HICOLM: High-Performance Platform of Physical Simulations by Using Low Computational Cost Methods

Flaviano Williams Fernandes

Abstract


For decades, computational simulation models have been used by scientists in search for new materials with technological applications in several areas of knowledge. For this, software based on several theoretical-computational models were developed in order to obtain an analysis of the physical properties at atomic levels. The objective of this work is proposing a widely functional software to analyze the physical properties of nanostructures based on carbon and condensed systems using theories of low computational cost. Therefore, a Fortran language computational program called HICOLM was developed, whose theoretical bases are based on two commonly known models (Tight-binding and Molecular Dynamics). The physical properties of condensed systems can be obtained in the thermodynamic equilibrium in several statistical ensembles, and possible to obtain an analysis of the properties of the material and its evolution in the time-dependent on its thermodynamic conditions like temperature and pressure. Moreover, from the tight-binding model, the HICOLM program is also capable of performing a physical analysis of carbon-based nanostructures from the calculation of the material band structure.


Keywords


Tight-binding; Molecular dynamics; Nanotechnology; Molecular structure

Full Text:

PDF

References


Castro Neto, A. H. et al. The electronic properties of graphene. Reviews of Modern Physics, American Physical Society, v. 81, n. 1, p. 109–162, jan 2009.

MCCANN, E.; KOSHINO, M. The electronic properties of bilayer graphene. Reports on Progress in Physics, IOP Publishing, v. 76, n. 5, p. 056503, may 2013.

KONSCHUH, S.; GMITRA, M.; FABIAN, J. Tight- binding theory of the spin-orbit coupling in graphene. Physi- cal Review B, v. 82, n. 24, p. 245412, 2010.

KONSCHUH, S. Spin-Orbit Coupling Effects From Graphene To Graphite. Tese (Doutorado), 2011.

SAMADIKHAH, K. et al. Continuum-molecular mod- elling of graphene. Computational Materials Science, Elsevier, v. 53, n. 1, p. 37–43, feb 2012.

CHOI, W. et al. Synthesis of Graphene and Its Applica- tions: A Review. Critical Reviews in Solid State and Materials Sciences, Taylor & Francis Group, v. 35, n. 1, p. 52–71, feb 2010.

D. Ghuge, A.; R. Shirode, A.; J. Kadam, V. Graphene: A Comprehensive Review. Current Drug Targets, v. 18, n. 6, p. 724–733, mar 2017.

RAJASEKARAN, G.; KUMAR, R.; PARASHAR, A. Tersoff potential with improved accuracy for simulating graphene in molecular dynamics environment. Materials Re- search Express, v. 3, n. 3, p. 035011, mar 2016.

GRUNEIS, A. et al. Tight-binding description of the quasiparticle dispersion of graphite and few-layer graphene. Physical Review B, American Physical Society, v. 78, n. 20, p. 205425, nov 2008.

SOOD, A. K. et al. Review of Graphene Technology and Its Applications for Electronic Devices. In: Graphene - New Trends and Developments. [S.l.]: InTech, 2015.

LI, H.; SHI, Y.; LI, L.-J. Synthesis and optoelectronic applications of graphene/transition metal dichalcogenides flat- pack assembly. Carbon, Pergamon, v. 127, p. 602–610, feb 2018 ́

SOLIS-FERNANDEZ, P.; BISSETT, M.; AGO, H. Synthesis, structure and applications of graphene-based 2D het- erostructures. Chemical Society Reviews, The Royal Society of Chemistry, v. 46, n. 15, p. 4572–4613, jul 2017.

ABRAHAM, M. J. et al. Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, Elsevier, v. 1-2, p. 19– 25, sep 2015.

SMITH, W.; YONG, C.; RODGER, P. DL POLY: Appli- cation to molecular simulation. Molecular Simulation, Taylor & Francis Group, v. 28, n. 5, p. 385–471, may 2002.

PLIMPTON, S. Fast Parallel Algorithms for Short-Range Molecular Dynamics. Journal of Computational Physics, Aca- demic Press, v. 117, n. 1, p. 1–19, mar 1995.

ALLEN, M. P.; TILDESLEY, D. J. Computer Simulation of Liquids. New York, NY, USA: Clarendon Press, 1989.

GUPTA, S. Computing aspects of molecular dynam- ics simulation. Computer Physics Communications, North- Holland, v. 70, n. 2, p. 243–270, jun 1992.

EWALD, P. P. Die Berechnung optischer und elek- trostatischer Gitterpotentiale. Annalen der Physik, Wiley- Blackwell, v. 369, n. 3, p. 253–287, jan 1921.

FENNELL, C. J.; GEZELTER, J. D. Is the Ewald sum- mation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics. The Journal of Chem- ical Physics, American Institute of Physics, v. 124, n. 23, p. 234104, jun 2006.

WOLF, D. et al. Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r-1 summation. The Journal of Chemical Physics, American In- stitute of Physics, v. 110, n. 17, p. 8254, apr 1999.

TERSOFF, J. Modeling solid-state chemistry: Inter- atomic potentials for multicomponent systems. Physical Re- view B, American Physical Society, v. 39, n. 8, p. 5566–5568, mar 1989.

BERENDSEN, H. J. C. et al. Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, American Institute of Physics, v. 81, n. 8, p. 3684–3690, oct 1984.

MORE et al. The MINPACK Project, in Sources and Development of Mathematical Software. 1984.

MORE, J. J.; GARBOW, B. S.; HILLSTROM, K. E. User Guide for MINPACK-1. Style DeKalb IL, Argonne National Laboratory, 1980.

ANDERSON, E. LAPACK users’ guide. [S.l.]: Society for Industrial and Applied Mathematics, 1999. 407 p.

GARCIA, A. et al. The SIESTA method for ab initio order- N materials simulation. Journal of Physics: Condensed Matter, IOP Publishing, v. 14, n. 11, p. 2745–2779, mar 2002.

WHITE, J. A. Lennard-Jones as a model for argon and test of extended renormalization group calculations. The Jour- nal of Chemical Physics, American Institute of Physics, v. 111, n. 20, p. 9352, nov 1999.

WU, Y.; TEPPER, H. L.; VOTH, G. A. Flexible simple point-charge water model with improved liquid-state proper- ties. The Journal of Chemical Physics, American Institute of Physics, v. 124, n. 2, p. 024503, jan 2006.

SAITO, R.; DRESSELHAUS, G.; DRESSELHAUS, M. S. Physical Properties of Carbon Nanotubes. [S.l.]: PUB- LISHED BY IMPERIAL COLLEGE PRESS AND DIS- TRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2012.

KHAN, A. A. Radial distribution functions of fluid argon. Physical Review, American Physical Society, v. 134, n. 2A, p. A367–A384, apr 1964.

William E. Acree, J. S. C. Phase Transition Enthalpy Measurements of Organic and Organometallic Compounds. In: NIST Chemistry WebBook, NIST Standard Reference Database Number 69, Eds. P.J. Linstrom and W.G. Mallard. Gaithersburg MD: [s.n.], 2019. p. 20899.

TEGELER, C.; SPAN, R.; WAGNER, W. A New Equa- tion of State for Argon Covering the Fluid Region for Tem- peratures From the Melting Line to 700 K at Pressures up to 1000 MPa. Journal of Physical and Chemical Reference Data, 1999.




DOI: https://doi.org/10.22456/2175-2745.92486

Copyright (c) 2019 Flaviano Williams Fernandes

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.