HTEM: High-throughput toolkit for elasticity modeling

IF 3.4 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer Physics Communications Pub Date : 2025-08-13 DOI:10.1016/j.cpc.2025.109814

Zhen Yang , Jiawei Xian , Yuanji Xu , De-Ye Lin , Qingchun Wang , Xingyu Gao , Fuyang Tian , Haifeng Song

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引用次数: 0

Abstract

Elasticity under varying temperatures and pressures is particularly significant for understanding mechanical properties and structural phase transitions. Consequently, there is an increasing demand for tools capable of determining elasticity across wide temperature and pressure ranges, either numerically or analytically. In this work, we propose HTEM, a comprehensive toolkit that automates input generation workflow, elastic calculations, modeling, and visualization within an integrated framework to solve the demand for elasticity across wide temperature and pressure ranges. HTEM performs simulations with four computational modes, allowing users to balance accuracy and efficiency. It incorporates a semi-analytic model for robust, high-precision elastic modeling with finite data combinations, even using sparse elasticity at high temperatures. To validate the algorithm and workflows for calculation and modeling, we performed HTEM to study the elasticity of Si across wide temperature and pressure ranges. The results show the high precision and high efficiency of HTEM. And modeling mitigates noise from constant pressure ensemble simulations. Furthermore, HTEM provides detailed visualizations of the elasticity and anisotropy as functions of temperature and pressure, providing a comprehensive insight into how the intrinsic properties of materials evolve under varying conditions.

Program summary

Program title: HTEM

CPC Library link to program files: https://doi.org/10.17632/8sfnsdvxyn.1

Licensing provisions: GNU General Public License 3

Programming language: Python 3.X (version > 3.7)

External routines/libraries: Numpy, Scipy, Matplotlib, Ase, Spglib, Imageio

Nature of problem: Through the coupling of toolkit with the first-principle approaches, the temperature and pressure dependent second-order elastic stiffness coefficients (SOESC) and elastic moduli of solid materials can be calculated and modeled with less cost, and the change of elastic and mechanical properties can be dynamically visualized with temperature and pressure.

Solution method: HTEM contains four simulation modes to obtain elasticity with high-throughput. The cold and QSA modes are based on VASP's ab

i n i t i o

calculations. NVT and NPT modes correspond to VASP's ab

i n i t i o

molecular dynamics (AIMD) simulations. Here, the cold mode is for zero-temperature calculations, while the QSA, NVT, and NPT modes are used to calculate the finite-temperature elasticity. This program is versatile for calculating SOESCs at various temperatures and pressures. In addition to the calculated SOESCs and elastic moduli based on ab

i n i t i o

calculations and AIMD simulations, we integrated the semi-analytic model, which allows us to efficiently estimate the elastic properties across a wide temperature and pressure range based on finite calculations or experimental measurements. Beyond basic elastic moduli, HTEM has advanced visualization capabilities and computes additional critical properties such as the Debye temperature and sound velocity. HTEM is a comprehensive toolkit for accelerated material design and modeling, especially for extreme conditions, and advanced visualization, offering both efficiency and depth in material property analysis.

Additional comments including restrictions and unusual features: HTEM is currently integrated with the Vienna Ab initio Simulation Package (VASP).

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HTEM：用于弹性建模的高吞吐量工具包

在不同温度和压力下的弹性对于理解机械性能和结构相变尤为重要。因此，对于能够在较宽的温度和压力范围内确定弹性的工具的需求越来越大，无论是数值还是分析。在这项工作中，我们提出了HTEM，这是一个全面的工具包，可以在集成框架内自动化输入生成工作流，弹性计算，建模和可视化，以解决宽温度和压力范围内的弹性需求。HTEM执行模拟与四种计算模式，允许用户平衡精度和效率。它结合了一个半解析模型，用于鲁棒，高精度的弹性建模，具有有限的数据组合，甚至使用高温下的稀疏弹性。为了验证计算和建模的算法和工作流程，我们使用高温透射电镜研究了Si在宽温度和压力范围内的弹性。结果表明，该方法精度高，效率高。并且建模可以减轻恒压集合模拟带来的噪声。此外，HTEM还提供了弹性和各向异性随温度和压力的详细可视化，从而全面了解材料的内在特性在不同条件下是如何演变的。程序摘要程序标题：HTEMCPC库链接到程序文件：https://doi.org/10.17632/8sfnsdvxyn.1Licensing条款：GNU通用公共许可证3编程语言：Python 3。外部例程/库：Numpy， Scipy, Matplotlib, Ase, Spglib， imageionproblem的性质：通过工具箱与第一性原理方法的耦合，可以以较低的成本计算和建模固体材料的依赖于温度和压力的二阶弹性刚度系数（SOESC）和弹性模量，并可以动态可视化其弹性和力学性能随温度和压力的变化。求解方法：HTEM包含四种仿真模式，以获得高通量的弹性。冷模和QSA模是基于VASP的从头计算。NVT和NPT模式对应VASP的从头算分子动力学（AIMD）模拟。其中，冷模式用于零温度计算，而QSA、NVT和NPT模式用于计算有限温度弹性。这个程序是通用的计算在各种温度和压力下的SOESCs。除了基于从头计算和AIMD模拟计算的soesc和弹性模量外，我们还集成了半解析模型，这使我们能够基于有限的计算或实验测量有效地估计在宽温度和压力范围内的弹性特性。除了基本的弹性模量外，HTEM还具有先进的可视化功能，可以计算额外的关键特性，如Debye温度和声速。HTEM是一个全面的工具箱，用于加速材料设计和建模，特别是在极端条件下，以及先进的可视化，提供材料性能分析的效率和深度。其他评论包括限制和不寻常的功能：HTEM目前与维也纳从头算模拟包（VASP）集成。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Computer Physics Communications 物理-计算机：跨学科应用

CiteScore

12.10

自引率

3.20%

发文量

287

审稿时长

5.3 months

期刊介绍： The focus of CPC is on contemporary computational methods and techniques and their implementation, the effectiveness of which will normally be evidenced by the author(s) within the context of a substantive problem in physics. Within this setting CPC publishes two types of paper. Computer Programs in Physics (CPiP) These papers describe significant computer programs to be archived in the CPC Program Library which is held in the Mendeley Data repository. The submitted software must be covered by an approved open source licence. Papers and associated computer programs that address a problem of contemporary interest in physics that cannot be solved by current software are particularly encouraged. Computational Physics Papers (CP) These are research papers in, but are not limited to, the following themes across computational physics and related disciplines. mathematical and numerical methods and algorithms; computational models including those associated with the design, control and analysis of experiments; and algebraic computation. Each will normally include software implementation and performance details. The software implementation should, ideally, be available via GitHub, Zenodo or an institutional repository.In addition, research papers on the impact of advanced computer architecture and special purpose computers on computing in the physical sciences and software topics related to, and of importance in, the physical sciences may be considered.