Issue regarding tri-clinic

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1

Dear All,

Can anyone explain how exactly lammps convert original triclinic to lammps-triclinic? I have read documentation about triclinic. (section6.12). For some material it cant convert it properly. I have attached both original and lammps triclinic boxes with atom co-ordinates. Is there some issue regarding alpha being less than 63?

File attached below have following description:

  1. Framework_0_final.pdb : original triclinic box.

! 31.372 A (tri)
! 48.392 B (tri)
! 48.392 C (tri)
! 61.15 alpha (tri)
! 83.80 beta (tri)
! 96.20 gamama (tri)

  1. co-ordinate.xyz : lammps triclinic box.

! 31.372 cell_a (lmptri)
! 48.673401 cell_b (lmptri)
! 48.684792 cell_c (lmptri)
! 89.428204 cell_alpha (lmptri)
! 83.837433 cell_beta (lmptri)
! 96.16402 cell_gamma (lmptri)

I have send you files, so you can visulise in VMD.

Thanks in advance.

Sincerely,

Viral

Framework_0_final.pdb (342 KB)

co-ordinate.xyz (122 KB)

2

From: Viral Solanki <[email protected]...>
Date: Thu, Jan 25, 2018 at 11:15 AM
Subject: Issue regarding tri-clinic
To: [email protected]

Dear All,

        Can anyone explain how exactly lammps convert original triclinic
to lammps-triclinic? I have read documentation about triclinic.
(section6.12). For some material it cant convert it properly. I have
attached both original and lammps triclinic boxes with atom co-ordinates.
Is there some issue regarding alpha being less than 63?

​you are not making much sense here. the lengths A, B, and C and the angles
alpha, beta, and gamma *must* be the same in your pdb file as well as in
LAMMPS. otherwise it would not be the same cell. what you are missing in
your description below is the fact, that a triclinic cell is not perfectly
described in space with these 6 parameters. what you are missing is the
orientation. this is where triclinic cells in LAMMPS are restricted as they
*require* a specific orientation. please see the LAMMPS manual for details.
you must have been seriously misreading something. in LAMMPS you don't
enter angles anyway, but three tilt factors: xy, xz, and yz.

in practice and as far as i can tell, your pdb file i​s conforming to the
LAMMPS orientation requirement.

axel.