pyHMA: A VASP post-processor for precise measurement of crystalline anharmonic properties using harmonically mapped averaging
pyHMA: A VASP post-processor for precise measurement of crystalline anharmonic properties using harmonically mapped averaging
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pyHMA：VASP 后处理器，用于使用谐波映射平均来精确测量晶体非谐波特性
DOI：
10.1016/j.cpc.2020.107554
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发表时间：
2021
影响因子：
6.3
通讯作者：
Kofke, David A.
中科院分区：
文献类型：
--
作者：
Moustafa, Sabry G.;Purohit, Apoorva;Schultz, Andrew J.;Kofke, David A.
我们介绍了一个新的Python包(PyHMA)，它与Vasp接口，通过对NVT Born-Oppenheimer从头算分子动力学(AIMD)模拟的数据进行后处理，计算晶体系统的(经典)非谐性质。它基于最近开发的调和映射平均(HMA)方法，该方法利用解析上已知的调和行为来重新表示直接/传统集成平均，以便在给定的CPU时间内显著提高精度。该程序包包括两个阶段：从Vasprun读取AIMD数据。XML文件(S)，然后计算非谐性质。虽然第一阶段依赖于MD包，但第二阶段是通用的，因为它以所需的格式接收数据。为了说明高温高压的应用，我们计算了铝面心立方晶体在高压(≈115 Gpa)和高达4000K(近熔化)下的非简谐能量和压力。利用HMA非简谐能量的热力学积分，进一步计算了非简谐自由能随温度的变化。尽管PYHMA目前与VASP对接以计算HMA非谐能量和压力，但它以这样的方式被模块化以允许通过添加新的读取器与其他代码(例如LAMMPS)对接，并且一旦相关数据可用，可以通过添加新的方法来计算其他HMA非谐属性(例如热容)。计划摘要计划标题：PYHMA CPC库程序文件链接：http://dx.多伊。Org/10.17632/bzgfk52msk。1许可条款：MPL-2.0编程语言：PYTHON 3.7问题的性质：晶体系统的理论动力学属性(例如，能量、压力和热容)可分解为：晶格(或，在0K时的属性)、准谐贡献和非谐贡献。虽然前两者只用几个单点密度泛函理论(DFT)计算是可行的，但测量非谐贡献需要进行从头计算分子动力学(AIMD)模拟，这在计算上要求非常高的直接系综平均。解决方法：在PYHMA中，我们采用调和映射平均(HMA)技术，与直接/传统(CONV)平均相比，该技术提供数量级(S)更高的精度。该程序包作为VASP AIMD输出的后处理器，为给定的DFT模型提供非常精确(和准确)的非谐波特性估计，并应用于能量和压力(此时)。补充说明：在文献中，术语非谐性通常用来定性地描述在0K(即虚频率)没有平衡构型的系统；换句话说，它指的是“非谐”势能面。然而，在这里，我们将某些性质X的非谐贡献定义为超过调和近似的残余量；X ah≡X−(Xlat+Xqh)。因此，如果系统在0K没有平衡晶格构型，那么这个特定的定义是没有意义的。为此，pyHMA检查第一个构型上的力，以确保系统具有平衡构型(即零力)。此外，当使用PYHMA测量非简谐自由能时，使用热力学积分从0K(SEC。3.3)，只能使用基态DFT；使用有限温度DFT(即费米-狄拉克涂抹；ISMEAR=-1和Sigma=k B T)不能使用，因为在这种情况下PES是温度相关的，这不在积分中考虑。然而，这种贡献仍然可以使用其他地方描述的自由能微扰方法[1]来考虑。另一方面，…
We introduce a new Python package (pyHMA) that interfaces with VASP to compute (classical) anharmonic properties of crystalline systems by post-processing data from NVT Born–Oppenheimer ab initio molecular dynamics (AIMD) simulation. It is based on the recently developed harmonically mapped averaging (HMA) method, which leverages the analytically known harmonic behavior to reformulate the direct/conventional ensemble averages in order to significantly improve precision, for a given CPU time. The package consists of two stages: reading AIMD data from vasprun. xml file (s) and then computing anharmonic properties. While the first stage is MD package-dependent, the second one is universal, given that it receives data in the required format. To demonstrate the usage of pyHMA, we compute anharmonic energy and pressure of aluminum fcc crystal at high pressure (≈ 115 GPa) and up to 4000 K (near melting). We further compute anharmonic free energy as a function of temperature, using thermodynamic integration of the HMA anharmonic energy. Although pyHMA currently interfaces with VASP to compute HMA anharmonic energy and pressure, it is moduled in such a way to allow for interfacing with other codes (eg, LAMMPS) by adding a new reader and can compute other HMA anharmonic properties (eg, heat capacity) by adding a new method, once relevant data are available. Program summary Program title: pyHMA CPC Library link to program files: http://dx. doi. org/10.17632/bzgfk52msk. 1 Licensing provisions: MPL-2.0 Programming language: Python 3.7 Nature of problem: Theormodynamic properties (eg, energy, pressure, and heat capacity) of crystalline systems can be decomposed into: lattice (or, property at 0 K), quasiharmonic, and anharmonic contributions. Although the first two are feasible to compute using only a few single-point density functional theory (DFT) calculations, measuring anharmonic contribution requires running ab initio molecular dynamics (AIMD) simulation, which is computationally very demanding using direct ensemble averaging. Solution method: In pyHMA, we are adopting the harmonically mapped averaging (HMA) technique that provides order (s) of magnitude higher precision, in comparison to direct/conventional (Conv) averaging. The package works as a post-processor to VASP AIMD output to provide very precise (and accurate) estimate of anharmonic properties, for a given DFT model, with application to energy and pressure (at this time). Additional comments: The term anharmonicity is commonly used in literature to qualitatively describe a system with no equilibrium configuration at 0 K (ie, imaginary frequencies); in other words, it refers to a “non-harmonic” potential-energy surface. Here, however, we define anharmonic contribution of some property X as the residual in excess of the harmonic approximation; X ah≡ X−(X lat+ X qh). Therefore, this specific definition is meaningless if the system does not have equilibrium lattice configuration at 0 K. For this reason, pyHMA checks forces on the first configuration to make sure the system has an equilibrium configuration (ie, zero forces). In addition, when using pyHMA to measure anharmonic free energy using thermodynamic integration from 0 K (Sec. 3.3), only ground-state DFT must be used; using finite-temperature DFT (ie, Fermi–Dirac smearing; ISMEAR=-1 and SIGMA= k B T), as often done with metals, cannot be used as the PES in this case is temperature-dependent, which is not accounted for in the integration. This contribution, however, can still be included using free-energy perturbation methods as described elsewhere [1]. On the other hand …
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DOI：
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发表时间：
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影响因子：
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