{
"id": "https://doi.org/10.5281/zenodo.1112289",
"doi": "10.5281/ZENODO.1112289",
"url": "https://zenodo.org/record/1112289",
"types": {
"ris": "JOUR",
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"schemaOrg": "ScholarlyArticle",
"resourceType": "Journal article",
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"creators": [
{
"name": "R. O. Ocaya",
"affiliation": []
},
{
"name": "J. J. Terblans",
"affiliation": []
}
],
"titles": [
{
"title": "Coding Considerations For Standalone Molecular Dynamics Simulations Of Atomistic Structures"
}
],
"publisher": {
"name": "Zenodo"
},
"container": {},
"subjects": [
{
"subject": "C-language"
},
{
"subject": "molecular dynamics"
},
{
"subject": "simulation"
},
{
"subject": "embedded atom method."
}
],
"contributors": [],
"dates": [
{
"date": "2016-02-02",
"dateType": "Issued"
}
],
"publicationYear": 2016,
"language": "en",
"identifiers": [
{
"identifier": "https://zenodo.org/record/1112290",
"identifierType": "URL"
}
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"rightsList": [
{
"rights": "Creative Commons Attribution 4.0",
"rightsUri": "https://creativecommons.org/licenses/by/4.0"
},
{
"rights": "Open Access",
"rightsUri": "info:eu-repo/semantics/openAccess"
}
],
"descriptions": [
{
"description": "The laws of Newtonian mechanics allow ab-initio
\nmolecular dynamics to model and simulate particle trajectories in
\nmaterial science by defining a differentiable potential function. This
\npaper discusses some considerations for the coding of ab-initio
\nprograms for simulation on a standalone computer and illustrates
\nthe approach by C language codes in the context of embedded
\nmetallic atoms in the face-centred cubic structure. The algorithms use
\nvelocity-time integration to determine particle parameter evolution
\nfor up to several thousands of particles in a thermodynamical
\nensemble. Such functions are reusable and can be placed in a
\nredistributable header library file. While there are both commercial
\nand free packages available, their heuristic nature prevents dissection.
\nIn addition, developing own codes has the obvious advantage of
\nteaching techniques applicable to new problems.",
"descriptionType": "Abstract"
},
{
"description": "{\"references\": [\"Mendelev MI, Han S, Srolovitz DJ, Ackland GJ, Sun DY, Asta M.\\nDevelopment of new interatomic potentials appropriate for crystalline\\nand liquid iron, Philosophical Magazine, 83:35 (2003), 3977-3994, DOI:\\n10.1080/14786430310001613264\", \"Sutton AP, Chen J. Long-range Finnis-Sinclair potentials. Philosophical\\nMagazine Letters, 1990 Vol. 61 (3), 139-156.\", \"Das A, Ghosh MM. MD simulation-based study on the melting\\nand thermal expansion behaviours of nanoparticles under heat\\nload. Computational Materials Science 101 (2015) 88-95. doi:\\n10.1016/j.commatsci.2015.01.008\", \"van der Walt C, Terblans JJ, Swart HC. Molecular dynamics study\\nof the temperature dependence and surface orientation dependence\\nof the calculated vacancy formation energies of Al, Ni, Cu, Pd,\\nAg, and Pt. Computational Materials Science 83 (2014) 7077. doi:\\n10.1016/j.commatsci.2013.10.039\", \"Abraham MJ, Murtolad T, Roland Schulz R, Palla S, JSmith JC, Hessa\\nB, Lindahl E. GROMACS: High performance molecular simulations\\nthrough multi-level parallelism from laptops to supercomputers.\\nSoftwareX (2015). doi: 10.1016/j.softx.2015.06.001\", \"Smirnov BM. Energetics of clusters with a face centered-cubic structure.\\nZh. Eksp. Teor. Fiz. 107 (1995), 2080-2091\", \"Terblans JJ. Calculating the bulk vacancy formation energy (Ev) for a\\nSchottky defect in a perfect Cu(111), Cu(100) and a Cu(110) single\\ncrystal. Surf. Interface Anal. 2002; 33: 767770 doi: 10.1002/sia.1451\", \"Mattsson TR, Mattsson AE. Calculating the vacancy formation energy\\nin metals: Pt, Pd, and Mo. Physical Review B 66 (2002) 214110.\", \"Sebastian IS, Aldazabal J, Capdevila C, Garcia-Mateo C. Diffusion\\nsimulation of CrFe bcc systems at atomic level using a random walk\\nalgorithm. p hys. stat. sol. (a) 205, No. 6, 13371342 (2008). doi:\\n10.1002/pssa.200778124\\n[10] Jian-Min Z, Fei M, Ke-Wei, X. Calculation of the surface energy of\\nfcc metals with modified embedded-atom method. Vol. 13 (7) 2004.\\n1009-1963/2004/13(07)/1082-09\\n[11] Griebel M, Knapek S, Zumbusch G, in Barth TJ et al.(Eds.), Numerical\\nSimulation in Molecular Dynamics, in: Texts in Computational Science\\nand Engineering 5, Springer, Berlin, 2007, ISBN 978-3-540-68094-9\\n[12] Car R, Parrinello M, Unified Approach for Molecular Dynamics and\\nDensity Functional Theory, Phys. Rev. Lett, 55(22), 1985, 2471-2474.\\n[13] Car R, Parrinello M, The Unified Approach for Molecular Dynamics\\nand Density Functional Theory, in Simple Molecular Systems at Very\\nHigh Density, vol. 186 of NATO ASI Series , series B, Physics, P.P.\\nLoubeyre and N. Boccara (Eds.) (Plenum Press, NY), 1989, 455-476.\\n[14] Remler DK, Madden PA, Molecular dynamics without effective\\npotentials via the Car-Parrinello approach, Mol. Phys., 70(6) 1990,\\n921-966.\\n[15] Tuckerman ME. Ab initio molecular dynamics: basic concepts, current\\ntrends and novel applications. J. Phys.: Condens. Matter 14 (2002)\\nR1297R1355 Online at stacks.iop.org/JPhysCM/14/R1297\\n[16] Finnis MW, Sinclair JE, Philos. Mag. A 50 (1984) 45.\\n[17] Daw MS, Foiles SM, Baskes MI, Mater. Sci. Rep. 9 (1993) 251.\\n[18] Daw MS, Baskes MI, Phys. Rev. B 29 (1984) 6443.\\n[19] Todd BD, Lynden-Bell RM. Surface and bulk properties of\\nmetals modelled with Sutton-Chen potentials. Surface Science 281,\\n1993,191-206.\\n[20] Chamati H, Papanicolaou NI, Mishin Y, Papaconstantopoulos DA.\\nEmbedded-atom potential for Fe and its application to self-diffusion on\\nFe (100). Surface Science; 2006, 1-11. doi:10.1016/j.susc.2006.02.10 [21] Mishin Y, in: Yip S (Ed.), Handbook of Materials Modeling, Springer,\\nThe Netherlands, 2005, p. 459.\\n[22] Doye JPK, Wales DJ. Global minima for transition metal clusters\\ndescribed by the Sutton-Chen potentials. New J. Chem. 1998, 733-744.\\n[23] Swope W, Andersen H, Berens P, Wilson K. A computer simulation\\nmethod for the calculation of equilibrium constants for the formation of\\nphysical clusters of molecules: Application to small water clusters, J.\\nChem. Phys., 76 (1982), pp. 637649.\\n[24] Landau L, Lifschitz E. Mechanics, Course of Theoretical Physics, Vol.\\n1, Pergamon Press, Oxford, 1976.\\n[25] Hockney, R. The potential calculation and some applications, Methods\\nComp. Phys., 9 (1970), pp. 136211.\\n[26] Verlet L. Computer experiments on classical fluids. I. Thermodynamical\\nproperties of Lennard-Jones molecules, Phys. Rev., 159 (1967), pp.\\n98103.\\n[27] Chandler D. Introduction to modern statistical mechanics, Oxford\\nUniversity Press, New York, 1987.\"]}",
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