diff --git a/doc/src/Bibliography.rst b/doc/src/Bibliography.rst index cf64eb46b9..75082eb37c 100644 --- a/doc/src/Bibliography.rst +++ b/doc/src/Bibliography.rst @@ -721,17 +721,14 @@ Bibliography **(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 - **(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, Macromolecules 53, 3007-3020 (2020). **(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 + J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, Comput. Phys. Commun., 185, 1987-1998 (2014). **(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 + J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014). **(Larsen)** Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016). @@ -782,7 +779,7 @@ Bibliography Liang, Phillpot, Sinnott Phys. Rev. B79 245110, (2009), Erratum: Phys. Rev. B85 199903(E), (2012) **(Lisal)** - M.\ Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.", + M.\ Lisal, J.K. Brennan, J. Bonet Avalos, J. Chem. Phys., 135, 204105 (2011). **(Liu1)** L.\ Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal of Physical Chemistry A, 115, 11016-11022 (2011). @@ -799,6 +796,15 @@ Bibliography **(Luding, 2008)** Luding, S. (2008). Cohesive, frictional powders: contact models for tension. Granular matter, 10(4), 235. +**(Lysogorskiy)** + Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021). + +**(Lysogorskiy21)** + Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021). + +**(Lysogorskiy23)** + Lysogorskiy, Bochkarev, Mrovec, Drautz, Phys Rev Mater, 7, 043801 (2023) / arXiv:2212.08716 (2022). + **(Maaravi)** T.\ Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017). @@ -817,12 +823,18 @@ Bibliography **(Maginn)** Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, 260, 218-231 (2007). +**(Mahoney)** + Mahoney, Jorgensen, J Chem Phys 112, 8910 (2000) + **(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. +**(Mandelli_1)** + D. Mandelli, W. Ouyang, M. Urbakh, and O. Hod, ACS Nano 13(7), 7603-7609 (2019). + **(Maras)** Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp Phys Comm, 205, 13-21 (2016). @@ -838,6 +850,9 @@ Bibliography **(Martyna1994)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). +**(Martyna2)** + G. Martyna, A. Hughes, M. Tuckerman, J. Chem. Phys. 110, 3275 (1999). + **(Mason)** J.\ K. Mason, Acta Cryst A65, 259 (2009). @@ -877,6 +892,9 @@ Bibliography **(Mie)** G.\ Mie, Ann Phys, 316, 657 (1903). +**(Milano)** + G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005). + **(Miller1)** T.\ F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002). @@ -907,12 +925,18 @@ Bibliography **(Mitchell2011a)** Mitchell. A Nonlocal, Ordinary, State-Based Plasticity Model for Peridynamics. Sandia National Lab Report, 3166:1-34 (2011). +**(Miyazaki)** + Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020). + **(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). +**(Monti)** + Monti, Clemmer, Srivastava, Silbert, Grest, and Lechman, Phys. Rev. E, (2022). + **(Moore)** Moore, J Chem Phys, 144, 104501 (2016). @@ -932,7 +956,7 @@ Bibliography 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) `_ + Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, `Phys. Rev. E [92], 043303 (2015) `_ **(Muller-Plathe1)** Muller-Plathe, J Chem Phys, 106, 6082 (1997). @@ -952,9 +976,6 @@ Bibliography **(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). @@ -964,12 +985,24 @@ Bibliography **(Neyts)** E.\ C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320 (2013). +**(Nguyen2023)** + Nguyen, Physical Review B, 107(14), 144103, (2023). + +**(Nguyen2024)** + Nguyen, Journal of Computational Physics, 113102, (2024). + +**(Nguyen and Rohskopf)** + Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023). + +**(Nguyen and Sema)** + Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024). + +**(NguyenTD)** + Nguyen, Li, Bagchi, Solis, Olvera de la Cruz, Comput Phys Commun 241, 80-19 (2019) + **(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). @@ -982,6 +1015,9 @@ Bibliography **(Niklasson2017)** A.\ M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017). +**(Nitol)** + Nitol, Dickel, and Barrett, Computational Materials Science 188 (2021): 110207. + **(Noid)** Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J Chem Phys 128, 134105 (2008). @@ -1003,6 +1039,9 @@ Bibliography **(O'Connor)** O'Connor et al., J. Chem. Phys. 142, 024903 (2015). +**(O'Hearn)** + O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1--C22 (2020). + **(Okabe)** T.\ Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001). @@ -1012,6 +1051,8 @@ Bibliography **(Omelyan)** Omelyan, Mryglod, and Folk. Phys. Rev. Lett. 86(5), 898. (2001). +**(OPLS-AA96)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996). + **(Oppelstrup)** Oppelstrup, unpublished, 2015. Oppelstrup and Moriarty, to be published. @@ -1033,14 +1074,17 @@ Bibliography **(Ouyang2)** W.\ Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020). -**(PASS)** - PASS webpage: https://www.sdu.dk/en/DPASS +**(Ouyang_1)** + W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020). -**(PLUMED)** - G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014) +**(Ouyang6)** + W. Ouyang, O. Hod, and R. Guerra, J. Chem. Theory Comput. 17, 7215 (2021). -**(Pavlov)** -D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024). +**(Ouyang7)** + W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021). + +**(Palkar)** + Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022 **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 `_. @@ -1051,21 +1095,33 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo **(Parks)** Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), 777-783 (2008). -**(Parrinello1981)** +**(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). +**(PASS)** + PASS webpage: https://www.sdu.dk/en/DPASS + **(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). +**(Pavlov1)** + D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024). + +**(Pavlov2)** + Pavlov, Galigerov, Kolotinskii, Nikolskiy, Stegailov, "GPU-based Molecular Dynamics of Fluid Flows: Reaching for Turbulence", Int. J. High Perf. Comp. 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Phys. 102, 511 (1995). + **(Silbert)** Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev E, 64, p 051302 (2001). @@ -1231,12 +1341,21 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo **(Silling 2000)** Silling, J Mech Phys Solids, 48, 175-209 (2000). +**(Silling 2005)** + Silling Askari, Computer and Structures, 83, 1526-1535 (2005). + **(Silling 2007)** Silling, Epton, Weckner, Xu, Askari, J Elasticity, 88, 151-184 (2007). **(Singh)** Singh and Warner, Acta Mater, 58, 5797-5805 (2010), +**(Singraber, Behler and Dellago 2019)** + Singraber, A.; Behler, J.; Dellago, C. J., Chem. Theory Comput. 2019, 15 (3), 1827-1840 + +**(Singraber et al 2019)** + Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C., J. Chem. Theory Comput. 2019, 15 (5), 3075-3092. + **(Sirk1)** Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J Chem Phys, 136 (13) 134903, 2012. @@ -1249,6 +1368,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo **(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015). +**(Son)** + Son, McDaniel, Cui and Yethiraj, J Phys Chem Lett, 10, 7523 (2019). + **(Srivastava)** Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417 (2005). @@ -1258,6 +1380,12 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo **(Steinhardt)** P.\ Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983). +**(Steward)** + Stewart, Spearot, Modelling Simul. Mater. Sci. Eng. 21, 045003, (2013). + +**(Stewart2018)** + J.A. Stewart, et al. 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Phys. 104, 9932 (1996). + **(Tersoff_1)** J.\ Tersoff, Phys Rev B, 37, 6991 (1988). @@ -1363,6 +1500,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo **(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018). +**(Tribello)** + G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014) + **(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), @@ -1381,6 +1521,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo **(Tuckerman4)** Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, 106, 5615 (1997). +**(Tyagi)** + Tyagi, Suzen, Sega, Barbosa, Kantorovich, Holm, J Chem Phys, 132, 154112 (2010) + **(Ulomek)** Ulomek, Brien, Foiles, Mohles, Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007 @@ -1390,6 +1533,15 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo **(Valone)** Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006). +**(vanWijk)** + M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014) + +**(Van Workum)** + K. Van Workum et al., J. Chem. Phys. 125 144506 (2006) + +**(Vargas and McCarthy 2001)** + Vargas, W.L. and McCarthy, J.J. (2001). + **(Varshalovich)** Varshalovich, Moskalev, Khersonskii, Quantum Theory of Angular Momentum, World Scientific, Singapore (1987). @@ -1402,6 +1554,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo **(Veld)** In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007). +**(Verstraelen)** + Verstraelen, Ayers, Speybroeck, Waroquier, J. Chem. Phys. 138, 074108 (2013). + **(Volkov1)** Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010). @@ -1426,6 +1581,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo **(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. +**(Wang2020)** + X. Wang, S. Ramirez-Hinestrosa, J. Dobnikar, and D. Frenkel, Phys. Chem. Chem. Phys. 22, 10624 (2020). + **(Wang1)** J.\ Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011). @@ -1465,6 +1623,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo **(Wicaksono2)** Wicaksono, figshare, https://doi.org/10.6084/m9.figshare.1488628.v1 (2015). +**(Winkler)** + Winkler, Wysocki, and Gompper, Soft Matter, 11, 6680 (2015). + **(Wirnsberger)** Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 (2015). @@ -1477,9 +1638,27 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo **(Wood)** Wood and Thompson, J Chem Phys, 148, 241721, (2018) +**(Xie23)** + Xie, S.R., Rupp, M. & Hennig, R.G. Ultra-fast interpretable machine-learning potentials. npj Comput Mater 9, 162 (2023). https://doi.org/10.1038/s41524-023-01092-7 + +**(Yade-DEM)** + V. Smilauer et al. (2021), Yade Documentation 3rd ed. + +**(Yanxon2020)** + Yanxon, Zagaceta, Tang, Matteson, Zhu, Mach. Learn.: Sci. Technol. 2, 027001 (2020). + **(Yeh)** Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999). +**(Yuan2010a)** + Yuan, Huang, Li, Lykotrafitis, Zhang, Phys. Rev. E, 82, 011905(2010). + +**(Yuan2010b)** + Yuan, Huang, Zhang, Soft. Matter, 6, 4571(2010). + +**(Zagaceta2020)** + Zagaceta, Yanxon, Zhu, J Appl Phys, 128, 045113 (2020). + **(ZBL)** J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges of Ions in Matter' Vol 1, 1985, Pergamon Press. @@ -1552,8 +1731,3 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo **(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) diff --git a/doc/src/Howto_moltemplate.rst b/doc/src/Howto_moltemplate.rst index bb068a2e93..1b34169a4f 100644 --- a/doc/src/Howto_moltemplate.rst +++ b/doc/src/Howto_moltemplate.rst @@ -367,5 +367,4 @@ And execute the simulation with the following: .. _OPLSAA96: -**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, -118(45), 11225-11236 (1996). +**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996). diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 44f569548b..90581babbb 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -643,5 +643,4 @@ checked, *maxtry* = 10, and *units* = lattice. .. _Roberts2019: -**(Roberts)** R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning. -``_ +**(Roberts)** R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning. ``_ diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index ef5a5ed073..284d8c0116 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -83,14 +83,8 @@ none .. _Lisal1: -**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative -particle dynamics at isothermal, isobaric, isoenergetic, and -isoenthalpic conditions using Shardlow-like splitting algorithms.", -J. Chem. Phys., 135, 204105 (2011). +**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, J. Chem. Phys., 135, 204105 (2011). .. _Larentzos3: -**(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 -Laboratory, Aberdeen Proving Ground, MD (2014). +**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014). diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index bc2684af53..3cbb4ae441 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -29,25 +29,28 @@ Description Specifies that the Shardlow splitting algorithm (SSA) is to be used to integrate the DPD equations of motion. The SSA splits the integration into a stochastic and deterministic integration step. The fix -*shardlow* performs the stochastic integration step and must be used -in conjunction with a deterministic integrator (e.g. :doc:`fix nve ` or :doc:`fix nph `). The stochastic -integration of the dissipative and random forces is performed prior to -the deterministic integration of the conservative force. Further -details regarding the method are provided in :ref:`(Lisal) ` and +*shardlow* performs the stochastic integration step and must be used in +conjunction with a deterministic integrator (e.g. :doc:`fix nve +` or :doc:`fix nph `). The stochastic integration of +the dissipative and random forces is performed prior to the +deterministic integration of the conservative force. Further details +regarding the method are provided in :ref:`(Lisal) ` and :ref:`(Larentzos1) `. -The fix *shardlow* must be used with the :doc:`pair_style dpd/fdt ` or :doc:`pair_style dpd/fdt/energy ` command to properly initialize the -fluctuation-dissipation theorem parameter(s) sigma (and kappa, if -necessary). +The fix *shardlow* must be used with the :doc:`pair_style dpd/fdt +` or :doc:`pair_style dpd/fdt/energy ` command +to properly initialize the fluctuation-dissipation theorem parameter(s) +sigma (and kappa, if necessary). Note that numerous variants of DPD can be specified by choosing an -appropriate combination of the integrator and :doc:`pair_style dpd/fdt ` command. DPD under isothermal conditions can -be specified by using fix *shardlow*, fix *nve* and pair_style -*dpd/fdt*\ . DPD under isoenergetic conditions can be specified by -using fix *shardlow*, fix *nve* and pair_style *dpd/fdt/energy*\ . DPD -under isobaric conditions can be specified by using fix shardlow, fix -*nph* and pair_style *dpd/fdt*\ . DPD under isoenthalpic conditions can -be specified by using fix shardlow, fix *nph* and pair_style +appropriate combination of the integrator and :doc:`pair_style dpd/fdt +` command. DPD under isothermal conditions can be specified +by using fix *shardlow*, fix *nve* and pair_style *dpd/fdt*\ . DPD +under isoenergetic conditions can be specified by using fix *shardlow*, +fix *nve* and pair_style *dpd/fdt/energy*\ . DPD under isobaric +conditions can be specified by using fix shardlow, fix *nph* and +pair_style *dpd/fdt*\ . DPD under isoenthalpic conditions can be +specified by using fix shardlow, fix *nph* and pair_style *dpd/fdt/energy*\ . Examples of each DPD variant are provided in the examples/PACKAGES/dpd-react directory. @@ -88,21 +91,12 @@ none .. _Lisal: -**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative -particle dynamics as isothermal, isobaric, isoenergetic, and -isoenthalpic conditions using Shardlow-like splitting algorithms.", -J. Chem. Phys., 135, 204105 (2011). +**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, J. Chem. Phys., 135, 204105 (2011). .. _Larentzos1sh: -**(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 -Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014). +**(Larentzos1)** J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, Comput. Phys. Commun., 185, 1987-1998 (2014). .. _Larentzos2sh: -**(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 -Laboratory, Aberdeen Proving Ground, MD (2014). +**(Larentzos2)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014). diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index efe7b3ed66..5d4d3ad1c0 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -183,7 +183,4 @@ none .. _Lisal3: -**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative -particle dynamics at isothermal, isobaric, isoenergetic, and -isoenthalpic conditions using Shardlow-like splitting algorithms.", -J. Chem. Phys., 135, 204105 (2011). +**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, J. Chem. Phys., 135, 204105 (2011). diff --git a/doc/src/pair_kolmogorov_crespi_z.rst b/doc/src/pair_kolmogorov_crespi_z.rst index 937d868b55..593a3896f4 100644 --- a/doc/src/pair_kolmogorov_crespi_z.rst +++ b/doc/src/pair_kolmogorov_crespi_z.rst @@ -86,5 +86,4 @@ none .. _vanWijk: -**(vanWijk)** M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, -Physical Review Letters, 113, 135504 (2014) +**(vanWijk)** M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014) diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst index 3d1498b769..282da39ff7 100644 --- a/doc/src/pair_spin_dmi.rst +++ b/doc/src/pair_spin_dmi.rst @@ -100,8 +100,6 @@ none .. _Tranchida5: -**(Rohart)** Rohart and Thiaville, -Physical Review B, 88(18), 184422. (2013). +**(Rohart)** Rohart and Thiaville, Physical Review B, 88(18), 184422. (2013). -**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, -Journal of Computational Physics, 372, 406-425, (2018). +**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018).