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https://catmap.readthedocs.io/en/latest/index.html
 
https://catmap.readthedocs.io/en/latest/index.html
  
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=== '''Installation:''' ===
 
CatMap can be installed directly via pip:
 
CatMap can be installed directly via pip:
 
  <code>pip install --upgrade <nowiki>https://github.com/SUNCAT-Center/catmap/zipball/master</nowiki></code>
 
  <code>pip install --upgrade <nowiki>https://github.com/SUNCAT-Center/catmap/zipball/master</nowiki></code>
  
 +
======  via add-to Path ======
 
To use the package add this directory to the PYTHONPATH, e.g. in bash shell:
 
To use the package add this directory to the PYTHONPATH, e.g. in bash shell:
 
  <code>export PYTHONPATH=$HOME/THIS_FOLDER_PATH:$PYTHONPATH</code>
 
  <code>export PYTHONPATH=$HOME/THIS_FOLDER_PATH:$PYTHONPATH</code>
  
=== Input File Structure ===
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=== '''Tutorials''' ===
 +
 
 +
== Input File ==
 +
 
 +
=== 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 TableParser accepts inputs in a tab-separated text file. An example of the header and first few lines are provided below:
 
[[File:Image.png|thumb]]
 
[[File:Image.png|thumb]]
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You can use the python script under /CATMAP/catmap/tutorials/1-generating_input_file/generate_input.py
 
You can use the python script under /CATMAP/catmap/tutorials/1-generating_input_file/generate_input.py
  
=== Creating a Microkinetic Model ===
+
==== Creating a Microkinetic Model ====
 
Check the example of CO oxidation in the path of /CATMAP/catmap/tutorials/2-creating_microkinetic_model
 
Check the example of CO oxidation in the path of /CATMAP/catmap/tutorials/2-creating_microkinetic_model
  

Revision as of 10:17, 12 January 2022

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.

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.

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 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

Installation:

CatMap can be installed directly via pip:

pip install --upgrade https://github.com/SUNCAT-Center/catmap/zipball/master
via add-to Path

To use the package add this directory to the PYTHONPATH, e.g. in bash shell:

export PYTHONPATH=$HOME/THIS_FOLDER_PATH:$PYTHONPATH

Tutorials

Input File

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

Formation Energy Approach

One key point for generating input files is that the energies are computed as a “generalized formation energy” relative to a common reference:

where  is the “generalized formation energy” of species ,  is the raw/DFT energy of species ,  is the number of atomic species  in , and  is the reference energy of that atomic species. Mathematically this looks a little confusing (especially with such crude notation) but in practice it is pretty easy. For example, say we want to find the energy of gas-phase CO relative to carbon (C) in methane (), oxygen (O) in , and hydrogen (H) in molecular hydrogen (). We first compute the reference energies () for each atomic species:

(where again U is a “raw” energy from an ab-initio calculation, or a “regular” formation energy from NIST).

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.

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.

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