auglat

This code makes the augmented lattice given the high symmetry unstable lattice and a local distortion close by. This module is part of the "Piecewise Polynomial Potential Partitioning (P4)" method introduced here.

-> Input files:
hs_lat.in The high-symmetry unstable lattice.
str_loc.in The local distortion structure geometry.

-> Output files:
lat.in The augmented lattice.

-> Structure and lattice file formats:
Both the lattice and the structure files have a similar structure.
First, the coordinate system a,b,c is specified, either as
[a] [b] [c] [alpha] [beta] [gamma]
or as:
[ax] [ay] [az]
[bx] [by] [bz]
[cx] [cy] [cz]
Then the lattice vectors u,v,w are listed, expressed in the coordinate system
just defined:
[ua] [ub] [uc]
[va] [vb] [vc]
[wa] [wb] [wc]
Finally, atom positions and types are given, expressed in the same coordinate system as the lattice vectors:
[atom1a] [atom1b] [atom1c] [atom1type]
[atom2a] [atom2b] [atom2c] [atom1type]
etc.

In the lattice file:
-The atom type is a comma-separated list of the atomic symbols of the atoms that can sit the lattice site.
-The atomic symbol 'Vac' or 'Va' is used to indicate a vacancy.

In the structure file:
-The atom type is just a single atomic symbol (which, of course, has to be among the atomic symbols given in the lattice file).
-Vacancies do not need to be specified.

Note: This module is used to generate the input files for other modules like vcrelax_vasp or mcmc. It is highly recommended that one uses this module instead of generating the augmented lattice by itself. Otherwise, unexpected errors might be observed in vcrelax_vasp or mcmc due to inconsistent input lattice and structure files.

Note: See genrndstr -h for more details on how to generate structure file given the augmented lattice.

-> Example 1: Unstable bcc Titanium

The bcc lattice of Ti system as the high-symmetry lattice:
3.24 3.24 3.24 90 90 90
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
0 0 0 Ti,Vac

Note: Always incldue vacancies in the high-symmetry lattice file to gaurantee the generation of a correct augmented lattice.

The local distortion structure nearby the high-symmetry lattice:
3.24 3.24 3.24 90 90 90
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
0.1443 0.1443 0.1443 Ti

Run the following command
auglat -l=hs_lat.in -loc=str_loc.in -ol=lat.in
The generated augmented lattice is written to lat.in file as the following:
3.24 0 0
1.98386e-16 3.24 0
1.98393e-16 1.98393e-16 3.24
1.9839e-16 1.62 1.62
1.62 9.91964e-17 1.62
1.62 1.62 0
0.6443 0.8557 0.6443 Ti,Vac
0.1443 0.3557 0.3557 Ti,Vac
0.1443 0.1443 0.1443 Ti,Vac
0.3557 0.3557 0.1443 Ti,Vac
0.6443 0.6443 0.8557 Ti,Vac
0.8557 0.8557 0.8557 Ti,Vac
0.3557 0.1443 0.3557 Ti,Vac
0.8557 0.6443 0.6443 Ti,Vac
1 1 1 Ti,Vac

-> End of example 1

-> Example 2: Unstable B2 ordered Ni-Ti compound:

The B2 lattice of Ti-Ni system as the high-symmetry lattice:
3.0 3.0 3.0 90 90 90
1 0.0 0.0
0.0 1 0.0
0.0 0.0 1
0 0 0 Ti,Vac
0.5 0.5 0.5 Ni,Vac

Note: Always incldue vacancies in the high-symmetry lattice file to gaurantee the generation of a correct augmented lattice.

The local distortion structure nearby the high-symmetry lattice:
3.0 3.0 3.0 90 90 90
1 0.0 0.0
0.0 1 0.0
0.0 0.0 1
0.1 0.1 0.1 Ti
0.4 0.4 0.4 Ni

Run the following command
auglat -l=hs_lat.in -loc=str_loc.in -ol=lat.in
The generated augmented lattice is written to lat.in file as the following:
3 0 0
1.83691e-16 3 0
1.83697e-16 1.83697e-16 3
1 0 0
0 1 0
-1.2326e-32 -1.2326e-32 1
0.1 0.1 0.1 Ti,Vac
0.4 0.4 0.4 Ni,Vac
0.1 0.1 0.9 Ti,Vac
0.4 0.4 0.6 Ni,Vac
0.1 0.9 0.1 Ti,Vac
0.4 0.6 0.4 Ni,Vac
0.1 0.9 0.9 Ti,Vac
0.4 0.6 0.6 Ni,Vac
0.9 0.1 0.1 Ti,Vac
0.6 0.4 0.4 Ni,Vac
0.9 0.1 0.9 Ti,Vac
0.6 0.4 0.6 Ni,Vac
0.9 0.9 0.1 Ti,Vac
0.6 0.6 0.4 Ni,Vac
0.9 0.9 0.9 Ti,Vac
0.6 0.6 0.6 Ni,Vac
1 1 1 Ti,Vac
0.5 0.5 0.5 Ni,Vac

-> End of example 2