CELSLC - Generation of multislice phase gratings

 

The purpose the program CELSLC is the calculation of complex valued phase grating data from atomic super-cell structure files. This program is compiled for single-thread calculations and can be called from command-line shell or from other programs on 64-bit operating systems.

 

Summary of program functions:

INPUT DATA : Required input data for phase grating calculations with CELSLC are atomic structure parameters in form of a super-cell containg atomic sites. The atomic structure data can be supplied either in form of a CEL file or a CIF file. Such files contain information about super-cell dimension, atom symbols, relative atom coordinates, atom site occupancies, and thermal vibration parameters, e.g. in terms of isotropic Biso parameters.

SLICE GENERATION : In order to calculate the elastic forward scattering of the incident electron wave by the electrostatic potential of the atomic object structure with a multislice algorithm, the crystal potential is projected to very thin volume slices. The elastic scattering potentials are calculated using the parameterization of Weickenmeier and Kohl [Acta Cryst. A47 (1991) p. 590-597]. An implementation of alternative potential models is implemented and may be explained to the interested user on request.
Within the small angle approximation the interaction of the fast electron with the screened Coulomb potential of the atomic core charge results in a phase shift of the electron wave function which is expressed numerically by a phase grating. A free discretization up to 2048 x 2048 pixels is possible by default. Higher pixel numbers are available on request. Thermal vibration models using a frozen lattice or Debye-Waller factors are implemented.
Two different options are provided to apply absorptive potentials:
 (1) Absorptive potentials as described by Weickenmeier and Kohl [Acta Cryst. A47 (1991) p. 590-597] - This approach is sufficient for low-angle scattering calculations as required for conventional high-resolution TEM and is availble only in conjunction with the application of Debye-Waller factors.
 (2) Constant but user defined absorption parameter, as proposed by Hashimoto, Howie, and Whelan [Proc. R. Soc. London Ser. A, 269 (1962) p. 80-103] - The absorption parameter is around 0.1 for low-angle scattering calculations. The respective absorption parameter for high-angle scattering calculations or low Z material should be significantly smaller on the order of 0.01 but may depend on the actual simulation setup.

PROGRAM CALLING : The program CELSLC can be run from a command-line shell, such as the console cmd.exe provided by the Windows OS or from other programs by executing celslc.exe. The program requires several command-line options to be specified with the call. The following table lists all command-line options of CELSLC of version 0.51 and provides sort descriptions of their meaning.

Option

Description of CELSLC options (Version 0.50+)

-cel <file name>

Specifies the input super-cell file containing the atomic structure data in CEL file format. Absolute or relative file names can be specified. Enclose the file name string using quotation marks if the file name contains space characters.
Example: -cel 'cel\cell 1.cel'

-cif <file name>

Specifies the input super-cell file containing the atomic structure data in CIF file format. Absolute or relative file names can be specified. Enclose the file name string using quotation marks if the file name contains space characters.
Example: -cif 'cel\crystal 2.cif'

-prj <u,v,w,u,v,w,a,b,c>

Re-orientation and re-sizing of the input structure model assuming a periodic crystal structure into an orthorhombic target cell. The orientation is given by the first 6 numbers, where the first tripple [uvw] defines the new projection direction in the input real-space lattice basis and the second triple [uvw] defines a perpendicular direction for the new y-axis of the projection. The size of the new orthorhombic super-cell is given by the last 3 numbers (a,b,c) defining the extension in nanometers along each of the 3 new axes x, y, and z, where z is the projection direction of the similation. The origin point of the structure is not changed.
Example: -prj 2,4,1,-2,2,-1,0.79289,0.79289,0.79289

-tla <fx,fy,fz>

Shift all atoms of the structure in the chosen final orthorhombic super-cell by a given amount in fractional coordinates (fx,fy,fz). All atoms are shifted by the same amount and their final fractional coordinates are wrapped back periodically into the range [0,1[.
Example: -tla 0,0.125,0.0625

-slc <file name>

Specifies the output slice file name prefix. Absolute or relative path names can be used. Enclose the file name string using quotation marks if the file name prefix or the disk path contains space characters. The slice file names will be suffixed by '_###.sli', where ### is a 3 digit number denoting the sequence of slices generated from the supercell.
Example: -slc 'slc\slices 1'

-nx <pixel number>

Number of horizontal samples for the phase grating. The same number of pixels is used to sample the wave function in multislice calculations based on the calculated phase gratings.
Example: -nx 768

-ny <pixel number>

Number of vertical samples for the phase grating. The same number of pixels is used to sample the wave function in multislice calculations based on the calculated phase gratings.
Example: -ny 768

-ht <number>

Accelerating voltage defining the kinetic energy of the incident electron beam in kV.
Example: -ht 300.0

-rev

(OPTIONAL) Switch reversing the order in which slices are generated from the input structure. When the option -rev is omitted, the slice sequence begins at the fractional z-coordinate z/c = 0 and stops at z/c = 1. When the option -rev is set, the slice sequence begins at z/c = 1 and stops at z/c = 0. When changing this option, the electron diffraction will not only be reversed along the z-coordinate, but will also change the rotational sense.

-fl

(OPTIONAL) Switch for applying random atomic displacements for frozen-lattice caluclations according to the specified thermal vibration parameter (Debye-Waller factor) B.
This option cannot be used in combination with the options -dwf and -abs.

-nv <variant number>

(Optional) Specifies the number of frozen lattice variants with random atom displacements generated per slice. Each slice file will contain several phase gratings of the same slice. Make sure to precalculate the required memory for stroing multiple variants. Do not exceed the physical size of the available RAM! Requires the option flag -fl.
Example: -nv 25

-nz <slice number>

(Optional) Equidistant slicing of the super-cell along the c-axis. Specify an explicit number of slices, or use -nz 0 to let CELSLC determine the number of equidistant slices automatically. Omitting the -nz option will lead to an automatic non-equidistant slicing.
Example: -nz 4

-dwf

(OPTIONAL) Switch for applying Debye-Waller factors which effectively dampen the atomic scattering potentials. Use this option for conventional HR-TEM, STEM bright-field, or STEM annular bright-field image simulations only.

-abs

(OPTIONAL) Switch for applying absorption potentials (imaginary part) according to Weickenmeier and Kohl [Acta Cryst. A47 (1991) p. 590-597]. This absorption calculation considers the loss of intensity in the elastic channel due to thermal diffuse scattering.
The option -abs cannot be used in combination with the options -fl and -abf.

-abf <number>

(OPTIONAL) Switch and value for applying absorption potentials. The absorption potential is set as imaginary part of the scattering potential, which is a copy of the potential real part multiplied by a factor given by the specified floating point number. A typical value is 0.1.
Example: -abf 0.085

-pot

(OPTIONAL) Switch for exporting projected potential slices to individual files (*.pot).

OUTPUT DATA : The phase gratings generated by CELSLC are saved as a sequence of separate files with file-name extension sli. These files contain a header with physical size and calculation parameters and the complex valued phase grating in uncompressed binary form. The sli-files are used as input data for multislice calculations with the Dr. Probe graphical user interface or with the command line program MSA.

 

Examples

Periodic SrTiO3 [001] with frozen phonons for HAADF-STEM image simulations:
Generate phase gratings of 2 slices sampled on a grid of 480 x 480 pixels for 300 keV electrons with 50 frozen phonon configurations per slice. The input structure data consists of 3 x 3 unit cells SrTiO3 in [001] orientation arranged in a square grid in the x-y plane. The output phase gratings will be stored in the files STO001-300kV_001.sli and STO001-300kV_002.sli.
celslc -cel STO_001_3x3.cel -slc STO001-300kV -nx 480 -ny 480 -nz 2 -nv 50 -fl -ht 300

Periodic SrTiO3 [110] for high-resolution TEM image simulations:
Generate phase gratings of 4 slices sampled on a grid of 108 x 80 pixels for 300 keV electrons with Debye-Waller factors and apsorptive potentials applied. The input structure data consists of 2 SrTiO3 unit cells in [110] orientation. The output phase gratings will be stored in the files STO100-300kV_001.sli, STO100-300kV_002.sli, STO100-300kV_003.sli and STO110-300kV_004.sli.
celslc -cel STO_110_2UC.cel -slc STO110-300kV -nx 108 -ny 80 -nz 4 -dwf -abs -ht 300

 


Last update: August 1, 2017

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