def test_pseudopotential_group_get_structure():
"""Test get_pseudos from structure"""
Pseudo = DataFactory("gaussian.pseudo")
PseudopotentialGroup = GroupFactory("gaussian.pseudo")
pseudogroup, created = PseudopotentialGroup.objects.get_or_create("test")
assert created
pseudogroup.store()
with open(TEST_DIR.joinpath("GTH_POTENTIALS.LiH"), "r") as fhandle:
pseudos = Pseudo.from_cp2k(fhandle)
pseudogroup.add_nodes([pseudo.store() for pseudo in pseudos])
StructureData = DataFactory("structure")
structure = StructureData(cell=[[4.796302, 0, 0], [0, 4.796302, 0],
[0, 0, 4.796302]],
pbc=True)
structure.append_atom(position=(0.000, 0.000, 0.000), symbols="Li")
structure.append_atom(position=(0.500, 0.500, 0.000), symbols="Li")
structure.append_atom(position=(0.500, 0.000, 0.500), symbols="Li")
structure.append_atom(position=(0.000, 0.500, 0.500), symbols="Li")
structure.append_atom(position=(0.000, 0.500, 0.000), symbols="H")
structure.append_atom(position=(0.000, 0.000, 0.500), symbols="H")
structure.append_atom(position=(0.500, 0.000, 0.000), symbols="H")
structure.append_atom(position=(0.500, 0.500, 0.500), symbols="H")
retrieved_pseudos = pseudogroup.get_pseudos(structure=structure)
assert retrieved_pseudos == {
"Li": [p for p in pseudos if p.element == "Li"],
"H": [p for p in pseudos if p.element == "H"],
}
def test_get_matching_empty():
Pseudo = DataFactory("gaussian.pseudo")
with open(TEST_DIR.joinpath("GTH_POTENTIALS.LiH"), "r") as fhandle:
pseudos = Pseudo.from_cp2k(fhandle)
with pytest.raises(NotExistent):
pseudos[0].get_matching_basisset()
def test_n_orbital_functions():
BasisSet = DataFactory("gaussian.basisset")
with open(TEST_DIR.joinpath("BASIS_MOLOPT.Hf"), "r") as fhandle:
bsets = BasisSet.from_cp2k(fhandle)
assert bsets
assert bsets[0].n_orbital_functions == 1 * 3 + 3 * 2 + 5 * 2 + 7 * 1 # l=0,1,2,3 with respective nshells=3,2,2,1
def test_get_matching_empty():
BasisSet = DataFactory("gaussian.basisset")
with open(TEST_DIR.joinpath("BASIS_MOLOPT.H"), "r") as fhandle:
bsets = BasisSet.from_cp2k(fhandle)
with pytest.raises(NotExistent):
bsets[0].get_matching_pseudopotential()
def test_lookup():
BasisSet = DataFactory("gaussian.basisset")
with open(TEST_DIR.joinpath("BASIS_MOLOPT.H"), "r") as fhandle:
bsets = BasisSet.from_cp2k(fhandle)
bsets[0].store()
basis_H = BasisSet.get(element="H", name="SZV-MOLOPT-GTH")
assert basis_H
def test_nlcc_import():
"""With the usage of the cp2k-input-tools for file handling we also gained support for the NLCC pseudos"""
Pseudopotential = DataFactory("gaussian.pseudo")
with open(TEST_DIR.joinpath("NLCC_POTENTIALS"), "r") as fhandle:
# get only the He PADE pseudo
pseudos = Pseudopotential.from_cp2k(
fhandle, filters={"element": lambda x: x == "C"})
assert len(pseudos) == 1
def test_import_from_cp2k():
BasisSet = DataFactory("gaussian.basisset")
with open(TEST_DIR.joinpath("BASIS_MOLOPT.H"), "r") as fhandle:
bsets = BasisSet.from_cp2k(fhandle)
assert len(bsets) == 1
bsets[0].store()
# check that the name is used for the node label
assert bsets[0].label == bsets[0].name
def test_to_cp2k():
"""Check whether writing a CP2K datafile works"""
Pseudo = DataFactory("gaussian.pseudo")
with open(TEST_DIR.joinpath("GTH_POTENTIALS.LiH"), "r") as fhandle:
pseudos = Pseudo.from_cp2k(fhandle)
fhandle = io.StringIO()
for pseudo in pseudos:
pseudo.to_cp2k(fhandle)
assert fhandle.getvalue()
def test_to_cp2k_nlcc_missing():
"""Check whether writing a CP2K datafile works, also with missing NLCC attribute"""
Pseudo = DataFactory("gaussian.pseudo")
with open(TEST_DIR.joinpath("GTH_POTENTIALS.LiH"), "r") as fhandle:
pseudos = Pseudo.from_cp2k(fhandle)
fhandle = io.StringIO()
for pseudo in pseudos:
del pseudo.attributes["nlcc"]
pseudo.to_cp2k(fhandle)
assert fhandle.getvalue()
def cp2k_basissets(bsdataset):
"""Returns basisset objects from the data above"""
fhandle = StringIO(BSET_DATA[bsdataset])
BasisSet = DataFactory("gaussian.basisset") # pylint: disable=invalid-name
bsets = {}
for bset in BasisSet.from_cp2k(fhandle):
bset.store(
) # store because the validator accesses it when raising an error
if bset.element in bsets:
# if we have multiple basissets per element, pass them as a list
if not isinstance(bsets[bset.element], list):
bsets[bset.element] = [bsets[bset.element]]
bsets[bset.element] += [bset]
else:
bsets[bset.element] = bset
return bsets
def test_lookup():
Pseudopotential = DataFactory("gaussian.pseudo")
with open(TEST_DIR.joinpath("GTH_POTENTIALS"), "r") as fhandle:
# get only the He PBE pseudo
pseudos = Pseudopotential.from_cp2k(fhandle,
filters={
"element":
lambda x: x == "He",
"tags":
lambda x: set(
("PBE", )).issubset(x)
})
pseudos[0].store()
assert Pseudopotential.get(element="He", name="GTH-PBE-q2")
assert Pseudopotential.get(element="He", name="GTH-PBE")
def test_pseudopotential_group_get():
Pseudo = DataFactory("gaussian.pseudo")
PseudopotentialGroup = GroupFactory("gaussian.pseudo")
pseudogroup, created = PseudopotentialGroup.objects.get_or_create("test")
assert created
pseudogroup.store()
with open(TEST_DIR.joinpath("GTH_POTENTIALS.LiH"), "r") as fhandle:
pseudos = Pseudo.from_cp2k(fhandle)
pseudogroup.add_nodes([pseudo.store() for pseudo in pseudos])
retrieved_pseudos = pseudogroup.get_pseudos(elements=["Li", "H"])
assert retrieved_pseudos == {
"Li": [p for p in pseudos if p.element == "Li"],
"H": [p for p in pseudos if p.element == "H"],
}
def test_import_from_cp2k():
Pseudopotential = DataFactory("gaussian.pseudo")
with open(TEST_DIR.joinpath("GTH_POTENTIALS"), "r") as fhandle:
# get only the He PADE pseudo
pseudos = Pseudopotential.from_cp2k(fhandle,
filters={
"element":
lambda x: x == "He",
"tags":
lambda x: set(
("PADE", )).issubset(x)
})
assert len(pseudos) == 1
pseudos[0].store()
# check that the name is used for the node label
assert pseudos[0].label == pseudos[0].name
def test_get():
from aiida.common.exceptions import MultipleObjectsError, NotExistent
BasisSet = DataFactory("gaussian.basisset")
with open(TEST_DIR.joinpath("MOLOPT_PBE.LiH"), "r") as fhandle:
bsets = BasisSet.from_cp2k(fhandle)
for bset in bsets:
bset.store()
# getting a single one should work
bset = BasisSet.get(element="H", name="DZVP-MOLOPT-PBE-GTH-q1")
assert bset.element == "H" and bset.name == "DZVP-MOLOPT-PBE-GTH-q1"
with pytest.raises(NotExistent):
BasisSet.get(element="C")
# leaving away the name should return multiple ones, raising an error
with pytest.raises(MultipleObjectsError):
BasisSet.get(element="H")
def test_get():
from aiida.common.exceptions import MultipleObjectsError, NotExistent
Pseudo = DataFactory("gaussian.pseudo")
with open(TEST_DIR.joinpath("GTH_POTENTIALS.LiH"), "r") as fhandle:
pseudos = Pseudo.from_cp2k(fhandle)
for pseudo in pseudos:
pseudo.store()
# getting a single one should work
pseudo = Pseudo.get(element="H", name="GTH-PBE-q1")
assert pseudo.element == "H" and pseudo.name == "GTH-PBE-q1"
with pytest.raises(NotExistent):
Pseudo.get(element="C")
# leaving away the name should return multiple ones, raising an error
with pytest.raises(MultipleObjectsError):
Pseudo.get(element="Li")
def load_data(prefix="MY-"):
"""
This is something the user will usually do only ONCE and most likely by
using the CLI of the aiida-gaussian-datatypes.
"""
# Note: the basissets and pseudos deliberately have a prefix to avoid matching
# any CP2K provided entries which may creep in via the DATA_DIR
bset_input = f"""\
H {prefix}AUTO-DZVP-MOLOPT-GTH {prefix}AUTO-DZVP-MOLOPT-GTH-q1
1
2 0 1 7 2 1
11.478000339908 0.024916243200 -0.012512421400 0.024510918200
3.700758562763 0.079825490000 -0.056449071100 0.058140794100
1.446884268432 0.128862675300 0.011242684700 0.444709498500
0.716814589696 0.379448894600 -0.418587548300 0.646207973100
0.247918564176 0.324552432600 0.590363216700 0.803385018200
0.066918004004 0.037148121400 0.438703133000 0.892971208700
0.021708243634 -0.001125195500 -0.059693171300 0.120101316500
O {prefix}AUTO-DZVP-MOLOPT-SR-GTH {prefix}AUTO-DZVP-MOLOPT-SR-GTH-q6
1
2 0 2 5 2 2 1
10.389228018317 0.126240722900 0.069215797900 -0.061302037200 -0.026862701100 0.029845227500
3.849621072005 0.139933704300 0.115634538900 -0.190087511700 -0.006283021000 0.060939733900
1.388401188741 -0.434348231700 -0.322839719400 -0.377726982800 -0.224839187800 0.732321580100
0.496955043655 -0.852791790900 -0.095944016600 -0.454266086000 0.380324658600 0.893564918400
0.162491615040 -0.242351537800 1.102830348700 -0.257388983000 1.054102919900 0.152954188700
"""
pseudo_input = f"""\
#
H {prefix}AUTO-GTH-PADE-q1 {prefix}AUTO-GTH-LDA-q1 {prefix}AUTO-GTH-PADE {prefix}AUTO-GTH-LDA
1
0.20000000 2 -4.18023680 0.72507482
0
O {prefix}AUTO-GTH-PADE-q6 {prefix}AUTO-GTH-LDA-q6 {prefix}AUTO-GTH-PADE {prefix}AUTO-GTH-LDA
2 4
0.24762086 2 -16.58031797 2.39570092
2
0.22178614 1 18.26691718
0.25682890 0
"""
BasisSet = DataFactory("gaussian.basisset") # pylint: disable=invalid-name
Pseudo = DataFactory("gaussian.pseudo") # pylint: disable=invalid-name
fhandle_bset = StringIO(bset_input)
fhandle_pseudo = StringIO(pseudo_input)
try:
bsets = {b.element: b for b in BasisSet.from_cp2k(fhandle_bset, duplicate_handling='error')}
pseudos = {p.element: p for p in Pseudo.from_cp2k(fhandle_pseudo, duplicate_handling='error')}
except UniquenessError: # if the user already ran the script, fetch the data from the db instead
bsets = {
"H": BasisSet.get("H", f"{prefix}AUTO-DZVP-MOLOPT-GTH"),
"O": BasisSet.get("O", f"{prefix}AUTO-DZVP-MOLOPT-SR-GTH"),
}
pseudos = {
"H": Pseudo.get("H", f"{prefix}AUTO-GTH-PADE-q1"),
"O": Pseudo.get("O", f"{prefix}AUTO-GTH-PADE-q6"),
}
return bsets, pseudos
def cp2k_pseudos(pdataset):
"""Returns pseudo objects from the data above"""
fhandle = StringIO(PSEUDO_DATA[pdataset])
Pseudo = DataFactory("gaussian.pseudo") # pylint: disable=invalid-name
return {p.element: p for p in Pseudo.from_cp2k(fhandle)}
