OVITO Forum
OVITO => Support Forum => Topic started by: rajdeep on March 14, 2019, 02:03:38 PM

Dear all,
I have a LAMMPS data file (unit cell) of TiAl which is a face centered tetragonal (FCT) lattice. In this data file my X, Y and Z axes are oriented along <100>, <010>, and <001>, respectively.
I would like to rotate the lattice in such a way so that my new X, Y and Z are aligned with <211>, <111>, and <011>, respectively. In order to accomplish this within OVITO, I applied the affine transformation option but the new lattice become triclinic. Please see the attached snapshot.
My question is does this affine transformation option can rotate my lattice in the desired crystallographic orientation? If so, after the transformation how I can wrap the atoms in a orthogonal cell?
Thanks,
Rajdeep

Dear Rajdeep,
note that the Affine Transformation modifier takes the transformation matrix that you enter and applies it onto your system. So what you need to enter there is the rotation matrix between your two coordinate systems.
Constanze

Dear Constanze,
Thank you very much for your reply. I would like to transform the coordinate system from (100, 010, 001) to (111, 110,112). So my rotation matrix is (111, 110, 112). If I provide this rotation matrix to OVITO along with 'Transform simulation cell' option, it gives me a triclinic box. Later on, I minimized the triclinic box in LAMMPS, and it seems that it has a large residual pressure even with stringent energy and force criterion which indicates that the rotated structure is not stable. In that case how I can wrap the rotated structure in a orthogonal box? Please see the initial and rotated structure. Thanks for your help.
Best regards,
Rajdeep

Dear Rajdeep,
Note that your transformation matrix is not a proper rotation matrix: ([111], [110], [112]), because its column vectors are not normalized. A rotation matrix must have unit column vectors, all orthogonal, and its determinant must be 1. Since your matrix doesn't fulfill these criteria, you are getting something that is not a pure rotation.
It should suffice to normalize each column vector to obtain a rotation matrix, i.e.
([111]/sqrt(3), [110]/sqrt(2), [112]/sqrt(6))
Alex

Dear Alexander,
Thank you for your email. Sorry for incorrect rotation matrix.
Now, I'm providing the normalized rotation matrix and the option "transform simulation cell" is selected. In the output it looks like the entire simulation box is rotated with respect to the X, Y and Z axis, but atom positions are not changed. I did minimization of the rotated structure and got exactly similar structure as the input structure was. It is expected that after rotation cell size along X, Y and Z should change, but it is not changed in the rotated system. Please find the attached figures of the initial and rotated structure. Am I missing anything or misunderstanding OVITO?
Thank you very much for your help.
Best regards,
Rajdeep

Hello Rajdeep,
instead of rotating everything you need to apply the rotation only on the atoms.
Constanze