How does CP2K define the cell around a molecule?

[rashe...@gmail.com]

How does CP2K define the cell around a molecule?

Does it centre the cell about the axes' origin (0,0,0)? 

Or does it define point (0,0,0) as a corner of the cell?

[Stein, Dr. Frederick]

Dear Rashed (?),
The coordinates are taken from the coordinates given by the respective
XYZ-file or the geometry defined in the &COORD-section. Coordinates are only
centred if the &CENTER_COORDINATES
(https://manual.cp2k.org/cp2k-2026_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/TOPOLOGY/CENTER_COORDINATES.html)
section is active).
HTH,
Frederick

Am Sat, 27 Jun 2026 22:53:15 -0700 (PDT) schrieb "rashe...@gmail.com"
<rashe...@gmail.com>:

> How does CP2K define the cell around a molecule?
> Does it centre the cell about the axes' origin (0,0,0)?
> Or does it define point (0,0,0) as a corner of the cell?
>

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Dr. Frederick Stein
Scientific Computing Core
CASUS - Center for Advanced Systems Understanding, Görlitz
Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)

[rashe...@gmail.com]

Thanks Frederick,

So, just for absolute clarification: 

Say I defined a molecule about the origin, with coordinates having positive and negative signs, and then used, say,  10*10*10 cell without the  &CENTER_COORDINATES option, then part of the molecule will not be included within the cell? This means the molecule must be shifted to lie within the first octant of the xyz space (?)

eftrsd

[Stein, Dr. Frederick]

Dear eftrsd,
For clarification: In the case of missing periodicity, all parts of
densities(!) outside of the box in the non-periodic directions, are not
considered. This leads to non-zero densities at the border of the cell and
potentially a source of error (depends on the magnitude). Some
Poisson-solvers will emit a warning in this case because they assume exactly
that. The &CENTER_COORDINATES section reduces the probability of it, i.e.
the cell must be large enough.
Best,
Frederick

Am Mon, 29 Jun 2026 11:57:52 -0700 (PDT) schrieb "rashe...@gmail.com"
<rashe...@gmail.com>:

>https://groups.google.com/d/msgid/cp2k/75569048-a0b8-4718-b14c-b9c562c9d4bfn%40googlegroups.com.