potentials.md

Interatomic potentials

This file contains a list of interatomic potentials implemented in Atomistica, and the parameter sets provided for them. The code fragments show Python code that instantiates an ASE calculator object for the respective potential/parameterization. Note that for all potentials listed below there is a default parameter set that is used if instantiated without an explicit database dictionary. This default is the first potential listed below.

Non-orthogonal tight-binding

Atomistica can carry out non-orthogonal tight-binding calculations with charge self-consistency. Parameter sets are not distributed with Atomistica but can be found for example at dftb.org. For more details, see the following publications:

• Marcus Elstner, Dirk Porezag, G. Jungnickel, J. Elsner, M. Haugk, Thomas Frauenheim, Sándor Suhai, Gotthard Seifert
  “Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties.”
  Phys. Rev. B 58, 7260 (1998) - http://dx.doi.org/10.1103/PhysRevB.58.7260

  from atomistica import TightBinding  
  calc = TightBinding(database_folder='/path/to/notb/database')
  

  Note: This code snippet runs calculations without charge self-consistency. See the examples folder for example how to run self-consistent calculations.

Empirical bond-order potentials

Potentials that employ Tersoff's functional form:

• Jerry Tersoff
  "Modeling solid-state chemistry: Interatomic potentials for multicomponent systems"
  Phys. Rev. B 39, 5566 (1989) - http://dx.doi.org/10.1103/PhysRevB.39.5566

  from atomistica import Tersoff, Tersoff_PRB_39_5566_Si_C  
  calc = Tersoff(**Tersoff_PRB_39_5566_Si_C)
  

  Note: This is the default parameter set for this potential. It gets loaded by the following code.

  from atomistica import Tersoff  
  calc = Tersoff()
  

• Souraya Goumri-Said, Mohammed Benali Kanoun, Abdelkarim E Merad, Ghouti Merad, Hafid Aourag
  "Prediction of structural and thermodynamic properties of zinc-blende AlN: molecular dynamics simulation" Chem. Phys. 302, 135 (2004) - http://dx.doi.org/10.1016/j.chemphys.2004.03.030

  from atomistica import Tersoff, Goumri_Said_ChemPhys_302_135_Al_N  
  calc = Tersoff(**Goumri_Said_ChemPhys_302_135_Al_N)
  

• Katsuyuki Matsunaga, Craig Fisher, Hideaki Matsubara
  "Tersoff potential parameters for simulating cubic boron carbonitrides"
  Jpn. J. Appl. Phys. 39, 48 (2000) - http://dx.doi.org/10.1143/JJAP.39.L48

  from atomistica import Tersoff, Matsunaga_Fisher_Matsubara_Jpn_J_Appl_Phys_39_48_B_C_N  
  calc = Tersoff(**Matsunaga_Fisher_Matsubara_Jpn_J_Appl_Phys_39_48_B_C_N)
  

Potentials that employ Brenner's functional form:

• Paul Erhart, Karsten Albe
  "Analytical potential for atomistic simulations of silicon, carbon, and silicon carbide"
  Phys. Rev. B 71, 035211 (2005) - http://dx.doi.org/10.1103/PhysRevB.71.035211

  from atomistica import Brenner, Erhart_PRB_71_035211_SiC  
  calc = Brenner(**Erhart_PRB_71_035211_SiC)
  

  Note: This is the default parameter set for this potential. It gets loaded by the following code.

  from atomistica import Brenner  
  calc = Brenner()
  

• Donald Brenner
  "Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films"
  Phys. Rev. B 42, 9458 (1990) - http://dx.doi.org/10.1103/PhysRevB.42.9458
  and Erratum Phys. Rev. B 46, 1948 (1992) - http://dx.doi.org/10.1103/PhysRevB.46.1948.2
  Warning: The original formulation uses look-up tables to correct the energies for radicals and hydrocarbons. This potential is implemented without these lookup tables.
  Note: The paper describes two parameter sets, denoted as I and II.
  Parameter set I:

  from atomistica import Brenner, Brenner_PRB_42_9458_C_I  
  calc = Brenner(**Brenner_PRB_42_9458_C_I)
  

  Parameter set II:

  from atomistica import Brenner, Brenner_PRB_42_9458_C_II  
  calc = Brenner(**Brenner_PRB_42_9458_C_II)
  

• Karsten Albe, Kai Nordlund, Robert S. Averback
  "Analytical bond-order potential for platinum-carbon"
  Phys. Rev. B 65, 195124 (2002) - http://dx.doi.org/10.1103/PhysRevB.65.195124

  from atomistica import Brenner, Albe_PRB_65_195124_PtC  
  calc = Brenner(**Albe_PRB_65_195124_PtC)
  

• Krister O.E. Henriksson, Kai Nordlund
  "Simulations of cementite: An analytical potential for the Fe-C system"
  Phys. Rev. B 79, 144107 (2009) - http://dx.doi.org/10.1103/PhysRevB.79.144107

  from atomistica import Brenner, Henriksson_PRB_79_114107_FeC  
  calc = Brenner(**Henriksson_PRB_79_114107_FeC)
  

• J. Kioseoglou, Ph. Komninou, Th. Karakostas
  "Interatomic potential calculations of III (Al, In)-N planar defects with a III‐species environment approach"
  Phys. Stat. Sol. (b) 245, 1118 (2008) - http://dx.doi.org/10.1002/pssb.200844122

  from atomistica import Brenner, Kioseoglou_PSSb_245_1118_AlN  
  calc = Brenner(**Kioseoglou_PSSb_245_1118_AlN)
  

Potentials that employ the REBO2 functional form:

• Donald W. Brenner, Olga A. Shenderova, Judith A. Harrison, Steven J. Stuart, Boris Ni, Susan B. Sinnott
  "A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons"
  J. Phys.: Condens. Matter 14, 783 (2002) - http://dx.doi.org/10.1088/0953-8984/14/4/312

  from atomistica import Rebo2  
  calc = Rebo2()
  

Special potentials:

• N. Juslin, Paul Erhart, P. Traskelin, J. Nord, Krister O.E. Henriksson, Kai Nordlund, E. Salonen, Karsten Albe
  "Analytical interatomic potential for modeling nonequilibrium processes in the W–C–H system"
  J. Appl. Phys. 98, 123520 (2005) - http://dx.doi.org/10.1063/1.2149492

  from atomistica import Juslin, Juslin_JAP_98_123520_WCH  
  calc = Juslin(**Juslin_JAP_98_123520_WCH)
  

  Note: This is the default parameter set for this potential. It gets loaded by the following code.

  from atomistica import Juslin  
  calc = Juslin()
  

• T. Kumagai, S. Izumi, S. Hara, S. Sakai
  "Development of bond-order potentials that can reproduce the elastic constants and melting point of silicon for classical molecular dynamics simulation"
  Comp. Mater. Sci. 39, 457 (2007) - http://dx.doi.org/10.1016/j.commatsci.2006.07.013

  from atomistica import Kumagai, Kumagai_CompMaterSci_39_457_Si  
  calc = Kumagai(**Kumagai_CompMaterSci_39_457_Si)
  

  Note: This is the default parameter set for this potential. It gets loaded by the following code.

  from atomistica import Kumagai  
  calc = Kumagai()
  

Screened empirical bond-order potentials

• Lars Pastewka, Pablo Pou, Ruben Perez, Peter Gumbsch, Michael Moseler
  "Describing bond-breaking processes by reactive potentials: Importance of an environment-dependent interaction range"
  Phys. Rev. B 78, 161402(R) (2008) - http://dx.doi.org/10.1103/PhysRevB.78.161402

  from atomistica import Rebo2Scr  
  calc = Rebo2Scr()
  

• Lars Pastewka, Andreas Klemenz, Peter Gumbsch, Michael Moseler
  "Screened empirical bond-order potential for Si-C"
  Phys. Rev. B 87, 205410 (2013) - http://dx.doi.org/10.1103/PhysRevB.87.205410
  arXiv:1301.2142 - http://arxiv.org/abs/1301.2142
  This paper describes screened versions of the Tersoff, Erhart & Albe and Kumagai potentials.

  from atomistica import TersoffScr, Tersoff_PRB_39_5566_Si_C__Scr  
  calc = TersoffScr(**Tersoff_PRB_39_5566_Si_C__Scr)  
  from atomistica import BrennerScr, Erhart_PRB_71_035211_SiC__Scr  
  calc = BrennerScr(**Erhart_PRB_71_035211_SiC__Scr)  
  from atomistica import KumagaiScr, Kumagai_CompMaterSci_39_457_Si__Scr  
  calc = KumagaiScr(**Kumagai_CompMaterSci_39_457_Si__Scr)
  

• A general overview on bond-order potentials can be found in
  Lars Pastewka, Matous Mrovec, Michael Moseler, Peter Gumbsch
  "Bond order potentials for fracture, wear, and plasticity"
  MRS Bulletin 37, 493 (2012) - http://dx.doi.org/10.1557/mrs.2012.94

Embedded-atom method potentials

• General EAM potentials tabulated in the DYNAMO 'setfl' format.
  See http://www.ctcms.nist.gov/~cbecker/ for a database of potential datafiles.