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QC model method contributions #160

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d436e95
add main and auxiliary basis set quantities to AtomCenteredBasisSet
EBB2675 Sep 24, 2024
022c1fa
formatting
EBB2675 Sep 24, 2024
bf1f6f4
Merge branch 'develop' into coupled_cluster
EBB2675 Sep 25, 2024
af88624
add a draft for AtomCenteredFunction
EBB2675 Sep 25, 2024
0a9d98b
add a quantity for number of primitives
EBB2675 Sep 25, 2024
a204ec4
add atoms_state reference to AtomCenteredBasisSet
EBB2675 Sep 26, 2024
a325753
Merge remote-tracking branch 'origin/develop' into 130-atom-centered-…
EBB2675 Oct 1, 2024
8866ab7
assign JSON format to basis set
EBB2675 Oct 2, 2024
c7b078a
add type and auxiliary_type quantities to AtomCenteredBasisSet
EBB2675 Oct 8, 2024
1208e88
reformatted basis_set.py
EBB2675 Oct 8, 2024
fbc13f9
add NAO and point charges to basis set types
EBB2675 Oct 8, 2024
ddab789
add cECPs and pointcharges to AtomCenteredBasisSet
EBB2675 Oct 9, 2024
8c6ae1a
fix point charge Quantity type
EBB2675 Oct 11, 2024
c94e995
a bit of a cleanup
EBB2675 Oct 14, 2024
a007e1e
merge develop
EBB2675 Oct 18, 2024
62de243
move GTOIntegralDecomposition to NumericalSettings
EBB2675 Oct 24, 2024
c12adac
Merge branch 'develop' into 130-atom-centered-basis-set
EBB2675 Nov 19, 2024
52d6b9a
merge develop
EBB2675 Nov 19, 2024
646430c
add Mesh, NumericalIntegration and MolecularHamiltonianSubTerms
EBB2675 Nov 19, 2024
cca109f
minor adjustments to Mesh and NumericalIntegration
EBB2675 Nov 19, 2024
42f4f38
add integration_thresh and weight_cutoff to NumericalIntegration
EBB2675 Nov 20, 2024
0f92eb9
check whether n_primitive matches the lengths of exponents and contra…
EBB2675 Nov 20, 2024
e8fb5ef
add tests for AtomCenteredBasisSet and AtomCenteredFunction
EBB2675 Nov 20, 2024
4826f0c
add tests for Mesh and NumericalIntegration
EBB2675 Nov 20, 2024
c5141ab
modify Mesh
EBB2675 Nov 20, 2024
23d7615
MEnum for MolecularHamiltonianContributions
EBB2675 Nov 21, 2024
9ef13ea
remove contributions
EBB2675 Nov 21, 2024
80c8b64
add a normalizer function for the AtomCenteredFunction to handle comb…
EBB2675 Nov 28, 2024
4ac1076
fix test_basis_set.py
EBB2675 Dec 4, 2024
10e782c
add OrbitalLocalization to numerical_settings.py
EBB2675 Dec 4, 2024
5c15e97
add method to LocalCorrelation
EBB2675 Dec 4, 2024
2fd6398
add total_charge and total_spin to ModelSystem
EBB2675 Dec 5, 2024
c9d6118
add a simple HF class
EBB2675 Dec 10, 2024
816c7ba
a placeholder for MO and LCAO
EBB2675 Dec 11, 2024
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assign JSON format to basis set
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EBB2675 committed Oct 2, 2024
commit 8866ab7785a103cf11c50698f4fccd9637adf6d1
46 changes: 43 additions & 3 deletions src/nomad_simulations/schema_packages/basis_set.py
Original file line number Diff line number Diff line change
@@ -13,7 +13,7 @@
from nomad import utils
from nomad.datamodel.data import ArchiveSection
from nomad.datamodel.metainfo.annotations import ELNAnnotation
from nomad.metainfo import MEnum, Quantity, SubSection
from nomad.metainfo import MEnum, Quantity, SubSection, JSON
from nomad.units import ureg

from nomad_simulations.schema_packages.atoms_state import AtomsState
@@ -191,7 +191,7 @@ class AtomCenteredFunction(ArchiveSection):
"""

function_type = Quantity(
type=MEnum('S', 'P', 'D', 'F', 'G', 'H', 'I', 'J'),
type=MEnum('s', 'p', 'd', 'f', 'g', 'h', 'i', 'j'),
description="""
the angular momentum of the shell to be added.
""",
@@ -224,7 +224,47 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
super().normalize(archive, logger)
# self.name = self.m_def.name

class AtomCenteredBasisSet(BasisSetComponent):
"""
Defines an atom-centered basis set, using a single JSON quantity for all basis set types,
while allowing different AtomState references for each basis set type.
"""

basis_set_data = Quantity(
type=JSON, # Use JSON to store basis set information, including atom references
description="""
JSON object containing all the basis set information along with atom references. Example:
{
"main_basis_set": {
"name": "cc-pVTZ",
"atoms_ref": [ref_to_atoms_1, ref_to_atoms_2]
},
"aux_c_basis_set": {
"name": "cc-pVTZ/C",
"atoms_ref": [ref_to_atoms_3]
},
"aux_j_basis_set": {
"name": "RIJ",
"atoms_ref": [ref_to_atoms_4]
},
"aux_jk_basis_set": {
"name": "aug-cc-pVTZ/JK",
"atoms_ref": [ref_to_atoms_1, ref_to_atoms_5]
}
}
""",
)

functional_composition = SubSection(
sub_section=AtomCenteredFunction.m_def, repeats=True
)

def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
super().normalize(archive, logger)



'''
class AtomCenteredBasisSet(BasisSetComponent):
"""
Defines an atom-centered basis set.
@@ -275,7 +315,7 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
# self.name = self.m_def.name
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Don't forget to do something with this.

Do we already have some sort of convention the names? It seems like most or at least a lot of classes have the line you are commenting out here, but I have also seen self.name = self.m_def.name if self.name is None else self.name which allows the parser to overwrite this name.

# TODO: set name based on basis functions
# ? use basis set names from Basis Set Exchange

'''

class APWBaseOrbital(ArchiveSection):
"""
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