Calculation for all
Calculations describing the properties of large molecular systems can take weeks or even months. Physicists and chemists at the Nicolaus Copernicus University in Toruń have found a way around this: they have created a quantum chemistry software package that significantly reduces this time. They are now sharing their tool with others, for free.
The Pythonic Black-box Electronic Structure Tool (PyBEST), as this is the full name of the tool created by researchers from the Faculty of Physics, Astronomy and Informatics and the Faculty of Chemistry of the Nicolaus Copernicus University in Toruń, is a modern, efficient and reliable platform for electron structure calculations at the intersection of physics and chemistry. And what is extremely important - it was created with the assumption of open access to science resources for everyone. It can be used by scientists and can also be successfully used in schools for educational purposes, e.g., during chemistry lessons.
Open science with the NCU
The main architects and creators of the platform are dr habil. Katharina Boguslawski, NCU Prof. and dr habil. Paweł Tecmer, NCU Prof. from the Department of Quantum Mechanics at the NCU Institute of Physics. Aleksandra Leszczyk, Artur Nowak, Filip Brzęk, as well as dr habil. Piotr Żuchowski, NCU Prof. and dr Dariusz Kędziera from the NCU Faculty of Chemistry, also contributed significantly to the development of PyBEST. All are members of the University Centre of Excellence "Astrophysics and Astrochemistry".
Before getting started, we had assumed that PyBEST should be, above all, easy to use, but also to modify and update, says Prof Pawel Tecmer. - PyBEST is written primarily in Python.
- Python is one of the most modern and rapidly developing programming languages, extremely common among programmers and researchers. Due to its popularity, PyBEST can therefore integrate well into different environments, which gives us the opportunity to disseminate it and continuously upgrade it, adds Prof Piotr Żuchowski.
Saving time and... money
Physicists stress that effectiveness is essential to their scientific research. However, some simulations can take weeks or even months.
When calculations are so time-consuming, they are often abandoned. Hence, the drive to create the most efficient codes possible to reduce computation time and hardware resources required, explains Prof. Tecmer. - The problem arises when we study multi-atom molecular systems, in which case the need to describe a large number of electrons results in calculations that can take an extremely long time.
PyBEST is also used in chemistry, for example to model compounds containing uranium and plutonium. Experiments with these are quite limited due to problems with the availability of materials and the safety issue for scientists conducting experiments. With a tool such as PyBEST, experiments and measurements can be simulated without entering the laboratory. All the researchers need is a computer and the code written by the Toruń researchers.
The software package developed at the NCU is unique in Poland - although we have many very good physicists and quantum chemists in Poland, no such comprehensive tool has been available on our market until now. So far Polish researchers have mainly used German and American programmes.
Most importantly, PyBEST is available free of charge and can be downloaded, installed and used by anyone interested. The code can be downloaded from pybest.fizyka.umk.pl
- Of course, there are also free programs available. Unfortunately, these are often based on old computer languages, dating back as far as the 1970s. Sometimes, when using them, we do not have access to the source code or it is difficult to access it. This becomes a major problem when you want to develop a new method or a new way of solving mathematical equations used to describe molecules, explains Prof Tecmer. - This is why we decided to write everything from scratch. And this is where you can really see the advantages of the fact that the software was developed in a modern programming language - this means that the code can be constantly and fairly easily modified and developed. Its modularity allows us to host additional libraries and software packages.
The flexible structure of the code allows for many modifications and upgrades. However, maintaining all the 'machinery', i.e., making sure everything works, takes a lot of time - the researchers are constantly working on modifications and also take into account suggestions for changes and feedback from users - after all, the program is supposed to respond to their needs.
This is a long-term project. New computing technologies are constantly emerging that we will use in PyBES. There are also new quantum chemistry methods being developed that are not yet available in other programs, which will be implemented in our software, says Prof. Tecmer. - We want to modify the PyBEST code in such a way that we will be able to describe increasingly larger molecular systems.