First-principles electronic structure calculations for large-scale material systems with defects or dopants remain a major computational bottleneck in atomistic simulations. Here, we propose a target-driven, non-learning-based method termed HaMLR (Hash-Matching-based Local density-matrix Reuse) to efficiently construct the density matrix of periodic atomic structures containing local defects or dopants. Leveraging the nearsightedness principle of electronic matter, the method systematically scans all atoms in the target system to extract local substructures within a defined nearsightedness radius, thereby covering the full sample space of local environments. Each substructure is encoded based on its geometric and chemical features, hashed, and deduplicated. Distinct substructures are then evaluated using self-consistent density functional theory (DFT) calculations to obtain the density-matrix blocks between the central atom and its neighbors within the cutoff radius. During reconstruction, the full-system density matrix is assembled by matching local environments via hash values and reusing the precomputed local density blocks—thereby avoiding full-scale DFT calculations. Unlike machine learning-based approaches, HaMLR does not require model training, offering improved physical consistency and computational efficiency. Validation on defective graphene, MoS2, and doped silicon demonstrates that HaMLR achieves high accuracy while significantly accelerating density-matrix construction, providing an efficient and robust alternative for large-scale electronic structure modeling.
33Topological Defects Induced High-Spin Quartet State in Truxene-Based Molecular Graphenoids
Topological Defects Induced High-Spin Quartet State in Truxene-Based Molecular Graphenoids
10Atomic-scale characterization of defects in oxygen plasma-treated graphene by scanning tunneling microscopy
Defects in graphene are important nanoscale pathways for metal atoms to enter the interface between epitaxial graphene and SiC in order to form stable ultrathin metal layers with new exotic physical properties. However, the atomic-scale details of defects that mainly govern the intercalation process remain modest. In this work, we present the first atomic investigation of point defects generated by oxygen plasma treatment on epitaxial graphene grown on SiC using low-temperature scanning tunneling microscopy, corroborated by density functional theory calculations. We found a broad spectrum of point defects that varies in size, shape, and symmetry and is dominated by triangular species. Tunneling spectroscopy identified defect-induced states in the vicinity of the Fermi level that significantly perturb the graphene electronic properties at the defect site. Based on the well-defined defect symmetry, we simulated the local density of states of the triangular defects and their corresponding scanning tunneling microscopy images which further helped us to identify the exact atomic configurations of monovacancy defects. The combination of atomic-scale scanning tunneling microscopy experiments and reliable density functional theory simulations provides ultimate microscopic details and opens a new way to identify the atomic configurations of defects in oxygen plasma-treated graphene. Our work might shed light on precise control of defect engineering in graphene for metal intercalation by controlling the defect types based on a deep understanding of each configuration.
Read more139A DFT study of CO adsorption on the pristine, defective, In-doped and Sb-doped graphene and the effect of applied electric field
A DFT study of CO adsorption on the pristine, defective, In-doped and Sb-doped graphene and the effect of applied electric field
Read more35Electronic structure and optical properties of noncentrosymmetric LiGaSe2: Experimental measurements and DFT band structure calculations
Electronic structure and optical properties of noncentrosymmetric LiGaSe2: Experimental measurements and DFT band structure calculations
Read more56Nickel Cluster Growth on Defect Sites of Graphene: A Computational Study
Watching the defectives: DFT studies on the growth of nickel clusters on different graphene substrates shows that graphene defects essentially determine the morphology of the clusters. Defects greatly improve the catalytic reactivity of the larger clusters Nin (5≤n≤10). Smaller clusters Nin (n<4) efficiently open the band gap of defective graphene, allowing a way to modulate the electronic properties of the graphene. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Read more1Crystal and electronic structure of the sub-stoichiometric photocatalyst Cu4Se6: DFT study
Crystal and electronic structure of the sub-stoichiometric photocatalyst Cu4Se6: DFT study
3Investigation of the Fe3+ centers in perovskite KMgF3 through a combination of ab initio (density functional theory) and semi-empirical (superposition model) calculations
Analyses of the local crystal and electronic structure in the vicinity of Fe3+ centers in perovskite KMgF3 crystal have been carried out in a comprehensive manner. A combination of density functional theory (DFT) and a semi-empirical superposition model (SPM) is used for a complete analysis of all Fe3+ centers in this study for the first time. Some quantitative information has been derived from the DFT calculations on both the electronic structure and the local geometry around Fe3+ centers. All of the trigonal (K-vacancy case, K-Li substitution case, and normal trigonal Fe3+ center case), FeF5O cluster, and tetragonal (Mg-vacancy and Mg-Li substitution cases) centers have been taken into account based on the previously suggested experimental and theoretical inferences. The collaboration between the experimental data and the results of both DFT and SPM calculations provides us to understand most probable structural model for Fe3+ centers in KMgF3.
Read moreDensity Functional Theory Investigations of Metal/Oxide Interfaces and Transition Metal Catalysts
Density Functional Theory Investigations of Metal/Oxide Interfaces and Transition Metal Catalysts
3All-electron density functional theory calculations of the zero-pressure properties of plutonium dioxide
The fluorite structure light-actinide dioxides, uranium dioxide and plutonium dioxide, are both known to be prototypical Mott-Hubbard insulators, with band gaps produced by strong Coulomb correlation effects that are not adequately accounted for in traditional density functional theory (DFT) calculations. Indeed, DFT electronic structure calculations for these two actinide dioxides have been shown to incorrectly predict metallic behavior. The highly-correlated electron effects exhibited by the actinide dioxides, combined with the large relativistic effects (including spin-orbit coupling) expected for any actinide compound, provide an extreme challenge for electronic structure theorists. For this reason, few fully-self-consistent DFT calculations have been carried out for the actinide dioxides, in general, and only one for plutonium dioxide. In that calculation, the troublesome 5f electrons were treated as core electrons, and spin-orbit coupling was ignored.
Read more26Comparison of SERRS and RRS excitation profiles of [Fe(tpy)2]2+ (tpy = 2,2':6',2''‐terpyridine) supported by DFT calculations: effect of the electrostatic bonding to chloride‐modified Ag nanoparticles on its vibrational and electronic structure
Nonresonance (or normal) Raman scattering (NRS), resonance Raman scattering (RRS), surface‐enhanced Raman scattering (SERS), and surface‐enhanced RRS (SERRS) spectra of [Fe(tpy)2]2+ complex dication (tpy = 2,2':6',2''‐terpyridine) are reported. The comparison of RRS/NRS and SERRS/SERS excitation profiles of [Fe(tpy)2]2+ spectral bands in the range of 445–780 nm is supported by density functional theory (DFT) calculations, Raman depolarization measurements, comparison of the solid [Fe(tpy)2](SO4)2 and solution RRS spectra, and characterization of the Ag nanoparticle (NP) hydrosol/[Fe(tpy)2]2+ SERS/SERRS active system by surface plasmon extinction spectrum and transmission electron microscopy image of the fractal aggregates (D = 1.82). By DFT calculations, both the Raman active modes and the electronic states of the complex have been assigned to the symmetry species of the D2d point group. It has been demonstrated that upon the electrostatic bonding of the complex dication to the chloride‐modified Ag NPs, the geometric and ground state electronic structure of the complex and the identity of the three different metal‐to‐ligand charge transfer (1MLCT) electronic transitions remain preserved. On the other hand, the effect of ion pairing manifests itself by a slight change in localization of one of the electronic transitions (with max. at 552 nm) as well as by promotion of the Herzberg–Teller activation of E modes resulting from coupling of E and B2 excited electronic states. Finally, the very low, 1 × 10−11 M SERRS spectral detection limit of [Fe(tpy)2]2+ at 532‐nm excitation is attributed to a concerted action of the electromagnetic and molecular resonance mechanism, in conjunction to the electrostatic bonding of the complex dication to the chloride‐modified Ag NP surface. Copyright © 2014 John Wiley & Sons, Ltd.
Read more65A combined ab initio and atomistic simulation study of the surface and interfacial structures and energies of hydrated scheelite: introducing a CaWO 4 potential model
A combined ab initio and atomistic simulation study of the surface and interfacial structures and energies of hydrated scheelite: introducing a CaWO 4 potential model
Read more27Interatomic potentials and defect properties of Fe–Cr–Al alloys
Interatomic potentials and defect properties of Fe–Cr–Al alloys
6Parallel Implementation of Large-Scale Linear Scaling Density Functional Theory Calculations With Numerical Atomic Orbitals in HONPAS.
Linear-scaling density functional theory (DFT) is an efficient method to describe the electronic structures of molecules, semiconductors, and insulators to avoid the high cubic-scaling cost in conventional DFT calculations. Here, we present a parallel implementation of linear-scaling density matrix trace correcting (TC) purification algorithm to solve the Kohn–Sham (KS) equations with the numerical atomic orbitals in the HONPAS package. Such a linear-scaling density matrix purification algorithm is based on the Kohn's nearsightedness principle, resulting in a sparse Hamiltonian matrix with localized basis sets in the DFT calculations. Therefore, sparse matrix multiplication is the most time-consuming step in the density matrix purification algorithm for linear-scaling DFT calculations. We propose to use the MPI_Allgather function for parallel programming to deal with the sparse matrix multiplication within the compressed sparse row (CSR) format, which can scale up to hundreds of processing cores on modern heterogeneous supercomputers. We demonstrate the computational accuracy and efficiency of this parallel density matrix purification algorithm by performing large-scale DFT calculations on boron nitrogen nanotubes containing tens of thousands of atoms.
Read more34Two-Dimensional Metal–Organic Frameworks with Unique Oriented Layers for Oxygen Reduction Reaction: Tailoring the Activity through Exposed Crystal Facets
Two-Dimensional Metal–Organic Frameworks with Unique Oriented Layers for Oxygen Reduction Reaction: Tailoring the Activity through Exposed Crystal Facets
Read more24Computational Study on Redox-Switchable Second-Order Nonlinear Optical Properties of Totally Inorganic Keggin-Type Polyoxometalate Complexes
The electronic structure and second-order nonlinear optical (NLO) property of a series of monoruthenium-substituted Keggin-type polyoxometalates (POMs) have been studied by using density functional theory (DFT) and time-dependent (TD)DFT calculations. The DFT calculation supports that these POM complexes possess donor-π-conjugated bridge-acceptor (D-π-A) structure, which the ruthenium atom acts as the role of electron donor and the three vanadium atoms in cap region of Keggin-type POM act as the role of electron acceptor. It is well-known that D-π-A structure, as a simple molecular scheme, has been successfully used in the development of organic NLO materials. However, the totally inorganic molecule having D-π-A structure is very rare. Thereby the second-order NLO properties of these POM complexes have been analyzed in this work. According to the calculations, introduction of the electron acceptor leads to a substantial enhancement on the second-order NLO response. The calculated βHRS(−2ω; ω, ω) value of ...
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