Abstract
ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, we present a major redevelopment of the ChemShell code, which provides a modern platform for advanced QM/MM embedding models. The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, new interfaces to high performance QM and MM programs, and a user interface written in the Python programming language. The redeveloped package is capable of performing QM/MM calculations on systems of significantly increased size, which we illustrate with benchmarks on zirconium dioxide nanoparticles of over 160000 atoms.
Highlights
Combined quantum mechanical/molecular mechanical (QM/ MM) calculations are an efficient means of calculating localized chemistry in complex molecular and solid systems
The ChemShell software package has been completely rewritten with the aim of providing a modern, scriptable platform for multiscale computational chemistry
This article describes the features of the code available in the initial public release in December 2017, which is focused on quantum mechanical and molecular mechanical (QM/MM) calculations for materials chemistry
Summary
Combined quantum mechanical/molecular mechanical (QM/ MM) calculations are an efficient means of calculating localized chemistry in complex molecular and solid systems. ChemShell implements a flexible, modular approach to QM/MM, where a variety of QM and MM programs (either built in as libraries or called through external interfaces) may be used to evaluate energies and gradients of the quantum and classical regions, while ChemShell takes on the task of coupling the results to obtain the combined QM/ MM energy and gradient, including an appropriate treatment of the boundary region that couples the two subsystems Highlevel tasks such as geometry optimization and molecular dynamics are handled at the ChemShell level, ensuring that these are carried out in a consistent way regardless of the choice of energy evaluator. The new Py-ChemShell package is available for download under the GNU LGPL v3 free software license at www.chemshell.org
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