High-throughput $ab$ $initio$ calculations are the indispensable parts of data-driven discovery of new materials with desirable properties, as reflected in the establishment of several online material databases. The accumulation of extensive theoretical data through computations enables data-driven discovery by constructing machine learning and artificial intelligence models to predict novel compounds and forecast their properties. Efficient usage and extraction of data from these existing online material databases can accelerate the next stage materials discovery that targets different and more advanced properties, such as electron-phonon coupling for phonon-mediated superconductivity. However, extracting data from these databases, generating tailored input files for different $ab$ $initio$ calculations, performing such calculations, and analyzing new results can be demanding tasks. Here, we introduce a software package named "HTESP" (High-Throughput Electronic Structure Package) written in Python and Bash languages, which automates the entire workflow including data extraction, input file generation, calculation submission, result collection and plotting. Our HTESP will help speed up future computational materials discovery processes.
We present M-SPARC: MATLAB-Simulation Package for Ab-initio Real-space Calculations. It can perform pseudopotential spin-polarized and unpolarized Kohn-Sham Density Functional Theory (DFT) simulations for isolated systems such as molecules as well as extended systems such as crystals, surfaces, and nanowires. M-SPARC provides a rapid prototyping platform for the development and testing of new algorithms and methods in real-space DFT, with the potential to significantly accelerate the rate of advancements in the field. It also provides a convenient avenue for the accurate first principles study…
We present SPARC: Simulation Package for Ab-initio Real-space Calculations. SPARC can perform Kohn-Sham density functional theory calculations for isolated systems such as molecules as well as extended systems such as crystals and surfaces, in both static and dynamic settings. It is straightforward to install/use and highly competitive with state-of-the-art planewave codes, demonstrating comparable performance on a small number of processors and increasing advantages as the number of processors grows. Notably, SPARC brings solution times down to a few seconds for systems with $\mathcal{O}(100-…
We develop a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts, water-based fluids, various supercritical fluids. The package is a collection of Python scripts that include two major libraries dealing with file formats and with crystallography. All the scripts are run at the command line. We propose a simplified format to store the atomic trajectories and relevant thermodynamic information of the simulations, which is saved in UMD…
Perturbo is a software package for first-principles calculations of charge transport and ultrafast carrier dynamics in materials. The current version focuses on electron-phonon interactions and can compute phonon-limited transport properties such as the conductivity, carrier mobility and Seebeck coefficient. It can also simulate the ultrafast nonequilibrium electron dynamics in the presence of electron-phonon scattering. Perturbo uses results from density functional theory and density functional perturbation theory calculations as input, and employs Wannier interpolation to reduce the computat…
QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between differ…
FHI-aims is a quantum mechanics software package based on numeric atom-centered orbitals (NAOs) with broad capabilities for all-electron electronic-structure calculations and ab initio molecular dynamics. It also connects to workflows for multi-scale and artificial intelligence modeling.
We discuss how to include our recently proposed thermopotentiostat technique [Phys. Rev. Lett. 126, 136803 (2021)] into any existing ab initio molecular dynamics (AIMD) package. Using thermopotentiostat AIMD simulations in the canonical NVTΦ ensemble at constant electrode potential, we compute the polarization bound charge and dielectric response of interfacial water from first principles.
This work provides the community with an easily executable open-source Python package designed to automize the evaluation of Interfacial Phonons (InterPhon). Its strategy of arbitrarily defining the interfacial region and periodicity alleviates the excessive computational cost in applying ab initio phonon calculations to interfaces and enables efficient extraction of interfacial phonons. InterPhon makes it possible to apply all of the phonon-based predictions that have been available for bulk systems, to interfacial systems. The first example, in which this package was applied to InAs surfaces…
This paper describes some applications of GPU acceleration in ab initio nuclear structure calculations. Specifically, we discuss GPU acceleration of the software package MFDn, a parallel nuclear structure eigensolver. We modify the matrix construction stage to run partly on the GPU. On the Titan supercomputer at the Oak Ridge Leadership Computing Facility, this produces a speedup of approximately 2.2x - 2.7x for the matrix construction stage and 1.2x - 1.4x for the entire run.
Hybrid density-functional calculation is one of the most commonly adopted electronic structure theory used in computational chemistry and materials science because of its balance between accuracy and computational cost. Recently, we have developed a novel scheme called NAO2GTO to achieve linear scaling (Order-N) calculations for hybrid density-functionals. In our scheme, the most time-consuming step is the calculation of the electron repulsion integrals (ERIs) part. So how to create an even distribution of these ERIs in parallel implementation is an issue of particular importance. Here, we pre…
SALMON (Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience, http://salmon-tddft.jp) is a software package for the simulation of electron dynamics and optical properties of molecules, nanostructures, and crystalline solids based on first-principles time-dependent density functional theory. The core part of the software is the real-time, real-space calculation of the electron dynamics induced in molecules and solids by an external electric field solving the time-dependent Kohn-Sham equation. Using a weak instantaneous perturbing field, linear response properties such as polariz…
The Chronus Quantum (ChronusQ) software package is an open source (under the GNU General Public License v2) software infrastructure which targets the solution of challenging problems that arise in ab initio electronic structure theory. Special emphasis is placed on the consistent treatment of time dependence and spin in the electronic wave function, as well as the inclusion of relativistic effects in said treatments. In addition, ChronusQ provides support for the inclusion of uniform finite magnetic fields as external perturbations through the use of gauge-including atomic orbitals (GIAO). Chr…
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 YR…
An existing hyperelastic membrane model for graphene calibrated from ab-initio data (Kumar and Parks, 2014) is adapted to curvilinear coordinates and extended to a rotation-free shell formulation based on isogeometric finite elements. Therefore, the membrane model is extended by a hyperelastic bending model that reflects the ab-inito data of Kudin et al. (2001). The proposed formulation can be implemented straight-forwardly into an existing finite element package, since it does not require the description of molecular interactions. It thus circumvents the use of interatomic potentials that ten…
Interpretation of vibrational inelastic neutron scattering spectra of complex systems is frequently reliant on accompanying simulations from theoretical models. Ab-initio codes can routinely generate force constants, but additional steps are required for direct comparison to experimental spectra. On modern spectrometers this is a computationally expensive task due to the large data volumes collected. In addition, workflows are frequently cumbersome as the simulation software and experimental data analysis software often do not easily interface to each other. Here a new package, Euphonic, is pr…
Jsymm: A Python package for symmetry analysis of exchange tensors in magnetic Hamiltonians
M.V. Lomonosov Moscow State University（莫斯科国立罗蒙诺索夫大学）；M.N. Mikheev Institute of Metal Physics, Ural Branch of Russian Academy of Sciences（俄罗斯科学院乌拉尔分校M.N.米凯耶夫金属物理研究所）
Titanium-based oxides are abundant, chemically stable, non-toxic, and highly versatile materials, with applications ranging from photovoltaics to catalysis. For rutile and anatase phases of Titanium dioxide (TiO2), the bandgap ranges from 3.0-3.2 eV, which are too large to absorb in the visible range (400 nm - 700 nm), resulting in poor photo-catalytic efficiency. Nitrogen doping into TiO2 has been able to narrow its bandgap, forming an absorption tail in the visible-light region. However, TiO2 has limits to which it can be doped, suggesting investigations of the oxygen-deficient Ti203. Using …
almaBTE is a software package that solves the space- and time-dependent Boltzmann transport equation for phonons, using only ab-initio calculated quantities as inputs. The program can predictively tackle phonon transport in bulk crystals and alloys, thin films, superlattices, and multiscale structures with size features in the nm-$μ$m range. Among many other quantities, the program can output thermal conductances and effective thermal conductivities, space-resolved average temperature profiles, and heat-current distributions resolved in frequency and space. Its first-principles character makes…
The CP-PAW code package for first-principles calculations from a user's perspective
Clausthal University of Technology（克劳斯塔尔工业大学）；Paderborn University（帕德博恩大学）；Lawrence Livermore National Laboratory（劳伦斯利弗莫尔国家实验室）；Georg-August University（格奥尔格-奥古斯特大学）；Helmholtz Zentrum Dresden-Rossendorf（亥姆霍兹德累斯顿-罗斯多夫中心）
The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix ($C_{ij}$) 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 u…
Module for ab initio structure evolution (MAISE) is an open-source package for materials modeling and prediction. The code's main feature is an automated generation of neural network (NN) interatomic potentials for use in global structure searches. The systematic construction of Behler-Parrinello-type NN models approximating ab initio energy and forces relies on two approaches introduced in our recent studies. An evolutionary sampling scheme for generating reference structures improves the NNs' mapping of regions visited in unconstrained searches, while a stratified training approach enables t…
TurboRVB is a computational package for {\it ab initio} Quantum Monte Carlo (QMC) simulations of both molecular and bulk electronic systems. The code implements two types of well established QMC algorithms: Variational Monte Carlo (VMC), and Diffusion Monte Carlo in its robust and efficient lattice regularized variant. A key feature of the code is the possibility of using strongly correlated many-body wave functions. The electronic wave function (WF) is obtained by applying a Jastrow factor, which takes into account dynamical correlations, to the most general mean-field ground state, written e…
The Wu-Wentzcovitch semi-analytical method (SAM) is a concise and predictive formalism to calculate the high-pressure and high-temperature (high-PT) thermoelastic tensor (Cij) of crystalline materials. This method has been successfully applied to materials across different crystal systems in conjunction with ab initio calculations of static elastic coefficients and phonon frequencies. Such results have offered first-hand insights into the composition and structure of the Earth's mantle. Here we introduce the cij package, a Python implementation of the SAM-Cij formalism. It enables a thermoelas…
CP2K: An electronic structure and molecular dynamics software package - Dynamics, Transport, and Spectroscopic Response
University of Regensburg（雷根斯堡大学）；Christian-Albrechts-University Kiel（基尔大学）；Paderborn University（帕德博恩大学）；University of Zurich（苏黎世大学）；Tata Institute of Fundamental Research（塔塔基础研究所）；Center for Advanced Systems Understanding (CASUS)（高级系统理解中心）；Helmholtz-Zentrum Dresden-Rossendorf（德累斯顿-罗斯多夫亥姆霍兹中心）
