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Distance warning for Rigid Body model with corner-sharing polyhedron
distance warning pops when refining a Rigid body model with constrained tilting direction
CLi #1
Member since Dec 2017 · 4 posts
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Subject: Distance warning for Rigid Body model with corner-sharing polyhedron
Dear All,

I am trying to refine a structure with cooperative tilting pattern, using the rigid body tool in TOPAS. The tilting direction has been set-up using the isodistort tool so that the polyhedron tilt would not break the corner-sharing polyhedron. During the refinement, the following warning pops:

“Warning; Site O4_1_1 of phase  has one of its
equivalent positions at a distance of 0 Angstroms”

The warning seems to be related with the rigid unit, the O4_1_1 sits in a special position and the warning goes away if the rigid unit is deleted from the model.

I guess the error is somehow related to that the rigid units try to move the atom away from the special position, prompting the warning, whilst the movement is restricted by the tilting direction in the script. Still, one wonders, is it necessary to modify the occupancy of the sites during the refinement? i.e. has the atom been treated as in general position, with a larger number of equivalent positions during the refinement?

I have included the .inp file in the attachment, any input for the matter is appreciated.

Best Regards,
CL
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AlanCoelho #2
Member since Aug 2011 · 280 posts
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The program is telling you that atoms lay on top of each other and probably, as you guessed, is due to a special position. Special position can be deal with by using occ_merge; search for this keyword in Technical_Reference.PDF.
CLi #3
Member since Dec 2017 · 4 posts
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Hi Alan,

Thanks for your response, occ_merge keyword works like a charm!

Best,
CL
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