MD Potential Files: Difference between revisions
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==Potential |
==Potential Types== |
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This table contains information about the potentials use in MD++. |
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| ⚫ | These are some potential files we used in our simulations of molecular structures. Please note that since we use a variety of codes, the potential files will be in a variety of |
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! Name of Potential || executable || Types of Materials |
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| Molecular Dynamics || md_$(SYS) || empty potential, for visualization and atom manipulation |
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| Finnis-Sinclair || fs_$(SYS) || BCC metals (Mo, Ta, W, ...) |
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| Embedded Atom Method || eam_$(SYS) || FCC metals (Cu, Au, ...) |
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| Aluminum Glue || alglue_$(SYS) || Al (FCC metal) |
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| Modified Embedded Atom Method || meam_$(SYS) || FCC metals, BCC metals, semiconductors |
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| Lennard-Jones || lj_$(SYS) || Noble gas (Ar, ...) |
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| Stillinger-Webber || sw_$(SYS) || Semiconductors (Si, Ge, C) |
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| Tersoff || tersoff_$(SYS) || Semiconductors (Si, Ge, C), PRB '''39''' 5566 (1989) |
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| Tersoff88 || tersoff88_$(SYS) || Si(B) - PRB '''37''' 6991 (1988), Si(C) - PRB '''38''' 9902 (1988) In default, the parameters are set to Si(C). The parameters can be reset to Si(B) by modifying source code, "tersoff88.cpp". |
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| Brenner || brenner_$(SYS) || C, hydrocarbons |
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|} |
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==Relation between the parameters in SW potential and in MD++ codes == |
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==Potentials== |
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The parameters in SW potential model and in MD++ codes are associated, following the rules described in table below. When changing values of the parameters in MD++ codes, make sure you know what you are changing and how. |
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{| class="wikitable" cellpadding="2" |
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! Parameters in Balamane et al (PRB 46 2250) || Parameters in original SW (PRB 31 5262) || Variables in MD++ |
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| A_1 || = ε*A*B*σ^p || bb = A_1/aa = B*σ^(p-q) |
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| A_2 || = ε*A*σ^q || = aa |
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| Z || = ε*λ || = plam |
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| μ || = σ || = pss |
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| α || = γ || pgam = γ*pss |
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| R_c || = a*σ || = acut |
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| λ_1 || = p || = rho |
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| λ_2 || = q || Not Used (0) |
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|} |
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=="Potential" Problems== |
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| ⚫ | These are some potential files we used in our simulations of molecular structures. Please note that since we use a variety of codes, the potential files will be in a variety of formats. The most common codes used by our group are LAMMPS ( and ParaDyne) and MD++. These codes use different file formats for EAM potentials, so all files should specify which file format. We will also try to provide a reference describing the potential. |
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==Potential Files== |
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===MD++ Files=== |
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Ref: Park, H. S., Zimmerman J. A., Modeling inelasticity and failure in gold nanowires. Phys. Rev. B 72, 054106 (2005). |
Ref: Park, H. S., Zimmerman J. A., Modeling inelasticity and failure in gold nanowires. Phys. Rev. B 72, 054106 (2005). |
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[[media:eamdata_cufoiles.txt | EAM Foiles potential for Copper.]] |
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Ref: Aubry, S. and Hughes, D. A., Reductions in stacking fault widths in fcc crystals: Semiempirical calculations. Phys. Rev. B 73, 224116 (2006). |
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===LAMMPS SET Files === |
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[[media:cufoiles_set.txt | EAM Foiles potential for Copper.]] |
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Ref: Aubry, S. and Hughes, D. A., Reductions in stacking fault widths in fcc crystals: Semiempirical calculations. Phys. Rev. B 73, 224116 (2006). |
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===LAMMPS FUNC Files=== |
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Latest revision as of 15:17, 10 January 2014
Potential Types[edit]
This table contains information about the potentials use in MD++.
| Name of Potential | executable | Types of Materials |
|---|---|---|
| Molecular Dynamics | md_$(SYS) | empty potential, for visualization and atom manipulation |
| Finnis-Sinclair | fs_$(SYS) | BCC metals (Mo, Ta, W, ...) |
| Embedded Atom Method | eam_$(SYS) | FCC metals (Cu, Au, ...) |
| Aluminum Glue | alglue_$(SYS) | Al (FCC metal) |
| Modified Embedded Atom Method | meam_$(SYS) | FCC metals, BCC metals, semiconductors |
| Lennard-Jones | lj_$(SYS) | Noble gas (Ar, ...) |
| Stillinger-Webber | sw_$(SYS) | Semiconductors (Si, Ge, C) |
| Tersoff | tersoff_$(SYS) | Semiconductors (Si, Ge, C), PRB 39 5566 (1989) |
| Tersoff88 | tersoff88_$(SYS) | Si(B) - PRB 37 6991 (1988), Si(C) - PRB 38 9902 (1988) In default, the parameters are set to Si(C). The parameters can be reset to Si(B) by modifying source code, "tersoff88.cpp". |
| Brenner | brenner_$(SYS) | C, hydrocarbons |
Relation between the parameters in SW potential and in MD++ codes[edit]
The parameters in SW potential model and in MD++ codes are associated, following the rules described in table below. When changing values of the parameters in MD++ codes, make sure you know what you are changing and how.
| Parameters in Balamane et al (PRB 46 2250) | Parameters in original SW (PRB 31 5262) | Variables in MD++ |
|---|---|---|
| A_1 | = ε*A*B*σ^p | bb = A_1/aa = B*σ^(p-q) |
| A_2 | = ε*A*σ^q | = aa |
| Z | = ε*λ | = plam |
| μ | = σ | = pss |
| α | = γ | pgam = γ*pss |
| R_c | = a*σ | = acut |
| λ_1 | = p | = rho |
| λ_2 | = q | Not Used (0) |
"Potential" Problems[edit]
These are some potential files we used in our simulations of molecular structures. Please note that since we use a variety of codes, the potential files will be in a variety of formats. The most common codes used by our group are LAMMPS ( and ParaDyne) and MD++. These codes use different file formats for EAM potentials, so all files should specify which file format. We will also try to provide a reference describing the potential.
Potential Files[edit]
MD++ Files[edit]
EAM Foiles potential for Gold. Ref: Park, H. S., Zimmerman J. A., Modeling inelasticity and failure in gold nanowires. Phys. Rev. B 72, 054106 (2005).
EAM Foiles potential for Copper. Ref: Aubry, S. and Hughes, D. A., Reductions in stacking fault widths in fcc crystals: Semiempirical calculations. Phys. Rev. B 73, 224116 (2006).
LAMMPS SET Files[edit]
EAM Foiles potential for Copper. Ref: Aubry, S. and Hughes, D. A., Reductions in stacking fault widths in fcc crystals: Semiempirical calculations. Phys. Rev. B 73, 224116 (2006).