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Nowadays, the interoperability and interfacing of codes and libraries have become crucial aspects of software development and engineering, and the basis for enabling and simplifying the sharing of methods and tools, both within and among communities. One of the most important bottlenecks that arises when developing and maintaining an interface of a library with an already existing software, is to keep it aligned with the development route of the latter. This might include significant changes, such as changes in the data structures used by the library, which are communicated through the interface. In this paper, an approach for inserting a new algorithm into existing software is presented, through a minimally invasive interface, that takes over an already present algorithm, and thus changes its original purpose. The approach is applied to the well-established Activation-Relaxation Technique nouveau (ARTn) algorithm, that is revisited and re-engineered to bias and take over the FIRE minimization algorithm, as presently implemented in two community codes for atomistic simulations, namely Quantum ESPRESSO (PWscf) and LAMMPS. ARTn is a well established single-ended saddle-point search algorithm that allows for the exploration of potential energy surfaces. The resulting algorithm acts as a plugin, and is distributed in the form of an external library (pARTn). Program Title: plugin Activation Relaxation Technique nouveau (pARTn) CPC Library link to program files: https://doi.org/10.17632/xpwr56d2yk.1 Developer's repository link: https://gitlab.com/mammasmias/artn-plugin Licensing provisions: Apache-2.0/GPLv3 Programming language: Modern Fortran and C++ Nature of problem: Original ARTn implementation was difficult to interface, port and maintain. Solution method: Full refactoring and re-engineering into a library, which utilizes and biases a minimization algorithm already implemented in the engine, to make it behave as ARTn. The biasing is done by reverse-engineering specific external conditions that drive the displacement of atoms. [ABSTRACT FROM AUTHOR]

In this paper, the model of chemical reactions on grained molecular level is presented. This model allows simulating simple chemical reactions of first- and second-order using the parallel approach. Proposed model has been implemented as an extension to the Dynamic Lattice Liquid (DLL) algorithm on the FPGA cluster – ARUZ (Analyzer of Real Complex Systems). An example simulation achieves a performance of 4,792 algorithm cycles per second, 17 × 10 9 Lattice Updates Per Second (LUPS), 3.7 times faster than the GPU cluster implementation, and its result agrees very well with theory and practical experiment. [ABSTRACT FROM AUTHOR]