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pastewka/lammps_to_data.py

Last active April 10, 2019 14:06
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Convert LAMMPS data files into NetCDF trajectory
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lammps_to_data.py
import glob
import os
from ase.io import NetCDFTrajectory, read
fns = glob.glob('/work/ws/nemo/fr_rj1011-18.07.03-GAP_low_density-0/18.10.15-aC_GAP-quasistatic-bond_breaking_B/quasistatic-2.7_B_*.lammps')
nc = NetCDFTrajectory('quasistatic_2.7.nc', 'w')
fns = sorted(fns, key=lambda x: int(os.path.basename(x).replace('quasistatic-2.7_B_', '').replace('.lammps', '')))
for fn in fns:
print(fn)
a = read(fn, format='lammps-data', style='atomic')
nc.write(a, arrays=['id', 'travel'])
nc.close()
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