[CP2K-user] [CP2K:22299] How does CP2K define the cell around a molecule?

[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... at gmail.com" 
<rashedeffat at 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
> 
> On Sunday, June 28, 2026 at 8:56:22 PM UTC+3 Stein, Dr. Frederick wrote:
> 
>> 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... at gmail.com" 
>> <rashe... at 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)
>>
> 
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Dr. Frederick Stein
Scientific Computing Core
CASUS - Center for Advanced Systems Understanding, Görlitz
Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)

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