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=== | ||
+ | [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 | ||
+ | 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
Contents
Software and resources
Structure and crystallography
ICSD database
Automatic login through EZproxy (www.ub.uio.no/english/using/remote-access.html).
Materials project
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
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
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
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
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.