Cell Optimization of triclinic cell
Aniruddha Dive
anirudd... at gmail.com
Tue Apr 17 23:03:43 UTC 2018
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:
*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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