arXiv subjects

Alessandro Genova

Publications and source records attributed to Alessandro Genova.

6 recordsLinked to original sources

arXiv2022

Real-time 3D analysis during electron tomography using tomviz

The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high quality tomogram is available within 30 minutes. Real time tomography is integrated into tomviz, an open source and cross platform 3D analysis tool that contains intuitive graphical user interfaces (GUI) to enable any scientist to characterize biological and material structure in 3D.

cond-mat.mtrl-sci↗

arXiv2021

eQE 2.0: Subsystem DFT Beyond GGA Functionals

By adopting a divide-and-conquer strategy, subsystem-DFT (sDFT) can dramatically reduce the computational cost of large-scale electronic structure calculations. The key ingredients of sDFT are the nonadditive kinetic energy and exchange-correlation functionals which dominate it's accuracy. Even though, semilocal nonadditive functionals find a broad range of applications, their accuracy is somewhat limited especially for those systems where achieving balance between exchange-correlation interactions on one side and nonadditive kinetic energy on the other is crucial. In eQE 2.0, we improve dramatically the accuracy of sDFT simulations by (1) implementing nonlocal nonadditive kinetic energy functionals based on the LMGP family of functionals; (2) adapting Quantum ESPRESSO's implementation of rVV10 and vdW-DF nonlocal exchange-correlation functionals to be employed in sDFT simulations; (3) implementing "deorbitalized" meta GGA functionals (e.g., SCAN-L). We carefully assess the performance of the newly implemented tools on the S22-5 test set. eQE 2.0 delivers excellent interaction energies compared to conventional Kohn-Sham DFT and CCSD(T). The improved performance does not come at a loss of computational efficiency. We show that eQE 2.0 with nonlocal nonadditive functionals retains the same linear scaling behavior achieved in eQE 1.0 with semilocal nonadditive functionals.

cond-mat.mtrl-sci↗

arXiv2020

DFTpy: An efficient and object-oriented platform for orbital-free DFT simulations

In silico materials design is hampered by the computational complexity of Kohn-Sham DFT, which scales cubically with the system size. Owing to the development of new-generation kinetic energy density functionals (KEDFs), orbital-free DFT (OFDFT, a linear-scaling method) can now be successfully applied to a large class of semiconductors and such finite systems as quantum dots and metal clusters. In this work, we present DFTpy, an open source software implementing OFDFT written entirely in Python 3 and outsourcing the computationally expensive operations to third-party modules, such as NumPy and SciPy. When fast simulations are in order, DFTpy exploits the fast Fourier transforms (FFTs) from PyFFTW. New-generation, nonlocal and density-dependent-kernel KEDFs are made computationally efficient by employing linear splines and other methods for fast kernel builds. We showcase DFTpy by solving for the electronic structure of a million-atom system of aluminum metal which was computed on a single CPU. The Python 3 implementation is object-oriented, opening the door to easy implementation of new features. As an example, we present a time-dependent OFDFT implementation (hydrodynamic DFT) which we use to compute the spectra of small metal cluster recovering qualitatively the time-dependent Kohn-Sham DFT result. The Python code base allows for easy implementation of APIs. We showcase the combination of DFTpy and ASE for molecular dynamics simulations (NVT) of liquid metals. DFTpy is released under the MIT license.

physics.comp-ph↗

arXiv2018

Nonlocal Kinetic Energy Functionals By Functional Integration

Since the seminal works of Thomas and Fermi, researchers in the Density-Functional Theory (DFT) community are searching for accurate electron density functionals. Arguably, the toughest functional to approximate is the noninteracting Kinetic Energy, $T_s[ρ]$, the subject of this work. The typical paradigm is to first approximate the energy functional, and then take its functional derivative, $\frac{δT_s[ρ]}{δρ(r)}$, yielding a potential that can be used in orbital-free DFT, or subsystem DFT simulations. Here, this paradigm is challenged by constructing the potential from the second-functional derivative via functional integration. A new nonlocal functional for $T_s[ρ]$ is prescribed (which we dub MGP) having a density independent kernel. MGP is constructed to satisfy three exact conditions: (1) a nonzero "Kinetic electron" arising from a nonzero exchange hole; (2) the second functional derivative must reduce to the inverse Lindhard function in the limit of homogenous densities; (3) the potential derives from functional integration of the second functional derivative. Pilot calculations show that MGP is capable of reproducing accurate equilibrium volumes, bulk moduli, total energy, and electron densities for metallic (BCC, FCC) and semiconducting (CD) phases of Silicon as well as of III-V semiconductors. MGP functional is found to be numerically stable typically reaching selfconsistency within 12 iteration of a truncated Newton minimization algorithm. MGP's computational cost and memory requirements are low and comparable to the Wang-Teter (WT) nonlocal functional or any GGA functional.

cond-mat.mtrl-sci↗

arXiv2015

Subsystem Density-Functional Theory as an Effective Tool for Modeling Ground and Excited States, their Dynamics, and Many-Body Interactions

Subsystem Density-Functional Theory (DFT) is an emerging technique for calculating the electronic structure of complex molecular and condensed phase systems. In this topical review, we focus on some recent advances in this field related to the computation of condensed phase systems, their excited states, and the evaluation of many-body interactions between the subsystems. As subsystem DFT is in principle an exact theory, any advance in this field can have a dual role. One is the possible applicability of a resulting method in practical calculations. The other is the possibility of shedding light on some quantum-mechanical phenomenon which is more easily treated by subdividing a supersystem into subsystems. An example of the latter is many-body interactions. In the discussion, we present some recent work from our research group as well as some new results, casting them in the current state-of-the-art in this review as comprehensively as possible.

physics.chem-ph↗

arXiv2014

Periodic Subsystem Density-Functional Theory

By partitioning the electron density into subsystem contributions, the Frozen Density Embedding (FDE) formulation of subsystem DFT has recently emerged as a powerful tool for reducing the computational scaling of Kohn--Sham DFT. To date, however, FDE has been employed to molecular systems only. Periodic systems, such as metals, semiconductors, and other crystalline solids have been outside the applicability of FDE, mostly because of the lack of a periodic FDE implementation. To fill this gap, in this work we aim at extening FDE to treat subsystems of molecular and periodic character. This goal is achieved by a dual approach. On one side, the development of a theoretical framework for periodic subsystem DFT. On the other, the realization of the method into a parallel computer code. We find that periodic FDE is capable of reproducing total electron densities and (to a lesser extent) also interaction energies of molecular systems weakly interacting with metallic surfaces. In the pilot calculations considered, we find that FDE fails in those cases where there is appreciable density overlap between the subsystems. Conversely, we find FDE to be in semiquantitative agreement (but still within chemical accuracy) with Kohn--Sham DFT when the inter-subsystem density overlap is low. We also conclude that to make FDE a suitable method for describing molecular adsorption at surfaces, kinetic energy density functionals that go beyond the GGA level must be employed.

cond-mat.mtrl-sci↗