ABACUS Tools

This directory contains various auxiliary tools for ABACUS calculations.

Directory Structure

tools/
├── README.md
│
├── 01_NAO_generation/                # Numerical atomic orbital generation tools
│   ├── SIAB/                         # Simulated Annealing method (C++)
│   ├── pytorch/                      # PyTorch gradient method V1
│   ├── pytorch_dpsi/                 # PyTorch gradient method V2 (with dpsi)
│   ├── pytorch_gradient_source/      # Original PyTorch gradient implementation
│   ├── lcao_bash/                    # LCAO basis set bash tools
│   ├── abfs_bash/                    # ABFS basis set bash tools
│   ├── qo/                           # Quasiatomic orbital (QO) generation
│   ├── Generate_Orbital_AllInOne.sh  # Main orbital generation script
│   └── examples/                     # Usage examples
│
├── 02_postprocessing/                # Post-processing and visualization tools
│   ├── rt-tddft-tools/               # Real-time TDDFT analysis
│   ├── stm/                          # STM image generation
│   ├── average_pot/                  # Average electrostatic potential
│   ├── selective_dynamics/           # ABACUS + Phonopy phonon calculation
│   └── plot-tools/                   # Band structure, DOS, dipole and absorption
│
├── 03_code_analysis/                 # Source code analysis tools
│   └── generate_include_analysis.py
│
└── 04_windows_installation/          # Windows one-click installer via WSL2
    ├── install-abacus.bat
    ├── uninstall-abacus.bat
    ├── provision.sh
    └── README.md

Quick Start

Generate Numerical Atomic Orbitals

cd 01_NAO_generation
./Generate_Orbital_AllInOne.sh ORBITAL_INPUT

RT-TDDFT Post-processing

cd 02_postprocessing/rt-tddft-tools
python plot_absorption.py --help

STM Image Generation

cd 02_postprocessing/stm
python stm.py --help

Average Electrostatic Potential

cd 02_postprocessing/average_pot
python aveElecStatPot.py --help

Windows Installation

Run as administrator:

04_windows_installation/install-abacus.bat

Tool Descriptions

01_NAO_generation/

• SIAB/ - Simulated Annealing method for NAO optimization (C++)
• pytorch/ - PyTorch gradient method V1 for NAO optimization
• pytorch_dpsi/ - PyTorch gradient method V2 with dpsi calculation
• pytorch_gradient_source/ - Original PyTorch gradient implementation
• lcao_bash/ - Bash tools for LCAO basis set generation
• abfs_bash/ - Bash tools for ABFS basis set generation
• qo/ - Quasiatomic orbital (QO) generation tool
• examples/ - Example input files and test cases

02_postprocessing/

• rt-tddft-tools/ - Tools for real-time time-dependent density functional theory analysis
• stm/ - Tools for generating STM images from LDOS cube files
• average_pot/ - Python script to calculate and plot average electrostatic potential
• selective_dynamics/ - Tools for selective dynamics with ABACUS + Phonopy
• plot-tools/ - Band structure, DOS, dipole and absorption plotting tools

03_code_analysis/

• generate_include_analysis.py - Header file dependency depth analysis tool

04_windows_installation/

• Windows one-click installer via WSL2 + conda-forge