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Nonadiabatic molecular dynamics (NAMD) is widely used to describe hot electron relaxation and nonradiative recombination processes, but high computational costs limit its application to large supercells. Here, we implement a nonadiabatic…
Field emission coupled with molecular dynamics simulation (FEcMD) software package is a computational tool for studying atomic structure evolution, structural deformation, phase transitions, recrystallization as well as electron emission…
Quantum computers hold promise to enable efficient simulations of the properties of molecules and materials; however, at present they only permit ab initio calculations of a few atoms, due to a limited number of qubits. In order to harness…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
We present SPARC: Simulation Package for Ab-initio Real-space Calculations. SPARC can perform Kohn-Sham density functional theory calculations for isolated systems such as molecules as well as extended systems such as crystals and surfaces,…
We introduce the pCI software package for high-precision atomic structure calculations. The standard method of calculation is based on the configuration interaction (CI) method to describe valence correlations, but can be extended to attain…
We present a method for electronic structure calculations that retains all of the advantages of real space and addresses the inherent inefficiency of a regular grid, which has equal precision everywhere. The computations are carried out on…
Pythonic Black-box Electronic Structure Tool (PyBEST) represents a fully-fledged modern electronic structure software package developed at Nicolaus Copernicus University in Toru\'n. The package provides an efficient and reliable platform…
Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and…
We describe CPMC-Lab, a Matlab program for the constrained-path and phaseless auxiliary-field Monte Carlo methods. These methods have allowed applications ranging from the study of strongly correlated models, such as the Hubbard model, to…
Generating energy functions for heterogeneous systems suitable for quantitative and predictive atomistic simulations is a challenging undertaking. The present work combines a cluster-based approach with electronic structure calculations at…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Ab initio electronic structure methods give accurate results for small systems, but do not scale well to large systems. Chemical insight tells us that molecular functional groups will behave approximately the same way in all molecules,…
Explicit structure-preserving geometric Particle-in-Cell (PIC) algorithm in curvilinear orthogonal coordinate systems is developed. The work reported represents a further development of the structure-preserving geometric PIC algorithm…
Constant potential methods (CPM) enable computationally efficient simulations of the solid-liquid interface at conducting electrodes in molecular dynamics (MD). They have been successfully used, for example, to realistically model the…
Perturbo is a software package for first-principles calculations of charge transport and ultrafast carrier dynamics in materials. The current version focuses on electron-phonon interactions and can compute phonon-limited transport…
Progress in the atomic-scale modelling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic…
While the treatment of chemically relevant systems containing hundreds or even thousands of electrons remains beyond the reach of quantum devices, the development of quantum-classical hybrid algorithms to resolve electronic correlation…
In the near future, material and drug design may be aided by quantum computer assisted simulations. These have the potential to target chemical systems intractable by the most powerful classical computers. However, the resources offered by…