Created
May 22, 2023 06:16
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NequIP data file from VASP OUTCAR file without ML
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#!/usr/bin/env python3.11 | |
''' | |
# AIB_EM | |
# Asif Iqbal | |
''' | |
import os, sys | |
import pandas as pd | |
import numpy as np | |
from ase.io import read, write | |
import dpdata | |
inpFilename = 'OUTCAR' | |
outFilename = 'heaData.extxyz' | |
os.system('rm -r ' + outFilename) | |
# | |
data = dpdata.LabeledSystem('OUTCAR', fmt = 'vasp/outcar') | |
print(f'# the data contains {len(data)} frames, {data["coords"].shape}') | |
# | |
all_atoms = read(inpFilename, format='vasp-out', index=':') | |
print("READING LATTICE DIM:: ", all_atoms[-1].get_positions().shape) | |
print("# of Frames:: ", len(all_atoms)) | |
for i, curr_atoms in enumerate(all_atoms): | |
write(outFilename, curr_atoms, append=True, format='extxyz') | |
# CHECK | |
dd = [] | |
rd = read(outFilename, format='extxyz', index=':') | |
for k, i in enumerate(rd): | |
dd.append({'Frame': k, | |
'Formula':i.get_chemical_formula(), | |
'TotENE':i.get_potential_energy()}) | |
df = pd.DataFrame(dd) | |
print(df) | |
minENEinMD = df['TotENE'].idxmin() | |
print('Min Frame idx and Frame TotENE:: ', minENEinMD, df['TotENE'].min()) | |
print(all_atoms[minENEinMD].get_potential_energy()) | |
write('CONTCAR_min', all_atoms[minENEinMD], format='vasp') |
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