Software | QTCOVI – Theoretical and Computational Chemistry

critic2

Mon, 01 Jan 2024 00:00:00 +0000

About

critic2 is an open-source program for the topological analysis of scalar fields—most commonly the electron density—in both molecular and periodic (crystal) systems. It supports a wide range of quantum chemistry and plane-wave DFT codes as input sources.

Key capabilities include:

Critical point search — bonds, rings, and cages from any scalar field.
QTAIM integration — atomic charges, volumes, and multipole moments.
Delocalization indices — from promolecular or DFT-level densities.
NCI visualisation — reduced density gradient isosurfaces for non-covalent interaction analysis.
Crystal structure analysis — symmetry, powder diffraction, intermolecular interaction energies.

Citation

A. Otero-de-la-Roza, E. R. Johnson, V. Luaña, Comput. Phys. Commun. 185, 1007 (2014). A. Otero-de-la-Roza, M. A. Blanco, A. M. Pendás, V. Luaña, Comput. Phys. Commun. 180, 157 (2009).

edf-omp

Mon, 01 Jan 2024 00:00:00 +0000

About

edf-omp computes Electron Number Distribution Functions (EDFs) — the probability distribution of finding n electrons in a QTAIM atomic basin. EDFs encode the full statistics of electron population fluctuations, giving direct access to:

Atomic mean electron populations (charges).
Electron localisation and delocalization indices.
Higher-order cumulants revealing multi-centre bonding and electron correlation.

The code is written in Fortran and parallelised with OpenMP, using LAPACK for the required linear algebra. It is designed for high-throughput calculations on large systems.

The compiled binary is also available at the companion GitHub Pages site.

MM2SF

Mon, 01 Jan 2024 00:00:00 +0000

About

MM2SF automatically generates optimised Atom-Centred Symmetry Functions (ACSFs) for use as descriptors in neural network interatomic potentials. Given a molecular dynamics trajectory or normal-mode sampling, it applies a Gaussian Mixture Model (GMM) to decompose the chemical space into well-defined clusters, then selects symmetry function parameters that accurately describe each region.

Supported symmetry function types:

Two-body (radial) — G^rad
Three-body (angular) — G^ang (modified functional form)

Installation

pip install git+https://github.com/m-gallegos/MM2SF.git

Or from a downloaded zip:

pip install MM2SF-main.zip

NNAIMQ

Mon, 01 Jan 2024 00:00:00 +0000

About

NNAIMQ predicts QTAIM (Bader) partial charges for C, H, O and N atoms in neutral, singlet-spin gas-phase organic and biological molecules. It comprises four Artificial Neural Networks (one per element) fitted to high-quality quantum chemical data.

Key features:

High-accuracy QTAIM charges without running a full topological analysis.
Supports standard .xyz geometry files as input.
Compatible with x86-64 and ARM (Apple M1) processors.

Requirements

Python ≥ 3.7.3
keras, matplotlib, numpy, pandas, seaborn, tensorflow

Usage

cd code/
python nnaimq.py input

where input is a plain-text file listing the .xyz geometry files to process.

PROMOLDEN

Mon, 01 Jan 2024 00:00:00 +0000

About

PROMOLDEN is our in-house code for the topological analysis of scalar fields derived from the electron density and pair density. It implements:

QTAIM basin integration — atomic charges, volumes, and energies from IQA.
IQA energy decomposition — intra-atomic self-energies and inter-atomic electrostatic/exchange–correlation interactions.
Delocalization and localisation indices — bond orders from the electron pair density.
Non-covalent interaction (NCI) index — identification and visualisation of van der Waals, hydrogen bond, and steric interaction regions.
Electron localisation function (ELF) — topological analysis of electron pairing.

Availability

PROMOLDEN is available for academic use upon request to the PI. Please contact ampendas@uniovi.es to obtain the code and documentation.

Citation

If you use PROMOLDEN in published work, please cite:

Á. Martín Pendás, E. Francisco, PROMOLDEN: A QTAIM/IQA code, University of Oviedo, 2021.

SchNet4AIM

Mon, 01 Jan 2024 00:00:00 +0000

About

SchNet4AIM is a code designed to train SchNet deep-learning models on atomic (1-body) and pairwise (2-body) properties formulated within the Quantum Theory of Atoms in Molecules (QTAIM). It is built as a targeted modification of SchNetPack, retaining only the components relevant for 1p/2p property training.

Key features:

Train on atomic (charges, energies, volumes) or pairwise (delocalization indices, IQA interaction energies) QTAIM properties.
Supports JSON and ASE-SQLite database formats.
Runs on CPU and GPU (GPU recommended for speed).

Installation

git clone https://github.com/QTCOVI/SchNet4AIM.git
cd SchNet4AIM
pip install -r requirements.txt

NNAIMGUI

Sun, 01 Jan 2023 00:00:00 +0000

About

NNAIMGUI (M. Gallegos, University of Oviedo, 2023) is a code for the prediction and visualisation of atomic properties using feed-forward neural network (FFNN) models. It ships with the built-in NNAIMQ model for predicting QTAIM charges of gas-phase neutral singlet molecules containing C, H, O and N atoms, and supports user-supplied custom models for any atomic property of interest.

Key features:

Graphical user interface for non-expert users, plus command-line mode.
Built-in charge equilibration to enforce molecular electroneutrality (13 algorithms included).
Supports user-defined FFNN models for any atomic property.
Compatible with Linux and Windows.

Installation

pip install git+https://github.com/m-gallegos/NNAIMGUI.git

Citation

M. Gallegos et al., J. Chem. Inf. Model. (2023). https://doi.org/10.1021/acs.jcim.3c00597

Software | QTCOVI – Theoretical and Computational Chemistry

critic2

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Citation

edf-omp

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MM2SF

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Installation

Links

NNAIMQ

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Requirements

Usage

Links

PROMOLDEN

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Availability

Citation

SchNet4AIM

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Installation

Links

NNAIMGUI

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Installation

Citation

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