NanoparticleAtomCounter 0.1.6

Estimates atom counts in monometallic nanoparticles given radius and contact angle

Treating a supported nanoparticle as a spherical cap, NanoparticleAtomCounter rapidly estimates the number of Total, Surface, Perimeter, and Interfacial atoms (see below). Only two inputs are mandatory: the radius and contact angle, readily obtainable from Transmission Electron Microscopy (TEM) images.

Can be used on the web app or on a command line.

Requirements

• numpy>=1.20,<2.3

• pandas>=1.4

• streamlit>=1.4,<2

• openpyxl>=3.1.0

• xlrd>=2.0.1

For testing, these are also required

• pytest>=8,<9

• ascii-colors

For benchmarking, these are also required

• ase>=3.22.0,<3.25

• tqdm<=4.67.1

• joblib<=1.5.1

Installation

First create and activate a new environment:

mamba create --name env_name "python>=3.10,<3.15"
mamba activate env_name

To install the latest version:

pip install NanoparticleAtomCounter

Alternatively:

git clone https://github.com/szilvasi-group/NanoparticleAtomCounter.git
cd NanoparticleAtomCounter/
pip install -e .

To be able to run tests:

pip install NanoparticleAtomCounter[test]

To be able to run benchmarks along with tests:

pip install NanoparticleAtomCounter[benchmark]

Usage

1) Prepare your input CSV

Upload a .csv with these headers:

r (A), R (A), Theta, Element, Interface Facet, Surface Facet

Definitions:

• r (A) = footprint radius (in Angstrom); R (A) = radius of curvature (in Angstrom)

r vs R

• Provide either r (A) or R (A) (if both are present, R (A) is ignored).

• Theta = contact angle (in degrees)

• Element = chemical symbol of the element that comprises the nanoparticle, e.g. Cr

• Interface Facet and Surface Facet are OPTIONAL; leave blank if unknown.

  • Interface Facet = facet at the nanoparticle-support interface, e.g. (1,1,1)

  • Surface Facet = dominant facet at the nanoparticle-gas/vacuum interface, e.g. (1,0,0)

• Here’s a sample input file

2) Use the web app

Upload your input file and download the output.

OR

2) Use the command line

nanoparticle-atom-count -i input_file.csv -o output_file.csv

Testing

If you have it installed with the tests, then run the following test and please let me know if there are any errors:

atom-count-test

If you have it installed with the benchmarks, then run the following and please let me know if there are any errors:

atom-count-benchmark

Contact

Any problems or questions?

• Email me at [e-mail]

• Or raise an issue right here