POMSimulator

• Introduction
• Installation
• Quickstart
• How to Cite
• License and Copyright Information
• Support and Contact

Introduction

POMSimulator is a software for predicting the aqueous speciation and self-assembly mechanism of polyoxometalates. Based on a pure Python framework, the method generates reaction maps using Graph Theory, and solves the non-linear equations related to the speciation models. The software creates a collection of formation constants for all the species in the simulation, and a list of the chemical reactions. The package also contains a set of python scripts for analysing and plotting this data.

Authors: Enric Petrus, Mireia Segado-Centellas, Carles Bo

Institution: research group of Carles Bo, at the Institute of Chemical Research of Catalonia (ICIQ) - Tarragona, Spain

Developer team: Jordi Buils, Diego Garay-Ruiz, Enric Petrus

Installation

POMSimulator can be installed via git and pip (see below).

git clone <pomsimulator-repo>
cd pomsimulator
pip install -e .

To ensure that the installation has been successful, we recommend to run the test python simulation_test.py from inside the Simulations folder.

Quickstart

The main simulation file of POMSimulator is stored in ./Simulations. The code reads the quantum mechanical outputs in ./Inputs and generates two output files in the folder ./Outputs. These two files correspond to the chemical reaction network, and the list predicted of formation constants. Hitherto, the code parses the input data from the calculations of the SCM ADF 2019 package. Nonetheless, the input data can also be introduced separately.

The run the code, the user has to set the simulation.py file, and the execute it. For example: python simulation_tungstates.py.

With the obtained results, the package offers a set of tools, in the folder ./Utilities, for analysing and plotting the results. Before plotting the speciation and/or phase diagrams, it is necessary to linearly scale the predicted formation constants. This is done with scale_constants.py. The scaling parameters are stored as a text file (scaling_params.pomsim), and then employed by speciation_diagram.py.

The user can find more information about the method in:

1. The PhD thesis of the author
2. The markdown manual in docs/manual.md
3. The documentation hosted at readthedocs.org

How to Cite

When publishing results generated with POMSimulator, we kindly request you to cite the original paper, and if possible the corresponding release as archived on Zenodo:

Petrus, E.; Segado, M.; Bo, C. Chem. Sci., 2020, 11, 8448-8456 doi.org/10.1039/D0SC03530K

List of peer-reviewed articles featuring POMSimulator:

• Petrus, E.; Bo, C. J. Phys. Chem. A. 2021, 125, 23, 5212-5219 doi.org/10.1021/acs.jpca.1c03292
• Petrus, E.; Segado, M.; Bo, C. Inorg. Chem. 2022, 61, 35, 13708-13718 doi.org/10.1021/acs.inorgchem.2c00925
• Petrus, E.; Garay-Ruiz, D.; Reiher, M.; Bo, C. J. Am. Chem. Soc, 2023, 145, 34, 18920-18930 doi.org/10.1021/jacs.3c05514
• Garay-Ruiz, D.; Petrus, E.; Bo, C. Revista de la Societat Catalana de Quimica 2023, 22, 23-38 doi.org/10.2436/20.2003.01.142
• Petrus, E.; Buils, J.; Garay-Ruiz, D.; Segado-Centellas, M.; Bo, C. J. Comput. Chem. 2024, 1-9 doi.org/10.1002/jcc.27389

License and Copyright Information

POMSimulator is distributed under the GNU AFFERO GENERAL PUBLIC LICENSE. For more license and copyright information, see the file LICENSE.txt

Support and Contact

In case you should encounter problems or bugs, please write a short message to one of the following addresses: enricpz@icloud.com, jbuils@iciq.es, dgaray@iciq.es.