Juri Barthel, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
Copyright (c) 2008 - 2023 - Forschungszentrum Jülich GmbH
Published under the GNU General Public License, version 3, see http://www.gnu.org/licenses/ and LICENSE!
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 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 is a program used for the calculation of high-reslolution TEM images from an input electron wave function.
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.
Solution and project files are included that should work with Visual Studio 2017+ and the Intel Parallel Studio or the Intel oneAPI.
The code is using the dfti module (mkl_dfti.f90) of the Intel MKL. This module must be compiled, which is not the case by default. Add the source file manually to the CELSLC project once and compile it with a release configuration. Then copy the mkl_dft*.mod files to the lp64 sub-folder of the MKL include folder (ilp64 for 64-bit integer code, default is 32-bit integers). Once the mod files are there, and you always use the same MKL version, mkl_dfti can be removed again from the project and CELSLC and MSA should both compile and link. This manual procedure is needed, since the MKL code folder can be different on different systems.
Check the makefiles for correct include folders. The setup given should work in most cases.
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.
- 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
- 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
The programs are written in Fortran 90 code for Intel Fortran compilers. CELSLC and MSA are linked against the Intel Math Kernel Libraries (MKL).
Current versions:
- CELSLC: 1.1
- MSA: 1.1
- WAVIMG: 1.0
- add slice loading on demand to MSA
- 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.