a['J'] - 5e0) < 1e-8 and a['func'] == 'U'
a = U("dudarev", 'd')
assert a['type'] == 2 and a['l'] == 2 and abs(a['U']) < 1e-8 \
and abs(a['J']) < 1e-8 and a['func'] == 'U'
a = U("dudarev", 'f')
assert a['type'] == 2 and a['l'] == 3 and abs(a['U']) < 1e-8 \
and abs(a['J']) < 1e-8 and a['func'] == 'U'
try:
U('shit')
except:
pass
else:
raise RuntimeError()
try:
U(l=4)
except:
pass
else:
raise RuntimeError()
try:
U(type=0)
except:
pass
else:
raise RuntimeError()
def load_FERE_species(vasp: Vasp, structure):
# See vasp/functional.py: elementName, fileName, max or min oxidation state
pseudoDir = '$PSEUDO_DIR'
vasp.add_specie = "Sc", pseudoDir + "/Sc_sv", U("dudarev", "d", 3) # FERE
vasp.add_specie = "Y", pseudoDir + "/Y_sv", U("dudarev", "d", 3) # FERE
# vasp.add_specie = "Ti", pseudoDir + "/Ti_pv", U("dudarev", "d", 4.35) # Wolverton 3+
# vasp.add_specie = "V", pseudoDir + "/V_pv", U("dudarev", "d", 4.9) # Wolverton 2+
# vasp.add_specie = "Cr", pseudoDir + "/Cr_pv", U("dudarev", "d", 3.04) # Wolverton 3+
vasp.add_specie = "Zr", pseudoDir + "/Zr_sv", U("dudarev", "d", 3) # FERE
# vasp.add_specie = "Mn", pseudoDir + "/Mn_pv", U("dudarev", "d", 2.98) # Wolverton 2+
# vasp.add_specie = "Mn3p", pseudoDir + "/Mn_pv", U("dudarev", "d", 4.54) # Wolverton 3+
vasp.add_specie = "Fe", pseudoDir + "/Fe_pv", U("dudarev", "d", 3) # FERE
vasp.add_specie = "Co", pseudoDir + "/Co_pv", U("dudarev", "d", 3) # Wolverton 2+
vasp.add_specie = "Ni", pseudoDir + "/Ni_pv", U("dudarev", "d", 3) # FERE
vasp.add_specie = "Cu", pseudoDir + "/Cu_pv", U("dudarev", "d", 5.0) # FERE
vasp.add_specie = "Nb", pseudoDir + "/Nb_pv", U("dudarev", "d", 3.0) # FERE
vasp.add_specie = "Ce", pseudoDir + "/Ce", U("dudarev", "f", 3.0) # Wolverton Ceria Paper
vasp.add_specie = "Zn", pseudoDir + "/Zn",
vasp.add_specie = "Ga", pseudoDir + "/Ga",
vasp.add_specie = "O", pseudoDir + "/O"
vasp.add_specie = "Al", pseudoDir + "/Al"
vasp.add_specie = "H", pseudoDir + "/H"
vasp.add_specie = "Nb", pseudoDir + "/Nb_pv"
vasp.add_specie = "Ta", pseudoDir + "/Ta_pv"
vasp.add_specie = "Hf", pseudoDir + "/Hf_pv"
vasp.add_specie = "Sr", pseudoDir + "/Sr_sv"
vasp.add_specie = "Si", pseudoDir + "/Si"
vasp.add_specie = "Cd", pseudoDir + "/Cd"
vasp.add_specie = "Ba", pseudoDir + "/Ba_sv"
vasp.add_specie = "Be", pseudoDir + "/Be"
vasp.add_specie = "Ba", pseudoDir + "/Ba_sv"
vasp.add_specie = "Bi", pseudoDir + "/Bi_d"
vasp.add_specie = "Ge", pseudoDir + "/Ge_d"
vasp.add_specie = "Se", pseudoDir + "/Se"
vasp.add_specie = "Sb", pseudoDir + "/Sb"
vasp.add_specie = "Na", pseudoDir + "/Na_pv"
vasp.add_specie = "Ca", pseudoDir + "/Ca_pv"
vasp.add_specie = "In", pseudoDir + "/In_d"
vasp.add_specie = "K", pseudoDir + "/K_sv"
vasp.add_specie = "Mg", pseudoDir + "/Mg"
vasp.add_specie = "Sn", pseudoDir + "/Sn_d"
vasp.add_specie = "Li", pseudoDir + "/Li_sv"
vasp.add_specie = "La", pseudoDir + "/La" # TODO Determine U
return (vasp)
def test():
from collections import namedtuple
from pickle import loads, dumps
from pylada.crystal.cppwrappers import Structure
from pylada.vasp.incar._params import UParams
from pylada.vasp.specie import U, nlep
u = 0.25
x, y = u, 0.25 - u
structure = Structure([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]]) \
.add_atom(5.000000e-01, 5.000000e-01, 5.000000e-01, "A") \
.add_atom(5.000000e-01, 2.500000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 5.000000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 2.500000e-01, 5.000000e-01, "A") \
.add_atom(8.750000e-01, 8.750000e-01, 8.750000e-01, "B") \
.add_atom(1.250000e-01, 1.250000e-01, 1.250000e-01, "B") \
.add_atom( x, x, x, "X") \
.add_atom( x, y, y, "X") \
.add_atom( y, x, y, "X") \
.add_atom( y, y, x, "X") \
.add_atom( -x, -x, -x, "X") \
.add_atom( -x, -y, -y, "X") \
.add_atom( -y, -x, -y, "X") \
.add_atom( -y, -y, -x, "X")
Vasp = namedtuple('Vasp', ['species'])
Specie = namedtuple('Specie', ['U'])
vasp = Vasp({
'A': Specie([U(2, 0, 0.5)]),
'B': Specie([U(2, 0, -0.5), nlep(2, 1, -1.0)]),
'X': Specie([])
})
a =\
"""\
LDAU = .TRUE.
LDAUPRINT = 0
LDAUTYPE = 2
LDUL1= 0 -1 0
LDUU1= 5.0000000000e-01 0.0000000000e+00 -5.0000000000e-01
LDUJ1= 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00
LDUO1= 1 1 1
LDUL2= -1 -1 1
LDUU2= 0.0000000000e+00 0.0000000000e+00 -1.0000000000e+00
LDUJ2= 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00
LDUO2= 1 1 2
"""
assert a == UParams('off').incar_string(vasp=vasp, structure=structure)
vasp = Vasp({
'A': Specie([U(2, 0, 0.5)]),
'B': Specie([U(2, 0, -0.5), nlep(2, 2, -1.0, -3.0)]),
'X': Specie([])
})
a =\
"""\
LDAU = .TRUE.
LDAUPRINT = 1
LDAUTYPE = 2
LDUL1= 0 -1 0
LDUU1= 5.0000000000e-01 0.0000000000e+00 -5.0000000000e-01
LDUJ1= 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00
LDUO1= 1 1 1
LDUL2= -1 -1 2
LDUU2= 0.0000000000e+00 0.0000000000e+00 -1.0000000000e+00
LDUJ2= 0.0000000000e+00 0.0000000000e+00 -3.0000000000e+00
LDUO2= 1 1 3
"""
assert a == UParams('on').incar_string(vasp=vasp, structure=structure)
vasp = Vasp({'A': Specie([]), 'B': Specie([]), 'X': Specie([])})
assert '# no LDA+U/NLEP parameters' == UParams('all').incar_string(
vasp=vasp, structure=structure)
assert repr(UParams('off')) == "UParams('off')"
assert repr(UParams('on')) == "UParams('on')"
assert repr(UParams(None)) == "UParams('off')"
assert repr(UParams('all')) == "UParams('all')"
assert repr(loads(dumps(UParams('off')))) == "UParams('off')"
assert repr(loads(dumps(UParams('on')))) == "UParams('on')"
assert repr(loads(dumps(UParams(None)))) == "UParams('off')"
assert repr(loads(dumps(UParams('all')))) == "UParams('all')"
def test():
from collections import namedtuple
from pickle import loads, dumps
from numpy import all, abs, array
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada.vasp.specie import U, nlep
import pylada
u = 0.25
x, y = u, 0.25 - u
structure = Structure([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]]) \
.add_atom(5.000000e-01, 5.000000e-01, 5.000000e-01, "A") \
.add_atom(5.000000e-01, 2.500000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 5.000000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 2.500000e-01, 5.000000e-01, "A") \
.add_atom(8.750000e-01, 8.750000e-01, 8.750000e-01, "B") \
.add_atom(1.250000e-01, 1.250000e-01, 1.250000e-01, "B") \
.add_atom( x, x, x, "X") \
.add_atom( x, y, y, "X") \
.add_atom( y, x, y, "X") \
.add_atom( y, y, x, "X") \
.add_atom( -x, -x, -x, "X") \
.add_atom( -x, -y, -y, "X") \
.add_atom( -y, -x, -y, "X") \
.add_atom( -y, -y, -x, "X")
a = Vasp()
Specie = namedtuple('Specie', ['U'])
a.species = {'A': Specie([]), 'B': Specie([]), 'X': Specie([])}
pylada.vasp_has_nlep = False
o = a._input['ldau']
d = {'LDAU': o.__class__}
assert a.ldau == True
assert o.output_map(vasp=a, structure=structure) is None
assert eval(repr(o), d)._value == True
assert eval(repr(o), d).keyword == 'LDAU'
assert loads(dumps(o)).keyword == 'LDAU'
assert loads(dumps(o))._value
# now disables U.
a.species = {'A': Specie([U(2, 0, 0.5)]), 'B': Specie([]), 'X': Specie([])}
a.ldau = False
assert a.ldau == False
print o
assert o.output_map(vasp=a) is None
# now prints U
a.ldau = True
map = o.output_map(vasp=a, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(abs(array(map['LDUJ'].split(), dtype='float64')) < 1e-8)
assert all(
abs(array(map['LDUU'].split(), dtype='float64') - [0.5, 0, 0]) < 1e-8)
assert all(
abs(array(map['LDUL'].split(), dtype='float64') - [0, -1, -1]) < 1e-8)
a.species = {
'A': Specie([U(2, 0, 0.5)]),
'B': Specie([U(2, 1, 0.6)]),
'X': Specie([])
}
map = o.output_map(vasp=a, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(abs(array(map['LDUJ'].split(), dtype='float64')) < 1e-8)
assert all(
abs(array(map['LDUU'].split(), dtype='float64') -
[0.5, 0, 0.6]) < 1e-8)
assert all(
abs(array(map['LDUL'].split(), dtype='float64') - [0, -1, 1]) < 1e-8)
# now tries NLEP
pylada.vasp_has_nlep = True
a.species = {
'A': Specie([U(2, 0, 0.5)]),
'B': Specie([U(2, 0, -0.5), nlep(2, 1, -1.0)]),
'X': Specie([])
}
a.ldau = False
assert a.ldau == False
assert o.output_map(vasp=a) is None
a.ldau = True
map = o.output_map(vasp=a, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(
abs(array(map['LDUL1'].split(), dtype='float64') - [0, -1, 0]) < 1e-8)
assert all(
abs(array(map['LDUU1'].split(), dtype='float64') -
[0.5, 0, -0.5]) < 1e-8)
assert all(
abs(array(map['LDUJ1'].split(), dtype='float64') - [0, 0, 0]) < 1e-8)
assert all(
abs(array(map['LDUO1'].split(), dtype='float64') - [1, 1, 1]) < 1e-8)
assert all(
abs(array(map['LDUL2'].split(), dtype='float64') - [-1, -1, 1]) < 1e-8)
assert all(
abs(array(map['LDUU2'].split(), dtype='float64') -
[0, 0, -1.0]) < 1e-8)
assert all(
abs(array(map['LDUJ2'].split(), dtype='float64') - [0, 0, 0]) < 1e-8)
assert all(
abs(array(map['LDUO2'].split(), dtype='float64') - [1, 1, 2]) < 1e-8)
a.species = {
'A': Specie([U(2, 0, 0.5)]),
'B': Specie([U(2, 0, -0.5), nlep(2, 2, -1.0, -3.0)]),
'X': Specie([])
}
a.ldau = True
map = o.output_map(vasp=a, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(
abs(array(map['LDUL1'].split(), dtype='float64') - [0, -1, 0]) < 1e-8)
assert all(
abs(array(map['LDUU1'].split(), dtype='float64') -
[0.5, 0, -0.5]) < 1e-8)
assert all(
abs(array(map['LDUJ1'].split(), dtype='float64') - [0, 0, 0]) < 1e-8)
assert all(
abs(array(map['LDUO1'].split(), dtype='float64') - [1, 1, 1]) < 1e-8)
assert all(
abs(array(map['LDUL2'].split(), dtype='float64') - [-1, -1, 2]) < 1e-8)
assert all(
abs(array(map['LDUU2'].split(), dtype='float64') -
[0, 0, -1.0]) < 1e-8)
assert all(
abs(array(map['LDUJ2'].split(), dtype='float64') -
[0, 0, -3.0]) < 1e-8)
assert all(
abs(array(map['LDUO2'].split(), dtype='float64') - [1, 1, 3]) < 1e-8)
def load_low_FERE_species(vasp: Vasp, structure):
pseudoDir = '$PSEUDO_DIR'
vasp.add_specie = "Fe", pseudoDir + "/Fe", U("dudarev", "d", 3) # FERE
vasp.add_specie = "O", pseudoDir + "/O_s"
vasp.add_specie = "Al", pseudoDir + "/Al"
return vasp
def load_optimized_U_species(vasp : Vasp, structure):
# See vasp/functional.py: elementName, fileName, max or min oxidation state
pseudoDir = '$PSEUDO_DIR'
vasp.add_specie = "Sc", pseudoDir + "/Sc_sv", U("dudarev", "d", 3) # FERE
vasp.add_specie = "Y", pseudoDir + "/Y_sv", U("dudarev", "d", 3) # FERE
vasp.add_specie = "Ti", pseudoDir + "/Ti_pv", U("dudarev", "d", 4.35) # Wolverton 3+
vasp.add_specie = "V", pseudoDir + "/V_pv", U("dudarev", "d", 4.9) # Wolverton 2+
vasp.add_specie = "Cr", pseudoDir + "/Cr_pv", U("dudarev", "d", 3.04) # Wolverton 3+
vasp.add_specie = "Zr", pseudoDir + "/Zr_sv", U("dudarev", "d", 3) # FERE
vasp.add_specie = "Mn", pseudoDir + "/Mn_pv", U("dudarev", "d", 2.98) # Wolverton 2+
vasp.add_specie = "Mn3p", pseudoDir + "/Mn_pv", U("dudarev", "d", 4.54) # Wolverton 3+
vasp.add_specie = "Mn4p", pseudoDir + "/Mn", U("dudarev", "d", 3.19) # Wolverton 3+
vasp.add_specie = "Fe", pseudoDir + "/Fe_pv", U("dudarev", "d", 4.04) # Wolverton 2+,
vasp.add_specie = "Co", pseudoDir + "/Co_pv", U("dudarev", "d", 3.75) # Wolverton 2+
vasp.add_specie = "Ni", pseudoDir + "/Ni_pv", U("dudarev", "d", 4.4) # Wolverton 2+
vasp.add_specie = "Cu", pseudoDir + "/Cu_pv", U("dudarev", "d" , 5.0) # FERE
vasp.add_specie = "Nb", pseudoDir + "/Nb_pv", U("dudarev", "d" , 3.0) # FERE
vasp.add_specie = "Ce", pseudoDir + "/Ce", U("dudarev", "f" , 3.0) # Wolverton Ceria Paper
vasp.add_specie = "Pr", pseudoDir + "/Pr", U("dudarev", "f" , 4.3) # https://doi.org/10.1016/j.actamat.2010.11.041
vasp.add_specie = "Nd", pseudoDir + "/Nd", U("dudarev", "f" , 6.0) # https://doi.org/10.1016/j.actamat.2010.11.041
vasp.add_specie = "Eu", pseudoDir + "/Eu", U("dudarev", "f" , 7.0) # https://doi.org/10.1016/j.actamat.2010.11.041
vasp.add_specie = "Sm", pseudoDir + "/Sm", U("dudarev", "f" , 8.0) # https://doi.org/10.1016/j.actamat.2010.11.041
vasp.add_specie = "Gd", pseudoDir + "/Gd", U("dudarev", "f" , 4.0) # https://doi.org/10.1002/jcc.23618
vasp.add_specie = "Tb", pseudoDir + "/Tb", U("dudarev", "f" , 10.0) # https://doi.org/10.1002/jcc.23618
vasp.add_specie = "Ho", pseudoDir + "/Ho", U("dudarev", "f" , 8.0) # https://doi.org/10.1002/jcc.24272
vasp.add_specie = "Er", pseudoDir + "/Er", U("dudarev", "f" , 8.4) # https://doi.org/10.1002/jcc.24272
vasp.add_specie = "Tm", pseudoDir + "/Tm", U("dudarev", "f" , 9.1) # https://doi.org/10.1002/jcc.24272
vasp.add_specie = "Yb", pseudoDir + "/Yb", U("dudarev", "f" , 6.4) # https://doi.org/10.1002/jcc.24272
vasp.add_specie = "Dy", pseudoDir + "/Dy", U("dudarev", "f" , 10.9) # https://doi.org/10.1002/jcc.23618
vasp.add_specie = "Gd", pseudoDir + "/Gd", U("dudarev", "f" , 4.5) # https://doi.org/10.1002/jcc.23618
vasp.add_specie = "Lu", pseudoDir + "/Lu", U("dudarev", "f" , 9.5) # https://doi.org/10.1002/jcc.24272
vasp.add_specie = "Zn", pseudoDir + "/Zn",
vasp.add_specie = "Ga", pseudoDir + "/Ga",
vasp.add_specie = "O", pseudoDir + "/O"
vasp.add_specie = "S", pseudoDir + "/S"
vasp.add_specie = "P", pseudoDir + "/P"
vasp.add_specie = "Al", pseudoDir + "/Al"
vasp.add_specie = "H", pseudoDir + "/H"
vasp.add_specie = "Hf", pseudoDir + "/Hf_pv", U("dudarev", "d", 3) # FERE
vasp.add_specie = "Ta", pseudoDir + "/Ta_pv", U("dudarev", "d", 3) # FERE
vasp.add_specie = "Sr", pseudoDir + "/Sr_sv"
vasp.add_specie = "F", pseudoDir + "/F"
vasp.add_specie = "C", pseudoDir + "/C"
vasp.add_specie = "Si", pseudoDir + "/Si"
vasp.add_specie = "Cd", pseudoDir + "/Cd"
vasp.add_specie = "Ba", pseudoDir + "/Ba_sv"
vasp.add_specie = "Be", pseudoDir + "/Be"
vasp.add_specie = "Ba", pseudoDir + "/Ba_sv"
vasp.add_specie = "Bi", pseudoDir + "/Bi_d"
vasp.add_specie = "Ge", pseudoDir + "/Ge_d"
vasp.add_specie = "Se", pseudoDir + "/Se"
vasp.add_specie = "Sb", pseudoDir + "/Sb"
vasp.add_specie = "Na", pseudoDir + "/Na_pv"
vasp.add_specie = "Ca", pseudoDir + "/Ca_pv"
vasp.add_specie = "In", pseudoDir + "/In_d"
vasp.add_specie = "K", pseudoDir + "/K_sv"
vasp.add_specie = "Mg", pseudoDir + "/Mg"
vasp.add_specie = "Sn", pseudoDir + "/Sn_d"
vasp.add_specie = "Li", pseudoDir + "/Li_sv"
vasp.add_specie = "La", pseudoDir + "/La" # TODO Determine U
las = ['Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb','Dy', 'Ho','Er','Tm','Yb','Lu']
for atom in structure:
if atom.type in las:
vasp.lmaxmix = 6
return(vasp)