Graphic user interface for molecular dynamics simulation of thin films

  • Héctor Barco-Ríos Universidad Nacional de Colombia Sede Manizales
  • Héctor D. Aristizábal-Soto Universidad Nacional de Colombia Sede Manizales
  • Elisabeth Restrepo-Parra Universidad Nacional de Colombia Sede Manizales
Keywords: Thin films, Molecular Dynamic, Graphic interface, dissociation energy, simulations, Software

Abstract

In this work, a software for simulating nanoindentation in thin films was implemented. For the software constructions, the Molecular Dynamics technique was used. The model applied for the graphic interface (software) is an approximation that reproduces the characteristic curves tendencies in test of materials hardness; on the other hand, the software was designed and built in a friendly environment, where the user can develop its own thin films, not only in monolayers, but also in multilayers. This interface allows to control the film thickness, the number of layers and other physical properties as the dissociation energy or the energy parameter in the sphere; furthermore, it is possible to control the steps of the dynamical time. For ensuring the proper working of the software, several simulations using the chromium parameters as the reference material were carried out, reproducing experimental tendencies.

Author Biographies

Héctor Barco-Ríos, Universidad Nacional de Colombia Sede Manizales
MSc. en Física, Departamento de Física y Química, Universidad Nacional de Colombia Sede Manizales, Manizales
Héctor D. Aristizábal-Soto, Universidad Nacional de Colombia Sede Manizales
Ingeniero Físico, PCM-Computational Applications, Departamento de Física y Química, Universidad Nacional de Colombia Sede Manizales, Manizales
Elisabeth Restrepo-Parra, Universidad Nacional de Colombia Sede Manizales
PhD. en Ingeniería, Línea Automática, PCM-Computational Applications, Departamento de Física y Química, Universidad Nacional de Colombia Sede Manizales, Manizales

References

B. H. Toby, “EXPGUI , a graphical user interface for GSAS,” J. Appl. Crystallogr., vol. 34, no. 2, pp. 210–213, Apr. 2001.

A. Kokalj, “Computer graphics and graphical user interfaces as tools in simulations of matter at the atomic scale,” Comput. Mater. Sci., vol. 28, no. 2, pp. 155–168, Oct. 2003.

K. Hinsen, “The molecular modeling toolkit: A new approach to molecular simulations,” J. Comput. Chem., vol. 21, no. 2, pp. 79–85, Jan. 2000.

P. Eastman and V. Pande, “OpenMM: A Hardware-Independent Framework for Molecular Simulations,” Comput. Sci. Eng., vol. 12, no. 4, pp. 34–39, Jul. 2010.

M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. Legrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, and V. S. Pande, “Accelerating molecular dynamic simulation on graphics processing units,” J. Comput. Chem., vol. 30, no. 6, pp. 864–872, Apr. 2009.

B. FrantzDale, S. J. Plimpton, and M. S. Shephard, “Software components for parallel multiscale simulation: an example with LAMMPS,” Eng. Comput., vol. 26, no. 2, pp. 205–211, Apr. 2010.

A. E. M. D. Spoel, E. Lindahl, B. Hess, G. Groenhof and J. C. Berendsen, “GROMACS: Fast, Flexible, and Free,” J. Comput. Chem, vol. 26, no. 16, pp. 1701–1718, 2005.

T. Nagata, “Molby: Graphical Molecular Modeling Software with Integrated Ruby Interpreter,” Bull. Chem. Soc. Jpn., vol. 87, no. 8, pp. 902–904, 2014.

A. V. Popov, Y. N. Vorobjev, and D. O. Zharkov, “MDTRA: A molecular dynamics trajectory analyzer with a graphical user interface,” J. Comput. Chem., vol. 34, no. 4, pp. 319–325, Feb. 2013.

R. Komanduri, N. Chandrasekaran, and L. M. Raff, “MD simulation of indentation and scratching of single crystal aluminum,” Wear, vol. 240, no. 1–2, pp. 113–143, May 2000.

M. B. Cai, X. P. Li, and M. Rahman, “Study of the mechanism of nanoscale ductile mode cutting of silicon using molecular dynamics simulation,” Int. J. Mach. Tools Manuf., vol. 47, no. 1, pp. 75–80, Jan. 2007.

R. T. Allen and P. Feuer, “Vibrational Energy Exchange for a Morse Potential Interaction,” J. Chem. Phys., vol. 40, no. 10, p. 2810, 1964.

H. Taseli, “Exact solutions for vibrational levels of the Morse potential,” J. Phys. A. Math. Gen., vol. 31, no. 2, pp. 779–788, Jan. 1998.

B. Molnár, P. Földi, M. G. Benedict, and F. Bartha, “Time evolution in the Morse potential using supersymmetry: Dissociation of the NO molecule,” Europhys. Lett., vol. 61, no. 4, pp. 445–451, Feb. 2003.

E. T. Lilleodden, J. A. Zimmerman, S. M. Foiles, and W. D. Nix, “Atomistic simulations of elastic deformation and dislocation nucleation during nanoindentation,” J. Mech. Phys. Solids, vol. 51, no. 5, pp. 901–920, May 2003.

T.-H. Fang, C.-I. Weng, and J.-G. Chang, “Molecular dynamics simulation of nano-lithography process using atomic force microscopy,” Surf. Sci., vol. 501, no. 1–2, pp. 138–147, Mar. 2002.

J. de Boer, “The non spherical potential field between two hydrogen molecules,” Physica, vol. 9, no. 3, pp. 363–382, Mar. 1942.

Y. Wang, D. Raabe, C. Klüber, and F. Roters, “Orientation dependence of nanoindentation pile-up patterns and of nanoindentation microtextures in copper single crystals,” Acta Mater., vol. 52, no. 8, pp. 2229–2238, May 2004.

R. E. Miller, L. . Shilkrot, and W. A. Curtin, “A coupled atomistics and discrete dislocation plasticity simulation of nanoindentation into single crystal thin films,” Acta Mater., vol. 52, no. 2, pp. 271–284, Jan. 2004.

G. S. Smith, E. B. Tadmor, N. Bernstein, and E. Kaxiras, “Multiscale simulations of silicon nanoindentation,” Acta Mater., vol. 49, no. 19, pp. 4089–4101, Nov. 2001.

A. Upadhyaya, J.-P. Rieu, J. A. Glazier, and Y. Sawada, “Anomalous diffusion and non-Gaussian velocity distribution of Hydra cells in cellular aggregates,” Phys. A Stat. Mech. its Appl., vol. 293, no. 3–4, pp. 549–558, Apr. 2001.

J. D. Vergados, S. H. Hansen, and O. Host, “Impact of going beyond the Maxwell distribution in direct dark matter detection rates,” Phys. Rev. D, vol. 77, no. 2, p. 023509, Jan. 2008.

L. V. Zhigilei and B. J. Garrison, “Velocity distributions of molecules ejected in laser ablation,” Appl. Phys. Lett., vol. 71, no. 4, p. 551, 1997.

A. M. Kapral and R., “Continuous-velocity lattice-gas model for fluid flow,” Eur. Lett, vol. 44, no. 5, pp. 552–558, 1998.

J. S. van Zon and F. C. MacKintosh, “Velocity Distributions in Dissipative Granular Gases,” Phys. Rev. Lett., vol. 93, no. 3, p. 038001, Jul. 2004.

K. Sun, L. Fang, Z. Yan, and J. Sun, “Atomistic scale tribological behaviors in nano-grained and single crystal copper systems,” Wear, vol. 303, no. 1–2, pp. 191–201, Jun. 2013.

T. Hilbig, W. Brostow, and R. Simoes, “Simulating scratch behavior of polymers with mesoscopic molecular dynamics,” Mater. Chem. Phys., vol. 139, no. 1, pp. 118–124, Apr. 2013.

L. Verlet, “Computer ‘Experiments’ on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules,” Phys. Rev., vol. 159, no. 1, pp. 98–103, Jul. 1967.

J. M. Meza, M. C. M. Farias, R. M. de Souza, and L. J. C. Riaño, “Using the ratio: maximum load over unload stiffness squared, Pm/Su2, on the evaluation of machine stiffness and area function of blunt indenters on depth-sensing indentation equipment,” Mater. Res., vol. 10, no. 4, pp. 437–447, Dec. 2007.

A. Bolshakov and G. M. Pharr, “Influences of pileup on the measurement of mechanical properties by load and depth sensing indentation techniques,” J. Mater. Res., vol. 13, no. 04, pp. 1049–1058, Apr. 1998.

A. G. B. J. C. Caicedo, P. Prieto, J. M. Caicedo. R, G. Bejarano and S. Gottschalk, “Deposición de películas de Zirconio/nitruro de zirconio en forma de multicapas por magnetrón sputtering reactivo,” Rev. Colomb. Fis, vol. 37, no. 2, pp. 388–392, 2005.

O. Z. V. Di Graci, M. Torres and E. S. Puchi, “Dureza en aceros aisi 304 laminados en tibio y en caliente,” Rev. Lat. Met. Mater, vol. 1, pp. 237–248, 2009.

Q. H. Tang, “MD simulation of dislocation mobility during cutting with diamond tip on silicon,” Mater. Sci. Semicond. Process., vol. 10, no. 6, pp. 270–275, Dec. 2007.

A. K. Nair, E. Parker, P. Gaudreau, D. Farkas, and R. D. Kriz, “Size effects in indentation response of thin films at the nanoscale: A molecular dynamics study,” Int. J. Plast., vol. 24, no. 11, pp. 2016–2031, Nov. 2008.

M. Shell De Guzman, G. Neubauer, P. Flinn, and W. D. Nix, “The Role of Indentation Depth on the Measured Hardness of Materials,” MRS Proc., vol. 308, p. 613, Jan. 1993.

J. R. Tuck, A. M. Korsunsky, S. J. Bull, and R. I. Davidson, “On the application of the work-of-indentation approach to depth-sensing indentation experiments in coated systems,” Surf. Coatings Technol., vol. 137, no. 2–3, pp. 217–224, Mar. 2001.

N. Chollacoop, M. Dao, and S. Suresh, “Depth-sensing instrumented indentation with dual sharp indenters,” Acta Mater., vol. 51, no. 13, pp. 3713–3729, Aug. 2003.

W. C. Oliver and G. M. Pharr, “Measurement of hardness and elastic modulus by instrumented indentation: Advances in understanding and refinements to methodology,” J. Mater. Res., vol. 19, no. 01, pp. 3–20, Jan. 2004.

A. H. W. Ngan and B. Tang, “Viscoelastic effects during unloading in depth-sensing indentation,” J. Mater. Res., vol. 17, no. 10, pp. 2604–2610, Oct. 2002.

P. Peng, G. Liao, T. Shi, Z. Tang, and Y. Gao, “Molecular dynamic simulations of nanoindentation in aluminum thin film on silicon substrate,” Appl. Surf. Sci., vol. 256, no. 21, pp. 6284–6290, Aug. 2010.

Y. Gao, C. J. Ruestes, and H. M. Urbassek, “Nanoindentation and nanoscratching of iron: Atomistic simulation of dislocation generation and reactions,” Comput. Mater. Sci., vol. 90, pp. 232–240, Jul. 2014.

J. V. Y. Gaillard, E. Jiménez-Piqué, J. A. Muñoz and M. Anglada, “Nanoindentación de circona dopada con itria expuesta a degradación hidrotérmica,” An. la Mecánica Fract., vol. 1, pp. 283–288, 2007.

J. Gubicza, A. Juhász, and J. Lendvai, “A new method for hardness determination from depth sensing indentation tests,” J. Mater. Res., vol. 11, no. 12, pp. 2964–2967, Dec. 1996.

B. Evans and C. Goetze, “The temperature variation of hardness of olivine and its implication for polycrystalline yield stress,” J. Geophys. Res., vol. 84, no. B10, p. 5505, 1979.

Y. . Milman, S. Luyckx, and I. Northrop, “Influence of temperature, grain size and cobalt content on the hardness of WC–Co alloys,” Int. J. Refract. Met. Hard Mater., vol. 17, no. 1–3, pp. 39–44, May 1999.

How to Cite
[1]
H. Barco-Ríos, H. D. Aristizábal-Soto, and E. Restrepo-Parra, “Graphic user interface for molecular dynamics simulation of thin films”, TecnoL., vol. 19, no. 36, pp. 113–123, Jan. 2016.

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Published
2016-01-30
Section
Research Papers

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