diff --git a/jose.00286/10.21105.jose.00286.crossref.xml b/jose.00286/10.21105.jose.00286.crossref.xml new file mode 100644 index 0000000..5adaf08 --- /dev/null +++ b/jose.00286/10.21105.jose.00286.crossref.xml @@ -0,0 +1,238 @@ + + + + 20250904145200-65c7d80fc9d546a236aa1c875e628b945f4f96a5 + 20250904145200 + + JOSS Admin + admin@theoj.org + + The Open Journal + + + + + Journal of Open Source Education + JOSE + 2577-3569 + + 10.21105/jose + https://jose.theoj.org + + + + + 09 + 2025 + + + 8 + + 91 + + + + PyQInt: A Teaching-Oriented Hartree–Fock Implementation in Python + + + + I. A. W. + Filot + + Inorganic Materials and Catalysis, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology + + https://orcid.org/0000-0003-1403-8379 + + + + 09 + 04 + 2025 + + + 286 + + + 10.21105/jose.00286 + + + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + + + + Software archive + 10.5281/zenodo.17055029 + + + GitHub review issue + https://github.com/openjournals/jose-reviews/issues/286 + + + + 10.21105/jose.00286 + https://jose.theoj.org/papers/10.21105/jose.00286 + + + https://jose.theoj.org/papers/10.21105/jose.00286.pdf + + + + + + New developments in molecular orbital theory + Roothaan + Reviews of Modern Physics + 23 + 10.1103/RevModPhys.23.69 + 1951 + Roothaan, C. C. J. (1951). New developments in molecular orbital theory. Reviews of Modern Physics, 23, 69–89. https://doi.org/10.1103/RevModPhys.23.69 + + + Spin-unrestricted character of kohn-sham orbitals for open-shell systems + Pople + International Journal of Quantum Chemistry + 4 + 56 + 10.1002/qua.560560414 + 1995 + Pople, J. A., Gill, P. M. W., & Handy, N. C. (1995). Spin-unrestricted character of kohn-sham orbitals for open-shell systems. International Journal of Quantum Chemistry, 56(4), 303–305. https://doi.org/10.1002/qua.560560414 + + + Convergence acceleration of iterative sequences. The case of scf iteration + Pulay + Chemical Physics Letters + 2 + 73 + 10.1016/0009-2614(80)80396-4 + 0009-2614 + 1980 + Pulay, P. (1980). Convergence acceleration of iterative sequences. The case of scf iteration. Chemical Physics Letters, 73(2), 393–398. https://doi.org/10.1016/0009-2614(80)80396-4 + + + Gaussian-expansion methods for molecular integrals + Taketa + Journal of the Physical Society of Japan + 11 + 21 + 10.1143/JPSJ.21.2313 + 1966 + Taketa, H., Huzinaga, S., & O-ohata, K. (1966). Gaussian-expansion methods for molecular integrals. Journal of the Physical Society of Japan, 21(11), 2313–2324. https://doi.org/10.1143/JPSJ.21.2313 + + + Crystal orbital hamilton populations (COHP): Energy-resolved visualization of chemical bonding in solids based on density-functional calculations + Dronskowski + The Journal of Physical Chemistry + 33 + 97 + 10.1021/j100135a014 + 1993 + Dronskowski, R., & Bloechl, P. E. (1993). Crystal orbital hamilton populations (COHP): Energy-resolved visualization of chemical bonding in solids based on density-functional calculations. The Journal of Physical Chemistry, 97(33), 8617–8624. https://doi.org/10.1021/j100135a014 + + + Students’ levels of explanations, models, and misconceptions in basic quantum chemistry: A phenomenographic study + Stefani + Journal of Research in Science Teaching + 46 + 10.1002/tea.20279 + 2009 + Stefani, C., & Tsaparlis, G. (2009). Students’ levels of explanations, models, and misconceptions in basic quantum chemistry: A phenomenographic study. Journal of Research in Science Teaching, 46, 520–536. https://doi.org/10.1002/tea.20279 + + + Reducing student misconceptions through problem-based learning with a computational chemistry-assisted question map approach + Hulyadi + Jurnal Penelitian Pendidikan IPA + 09 + 10.29303/jppipa.v9i12.5936 + 2023 + Hulyadi, H., Muhali, M., & Gargazi, G. (2023). Reducing student misconceptions through problem-based learning with a computational chemistry-assisted question map approach. Jurnal Penelitian Pendidikan IPA, 09, 11207–11217. https://doi.org/10.29303/jppipa.v9i12.5936 + + + Density-functional thermochemistry. III. The role of exact exchange + Becke + The Journal of Chemical Physics + 7 + 98 + 10.1063/1.464913 + 0021-9606 + 1993 + Becke, A. D. (1993). Density-functional thermochemistry. III. The role of exact exchange. The Journal of Chemical Physics, 98(7), 5648–5652. https://doi.org/10.1063/1.464913 + + + Development of the colle-salvetti correlation-energy formula into a functional of the electron density + Lee + Physical Review B + 37 + 10.1103/PhysRevB.37.785 + 1988 + Lee, C., Yang, W., & Parr, R. G. (1988). Development of the colle-salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37, 785–789. https://doi.org/10.1103/PhysRevB.37.785 + + + General performance of density functionals + Sousa + The Journal of Physical Chemistry A + 42 + 111 + 10.1021/jp0734474 + 2007 + Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2007). General performance of density functionals. The Journal of Physical Chemistry A, 111(42), 10439–10452. https://doi.org/10.1021/jp0734474 + + + Construction of some molecular orbitals to be approximately invariant for changes from one molecule to another + Boys + Reviews of Modern Physics + 32 + 10.1103/RevModPhys.32.296 + 1960 + Boys, S. F. (1960). Construction of some molecular orbitals to be approximately invariant for changes from one molecule to another. Reviews of Modern Physics, 32, 296–299. https://doi.org/10.1103/RevModPhys.32.296 + + + Editorial: Modern architectures and their impact on electronic structure theory + Gordon + Chemical Reviews + 17 + 120 + 10.1021/acs.chemrev.0c00700 + 2020 + Gordon, M. S., & Windus, T. L. (2020). Editorial: Modern architectures and their impact on electronic structure theory. Chemical Reviews, 120(17), 9015–9020. https://doi.org/10.1021/acs.chemrev.0c00700 + + + Modern quantum chemistry: Introduction to advanced electronic structure theory + Szabo + 1996 + Szabo, A., & Ostlund, N. S. (1996). Modern quantum chemistry: Introduction to advanced electronic structure theory. Dover. + + + Elements of electronic structure theory + Filot + 978-90-386-6477-4 + 2025 + Filot, I. A. W. (2025). Elements of electronic structure theory. Eindhoven University of Technology Library. ISBN: 978-90-386-6477-4 + + + PyQInt documentation + Filot + 2025 + Filot, I. A. W. (2025). PyQInt documentation. https://ifilot.github.io/pyqint/index.html + + + Matplotlib: A 2D graphics environment + Hunter + Computing in Science & Engineering + 3 + 9 + 10.1109/MCSE.2007.55 + 2007 + Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science & Engineering, 9(3), 90–95. https://doi.org/10.1109/MCSE.2007.55 + + + + + + diff --git a/jose.00286/10.21105.jose.00286.pdf b/jose.00286/10.21105.jose.00286.pdf new file mode 100644 index 0000000..d70941a Binary files /dev/null and b/jose.00286/10.21105.jose.00286.pdf differ diff --git a/jose.00286/paper.jats/10.21105.jose.00286.jats b/jose.00286/paper.jats/10.21105.jose.00286.jats new file mode 100644 index 0000000..81a233d --- /dev/null +++ b/jose.00286/paper.jats/10.21105.jose.00286.jats @@ -0,0 +1,561 @@ + + +
+ + + + +Journal of Open Source Education +JOSE + +2577-3569 + +Open Journals + + + +286 +10.21105/jose.00286 + +PyQInt: A Teaching-Oriented Hartree–Fock Implementation +in Python + + + +https://orcid.org/0000-0003-1403-8379 + +Filot +I. A. W. + + +* + + + +Inorganic Materials and Catalysis, Department of Chemical +Engineering and Chemistry, Eindhoven University of +Technology + + + + +* E-mail: + + +3 +9 +2023 + +8 +91 +286 + +Authors of papers retain copyright and release the +work under a Creative Commons Attribution 4.0 International License (CC +BY 4.0) +2025 +The article authors + +Authors of papers retain copyright and release the work under +a Creative Commons Attribution 4.0 International License (CC BY +4.0) + + + +Quantum chemistry +Electronic structure theory +Hartree-Fock +Gaussian basis functions +Molecular integrals +SCF method + + + + + + Summary +

PyQInt is a modular Python package for + learning and prototyping quantum chemistry methods, with a particular + focus on the Hartree-Fock formalism + (Roothaan, + 1951) using Gaussian-type orbitals + (Pople + et al., 1995). Designed to prioritize educational transparency, + PyQInt exposes all computational building + blocks—integrals, matrices, Hamiltonians, SCF procedures, and + gradients—through a clean, inspectable API.

+

Users can evaluate molecular integrals + (Taketa + et al., 1966), perform self-consistent field calculations with + direct inversion of iterative subspace (DIIS) + (Pulay, + 1980), construct and localize orbitals, compute crystal orbital + Hamilton population (COHP) coefficients + (Dronskowski + & Bloechl, 1993), and optimize molecular geometries. + PyQInt is especially well suited for students + and researchers who want to interact with and understand the + underlying steps of electronic structure theory, offering full access + to intermediate data structures and algorithmic pathways.

+

While numerical efficiency is not the primary goal, + PyQInt connects to a C++ backend for integral + evaluation, enabling practical computations on small molecules. The + package is fully documented and tested, and is ideal for use in + courses, tutorials, or prototyping new electronic structure ideas.

+ + + Statement of need +

Electronic structure theory plays a foundational role in modern + computational chemistry, with widespread applications in materials + discovery, catalyst design, drug development, and the prediction of + molecular properties. As simulation tools become increasingly powerful + and accessible, they are now integral to both academic research and + industrial workflows + (Gordon + & Windus, 2020).

+

However, many students and early-career researchers engage with + these tools as users—relying on established software packages—without + gaining a clear understanding of the underlying theoretical models, + numerical procedures, or methodological limitations. This lack of + transparency can lead to misinterpretation of results, inappropriate + method selection, and an underappreciation of the approximations + involved in electronic structure calculations + (Hulyadi + et al., 2023; + Stefani + & Tsaparlis, 2009).

+

Although the Hartree-Fock (HF) method is rarely used in isolation + for practical applications, it remains a critical pedagogical + foundation for understanding more advanced approaches such as Density + Functional Theory (DFT) and post-Hartree-Fock correlation methods + (Szabo + & Ostlund, 1996). In particular, the explicit evaluation of + the exchange energy in Hartree-Fock forms the conceptual and + mathematical basis for hybrid functionals like B3LYP + (Becke, + 1993; + Lee + et al., 1988), which are among the most widely used methods in + applied quantum chemistry + (Sousa + et al., 2007).

+

PyQInt is designed to support education and + exploration in electronic structure theory through a modular and + transparent implementation of Hartree–Fock methodology using + Gaussian-type orbitals. In contrast to software packages that abstract + away computational details, PyQInt provides access to individual steps + such as integral evaluation, matrix construction, SCF procedures, and + orbital manipulation. This structure makes the program suitable for + instructional use as well as for prototyping and method + development.

+ +

Visualization of the coefficient matrix from a + Hartree–Fock calculation of the CO molecule using an STO-3g basis + set, obtained using PyQInt. The numeric + values shown along the x-axis correspond to orbital energies. +

+ + + + + Features +

PyQInt is a Python-based software package + developed to support instruction and exploration in electronic + structure theory. It implements the Hartree–Fock method using + Gaussian-type orbitals, with a particular emphasis on clarity, + inspectability, and modularity. Designed as both a pedagogical tool + and a platform for method prototyping, PyQInt + exposes the underlying components of electronic structure calculations + in a form that facilitates learning and experimentation. In addition + to its modular structure, the source code is richly commented + throughout, with the explicit intention that students and early-stage + researchers can read and understand the implementation details. This + transparency allows users not only to use the code but also to study + it as an educational resource, reinforcing theoretical concepts + through hands-on engagement with working algorithms.

+

The package provides functionality for constructing and + manipulating Gaussian basis functions, along with the evaluation of + the corresponding one- and two-electron integrals. These integrals are + computed using a C++ backend with OpenMP parallelization, which + ensures efficient performance suitable for small to medium-sized + systems. This low-level access supports detailed exploration of + integral evaluation and basis set structure. In addition, PyQInt + includes higher-level capabilities such as self-consistent field (SCF) + Hartree–Fock calculations with DIIS acceleration, orbital localization + using the Foster–Boys method + (Boys, + 1960), Crystal Orbital Hamilton Population (COHP) analysis + (Dronskowski + & Bloechl, 1993), and geometry optimization based on + analytic energy gradients.

+

A key design feature is that all calculations return structured + Python dictionary objects, which expose the internal matrices and + multidimensional arrays used during computation. These include, for + example, the overlap, kinetic energy, Coulomb, coefficient (see + [fig:co-coefficient]), + and Fock matrices, as well as the four-dimensional array representing + the two-electron repulsion integrals. By providing this level of + access, the program allows users to inspect, manipulate, and recompute + quantities such as electronic energy and orbital-specific + contributions using standard tools such as NumPy. This design supports + a more detailed understanding of the theoretical framework and + computational procedures that underpin quantum chemical models.

+

PyQInt also supports molecular orbital + visualization through both two-dimensional contour plots + ([fig:co-contour]) + via Matplotlib + (Hunter, + 2007) and three-dimensional isosurface rendering + ([fig:co-isosurface]). + These features aid in connecting computational results to chemical + concepts and spatial representations.

+ +

Two-dimensional contour plots of selected molecular + orbitals of the CO molecule, visualized using + PyQInt. The titles of the subplots indicate + the corresponding orbital + energies.

+ + + +

Three-dimensional isosurface representations of selected + molecular orbitals of the CO molecule, generated with PyQInt and + rendered using + Blender.

+ + +

All features of PyQInt are accompanied by comprehensive + documentation, which includes numerous examples and explanatory + materials. The documentation is designed to guide users through both + basic and advanced functionality, with an emphasis on clarity and + reproducibility. Many of the examples are presented as richly + commented Python code snippets, illustrating typical use cases and + highlighting key computational steps. This approach allows users to + connect theoretical concepts with practical implementation and lowers + the barrier to entry for students and early-stage researchers engaging + with electronic structure theory through programming.

+ + + Use in Teaching and Curriculum +

PyQInt is one of two computational tools + used throughout the open-access textbook Elements of + Electronic Structure Theory + (Filot, + 2025a), which is freely available online. The textbook combines + theoretical instruction with practical Python-based exercises, aiming + to provide students with both a conceptual foundation and a working + familiarity with electronic structure methods. + PyQInt is introduced as a lightweight and + readable implementation of Hartree–Fock theory, enabling learners to + explore the mathematical and computational framework of quantum + chemistry from first principles.

+

The software supports exercises focused on basis function + construction, integral evaluation, self-consistent field procedures, + and orbital analysis. These activities are intended to promote active + engagement with the subject matter by encouraging students to + investigate and manipulate the internal components of electronic + structure calculations, rather than relying exclusively on + preconfigured, black-box software. The modular architecture of + PyQInt is consistent with the pedagogical + progression adopted in the accompanying textbook, facilitating + incremental learning and conceptual reinforcement through hands-on, + code-based experimentation.

+

PyQInt has been used in four iterations of + the course Theoretical and Computational Chemistry at + Eindhoven University of Technology, where it was + integrated into lectures and assignments. Student feedback collected + through course evaluations indicates a high level of appreciation for + the tool, with many students identifying it as instrumental in + developing their understanding of electronic structure calculations. + The transparency of the code and the accessibility of key + computational elements have been noted as particularly valuable for + clarifying how abstract theoretical concepts are translated into + numerical procedures.

+

This integration highlights the effectiveness of + PyQInt as an educational resource, particularly + in settings where algorithmic transparency and practical skill + development are prioritized. By facilitating direct interaction with + core matrices, energy terms, and orbital visualizations, the software + supports deeper insight into both the theory and implementation of + electronic structure methods. It is well suited for use in + introductory courses, flipped classroom environments, and independent + study contexts.

+ + + Availability and Deployment +

In addition to its educational utility, + PyQInt is distributed through widely used + package managers, including PyPI and Anaconda, which simplifies + installation and integration across a range of computing environments. + This accessibility ensures that students and instructors can easily + incorporate the software into classroom exercises, Jupyter Notebooks, + or larger Python-based projects without the need for complex setup + procedures. The ability to install PyQInt with + a single command facilitates its use in teaching environments where + consistency and ease of deployment are critical, while also making it + suitable for use in virtual labs, remote instruction, and open science + workflows. Detailed documentation, including the installation + procedure, are available online + (Filot, + 2025b).

+ + + + + + + + + RoothaanC. C. J. + + New developments in molecular orbital theory + Reviews of Modern Physics + American Physical Society + 195104 + 23 + https://link.aps.org/doi/10.1103/RevModPhys.23.69 + 10.1103/RevModPhys.23.69 + 69 + 89 + + + + + + PopleJohn A. + GillPeter M. W. + HandyNicholas C. + + Spin-unrestricted character of kohn-sham orbitals for open-shell systems + International Journal of Quantum Chemistry + 1995 + 56 + 4 + https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.560560414 + 10.1002/qua.560560414 + 303 + 305 + + + + + + PulayPéter + + Convergence acceleration of iterative sequences. The case of scf iteration + Chemical Physics Letters + 1980 + 73 + 2 + 0009-2614 + https://www.sciencedirect.com/science/article/pii/0009261480803964 + 10.1016/0009-2614(80)80396-4 + 393 + 398 + + + + + + TaketaHiroshi + HuzinagaSigeru + O-ohataKiyosi + + Gaussian-expansion methods for molecular integrals + Journal of the Physical Society of Japan + 1966 + 21 + 11 + https://doi.org/10.1143/JPSJ.21.2313 + 10.1143/JPSJ.21.2313 + 2313 + 2324 + + + + + + DronskowskiRichard + BloechlPeter E. + + Crystal orbital hamilton populations (COHP): Energy-resolved visualization of chemical bonding in solids based on density-functional calculations + The Journal of Physical Chemistry + 1993 + 97 + 33 + 10.1021/j100135a014 + 8617 + 8624 + + + + + + StefaniChristina + TsaparlisGeorgios + + Students’ levels of explanations, models, and misconceptions in basic quantum chemistry: A phenomenographic study + Journal of Research in Science Teaching + 200905 + 46 + 10.1002/tea.20279 + 520 + 536 + + + + + + HulyadiHulyadi + MuhaliMuhali + GargaziGargazi + + Reducing student misconceptions through problem-based learning with a computational chemistry-assisted question map approach + Jurnal Penelitian Pendidikan IPA + 202312 + 09 + 10.29303/jppipa.v9i12.5936 + 11207 + 11217 + + + + + + BeckeAxel D. + + Density-functional thermochemistry. III. The role of exact exchange + The Journal of Chemical Physics + 199304 + 98 + 7 + 0021-9606 + 10.1063/1.464913 + 5648 + 5652 + + + + + + LeeChengteh + YangWeitao + ParrRobert G. + + Development of the colle-salvetti correlation-energy formula into a functional of the electron density + Physical Review B + American Physical Society + 198801 + 37 + https://link.aps.org/doi/10.1103/PhysRevB.37.785 + 10.1103/PhysRevB.37.785 + 785 + 789 + + + + + + SousaSérgio Filipe + FernandesPedro Alexandrino + RamosMaria João + + General performance of density functionals + The Journal of Physical Chemistry A + 2007 + 111 + 42 + https://doi.org/10.1021/jp0734474 + 10.1021/jp0734474 + 10439 + 10452 + + + + + + BoysS. F. + + Construction of some molecular orbitals to be approximately invariant for changes from one molecule to another + Reviews of Modern Physics + American Physical Society + 196004 + 32 + https://link.aps.org/doi/10.1103/RevModPhys.32.296 + 10.1103/RevModPhys.32.296 + 296 + 299 + + + + + + GordonMark S. + WindusTheresa L. + + Editorial: Modern architectures and their impact on electronic structure theory + Chemical Reviews + 2020 + 120 + 17 + https://doi.org/10.1021/acs.chemrev.0c00700 + 10.1021/acs.chemrev.0c00700 + 9015 + 9020 + + + + + + SzaboAttila + OstlundNeil S. + + Modern quantum chemistry: Introduction to advanced electronic structure theory + Dover + Mineola, New York + 1996 + + + + + + FilotIvo A. W. + + Elements of electronic structure theory + Eindhoven University of Technology Library + Eindhoven, The Netherlands + 2025 + 978-90-386-6477-4 + + + + + + FilotIvo A. W. + + PyQInt documentation + 2025 + 20250818 + https://ifilot.github.io/pyqint/index.html + + + + + + HunterJ. D. + + Matplotlib: A 2D graphics environment + Computing in Science & Engineering + IEEE COMPUTER SOC + 2007 + 9 + 3 + 10.1109/MCSE.2007.55 + 90 + 95 + + + + +
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