ChemRxiv | [Paper]
Welcome to POMFinder!
This is a simple machine learning tool for structure characterisation of polyoxometalate clusters using total scattering Pair
Distribution Function (PDF) analysis.
Simply provide a PDF and the model will output best best structural models from it structure catalog which contains 443 polyoxometalate clusters.
You can use POMFinder on a single PDF on the following HuggingFace App: https://huggingface.co/spaces/AndySAnker/POMFinder
Install POMFinder with PyPi:
pip install POMFinder==1.0.2
More details about which Python versions are supported etc. can be found at https://pypi.org/project/POMFinder/1.0.2/.
To verify that POMFinder has been installed properly, try calling the help argument.
POMFinder --help
>>> usage: POMFinder [-h] -d DATA [-n NYQUIST] [-i QMIN] [-a QMAX] [-m QDAMP] [-f FILE_NAME]
>>>
>>> This is a package which takes a directory of PDF files
>>> or a specific PDF file. It then determines the best structural
>>> candidates based on a polyoxometalate catalog. Results can
>>> be fitted to the PDF.
This should output a list of possible arguments for running POMFinder and indicate that it could find the package!
Now that POMFinder is installed and ready to use, let's discuss the possible arguments.
| Arg | Description | Default |
|---|---|---|
| Required argument | ||
-h or --help |
Prints help message. | |
-n or --nyquist |
Is the data nyquist sampled. bool | -n True |
-i or --Qmin |
Qmin value of the experimental PDF. float | -i 0.7 |
-a or --Qmax |
Qmax value of the experimental PDF. float | -a 30 |
-m or --Qdamp |
Qdamp value of the experimental PDF. float | -m 0.04 |
-f or --file_name |
Name of the output file. str | -o '' |
-d or --data |
A directory of PDFs or a specific PDF file. str | -d 5 |
For example
POMFinder --data "Experimental_Data/DanMAX_AlphaKeggin.gr" --nyquist "no" --Qmin 0.7 --Qmax 20 --Qdamp 0.02
>>> The 1st guess from the model is: icsd_427457_1_0.9rscale.xyz
>>> The 2nd guess from the model is: icsd_427379_0_0.9rscale.xyz
>>> The 3rd guess from the model is: icsd_281447_0_1.0rscale.xyz
>>> The 4th guess from the model is: icsd_423775_0_0.9rscale.xyz
>>> The 5th guess from the model is: icsd_172542_0_1.1rscale.xyz
OBS: As demonstrated in section E of the supplementary information, the Qmin, Qmax, and Qdamp values have only a minor impact on the prediction and can thus be omitted.
Andy S. Anker1
Emil T. S. Kjær1
Kirsten M. Ø. Jensen1
1 Department of Chemistry and Nano-Science Center, University of Copenhagen, 2100 Copenhagen Ø, Denmark.
Should there be any question, desired improvement or bugs please contact us on GitHub or through email: ansoan@dtu.dk.
If you use our code or our results, please consider citing our paper. Thanks in advance!
https://chemrxiv.org/engage/chemrxiv/article-details/64e5fef7dd1a73847f5951b9
This project is licensed under the Apache License Version 2.0, January 2004 - see the LICENSE file for details.