Crystal structure
Structure databases
Density functional theory (DFT) calculations are ab-initio meaning the
calculation is done from the scratch based on given input parameters. We need to
provide the crystal structure in order to calculate DFT. Crystal structures are
widely available in Crystallographic Information File (.CIF) format. There are
several databases where you can look for crystal structures.
- http://crystallography.net/cod/
- https://materialsproject.org
- https://mpds.io/
- https://icsd.fiz-karlsruhe.de/index.xhtml
- http://aflowlib.org/CrystalDatabase/
- http://crystdb.nims.go.jp/crystdb/search-materials
In Quantum Espresso, the structure information is provided by ibrav number,
and corresponding celldm values or lattice constants and cosines of angle
between the axes. It is also possible to set ibrav=0 and provide lattice
vectors in CELL_PARAMETERS.
When set ibrav=0, the lattice vectors must be provided with sufficiently large
number of decimal accuracy, otherwise symmetry detection may fail and strange
problems may arrise.
ibrav numbers for different lattice types:
ibrav | Lattice type |
|---|---|
| 1 | Simple cubic |
| 2 | Face centered cubic |
| 3,-3 | Body centered cubic |
| 4 | Hexagonal |
| 5 | Trigonal with c as 3-fold axis |
| -5 | Trigonal with <111> as 3-fold axis |
| 6 | Simple tetragonal |
| 7 | Centered tetragonal |
| 8 | Simple orthorhombic |
| 9,-9,91 | One-face centered orthorhombic |
| 10 | Face centered orthorhombic |
| 11 | Body centered orthorhombic |
| 12 | Simple monoclinic, c unique |
| -12 | Simple monoclinic, b unique |
| 13 | One base centered monoclinic, c unique |
| -13 | One base centered monoclinic, b unique |
| 14 | Triclinic |
Useful tools:
Vesta - https://jp-minerals.org/vesta/en/. It helps you visualize crystal structure, create and modify supercells, crystal structures, and many other useful functionalities.
We can prepare our Quantum Espresso input file using cif2cell utility. If you do not have cif2cell installed, you can use pip to install:
sudo pip3 install cif2cell
You may need to add it to the path in your .bashrc manually:
export PATH="/home/pranab/.local/lib/python3.8/site-packages/:$PATH"
Running cif2cell command:
cif2cell file.cif -p quantum-espresso -o inputfile.in
Xcrysdens
You can explore the crystal structure, find out k-path and many more using Xcrysdens application - http://www.xcrysden.org
For certain functionality, Xcrysdens requires basic calculator program. On Ubuntu/ Debian:
sudo apt update
sudo apt install bc xcrysden
Manual installation:
# install dependencies
sudo apt install --no-install-recommends bc tk libglu1-mesa libtogl2 \
libfftw3-3 libxmu6 imagemagick openbabel libgfortran5
# download the latest version of xcrysden and extract
wget http://www.xcrysden.org/download/xcrysden-1.6.2-linux_x86_64-shared.tar.gz
tar -zxvf xcrysden-1.6.2-linux_x86_64-shared.tar.gz
# launch (provided you extracted under your home directory)
~/xcrysden-1.6.2-bin-shared/xcrysden
If you are on WSL, you need to install X-server (X-ming for Windows) on the host
and set export DISPLAY=:0 in your WSL instance.
QE Input generator
You can generate PWscf input files using tools in this website as well https://www.materialscloud.org/work/tools/qeinputgenerator
The same website also has a tool for k-path visualization and generation https://www.materialscloud.org/work/tools/seekpath