Quantum chemistry part I - single reference methods #187

EBB2675 · 2025-05-12T09:48:47Z

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coveralls · 2025-05-12T12:07:49Z

Pull Request Test Coverage Report for Build 16907926789

Details

189 of 231 (81.82%) changed or added relevant lines in 5 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage increased (+0.8%) to 70.496%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/nomad_simulations/schema_packages/numerical_settings.py	16	17	94.12%
src/nomad_simulations/schema_packages/properties/molecular_orbitals.py	29	31	93.55%
src/nomad_simulations/schema_packages/basis_set.py	52	59	88.14%
src/nomad_simulations/schema_packages/model_method.py	62	94	65.96%

Totals
Change from base Build 16906847440:	0.8%
Covered Lines:	2148
Relevant Lines:	3047

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JFRudzinski · 2025-05-13T13:16:29Z

will review tomorrow 😅

EBB2675 · 2025-05-13T13:56:20Z

hi again,

this is the basis for Quantum Chemistry support. Later on, I can build all the remaining methods while using these building blocks.

When you are done with reviewing the QC-base, I will then add all the remaining (single-reference) post-HF methods.

JFRudzinski · 2025-05-14T05:52:25Z

src/nomad_simulations/schema_packages/basis_set.py

+        """,
+    )
+
+    function_type = Quantity(


Is "type" clear enough, or should ang-mom someone be in the name?

JFRudzinski · 2025-05-14T05:56:07Z

src/nomad_simulations/schema_packages/basis_set.py

+        """,
+    )
+
+    exponents = Quantity(


"primitive_exponents"? I just have no idea of the context/clarity, so feel free to reject these naming questions

both TREXIO and basis set exchange library uses exponents

JFRudzinski · 2025-05-14T05:59:25Z

src/nomad_simulations/schema_packages/basis_set.py

+    )
+
+    primitive_normalization = Quantity(
+        type=MEnum('L2', 'none', 'contracted', 'custom'),


Move none to the end of the list

You might want to use all lower case for consistency ie l2

JFRudzinski · 2025-05-14T06:01:15Z

src/nomad_simulations/schema_packages/basis_set.py

+
+    primitive_normalization = Quantity(
+        type=MEnum('L2', 'none', 'contracted', 'custom'),
+        default='L2',


I would have thought the default should be none?

its kind of a standard convention that each primitive basis function is L²-normalized before forming any contracted orbital

Even so, I think it is not good practice to populated with a parameter that is not explicitly parsed from the files. It's safer to leave the default out so that it is not populated unless this metadata is actually there

JFRudzinski · 2025-05-14T07:25:42Z

src/nomad_simulations/schema_packages/basis_set.py

+        description="""
+        **Extra scaling factors for each primitive** (dimensionless).
+
+        - Let ϕₖ(r) be the *analytic* primitive basis function (Gaussian or


Can you check at some point if the greek letters are displayed properly in the GUI metainfo browser and DATA tab?

JFRudzinski · 2025-05-14T07:28:32Z

src/nomad_simulations/schema_packages/basis_set.py

+        contracted function so that
+
+        \\[
+            \\int_{\\mathbb{R}^3} |χ(r)|^2 \\,dr = 1.


same here, does this display? I remember looking into putting equations in the descriptions but I can't remember the outcome now.

I'm not suggesting you change anything, but if it doesn't display in the GUI we could talk to Area D about a feature for this

JFRudzinski · 2025-05-14T07:30:30Z

src/nomad_simulations/schema_packages/basis_set.py

+        """
+        super().normalize(archive, logger)
+
+        # ---------------- infer component / primitive counts -------------


I like this syntax for section separation comments, very nice readability 👍

JFRudzinski · 2025-05-14T07:56:27Z

src/nomad_simulations/schema_packages/properties/molecular_orbitals.py

+from nomad_simulations.schema_packages.variables import Variables
+
+
+class MolecularOrbitals(PhysicalProperty):


Is there a "main" value for this property? Does it even make sense in this case?

I am wondering in the context of using value or some sub-section for different types of the "main" value. I guess we never discussed what to do if the property is only really defined in terms of a set of equally-important metadata

JFRudzinski

This has developed into a really nice, clear and extensive(-looking) schema 🙌 The comments and descriptions are particularly good, these should serve as a reference point as we continue to refine and extend the schema

I presume that at this point Denis is already well versed with the schema and approves? I think you said you would also run it by your PhD advisor? Or will you do that later? And what about Nathan, did he review it?

Let's finalize all these things and also a few of my below comments later today, and then I would say you can go ahead and merge it

src/nomad_simulations/schema_packages/basis_set.py

ladinesa · 2025-05-14T09:17:36Z

src/nomad_simulations/schema_packages/basis_set.py

+
+    # ---------------- property: matrix view (read‑only) ------------------
+    @property
+    def coeff_matrix(self) -> np.ndarray:


is this really not a section quantity? at least the name looks like.

ladinesa · 2025-05-14T09:19:41Z

src/nomad_simulations/schema_packages/basis_set.py

+        """,
+    )
+
    functional_composition = SubSection(


is this plural? what is the convention when sub-sections repeat?

src/nomad_simulations/schema_packages/basis_set.py

src/nomad_simulations/schema_packages/model_method.py

src/nomad_simulations/schema_packages/basis_set.py

…ients

This was linked to issues May 12, 2025

Add post-HF methods #26

Closed

Add AtomCenteredBasisSet and AtomCenteredFunction to basis_set.py #130

Closed

Add Hartree Fock #133

Closed

Add IntegrationGrid settings #137

Open

EBB2675 marked this pull request as ready for review May 12, 2025 13:09

EBB2675 requested review from JFRudzinski, ladinesa and ndaelman-hu May 13, 2025 12:11

JFRudzinski reviewed May 14, 2025

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EBB2675 added 27 commits August 12, 2025 13:47

add utils.mo_convert helpers for MolecularOrbital I/O

4409e43

fix(utils): remove eager import of to break circular dependency

f98f2fb

add tests for mo_convert

8e5e9f9

remove two spin channel test

555d2b1

add a draft implemention for One and TwoElectronIntegral

71618e4

fix MO path

a1d8ce4

disable SectionProxy for MOs

6eb9ce6

IntegralDecomposition should be an ArchiveSection

f92459d

add a draft for SolvationModel and DispersionModel

823afa5

LocalCorrelation is an ArchiveSection

540f300

add a draft for OrbitalLocalization

a5ea38f

add DispersionModel and SolvationModel to ModelMethodMolecular

79275c9

remove redundant HartreeFock.type

c668503

add RelativityModel, minor corrections to FrozenCore

21d6e82

rename Mesh.mesh_type to Mesh.type

318eb6e

add TREXIO paper to relevant docstrings

0ec21ad

mo_energies should be in electronvolts

f6145ae

add a note on MolecularOrbitals.value (= MolecularOrbitals.mo_coeffic…

6df3a6b

…ients

Mesh.type : 'tangent' instead of 'tan'

f7074f0

remove value from MOs

a5333f7

add imaginary part of the mo coefficients

7dece9f

finalize MolecularOrbitals, full compatibility with TREXIO

a522877

cleanup integrals

3e2109d

remove mo_utils and related tests

5dfb743

add MolecularOrbitals.normalize

c0cd11a

create test_molecular_orbitals.py

60014e9

add test_integrals.py, fix the unit

609f5c7

EBB2675 force-pushed the qc-single-reference branch from 0e2a43e to 609f5c7 Compare August 12, 2025 11:48

This was unlinked from issues Nov 4, 2025

Add Hartree Fock #133

Closed

Add post-HF methods #26

Closed

		from nomad_simulations.schema_packages.variables import Variables


		class MolecularOrbitals(PhysicalProperty):

Quantum chemistry part I - single reference methods #187

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Quantum chemistry part I - single reference methods #187

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