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`znh5md convert` support `*.gro` and `.xtc` #84

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PythonFZ opened this issue Nov 6, 2023 · 0 comments

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PythonFZ commented Nov 6, 2023

ref = ase.io.read("nvt_eq.gro")

reader = znh5md.io.ChemfilesReader("nvt_eq.xtc")
db = znh5md.io.DataWriter("nvt_eq.h5")
db.initialize_database_groups()
db.add(reader)

x = znh5md.ASEH5MD("nvt_eq.h5")
for atoms in x.get_atoms_list():
    atoms.set_atomic_numbers(ref.get_atomic_numbers())
ase.io.write("nvt_eq.xyz", atoms_list)

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