QC model method contributions by EBB2675 · Pull Request #160 · FAIRmat-NFDI/nomad-simulations

EBB2675 · 2024-12-16T15:36:28Z

The first part of ModelMethod contributions for chemistry.

Up until now:

HartreeFock
PerturbationMethod
MolecularOrbital
LCAO
LocalCorrelation
AtomCenteredBasisSet
GTOIntegralDecomposition
NumericalIntegration
OrbitalLocalization

…basis-set

…ction coefficients

…ined orbital types

JFRudzinski

Looks very nice! I only gave some minor formatting suggestions.

To fully assess the schema, it would help to see the parser alongside or even better an example upload that I can use the metainfo browser to inspect.

@ndaelman-hu should of course approve before you merge.

JFRudzinski · 2024-12-18T08:29:14Z

src/nomad_simulations/schema_packages/basis_set.py


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


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.

JFRudzinski · 2024-12-18T08:30:26Z

src/nomad_simulations/schema_packages/model_method.py

+
+    energy = Quantity(
+        type=np.float64,
+        # unit='electron_volt',


JFRudzinski · 2024-12-18T08:31:48Z

src/nomad_simulations/schema_packages/model_method.py

+        - canonical: Default canonical molecular orbitals.
+        - natural: Natural orbitals obtained from the density matrix.
+        - localized: Localized orbitals such as Boys or Foster-Boys localization.
+        TODO: this will be later connected to many other things.


move TODO outside of description

and be a bit more explicit to what you'd like to connect

JFRudzinski · 2024-12-18T08:32:39Z

src/nomad_simulations/schema_packages/model_method.py

+        type=np.float64,
+        description="""
+        Total spin of the system defined as S = (n_alpha_electrons - n_beta_electrons) / 2.
+        Connect to the model system.


Is this a TODO? Clarify or move out of description

JFRudzinski · 2024-12-18T08:33:41Z

src/nomad_simulations/schema_packages/model_method.py

+                    f'For {self.reference_type}, the number of alpha and beta electrons must be equal.'
+                )
+                return False
+        if self.reference_type in ['ROHF', 'ROKS']:


JFRudzinski · 2024-12-18T08:38:41Z

src/nomad_simulations/schema_packages/model_method.py

+    density = Quantity(
+        type=MEnum('relaxed', 'unrelaxed'),
+        description="""
+        unrelaxed density: MP2 expectation value density


Capitals and periods, or make a table as above

JFRudzinski · 2024-12-18T08:38:58Z

src/nomad_simulations/schema_packages/model_method.py

+            - DLPNO-CCSD(T): Domain-Based Local Pair Natural Orbital CCSD(T)
+            - LocalDFT: Local Density Functional Theory.
+
+            # TODO: improve list!


move TODO out of description

JFRudzinski · 2024-12-18T08:41:25Z

src/nomad_simulations/schema_packages/numerical_settings.py

+        """,
+    )
+
+    integration_thresh = Quantity(


rename to "integration_threshold" (if there are other quantities named "thresh" throughout the schema, I would also like to rename those), maybe add a TODO for this

JFRudzinski · 2024-12-18T08:42:07Z

src/nomad_simulations/schema_packages/numerical_settings.py

+    orbital_window = Quantity(
+        shape=['*'],
+        description="""
+        the Molecular orbital range to be localized.


Capital "The"

JFRudzinski · 2024-12-18T08:42:17Z

src/nomad_simulations/schema_packages/numerical_settings.py

+    core_threshold = Quantity(
+        type=np.float64,
+        description="""
+        the energy window for the first occupied MO to be localized (in a.u.).


Capital "The"

ndaelman-hu

Covered model_method and mode_system now. Will do the rest in a future review.
You can resolve these comments in the meantime.

ndaelman-hu · 2024-12-19T11:50:05Z

src/nomad_simulations/schema_packages/model_method.py

+    symmetry_label = Quantity(
+        type=str, description='Symmetry label of the molecular orbital.'
+    )


consider type=MEnum, so you can better distinguish with the atoms state

ndaelman-hu · 2024-12-19T11:51:52Z

src/nomad_simulations/schema_packages/model_method.py

+    A section representing a single molecular orbital.
+    """
+
+    energy = Quantity(


This is also covered by ElectronicEigenvalues, which lists the values and occupations.
Is the energy meant here to simply identify the state?

ndaelman-hu · 2024-12-19T11:56:17Z

src/nomad_simulations/schema_packages/model_method.py

+    A base section for Hartree Fock ansatz.
+    """
+
+    reference_determinant = Quantity(


Maybe you also want to store a reference to the matching DFT calculation?
Then you could even extract this label with normalization.

ndaelman-hu · 2024-12-19T12:00:15Z

src/nomad_simulations/schema_packages/model_method.py

+
+            # TODO: improve list!
+        """,
+        a_eln=ELNAnnotation(component='EnumEditQuantity'),


Note that this does not yet provide any logic for saving the user input.

ndaelman-hu · 2024-12-19T15:33:42Z

src/nomad_simulations/schema_packages/model_method.py

The methodologies are fine, just minor comments.

I'd introduce a single ElectronicState instead of OrbitalState or MolecularOrbital...
Don't get me wrong, these may keep on existing (for now), but they should specialize ElectronicState via inheritance. This can be covered in a follow-up PR, but pls bear this in mind for your current approach.

ndaelman-hu · 2024-12-20T15:36:23Z

src/nomad_simulations/schema_packages/model_system.py

Thx for adding these quantities. I take it that the actual normalization will be in a follow-up PR?

ndaelman-hu · 2024-12-20T15:43:26Z

src/nomad_simulations/schema_packages/model_method.py

+    method = Quantity(
+        type=MEnum('LMP2', 'LCCD', 'LCCSD', 'LCCSD(T)', 'DLPNO-CCSD(T)', 'LocalDFT'),
+        description="""
+        The local correlation method applied. For example:


Pls elaborate a bit more here. Feel free to also add references for specific methods.

ndaelman-hu · 2024-12-20T15:44:44Z

src/nomad_simulations/schema_packages/model_method.py

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


The normalization is redundant here

ndaelman-hu · 2024-12-20T15:45:37Z

src/nomad_simulations/schema_packages/model_method.py

+        | `'BW'`       | Brillouin-Wigner |
+        """,
+        a_eln=ELNAnnotation(component='EnumEditQuantity'),
+    )  # TODO: check if the special symbols are supported


Latex is indeed supported

ndaelman-hu · 2024-12-20T15:49:15Z

src/nomad_simulations/schema_packages/numerical_settings.py

Your changes to Mesh only affect the quantity names and descriptions, correct?
This is fine, but in general I'd leave this for a separate, quick PR. Now we have to check whether all other places that use this interface have been updated too.

The new sections I'll cover in a future review.

coveralls · 2025-01-02T08:30:57Z

Pull Request Test Coverage Report for Build 13011770671

Details

78 of 106 (73.58%) changed or added relevant lines in 5 files are covered.
1 unchanged line in 1 file lost coverage.
Overall coverage decreased (-0.3%) to 79.806%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/nomad_simulations/schema_packages/numerical_settings.py	23	27	85.19%
src/nomad_simulations/schema_packages/model_method.py	27	38	71.05%
src/nomad_simulations/schema_packages/basis_set.py	16	29	55.17%

Files with Coverage Reduction	New Missed Lines	%
src/nomad_simulations/schema_packages/numerical_settings.py	1	76.43%

Totals
Change from base Build 12272374018:	-0.3%
Covered Lines:	2142
Relevant Lines:	2684

💛 - Coveralls

…rtreeFock section

JFRudzinski · 2025-08-11T10:40:20Z

@EBB2675 Is this still relevant? Or it was only a precursor to #187 ?

EBB2675 · 2025-08-11T11:24:24Z

not entirely relevant, but I wish to keep it for a while

EBB2675 added 30 commits September 24, 2024 14:26

add main and auxiliary basis set quantities to AtomCenteredBasisSet

d436e95

formatting

022c1fa

Merge branch 'develop' into coupled_cluster

bf1f6f4

add a draft for AtomCenteredFunction

af88624

add a quantity for number of primitives

0a9d98b

add atoms_state reference to AtomCenteredBasisSet

a204ec4

Merge remote-tracking branch 'origin/develop' into 130-atom-centered-…

a325753

…basis-set

assign JSON format to basis set

8866ab7

add type and auxiliary_type quantities to AtomCenteredBasisSet

c7b078a

reformatted basis_set.py

1208e88

add NAO and point charges to basis set types

fbc13f9

add cECPs and pointcharges to AtomCenteredBasisSet

ddab789

fix point charge Quantity type

8c6ae1a

a bit of a cleanup

c94e995

merge develop

a007e1e

move GTOIntegralDecomposition to NumericalSettings

62de243

Merge branch 'develop' into 130-atom-centered-basis-set

c12adac

merge develop

52d6b9a

add Mesh, NumericalIntegration and MolecularHamiltonianSubTerms

646430c

minor adjustments to Mesh and NumericalIntegration

cca109f

add integration_thresh and weight_cutoff to NumericalIntegration

42f4f38

check whether n_primitive matches the lengths of exponents and contra…

0f92eb9

…ction coefficients

add tests for AtomCenteredBasisSet and AtomCenteredFunction

e8fb5ef

add tests for Mesh and NumericalIntegration

4826f0c

modify Mesh

c5141ab

MEnum for MolecularHamiltonianContributions

23d7615

remove contributions

9ef13ea

add a normalizer function for the AtomCenteredFunction to handle comb…

80c8b64

…ined orbital types

fix test_basis_set.py

4ac1076

add OrbitalLocalization to numerical_settings.py

10e782c

EBB2675 added 4 commits December 4, 2024 13:36

add method to LocalCorrelation

5c15e97

add total_charge and total_spin to ModelSystem

2fd6398

add a simple HF class

c9d6118

a placeholder for MO and LCAO

816c7ba

JFRudzinski reviewed Dec 18, 2024

View reviewed changes

ndaelman-hu reviewed Dec 20, 2024

View reviewed changes

add MEnum for GTOIntegralDecomposition

09b0dfc

EBB2675 added 6 commits January 2, 2025 10:53

modify reference determinants in HF base class

271f69c

fix ROKS issue, minor modifications in model_method

d90eac1

enhance LocalCorrelation and CoupledCluster

95e319c

add a placeholder MolecularOrbitalsState

6f3e30b

improved class descriptions, new MolecularOrbitals class, improved Ha…

92fd95e

…rtreeFock section

minor modifications

b0eb159

EBB2675 added the pr:stale A PR has had no meaningful activity for > 10 days label Dec 16, 2025

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

Conversation

EBB2675 commented Dec 16, 2024

Uh oh!

JFRudzinski left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

ndaelman-hu left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

ndaelman-hu Dec 20, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

coveralls commented Jan 2, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Pull Request Test Coverage Report for Build 13011770671

Details

💛 - Coveralls

Uh oh!

JFRudzinski commented Aug 11, 2025

Uh oh!

EBB2675 commented Aug 11, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

ndaelman-hu Dec 20, 2024 •

edited

Loading

coveralls commented Jan 2, 2025 •

edited

Loading