shdchen / gpumd-wizard

Material structure processing software based on ASE (Atomic Simulation Environment)

GPUMD-Wizard

Material structure processing software based on ASE (Atomic Simulation Environment). It provides automation capabilities for calculating various properties of metals.

Features

• Based on the ASE package, MetalProperties-Automator supports different calculators such as PyNEP, calorine, DP, and LAMMPS.
• Allows for automated batch calculations of metal properties.
• Enables batch processing of files in the XYZ format.
• Integrated with GPUMD for performing molecular dynamics simulations, such as irradiation damage.

Installation

Requirements

Package	version
Python	>= 3.8
ase	>= 3.18.0
elastic
PyNEP

From Source

$ git clone --recursive https://github.com/Jonsnow-willow/GPUMD-Wizard.git

Add GPUMD-Wizard to your PYTHONPATH environment variable in your ~/.bashrc file.

$ export PYTHONPATH=<path-to-GPUMD-Wizard-package>:$PYTHONPATH

Usage

from wizard.atoms import SymbolInfo, MaterialCalculator
from pynep.calculate import NEP
#from deepmd.calculator import DP
#from ase.calculators.lammpslib import LAMMPSlib


def main():
    # Create calculator object 
    calc = NEP('nep.txt')
    # calc = DP('dp.pb')
    # cmds = ["pair_style eam/alloy",
    #         "pair_coeff * * W.eam.alloy W]
    # calc = LAMMPSlib(lmpcmds=cmds, log_file='log.' + symbol_info.symbol, keep_alive=True)

    # Set properties-related parameters
    millers = [(1,1,0),(0,0,1),(1,1,1),(1,1,2)]
    sia_vectors = [(1/2,1/2,1/2),(1,0,0),(1,1,0)]
    nths = [1,2,3]

    # Generate bulk atoms and calculate properties
    symbol_info = SymbolInfo('W', 'bcc', 3.185)    
    atoms = symbol_info.create_bulk_atoms()
    material_calculator = MaterialCalculator(atoms, calc, symbol_info.symbol, symbol_info.structure)
    material_calculator.lattice_constant()
    material_calculator.elastic_constant()
    material_calculator.eos_curve()
    material_calculator.phonon_dispersion()
    material_calculator.formation_energy_vacancy()
    material_calculator.migration_energy_vacancy()
    for nth in nths:
        material_calculator.formation_energy_divacancies(nth)
    for miller in millers:
        material_calculator.formation_energy_surface(miller)
    material_calculator.stacking_fault(a = (1,1,-1), b = (1,-1,0), miller = [1,1,2], distance = 3.185/2)
    material_calculator.stacking_fault(a = (1,1,-1), b = (1,1,2), miller = [1,-1,0], distance = 3.185/2)
    material_calculator.pure_bcc_metal_screw_dipole_move()
    material_calculator.pure_bcc_metal_screw_one_move()
    for vector in sia_vectors:
        material_calculator.formation_energy_sia(vector)
    material_calculator.formation_energy_interstitial_atom('W',[0,0,1/2],'octahedral')
    material_calculator.formation_energy_interstitial_atom('W',[1/4,0,1/2],'tetrahedral')

if __name__ == "__main__":
    main()