Dr. Probe command-line tools for HR-(S)TEM image simulation
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README.md

Dr. Probe command-line tools (drprobe_clt)

Authors and Copyright

Juri Barthel, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany

Copyright (c) 2008 - 2019 - Forschungszentrum Jülich GmbH

Published under the GNU General Public License, version 3, see http://www.gnu.org/licenses/ and LICENSE!

CELSLC

CELSLC is a program to calculate object transmission functions to be used as phase gratings in a multislice algorithm for electron diffraction calculations. The calculations require an atomic structure model as input, including the definition of a calculation box, atomic coordinates, thermal vibration parameters, and partial occupancy factors. Further parameters concern numerical sampling and the probing electron energy. The output produced can be used as input of the program MSA.

MSA

MSA is a program to calculate the diffraction of beam of probing electrons through a crystal. The crystal data is input in form of phase gratings or projected scattering potentials as calculated by the program CELSLC. Further parameters concern the probe forming, sample thickness, scan settings etc. Output are electron wave functions or STEM images.

WAVIMG

WAVIMG is a program used for the calculation of high-reslolution TEM images from an input electron wave function.

Documentation

Documentation and a few examples can be found on the Dr. Probe website. In addition, each tool has its own "howto" text file. These files are used as the primary source of documentation.

Testing

Example input data is provided in the subfolder "test". The following calls are simple test cases. Please, adopt folders and file names according to your local situation.

STEM image simulations

  • HAADF, ABF and BF thickness series simulation with subsequent source convolutions:
celslc -cif test/STO_001_4x4.cif -nx 625 -ny 625 -nz 2 -nv 50 -ht 300 -slc test/sto_001_4x4_300keV_fl50 -fl
msa -prm test/msa-1.prm -out test/img.dat /3dout
msa -prm test/msa-1.prm -in test/img_HAADF.dat -out test/img_HAADF_psc.dat /3dout
msa -prm test/msa-1.prm -in test/img_ABF.dat -out test/img_ABF_psc.dat /3dout
msa -prm test/msa-1.prm -in test/img_BF.dat -out test/img_BF_psc.dat /3dout
  • HAADF thickness series simulation with subsequent source convolutions including separation of elastic and thermal-diffuse scattering with 5 processes running in parallel, each solving a set of different scan lines:
celslc -cif test/STO_001_4x4.cif -nx 625 -ny 625 -nz 2 -nv 50 -ht 300 -slc test/sto_001_4x4_300keV_fl50 -fl
start msa -prm test/msa-1-avg.prm -out test/img.dat /3dout -py 0 -ly 3 /silavwaveft /verbose
start msa -prm test/msa-1-avg.prm -out test/img.dat /3dout -py 4 -ly 7 /silavwaveft /verbose
start msa -prm test/msa-1-avg.prm -out test/img.dat /3dout -py 8 -ly 11 /silavwaveft /verbose
start msa -prm test/msa-1-avg.prm -out test/img.dat /3dout -py 12 -ly 15 /silavwaveft /verbose
start msa -prm test/msa-1-avg.prm -out test/img.dat /3dout -py 16 -ly 19 /silavwaveft /verbose
msa -prm test/msa-1.prm -in test/img_HAADF_tot.dat -out test/img_HAADF_tot_psc.dat /3dout
msa -prm test/msa-1.prm -in test/img_HAADF_ela.dat -out test/img_HAADF_ela_psc.dat /3dout
msa -prm test/msa-1.prm -in test/img_HAADF_tds.dat -out test/img_HAADF_tds_psc.dat /3dout

HR-TEM image simulations

  • NCSI image:
celslc -cif test/STO_001_4x4.cif -nx 256 -ny 256 -nz 2 -ht 300 -slc test/sto_001_4x4_300keV_dwf -dwf -abf 0.07
msa -prm test/msa-2.prm -out test/img.dat /ctem
wavimg -prm test/wavimg-2.prm -out test/img_ctem.dat

Development

The programs are written in Fortran 90 code for Intel Fortran compilers.

Current versions:

  • CELSLC: 0.70
  • MSA: 0.92
  • WAVIMG: 0.70

The code of the program MSA links to "libfftwf-3.3.lib" MSA uses data output by FFTW and is in no form based on work represented by the FFTW project. Source code and library binary code of FFTW are available from http://www.fftw.org/ (accessed April 2018).

TODOs

  • keep up with new code from JMultiSlice
    • investigate if the CUDA code can be used in this project
  • add notes on experimental and undocumented features to the howto files.
  • add a wrapper tool for applying external transition potentials for EELS and EDX
  • add partial import of wavefunctions and images from 3d data sets with MSA and WAVIMG.