Density Functional Theory Software Research Articles

Software implementation for calculating Chern and [formula omitted] topological invariants of crystalline solids with WIEN2k all-electron density functional package

We present two modules that expand functionalities of the all-electron full-potential density functional theory package WIEN2k for computation of the Chern and Z2 topological invariants. Characterization of topological properties relies on two methods: computing an evolution of hybrid Wannier charge centers for Z2 topological insulators (construction of maximally localized Wannier functions is not needed) and computing the Berry phase for a multitude of Wilson loops that discretize a 2D Brillouin zone for Chern insulators as well as for mapping the Berry curvature. The implementation is validated by testing on well-known materials that feature topologically non-trivial electronic states.

Density Functional Theory for Buckyballs within Symmetrized Icosahedral Basis

We have developed a highly efficient computation method based on density functional theory (DFT) within a set of fully symmetrized basis functions for the C60 buckyball, which possesses the icosahedral () point-group symmetry with 120 symmetry operations. We demonstrate that our approach is much more efficient than the conventional approach based on three-dimensional plane waves. When applied to the calculation of optical transitions, our method is more than one order of magnitude faster than the existing DFT package with a conventional plane-wave basis. This makes it very convenient for modeling optical and transport properties of quantum devices related to buckyball crystals. The method introduced here can be easily extended to other fullerene-like materials.

A DFT study of electron–phonon interactions for the and defects in hexagonal boron nitride: investigating the role of the transition dipole direction

Quantum emitters in two-dimensional hexagonal boron nitride (h-BN) have generated significant interest due to observations of ultra-bright emission made at room temperature. The expectation that solid-state emitters exhibit broad zero-phonon lines at elevated temperatures has been put in question by recent observations of Fourier transform (FT) limited photons emitted from h-BN flakes at room temperature. All decoupled emitters produce photons that are directed in-plane, suggesting that the dipoles are perpendicular to the h-BN plane. Motivated by the promise of an efficient and scalable source of indistinguishable photons that can operate at room temperature, we have developed an approach using density functional theory (DFT) to determine the electron-phonon coupling for defects that have in- and out-of-plane transition dipole moments. Our DFT calculations reveal that the transition dipole for the defect is parallel to the h-BN plane, and for the defect is perpendicular to the plane. We calculate both the phonon density of states and the electron–phonon matrix elements associated with the h-BN defective structures. We find no indication that an out-of-plane transition dipole by itself will result in the low electron–phonon coupling that is expected to produce FT-limited photons at room temperature. Our work provides direction to future DFT software developments and adds to the growing list of calculations relevant to researchers in the field of solid-state quantum information processing.

All-electron APW+lo calculation of magnetic molecules with the SIRIUS domain-specific package.

We report APW+lo (augmented plane wave plus local orbital) density functional theory (DFT) calculations of large molecular systems using the domain specific SIRIUS multi-functional DFT package. The APW and FLAPW (full potential linearized APW) task and data parallelism options and the advanced eigen-system solver provided by SIRIUS can be exploited for performance gains in ground state Kohn-Sham calculations on large systems. This approach is distinct from our prior use of SIRIUS as a library backend to another APW+lo or FLAPW code. We benchmark the code and demonstrate performance on several magnetic molecule and metal organic framework systems. We show that the SIRIUS package in itself is capable of handling systems as large as a several hundred atoms in the unit cell without having to make technical choices that result in the loss of accuracy with respect to that needed for the study of magnetic systems.

Band unfolding with a general transformation matrix: From code implementation to interpretation of photoemission spectra

Unfolding of a supercell band structure into a primitive Brillouin zone is important for understanding implications of structural distortions, disorder, defects, and solid solutions on materials electronic structure. The necessity of band unfolding is also recognized in the interpretation of angle-resolved photoemission spectroscopy (ARPES) measurements. We describe an extension of the fold2Bloch package by implementing an arbitrary transformation matrix used to establish a relation between the primitive cell and supercell. This development allows us to overcome limitations of supercells constructed exclusively by scaling of primitive cell lattice vectors. It becomes possible to transform between primitive and conventional cells as well as include rotations. The fold2Bloch is publicly available from a GitHub repository as a FORTRAN code. It interfaces with the all-electron full-potential WIEN2k and the pseudopotential VASP density functional theory packages. The fold2Bloch is supplemented by additional pre- and post-processing utilities that aid in generating k points in the supercell (such that they later fall onto a desired path in the primitive Brillouin zone after unfolding) and plotting the unfolded band structure. We selected ▪ as an illustrative example and, for the first time, present its properly unfolded band structure in direct comparison with ARPES measurements. In addition, critical importance of the band unfolding for interpretation of ▪ ARPES data is illustrated and discussed as a perspective.

Quantum Behaviour of Mg and Mg-Al-Zn Microstructure

Magnesium is an essential element because of its many beneficial properties and advantages over other metals, including its lack of risk to people’s health and its reasonable cost. However, Mg has several disadvantages, one of which is its high corrosion rate. This work analysed magnesium alloy characteristics and quantum behaviour, including band structure, molecular orbital, and corrosion behaviour in the presence of water. Magnesium was characterised by density functional theory software using CASTEP and Dmol3. Results showed no Mg band structure displays a conductive Fermi level of 8.85 eV. Curvature studies revealed that Mg has strong curvature and electron mobility. The density of state (DOS) of Mg-Al-Zn changes with Al and Zn alloy atoms, and the electron density increases to −7.5 eV compared with pure Mg. HOMO–LUMO analysis elucidated that Mg-Al-Zn* has a large gap (0.419 eV), leading to its stability and low chemical reactivity. This study analysed the properties of Mg and then examines the effect of corrosion on Mg alloys using DFT at different element positions. Corrosion analysis indicated that Mg-Al-Zn has the highest activation energy, implying that its corrosion is less likely than that of other alloys.

WanTiBEXOS: A Wannier based Tight Binding code for electronic band structure, excitonic and optoelectronic properties of solids

The Bethe–Salpeter equation (BSE) approach becomes a methodology commonly used for simulating excitonic and optical properties in computer materials sciences. However, BSE approach based directly on first principles demands a high computational cost, being prohibitive for larger systems. In order to overcome this challenge, we have developed WanTiBEXOS, a parallel computational FORTRAN code, constituted of a maximally localized Wannier functions based tight-binding (MLWF-TB) model in conjunction with BSE framework. The MLWF-TB Hamiltonian used in WanTiBEXOS package can be obtained via any density functional theory package interfaced with Wannier90 code. It's expected, due MLWF-TB formalism, a computational time reduction around one or more orders of magnitude in comparison with BSE ab initio implementations. In order to demonstrate its reliability, flexibility, efficiency and versatility of WanTiBEXOS, we simulate electronic and optical property calculations for the representative materials, including conventional bulk semiconductors, perovskites, nano-monolayer materials and van der Waals heterostructures. Program summaryProgram Title: WanTiBEXOSCPC Library link to program files:https://doi.org/10.17632/4vh76mnkv5.1Developer's repository link:https://github.com/ac-dias/wantibexosLicensing provisions: GNU General Public Licence 3.0Programming language: Fortran90 (Intel compiler)External routines: OpenMP and Intel Math Kernel Library (MKL)Nature of problem: Calculate electronic, optical, and excitonic properties of solids.Solution method: Tight-binding approach under maximally localized Wannier functions (MLWF) parametrization to describe standard electronic properties and the Bethe–Salpeter formalism for excitonic properties.

DeePKS + ABACUS as a Bridge between Expensive Quantum Mechanical Models and Machine Learning Potentials.

Recently, the development of machine learning (ML) potentials has made it possible to perform large-scale and long-time molecular simulations with the accuracy of quantum mechanical (QM) models. However, for different levels of QM methods, such as density functional theory (DFT) at the meta-GGA level and/or with exact exchange, quantum Monte Carlo, etc., generating a sufficient amount of data for training an ML potential has remained computationally challenging due to their high cost. In this work, we demonstrate that this issue can be largely alleviated with Deep Kohn-Sham (DeePKS), an ML-based DFT model. DeePKS employs a computationally efficient neural network-based functional model to construct a correction term added upon a cheap DFT model. Upon training, DeePKS offers closely matched energies and forces compared with high-level QM method, but the number of training data required is orders of magnitude less than that required for training a reliable ML potential. As such, DeePKS can serve as a bridge between expensive QM models and ML potentials: one can generate a decent amount of high-accuracy QM data to train a DeePKS model and then use the DeePKS model to label a much larger amount of configurations to train an ML potential. This scheme for periodic systems is implemented in a DFT package ABACUS, which is open source and ready for use in various applications.

Empathes: A general code for nudged elastic band transition states search

An easy and flexible interface, Empathes (Extensible Minimum PATH EStimator), that allows to perform Nudged Elastic Band calculation for the determination of transition states is presented. The code is designed to be easily modified, in order to be associated with the user's preferred calculation software, even with those which implement composite approaches. In particular, the interfaces to Gaussian and Siesta programs are discussed in details, being the former only used for testing purpose, while the latter can be productively employed for transition states search with that commonly used density functional theory software for periodic calculations. Program summaryProgram Title:EmpathesCPC Library link to program files:https://doi.org/10.17632/v525mwf3cc.1Developer's repository link:https://github.com/marberti/empathesCode Ocean capsule:https://codeocean.com/capsule/2394233Licensing provisions: GPLv3Programming language: Fortran 08Nature of problem: The search for the structure of transition states through computational methods, essentially based on Density Functional Theory, is of overwhelming importance for the determination of the elementary steps forming a reaction mechanism. Allowing to develop basic knowledge, these investigations can be used to direct experimentalists towards a more efficient realization of chemical compounds synthetic processes. In cases where it is necessary to describe the reactive system through periodic calculations, which is very common in heterogeneous catalysis, this research must be done through the use of non-analytical methods.Solution method: In case of lacking of analytical procedures, the search for the transition states associated with the elementary stages that make up chemical reactions must take place through numerical methods. The Nudged Elastic Band (NEB) approach is, together with its variants, one of the most used for this purpose. In accordance with the NEB algorithm, a chain of geometric structures, generated by interpolating between the reactant and product geometries and joined by fictitious springs, is relaxed on the minimum energy path, allowing the association of the transition state to the maximum along this path. The NEB method involves the determination of molecular energies and forces acting on the nuclei of the system, which is generally carried out through a program for electronic structure calculation. The present code is a useful general interface.

Density functional theory calculations of large systems: Interplay between fragments, observables, and computational complexity

AbstractIn the past decade, developments of computational technology around density functional theory (DFT) calculations have considerably increased the system sizes which can be practically simulated. The advent of robust high performance computing algorithms which scale linearly with system size has unlocked numerous opportunities for researchers. This fact enables computational physicists and chemists to investigate systems of sizes which are comparable to systems routinely considered by experimentalists, leading to collaborations with a wide range of techniques and communities. This has important consequences for the investigation paradigms which should be applied to reduce the intrinsic complexity of quantum mechanical calculations of many thousand atoms. It becomes important to consider portions of the full system in the analysis, which have to be identified, analyzed, and employed as building‐blocks from which decomposed physico‐chemical observables can be derived. After introducing the state‐of‐the‐art in the large scale DFT community, we will illustrate the emerging research practices in this rapidly expanding field, and the knowledge gaps which need to be bridged to face the stimulating challenge of the simulation of increasingly realistic systems.This article is categorized under: Electronic Structure Theory > Density Functional Theory Software > Simulation Methods Structure and Mechanism > Computational Materials Science

Comparison of optical response from DFT random phase approximation and a low-energy effective model: Strained phosphorene

The engineering of the optical response of materials is a paradigm that demands microscopic-level accuracy and reliable predictive theoretical tools. Here we compare and contrast the dispersive permittivity tensor, using both a low-energy effective model and density functional theory (DFT). As a representative material, phosphorene subject to strain is considered. Employing a low-energy model Hamiltonian with a Green's function current-current correlation function, we compute the dynamical optical conductivity and its associated permittivity tensor. For the DFT approach, first-principles calculations make use of the first-order random phase approximation. Our results reveal that although the two models are generally in agreement within the low-strain and low-frequency regime, the intricate features associated with the fundamental physical properties of the system and optoelectronics devices implementation such as band gap, Drude absorption response, vanishing real part, absorptivity, and sign of permittivity over the frequency range show significant discrepancies. Our results suggest that the random phase approximation employed in widely used DFT packages should be revisited and improved to be able to predict these fundamental electronic characteristics of a given material with confidence. Furthermore, employing the permittivity results from both models, we uncover the pivotal role that phosphorene can play in optoelectronics devices to facilitate highly programable perfect absorption of electromagnetic waves by manipulating the chemical potential and exerting strain and illustrate how reliable predictions for the dielectric response of a given material are crucial to precise device design.

Baltimore SCIART: A Fully Virtual Undergraduate Research Experience at the Interface of Computational Chemistry and Art

From its inception in 2016 through 2019, the Baltimore SCIART Consortium offered an annual 10-week interdisciplinary summer research program for undergraduate students. Each year, the program mentored approximately 10 students, many from primarily undergraduate institutions including minority serving institutions and historically black colleges and universities. Throughout the sessions, the students were exposed to the career paths of art conservation and art conservation science as they worked in the laboratories of scientists, engineers, art conservators, and art conservation scientists at the University of Maryland Baltimore County, Johns Hopkins University, and the Walters Art Museum in Baltimore. Preparations for the 2020 program were underway when the COVID-19 pandemic shifted the undergraduate research paradigm to a virtual experience. An in-person, laboratory-based program was no longer an option, and this challenged the SCIART team to investigate novel ways to offer a rigorous, engaging undergraduate research program in a fully virtual setting. The result was an intensive, three-week pilot program in which four SCIART students learned about and successfully applied open-source periodic density functional theory software packages to explore the interactions between small molecule adsorbates and mineral-based surfaces relevant to art conservation. This case study exemplifies how educators and research leaders were able to strategically pivot and provide an adapted curriculum for a unique, interdisciplinary, and fully virtual undergraduate research experience. The implication is a potential (scalable) model for culturally engaging research opportunities for historically underrepresented students in STEM, both during and beyond the COVID-19 pandemic.

WloopPHI: A tool for ab initio characterization of Weyl semimetals

WloopPHI is a Python code that expands the features of WIEN2k, a full-potential all-electron density functional theory package, by the characterization of Weyl semimetals. It enables the calculation of the chirality (or “monopole charge”) associated with Weyl nodes and nodal lines. The theoretical methodology for the calculation of the chirality is based on an extended Wilson loop method and a Berry phase approach. We validate the code using TaAs, which is a well-characterized Weyl semimetal, both theoretically and experimentally. Afterwards, we applied the method to the characterization of YRh6Ge4 and found two sets of Weyl points (ca. 0.2 eV below the Fermi energy) together with a topological nodal line (protected by mirror symmetry) crossing the Fermi energy and mapped their chiralities.

Measuring Shared Electrons in Extended Molecular Systems: Covalent Bonds from Plane-Wave Representation of Wave Function.

In the study of materials and macromolecules by first-principle methods, the bond order is a useful tool to represent molecules, bulk materials and interfaces in terms of simple chemical concepts. Despite the availability of several methods to compute the bond order, most applications have been limited to small systems because a high spatial resolution of the wave function and an all-electron representation of the electron density are typically required. Both limitations are critical for large-scale atomistic calculations, even within approximate density-functional theory (DFT) approaches. In this work, we describe our methodology to quickly compute delocalization indices for all atomic pairs, while keeping the same representation of the wave function used in most compute-intensive DFT calculations on high-performance computing equipment. We describe our implementation into a post-processing tool, designed to work with Quantum ESPRESSO, a popular open-source DFT package. In this way, we recover a description in terms of covalent bonds from a representation of wave function containing no explicit information about atomic types and positions.

A machine learning platform for the discovery of materials

For photovoltaic materials, properties such as band gap E_{g} are critical indicators of the material’s suitability to perform a desired function. Calculating E_{g} is often performed using Density Functional Theory (DFT) methods, although more accurate calculation are performed using methods such as the GW approximation. DFT software often used to compute electronic properties includes applications such as VASP, CRYSTAL, CASTEP or Quantum Espresso. Depending on the unit cell size and symmetry of the material, these calculations can be computationally expensive. In this study, we present a new machine learning platform for the accurate prediction of properties such as E_{g} of a wide range of materials.

TB2J: A python package for computing magnetic interaction parameters

We present TB2J, a Python package for the automatic computation of magnetic interactions, including exchange and Dzyaloshinskii–Moriya, between atoms of magnetic crystals from the results of density functional calculations. The program is based on the Green’s function method with the local rigid spin rotation treated as a perturbation. As input, the package uses the output of either Wannier90, which is interfaced with many density functional theory packages, or of codes based on localized orbitals. One of the main interests of the code is that it requires only one first-principles electronic structure calculation in the non-relativistic case (or three in the relativistic case) and from the primitive cell only to obtain the magnetic interactions up to long distances, instead of first-principles calculations of many different magnetic configurations and large supercells. The output of TB2J can be used directly for the adiabatic magnon band structure and spin dynamics calculations. A minimal user input is needed, which allows for easy integration into high-throughput workflows. Program summaryProgram Title: TB2JCPC Library link to program files:https://doi.org/10.17632/dm45fcn69d.1Developer’s repository link:https://github.com/mailhexu/TB2JCode Ocean capsule:https://codeocean.com/capsule/6486145Licensing provisions: BSD 2-clauseProgramming language: PythonNature of problem: TB2J is a package for the computing of parameters in the extended Heisenberg model of the magnetic interaction, including the isotropic exchange, anisotropic exchange and Dzyaloshinskii–Moriya interactions from first principles result. It can make use of the Wannier function Hamiltonian, which can be constructed from many first principles codes, or localized orbital based codes.Solution method: It uses the magnetic force theorem and takes the rigid spin rotation as a perturbation to the electronic structure. The energy variation is calculated from the Green’s functions from tight-binding like Hamiltonian based on Wannier functions or localized orbitals.Additional comments including restrictions and unusual features: Isotropic exchange, anisotropic exchange, and Dzyaloshinskii–Moriya interactions can all be computed with the input of many DFT codes through the interface of Wannier90, or directly from localized orbital codes. The magnetic interaction parameters up to any distance can be computed from one DFT calculation. A minimum user-input is required which provides a black-box like experience. It generates output for several spin dynamics codes and thus bridges the first principles electronic structure simulation with the large scale spin dynamics simulation.

DMFTwDFT: An open-source code combining Dynamical Mean Field Theory with various density functional theory packages

Dynamical Mean Field Theory (DMFT) is a successful method to compute the electronic structure of strongly correlated materials, especially when it is combined with density functional theory (DFT). Here, we present an open-source computational package (and a library) combining DMFT with various DFT codes interfaced through the Wannier90 package. The correlated subspace is expanded as a linear combination of Wannier functions introduced in the DMFT approach as local orbitals. In particular, we provide a library mode for computing the DMFT density matrix. This library can be linked and then internally called from any DFT package, assuming that a set of localized orbitals can be generated in the correlated subspace. The existence of this library allows developers of other DFT codes to interface with our package and achieve the charge-self-consistency within DFT+DMFT loops. To test and check our implementation, we computed the density of states and the band structure of well-known solid-state correlated materials, namely LaNiO3, SrVO3, and NiO. The obtained results are compared to those obtained from other DFT+DMFT implementations. Program summaryProgram title: DMFTwDFTCPC Library link to program files:https://doi.org/10.17632/y27fngtkdw.1Licensing provisions: GNU General Public License 3Programming language: Python2/3, C++, and FORTRANExternal routines: MPI, FFTW, BLAS, LAPACK, Numpy, Scipy, mpi4py, Glib, gsl, weave, PyProcar, and PyChemiaSubprograms used: Wannier90 (v3.0), Siesta (v4.1-b4), VASP (v5.4.4), Quantum Espresso (v6.5), CTQMCNature of problem: Need for a simple, efficient, higher-level, and open-source package to study strongly correlated materials interfacing to various DFT codes regardless of basis sets used in DFT.Solution method: We present an open-source Python code which can be easily interfaced with Wannier90 and different DFT packages and perform a full charge-self-consistent DFT+DMFT calculation using a modern continuous-time quantum Monte Carlo (CTQMC) impurity solver.

On the top rung of Jacob's ladder of density functional theory: Toward resolving the dilemma of SIE and NCE

AbstractAccording to the classification of Jacob's Ladder proposed by Perdew, density functional approximations (DFAs) on the top (fifth) rung add the information of the unoccupied Kohn–Sham orbitals, which hold the promise to enter the heaven of chemical accuracy. In other words, we expect that a much higher accuracy with a broader applicability than the existing DFAs would eventually be achieved on the fifth rung. Nonetheless, Jacob's Ladder itself does not offer a recipe for how to manipulate the unoccupied Kohn–Sham orbitals on the construction of a successful fifth rung DFA. In this article, we briefly review two successful types of the fifth rung DFAs, that is, random‐phase approximation (RPA) and doubly hybrid approximation (DHA). The limitations of RPA and DHA will be introduced in the context of the so‐called self‐interaction error (SIE)/nondynamic correlation error (NCE) dilemma in the world of density functional theory. We propose the development strategy for DHAs to address the general concern about the future of advanced DFAs on the fifth rung. We share our experience here, based on the relevant efforts recently made by the authors and their co‐workers, aiming to resolve the SIE/NCE dilemma and to extend the applicability of DHAs from the chemistry of the main group elements to that of the transition metals.This article is categorized under: Electronic Structure Theory > Density Functional Theory Software > Quantum Chemistry

ONETEP + TOSCAM: Uniting Dynamical Mean Field Theory and Linear-Scaling Density Functional Theory.

We introduce the unification of dynamical mean field theory (DMFT) and linear-scaling density functional theory (DFT), as recently implemented in ONETEP, a linear-scaling DFT package, and TOSCAM, a DMFT toolbox. This code can account for strongly correlated electronic behavior while simultaneously including the effects of the environment, making it ideally suited for studying complex and heterogeneous systems that contain transition metals and lanthanides, such as metalloproteins. We systematically introduce the necessary formalism, which must account for the nonorthogonal basis set used by ONETEP. In order to demonstrate the capabilities of this code, we apply it to carbon monoxide ligated iron porphyrin and explore the distinctly quantum-mechanical character of the iron 3d electrons during the process of photodissociation.

Multi‐coefficients correlation methods

AbstractA composite quantum chemical method is an approximated computational protocol designed to obtain highly accurate energies for different types of interactions. In this review, we summarize the recent advance in the evolution, assessments, and applications of the multi‐coefficients correlation methods (MCCMs) and doubly hybrid MCCMs, especially the recent Wuhan‐Minnesota‐Scaling method, for accurate calculations of Born–Oppenheimer energies of molecular systems. The review gives an overview of the methods along with their performance on the W4‐17 database.This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Electronic Structure Theory > Density Functional Theory Software > Quantum Chemistry