The super cell file format (CEL)

 

Dr. Probe image simulations require atomic structure data as input. This input is provided in form of a text file, which contains general super-cell parameters, as well as atom type, position, occupancy, and thermal vibration data.

A super-cell structure file has the following general form:

Text line number

Text line content, structure parameters

1

Comment string, not used to define the structure.

2

Super-cell parameters: "0" <space> super cell size x <space> y <space> z in [nm] <space> cell basis vector angles alpha <space> beta <space> gamma in [deg]

3 ... # atoms

Atom site parameters: Symbol string <space> fractional cell coordinate x <space> y <space> z <space> site occupancy <space> Debye-Waller factor parameter Biso [nm2] <space> "0" <space> "0" <space> "0"

Last

"*"

 

The three "0" (zero) characters of the atom site parameters are placeholders which may be used in future versions to define directional thermal vibration parameters.

 

SrTiO3 110
  0  0.3905  0.5523  0.5523 90.0000 90.0000 90.0000
 Ti   0.000000  0.000000  0.500000  1.000000  0.005100  0.000000  0.000000  0.000000
 O    0.000000  0.250000  0.250000  1.000000  0.010800  0.000000  0.000000  0.000000
 O    0.000000  0.250000  0.750000  1.000000  0.010800  0.000000  0.000000  0.000000
 Ti   0.000000  0.500000  0.000000  1.000000  0.005100  0.000000  0.000000  0.000000
 O    0.000000  0.750000  0.250000  1.000000  0.010800  0.000000  0.000000  0.000000
 O    0.000000  0.750000  0.750000  1.000000  0.010800  0.000000  0.000000  0.000000
 Sr   0.500000  0.000000  0.000000  1.000000  0.006600  0.000000  0.000000  0.000000
 O    0.500000  0.000000  0.500000  1.000000  0.010800  0.000000  0.000000  0.000000
 O    0.500000  0.500000  0.000000  1.000000  0.010800  0.000000  0.000000  0.000000
 Sr   0.500000  0.500000  0.500000  1.000000  0.006600  0.000000  0.000000  0.000000
*

[Example super cell file for SrTiO3 in [110] zone axis orientation]

 

Example: Creation of a SrTiO3 [110] super cell for STEM simulations.

 


Last update: August 1, 2017

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