Center for Molecular Modeling - M. Chan

Grid: A Python library for molecular integration, interpolation, differentiation, and more

toon — Thu, 22 Jan 2026 11:40:44 +0000

A. Tehrani, X.D. Yang, M. Martinez-Gonzales, L. Pujal, R. Hernández-Esparza, M. Chan, E. Vohringer-Martinez, T. Verstraelen, P.W. Ayers, F. Heidar-Zadeh

The Journal of Chemical Physics

160(17), 172503

2024

DOI

https://doi.org/10.1063/5.0202240

The Tale of HORTON: Lessons Learned in a Decade of Scientific Software Development

leen — Thu, 25 Apr 2024 09:47:15 +0000

M. Chan, T. Verstraelen, A. Tehrani, M. Richer, X. D. Yang, T. D. Kim, E. Vohringer-Martinez, F. Heidar-Zadeh, P. W. Ayers

Journal of Chemical Physics

Volume 160, Issue 16

2024

Abstract

HORTON is a free and open-source electronic-structure package written primarily in Python 3 with some underlying C++ components. While HORTON’s development has been mainly directed by the research interests of its leading contributing groups, it is designed to be easily modified, extended, and used by other developers of quantum chemistry methods or post-processing techniques. Most importantly, HORTON adheres to modern principles of software development, including modularity, readability, flexibility, comprehensive documentation, automatic testing, version control, and quality-assurance protocols. This article explains how the principles and structure of HORTON have evolved since we started developing it more than a decade ago. We review the features and functionality of the latest HORTON release (version 2.3) and discuss how HORTON is evolving to support electronic structure theory research for the next decade. Keywords: quantum chemistry software, computational chemistry, Hartree-Fock method, model hamiltonians, Density Functional Theory (DFT) methods, numerical integration grids, periodic boundary conditions, Gaussian integrals, atoms-inmolecules partitioning schemes, Hirshfeld partitioning, population analysis, electrostatic potential fitting, parsing and converting computational chemistry file formats, theoretical chemistry Python library

DOI

http://dx.doi.org/10.1063/5.0196638

Private attachment

paper_release_horton.pdf

IOData: A python library for reading, writing, and converting computational chemistry file formats and generating input files

toon — Mon, 22 Feb 2021 18:50:35 +0000

T. Verstraelen, W. Adams, L. Pujal, A. Tehrani, B. D. Kelly, L. Macaya, F. Meng, M. Richer, R. Hernández-Esparza, X. D. Yang, M. Chan, T. D. Kim, M. Cools-Ceuppens, V. Chuiko, E. Vohringer-Martinez, P.W. Ayers, F. Heidar-Zadeh

Journal of Computational Chemistry

45, 6, 458--464

2021

Abstract

IOData is a free and open‐source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane‐wave density‐functional‐theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and released for stand‐alone use, its original purpose was to facilitate the interoperability of various modules in the HORTON and ChemTools software packages with external (third‐party) molecular quantum chemistry and solid‐state density‐functional‐theory packages. IOData is designed to be easy to use, maintain, and extend; this is why we wrote IOData in Python and adopted many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note of the IOData library.

DOI

http://dx.doi.org/

Private attachment

jcc.26468.pdf

An Explicit Approach to Conceptual Density Functional Theory Descriptors of Arbitrary Order

toon — Thu, 30 Jun 2016 08:16:28 +0000

F. Heidar-Zadeh, M. Richer, S. Fias, R.A. Miranda-Quintana, M. Chan, M. Franco-Perez, C. Gonzalez-Espinoza, T.D. Kim, C. Lanssens, A.H.G. Patel, X.D. Yang, E. Vohringer-Martinez, C. Cárdenas, T. Verstraelen, P.W. Ayers

Chemical Physics Letters

660, 307–312

2016

Abstract

We present explicit formulas for arbitrary-order derivatives of the energy, grand potential, electron density, and higher-order response functions with respect to the number of electrons, and the chemical potential for any smooth and differentiable model of the energy versus the number of electrons. The resulting expressions for global reactivity descriptors (hyperhardnesses and hypersoftnesses), local reactivity descriptors (hyperFukui functions and local hypersoftnesses), and nonlocal response functions are easy to evaluate computationally. Specifically, the explicit formulas for global/local/nonlocal hypersoftnesses of arbitrary order are derived using Bell polynomials. Explicit expressions for global and local hypersoftness indicators up to fifth order are presented.

DOI

http://dx.doi.org/10.1016/j.cplett.2016.07.039

Private attachment

1-s2.0-S0009261416305280-main.pdf

Assessing The Accuracy Of New Geminal-Based Approaches

toon — Tue, 22 Apr 2014 08:47:18 +0000

P. Tecmer, K. Boguslawski, P.A. Johnson, P.A. Limacher, M. Chan, T. Verstraelen, P.W. Ayers

Journal of Physical Chemistry A

118 (39), 9058–9068

2014

Abstract

We present a systematic theoretical study on the dissociation of diatomic molecules and their spectroscopic constants using our recently presented geminal-based wave function ansätze. Specifically, the performance of the antisymmetric product of rank two geminals (APr2G), the antisymmetric product of 1-reference-orbital geminals (AP1roG) and its orbital-optimized variant (OO-AP1roG) are assessed against standard quantum chemistry methods. Our study indicates that these new geminal-based approaches provide a cheap, robust, and accurate alternative for the description of bond-breaking processes in closed-shell systems requiring only mean-field-like computational cost. In particular, the spectroscopic constants obtained from OO-AP1roG are in very good agreement with reference theoretical and experimental data.