ASE-CHGNet（Cu-Au）

2025 June 16

Info

CHGNet needs to be installed.

The files used in this tutorial can be downloaded from CrySPY_utility/examples/ase_chgnet_Cu-Au_EA-vc. In this tutorial, we assume that a computing cluster with a job scheduler is used together with the machine learning potential CHGNet. The calculation can also be performed on a local PC, so if you prefer this, please modify the input settings accordingly. The target system is the binary Cu-Au system.

Pre-calculation

In EA-vc, the per-atom energies of each elemental phase must be used as the reference in the end_point setting of cryspy.in, so they need to be calculated beforehand. There should be two directories inside the example.

Au-fcc
├── POSCAR
├── chgnet_in.py
└── job_cryspy

Cu-fcc
├── POSCAR
├── chgnet_in.py
└── job_cryspy

Each directory contains a crystal structure file (POSCAR), a Python script (chgnet_in.py) to perform structure relaxation and calculate energy, and a job script (job_cryspy). Please modify these files according to your computing environment.

Submit the job (replace the job submission command as appropriate for your system).

cd Au-fcc
qsub job_cryspy
cd ../Cu-fcc
qsub job_cryspy
cd ..

When the calculations finish successfully, a file named end_point will be created in each directory, containing the energy per atom (eV/atom) after structure relaxation.

cat Au-fcc/end_point
-3.2357187271118164

cat Cu_fcc/end_point
-4.083529472351074

These values are then used as input for the cryspy.in file.

cryspy.in

[basic]
algo = EA-vc
calc_code = ASE
nstage = 1
njob = 20
jobcmd = qsub
jobfile = job_cryspy

[structure]
atype = Cu Au
ll_nat = 0 0
ul_nat = 8 8

[ASE]
ase_python = chgnet_in.py

[EA]
n_pop = 20
n_crsov = 5
n_perm = 2
n_strain = 2
n_rand = 2
n_add = 3
n_elim = 3
n_subs = 3
target = random
n_elite = 2
n_fittest = 10
slct_func = TNM
t_size = 2
maxgen_ea = 0
end_point = -4.08352709  -3.23571777

[option]

calc_in/

The contents under calc_in/ are the same as those in Tutorial > Random Search (RS) > ASE on your local PC, with minor modifications for CHGNet. Be sure to adjust paths such as the Python executable in the job script to match your computing environment. Be sure to adjust the Python executable path in the job script.

calc_in/chgnet_in.py_1

# ---------- import
from ase.constraints import FixSymmetry
from ase.filters import FrechetCellFilter
from ase.io import read, write
from ase.optimize import FIRE, BFGS, LBFGS
from chgnet.model import CHGNetCalculator

# ---------- input structure
# CrySPY outputs 'POSCAR' as an input file in work/xxxxxx directory
atoms = read('POSCAR')

# ---------- set up
atoms.calc = CHGNetCalculator()
atoms.set_constraint([FixSymmetry(atoms)])
cell_filter = FrechetCellFilter(atoms)
opt = BFGS(cell_filter, trajectory='opt.traj')

# ---------- run
opt.run(fmax=0.01, steps=2000)

# ---------- write structure
write('opt_struc.vasp', cell_filter.atoms, format='vasp', direct=True)

# ---------- opt. structure and energy
# [rule in ASE interface]
# output file for energy: 'log.tote' in eV/cell
#                         CrySPY reads the last line of 'log.tote'
# output file for structure: 'CONTCAR' in vasp format
# ------ energy
e = cell_filter.atoms.get_total_energy()    # eV/cell
with open('log.tote', mode='w') as f:
    f.write(str(e))

# ------ struc
opt_atoms = cell_filter.atoms.copy()
opt_atoms.set_constraint(None)    # remove constraint for pymatgen
write('CONTCAR', opt_atoms, format='vasp', direct=True)

calc_in/job_cryspy

#!/bin/sh
#$ -cwd
#$ -V -S /bin/bash
####$ -V -S /bin/zsh
#$ -N CuAu_CrySPY_ID
#$ -pe smp 2

# ---------- OpenMP
export OMP_NUM_THREADS=2

# ---------- ASE
/usr/local/Python-3.10.13/bin/python3 chgnet_in.py > out.log

# --------- CrySPY
sed -i -e '3 s/^.*$/done/' stat_job