Mathematica notebooks for processing, plotting and visualizition of outputs (and sometimes also inputs) of DFT codes (VASP, FHI-AIMS, Fireball, GPAW and maybe others) and results of SPM (simulations)
atomic_prop.dat : text file with colours and radii for elements.
Bader_analysis_view.nb : Visualization of charges from Bader analysis. Notebook can operate with outputs of "bader" script ( theory.cm.utexas.edu/henkelman/research/bader/ ) from VASP and FHI-AIMS .
BAS_to_XYZ_to_IN_to_CAR.nb : Notebook for fast switching of geometry from xyz, bas, geometry.in, CONTCAR & POSCAR files. Possibility to change atomic order, according to element and/or x and/or y and/or z coordinates.
DOS_plot_and_view.nb : The notebook can read PDOS from different DFT codes (Fireball, VASP, GPAW, FHI-AIMS, CP2K) and plot them in the same way. In the second part (VIEW) there is possibility to visualize the amount of PDOS per atom in 3D balls & sticks model.
DOS_plot_and_view_spinpol.nb : The notebook can read spin-polarized PDOS from different DFT codes (VASP, FHI - AIMS and CP2K) and plot them in the same way. For VASP also polarization in case of spin-orbit coupling can be plotted. In the second part (VIEW) there is possibility to visualize the amount of PDOS per atom in 3 D balls & sticks model.
energy_path_plot.nb : Plotting of energy diagrams and barriers for Nudged Elastic Band calculations.
Fast_WSxM_2D_view.nb : Notebook for 2D visualization of SPM data stored in WSxM format.
Fast_XYZ_view.nb : Notebook for fast balls and sticks plotting of geometry from *.xyz file.
geom_view_and_edit.nb : Notebook for view (balls and sticks) and possible edits of geometry from xyz, bas, geometry.in CONTCAR & POSCAR files.
molecular_assembly_simple_check.nb : Simple check for supercell creation - if adsorbed molecule is affecting its periodical image.
PP_XY_view_via_XSF.nb : ProbeParticle position view. This notebook is basically doing the same thing plot_results.py -- pos but in Mathematica Style. Done loong time ago.
WSxM_and_geom_2n3D_view.nb : Notebook for 2D & 3D visualization of SPM (simulated) data stored in WSxM format together with balls and sticks model of geometry (from DFT calculations). Possible to obtain also any line-profile from SPM data.
If there are some chapter-titles (Black bold texts) without any cells afterwards it means, that these chapters are closed. It is possible to open them by double-click to the second line/parentheses on the right side.