SICAT

Scripts designed to streamline and automate data analysis workflows in computational simulations of the ab initio kind. The repository provides tools to simplify repetitive tasks, improve efficiency, and support analysts in managing and interpreting simulation outputs.

Folders and Contents

ELF - Electron Localization Function

Tools for analyzing the Electron Localization Function (ELF) and other real-space functions in specific planes.

• ELF_c.txt: Multiwfn command script for plotting and exporting real-space properties (like promolecular density or ELF) on defined planes (XY, XZ, YZ).

ESP - Electrostatic Potential Analysis

Tools for quantitative analysis of molecular surfaces based on Electrostatic Potential (ESP).

• ESP_c.txt: Multiwfn command script for surface analysis, exporting extrema and vertices.
• ESP_Mwfn_vmd.bat: Automation script that runs Multiwfn analysis and launches VMD for visualization.
• ESP.vmd: VMD visualization script for ESP surfaces and extrema.

IRI - Interaction Region Indicator

Tools for Interaction Region Indicator (IRI) and IRI-pi analysis of weak interactions.

• IRI_c.txt: Multiwfn command script for IRI and IRI-pi analysis, including scatter data export and cube generation.
• IRI_Mwfn_vmd.bat: Automation script that runs Multiwfn, generates the IRI scatter plot with Python, and launches VMD visualizations.
• scatter_iri.py: Python script for processing output.txt and generating IRI scatter plots in PDF and PNG formats.
• IRIfill.vmd / IRIpifill.vmd: VMD scripts for visualizing IRI and IRI-pi isosurfaces.

NCI-RDG - Non-Covalent Interactions & Reduced Density Gradient

Tools for studying non-covalent interactions using the RDG method.

• NCI_c.txt: Multiwfn command script for RDG analysis (including promolecular approximation).
• NCI_Mwfn_vmd.bat: Main automation script that executes Multiwfn, processes scatter plots with Python, and launches VMD.
• NCI_Mwfn.bat: Script to run only the Multiwfn analysis part.
• scatter_rdg.py: Python script for processing and plotting RDG scatter data.
• RDGfill.vmd / RDGfill_pro.vmd: VMD scripts for visualizing RDG isosurfaces.

QTAIM - Quantum Theory of Atoms in Molecules

Tools for topological analysis of electron density.

• QTAIM_c.txt: Multiwfn command script for topology analysis, searching Critical Points (CPs), and generating bond paths.
• QTAIM_Mwfn_vmd.bat: Automation script that runs QTAIM analysis and launches VMD.
• QTAIM_Vmd.bat: Dedicated script for VMD visualization of QTAIM results.
• QTAIM.vmd: Comprehensive VMD script for visualizing Critical Points and bond paths.

Requirements

• Multiwfn: For electronic structure analysis.
• VMD (Visual Molecular Dynamics): For 3D visualization of results.
• Python: Required for scatter plot processing in NCI-RDG and IRI.
• Python packages: numpy and matplotlib for scatter plot generation.