lammps/doc/src/Bibliography.rst

Bibliography
************

**(Ackland)**
   Ackland, Jones, Phys Rev B, 73, 054104 (2006).

**(Ackland1)**
   Ackland, Condensed Matter (2005).

**(Ackland2)**
   Ackland, Mendelev, Srolovitz, Han and Barashev, Journal of Physics: Condensed Matter, 16, S2629 (2004).

**(Addington)**
   Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018).

**(Adhikari et al.)**
   Adhikari, R., Stratford, K.,  Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479.

**(Afshar)**
   Afshar, F. Schmid, A. Pishevar, S. Worley, Comput Phys Comm, 184, 1119-1128 (2013).

**(Agnolin and Roux 2007)**
   Agnolin, I. & Roux, J-N. (2007). Internal states of model isotropic granular packings. I. Assembling process, geometry, and contact networks. Phys. Rev. E, 76, 061302.

**(Aktulga)**
   Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012).

**(Albe)**
   J.\  Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003).

**(Albe)**
   K.\  Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002).

**(Allen)**
   Allen and Germano, Mol Phys 104, 3225-3235 (2006).

**(Allen)**
   Allen and Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987.

**(AllenTildesley)**
   Allen and Tildesley, Computer Simulation of Liquids, Oxford University Press (1987)

**(Allinger)**
   Allinger, Yuh, Lii, JACS, 111(23), 8551-8566 (1989),

**(Andersen)**
   H.\  Andersen, J of Comp Phys, 52, 24-34 (1983).

**(Anderson)**
   Anderson, Mukherjee, Critchley, Ziegler, and Lipton "POEMS: Parallelizable Open-source Efficient Multibody Software ", Engineering With Computers (2006).

**(Avendano)**
   C.\  Avendano, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011).

**(Axilrod)**
   Axilrod and Teller, J Chem Phys, 11, 299 (1943); Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943).

**(Babadi)**
   Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).

**(Babadi)**
   Babadi and Ejtehadi, EPL, 77 (2007) 23002.

**(Baczewski)**
   A.D. Baczewski and S.D. Bond, J. Chem. Phys. 139, 044107 (2013).

**(Bal)**
   K.\  M Bal and E. C. Neyts, J. Chem. Phys. 141, 204104 (2014).

**(Ball)**
   Ball and Melrose, Physica A, 247, 444-472 (1997).

**(Ballenegger)**
   Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107 (2009).

**(Banna)**
   Volkov, Banna, Comp. Mater. Sci. 176, 109410 (2020).

**(Barrat)**
   Barrat and Rodney, J. Stat. Phys, 144, 679 (2011).

**(Barrett)**
   Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012).

**(Bartok)**
   Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).

**(Bartok2010)**
   Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).

**(Bartok_2010)**
   AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical Review Letters 104, 136403 (2010).

**(Bartok_PhD)**
   A Bartok-Partay, PhD Thesis, University of Cambridge, (2010).

**(Baskes)**
   Baskes, Phys Rev B, 46, 2727-2742 (1992).

**(Beck)**
   Beck, Molecular Physics, 14, 311 (1968).

**(Bennet)**
   Bennet, J Comput Phys, 22, 245 (1976)

**(Berardi)**
   Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998). Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).

**(Berendsen)**
   Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).

**(Berendsen)**
   Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984).

**(Bessarab)**
   Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, 335-347 (2015).

**(Beutler)**
   Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem Phys Lett, 222, 529 (1994).

**(Bialke)**
   J.\  Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.

**(Bird)**
   G.\  A. Bird, "Molecular Gas Dynamics and the Direct Simulation of Gas Flows" (1994).

**(Bitzek)**
   Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, 97, 170201 (2006).

**(Bond)**
   Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007).

**(Boone)**
   Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019).

**(BoreschKarplus)**
   Boresch and Karplus, J Phys Chem A, 103, 103 (1999)

**(Botu1)**
   V.\  Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015).

**(Botu2)**
   V.\  Botu and R. Ramprasad, Phys. Rev. B, 92(9), 094306 (2015).

**(Botu3)**
   V.\  Botu, R. Batra, J. Chapman and R. Ramprasad, https://arxiv.org/abs/1610.02098 (2016).

**(Branicio2009)**
   Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002

**(Brennan)**
   Brennan, J Chem Phys Lett, 5, 2144-2149 (2014).

**(Brenner)**
   Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J Physics: Condensed Matter, 14, 783-802 (2002).

**(Brilliantov)**
   Brilliantov, Spahn, Hertzsch, Poschel, Phys Rev E, 53, p 5382-5392 (1996).

**(Brooks)**
   Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).

**(Brooks)**
   Brooks, et al, J Comput Chem, 30, 1545 (2009).

**(Brown)**
   Brown et al. International Tables for Crystallography Volume C: Mathematical and Chemical Tables, 554-95 (2004).

**(Buck)**
   Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36 (2006).

**(Bussi)**
   G.\  Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007)

**(Bussi1)**
   Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)

**(Bussi2)**
   Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)

**(COMB)**
   T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)

**(COMB3)**
   T.\  Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek, Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74, 255-279 (2013).

**(COMB_1)**
   J.\  Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),

**(Calhoun)**
   A.\  Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996).

**(Campana)**
   C.\  Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_

**(Cao1)**
   J.\  Cao and B. Berne, J Chem Phys, 99, 2902 (1993).

**(Cao2)**
   J.\  Cao and G. Voth, J Chem Phys, 100, 5093 (1994).

**(Caro)**
   A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)

**(CasP)**
   CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html

**(Cawkwell2012)**
   A.\  M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012).

**(Cercignani)**
   C.\  Cercignani and M. Lampis. Trans. Theory Stat. Phys. 1, 2, 101 (1971).

**(Cerda)**
   Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)

**(Ceriotti)**
   Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6, 1170-80 (2010)

**(Ceriotti2)**
   Ceriotti, Bussi and Parrinello, Phys Rev Lett 103, 030603 (2009)

**(Cerutti)**
   Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory and Computation 5, 2322 (2009)

**(Chen)**
   J Chen, D Tzou and J Beraun, Int. J. Heat Mass Transfer, 49, 307-316 (2006).

**(Chenoweth_2008)**
   Chenoweth, van Duin and Goddard, Journal of Physical Chemistry A, 112, 1040-1053 (2008).

**(Clarke)**
   Clarke and Smith, J Chem Phys, 84, 2290 (1986).

**(Coleman)**
   Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013).

**(Colliex)**
   Colliex et al. International Tables for Crystallography Volume C: Mathematical and Chemical Tables, 249-429 (2004).

**(Cooke)**
   "Cooke, Kremer and Deserno, Phys. Rev. E, 72, 011506 (2005)"

**(Cornell)**
   Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).

**(Cusentino)**
   Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)

**(Daivis and Todd)**
   Daivis and Todd, J Chem Phys, 124, 194103 (2006).

**(Daivis and Todd)**
   Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

**(Dammak)**
   Dammak, Chalopin, Laroche, Hayoun, and Greffet, Phys Rev Lett, 103, 190601 (2009).

**(Darden)**
   Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).

**(Davidchack)**
   R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).

**(Daw1)**
   Daw, Baskes, Phys Rev Lett, 50, 1285 (1983). Daw, Baskes, Phys Rev B, 29, 6443 (1984).

**(Daw2)**
   M.\  S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984).

**(DeVane)**
   Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).

**(Deserno)**
   Deserno and Holm, J Chem Phys, 109, 7694 (1998).

**(Destree)**
   M.\  Destree, F. Laupretre, A. Lyulin, and J.-P.  Ryckaert, J Chem Phys, 112, 9632 (2000).

**(Dobson)**
   Dobson, J Chem Phys, 141, 184103 (2014).

**(Duffy)**
   D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19, 016207-016218 (2007).

**(Dullweber)**
   Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, 5840 (1997).

**(Dunn1)**
   Dunn and Noid, J Chem Phys, 143, 243148 (2015).

**(Dunn2)**
   Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).

**(Dunweg)**
   Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).

**(EDIP)**
   J F Justo et al, Phys Rev B 58, 2539 (1998).

**(Eike)**
   Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006).

**(Elliott)**
   Elliott, Tadmor and Bernstein, `https://openkim.org/kim-api <https://openkim.org/kim-api>`_ (2011) doi: `https://doi.org/10.25950/FF8F563A <https://doi.org/10.25950/FF8F563A>`_

**(Elstner)**
   M.\  Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998).

**(Erdmann)**
   U.\  Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, Eur. Phys. J. B 15, 105-113, 2000.

**(Espanol and Revenga)**
   Espanol, Revenga, Physical Review E, 67, 026705 (2003).

**(Espanol1997)**
   Espanol, Europhys Lett, 40(6): 631-636 (1997).  DOI: 10.1209/epl/i1997-00515-8

**(Evans and Morriss)**
   Evans and Morriss, Phys Rev A, 30, 1528 (1984).

**(Evans)**
   Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986).

**(Everaers)**
   Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).

**(Faken)**
   Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).

**(Fath)**
   Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017).

**(Fennell)**
   C.\  J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006).

**(Feynman)**
   R.\  Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and Path Integrals, McGraw-Hill, New York (1965).

**(Fichthorn)**
   Fichthorn, Balankura, Qi, CrystEngComm, 18(29), 5410-5417 (2016).

**(Fily)**
   Y.\  Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012.  Default

**(Fincham)**
   Fincham, Mackrodt and Mitchell, J Phys Condensed Matter, 6, 393-404 (1994).

**(Finnis1)**
   Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).

**(Finnis2)**
   M.\  W. Finnis, A. T. Paxton, M. Methfessel, and M. van Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998).

**(Fiorin)**
   Fiorin, Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594

**(Fox)**
   Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93 (1989).

**(Fraige)**
   F.\  Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, Particuology, 6, 455 (2008).

**(Freitas)**
   Freitas, Asta, and de Koning, Computational Materials Science, 112, 333 (2016).

**(Frenkel)**
   Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.

**(GLE4MD)**
   `http://gle4md.org/ <http://gle4md.org/>`_

**(Gao)**
   Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.

**(Gissinger)**
   Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).

**(Glosli)**
   Glosli, unpublished, 2005. Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference Series, 46, 254 (2006).

**(Goldman1)**
   Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009)

**(Goldman2)**
   Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner, J. Phys. Chem. C, 117, 7885 (2013).

**(Grime)**
   Grime and Voth, to appear in J Chem Theory & Computation (2014).

**(Grimme)**
   Grimme, J Comput Chem, 27(15), 1787-1799 (2006).

**(Gronbech-Jensen1)**
   Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511 (2019)

**(Gronbech-Jensen2)**
   Gronbech-Jensen and Farago, Mol Phys, 111, 983 (2013)

**(Gronbech-Jensen3)**
   Hayre, and Farago, Comp Phys Comm, 185, 524 (2014)

**(Groot)**
   Groot and Warren, J Chem Phys, 107: 4423-4435 (1997).  DOI: 10.1063/1.474784

**(Guenole)**
   Guenole, Noehring, Vaid, Houlle, Xie, Prakash, Bitzek, Comput Mater Sci, 175, 109584 (2020).

**(Gullet)**
   Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).

**(Guo)**
   Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).

**(Hardy)**
   David Hardy thesis: Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006).

**(Hardy2)**
   Hardy, Stone, Schulten, Parallel Computing, 35, 164-177 (2009).

**(Hecht)**
   Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005).

**(Henkelman1)**
   Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).

**(Henkelman2)**
   Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, 9901-9904 (2000).

**(Henkes)**
   Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011.

**(Henrich)**
   O.\  Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).

**(Hess)**
   Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.

**(Heyes)**
   Heyes, Phys Rev B, 49, 755 (1994).

**(Hijazi)**
   M.\  Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018)

**(Hockney)**
   Hockney and Eastwood, Computer Simulation Using Particles, Adam Hilger, NY (1989).

**(Holian)**
   Holian and Ravelo, Phys Rev B, 51, 11275 (1995).

**(Hone)**
   T.\  Hone, P. Rossky, G. Voth, J Chem Phys, 124, 154103 (2006).

**(Hoover)**
   Hoover, Phys Rev A, 31, 1695 (1985).

**(Hummer)**
   Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)

**(Hunt)**
   Hunt, Mol Simul, 42, 347 (2016).

**(IPI)**
   `http://epfl-cosmo.github.io/gle4md/index.html?page=ipi <http://epfl-cosmo.github.io/gle4md/index.html?page=ipi>`_

**(IPI-CPC)**
   Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).

**(Ikeshoji)**
   Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).

**(In 't Veld)**
   In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).

**(Isele-Holder)**
   Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012).

**(Isele-Holder2)**
   Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory Comput 9, 5412 (2013).

**(Ismail)**
   Ismail, Tsige, In 't Veld, Grest, Molecular Physics (accepted) (2007).

**(Ivanov)**
   Ivanov, Uzdin, Jonsson. arXiv preprint arXiv:1904.02669, (2019).

**(Izrailev)**
   Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar, Wriggers, Schulten. Computational Molecular Dynamics: Challenges, Methods, Ideas, volume 4 of Lecture Notes in Computational Science and

**(Izvekov)**
   Izvekov, Voth, J Chem Phys 123, 134105 (2005).

**(Janssens)**
   Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature Materials, 5, 124-127 (2006).

**(Jaramillo-Botero)**
   Jaramillo-Botero, Su, Qi, Goddard, Large-scale, Long-term Non-adiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments, J Comp

**(Jarzynski)**
   Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)

**(Jiang)**
   Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,  J Phys Chem Lett, 2, 87-92 (2011).

**(Johnson et al, 1971)**
   Johnson, K. L., Kendall, K., & Roberts, A. D. (1971).  Surface energy and the contact of elastic solids. Proc. R. Soc. Lond. A, 324(1558), 301-313.

**(Jones)**
   Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940.

**(Jonsson)**
   Jonsson, Mills and Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti, and Coker World Scientific, Singapore, 1998, p 385.

**(Jorgensen)**
   Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983).

**(Jusufi)**
   Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, 13783 (2008).

**(Kamberaj)**
   Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).

**(Katsura)**
   H.\  Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005)

**(Kelchner)**
   Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).

**(Khrapak)**
   Khrapak, Chaudhuri, and Morfill, J Chem Phys, 134, 054120 (2011).

**(Kim)**
   Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010).

**(Klapp)**
   Klapp, Schoen, J Chem Phys, 117, 8050 (2002).

**(Kolafa)**
   Kolafa and Perram, Molecular Simulation, 9, 351 (1992).

**(Kolmogorov)**
   A.\  N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).

**(Kong)**
   L.T. Kong, G. Bartels, C. Campana, C. Denniston, and Martin H. Muser, `Computer Physics Communications [180](6):1004-1010 (2009). <https://doi.org/10.1016/j.cpc.2008.12.035>`_

**(Kong2011)**
   L.T. Kong, `Computer Physics Communications [182](10):2201-2207, (2011). <https://doi.org/10.1016/j.cpc.2011.04.019>`_

**(Kremer)**
   Kremer, Grest, J Chem Phys, 92, 5057 (1990).

**(Kuhn and Bagi, 2005)**
   Kuhn, M. R., & Bagi, K. (2004). Contact rolling and deformation in granular media.  International journal of solids and structures, 41(21), 5793-5820.

**(Kumagai)**
   T.\  Kumagai, S. Izumi, S. Hara, S. Sakai, Comp. Mat. Science, 39, 457 (2007).

**(Kumar)**
   Kumar and Higdon, Phys Rev E, 82, 051401 (2010).

**(Kumar)**
   Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008)

**(Lamoureux and Roux)**
   G.\  Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)

**(Lamoureux)**
   Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003).

**(Larentzos)**
   J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research

**(Larentzos1)**
   J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic Dissipative Particle Dynamics Using Shardlow-Like Splitting

**(Larentzos2)**
   J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research

**(Larsen)**
   Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).

**(Lebedeva et al.)**
   I.\  V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)

**(Lechman)**
   Lechman, et al, in preparation (2010).

**(Lee)**
   Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000).

**(Lee2)**
   Lee, Baskes, Kim, Cho.  Phys. Rev. B, 64, 184102 (2001).

**(Lenart)**
   Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, 044509 (2007).

**(Lenosky)**
   Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, Kress, Modelling Simulation Materials Science Engineering, 8, 825 (2000).

**(Leven1)**
   I.\  Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).

**(Leven2)**
   I.\  Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).

**(Li2013_POF)**
   Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). DOI: 10.1063/1.4812366.

**(Li2014_JCP)**
   Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014).  DOI: 10.1016/j.jcp.2014.02.003.

**(Li2015_CC)**
   Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 (2015).  DOI: 10.1039/C5CC01684C.

**(Li2015_JCP)**
   Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015).  DOI: 10.1063/1.4923254.

**(Lisal)**
   M.\  Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.",

**(Liu1)**
   L.\  Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal of Physical Chemistry A, 115, 11016-11022 (2011).

**(Liu2)**
   Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8) 2798 (2009)

**(Los and Fasolino)**
   J.\  H. Los and A. Fasolino, Phys. Rev. B 68, 024107 (2003).

**(Los2017)**
   J.\  H. Los et al. "Extended Tersoff potential for boron nitride: Energetics and elastic properties of pristine and defective h-BN", Phys. Rev. B 96 (184108), 2017.

**(Luding, 2008)**
   Luding, S. (2008). Cohesive, frictional powders: contact models for tension. Granular matter, 10(4), 235.

**(Maaravi)**
   T.\  Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).

**(MacKerell)**
   MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).

**(Mackay and Denniston)**
   Mackay, F. E., and Denniston, C., Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces, J. Comput. Phys. 237 (2013) 289-298.

**(Mackay et al.)**
   Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.

**(Magda)**
   Magda, Tirrell, Davis, J Chem Phys, 83, 1888-1901 (1985); erratum in JCP 84, 2901 (1986).

**(Maginn)**
   Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, 260, 218-231 (2007).

**(Malolepsza)**
   Malolepsza, Secor, Keyes, J Phys Chem B 119 (42), 13379-13384 (2015).

**(Mandadapu)**
   Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.  Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.

**(Maras)**
   Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp Phys Comm, 205, 13-21 (2016).

**(Marrink)**
   Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).

**(Marshall, 2009)**
   Marshall, J. S. (2009). Discrete-element modeling of particulate aerosol flows.  Journal of Computational Physics, 228(5), 1541-1561.

**(Martyna1992)**
   Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992); Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.

**(Martyna1994)**
   Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).

**(Mason)**
   J.\  K. Mason, Acta Cryst A65, 259 (2009).

**(Mattice)**
   Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994.

**(Maxwell)**
   J.C. Maxwell, Philos. Tans. Royal Soc. London, 157: 49-88 (1867).

**(Mayergoyz)**
   I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009)

**(Mayo)**
   Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990).

**(Mees)**
   M.\  J. Mees, G. Pourtois, E. C. Neyts, B. J. Thijsse, and A. Stesmans, Phys. Rev. B 85, 134301 (2012).

**(Mei)**
   Mei, Davenport, Fernando, Phys Rev B, 43 4653 (1991)

**(Melchor)**
   Gonzalez-Melchor, Mayoral, Velazquez, and Alejandre, J Chem Phys, 125, 224107 (2006).

**(Meloni)**
   Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).

**(Meremianin)**
   Meremianin, J. Phys. A,  39, 3099 (2006).

**(Mezei)**
   Mezei, J Chem Phys, 86, 7084 (1987)

**(Mickel)**
   W.\  Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).

**(Mie)**
   G.\  Mie, Ann Phys, 316, 657 (1903).

**(Miller1)**
   T.\  F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).

**(Miller2)**
   Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys, 144, 184107 (2016).

**(Minary)**
   Minary, Martyna, and Tuckerman, J Chem Phys, 18, 2510 (2003).

**(Mindlin and Deresiewicz, 1953)**
   Mindlin, R.D., & Deresiewicz, H (1953). Elastic Spheres in Contact under Varying Oblique Force. J. Appl. Mech., ASME 20, 327-344.

**(Mindlin, 1949)**
   Mindlin, R. D. (1949). Compliance of elastic bodies in contact.  J. Appl. Mech., ASME 16, 259-268.

**(Miron)**
   R.\  A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003).

**(Mishin)**
   Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029 (2005).

**(Mitchell and Finchham)**
   Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993).

**(Mitchell2011)**
   Mitchell. A non-local, ordinary-state-based viscoelasticity model for peridynamics. Sandia National Lab Report, 8064:1-28 (2011).

**(Mitchell2011a)**
   Mitchell. A Nonlocal, Ordinary, State-Based Plasticity Model for Peridynamics. Sandia National Lab Report, 3166:1-34 (2011).

**(Mniszewski)**
   S.\  M. Mniszewski, M. J. Cawkwell, M. E. Wall, J. Mohd-Yusof, N. Bock, T. C.  Germann, and A. M. N. Niklasson, J. Chem. Theory Comput., 11, 4644 (2015).

**(Monaghan)**
   Monaghan and Gingold, Journal of Computational Physics, 52, 374-389 (1983).

**(Moore)**
   Moore, J Chem Phys, 144, 104501 (2016).

**(Mori)**
   Y.\  Mori, Y. Okamoto, J. Phys. Soc. Jpn., 7, 074003 (2010).

**(Moriarty1)**
   Moriarty, Physical Review B, 38, 3199 (1988).

**(Moriarty2)**
   Moriarty, Physical Review B, 42, 1609 (1990). Moriarty, Physical Review B 49, 12431 (1994).

**(Moriarty3)**
   Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang, Journal of Materials Research, 21, 563 (2006).

**(Morris)**
   Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).

**(Moustafa)**
   Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*\ , `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_

**(Muller-Plathe1)**
   Muller-Plathe, J Chem Phys, 106, 6082 (1997).

**(Muller-Plathe2)**
   Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).

**(Murdick)**
   D.A. Murdick, X.W. Zhou, H.N.G. Wadley, D. Nguyen-Manh, R. Drautz, and D.G. Pettifor, Phys. Rev. B, 73, 45206 (2006).

**(Murty)**
   M.V.R. Murty, H.A. Atwater, Phys Rev B, 51, 4889 (1995).

**(Nakano)**
   A.\  Nakano, Computer Physics Communications, 104, 59-69 (1997).

**(Neelov)**
   Neelov, Holm, J Chem Phys 132, 234103 (2010)

**(Negre2016)**
   C.\  F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp., 12, 3063 (2016).

**(Nelson)**
   Nelson, Halperin, Phys Rev B, 19, 2457 (1979).

**(Nettleton)**
   Nettleton and Green, J Chem Phys, 29, 6 (1958).

**(Neyts)**
   E.\  C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320 (2013).

**(Nicholson and Rutledge)**
   Nicholson and Rutledge, J Chem Phys, 145, 244903 (2016).

**(Nicklas)**
   The spline-based MEAM+SW format was first devised and used to develop potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,

**(Niklasson2002)**
   A.\  M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002).

**(Niklasson2008)**
   A.\  M. N. Niklasson, Phys. Rev. Lett., 100, 123004 (2008).

**(Niklasson2014)**
   A.\  M. N. Niklasson and M. Cawkwell, J. Chem. Phys., 141, 164123, (2014).

**(Niklasson2017)**
   A.\  M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).

**(Noid)**
   Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J Chem Phys 128, 134105 (2008).

**(Nordlund95)**
   Nordlund, Kai. Computational materials science 3.4 (1995): 448-456.

**(Nordlund98)**
   Nordlund, Kai, et al.  Physical Review B 57.13 (1998): 7556.

**(Norman)**
   G E Norman, S V Starikov, V V Stegailov et al., Contrib. Plasma Phys., 53, 129-139 (2013).

**(Noskov)**
   Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).

**(Nurdin)**
   Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000)

**(O'Connor)**
   O'Connor et al., J. Chem. Phys. 142, 024903 (2015).

**(Okabe)**
   T.\  Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001).

**(Ollila et al.)**
   Ollila, S.T.T., Denniston, C., Karttunen, M., and Ala-Nissila, T., Fluctuating lattice-Boltzmann model for complex fluids, J. Chem. Phys. 134 (2011) 064902.

**(Omelyan)**
   Omelyan, Mryglod, and Folk. Phys. Rev. Lett. 86(5), 898. (2001).

**(Oppelstrup)**
   Oppelstrup, unpublished, 2015. Oppelstrup and Moriarty, to be published.

**(Orsi)**
   Orsi & Essex, The ELBA force field for coarse-grain modeling of lipid membranes, PloS ONE 6(12): e28637, 2011.

**(Otis R. Walton)**
   Walton, O.R., Personal Communication

**(Ouldridge)**
   T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

**(Ouldridge-DPhil)**
   T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).

**(Ouyang1)**
   W.\  Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

**(Ouyang2)**
   W.\  Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).

**(PASS)**
   PASS webpage: https://www.sdu.dk/en/DPASS

**(PLUMED)**
   G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)

**(Paquay)**
   Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.

**(Park)**
   Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)

**(Parks)**
   Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), 777-783 (2008).

**(Parrinello1981)**
   Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).

**(Paula Leite2016)**
   Paula Leite , Freitas, Azevedo, and de Koning, J Chem Phys, 126, 044509 (2016).

**(Paula Leite2017)**
   Paula Leite, Santos-Florez, and de Koning, Phys Rev E, 96, 32115 (2017).

**(Pearlman)**
   Pearlman, J Chem Phys, 98, 1487 (1994)

**(Pedersen)**
   Pedersen, J. Chem. Phys., 139, 104102 (2013).

**(Peng)**
   Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76 (1996).

**(Perram)**
   Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).

**(Petersen)**
   Petersen, J Chem Phys, 103, 3668 (1995).

**(Petersen)**
   Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J Chem Phys, 132, 174106 (2010).

**(Pettifor_1)**
   D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487 (1999).

**(Pettifor_2)**
   D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84, 4124 (2000).

**(Pettifor_3)**
   D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 (2002).

**(Phillips)**
   C.\  L. Phillips, J. A. Anderson, S. C. Glotzer, Comput Phys Comm, 230, 7191-7201 (2011).

**(Piaggi)**
   Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017).

**(Pisarev)**
   V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26, 475401 (2014).

**(Pollock)**
   Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).

**(Price1)**
   Price and Brooks, J Chem Phys, 121, 10096 (2004).

**(Price2)**
   Price, Stone and Alderton, Mol Phys, 52, 987 (1984).

**(QEq/Fire)**
   T.-R. Shan, A. P. Thompson, S. J. Plimpton, in preparation

**(Qi)**
   Qi and Reed, J. Phys. Chem. A 116, 10451 (2012).

**(Ramirez)**
   J.\  Ramirez, S.K. Sukumaran, B. Vorselaars and A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010).

**(Rappe)**
   Rappe and Goddard III, Journal of Physical Chemistry, 95, 3358-3363 (1991).

**(Ravelo)**
   Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004).

**(ReaxFF)**
   A.\  C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J Physical Chemistry, 105, 9396-9049 (2001)

**(Rector)**
   Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).

**(Ree)**
   Ree, Journal of Chemical Physics, 73, 5401 (1980).

**(Reed)**
   Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003).

**(Reed2)**
   Reed, J. Phys. Chem. C, 116, 2205 (2012).

**(Rick)**
   S.\  W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141 (1994).

**(Rohart)**
   Rohart and Thiaville, Physical Review B, 88(18), 184422. (2013).

**(Rosenberger)**
   Rosenberger, Sanyal, Shell and van der Vegt,  Journal of Chemical Physics, 2019, 151 (4), 044111.

**(Rubensson)**
   E.\  H. Rubensson, A. M. N. Niklasson, SIAM J. Sci. Comput. 36 (2), 147-170, (2014).

**(Rutherford)**
   A M Rutherford and D M Duffy, J. Phys.: Condens. Matter, 19, 496201-496210 (2007).

**(Ryckaert)**
   J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen, J of Comp Phys, 23, 327-341 (1977).

**(SMTB-Q_1)**
   N.\  Salles, O. Politano, E. Amzallag, R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189

**(SMTB-Q_2)**
   E.\  Maras, N. Salles, R. Tetot, T. Ala-Nissila, H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399

**(SMTB-Q_3)**
   R.\  Tetot, N. Salles, S. Landron, E. Amzallag, Surface Science 616, 19-8722 28 (2013)

**(SRIM)**
   SRIM webpage: http://www.srim.org/

**(SW)**
   F.\  H. Stillinger, and T. A. Weber, Phys. Rev. B, 31, 5262 (1985).

**(SWM4-NDP)**
   Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys Let, 418, 245-249 (2006)

**(Sadigh)**
   B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).

**(Safran)**
   Safran, Statistical Thermodynamics of Surfaces, Interfaces, And Membranes, Westview Press, ISBN: 978-0813340791 (2003).

**(Salerno)**
   Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).

**(Sanyal1)**
   Sanyal and Shell, Journal of Chemical Physics, 2016, 145 (3), 034109.

**(Sanyal2)**
   Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693.

**(Schelling)**
   Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).

**(Schlitter1)**
   Schlitter, Swegat, Mulders, "Distance-type reaction coordinates for modelling activated processes", J Molecular Modeling, 7, 171-177 (2001).

**(Schlitter2)**
   Schlitter and Klahn, "The free energy of a reaction coordinate at multiple constraints: a concise formulation", Molecular Physics, 101, 3439-3443 (2003).

**(Schmid)**
   S.\  Bureekaew, S. Amirjalayer, M. Tafipolsky, C. Spickermann, T.K. Roy and R. Schmid, Phys. Status Solidi B, 6, 1128 (2013).

**(Schneider)**
   Schneider and Stoll, Phys Rev B, 17, 1302 (1978).

**(Schratt & Mohles)**
   Schratt, Mohles. Comp. Mat. Sci. 182 (2020) 109774  ----------

**(Schroeder)**
   Schroeder and Steinhauser, J Chem Phys, 133, 154511 (2010).

**(Semaev)**
   Semaev, Cryptography and Lattices, 181 (2001).

**(Sheppard)**
   Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 (2008).  See ref 1 in this paper for original reference to Qmin in Jonsson, Mills, Jacobsen.

**(Shinoda)**
   Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).

**(Shinoda)**
   Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).

**(Sides)**
   Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42, 199-208 (2004).

**(Silbert)**
   Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev E, 64, p 051302 (2001).

**(Silbert, 2001)**
   Silbert, L. E., Ertas, D., Grest, G. S., Halsey, T. C., Levine, D., & Plimpton, S. J. (2001).  Granular flow down an inclined plane: Bagnold scaling and rheology. Physical Review E,

**(Silling 2000)**
   Silling, J Mech Phys Solids, 48, 175-209 (2000).

**(Silling 2007)**
   Silling, Epton, Weckner, Xu, Askari, J Elasticity, 88, 151-184 (2007).

**(Singh)**
   Singh and Warner, Acta Mater, 58, 5797-5805 (2010),

**(Sirk1)**
   Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J Chem Phys, 136 (13) 134903, 2012.

**(Sirk2)**
   Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013).

**(Skomski)**
   Skomski, R. (2008). Simple models of magnetism. Oxford University Press.

**(Snodin)**
   B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).

**(Srivastava)**
   Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417 (2005).

**(Steinbach)**
   Steinbach, Brooks, J Comput Chem, 15, 667 (1994).

**(Steinhardt)**
   P.\  Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).

**(Stiles)**
   Stiles , Hubbard, and Kayser, J Chem Phys, 77, 6189 (1982).

**(Stillinger)**
   Stillinger, Weber, Phys. Rev. B 31, 5262 (1985).

**(Stoddard)**
   Stoddard and Ford, Phys Rev A, 8, 1504 (1973).

**(Streitz)**
   F.\  H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003 (1994).

**(Strong)**
   Strong and Eaves, J. Phys. Chem. B 121, 189 (2017).

**(Stuart)**
   Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486 (2000).

**(Stukowski)**
   Stukowski, Sadigh, Erhart, Caro; Modeling Simulation Materials Science & Engineering, 7, 075005 (2009).

**(Su)**
   Su and Goddard, Excited Electron Dynamics Modeling of Warm Dense Matter, Phys Rev Lett, 99:185003 (2007).

**(Sulc1)**
   P.\  Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).

**(Sulc2)**
   P.\  Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).

**(Sun)**
   Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).

**(Surblys)**
   Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).

**(Sutmann)**
   Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)

**(Swinburne)**
   Swinburne and Marinica, Physical Review Letters, 120, 1 (2018)

**(Tadmor)**
   Tadmor, Elliott, Sethna, Miller and Becker, JOM, 63, 17 (2011). doi: `https://doi.org/10.1007/s11837-011-0102-6 <https://doi.org/10.1007/s11837-011-0102-6>`_

**(Tainter 2011)**
   Tainter, Pieniazek, Lin, and Skinner, J. Chem. Phys., 134, 184501 (2011)

**(Tainter 2015)**
   Tainter, Shi, and Skinner, 11, 2268 (2015)

**(Templeton2010)**
   Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.

**(Templeton2011)**
   Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.

**(Tersoff_1)**
   J.\  Tersoff, Phys Rev B, 37, 6991 (1988).

**(Tersoff_2)**
   J.\  Tersoff, Phys Rev B, 38, 9902 (1988).

**(Tersoff_3)**
   J.\  Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)

**(Theodorou)**
   Theodorou, Suter, Macromolecules, 18, 1206 (1985).

**(Thole)**
   Chem Phys, 59, 341 (1981).

**(Thompson1)**
   Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).

**(Thompson2)**
   Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316 (2015).

**(Thornton et al, 2013)**
   Thornton, C., Cummins, S. J., & Cleary, P. W. (2013).  An investigation of the comparative behavior of alternative contact force models during inelastic collisions. Powder

**(Thornton, 1991)**
   Thornton, C. (1991). Interparticle sliding in the presence of adhesion.  J. Phys. D: Appl. Phys. 24 1942

**(To)**
   Q.D. To, V.H. Vu, G. Lauriat, and C. Leonard. J. Math. Phys. 56, 103101 (2015).

**(Todd)**
   B.\  D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", Phys. Rev. E 52, 1627 (1995).

**(Toukmaji)**
   Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113, 10913 (2000).

**(Toxvaerd)**
   Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).

**(Tranchida)**
   Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018).

**(Tsuji et al, 1992)**
   Tsuji, Y., Tanaka, T., & Ishida, T. (1992). Lagrangian numerical simulation of plug flow of cohesionless particles in a horizontal pipe. Powder technology, 71(3),

**(Tsuzuki)**
   Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).

**(Tuckerman1)**
   M.\  Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993).

**(Tuckerman2)**
   Tuckerman, Alejandre, Lopez-Rendon, Jochim, and Martyna, J Phys A: Math Gen, 39, 5629 (2006).

**(Tuckerman3)**
   Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990 (1992).

**(Tuckerman4)**
   Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, 106, 5615 (1997).

**(Ulomek)**
   Ulomek, Brien, Foiles, Mohles, Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007

**(Vaiwala)**
   Vaiwala, Jadhav, and Thaokar, J Chem Phys, 146, 124904 (2017).

**(Valone)**
   Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).

**(Varshalovich)**
   Varshalovich, Moskalev, Khersonskii, Quantum Theory of Angular Momentum, World Scientific, Singapore (1987).

**(Vashishta1990)**
   P.\  Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990).

**(Vashishta2007)**
   P.\  Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007).

**(Veld)**
   In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).

**(Volkov1)**
   Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010).

**(Volkov2)**
   Volkov, Simov and Zhigilei, APS Meeting Abstracts, Q31.013 (2008).

**(Voter1998)**
   Voter, Phys Rev B, 57, 13985 (1998).

**(Voter2000)**
   Sorensen and Voter, J Chem Phys, 112, 9599 (2000)

**(Voter2002)**
   Voter, Montalenti, Germann, Annual Review of Materials Research 32, 321 (2002).

**(Voter2013)**
   S.\  Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139, 144110 (2013).

**(Wagner)**
   Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.

**(Wang et al, 2015)**
   Wang, Y., Alonso-Marroquin, F., & Guo, W. W. (2015).  Rolling and sliding in 3-D discrete element models. Particuology, 23, 49-55.

**(Wang1)**
   J.\  Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011).

**(Wang2)**
   J.\  Wang, and A. Rockett, Phys. Rev. B, 43, 12571 (1991).

**(Wang3)**
   Wang and Holm, J Chem Phys, 115, 6277 (2001).

**(Wang4)**
   Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004).

**(Ward)**
   D.K. Ward, X.W. Zhou, B.M. Wong, F.P. Doty, and J.A. Zimmerman, Phys. Rev. B, 85,115206 (2012).

**(Warren)**
   Warren, Phys Rev E, 68, 066702 (2003).

**(Watkins)**
   Watkins and Jorgensen, J Phys Chem A, 105, 4118-4125 (2001).

**(Weeks)**
   Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)

**(WeinanE)**
   E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).

**(Wen)**
   M.\  Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, 98, 235404 (2018)

**(Wennberg)**
   Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, 9, 3527 (2013).

**(Who)**
   Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 (2012).

**(Wicaksono1)**
   Wicaksono, Sinclair, Militzer, Computational Materials Science, 117, 397-405 (2016).

**(Wicaksono2)**
   Wicaksono, figshare, https://doi.org/10.6084/m9.figshare.1488628.v1 (2015).

**(Wirnsberger)**
   Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 (2015).

**(Wolf)**
   D.\  Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem Phys, 110, 8254 (1999).

**(Wolff)**
   Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).

**(Wood)**
   Wood and Thompson, J Chem Phys, 148, 241721, (2018)

**(Yeh)**
   Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).

**(ZBL)**
   J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges of Ions in Matter' Vol 1, 1985, Pergamon Press.

**(Zhang1)**
   Zhang and Makse, Phys Rev E, 72, p 011301 (2005).

**(Zhang2)**
   Zhang and Trinkle, Computational Materials Science, 124, 204-210 (2016).

**(Zhang3)**
   Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).

**(Zhang4)**
   Zhang, J Chem Phys, 106, 6102 (1997).

**(Zhang5)**
   Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B, 109, 15060-15067 (2005).

**(Zhigilei1)**
   Volkov and Zhigilei, ACS Nano 4, 6187 (2010).

**(Zhigilei2)**
   Volkov, Simov, Zhigilei, ASME paper IMECE2008, 68021 (2008).

**(Zhigilei3)**
   Volkov, Zhigilei, J. Phys. Chem. C 114, 5513 (2010).

**(Zhigilei4)**
   Wittmaack, Banna, Volkov, Zhigilei, Carbon 130, 69 (2018).

**(Zhigilei5)**
   Wittmaack, Volkov, Zhigilei, Compos. Sci. Technol. 166, 66 (2018).

**(Zhigilei6)**
   Wittmaack, Volkov, Zhigilei, Carbon 143, 587 (2019).

**(Zhigilei7)**
   Volkov, Zhigilei, Phys. Rev. Lett. 104, 215902 (2010).

**(Zhigilei8)**
   Volkov, Shiga, Nicholson, Shiomi, Zhigilei, J. Appl. Phys. 111, 053501 (2012).

**(Zhigilei9)**
   Volkov, Zhigilei, Appl. Phys. Lett. 101, 043113 (2012).

**(Zhigilei10)**
   Jacobs, Nicholson, Zemer, Volkov, Zhigilei, Phys. Rev. B 86, 165414 (2012).

**(Zhou1)**
   Zhou, Saidi, Fichthorn, J Phys Chem C, 118(6), 3366-3374 (2014).

**(Zhou3)**
   X.\  W. Zhou, M. E. Foster, R. E. Jones, P. Yang, H. Fan, and F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015).

**(Zhou4)**
   X.\  W. Zhou, M. E. Foster, J. A. Ronevich, and C. W. San Marchi, J. Comp. Chem., 41, 1299 (2020).

**(Zhu)**
   Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).

**(Ziegler)**
   J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.

**(Zimmerman2004)**
   Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319.

**(Zimmerman2010)**
   Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.

**(de Buyl)**
   de Buyl, Colberg and Hofling, H5MD: A structured, efficient, and portable file format for molecular data, Comp. Phys. Comm. 185(6), 1546-1553 (2014) -

**(de Koning)**
   de Koning and Antonelli, Phys Rev E, 53, 465 (1996).

**(electronic stopping)**
   Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29

**(tenWolde)**
   P.\  R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).

**(vanWijk)**
   M.\  M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014)