Cell Optimization of triclinic cell
Matt W
mattwa... at gmail.com
Tue Apr 17 23:34:12 UTC 2018
Hi,
you should either specify
ABC and alpha, beta, gamma
or
give the whole set of vectors, not both.
If the set of A, B, C vectors are given any angles are ignored.
Also, I suspect your supercell likely isn't large enough. By default cp2k
only uses gamma point to sample the Brillouin zone. You should probably use
a 2x2x1 supercell to get reasonably accurate results.
Matt
On Wednesday, April 18, 2018 at 12:03:43 AM UTC+1, Aniruddha Dive wrote:
>
> Hi All,
>
> I am trying to do cell optimization of a SiS2 crystal structure which has
> a triclinic symmetry. Below is the section of input file where I specify
> the cell vectors and the angles:
>
> &SUBSYS
> &CELL
>
>
>
>
>
> *SYMMETRY TRICLINIC A 5.58515 0.00000 0.00000 B 0.00000
> 6.21427 0.00000 C 0.00000 0.00000 10.92676 ALPHA_BETA_GAMMA
> 116.86 113.96 90.00 PERIODIC XYZ*
> &END
> ! unit cells that are orthorhombic are more efficient with CP2K
> ! atom coordinates can be in the &COORD section,
> ! or provided as an external file.
> &TOPOLOGY
> COORD_FILE_FORMAT PDB
> COORD_FILE_NAME SiS2_computed.pdb
> CONNECTIVITY OFF
> &CENTER_COORDINATES
> &END CENTER_COORDINATES
> &END
>
> When I try to run the calculations, in the output file I can see the
> correct vectors a,b and c but the angles are still 90.0 90.0 and 90.0.
> Below is the portion from output file:
>
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> *CELL_TOP| Volume [angstrom^3]:
> 379.242 CELL_TOP| Vector a [angstrom 5.585 0.000 0.000 |a|
> = 5.585 CELL_TOP| Vector b [angstrom 0.000 6.214 0.000
> |b| = 6.214 CELL_TOP| Vector c [angstrom 0.000 0.000
> 10.927 |c| = 10.927 CELL_TOP| Angle (b,c), alpha
> [degree]: 90.000 CELL_TOP| Angle (a,c),
> beta [degree]: 90.000 CELL_TOP| Angle
> (a,b), gamma [degree]: 90.000 CELL_TOP|
> Requested initial symmetry:
> TRICLINIC CELL_TOP| Numerically
> orthorhombic: YES CELL| Volume
> [angstrom^3]: 379.242 CELL|
> Vector a [angstrom]: 5.585 0.000 0.000 |a| =
> 5.585 CELL| Vector b [angstrom]: 0.000 6.214 0.000 |b|
> = 6.214 CELL| Vector c [angstrom]: 0.000 0.000 10.927
> |c| = 10.927 CELL| Angle (b,c), alpha
> [degree]: 90.000 CELL| Angle (a,c),
> beta [degree]: 90.000 CELL| Angle
> (a,b), gamma [degree]: 90.000 CELL|
> Requested initial symmetry:
> TRICLINIC CELL| Numerically
> orthorhombic: YES CELL_REF|
> Volume [angstrom^3]:
> 379.242 CELL_REF| Vector a [angstrom 5.585 0.000 0.000 |a|
> = 5.585 CELL_REF| Vector b [angstrom 0.000 6.214 0.000
> |b| = 6.214 CELL_REF| Vector c [angstrom 0.000 0.000
> 10.927 |c| = 10.927 CELL_REF| Angle (b,c), alpha
> [degree]: 90.000 CELL_REF| Angle (a,c),
> beta [degree]: 90.000 CELL_REF| Angle
> (a,b), gamma [degree]: 90.000 CELL_REF|
> Requested initial symmetry:
> TRICLINIC CELL_REF| Numerically
> orthorhombic: YES*
>
> Because of this the complete geometry of the cell has changed during the
> optimization giving me weird results. Please find attached input files as
> well as the coordinate file.
>
> Kindly let me know how to fix the issue.
>
> Regards,
> Aniruddha M Dive
> PhD Candidate, Washington State University
>
>
>
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