[CP2K-user] Structure error when calculating PDOS

[Fabian Ducry]

The error message is correct, you are not creating the structure that you 
need.

Let me illustrate this with the atom Cu 0 0 0:

You request a periodic simulation with cell size ABC [angstrom] 3.810000 
3.810000 3.810000
This implies that the Cu atom (0,0,0) is repeated every 3.81 angstrom in 
every direction periodically. Because of this, a periodic image of the atom 
also exist, for instance, at (-3.81,-3.81,-3.81).
At the same time you specify the fractional coordinates for the first atom 
in your structure with Cu -1 -1 -1, this is equivalent to 
(-3.81,-3.81,-3.81).

Because of the periodic boundary condition (PBC) you now have both atoms at 
the same location, Cu 0 0 0 because of the PBC and Cu -1 -1 -1. Therefore, 
the distance between these two atoms is 0.

To fix this problem you can do the following:
 - convert the scaled to cartesian coordinates
 - increase the box size by a factor of 3
 I.e.
ABC [angstrom] 11.43 11.43 11.43
and 
      &COORD
        SCALED FALSE
        Cu -3.81 -3.81 -3.81
        O -3.81 -1.905 -3.81
[...]
      &END COORD

Best,
Fabian
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