Fixed Atom and Fixed Cell Parameters

[kyleb...@berkeley.edu]

Hi there,

I am currently working on an optimization problem that requires a fixed cell size and some fixed atoms. I am interfacing with VASP. When I ran Calypso, however, the generated POSCAR contained several nonsense positions "nan nan nan" equal to the number of positions I wanted to allow Calypso to work on. I did some testing and determined that this error occurs if and only if one element has only some of its positions fixed. For example, if I fix all 4 carbons in C4Si4, there's no problem, but if I want to fix 2 carbons, a POSCAR is generated which contains the two fixed carbon positions, two "nan nan nan" lines, and four PSO-generated Si positions. I cannot find any error output from Calypso to suggest why the POSCARs were generated this way.

Is Calypso's fixed atom setting intended to support fixing only some positions for a given element, or is it necessary to fix all or none of the positions for a given element? If fixing only some positions for an element is supported, does anyone have any idea what might be going wrong?

Thank you very much for any advice you can offer!

Kyle