Software and resources
- 1 Software and resources
- 1.1 Structure and crystallography
- 1.2 Catalysis
- 1.3 Visualization
- 1.4 Packages
- 1.5 References
Software and resources
Structure and crystallography
Automatic login through EZproxy (www.ub.uio.no/english/using/remote-access.html).
Contains structures optimized by DFT that can be downloaded in several formats including .cif or POSCAR. Choose 'Conventional Standard' CIF.
Login with a Google account (available with UiO username www.uio.no/english/services/it/store-collaborate/gsuite/).
International Tables for Crystallography
Complete overview of space-group symmetry and more.
Shannon Ionic Radii
Binding energies of molecules
Todo: Table of binding energies with reference (e.g., NIST)
Database of reaction energies and barriers from DFT calculations.
No entropy found
jp-minerals.org/vesta/en/ (Windows, macOS, Linux)
View periodic structures, charge densities and more.
Recommended settings for improved figures
Objects > Properties > Atoms/Bonds/Polyhedra Specular: 40 40 40 Shininess (%): 1 View > Overall Appearance... Ambient: 10 Diffuse: 70
avogadro.cc (Windows, macOS, Linux)
View and edit molecular structures and optimize molecular geometry through molecular mechanics.
www.crystalimpact.com/diamond/ (Windows: Licence)
View and edit periodic and molecular structures.
www.ks.uiuc.edu/Research/vmd/ (Windows, macOS, Linux)
View and animate structures from molecular dynamics simulations.
github.com/orest-d/p4vasp (macOS, Linux)
Visualizing periodic structures, density of states and band structures.
OVITO is a visualization and analysis software for output data generated in molecular dynamics, atomistic Monte-Carlo and other particle-based simulations.
www.spyder-ide.org (Windows, macOS, Linux)
Scientific python developer environment.
Atomic Simulation Environment (ASE)
Set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
ASE modules are available on Saga
module avail ase
Example of a script for generating an (1 1 1) surface slab of palladium
#!/opt/local/bin/python from ase.io import read from ase.io import write from ase.build import fcc111 from ase.build import fcc100 from ase.build import fcc111_root
slab = fcc111_root('Pd', 3, size=(1,2,7), a=3.9438731474981594, vacuum=5.0)
write('Pd-111.cif', slab, 'cif')
VASPKIT provides a powerful and user-friendly interface to perform high throughput analysis of various material properties from the raw calculated data using the widely-used VASP code.
- Generate KPOINTS, POTCAR and INCAR for a given POSCAR file;
- Elastic-constants of 2D and bulk materials using stress-strain or energy-strain methods;
- Equation-of-state fitting;
- Suggested k-paths for a given crystal structure;
- Optical adsorption coefficient of 2D and bulk materials;
- Band structure unfolding;
- Fermi surface;
- Density-of-states and band-structure;
- Charge/spin density, Charge density difference;
- Vacuum level and work function;
- Wave-function analysis;
- Molecular-dynamics analysis;
- Effective mass of carrier;
- Symmetry finding and operations;
- 3D band structures;
- Magnetocrystalline anisotropy energy;
- Currently, only VASP raw data are fully supported.
CatMap is a catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic models used for studying kinetics and screening new catalysts.
CatMap can be installed directly via pip:
pip install --upgrade https://github.com/SUNCAT-Center/catmap/zipball/master
You may need to add the install directory to the PYTHONPATH, e.g. in bash shell or .bash_profile
Input File Structure
The TableParser accepts inputs in a tab-separated text file. An example of the header and first few lines are provided below:
The following column titles are required for a functional input file:
Generating input file for formation energy
You can use the python script under /CATMAP/catmap/tutorials/1-generating_input_file/generate_input.py
Creating a Microkinetic Model
Check the example of CO oxidation in the path of /CATMAP/catmap/tutorials/2-creating_microkinetic_model
One of the most important aspects of the “setup file” is the “rxn_expressions” variable which defines the elementary steps in the model. For this simplified CO oxidation model we will specify these as:
rxn_expressions = [ '*_s + CO_g -> CO*', '2*_s + O2_g <-> O-O* + *_s -> 2O*', 'CO* + O* <-> O-CO* + * -> CO2_g + 2*', ]
The first expression includes CO adsorption without any activation barrier. The second includes an activated dissociative chemisorption of the oxygen molecule, and the final is an activated associative desorption of CO2. More complex models for CO oxidation could be imagined, but these elementary steps capture the key features. Note that we have only included “
*” and “
*_s” sites since this is a single-site model for CO oxidation. This means that all intermediates will be adsorbed at a site designated as “
s”. These reaction expressions will be parsed automatically in order to define the adsorbates, transition-states, gasses, and surface sites in the model.
Phonopy and Phono3py
Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels. Phono3py is another open source package for phonon-phonon interaction and lattice thermal conductivity calculations.
- Phonon band structure, phonon DOS and partial-DOS
- Phonon thermal properties: Free energy, heat capacity (Cv), and entropy
- Phonon group velocity
- Thermal ellipsoids / Mean square displacements
- Irreducible representations of normal modes
- Dynamic structure factor for INS and IXS
- Non-analytical-term correction: LO-TO splitting (Born effective charges and dielectric constant are required.)
- Mode Grüneisen parameters
- Quasi-harmonic approximation: Thermal expansion, heat capacity at constant pressure (Cp)
- Interfaces to calculators: VASP, VASP DFPT, ABINIT, Quantu ESPRESSO, SIESTA, Elk, WIEN2k, CRYSTAL, DFTB+, TURBOMOLE, CP2K, FHI-aims, CASTEP, Fleur, LAMMPS (external)
- Phonopy API for Python
Extract force constants, phonon dispersion relations, thermal conductivity, and generate special quasirandom structures (SQS)
Available on Saga (/cluster/shared/tdep/bin). Use the following modules
module purge module load Anaconda3/2019.03 module load intel/2018b module load imkl/2018.3.222-iimpi-2018b module load HDF5/1.10.2-intel-2018b
Generate SQS supercell from from a unit cell POSCAR file named 'infile.ucposcar'
Example of 'infile.ucposcar' for a A-site doped SrTiO3 unit cell where the disordered site is designated 'ALLOY' (2 elements: 52% Sr and 48% Ca)
Sr1 Ti1 O3 1.0 3.945130 0.000000 0.000000 0.000000 3.945130 0.000000 0.000000 0.000000 3.945130 ALLOY Ti O 1 1 3 direct 0.000000 0.000000 0.000000 2 Sr 0.52 Ca 0.48 0.500000 0.500000 0.500000 0.500000 0.000000 0.500000 0.500000 0.500000 0.000000 0.000000 0.500000 0.500000
Generate 2x2x2 SQS supercells (five supercells will be generated outfile.sqs_001-005)
generate_structure -d 2 2 2
Python package dedicated to the study of point defects in solids. Can be used to calculate the correction energy due to electrostatic finite-size-effects in charged supercells, defect formation energies and transition levels, and defects concentrations.
Sumo is a Python toolkit for plotting and analysis of ab initio solid-state calculation data, built on existing Python packages from the solid-state chemistry/physics community. SUMO can plot projected DOS directly from DOSCAR and vasprun.xml
Installation on Saga works with the following python module (consider loading it in ~/.bash_profile)
module load Python/3.9.6-GCCcore-11.2.0
pip install sumo
The installation folder will be ~/.local/lib/python3.9/site-packages/
Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis.
Generate a POTCAR with symbols Li_sv O and the PBE functional
pmg potcar --symbols Li_sv O --functional PBE
- R.D. Shannon, Revised Effective Ionic Radii and Systematic Studies of Interatomic Distances in Halides and Chalcogenides, Acta Cryst. 1976 (A32) 751-767