Density Functional Theory Code Research Articles

Towards Ab-Initio Simulations of Crystalline Defects at the Exascale Using Spectral Quadrature Density Functional Theory

Defects in crystalline solids play a crucial role in determining properties of materials at the nano, meso- and macroscales, such as the coalescence of vacancies at the nanoscale to form voids and prismatic dislocation loops or diffusion and segregation of solutes to nucleate precipitates, phase transitions in magnetic materials via disorder and doping. First principles Density Functional Theory (DFT) simulations can provide a detailed understanding of these phenomena. However, the number of atoms needed to correctly simulate these systems is often beyond the reach of many widely used DFT codes. The aim of this article is to discuss recent advances in first principles modeling of crystal defects using the spectral quadrature method. The spectral quadrature method is linear scaling with respect to the number of atoms, permits spatial coarse-graining, and is capable of simulating non-periodic systems embedded in a bulk environment, which allows the application of appropriate boundary conditions for simulations of crystalline defects. In this article, we discuss the state-of-the-art in ab-initio modeling of large metallic systems of the order of several thousand atoms that are suitable for utilizing exascale computing resourses.

Effects of thermal, elastic, and surface properties on the stability of SiC polytypes

SiC polytypes have been studied for decades, both experimentally and with atomistic simulations, yet no consensus has been reached on the factors that determine their stability and growth. Proposed governing factors are temperature-dependent differences in the bulk energy, biaxial strain induced through point defects, and surface properties. In this work, we investigate the thermodynamic stability of the 3C, 2H, 4H, and 6H polytypes with density functional theory (DFT) calculations. The small differences of the bulk energies between the polytypes can lead to intricate changes in their energetic ordering depending on the computational method. Therefore, we employ and compare various DFT codes, i.e., vasp, cp2k, and fhi-aims; exchange-correlation functionals, i.e., LDA, PBE, PBEsol, PW91, HSE06, SCAN, and RTPSS; and nine different van der Waals (vdW) corrections. At $T=0$ K, 4H-SiC is marginally more stable than 3C-SiC, and the stability further increases with temperature by including entropic effects from lattice vibrations. Neither the most advanced vdW corrections nor strain on the lattice have a significant effect on the relative polytype stability. We further investigate the energies of the (0001) polytype surfaces that are commonly exposed during epitaxial growth. For Si-terminated surfaces, we find 3C-SiC to be significantly more stable than 4H-SiC. We conclude that the difference in surface energy is likely the driving force for 3C-nucleation, whereas the difference in the bulk thermodynamic stability slightly favors the 4H and 6H polytypes. In order to describe the polytype stability during crystal growth correctly, it is thus crucial to take into account both of these effects.

DFT-FE 1.0: A massively parallel hybrid CPU-GPU density functional theory code using finite-element discretization

We present DFT-FE 1.0, building on DFT-FE 0.6 Motamarri et al. (2020) [28], to conduct fast and accurate large-scale density functional theory (DFT) calculations (reaching ∼100,000 electrons) on both many-core CPU and hybrid CPU-GPU computing architectures. This work involves improvements in the real-space formulation—via an improved treatment of the electrostatic interactions that substantially enhances the computational efficiency—as well high-performance computing aspects, including the GPU acceleration of all the key compute kernels in DFT-FE. We demonstrate the accuracy by comparing the ground-state energies, ionic forces and cell stresses on a wide-range of benchmark systems against those obtained from widely used DFT codes. Further, we demonstrate the numerical efficiency of our GPU acceleration, which yields ∼20× speed-up on hybrid CPU-GPU nodes of the Summit supercomputer. Notably, owing to the parallel-scaling of the GPU implementation, we obtain wall-times of 80−140 seconds for full ground-state calculations, with stringent accuracy, on benchmark systems containing ∼6,000−15,000 electrons using 64−224 nodes of the Summit supercomputer. Program summaryProgram Title: DFT-FECPC Library link to program files:https://doi.org/10.17632/c5ghfc6ctn.1Developer's repository link:https://github.com/dftfeDevelopers/dftfeLicensing provisions: LGPL v3Programming language: C/C++External routines/libraries: p4est (http://www.p4est.org/), deal.II (https://www.dealii.org/), BLAS (http://www.netlib.org/blas/), LAPACK (http://www.netlib.org/lapack/), ELPA (https://elpa.mpcdf.mpg.de/), ScaLAPACK (http://www.netlib.org/scalapack/), Spglib (https://atztogo.github.io/spglib/), ALGLIB (http://www.alglib.net/), LIBXC (http://www.tddft.org/programs/libxc/), PETSc (https://www.mcs.anl.gov/petsc), SLEPc (http://slepc.upv.es), NCCL (optional-https://github.com/NVIDIA/nccl).Nature of problem: Density functional theory calculations.Solution method: We employ a local real-space variational formulation of Kohn-Sham density functional theory that is applicable for both pseudopotential and all-electron calculations on periodic, semi-periodic and non-periodic geometries. Higher-order adaptive spectral finite-element basis is used to discretize the Kohn-Sham equations. Chebyshev polynomial filtered subspace iteration procedure (ChFSI) is employed to solve the nonlinear Kohn-Sham eigenvalue problem self-consistently. ChFSI in DFT-FE employs Cholesky factorization based orthonormalization, and spectrum splitting based Rayleigh-Ritz procedure in conjunction with mixed precision arithmetic. Configurational force approach is used to compute ionic forces and periodic cell stresses for geometry optimization.Additional comments including restrictions and unusual features: Exchange correlation functionals are restricted to Local Density Approximation (LDA) and Generalized Gradient Approximation (GGA), with and without spin. The pseudopotentials available are optimized norm conserving Vanderbilt (ONCV) pseudopotentials and Troullier–Martins (TM) pseudopotentials. Calculations are non-relativistic.DFT-FE handles all-electron and pseudopotential calculations in the same framework, while accommodating periodic, non-periodic and semi-periodic boundary conditions.

A General Algorithm for Calculating Irreducible Brillouin Zones

Calculations of properties of materials require performing numerical integrals over the Brillouin zone (BZ). Integration points in density functional theory codes are uniformly spread over the BZ (despite integration error being concentrated in small regions of the BZ) and preserve symmetry to improve computational efficiency. Integration points over an irreducible Brillouin zone (IBZ), a rotationally distinct region of the BZ, do not have to preserve crystal symmetry for greater efficiency. This freedom allows the use of adaptive meshes with higher concentrations of points at locations of large error, resulting in improved algorithmic efficiency. We have created an algorithm for constructing an IBZ of any crystal structure in 2D and 3D. The algorithm uses convex hull and half-space representations for the BZ and IBZ to make many aspects of construction and symmetry reduction of the BZ trivial. The algorithm is simple, general, and available as open-source software.

Modeling fission spikes in nuclear fuel using a multigroup model of electronic energy transport

In fission based nuclear reactors the fuel is subject to an intense neutron environment that drives the fission chain reaction. Due to this process fission fragments are created with energies reaching 1 MeV/amu that lose energy primarily through inelastic interactions with the electronic structure producing electronic excitations. Subsequently, these excitations thermalize through electron-phonon interactions resulting in the formation of a high temperature thermal spike and associated pressure spike. This process promotes atomic mobility that is expected to evolve lattice defects, including the annealing of latent ion tracks. In this work, a multigroup model for electron energy transport is developed and applied to molecular dynamics simulations in the LAMMPS code to examine fission energy deposition and fission effects in nuclear fuel. This technique utilizes MCNP Monte Carlo electron transport calculations to determine the initial injection of fission energy. To provide a more predictive approach than semi-empirical two-temperature models, the electron-phonon interactions are defined to include multiphonon energy transfer as a function of atomic and electron temperature, and are evaluated from electronic structure calculations using the VASP density functional theory code and PHONON lattice dynamics code. Application of this model to fission energy deposition in uranium dioxide predicts ion track formation and fission enhanced atomic mobility behavior within reasonable agreement of experimental trends. Furthermore, simulations of fission fragment interactions with latent ion tracks demonstrate an annealing effect due to this enhanced mobility.

Vibrational Modes and Terahertz Phenomena of the Large-Cage Zeolitic Imidazolate Framework-71.

The zeolitic imidazole framework ZIF-71 has the potential to outperform other well-studied metal–organic frameworks due to its intrinsic hydrophobicity and relatively large pore size. However, a detailed description of its complex physical phenomena and structural dynamics has been lacking thus far. Herein, we report the complete assignment of the vibrational modes of ZIF-71 using high-resolution inelastic neutron scattering measurements and synchrotron radiation infrared spectroscopy, corroborated by density functional theory (DFT) calculations. With its 816 atoms per unit cell, ZIF-71 is the largest system yet for which frequency calculations have been accomplished employing the CRYSTAL17 DFT code. We discover low-energy terahertz dynamics such as gate-opening and shearing modes that are central to the functions and stability of the ZIF-71 framework structure. Nanoscale analytical methods based on atomic force microscopy (near-field infrared spectroscopy and AFM nanoindentation) further unravel the local chemical and mechanical properties of ZIF-71 single crystals.

Ab-Initio Investigation of Finite Size Effects in Rutile Titania Nanoparticles with Semilocal and Nonlocal Density Functionals

In this work, we employ hybrid and generalized gradient approximation (GGA) level density functional theory (DFT) calculations to investigate the convergence of surface properties and the electronic gap of rutile titania (TiO2) nanoparticles with particle size. The surface energies and electronic gaps are calculated for cuboidal particles with minimum dimension ranging from 3.7 Å (24 atoms) to 10.3 Å (384 atoms) using a highly parallel real-space DFT code to enable hybrid-level DFT calculations of larger nanoparticles than are typically practical. We deconvolute the geometric and electronic finite size effects in surface energy and evaluate the influence of defects on the electronic gap and density of states (DOS). The electronic finite size effects in surface energy vanish when the minimum length scale of the nanoparticles becomes greater than 10 Å. We show that this length scale is consistent with a computationally efficient numerical analysis of the characteristic length scale of electronic interactions. The surface energy of nanoparticles having a minimum dimension beyond this characteristic length can be approximated using slab calculations that account for the geometric defects. In contrast, the finite size effects on the electronic gap and DOS are highly dependent on the shape and size of these particles. The DOS for cuboidal particles and more realistic particles constructed using the Wulff algorithm reveal that defect states within the electronic gap play a key role in determining the eigenvalue distribution of nanoparticles and the electronic gap does not converge to the bulk limit for the particle sizes investigated.

Complex band structure with non-orthogonal basis set: analytical properties and implementation in the SIESTA code

The complex band structure (CBS), although not directly observable, determines many properties of a material where the periodicity is broken, such at surfaces, interfaces and defects. Furthermore, its knowledge helps in the interpretation of electronic transport calculations and in the study of topological materials. Here we extend the transfer matrix method, often used to compute the complex bands, to electronic structures constructed using an atomic non-orthogonal basis set. We demonstrate that when the overlap matrix is not the identity, the non-orthogonal case, spurious features appear in the analytic continuation of the band structure to the complex plane. The properties of these are studied both numerically and analytically and discussed in the context of existing literature. Finally, a numerical implementation to extract the CBS from periodic calculations carried out with the density functional theory code siesta is presented. This is constructed as a simple post-processing tool, and it is therefore amenable to high-throughput studies of insulators and semiconductors.

ReaxFF Force Field Development and Application for Toluene Adsorption on MnMOx (M = Cu, Fe, Ni) Catalysts.

In numerous studies, the application of the molecular dynamics scheme based on the reactive force field (ReaxFF) method has been proven effective in modeling the catalytic behavior of metal–organic compounds. Recently, this method has been successfully applied for MxOy (M = Cu, Fe, Mn, Ni) transition-metal oxides. Yet, bimetallic metal oxides of the type MnMOx (M = Cu, Fe, Ni) were also present in the experimental system but could not be modeled since not all of the force field parameters were available at the time. To bridge this gap, the force field for modeling bimetallic metal oxides had to be developed. Here, we establish the needed force field parameter sets (namely, Cu/Mn/O, Fe/Mn/O, and Ni/Mn/O) and apply them to the problem of toluene adsorption on bimetallic oxide catalyst surfaces to verify their validity. Each training set consisted of at least 10 crystal structures containing at least Cu–Mn–O, Fe–Mn–O, or Ni–Mn–O atoms in contact obtained from the available structure databases. The parameter training has been done using the in-home-compiled version of the ReaxFF code. After training the force fields for geometry reproduction, the parameters were refined using the optimization by atom charges, comparing the ReaxFF values to those obtained for the respective structures using periodic crystal density functional theory (DFT) codes. The as-developed force fields were then applied to the process of toluene adsorption/degradation on MnMOx catalysts. Results obtained show agreement with previous experimental expectations, although some remarks are given since the initially presumed crystal structure of bimetallic oxide Mn1–xMxOy crystallites may still have an impact on theoretical predictions. The presented are, to the best of the authors’ knowledge, the first applications of the ReaxFF approach to the Mn–(Cu|Fe|Ni)–O–C–H interaction.

Coupling of photoactive transition metal complexes to a functional polymer matrix*.

Conductive polymers represent a promising alternative to semiconducting oxide electrodes typically used in dye‐sensitized cathodes as they more easily allow a tuning of the physicochemical properties. This can then also be very beneficial for using them in light‐driven catalysis. In this computational study, we address the coupling of Ru‐based photosensitizers to a polymer matrix by combining two different first‐principles electronic structure approaches. We use a periodic density functional theory code to properly account for the delocalized nature of the electronic states in the polymer. These ground state investigations are complemented by time‐dependent density functional theory simulations to assess the Franck‐Condon photophysics of the present photoactive hybrid material based on a molecular model system. Our results are consistent with recent experimental observations and allow to elucidate the light‐driven redox chemical processes – eventually leading to charge separation – in the present functional hybrid systems with potential application as photocathode materials.

IrRep: Symmetry eigenvalues and irreducible representations of ab initio band structures

We present IrRep – a Python code that calculates the symmetry eigenvalues of electronic Bloch states in crystalline solids and the irreducible representations under which they transform. As input it receives bandstructures computed with state-of-the-art Density Functional Theory codes such as VASP, Quantum Espresso, or Abinit, as well as any other code that has an interface to Wannier90. Our code is applicable to materials in any of the 230 space groups and double groups preserving time-reversal symmetry with or without spin-orbit coupling included, for primitive or conventional unit cells. This makes IrRep a powerful tool to systematically analyze the connectivity and topological classification of bands, as well as to detect insulators with non-trivial topology, following the Topological Quantum Chemistry formalism: IrRep can generate the input files needed to calculate the (physical) elementary band representations and the symmetry-based indicators using the ▪ routine of the Bilbao Crystallographic Server. It is also particularly suitable for interfaces with other plane-waves based codes, due to its flexible structure. Program summaryProgram Title:IrRepCPC Library link to program files::https://doi.org/10.17632/yznd2ky9r6.1Developer's repository link:https://github.com/stepan-tsirkin/irrepLicensing provisions: GPLv3Programming language: PythonNature of problem: Symmetry properties of electronic band structures in solids are tightly related to their topological features. This relation is set mathematically by the formalisms of Topological Quantum Chemistry [1,2] and symmetry-based indicators of topology [3], but their application requires knowledge of the irreducible representations of the bands. Therefore, a code to calculate irreducible representations of ab initio bands is essential for a systematic theoretical search and classification of topological materials.Solution method:IrRep reads wave functions from files generated by VASP, Abinit, or Quantum Espresso (also files written as input for Wannier90), determines the space group and symmetry operations via the spglib library, evaluates the eigenvalues of the symmetry operations for the selected bands, and applies Group Theory to determine their irreducible representations.

PyPhotonics: A python package for the evaluation of luminescence properties of defects

The prediction of the photoluminescence line-shape of defect systems from first principles is becoming an important tool for the discovery of quantum emission defects in semiconductors. Using a sequence of density functional theory calculations based on the VASP code, PyPhotonics calculates the Huang-Rhys factor and plots the photoluminescence line-shape of the defect by processing the VASP output. Program summaryProgram title: PyPhotonicsCPC Library link to program files:https://doi.org/10.17632/vy4ccz4hxz.1Developer's repository link:https://github.com/sheriftawfikabbas/pyphotonicsLicensing provisions: GNU General Public License 3Programming language: Python 3.9Nature of problem: While density functional theory (DFT) codes can calculate properties of crystal defects, there are no available codes to calculate the photoluminescence line-shape and the Huang-Rhys factors for the defects computed using DFT.Solution method: The PyPhotonics python code is a post-processing library written entirely in python, which takes as input the output files of the VASP and phonopy codes for a defect system, and calculates the Huang-Rhys factor and the PL lineshapes for that system.

Surface Corrugations and Layer Thickness Dependent Frictional Behavior of MoS2 – A Computational Study

2D materials are at the core of nano/micro-electro-mechanical systems (MEMS/NEMS). However, surface corrugations are unavoidable in 2D materials because of operational inefficiencies involved in the synthesis procedures. Engineering the mechanical properties of the 2D materials are highly sought-after because they are the driving mechanism behind the nanodevices' functionality. So far, most related works focus on single planar 2D materials, i.e., Graphene. The existing Transient Metal Dichalcogenide (TMD) analyses do not include torque implications on the frictional force and multiple different variables simultaneously. In this work, we have combined the two aspects, i.e., surface irregularities with the need for tuning the mechanical properties. We have studied tuning the frictional properties of Molybdenum Disulfide (MoS2) by reactive molecular dynamics (rMD) modeling, which is further analyzed by density functional theory (DFT) code. We analyzed BADER charge and molecular orbitals by DFT code. The MoS2 layer(s) are indented by using an in-built library in Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to obtain different conformations of the system. We considered multiple cases, i.e., varying number of the layers (1-3), the number of dents (2-8), the radius of each dent (12-24 Å), and the pattern of the dents (in-line and zigzag). Next, we performed MD simulations to pass a hemispherical diamond probe across the indented surface to measure all spatial components of the reactional force and torque experienced by the probe during its movement. The probe is modeled by spring support on six axes to stabilize the movement. In total, 16 different systems are studied with different combinations of the dent's radius, pattern, quantity, and the number of layers. We hypothesize the frictional force experienced by the probe is affected by the materials’ geometry, both adjacent to and along the line of contact. Our torque plots validate our hypothesis. The major fluctuations in torque plots correlate with the fluctuations in force plots after neglecting the data noise. Our approach is useful for any other 2D materials. Our results provide insight into the characterization of the frictional dependence on locale surface corrugations.

Ab initio calculations of structural, electronic, magnetic and thermoelectric properties of Cr 1-x Al x P

ABSTRACT In the present study, the structural, electronic, magnetic and thermo electric (TE) properties of ) have been performed using first principle calculations based on the density functional theory (DFT) and BoltzTraP code. The obtained results show that is ferromagnetic with a lattice constant of 5.41 Å and the magnetic moment of equal 3µB. Density of states (DOS) of show a metallic behavior for , half metallic for , and semiconductor for . The TE properties such as Seebeck coefficient, electrical conductivity, electronic thermal conductivity, power factor, figure of merit and electronic specific heat are calculated. Negative values of Seebeck coefficient indicate that are n-type carriers. The obtained results show that doping of with has a great influence on the thermoelectric properties.

The application and development of the first principles calculation in nonlinear optical materials

<p indent=0mm>Nonlinear optical (NLO) crystals need to meet multiple criteria, so it is a challenging and time-consuming task to find new NLO materials. The computational method that based on first-principles can screen out materials from a large number of materials by predicting their properties. In addition, the NLO-active groups of the materials can be identified by studying the “composition-structure-properties” relationship, which provides guidance for the synthesis of new materials. This paper summarizes the role and recent cases of computational materials in the discovery of new NLO materials. The first-principles high-throughput screening pipeline system for nonlinear optical materials (FHSP-NLO) is introduced emphatically. The system combines density functional theory (DFT) codes, linear and nonlinear optical property calculation codes, and data transformation and extraction codes, and can be automatically run to calculate and analyze a large number of materials at once. It has been successfully applied in systems including borates, germanates and nitride silicates, which provide a powerful and effective tool for searching new NLO materials.

Quantitative assessment of the role of spin fluctuations in 2D Ising superconductor NbSe2

Accurate determination of the full momentum-dependent spin susceptibility χ(q) is very important for the description of magnetism and superconductivity. While in principle the formalism for calculating χ(q) in the linear response density functional theory (DFT) is well established, hardly any publicly available code includes this capability. Here, we describe an alternative way to calculate the static χ(q), which can be applied to most common DFT codes without additional programming. The method combines standard fixed-spin-moment calculations of χ(0) with direct calculations of the energy of spin spirals stabilized by an artificial Hubbard interaction. From these calculations, χDFT(q) can be extracted by inverting the RPA formula. We apply this recipe to the recently discovered Ising superconductivity in NbSe2 monolayer, one of the most exciting findings in superconductivity in recent years. It was proposed that spin fluctuations may strongly affect the parity of the order parameter. Previous estimates suggested proximity to ferromagnetism, i.e., χ(q) peaked at q=0. We find that the structure of spin fluctuations is more complicated, with the fluctuation spectrum sharply peaked at q≈(0.2,0). Such a spectrum would change the interband pairing interaction and considerably affect the superconducting state.

광전자소자로 이용가능한 나노구조 poly(4-phenylenediamine-co-2-aminophenol) 박막의 제조 및 분석

The dependence of structural and optical characteristics on the thermal annealing of a doped poly(4-phenylenediamine-co-2-aminophenol) nanostructured thin film [P4D2AP]<SUP>TF</SUP> as a doped polymer conductor nanostructured thin film was studied. [P4D2AP]<SUP>TF</SUP> was fabricated as a thin film (100 ± 2 ㎚) using the spin coating method. Various characterization methods for [P4A2AP]<SUP>TF</SUP> like Fourier-transform infrared spectroscopy (FTIR), ultraviolet-visible spectroscopic (UV-Vis), thermogravimetric analysis (TGA), and optical characteristics have been studied. The resulted X-ray diffraction (XRD) and scanning electron microscope (SEM) data have been employed to study interface composites. Density functional theory (DFT) was used for optimization by atomic orbital DFT code (DMol³) and Cambridge serial total energy package (CASTEP). Spectroscopic and structural characteristics for the thin film have confirmed the chemical composition and XRD observations revealed the same crystal structure. The fabricated film was annealed in the air for 1h at 100 and 200 ℃. XRD examination of [P4D2AP]<SUP>TF</SUP> displayed that symmetry is an orthorhombic with a space group (P<SUB>mcn</SUB>). The optical characteristics demonstrated that the thin film has a relatively high absorbance of 95%. The calculated energy gaps are 2.523 eV and 2.504 eV for DFT and experimental, respectively. In addition, the optoelectrical parameters of the film have been calculated for absorption index (k(λ)), refractive index (n(λ)), dielectric constant, and optical conductivity. CASTEP simulated values are consistent with the experimental values for optical parameters of [P4A2AP]<SUP>TF</SUP>. The findings of the structural and optical characteristics described the fabricated thin film can be utilized as a candidate material for optoelectronic devices and solar cells.

Effectiveness of smearing and tetrahedron methods: best practices in DFT codes

Density functional theory (DFT) codes are commonly treated as a ‘black box’ in high-throughput screening of materials, with users opting for the default values of the input parameters. Often, non-experts may not sufficiently consider the effect of these parameters on prediction quality. In this work, we attempt to identify a robust set of parameters related to smearing and tetrahedron methods that return numerically accurate and efficient results for a wide variety of metallic systems. The effects of smearing and tetrahedron methods on the total energy, number of self-consistent field cycles, and forces on atoms are studied in two popular DFT codes: the Vienna ab initio Simulation Package and Quantum Espresso. From nearly 40 000 computations, it is apparent that the optimal smearing depends on the system, smearing method, smearing parameter, and k-point density. The benefit of smearing is a minor reduction in the number of self-consistent field cycles, which is independent of the smearing method or parameter. A large smearing parameter—what is considered large is system dependent—leads to inaccurate total energies and forces. Blöchl’s tetrahedron method leads to small improvements in total energies. When treating diverse systems with the same input parameters, we suggest using as little smearing as possible due to the system dependence of smearing and the risk of selecting a parameter that gives inaccurate energies and forces.

MechElastic: A Python library for analysis of mechanical and elastic properties of bulk and 2D materials

The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix (Cij) obtained from any ab-initio density-functional theory (DFT) code. The current version of this package reads the output of VASP, ABINIT, and Quantum Espresso codes (but it can be easily generalized to any other DFT code) and performs the appropriate post-processing of elastic constants as per the requirement of the user. This program can also detect the input structure's crystal symmetry and test the mechanical stability of all crystal classes using the Born-Huang criteria. Various useful material-specific properties such as elastic moduli, longitudinal and transverse elastic wave velocities, Debye temperature, elastic anisotropy, 2D layer modulus, hardness, Pugh's ratio, Cauchy's pressure, Kleinman's parameter, and Lame's coefficients, can be estimated using this program. Another existing feature of this program is to employ the ELATE package (2016) [29] and plot the spatial variation of several elastic properties such as Poisson's ratio, linear compressibility, shear modulus, and Young's modulus in three dimensions. Further, the MechElastic package can plot the equation of state (EOS) curves for energy and pressure for a variety of EOS models such as Murnaghan, Birch, Birch-Murnaghan, and Vinet, by reading the inputted energy/pressure versus volume data obtained via numerical calculations or experiments. This package is particularly useful for the high-throughput analysis of elastic and mechanical properties of materials. Program summaryProgram Title:MechElasticCPC Library link to program files:https://doi.org/10.17632/y9zc7zybrm.1Developer's repository link:https://github.com/romerogroup/MechElasticLicensing provisions: GPLv3Programming language: PythonNature of problem: To automatize and simplify the analysis of elastic and mechanical properties for bulk and 2D materials, especially for high-throughput DFT calculations.Solution method: This Python program addresses the above problem by parsing the elastic coefficient matrix obtained from the first-principles DFT calculations, does the appropriate post-processing to evaluate the elastic properties, and performs the mechanical stability tests for all crystal classes using the generalized Born-Huang criteria. It can also be used to carry out the equation of state analysis to study the structural phase transitions.Additional comments:MechElastic can be downloaded using the below link: https://github.com/romerogroup/MechElasticInstallation (via PyPI): pip install mechelastic, or pip3 install mechelastic

The abTEM code: transmission electron microscopy from first principles.

Simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret experimental data. Since nuclear cores dominate electron scattering, the scattering potential is typically described using the independent atom model, which completely neglects valence bonding and its effect on the transmitting electrons. As instrumentation has advanced, new measurements have revealed subtle details of the scattering potential that were previously not accessible to experiment. We have created an open-source simulation code designed to meet these demands by integrating the ability to calculate the potential via density functional theory (DFT) with a flexible modular software design. abTEM can simulate most standard imaging modes and incorporates the latest algorithmic developments. The development of new techniques requires a program that is accessible to domain experts without extensive programming experience. abTEM is written purely in Python and designed for easy modification and extension. The effective use of modern open-source libraries makes the performance of abTEM highly competitive with existing optimized codes on both CPUs and GPUs and allows us to leverage an extensive ecosystem of libraries, such as the Atomic Simulation Environment and the DFT code GPAW. abTEM is designed to work in an interactive Python notebook, creating a seamless and reproducible workflow from defining an atomic structure, calculating molecular dynamics (MD) and electrostatic potentials, to the analysis of results, all in a single, easy-to-read document. This article provides ongoing documentation of abTEM development. In this first version, we show use cases for hexagonal boron nitride, where valence bonding can be detected, a 4D-STEM simulation of molybdenum disulfide including ptychographic phase reconstruction, a comparison of MD and frozen phonon modeling for convergent-beam electron diffraction of a 2.6-million-atom silicon system, and a performance comparison of our fastimplementation of thePRISM algorithm for a decahedral 20000-atom gold nanoparticle.