Ab-initio Package Research Articles

CELL: a Python package for cluster expansion with a focus on complex alloys

We present the Python package CELL, which provides a modular approach to the cluster expansion (CE) method. CELL can treat a wide variety of substitutional systems, including one-, two-, and three-dimensional alloys, in a general multi-component and multi-sublattice framework. It is capable of dealing with complex materials comprising several atoms in their parent lattice. CELL uses state-of-the-art techniques for the construction of training data sets, model selection, and finite-temperature simulations. The user interface consists of well-documented Python classes and modules (http://sol.physik.hu-berlin.de/cell/). CELL also provides visualization utilities and can be interfaced with virtually any ab initio package, total-energy codes based on interatomic potentials, and more. The usage and capabilities of CELL are illustrated by a number of examples, comprising a Cu-Pt surface alloy with oxygen adsorption, featuring two coupled binary sublattices, and the thermodynamic analysis of its order-disorder transition; the demixing transition and lattice-constant bowing of the Si-Ge alloy; and an iterative CE approach for a complex clathrate compound with a parent lattice consisting of 54 atoms.

Impact of electronic correlation on strong laser-induced bound-state transitions.

Electron correlation (EC) plays a crucial role in all multi-electron systems and dynamic processes. In this work, we focus on strong laser-induced bound-bound transitions (BBT), which are fundamental to optical absorption measurements. We use the helium atom, the simplest two-electron system, as our test case, utilizing the ab initio code package HeTDSE. We examined the bound state energy levels, transition dipole moments (TDMs), and the dynamics of strong laser-induced BBT, both with and without considering EC. Our results indicate that EC significantly impacts the energy levels of the bound states and the TDMs. These effects collectively influence the transition dynamics of the excited states. Although EC does not alter the quantum transition pathways between resonance states, it generally increases the probability of resonance transitions in most cases. Our findings provide a quantitative description of EC in laser-induced BBT.

Computational investigation of elastic properties of hypothetical Half-Heusler compounds XNbSn under hydrostatic pressures

We investigated the electronic, elastic, and magnetic properties of the hypothetical half- Heusler alloys with Niobium base atom, XNbSn with (X= Cr, Mn, Co, Fe, V) uses the full-potential (linearized) augmented plane-wave and local-orbitals [FP-(L)APW + lo] basis set in the WIEN2K ab-initio package based on density functional theory (DFT). We investigated the elastic constants, Shear modulus, young modulus, and bulk modulus of these alloys under different pressures (0, 20, 40, and 80 GPa). We predicted that CoNbSn behaves as a semiconductor with a direct energy gap of 0.99 eV, while the other half- Heusler alloys show a metallic behavior. CoNbSn keeps its semiconductor behavior under higher pressures up to 80 GPa. Both of VNbSn and CrNbSn have a high value of magnetic moments of 2.158 and 3.002 µB respectively. All XNbSn alloys are stable mechanically at different pressures according to the Born-Huang conditions. CoNbSn, FeNbSn, CrNbSn, and MnNbSn behave as a ductile material at ambient pressure.

Ideas of lattice-basis reduction theory for error-stable Bravais lattice determination and abinitio indexing.

In ab initio indexing, for a given diffraction/scattering pattern, the unit-cell parameters and the Miller indices assigned to reflections in the pattern are determined simultaneously. `Ab initio' means a process performed without any good prior information on the crystal lattice. Newly developed ab initio indexing software is frequently reported in crystallography. However, it is not widely recognized that use of a Bravais lattice determination method, which is tolerant of experimental errors, can simplify indexing algorithms and increase their success rates. One of the goals of this article is to collect information on the lattice-basis reduction theory and its applications. The main result is a Bravais lattice determination algorithm for 2D lattices, along with a mathematical proof that it works even for parameters containing large observational errors. It uses two lattice-basis reduction methods that seem to be optimal for different symmetries, similarly to the algorithm for 3D lattices implemented in the CONOGRAPH software. In indexing, a method for error-stable unit-cell identification is also required to exclude duplicate solutions. Several methods are introduced to measure the difference in unit cells known in crystallography and mathematics.

High-entropy carbide (Ti0.2Zr0.2Hf0.2Nb0.2Ta0.2)C mechanical properties prediction with the use of machine learning potential

The six-component high-entropy carbide (HEC) (Ti0.2Zr0.2Hf0.2Nb0.2Ta0.2)C has been studied. The electronic structure was calculated by using the ab initio package VASP for a supercell with 512 atoms constructed by using special quasi-random structures. The artificial neural networks potential (ANN-potential) was obtained by deep machine learning. The quality of the ANN-potential was estimated by the value of the energies, forces, and virials standard deviations. The generated ANN-potential was used to analyze both a defect-free model of the specified alloy, with 4096 atoms, and for the first time a polycrystalline HEC model, with 4603 atoms, by using the LAMMPS classical molecular dynamics package. The simulation of uniaxial cell tension was carried out, the elasticity coefficients, the all-round compression modulus, the elasticity modulus, and Poisson’s ratio were determined. The obtained values are in good agreement with the experimental and calculated data, which indicates a good predictive ability of the generated ANN-potential.

Defects in Se, As2S3, and GeS2 glasses: Ab initio analyses of related clusters

Dangling bonds in Se, As2S3, and GeS2 glasses and wrong bonds in the compounds have been comparatively studied using an ab initio molecular-orbital software. Defect energies and the densities in the chalcogenide glasses are estimated from the total energy Et of small clusters such as H-nSe-H, As3S4H, and Ge4S4H. Properties of corner- and edge-shared connections are also explored for the As-S and Ge-S systems. The three kinds of clusters show for a meta-stable energy ΔEt, relative to the total energy Et of normal bonding structures, a magnitude order of ΔEt(IVAP) < ΔEt(2D0) < ΔEt(D+/D−). Based on this result, we discuss why only GeS2 exhibits unpaired electron spins. The analysis also manifests that ΔEts of clusters containing wrong bonds (As-As, Ge-Ge, and S-S) are comparable with those of ΔEt(IVAP). Regarding electronic levels, the three glasses seem to possess marked gap states having different origins.

TRACK: A python code for calculating the transport properties of correlated electron systems using Kubo formalism

Exploring the transport properties of different materials brings new avenue for basic understanding of emergent phenomena and practical applications in many different fields. Here, we report a program named as TRACK (TRAnsport properties for Correlated materials using Kubo formalism) which is written in Python 3 for calculating temperature dependent electrical conductivity, electronic part of thermal conductivity, Seebeck coefficient and Lorenz number. In this code, Kubo linear-response formalism is utilized for computing these parameters using both interacting and non-interacting electronic structure methods. The formula for transport coefficients is accordingly modified to obtain the transport parameters under relaxation time approximation using band-theory. The basic inputs of this program are the structural information, dense k-points sampling in the irreducible part of the Brillouin zone and the information of velocity matrix elements, which can be calculated using third-party ab-initio package. TRACK is expected to calculate the transport properties of different class of materials. The code has been benchmarked by performing calculation on three different types of materials namely Vanadium (V), FeSi and LaCoO3, which are metal, semiconductor and Mott insulator, respectively. The temperature dependent behaviour of the transport coefficients for these materials show fairly good agreement with the corresponding experimental data. Program summaryProgram Title: TRACKCPC Library link to program files:https://doi.org/10.17632/jdt9tfkt4v.1Developer's repository link:https://sourceforge.net/projects/track-code/files/TRACK.zip/downloadLicensing provisions: GPLv3Programming language: Python3External routines/libraries: NumPy, SciPy, TimeNature of problem: Calculating the transport parameters using the Kubo linear-response formalism.Solution method: We present a Python3 open source code for calculating transport coefficients using Kubo formalism. Both interacting and non-interacting electronic structure methodology are possible to be used for computing transport parameters.

Analysis of the Magnetic Coupling in a Mn(II)-U(V)-Mn(II) Single Molecule Magnet.

[{Mn(TPA)I}{UO2(Mesaldien)}{Mn(TPA)I}]I formula (here TPA=tris(2-pyridylmethyl)amine and Mesaldien=N,N'-(2-aminomethyl)diethylenebis(salicylidene imine)) reported by Mazzanti and coworkers (Chatelain et al. Angew. Chem. Int. Ed. 2014, 53, 13434) is so far the best Single Molecule Magnet (SMM) in the {3d-5f} class of molecules exhibiting barrier height of magnetization reversal as high as 81.0 K. In this work, we have employed a combination of ab initio CAS and DFT methods to fully characterize this compound and to extract the relevant spin Hamiltonian parameters. We show that the signs of the magnetic coupling and of the g-factors of the monomers are interconnected. The central magnetic unit [UV O2 ]+ is described by a Kramers Doublet (KD) with negative g-factors, due to a large orbital contribution. The magnetic coupling for the {Mn(II)-U(V)} pair is modeled by an anisotropic exchange Hamiltonian: all components are ferromagnetic in terms of spin moments, the parallel component JZ twice larger as the perpendicular one J⊥ . The spin density distribution suggests that spin polarization on the U(V) center favors the ferromagnetic coupling. Further, the JZ /J⊥ ratio, which is related to the barrier height, was found to correlate to the corresponding spin contribution of the g-factors of the U(V) center. This correlation established for the first time offers a direct way to estimate this important ratio from the corresponding gS -values, which can be obtained using traditional ab initio packages and hence has a wider application to other {3d-5f} magnets. It is finally shown that the magnetization barrier height is tuned by the splitting of the [UV O2 ]+ 5 f orbitals.

Laser-assisted rapid synthesis of anatase/rutile TiO2 heterojunction with Function-specified micro-zones for the effective photo-oxidation of sulfamethoxazole

A solid-state laser scanning treatment (SLST) was adopted to synthesize anatase/rutile TiO2 heterojunction with effective charge carrier separation and high surface adsorption performances for the photodegradation of sulfamethoxazole (SMX). The 1064 nm pulsed fiber laser could in-situ generate rutile zones on the pristine sheet-like anatase crystal enclosed by (001) facets, which could form the well-defined anatase/rutile interface to promote the formation of dominating active species (h+ and ∙OH) on the anatase zones. X-ray absorption fine structure (XAFS) measurements, low temperature electron paramagnetic resonance (LT-EPR) as well as the density functional theory (DFT) simulation proved that the oxygen vacancies (VO) could both introduce defective energy states to promote the light absorption and enhance the SMX adsorption on anatase zones. Based on the delicately designed micro-zones, the photodegradation efficiency of the optimized catalyst could reach 99.3 %, which demonstrated ∼7 times higher performance than that of pristine TiO2 and exhibited robust stability under environmental conditions. Gaussian and Vienna Ab Initio Package (VASP) programs were used to provide detailed degradation pathways and mechanism for SMX. This SLST could be potentially employed to create function-specified zones on various catalysts for different applicational aims.

Extended first‐principles molecular dynamics simulations of hot dense boron: equation of state and ionization

AbstractThe extended first‐principles molecular dynamics (Ext. FPMD) model introduced by Shen Zhang et al. has been implemented within the ab initio DFT software package ABINIT and is now publicly available. This model allows performing quantum molecular dynamics simulations (QMD) at high temperatures bypassing the well‐known orbitals wall. QMD simulations can be done smoothly in the full range of temperatures from cold condensed matter to hot plasmas (&gt;100 eV) passing by the warm dense matter regime. At high temperature, a minimum of Kohn‐Sham orbitals is kept, allowing for deep ionization effects to manifest, such as the Schottky anomaly of the specific heat, in contrast with orbital‐free approaches for which this effect is absent. Using the new 9.6 ABINIT version, we present extensive simulations of boron along isochores, from a few Kelvins to thousands of eVs, in the Gigabar regime and construct a table. The Hugoniot curve is found in close agreement with the FPEOS model, for a much lower computational intensity. An ionization analysis, deduced from the pressure or from the structure, emphasizes the crucial contribution of the very deep 1s shell in the maximum compression regime.

DASP: Defect and Dopant ab-initio Simulation Package

Abstract In order to perform automated calculations of defect and dopant properties in semiconductors and insulators, we developed a software package, the Defect and Dopant ab-initio Simulation Package (DASP), which is composed of four modules for calculating: (i) elemental chemical potentials, (ii) defect (dopant) formation energies and charge-state transition levels, (iii) defect and carrier densities and (iv) carrier dynamics properties of high-density defects. DASP uses the materials genome database for quick determination of competing secondary phases when calculating the elemental chemical potential that stabilizes compound semiconductors. DASP calls the ab-initio software to perform the total energy, structural relaxation and electronic structure calculations of the defect supercells with different charge states, based on which the defect formation energies and charge-state transition levels are calculated. Then DASP can calculate the equilibrium densities of defects and electron and hole carriers as well as the Fermi level in semiconductors under different chemical potential conditions and growth/working temperature. For high-density defects, DASP can calculate the carrier dynamics properties such as the photoluminescence (PL) spectrum and carrier capture cross sections which can interpret the deep level transient spectroscopy (DLTS). Here we will show three application examples of DASP in studying the undoped GaN, C-doped GaN and quasi-one-dimensional SbSeI.

Extended first-principles molecular dynamics model for high temperature simulations in the Abinit code: Application to warm dense aluminum

The extended first-principles molecular dynamics (Extended FPMD) model introduced by Zhang et al. [2], based on an analytical single plane wave description of electronic orbitals for high energy electrons, has been implemented within the ab initio DFT software package Abinit and is now available. This model allows quantum simulations to be done smoothly on the full range of temperatures from cold condensed matter to hot dense plasmas passing through the warm dense matter regime which was currently not possible within the same ab initio model due to numerical limitations. In addition to presenting a brief theoretical background of the Zhang et al. method, we propose some improvements to the model. We then present the details of the implementation, and finally offer an application to the aluminum simulations for multiple densities, from room temperature to hot (thousands of eVs) temperature ranges, with a resulting Hugoniot equation of state that we compare with other methods.

An investigation of high entropy alloy conductivity using first-principles calculations

The Kubo–Greenwood equation, in combination with the first-principles Korringa–Kohn–Rostoker coherent potential approximation (KKR-CPA) can be used to calculate the DC residual resistivity of random alloys at T = 0 K. We implemented this method in a multiple scattering theory based ab initio package, MuST, and applied it to the ab initio study of the residual resistivity of the high entropy alloy AlxCoCrFeNi as a function of x. The calculated resistivities are compared with experimental data. We also predict the residual resistivity of refractory high entropy alloy MoNbTaVxW. The calculated resistivity trends are also explained using theoretical arguments.

DFT Study of Electronic Structure and Optical Properties of Kaolinite, Muscovite, and Montmorillonite

Clay mineral materials have attracted attention due to their many properties and applications. The applications of clay minerals are closely linked to their structure and composition. In this paper, we studied the electronic structure properties of kaolinite, muscovite, and montmorillonite crystals, which are classified as clay minerals, by using DFT-based ab initio packages VASP and the OLCAO. The aim of this work is to have a deep understanding of clay mineral materials, including electronic structure, bond strength, mechanical properties, and optical properties. It is worth mentioning that understanding these properties may help continually result in new and innovative clay products in several applications, such as in pharmaceutical applications using kaolinite for their potential in cancer treatment, muscovite used as insulators in electrical appliances, and engineering applications that use montmorillonite as a sealant. In addition, our results show that the role played by hydrogen bonds in O-H bonds has an impact on the hydration in these crystals. Based on calculated total bond order density, it is concluded that kaolinite is slightly more cohesive than montmorillonite, which is consistent with the calculated mechanical properties.

Role of the C4 protein PepYLCV in viral symptom determinant: In silico approach

The C4 protein of the monopartite begomovirus pepper yellow leaf curl virus [PepYLCV] plays a major role in the pathogenicity of plant virus infection. Complement gene [C4], in virus, is overlapped with complement gene 1 [C1] or known as Replicase gene [Rep]. The C1 protein is directly involved in virus DNA replication, but not the C4 protein. Recent studies suggested that the C4 is a viral symptom determinant but the molecular mechanism has not been elucidated. In this study, the C4 gene of the novel PepYLCV Alahan Panjang was isolated. To further investigate the role of C4 in symptom determinants, in silico approached was used. Computational modeling of C4 was constructed with homology and ab initio modeling software and the model was checked with Ramachandran Plot. The optimum model of the C4 was used in the surface analysis to predict binding sites and key residues. The mutant structure of the C4 protein and its prospect for CRISPR-Cas9 utilization are discussed.

Intramolecular interactions in a target specific anti-tumor nanodrug: a theoretical study

Through this authoritative report, an application of fragment molecular orbital (FMO) method on a functionalized carbon nanotube (CNT) has been proposed. A targeted anti-tumor nanodrug, based on CNT that converges towards cancerous cells, has been innovated in this regard. The anticancer drug cisplatin and the target selector arginine-aspartate-glycine acid (RGD) have been attached via poly ethylene glycol (PEG) on CNT. This nanodrug has been divided into 12 fragments including CNT as one of them. General atomic molecular electronic structure system (GAMESS), an ab initio package, has been used for calculations. The contributions of various fragments have been discussed in terms of inter-fragment interactions. Results indicate that the CNT shares the important role in stabilizing the different parts of its derivatives. In addition, this report proves CNT as a fragment for FMO method.

Irvsp: To obtain irreducible representations of electronic states in the VASP

We present an open-source program irvsp, to compute irreducible representations of electronic states for all 230 space groups with an interface to the Vienna ab-initio Simulation Package. This code is fed with plane-wave-based wavefunctions (e.g. WAVECAR) and space group operators (listed in OUTCAR), which are generated by the VASP package. This program computes the traces of matrix presentations and determines the corresponding irreducible representations for all energy bands and all the k-points in the three-dimensional Brillouin zone. It also works with spin–orbit coupling (SOC), i.e., for double groups. It is in particular useful to analyze energy bands, their connectivities, and band topology, after the establishment of the theory of topological quantum chemistry. Accordingly, the associated library – irrep_bcs.a – is developed, which can be easily linked to by other ab-initio packages. In addition, the program has been extended to orthogonal tight-binding (TB) Hamiltonians, e.g. electronic or phononic TB Hamiltonians. A sister program ir2tb is presented as well. Program summaryProgram title: irvspCPC Library link to program files:https://doi.org/10.17632/y9ds5nnm2f.1Licensing provisions: GNU Lesser General Public LicenseProgramming language: Fortran 90/77Nature of problem: Determining irreducible representations for all energy bands and all the k-points in 230 space groups. It is in particular useful to analyze energy bands, their connectivities, and band topology.Solution method: By computing the traces of matrix presentations of space group operators for the eigen-wavefunctions at a certain k-point in a given space group, one can determine irreducible representations for them.

High-Throughput DFT Screening Method Via Local Bonding Model for Corrosion Resistant Alloy Designed for Naval Applications

In this talk, first principles density functional theory (DFT) implemented in the Vienna Ab-initio Package (VASP)1,2 is employed to compile a reproducible and high-fidelity adsorption energy database to lend insights into searching and designing for corrosion resistant alloys (CRAs) on the atomic scale3–6. The current compilation and theory development begin with the high entropy alloy (HEA). Since the independent investigation of HEA by Yeh7 and Cantor8, this class of alloy has shown a range of desirable features, such as good mechanical properties, phase stability at high temperature, and excellent corrosion resistance7,9,10. For these reasons, HEA has drawn attentions as possible candidate to supersede stainless steel for naval applications. One of the outstanding challenges to investigate HEA at the atomic scale, however, is the manifestation of randomness in the individual atoms that occupy the lattice sites. Two popular schools of theories have emerged over the years to tackle this issue. One is to overlay the potential fields of constituent atoms on top of the same lattice site, thereby ensuring “true” randomness11. The other is to score correlation function between first, second, third and so on nearest neighbor atoms with an Ising model approach to explicitly represent atoms within reasonable number for DFT computation12. Upon surveying the literature, both theories have been employed to mainly investigate the mechanical behavior of HEA13,14, while comparatively less has been adapted to study the corrosion resistant properties15. Herein, we propose a local bonding model to aid high throughput calculations that is necessary for both establishing a database and the subsequent screening of beneficial dopant elements in the design of CRAs. Our local bonding model is derived from the observation that the outer most layer atoms that come into contact with environment contribute the most to the computed adsorption energies. For HEA that has face-center-cubic (fcc) lattice, the local bonding model reduces to account for the most frequently occurring low-index fcc (111) surface, and the adsorption position on the three-fold fcc site. We will show that within this approach, the total number of DFT calculations become much more manageable and tractable. Furthermore, we expand upon the previously established concepts of aqueous species surface coverage16 and chloride susceptibility index17 , and include the alloy surface affinity for hydron and oxygen atoms. Altogether, we believe that the surface competition amongst chloride, hydrogen, and oxygen species can lend useful insights into re-passivation potential framework18–22 for the CRAs of interest by establishing an unforeseen correlation. Reference G. Kresse and J. 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PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids.

Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL plugin called PyVibMS for visualizing the vibrational motions for both molecular and solid systems calculated by mainstream quantum chemical computer programs including Gaussian, Q-Chem, VASP, and CRYSTAL. Benefiting from the continuing development of the PyMOL platform, PyVibMS provides powerful functionalities and user-friendly interface. PyVibMS was written in Python and its open-source nature makes it flexible and sustainable. As an example, the motions of the Konkoli-Cremer local vibrational modes are shown in this work for the first time. PyVibMS is freely available at https://github.com/smutao/PyVibMS . Graphical abstract In this work, a PyMOL plugin named PyVibMS is developed to visualize molecular and lattice vibrations.

Exact quasi-relativistic wavefunctions of Hydrogen-like atoms

Exact solutions of a novel quasi-relativistic quantum mechanical wave equation are found for Hydrogen-like atoms. This includes both, an exact analytical expression for the energies of the bound states, and exact analytical expressions for the wavefunctions, which successfully describe quantum particles with mass and spin-0 up to energies comparable to the energy associated to the mass of the particle. These quasi-relativistic atomic orbitals may be used for improving ab-initio software packages dedicated to numerical simulations in physical-chemistry and atomic and solid-state physics.