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Michele Nottoli

Publications and source records attributed to Michele Nottoli.

4 recordsLinked to original sources

CP2K: An electronic structure and molecular dynamics software package - Dynamics, Transport, and Spectroscopic Response

One of the distinguishing aspects of CP2K is its seamless integration of diverse structural and transition-state optimization techniques with advanced sampling approaches including Monte Carlo, molecular dynamics, and metadynamics, enabling the efficient exploration of complex potential- and free-energy landscapes, including rare events. These capabilities are combined with a broad hierarchy of energy and force evaluation methods, ranging from classical and machine-learned interaction potentials and mixed quantum-classical multiscale and semiempirical schemes, to highly accurate quantum-mechanical electronic-structure approaches. At the heart of the latter lies the Gaussian and plane-wave framework, along with its augmented all-electron generalization, which have been described in detail in our previous code review [T. D. K\"uhne et al., J. Chem. Phys. 152, 194103 (2020)]. Building on this foundation, the present work revisits the methods within CP2K that turn electronic structure into dynamics, transport, and spectroscopic response. Particular emphasis is placed on the coupling between static response calculations and nuclear motion: spectra may be evaluated at optimized structures, averaged over thermally sampled configurations, obtained from time-correlation functions along ab-initio or path integral molecular trajectories, or followed in real time together with electronic and nuclear dynamics. The same modular structure also enables equilibrium and biased transport simulations, from Kubo-type linear response to open-boundary approaches under external potentials, highlighting CP2K's unique capability to unify quantum chemistry with quantum and statistical mechanics within a versatile, holistic simulation environment.

physics.chem-ph

A symmetry-preserving and transferable representation for learning the Kohn-Sham density matrix

The Kohn-Sham (KS) density matrix is one of the most essential properties in KS density functional theory (DFT), from which many other physical properties of interest can be derived. In this work, we present a parameterized representation for learning the mapping from a molecular configuration to its corresponding density matrix using the Atomic Cluster Expansion (ACE) framework, which preserves the physical symmetries of the mapping, including isometric equivariance and Grassmannianity. Trained on several typical molecules, the proposed representation is shown to be systematically improvable with the increase of the model parameters and is transferable to molecules that are not part of and even more complex than those in the training set. The models generated by the proposed approach are illustrated as being able to generate reasonable predictions of the density matrix to either accelerate the DFT calculations or to provide approximations to some properties of the molecules.

physics.chem-ph

The OpenMMPol Library for Polarizable QM/MM Calculations of Properties and Dynamics

We present a new library designed to provide a simple and straightforward way to implement QM/AMOEBA and other polarizable QM/MM methods based on induced point dipoles. The library, herein referred to as OpenMMPol, is free and open-sourced and is engineered to address the increasing demand for accurate and efficient QM/MM simulations. OpenMMPol is specifically designed to allow polarizable QM/MM calculations of ground state energies and gradients, and excitation properties. Key features of OpenMMPol include a modular architecture facilitating extensibility, parallel computing capabilities for enhanced performance on modern cluster architectures, and a user-friendly interface for intuitive implementation and a simple and flexible structure for providing input data. To show the capabilities of fered by the library we present an interface with PySCF to perform QM/AMOEBA molecular dynamics, geometry optimization and excited state calculation based on (TD)DFT.

physics.chem-ph

Linear scaling computation of forces for the domain-decomposition linear Poisson--Boltzmann method

The Linearized Poisson--Boltzmann (LPB) equation is a popular and widely accepted model for accounting solvent effects in computational (bio-) chemistry. In the present article we derive the analytical forces of the domain-decomposition-based ddLPB-method with vdW or SAS surface. We present an efficient strategy to compute the forces and its implementation, allowing linear scaling of the method with respect to the number of atoms using the fast multipole method (FMM). Numerical tests illustrates the accuracy of the computation of the analytical forces and compares efficiency with other available methods.

math.NA