Introduction

by Joseph Wong 5/26/2019

This notebook demonstrates the basic usage of aimsgb in the Linux/UNIX command line with MgO and Co2VGa as examples. The command line version of aimsgb allows for quick generation of a small number of grain boundary structures. All this information and example usage can be viewed in the command line with aimsgb -h

In [1]:
$ aimsgb -h
$ aimsgb list -h
$ aimsgb gb -h
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list

To construct a grain boundary, the Σ value, rotation-axis, and grain boundary plane must first be known. If these values are not known beforehand, the list command can provide a list of possible values for a particular rotation-axis for Σ values up to a certain cutoff.

In [2]:
$ aimsgb list 001 20
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gb

The gb command constructs the grain boundary from a given structure file with a specified rotation axis (001), Σ value (5), and grain boundary plane (1 2 0).

In [3]:
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO
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The grain size of each half (grain a and grain b) can be specified with the -ua option

In [4]:
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -ua 1 -ub 1
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -ua 1 -ub 2
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -ua 2 -ub 1
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Individual layers can be deleted with -dl #b#t#b#t, where b and t refer to bottom and top layer of each grain respectively and # refers to the number of layers to be deleted.

In [5]:
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -dl 0b0t0b0t
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -dl 0b0t0b1t
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -dl 0b0t1b0t
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -dl 0b1t0b0t
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -dl 1b0t0b0t
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A vacuum layer can be added at both grain boundary planes with -ad. Similarly, a vacuum layer can be added at only one grain boundary plane with -v.

In [6]:
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -ad 0
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -ad 0.75
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The tolerance factor for assigning atoms to layers during the grain grain construction can be specified with -t. If no structural manipulation is performed, this parameter will not have any effect on the grain boundary structure. This is primarily useful in cases where layer deletion is involved. In most cases, the default value of 0.25 angstroms is sufficient, but in cases of structurally relaxed or distorted structures, increasing this value may be appropriate. A tolerance factor that is too large can lead to unexpected results.

In [7]:
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -t 0.25
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -t 0.25 -dl 0b0t0b1t
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -t 0.5 -dl 0b0t0b1t
$ aimsgb gb 001 5 1 2 0 POSCAR_MgO -t 1.5 -dl 0b0t0b1t
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By default, aimsgb will generate the primitive grain boundary structure. The conventional structure can be generated by specifying -c

In [8]:
$ aimsgb gb 001 5 1 2 0 POSCAR_Co2VGa -c
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