Difference between revisions of "Software and resources"

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  R.D. Shannon, Revised Effective Ionic Radii and Systematic Studies of Interatomic Distances in Halides and Chalcogenides, Acta Cryst. 1976 (A32) 751-767
 
  R.D. Shannon, Revised Effective Ionic Radii and Systematic Studies of Interatomic Distances in Halides and Chalcogenides, Acta Cryst. 1976 (A32) 751-767
 +
 +
==Catalysis==
 +
===Catalysis Hub===
 +
[https://www.catalysis-hub.org www.catalysis-hub.org]
 +
 +
Database of reaction energies and barriers from DFT calculations.
  
 
==Visualization==
 
==Visualization==
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Visualizing periodic structures, density of states and band structures.
 
Visualizing periodic structures, density of states and band structures.
 +
 +
==Packages==
 +
===Spyder===
 +
[https://www.spyder-ide.org www.spyder-ide.org] (Windows, macOS, Linux)
 +
 +
Scientific python developer environment.
 +
 +
===Atomic Simulation Environment (ASE)===
 +
[https://wiki.fysik.dtu.dk/ase/ wiki.fysik.dtu.dk/ase/] (Module available on Saga)
 +
 +
Set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
 +
 +
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-gb.cif', slab, 'cif')
 +
 +
===VASPKIT===
 +
[https://vaspkit.com vaspkit.com] (macOS, Linux)
 +
 +
Generate input files and data processing.
 +
 +
===CatMAP===
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[https://catmap.readthedocs.io/ catmap.readthedocs.io/] (macOS, Linux)
 +
 +
Create microkinetic models.
 +
 +
===TDEP===
 +
[https://ollehellman.github.io 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
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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 SrTiO<sub>3</sub> 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)
 +
 +
<code> generate_structure -d 2 2 2 </code>
 +
 +
===Spinney===
 +
[https://spinney.readthedocs.io/ 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.

Revision as of 10:50, 27 September 2021

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/ 

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

Catalysis

Catalysis Hub

www.catalysis-hub.org

Database of reaction energies and barriers from DFT calculations.

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
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.

Packages

Spyder

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

Scientific python developer environment.

Atomic Simulation Environment (ASE)

wiki.fysik.dtu.dk/ase/ (Module available on Saga)

Set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.

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-gb.cif', slab, 'cif')

VASPKIT

vaspkit.com (macOS, Linux)

Generate input files and data processing.

CatMAP

catmap.readthedocs.io/ (macOS, Linux)

Create microkinetic models.

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.

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