QMatSim: Advanced Strain Engineering Framework for 2D Quantum Materials

Multiscale simulation framework for strain engineering in 2D materials. Combines DFT and MD calculations to study flat bands, lateral heterostructures, and electronic phases in transition metal dichalcogenides.

Capabilities

• Strain-induced flat band emergence and hole localization in 2D materials
• DFT calculations with spin-orbit coupling and band engineering
  
• LAMMPS-based mechanical deformation and systematic strain protocols
• Transition metal dichalcogenides (TMDCs) with comprehensive material libraries
• DFT-MD integration for strain-electronic property correlations

Overview

QMatSim implements the computational framework from "Strain-induced lateral heterostructures: Hole localization and the emergence of flat bands in rippled MoS monolayers" (Alawein et al., Physical Review Materials 2025). The framework combines SIESTA density functional theory calculations with LAMMPS molecular dynamics simulations for studying strain effects in 2D materials.

Provides workflows from atomic-scale deformation to electronic structure analysis, focusing on flat band physics and lateral heterostructures in transition metal dichalcogenides.

Features

• Automated discovery of flat bands and lateral heterostructures
• DFT calculations with spin-orbit coupling for band engineering
• Systematic rippling and compression strain studies
• DFT-MD coupling for strain-electronic correlations
• SLURM automation with resource management
• Band structure and LDOS visualization tools
• Complete libraries for MoS, MoSe, WS, WSe systems

Installation

Prerequisites

• Python 3.9+ with NumPy, Matplotlib
• SIESTA 4.1+ for DFT calculations
• LAMMPS (stable) for MD simulations
• SLURM (optional) for HPC job submission

Setup

```bash

Clone the repository

git clone https://github.com/alaweimm90/QMatSim.git cd QMatSim

Install in development mode

pip install -e .

Install additional dependencies

pip install numpy matplotlib pytest

Verify installation

qmatsim --help ```

Usage

```bash

Strain-Induced Electronic Structure (DFT)

qmatsim relax --material MoS2 --structure 1x10_rectangular

Mechanical Deformation Studies (MD)

qmatsim minimize --structure ripple10 --mode compress qmatsim minimize --structure ripple10 --mode all

Flat Band Discovery & Analysis

qmatsim analyze --material MoS2 --structure 1x10_rectangular ```

Directory Structure

QMatSim/ qmatsim/ # Core Python CLI framework __init__.py # Package initialization __main__.py # CLI entry point and argument parsing py.typed # Type hints marker scripts/ # Bash automation tools run-DFT.sh # SIESTA workflow automation run-MD.sh # LAMMPS simulation control run-postprocessing.sh # Analysis pipeline automation template-*.sh # Input file generation scripts config.sh # Configuration management siesta/ # DFT calculation infrastructure io_templates/ # SIESTA input file templates pseudopotentials/ # Element pseudopotentials (GGA/LDA/SOC) materials/ # Material-specific calculation setups python-utilities/ # Analysis and plotting scripts bin/ # SIESTA utilities and tools lammps/ # MD simulation infrastructure data/ # Atomic structure files (.data format) in/ # LAMMPS input scripts and protocols potentials/ # Interatomic potential files tests/ # Test suite test_cli_basic.py # Basic CLI functionality tests test_qmatsim_cli.py # Advanced CLI integration tests docs/ # Documentation dev-guide.md # Development guide and architecture index.md # Documentation index pyproject.toml # Modern Python build configuration setup.py # Legacy Python setup LICENSE # MIT License

Testing

```bash

Run complete test suite

pytest tests/

Run specific test modules

pytest tests/testclibasic.py pytest tests/testqmatsimcli.py

Test CLI functionality

python -m qmatsim --help

Integration tests (requires SIESTA/LAMMPS installations)

qmatsim relax --help qmatsim minimize --help qmatsim analyze --help ```

Validation Examples

• Flat band physics: reproduces strain-induced emergence in rippled MoS (Phys. Rev. Materials 2025)
• Lateral heterostructures: hole localization and electronic phase transitions
• Strain engineering: systematic deformation studies up to 20% strain
• Spin-orbit effects: SOC-dependent band modifications in TMDCs
• Multiscale coupling: DFT-MD correlation studies

Documentation

The docs/ folder contains: - dev-guide.md: development guide with architecture overview and testing - Template system documentation: SIESTA input file generation and variable substitution - Material libraries: TMDC parameters and pseudopotential usage

Plotting Standards

Uses UC Berkeley color scheme: - Berkeley Blue #003262 (primary) - California Gold #FDB515 (accent)
- Neutral Gray #888888 (secondary) - Publication quality: serif fonts, inward ticks, no grid - Saves plots as .pdf and .png to /plots/ directories

Citation

If you use QMatSim in your research, please cite:

```bibtex @article{alawein2025strain, title={Strain-induced lateral heterostructures: Hole localization and the emergence of flat bands in rippled MoS monolayers}, author={Alawein, Meshal and Ager, Joel W and Javey, Ali and Chrzan, DC}, journal={Physical Review Materials}, volume={9}, number={2}, pages={L021002}, year={2025}, publisher={APS} }

@software{alawein2025qmatsim, author = {Meshal Alawein}, title = {QMatSim: Advanced Strain Engineering Framework for 2D Quantum Materials}, url = {https://github.com/alaweimm90/QMatSim}, year = {2025}, institution = {University of California, Berkeley} } ```

License

This project is licensed under the MIT License see the LICENSE file for details.
2025 Meshal Alawein All rights reserved.

Author

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