MEAMfit: A reference-free modified embedded atom method (RF-MEAM) energy and force-fitting code

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• 作者：Andrew Ian Duff ^{andrew.duff@imperial.ac.uk" class="auth_mail" title="E-mail the corresponding author}
• 关键词：Interatomic potential ; Fitting ; Lattice vibrations
• 刊名：Computer Physics Communications
• 出版年：2016
• 出版时间：June 2016
• 年：2016
• 卷：203
• 期：Complete
• 页码：354-355
• 全文大小：294 K

文摘

MEAMfit v1.02. Changes: various bug fixes; speed of single-shot energy and force calculations (not optimization) increased by class="mathmlsrc">class="formulatext stixSupport mathImg" data-mathURL="/science?_ob=MathURL&_method=retrieve&_eid=1-s2.0-S0010465516300303&_mathId=si1.gif&_user=111111111&_pii=S0010465516300303&_rdoc=1&_issn=00104655&md5=67efc70eda5ae3e7168d003c1f6e5aed" title="Click to view the MathML source">×10class="mathContainer hidden">class="mathCode">$\times 10$; elements up to Cn (class="mathmlsrc">class="formulatext stixSupport mathImg" data-mathURL="/science?_ob=MathURL&_method=retrieve&_eid=1-s2.0-S0010465516300303&_mathId=si2.gif&_user=111111111&_pii=S0010465516300303&_rdoc=1&_issn=00104655&md5=508093a13b80ac7a556691584b0d528c" title="Click to view the MathML source">Z=112class="mathContainer hidden">class="mathCode">$Z=112$) now correctly read from vasprun.xml files; EAM fits now produce Camelion output files; changed max number of vasprun.xml files to 10,000 (an unnecessary lower limit of 10 was allowed in the previous version).

New version program summary

Program title: MEAMfit

Catalogue identifier: AEWY_v1_1

Program summary URL:class="interref" data-locatorType="url" data-locatorKey="http://cpc.cs.qub.ac.uk/summaries/AEWY_v1_1.html">http://cpc.cs.qub.ac.uk/summaries/AEWY_v1_1.html

Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland

Licensing provisions: BSD 2-Clause License

No. of lines in distributed program, including test data, etc.: 5202334

No. of bytes in distributed program, including test data, etc.: 66637698

Distribution format: tar.gz

Programming language: Fortran.

Computer: Linux based workstations.

Operating system: Linux.

RAM: 120 MB

Classification: 16.1.

Catalogue identifier of previous version: AEWY_v1_0

Journal reference of previous version: Comput. Phys. Comm. 196 (2015) 439

External routines: TOMS611 Unconstrained Minimization [1] included in the MEAMfit code.

Does the new version supersede the previous version?: Yes

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.

Reasons for new version: Bugs fixed; improvements made.

Summary of revisions:   Various bug fixes; speed of single-shot energy and force calculations (not optimization) increased by class="mathmlsrc">class="formulatext stixSupport mathImg" data-mathURL="/science?_ob=MathURL&_method=retrieve&_eid=1-s2.0-S0010465516300303&_mathId=si1.gif&_user=111111111&_pii=S0010465516300303&_rdoc=1&_issn=00104655&md5=67efc70eda5ae3e7168d003c1f6e5aed" title="Click to view the MathML source">×10class="mathContainer hidden">class="mathCode">$\times 10$; elements up to Cn (class="mathmlsrc">class="formulatext stixSupport mathImg" data-mathURL="/science?_ob=MathURL&_method=retrieve&_eid=1-s2.0-S0010465516300303&_mathId=si2.gif&_user=111111111&_pii=S0010465516300303&_rdoc=1&_issn=00104655&md5=508093a13b80ac7a556691584b0d528c" title="Click to view the MathML source">Z=112class="mathContainer hidden">class="mathCode">$Z=112$) now correctly read from vasprun.xml files; EAM fits now produce Camelion output files; changed max number of vasprun.xml files to 10,000 (an unnecessary lower limit of 10 was allowed in the previous version).

Additional comments:

User manual provided.

!!!!! The distribution file for this program is over 65 MB 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 class="mathmlsrc">class="formulatext stixSupport mathImg" data-mathURL="/science?_ob=MathURL&_method=retrieve&_eid=1-s2.0-S0010465516300303&_mathId=si5.gif&_user=111111111&_pii=S0010465516300303&_rdoc=1&_issn=00104655&md5=221209041df49292aad6e1870b6f9a16" title="Click to view the MathML source">R=12%–13%class="mathContainer hidden">class="mathCode">$R=12\%\text{–}13\%$ (see Equation. 9 in main-text for definition). To ensure a maximally optimized potential however (class="mathmlsrc">class="formulatext stixSupport mathImg" data-mathURL="/science?_ob=MathURL&_method=retrieve&_eid=1-s2.0-S0010465516300303&_mathId=si6.gif&_user=111111111&_pii=S0010465516300303&_rdoc=1&_issn=00104655&md5=2b62c43dc124597aa9bf1a0646aaf8ec" title="Click to view the MathML source">R=12%class="mathContainer hidden">class="mathCode">$R=12\%$), a run-time of 24 h is recommended. To optimize a RF-MEAM potential, a further 24 h 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:

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J. E. Dennis, D. Gay and R. E. Welsch, ACM Trans. on Math. Soft., 7 (1981) 348–368.

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M. I. Baskes, Materials Science and Engineering A, 261 (1999), 165.

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M. Timonova and B. J. Thijsse, Modelling Simul. Mater. Sci. Eng., 19 (2011) 015003

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G. Kresse, J. Hafner, Phys. Rev. B 47 (1993) 558.

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G. Kresse, J. Hafner, Phys. Rev. B 49 (1994) 14251.

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G. Kresse, J. Furthmüller, Comput. Mat. Sci. 6 (1996) 15.

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G. Kresse, J. Furthmüller, Phys. Rev. B 54 (1996) 11169.

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S. Plimpton, J. Comp. Phys. 117 (1995)

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http//://tinyurl.com/camelion11-53