DELTA: Differential Evolution algorithm for Large-scale Tailored Atomistic structures

Overview

DELTA is a Python package designed to search for the minimum energy configurations of crystal structures using DDE algorithms and various computational chemistry tools.

Features

• Load configuration from JSON files
• Setup and display logging information
• Process atomic structures using the ASE library
• Generate and evolve populations of crystal structures
• Handle VASP and LAMMPS file formats
• Perform parallel computations

Installation

1. Create a virtual environment:

   conda create -n delta python=3.9   #choose your python version and env name
   conda activate delta # 

2. Clone the repository:

   git clone https://github.com/luowh35/delta.git

3. Install DELTA:

   cd DELTA
   pip install .

how to use

1. Example for the Al2O3 structure searching:

   cd example
   cat param.json

   Then you will get this output, which is about the input parameters:

       "input_file" : "./input/POSCAR",
       "lammps_in_file": "./input/in.lammps",
       "run_lammps_file": "./input/submit.sh",
       "output_dir" : "./out",
       "atoms" : 64,
       "total" : 264,
       "pop_size" : 4,
       "generation" : 3,
       "mpi_tasks" : 4,
       "CR_start" : 0.8,
       "CR_end" : 0.2,
       "F_start" : 0.8,
       "F_end" : 0.2,
       "restart" : 0

2. Explanation of parameters: input_file: Path to the POSCAR, which is filled with all possible positions.

   output_dir: Output director.

   atoms: Real atoms, now only support Al.

   total: All the Al + vacancy.

   pop_size: The total population of each generation.

   generation: The total generation.

   mpi_tasks: It determines how many tasks run at the same time.

   CR_start and CR_end: The starting and ending crossrate ​​of the DDE algorithm.

   F_start and F_end: The starting and ending Mutation Factor ​​of the DDE algorithm.

   restart: The flag to set continue calculation, only can be set to 0 or 1.

3. Run the main script:

   delta

   Or use nohup delta to prevent printing log information to the screen.

   You can also submit delta to the queue system, eg: PBS, Slurm.

   qsub rundelta.sh

OUTPUT

The OUTPUT logfile is Generation.log, which contains the necessary output