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xsd.py: fixed a minor xsd file reading bug

username-removed-562254 requested to merge googhgoo/ase:xsd-read-fix into master

Some programs that uses xsd format sometimes does not provide xyz coordinate for atoms located at the origin (e.g., [0,0,0]). ASE runs into error when xyz coordinate is not found. Now, the ASE assumes that the atom is at the origin if the xyz coordinate is not provided.

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