The Visualization Toolkit for Analyzing Defects in Materials (VTAnDeM)

VTAnDeM is a post-processing plotting toolkit for DFT calculations of defects in materials. The toolkit allows simultaneous visualization of interconnected thermodynamic and electronic properties of materials, including phase stability, defects, and carrier concentrations.

Python Version

python >= 3.5

Required Packages

Numpy >= 1.16
Matplotlib >= 3.0
Click
- pip3 install click
LabelLines
- pip3 install matplotlib-label-lines
PeriodicTable
- pip3 install periodictable
Pymatgen >= 2019.5.8
- pip3 install pymatgen
PyQt5 >= 5.11.3
- pip3 install PyQt5
PyPolyhedron (Courtesy of Dr. Pearu Peterson and Dr. Sunghyun Kim, https://github.com/frssp/PyPolyhedron)
- Steps:
  1. git clone https://github.com/frssp/PyPolyhedron
  2. cd /path/to/PyPolyhedron
  3. python3 setup.py install

Installation

Download all VTAnDeM files.
- git clone https://github.com/ertekin-research-group/VTAnDeM
Run python3 setup.py install in the downloaded VTAnDeM folder.

Examples:

Example VTAnDeM projects can be found in the Examples folder for the following materials:

Mg₂Si
Hg₂GeTe₄
Cu₂HgGeTe₄

Usage:

VTAnDeM must be called from the command terminal. The steps are as follows:

Create a VTAnDeM project in a directory of your choice.

mkdir vtandem_project
cd vtandem_project
vtandem --new

Import all of your DFT data. This can be done in one of three ways:

Open the VTAnDeM user interface.
```
vtandem --open
```
(Help can be found in the help buttons, which are included in the import dialogs.)

Import data from the command line.

Phase Stability Data:

 vtandem --import_element Cu PhaseStability/Cu
 vtandem --import_element Hg PhaseStability/Hg
 vtandem --import_element Ge PhaseStability/Ge
 vtandem --import_element Te PhaseStability/Te
 vtandem --import_compound CuTe PhaseStability/CuTe
 vtandem --import_compound GeTe PhaseStability/GeTe
 vtandem --import_compound HgTe PhaseStability/HgTe
 vtandem --import_compound Hg2GeTe4 PhaseStability/Hg2GeTe4
 vtandem --import_compound Cu2GeTe3 PhaseStability/Cu2GeTe3

Defects Data:

 vtandem --import_defects Cu2HgGeTe4 Cu2HgGeTe4_Defects

Defect Energy Corrections:

 vtandem --import_defect_energy_corrections Cu2HgGeTe4 CHGT_EnergyCorrections.csv

DOS Data:

 vtandem --import_dos Cu2HgGeTe4 DOSCAR

Import data from Python interface.

Phase Stability Data:

 from vtandem.dft import import_dft
 x = import_dft.Compounds_Import()
 x.Add_Element("Cu", "PhaseStability/Cu")
 x.Add_Element("Hg", "PhaseStability/Hg")
 x.Add_Element("Ge", "PhaseStability/Ge")
 x.Add_Element("Te", "PhaseStability/Te")
 x.Add_Compound("CuTe", "PhaseStability/CuTe")
 x.Add_Compound("GeTe", "PhaseStability/GeTe")
 x.Add_Compound("HgTe", "PhaseStability/HgTe")
 x.Add_Compound("Hg2GeTe4", "PhaseStability/Hg2GeTe4")
 x.Add_Compound("Cu2GeTe3", "PhaseStability/Cu2GeTe3")
 x.Update_Compounds_Database()

Defects Data:

 from vtandem.dft import import_dft
 x = import_dft.Defects_Import()
 x.Add_Defects("Cu2HgGeTe4", "Cu2HgGeTe4_Defects")
 x.Add_Energy_Corrections("Cu2HgGeTe4", "CHGT_EnergyCorrections.csv")
 x.Update_Defects_Database()

DOS Data:

 from vtandem.dft import import_dft
 x = import_dft.DOS_Import()
 x.Add_DOS("Cu2HgGeTe4", "DOSCAR")
 x.Update_DOS_Database()

Open the VTAnDeM interface.
```
vtandem --visualize
```
(Note that this step is not necessary if you opened the VTAnDeM UI in step 2.i)

Help:

Help with the necessary data structure can be found readily on the command terminal.

vtandem --help

kavanase / VTAnDeM