Problem with numerical frequency calculation

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Thank you for your reply, Sean.

I just got chance to try today. I found if I define a new geometry with just active atom, the normal mode frequencies will all be zero. From the xyz file it's clear that the only atom in the geometry is not moving at all.
The script in my first post can do the job, but it will generate thousands of xyz files. That's why it made me think if I did something wrong.

I understand now to the second question, thank you!
Edited On 1:57:05 PM PDT - Wed, Mar 16th 2016 by Olanky

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