Software and resources

From mn.kjemi.vaspwiki
Jump to: navigation, search

Software and resources

Structure and crystallography

ICSD database

icsd.fiz-karlsruhe.de/

Automatic login through EZproxy (www.ub.uio.no/english/using/remote-access.html).

Materials project

www.materialsproject.org

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

it.iucr.org

Complete overview of space-group symmetry and more.

Shannon Ionic Radii

abulafia.mt.ic.ac.uk/shannon/

Reference [1]

Binding energies of molecules

Todo: Table of binding energies with reference (e.g., NIST)

Catalysis

Catalysis Hub

www.catalysis-hub.org

Database of reaction energies and barriers from DFT calculations.

No entropy found

Visualization

VESTA

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

avogadro.cc (Windows, macOS, Linux)

View and edit molecular structures and optimize molecular geometry through molecular mechanics.

Diamond

www.crystalimpact.com/diamond/ (Windows: Licence)

View and edit periodic and molecular structures.

VMD

www.ks.uiuc.edu/Research/vmd/ (Windows, macOS, Linux)

View and animate structures from molecular dynamics simulations.

P4vasp

github.com/orest-d/p4vasp (macOS, Linux)

Visualizing periodic structures, density of states and band structures.

OVITO

https://www.ovito.org/about/

OVITO is a visualization and analysis software for output data generated in molecular dynamics, atomistic Monte-Carlo and other particle-based simulations.

Packages

Spyder

www.spyder-ide.org (Windows, macOS, Linux)

Scientific python developer environment.

Atomic Simulation Environment (ASE)

wiki.fysik.dtu.dk/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

vaspkit.com/

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

CatMap is a catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic models used for studying kinetics and screening new catalysts.

https://catmap.readthedocs.io/en/latest/index.html

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

export PYTHONPATH=$HOME/THIS_FOLDER_PATH:$PYTHONPATH

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:

Image.png

The following column titles are required for a functional input file:

  • surface_name
  • site_name
  • species_name
  • formation_energy
  • frequencies
  • reference

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.github.io/phonopy/

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.

Features

  • 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

TDEP

ollehellman.github.io

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

Spinney

spinney.readthedocs.io/

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

smtg-ucl.github.io/sumo/

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

pymatgen.org/

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

References

  1. R.D. Shannon, Revised Effective Ionic Radii and Systematic Studies of Interatomic Distances in Halides and Chalcogenides, Acta Cryst. 1976 (A32) 751-767