MMM-Resources

Molecular modelling scripts, LAMMPS/ReaxFF simulation inputs and outputs, and structure files from PhD research into amorphous oxide systems (SiO2, Ta2O5, GaO), covering molecular dynamics, DFT post-processing, and structural characterisation.

Repository structure

Folder	Contents
scripts/	Analysis and post-processing scripts (Python)
simulations/lammps/inputs/	LAMMPS/ReaxFF input decks and data files
simulations/lammps/outputs/	Raw simulation logs and run outputs
simulations/lammps/forcefields/	ReaxFF force field parameter file
simulations/lammps/hpc-jobs/	HPC batch job scripts and their SLURM output
structures/models/	Atomic structure files (.xyz, .lmp)
structures/lattice-parameters/	Extracted lattice parameter datasets
structures/archives/	Bulk archives of generated amorphous structure sets
data/	Derived datasets (density, coordination number) in spreadsheet form
references/	Supporting literature and supplementary information

Scripts

Script	Purpose	Dependencies
scripts/coordination_number_analysis.py	Computes coordination numbers from an atomic structure using a neighbour-list cutoff	ase, numpy, matplotlib — expects an input file (e.g. 44.xyz) not currently in this repo; update the path before running
scripts/calculate_density.py	Calculates unit cell density from lattice parameters and molar mass	math (stdlib)
scripts/optical_absorption.py	Builds a Gaussian-broadened optical absorption spectrum from TDDFT log output	numpy, matplotlib — expects tddft_silicon.log as input
scripts/pdos/pdos.py	Module defining the pdos class for handling CP2K projected density of states output	numpy
scripts/pdos/get_smearing_pdos.py	CLI wrapper around pdos.py — smears one or a pair of alpha/beta CP2K .pdos files into smeared.dat	imports pdos.py (same folder)

Simulations

LAMMPS runs using the ReaxFF force field (ffield.reax) for silica and gallium oxide systems, run on an HPC cluster via short.slurm. Inputs, outputs, and job scripts are separated so a given run's full provenance (input → job script → output) can be traced.

Structures

Atomic models and lattice parameter datasets from amorphous structure generation runs, plus the bulk archives (.tar/.zip) containing multiple generated structure sets.

Data

Spreadsheet outputs summarising computed properties (coordination numbers, densities) across the modelled systems.

References

• ReaxFF_Si_Silica_Systems_2019.pdf — ReaxFF force field reference for Si/silica systems
• jp3086649_si_002.txt — supplementary information referenced in the modelling work

Known gaps

• scripts/coordination_number_analysis.py references a structure file (44.xyz) that isn't included in this repo — it will raise a FileNotFoundError as-is.
• scripts/optical_absorption.py similarly expects a tddft_silicon.log not present here.

Both are flagged rather than fixed, since the correct input files depend on which run they were originally generated from.