MEAMfit: A reference-free modified embedded atom method (RF-MEAM) energy and force-fitting code
MEAMfit: A reference-free modified embedded atom method (RF-MEAM) energy and force-fitting code
复制标题
MEAMfit：无参考修改嵌入式原子方法 (RF-MEAM) 能量和力拟合代码
DOI：
10.1016/j.cpc.2015.05.016
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发表时间：
2015
影响因子：
6.3
通讯作者：
Duff A
中科院分区：
文献类型：
--
作者：
Duff A
近年来，由于密度泛函理论（DFT）的成功，材料的从头算建模已经成为常规。然而，对于材料中的许多过程，只有在考虑数百万原子时才能实现真实感。目前，如此大规模的模拟超出了从头算的能力，因此人们必须求助于有效的原子间势，以便在较小的尺度上很好地表示从头算数据。两种更广泛使用的原子间电位类型是嵌入原子法（EAM）和修饰嵌入原子法（MEAM）电位。在这里，我们提出了一个代码，可以使用从头算产生的能量和力来获得具有代表性的EAM和无参考的MEAM型有效原子间势。我们用从头计算ZrC中的热激励来说明这个代码的使用。项目摘要项目名称：MEAMfit目录标识符：AEWY_v1_0项目摘要URL: http://cpc。cs。qub。英国/摘要/ AEWY_v1_0 ac.。程序可从：北爱尔兰贝尔法斯特女王大学CPC程序库获得许可条款：标准CPC许可，http://cpc。cs。qub。英国ac. /许可证/许可证。html没有。，包括测试数据等：4467841号。分布程序中包含测试数据等的字节数：56403685分布格式：tar。程序设计语言：Fortran。计算机：基于Linux的工作站。操作系统：Linux。内存：120mb分类：16.1外部例程：TOMS611无约束最小化[1]包含在MEAMfit代码中。问题性质：拟合嵌入原子法（EAM）和无参考修正嵌入原子法（RF-MEAM）电位[2-3]与VASP产生的能量和力[4-7]。求解方法：提出了一个计算机程序，该程序使用共轭梯度最小化器与遗传算法配对，将EAM和RF-MEAM电位拟合到直接从VASP输出文件中读取的能量和/或原子力。代码产生的电位可直接用于LAMMPS[8]或Camelion[9]分子动力学包。附加说明：提供的用户手册。！！！！！该程序的分发文件超过56兆字节，因此在请求下载或电子邮件时不会直接交付。而是发送一个html文件，详细说明如何获得该程序运行时：运行时取决于所要求的最终电位的准确度水平。对于适合670能量的EAM电势，在单个磁芯上运行几个小时通常足以产生R= 12%-13%的电势（定义见正文中的公式9）。然而，为了确保最大限度地优化潜力（R= 12%），建议运行时间为24小时。为了优化RF-MEAM的潜力，应该再允许24小时。我们已经发现仅使用单个核心比EAM有改进，但是为了确保最大限度地优化潜力，应该并行运行多个MEAMfit实例。参考文献：[1]JE Dennis， D. Gay和RE Welsch， ACM译。在数学。柔软。科学进展，7 (1981):348-368杨建军，刘建军，刘建军，等。材料工程学报，33 (1),391 - 391M. Timonova和BJ Thijsse，建模模拟。板牙。科学。Eng。浙江农业学报，19 (2011):015003G.克雷斯，J.哈夫纳，物理学家。Rev. b47 (1993) 558. bb0G.克雷斯，J.哈夫纳，物理学家。Rev. B 49 (1994) 14251G. Kresse， J. furthm<e:1> ller，计算机。自然科学6 (1996)15G. Kresse， J. furthm<e:1> ller，物理学家。Rev. B 54 (1996) 11169林普林顿，J. Comp.物理，117(1995)1-19。[9] http://tinyurl。com/camelion11-53。
Ab initio modeling of materials has become routine in recent years, largely due to the success of density functional theory (DFT). However, for many processes in materials, realism is achieved only when millions of atoms are considered. Currently, such large scale simulations are beyond ab initio capabilities so that one has to resort to effective interatomic potentials that well represent ab initio data on smaller scales. Two of the more widely used types of interatomic potentials are embedded atom method (EAM) and modified embedded atom method (MEAM) potentials. Here we present a code that can use ab initio generated energies and forces to obtain representative EAM and reference-free MEAM type effective interatomic potentials. We illustrate the use of this code with ab initio computed thermal excitations in ZrC. Program summary Program title: MEAMfit Catalogue identifier: AEWY_v1_0 Program summary URL: http://cpc. cs. qub. ac. uk/summaries/AEWY_v1_0. html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc. cs. qub. ac. uk/licence/licence. html No. of lines in distributed program, including test data, etc.: 4467841 No. of bytes in distributed program, including test data, etc.: 56403685 Distribution format: tar. gz Programming language: Fortran. Computer: Linux based workstations. Operating system: Linux. RAM: 120 Megabytes Classification: 16.1. External routines: TOMS611 Unconstrained Minimization [1] included in the MEAMfit code. Nature of problem: Fitting embedded atom method (EAM) and reference-free modified embedded atom method (RF-MEAM) potentials [2-3] to energies and forces produced by VASP [4-7]. Solution method: A computer program is presented which uses a conjugate-gradient minimizer paired with a genetic algorithm to fit EAM and RF-MEAM potentials to energies and/or atomic forces read directly from VASP output files. Potentials produced by the code are directly usable with the LAMMPS [8] or Camelion [9] molecular-dynamics packages. Additional comments: User manual provided.!!!!! The distribution file for this program is over 56 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent.!!!!! Running time: The run-time depends on the required level of accuracy of the final potential. For an EAM potential fit to 670 energies, a few hours on a single core is usually sufficient to produce a potential with R= 12%–13%(see Equation. 9 in main-text for definition). To ensure a maximally optimized potential however (R= 12%), a run-time of 24 hours is recommended. To optimize a RF-MEAM potential, a further 24 hours should be allowed. One will already find an improvement over the EAM using just a single core, however to ensure a maximally optimized potential, one should run several instances of MEAMfit in parallel. References:[1] JE Dennis, D. Gay and RE Welsch, ACM Trans. on Math. Soft., 7 (1981) 348-368.[2] MI Baskes, Materials Science and Engineering A, 261 (1999), 165.[3] M. Timonova and BJ Thijsse, Modelling Simul. Mater. Sci. Eng., 19 (2011) 015003.[4] G. Kresse, J. Hafner, Phys. Rev. B 47 (1993) 558.[5] G. Kresse, J. Hafner, Phys. Rev. B 49 (1994) 14251.[6] G. Kresse, J. Furthmüller, Comput. Mat. Sci. 6 (1996) 15.[7] G. Kresse, J. Furthmüller, Phys. Rev. B 54 (1996) 11169.[8] S. Plimpton, J. Comp. Phys. 117 (1995) 1–19.[9] http://tinyurl. com/camelion11-53.
影响因子：
3.7
作者：
Togo, Atsushi;Oba, Fumiyasu;Tanaka, Isao
通讯作者：
Tanaka, Isao