VASPKIT: A user-friendly interface facilitating high-throughput computing and analysis using VASP code

Elastic mechanics; Electronic properties; High-throughput; Molecular dynamics; Optical properties; Wave-function; Command line; High-throughput analysis; Input files; Interactive user interfaces; Optical-; Property; User friendly interface; Hardware and Architecture; Physics and Astronomy (all); Physics - Materials Science; General Physics and Astronomy

Abstract :

[en] We present the VASPKIT, a command-line program that aims at providing a robust and user-friendly interface to perform high-throughput analysis of a variety of material properties from the raw data produced by the VASP code. It consists of mainly the pre- and post-processing modules. The former module is designed to prepare and manipulate input files such as the necessary input files generation, symmetry analysis, supercell transformation, k-path generation for a given crystal structure. The latter module is designed to extract and analyze the raw data about elastic mechanics, electronic structure, charge density, electrostatic potential, linear optical coefficients, wave function plots in real space, etc. This program can run conveniently in either interactive user interface or command line mode. The command-line options allow the user to perform high-throughput calculations together with bash scripts. This article gives an overview of the program structure and presents illustrative examples for some of its usages. The program can run on Linux, macOS, and Windows platforms. The executable versions of VASPKIT and the related examples and tutorials are available on its official website vaspkit.com. Program summary: Program title: VASPKIT CPC Library link to program files: https://doi.org/10.17632/v3bvcypg9v.1 Licensing provisions: GPLv3 Programming language: Fortran, Python Nature of problem: This program has the purpose of providing a powerful and user-friendly interface to perform high-throughput calculations together with the widely-used VASP code. Solution method: VASPKIT can extract, calculate and even plot the mechanical, electronic, optical and magnetic properties from density functional calculations together with bash and python scripts. It can run in either interactive user interface or command line mode.

Disciplines :

Materials science & engineering

Author, co-author :

Wang, Vei ; Department of Applied Physics, Xi'an University of Technology, Xi'an, China

Xu, Nan; College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China

Liu, Jin-Cheng ; Department of Chemistry, Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Tsinghua University, Beijing, China

Tang, Gang ; Université de Liège - ULiège > Département de physique > Physique théorique des matériaux

Geng, Wen-Tong ; School of Materials Science & Engineering, University of Science and Technology Beijing, Beijing, China

Language :

English

Title :

VASPKIT: A user-friendly interface facilitating high-throughput computing and analysis using VASP code

Publication date :

October 2021

Journal title :

Computer Physics Communications

ISSN :

0010-4655

eISSN :

1879-2944

Publisher :

Elsevier B.V.

Volume :

267

Pages :

108033

Peer reviewed :

Peer Reviewed verified by ORBi

Additional URL :

https://api.elsevier.com/content/article/PII:S0010465521001454?httpAccept=text/xml

Funding text :

We acknowledge other contributors (in no particular order) including Peng-Fei Liu, Xue-Fei Liu, Zhao-Fu Zhang, Tian Wang, Dao-Xiong Wu, Ya-Chao Liu, Jiang-Shan Zhao, Yue Qiu and Qiang Li. We gratefully acknowledge helpful discussions with Zhe-Yong Fan, Qi-Jing Zheng and Ming-Qing Liao. We also thank various researchers worldwide for reporting bugs and suggesting features, which have led to significant improvements in the accuracy and robustness of the package. V.W. gratefully appreciates Yoshiyuki Kawazoe and Shigenobu Ogata for their invaluable support. V.W. also thanks The Youth Innovation Team of Shaanxi Universities.

Available on ORBi :

since 24 April 2022

Statistics

Number of views

49 (1 by ULiège)

Number of downloads

54 (0 by ULiège)

More statistics

Scopus citations^®

2344

Scopus citations^®
without self-citations

2323

OpenCitations

820

Bibliography

Hohenberg, P., Kohn, W., Phys. Rev. 136 (1964), B864–B871, 10.1103/PhysRev.136.B864.
Kohn, W., Sham, L.J., Phys. Rev. 140 (1965), A1133–A1138, 10.1103/PhysRev.140.A1133.
Payne, M.C., Teter, M.P., Allan, D.C., Arias, T.A., Joannopoulos, J.D., Rev. Mod. Phys. 64 (1992), 1045–1097, 10.1103/RevModPhys.64.1045.
Jones, R.O., Gunnarsson, O., Rev. Mod. Phys. 61 (1989), 689–746, 10.1103/RevModPhys.61.689.
Jones, R.O., Rev. Mod. Phys. 87 (2015), 897–923, 10.1103/RevModPhys.87.897.
Sato, K., Bergqvist, L., Kudrnovský, J., Dederichs, P.H., Eriksson, O., Turek, I., Sanyal, B., Bouzerar, G., Katayama-Yoshida, H., Dinh, V.A., Fukushima, T., Kizaki, H., Zeller, R., Rev. Mod. Phys. 82 (2010), 1633–1690, 10.1103/RevModPhys.82.1633.
Dietl, T., Ohno, H., Rev. Mod. Phys. 86 (2014), 187–251, 10.1103/RevModPhys.86.187.
Jain, A., Shin, Y., Persson, K.A., Nat. Rev. Mater., 1(1), 2016, 15004, 10.1038/natrevmats.2015.4.
Freysoldt, C., Grabowski, B., Hickel, T., Neugebauer, J., Kresse, G., Janotti, A., Van de Walle, C.G., Rev. Mod. Phys. 86 (2014), 253–305, 10.1103/RevModPhys.86.253.
Pokluda, J., Černỳ, M., Šob, M., Umeno, Y., Prog. Mater. Sci. 73 (2015), 127–158, 10.1016/j.pmatsci.2015.04.001.
Zhang, L., Wang, Y., Lv, J., Ma, Y., Nat. Rev. Mater., 2(4), 2017, 17005, 10.1038/natrevmats.2017.5.
Oganov, A.R., Pickard, C.J., Zhu, Q., Needs, R.J., Nat. Rev. Mater. 4:5 (2019), 331–348, 10.1038/s41578-019-0101-8.
Gonze, X., Jollet, F., Araujo, F.A., Adams, D., Amadon, B., Applencourt, T., Audouze, C., Beuken, J.-M., Bieder, J., Bokhanchuk, A., et al. Comput. Phys. Commun. 205 (2016), 106–131, 10.1016/j.cpc.2016.04.003.
Clark, S.J., Segall, M.D., Pickard, C.J., Hasnip, P.J., Probert, M.I., Refson, K., Payne, M.C., Z. Kristallogr. 220:5–6 (2005), 567–570, 10.1524/zkri.220.5.567.65075.
Kresse, G., Furthmüller, J., Comput. Mater. Sci. 6:1 (1996), 15–50, 10.1016/0927-0256(96)00008-0.
Kresse, G., Furthmüller, J., Phys. Rev. B 54 (1996), 11169–11186, 10.1103/PhysRevB.54.11169.
Soler, J.M., Artacho, E., Gale, J.D., García, A., Junquera, J., Ordejón, P., Sánchez-Portal, D., J. Phys. Condens. Matter 14:11 (2002), 2745–2779, 10.1088/0953-8984/14/11/302.
Giannozzi, P., Baroni, S., Bonini, N., Calandra, M., Car, R., Cavazzoni, C., Ceresoli, D., Chiarotti, G.L., Cococcioni, M., Dabo, I., Corso, A.D., de Gironcoli, S., Fabris, S., Fratesi, G., Gebauer, R., Gerstmann, U., Gougoussis, C., Kokalj, A., Lazzeri, M., Martin-Samos, L., Marzari, N., Mauri, F., Mazzarello, R., Paolini, S., Pasquarello, A., Paulatto, L., Sbraccia, C., Scandolo, S., Sclauzero, G., Seitsonen, A.P., Smogunov, A., Umari, P., Wentzcovitch, R.M., J. Phys. Condens. Matter, 21(39), 2009, 395502, 10.1088/0953-8984/21/39/395502.
Giannozzi, P., Andreussi, O., Brumme, T., Bunau, O., Nardelli, M.B., Calandra, M., Car, R., Cavazzoni, C., Ceresoli, D., Cococcioni, M., et al. J. Phys. Condens. Matter, 29(46), 2017, 465901, 10.1088/1361-648x/aa8f79.
Dewhurst, K., Sharma, S., Nordstrom, L., Cricchio, F., Bultmark, F., Gross, H., Ambrosch-Draxl, C., Persson, C., Brouder, C., Armiento, R., et al. The elk fp-lapw code. http://elk.sourceforge.net/. (Accessed 4 April 2020)
Blaha, P., Schwarz, K., Tran, F., Laskowski, R., Madsen, G.K.H., Marks, L.D., J. Chem. Phys., 152(7), 2020, 074101, 10.1063/1.5143061.
Dassault system̀es biovia, materials studio, 7.0, dassault system̀es, San Diego https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-materials-studio, 2017. (Accessed 4 April 2020)
Smidstrup, S., Markussen, T., Vancraeyveld, P., Wellendorff, J., Schneider, J., Gunst, T., Verstichel, B., Stradi, D., Khomyakov, P.A., Vej-Hansen, U.G., et al. J. Phys. Condens. Matter, 32(1), 2019, 015901, 10.1088/1361-648x/ab4007.
Ong, S.P., Richards, W.D., Jain, A., Hautier, G., Kocher, M., Cholia, S., Gunter, D., Chevrier, V.L., Persson, K.A., Ceder, G., Comput. Phys. Sci. 68 (2013), 314–319, 10.1016/j.commatsci.2012.10.028.
Larsen, A.H., Mortensen, J.J., Blomqvist, J., Castelli, I.E., Christensen, R., Dułak, M., Friis, J., Groves, M.N., Hammer, B., Hargus, C., et al. J. Phys. Condens. Matter, 29(27), 2017, 273002, 10.1088/1361-648x/aa680e.
Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Munoz, F., Romero, A.H., Comput. Phys. Commun., 251, 2020, 107080, 10.1016/j.cpc.2019.107080.
Kantorovich, L.N., Lev00 & tetr: user-friendly packages for dft codes vasp/siesta/quickstep/crystal/quantum espresso. https://nms.kcl.ac.uk/lev.kantorovitch/codes/lev00/index.html. (Accessed 4 April 2020)
Yi, W., Tang, G., Chen, X., Yang, B., Liu, X., Comput. Phys. Commun., 257, 2020, 107535, 10.1016/j.cpc.2020.107535.
Wang, V., Liang, Y., Kawazoe, Y., Geng, W., High-throughput computational screening of two-dimensional semiconductors. preprint arXiv:1806.04285, 2018.
Togo, A., Tanaka, I., Spglib: a software library for crystal symmetry search. preprint arXiv:1808.01590, 2018.
Kokalj, A., Comput. Mater. Sci. 28:2 (2003), 155–168, 10.1016/S0927-0256(03)00104-6.
Hall, S.R., Allen, F.H., Brown, I.D., Acta Crystallogr. A 47:6 (1991), 655–685.
Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M., J. Mol. Biol. 112:3 (1977), 535–542, 10.1016/S0022-2836(77)80200-3.
Hinuma, Y., Pizzi, G., Kumagai, Y., Oba, F., Tanaka, I., Comput. Phys. Sci. 128 (2017), 140–184, 10.1016/j.commatsci.2016.10.015.
Setyawan, W., Curtarolo, S., Comput. Mater. Sci. 49:2 (2010), 299–312, 10.1016/j.commatsci.2010.05.010.
Hunter, J.D., Comput. Sci. Eng. 9:3 (2007), 90–95, 10.1109/MCSE.2007.55.
Voigt, W., et al. Lehrbuch der kristallphysik. vol. 962, 1928, Teubner, Leipzig.
Nielsen, O.H., Martin, R.M., Phys. Rev. Lett. 50 (1983), 697–700, 10.1103/PhysRevLett.50.697.
Nielsen, O., Martin, R.M., Phys. Rev. B, 32(6), 1985, 3792, 10.1103/PhysRevB.32.3792.
Zhang, S., Zhang, R., Comput. Phys. Commun. 220 (2017), 403–416, 10.1016/j.cpc.2017.07.020.
Golesorkhtabar, R., Pavone, P., Spitaler, J., Puschnig, P., Draxl, C., Comput. Phys. Commun. 184:8 (2013), 1861–1873, 10.1016/j.cpc.2013.03.010.
Nye, J.F., et al. Physical Properties of Crystals: Their Representation by Tensors and Matrices. 1985, Oxford University Press.
Le Page, Y., Saxe, P., Phys. Rev. B, 63(17), 2001, 174103, 10.1103/PhysRevB.63.174103.
Yu, R., Zhu, J., Ye, H., Comput. Phys. Commun. 181:3 (2010), 671–675, 10.1016/j.cpc.2009.11.017.
Le Page, Y., Saxe, P., Phys. Rev. B, 65, 2002, 104104, 10.1103/PhysRevB.65.104104.
Hashin, Z., Shtrikman, S., J. Mech. Phys. Solids 10:4 (1962), 343–352, 10.1016/0022-5096(62)90005-4.
Mouhat, F., Coudert, F.m.c.-X., Phys. Rev. B, 90, 2014, 224104, 10.1103/PhysRevB.90.224104.
Reuss, A., Angnew, Z., Math. Meth., 9, 1929, 55, 10.1007/BF00544497.
Hill, R., Proc. Phys. Soc. A 65:5 (1952), 349–354, 10.1088/0370-1298/65/5/307.
Maździarz, M., 2D Mater., 6(4), 2019, 048001, 10.1088/2053-1583/ab2ef3.
Landau, L.D., Lifshitz, E.M., Course of Theoretical Physics Vol 7: Theory and Elasticity. 1959, Pergamon Press.
Wei, X., Fragneaud, B., Marianetti, C.A., Kysar, J.W., Phys. Rev. B, 80, 2009, 205407, 10.1103/PhysRevB.80.205407.
Haastrup, S., Strange, M., Pandey, M., Deilmann, T., Schmidt, P.S., Hinsche, N.F., Gjerding, M.N., Torelli, D., Larsen, P.M., Riis-Jensen, A.C., et al. 2D Mater., 5(4), 2018, 042002, 10.1088/2053-1583/aacfc1.
Wang, L., Kutana, A., Zou, X., Yakobson, B.I., Nanoscale 7 (2015), 9746–9751, 10.1039/C5NR00355E.
Latimer, K., Dwaraknath, S., Mathew, K., Winston, D., Persson, K.A., npj Comput. Mater., 4(1), 2018, 40, 10.1038/s41524-018-0091-x.
Anderson, O.L., Anderson, O.L., et al. Equations of State of Solids for Geophysics and Ceramic Science. vol. 31, 1995, Oxford University Press on Demand.
Murnaghan, F.D., Proc. Natl. Acad. Sci. USA 30:9 (1944), 244–247, 10.1073/pnas.30.9.244.
Birch, F., Phys. Rev. 71 (1947), 809–824, 10.1103/PhysRev.71.809.
Dymond, J.H., Malhotra, R., Int. J. Thermophys. 9:6 (1988), 941–951, 10.1007/BF01133262.
Vinet, P., Ferrante, J., Rose, J.H., Smith, J.R., J. Geophys. Res. 92:B9 (1987), 9319–9325, 10.1029/JB092iB09p09319.
Hebbache, M., Zemzemi, M., Phys. Rev. B, 70, 2004, 224107, 10.1103/PhysRevB.70.224107.
Roy, P.B., Roy, S.B., J. Phys. Condens. Matter 17:39 (2005), 6193–6216, 10.1088/0953-8984/17/39/007.
Pack, D.C., Evans, W.M., James, H.J., Proc. Phys. Soc. 60:1 (1948), 1–8, 10.1088/0959-5309/60/1/302.
Poirier, J.-P., Tarantola, A., Phys. Earth Planet. Inter. 109:1 (1998), 1–8, 10.1016/S0031-9201(98)00112-5.
Whalley, L.D., Frost, J.M., Morgan, B.J., Walsh, A., Phys. Rev. B, 99, 2019, 085207, 10.1103/PhysRevB.99.085207.
Williamson, A.J., Wang, L.W., Zunger, A., Phys. Rev. B 62 (2000), 12963–12977, 10.1103/PhysRevB.62.12963.
Naka, N., Fukai, K., Handa, Y., Akimoto, I., Phys. Rev. B, 88, 2013, 035205, 10.1103/PhysRevB.88.035205.
Momma, K., Izumi, F., J. Appl. Crystallogr. 44:6 (2011), 1272–1276, 10.1107/S0021889811038970.
Frisch, M., Trucks, G., Schlegel, H.B., Scuseria, G., Robb, M., Cheeseman, J., Scalmani, G., Barone, V., Mennucci, B., Petersson, G., et al. Gaussian 09. Revision a. 02, vol. 200, 2009, Gaussian, Inc., Wallingford, CT, 28.
Peressi, M., Binggeli, N., Baldereschi, A., J. Phys. D, Appl. Phys. 31:11 (1998), 1273–1299, 10.1088/0022-3727/31/11/002.
Dugdale, S.B., Phys. Scr., 91(5), 2016, 053009, 10.1088/0031-8949/91/5/053009.
Kawamura, M., Comput. Phys. Commun. 239 (2019), 197–203, 10.1016/j.cpc.2019.01.017.
Popescu, V., Zunger, A., Phys. Rev. Lett., 104, 2010, 236403, 10.1103/PhysRevLett.104.236403.
Popescu, V., Zunger, A., Phys. Rev. B, 85, 2012, 085201, 10.1103/PhysRevB.85.085201.
Gajdoš, M., Hummer, K., Kresse, G., Furthmüller, J., Bechstedt, F., Phys. Rev. B, 73, 2006, 045112, 10.1103/PhysRevB.73.045112.
M. Fox, Optical properties of solids, 2002.
Hedin, L., Phys. Rev., 139(3A), 1965, A796, 10.1103/PhysRev.139.A796.
Fuchs, F., Furthmüller, J., Bechstedt, F., Shishkin, M., Kresse, G., Phys. Rev. B, 76(11), 2007, 115109, 10.1103/PhysRevB.76.115109.
Onida, G., Reining, L., Rubio, A., Rev. Mod. Phys. 74 (2002), 601–659, 10.1103/RevModPhys.74.601.
Hüser, F., Olsen, T., Thygesen, K.S., Phys. Rev. B, 88, 2013, 245309, 10.1103/PhysRevB.88.245309.
Cudazzo, P., Tokatly, I.V., Rubio, A., Phys. Rev. B, 84, 2011, 085406, 10.1103/PhysRevB.84.085406.
Matthes, L., Pulci, O., Bechstedt, F., New J. Phys., 16(10), 2014, 105007, 10.1088/1367-2630/16/10/105007.
Matthes, L., Pulci, O., Bechstedt, F., Phys. Rev. B, 94, 2016, 205408, 10.1103/PhysRevB.94.205408.
Torbatian, Z., Asgari, R., Phys. Rev. B, 98, 2018, 205407, 10.1103/PhysRevB.98.205407.
M.S. Dresselhaus, Solid state physics part ii optical properties of solids, 2001.
Yin, W.-J., Shi, T., Yan, Y., Adv. Mater. 26:27 (2014), 4653–4658, 10.1002/adma.201306281.
Transition dipole moment https://en.wikipedia.org/w/index.php?title=Transition_dipole_moment&oldid=902785194/. (Accessed 4 April 2020)
Meng, W., Wang, X., Xiao, Z., Wang, J., Mitzi, D.B., Yan, Y., J. Phys. Chem. Lett. 8:13 (2017), 2999–3007, 10.1021/acs.jpclett.7b01042.
Nørskov, J.K., Studt, F., Abild-Pedersen, F., Bligaard, T., Fundamental Concepts in Heterogeneous Catalysis. 1st edition, 2014, Wiley.
Hammer, B., Nørskov, J., Surf. Sci. 343:3 (1995), 211–220, 10.1016/0039-6028(96)80007-0.
Hammer, B., Nørskov, J., Impact of Surface Science on Catalysis Advances in Catalysis, vol. 45, 2000, Academic Press, 71–129, 10.1016/S0360-0564(02)45013-4.
D.A. McQuarrie, J.D. Simon, Molecular thermodynamics, 1999.
Ochterski, J.W., Thermochemistry in Gaussian. 2000, Gaussian Inc., 1–19.
Chase, M., J. Phys. Chem. Ref. Data, Monogr., 9, 1998, 12.
Kneller, G.R., Keiner, V., Kneller, M., Schiller, M., Comput. Phys. Commun. 91:1 (1995), 191–214, 10.1016/0010-4655(95)00048-K.
Róg, T., Murzyn, K., Hinsen, K., Kneller, G.R., J. Comput. Chem. 24:5 (2003), 657–667, 10.1002/jcc.10243.
Lin, S.-T., Blanco, M., Goddard, W.A., J. Chem. Phys. 119:22 (2003), 11792–11805, 10.1063/1.1624057.
Dickey, J.M., Paskin, A., Phys. Rev. 188 (1969), 1407–1418, 10.1103/PhysRev.188.1407.
Soper, A.K., Benmore, C.J., Phys. Rev. Lett., 101, 2008, 065502, 10.1103/PhysRevLett.101.065502.
Imoto, S., Xantheas, S.S., Saito, S., J. Chem. Phys., 138(5), 2013, 054506, 10.1063/1.4789951.