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Updates to BibTeX syntax for anything that needed it that I caught and fixes to address Issue #2597

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This commit is contained in:
Karl Hammond
2022-08-13 04:51:54 -05:00
parent c7dd679fcd
commit 29e1595fb4
64 changed files with 285 additions and 256 deletions
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6
src/ASPHERE/pair_gayberne.cpp
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@ -36,9 +36,9 @@ using namespace LAMMPS_NS;
static const char cite_pair_gayberne[] =
"pair gayberne command: doi:10.1063/1.3058435\n\n"
"@Article{Brown09,\n"
" author = {W. M. Brown, M. K. Petersen, S. J. Plimpton, and G. S. Grest},\n"
" title = {Liquid crystal nanodroplets in solution},\n"
" journal = {J.~Chem.~Phys.},\n"
" author = {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},\n"
" title = {Liquid Crystal Nanodroplets in Solution},\n"
" journal = {J.~Chem.\\ Phys.},\n"
" year = 2009,\n"
" volume = 130,\n"
" number = 4,\n"

3
src/BOCS/fix_bocs.cpp
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@ -44,7 +44,8 @@ using namespace FixConst;
static const char cite_user_bocs_package[] =
"BOCS package: doi:10.1021/acs.jpcb.7b09993\n\n"
"@Article{Dunn2018,\n"
" author = {NJH Dunn, KM Lebold, MR DeLyser, JF Rudzinski, WG Noid},\n"
" author = {N. J. H. Dunn and K. M. Lebold and M. R. {DeLyser} and\n"
" J. F. Rudzinski and W. G. Noid},\n"
" title = {{BOCS}: Bottom-Up Open-Source Coarse-Graining Software},\n"
" journal = {J.~Phys.\\ Chem.~B},\n"
" year = 2018,\n"

12
src/DIELECTRIC/atom_vec_dielectric.cpp
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@ -21,13 +21,13 @@
using namespace LAMMPS_NS;
static const char cite_user_dielectric_package[] =
"DIELECTRIC package:\n\n"
"DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006\n\n"
"@Article{TrungCPC19,\n"
" author = {Trung Dac Nguyen, Honghao Li, Debarshee Bagchi,"
" Francisco J. Solis, Monica Olvera de la Cruz,\n"
" title = {Incorporating surface polarization effects into large-scale"
" coarse-grained Molecular Dynamics simulation},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and"
" Francisco J. Solis and Olvera de la Cruz, Monica}\n"
" title = {Incorporating Surface Polarization Effects Into Large-Scale"
" Coarse-Grained Molecular Dynamics Simulation},\n"
" journal = {Comput.\\ Phys.\\ Commun.},\n"
" year = 2019,\n"
" volume = 241,\n"
" pages = {80--91}\n"

4
src/DIFFRACTION/compute_saed.cpp
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@ -39,8 +39,8 @@ using namespace MathConst;
static const char cite_compute_saed_c[] =
"compute_saed command: doi:10.1088/0965-0393/21/5/055020\n\n"
"@Article{Coleman13,\n"
" author = {S. P. Coleman, D. E. Spearot, L. Capolungo},\n"
" title = {Virtual diffraction analysis of Ni [010] symmetric tilt grain boundaries},\n"
" author = {S. P. Coleman and D. E. Spearot and L. Capolungo},\n"
" title = {Virtual Diffraction Analysis of {Ni} [010] Symmetric Tilt Grain Boundaries},\n"
" journal = {Modelling and Simulation in Materials Science and Engineering},\n"
" year = 2013,\n"
" volume = 21,\n"

4
src/DIFFRACTION/compute_xrd.cpp
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@ -40,8 +40,8 @@ using namespace MathConst;
static const char cite_compute_xrd_c[] =
"compute_xrd command: doi:10.1088/0965-0393/21/5/055020\n\n"
"@Article{Coleman13,\n"
" author = {S. P. Coleman, D. E. Spearot, L. Capolungo},\n"
" title = {Virtual diffraction analysis of Ni [010] symmetric tilt grain boundaries},\n"
" author = {S. P. Coleman and D. E. Spearot and L. Capolungo},\n"
" title = {Virtual Diffraction Analysis of {Ni} [010] Symmetric Tilt Grain Boundaries},\n"
" journal = {Modelling and Simulation in Materials Science and Engineering},\n"
" year = 2013,\n"
" volume = 21,\n"

4
src/DPD-MESO/pair_edpd.cpp
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@ -44,7 +44,7 @@ static const char cite_pair_edpd[] =
"pair edpd command: doi:10.1016/j.jcp.2014.02.003\n\n"
"@Article{ZLi2014_JCP,\n"
" author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G.E.},\n"
" title = {Energy-conserving dissipative particle dynamics with temperature-dependent properties},\n"
" title = {Energy-Conserving Dissipative Particle Dynamics with Temperature-Dependent Properties},\n"
" journal = {Journal of Computational Physics},\n"
" year = {2014},\n"
" volume = {265},\n"
@ -52,7 +52,7 @@ static const char cite_pair_edpd[] =
"}\n\n"
"@Article{ZLi2015_CC,\n"
" author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G.E.},\n"
" title = {Mesoscale modeling of phase transition dynamics of thermoresponsive polymers},\n"
" title = {Mesoscale Modeling of Phase Transition Dynamics of Thermoresponsive Polymers},\n"
" journal = {Chemical Communications},\n"
" year = {2015},\n"
" volume = {51},\n"

4
src/DPD-MESO/pair_mdpd.cpp
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@ -39,8 +39,8 @@ using namespace LAMMPS_NS;
static const char cite_pair_mdpd[] =
"pair mdpd command: doi:10.1063/1.4812366\n\n"
"@Article{ZLi2013_POF,\n"
" author = {Li, Z. and Hu, G.H. and Wang, Z.L. and Ma Y.B. and Zhou, Z.W.},\n"
" title = {Three dimensional flow structures in a moving droplet on substrate: a dissipative particle dynamics study},\n"
" author = {Li, Z. and Hu, G. H. and Wang, Z. L. and Ma Y. B. and Zhou, Z. W.},\n"
" title = {Three Dimensional Flow Structures in a Moving Droplet on Substrate: a Dissipative Particle Dynamics Study},\n"
" journal = {Physics of Fluids},\n"
" year = {2013},\n"
" volume = {25},\n"

4
src/DPD-MESO/pair_tdpd.cpp
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@ -42,8 +42,8 @@ using namespace LAMMPS_NS;
static const char cite_pair_tdpd[] =
"pair tdpd command: doi:10.1063/1.4923254\n\n"
"@Article{ZLi2015_JCP,\n"
" author = {Li, Z. and Yazdani, A. and Tartakovsky, A. and Karniadakis, G.E.},\n"
" title = {Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems},\n"
" author = {Li, Z. and Yazdani, A. and Tartakovsky, A. and Karniadakis, G. E.},\n"
" title = {Transport Dissipative Particle Dynamics Model for Mesoscopic Advection-Diffusion-Reaction Problems},\n"
" journal = {The Journal of Chemical Physics},\n"
" year = {2015},\n"
" volume = {143},\n"

17
src/DPD-REACT/fix_shardlow.cpp
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@ -63,21 +63,22 @@ using namespace random_external_state;
#define EPSILON_SQUARED ((EPSILON) * (EPSILON))
static const char cite_fix_shardlow[] =
"fix shardlow command:\n\n"
"fix shardlow command: doi:10.1016/j.cpc.2014.03.029, doi:10.1063/1.3660209\n\n"
"@Article{Larentzos14,\n"
" author = {J. P. Larentzos, J. K. Brennan, J. D. Moore, M. Lisal, W. D. Mattson},\n"
" title = {Parallel implementation of isothermal and isoenergetic Dissipative Particle Dynamics using Shardlow-like splitting algorithms},\n"
" journal = {Computer Physics Communications},\n"
" author = {J. P. Larentzos and J. K. Brennan and J. D. Moore and M. Lisal and W. D. Mattson},\n"
" title = {Parallel Implementation of Isothermal and Isoenergetic Dissipative Particle Dynamics Using {S}hardlow-Like Splitting Algorithms},\n"
" journal = {Comput.\\ Phys.\\ Commun.},\n"
" year = 2014,\n"
" volume = 185\n"
" pages = {1987--1998}\n"
"}\n\n"
"@Article{Lisal11,\n"
" author = {M. Lisal, J. K. Brennan, J. Bonet Avalos},\n"
" title = {Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms},\n"
" journal = {Journal of Chemical Physics},\n"
" author = {M. Lisal and J. K. Brennan and J. Bonet Avalos},\n"
" title = {Dissipative Particle Dynamics at Isothermal, Isobaric, Isoenergetic, and Isoenthalpic Conditions Using {S}hardlow-Like Splitting Algorithms},\n"
" journal = {J.~Chem.\\ Phys.},\n"
" year = 2011,\n"
" volume = 135\n"
" volume = 135,\n"
" number = 20,\n"
" pages = {204105}\n"
"}\n\n";

9
src/DPD-REACT/pair_multi_lucy.cpp
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@ -44,13 +44,14 @@ enum{NONE,RLINEAR,RSQ};
#define MAXLINE 1024
static const char cite_pair_multi_lucy[] =
"pair_style multi/lucy command:\n\n"
"pair_style multi/lucy command: doi:10.1063/1.4942520\n\n"
"@Article{Moore16,\n"
" author = {J.D. Moore, B.C. Barnes, S. Izvekov, M. Lisal, M.S. Sellers, D.E. Taylor and J. K. Brennan},\n"
" title = {A coarse-grain force field for RDX: Density dependent and energy conserving},\n"
" journal = {J. Chem. Phys.},\n"
" author = {J. D. Moore and B. C. Barnes and S. Izvekov and M. Lisal and M. S. Sellers and D. E. Taylor and J. K. Brennan},\n"
" title = {A Coarse-Grain Force Field for {RDX}: Density Dependent and Energy Conserving},\n"
" journal = {J.~Chem.\\ Phys.},\n"
" year = 2016,\n"
" volume = 144\n"
" number = 10,\n"
" pages = {104501}\n"
"}\n\n";

8
src/DPD-REACT/pair_multi_lucy_rx.cpp
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@ -55,11 +55,11 @@ enum{NONE,RLINEAR,RSQ};
#define isOneFluid(_site) ( (_site) == oneFluidParameter )
static const char cite_pair_multi_lucy_rx[] =
"pair_style multi/lucy/rx command:\n\n"
"pair_style multi/lucy/rx command: doi:10.1063/1.4942520\n\n"
"@Article{Moore16,\n"
" author = {J.D. Moore, B.C. Barnes, S. Izvekov, M. Lisal, M.S. Sellers, D.E. Taylor and J. K. Brennan},\n"
" title = {A coarse-grain force field for RDX: Density dependent and energy conserving},\n"
" journal = {J. Chem. Phys.},\n"
" author = {J. D. Moore and B. C. Barnes and S. Izvekov and M. Lisal and M. S. Sellers and D. E. Taylor and J. K. Brennan},\n"
" title = {A Coarse-Grain Force Field for {RDX}: {D}ensity Dependent and Energy Conserving},\n"
" journal = {J.~Chem.\\ Phys.},\n"
" year = 2016,\n"
" volume = 144\n"
" pages = {104501}\n"

5
src/EFF/atom_vec_electron.cpp
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@ -23,14 +23,15 @@
using namespace LAMMPS_NS;
static const char cite_user_eff_package[] =
"EFF package:\n\n"
"EFF package: doi:10.1002/jcc.21637\n\n"
"@Article{Jaramillo-Botero11,\n"
" author = {A. Jaramillo-Botero, J. Su, A. Qi, W. A. Goddard III},\n"
" author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},\n"
" title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing "
"Material Properties and Phenomena in Extreme Environments},\n"
" journal = {J.~Comp.~Chem.},\n"
" year = 2011,\n"
" volume = 32,\n"
" number = 3,\n"
" pages = {497--512}\n"
"}\n\n";

6
src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
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@ -37,10 +37,10 @@ using namespace LAMMPS_NS;
------------------------------------------------------------------------------------*/
static const char cite_compute_stress_cartesian[] =
"compute stress/cartesian:\n\n"
"compute stress/cartesian: doi:10.3390/nano11010165\n\n"
"@article{galteland2021nanothermodynamic,\n"
"title={Nanothermodynamic description and molecular simulation of a single-phase fluid in a "
"slit pore},\n"
"title={Nanothermodynamic Description and Molecular Simulation of a Single-Phase Fluid in a "
"Slit Pore},\n"
"author={Galteland, Olav and Bedeaux, Dick and Kjelstrup, Signe},\n"
"journal={Nanomaterials},\n"
"volume={11},\n"

9
src/EXTRA-COMPUTE/compute_stress_cylinder.cpp
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@ -43,13 +43,14 @@ using MathSpecial::square;
------------------------------------------------------------------------------------*/
static const char cite_compute_stress_cylinder[] =
"compute stress/cylinder:\n\n"
"compute stress/cylinder: doi:10.1063/1.5037054\n\n"
"@Article{Addington,\n"
" author = {C. K. Addington, Y. Long, K. E. Gubbins},\n"
" title = {The pressure in interfaces having cylindrical geometry},\n"
" journal = {J.~Chem.~Phys.},\n"
" author = {C. K. Addington and Y. Long and K. E. Gubbins},\n"
" title = {The Pressure in Interfaces Having Cylindrical Geometry},\n"
" journal = {J.~Chem.\\ Phys.},\n"
" year = 2018,\n"
" volume = 149,\n"
" number = 8,\n"
" pages = {084109}\n"
"}\n\n";

6
src/EXTRA-COMPUTE/compute_stress_spherical.cpp
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@ -46,11 +46,11 @@ using MathSpecial::square;
------------------------------------------------------------------------------------*/
static const char cite_compute_stress_sphere[] =
"compute stress/spherical:\n\n"
"compute stress/spherical: doi:10.48550/arXiv.2201.13060\n\n"
"@article{galteland2022defining,\n"
"title={Defining the pressures of a fluid in a nanoporous, heterogeneous medium},\n"
"title={Defining the Pressures of a Fluid in a Nanoporous, Heterogeneous Medium},\n"
"author={Galteland, Olav and Rauter, Michael T and Varughese, Kevin K and Bedeaux, Dick and "
"Kjelstrup, Signe},\n"
" Kjelstrup, Signe},\n"
"journal={arXiv preprint arXiv:2201.13060},\n"
"year={2022}\n"
"}\n\n";

7
src/EXTRA-FIX/fix_ave_correlate_long.cpp
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@ -43,13 +43,14 @@ using namespace FixConst;
enum{AUTO,UPPER,LOWER,AUTOUPPER,AUTOLOWER,FULL};
static const char cite_fix_ave_correlate_long[] =
"fix ave/correlate/long command:\n\n"
"fix ave/correlate/long command: doi:10.1063/1.3491098\n\n"
"@Article{Ramirez10,\n"
" author = {Jorge Rami{\'}rez and Sathish K. Sukumaran and Bart Vorselaars and Alexei E. Likhtman},\n"
" title = {Efficient on the fly calculation of time correlation functions in computer simulations},"
" journal = {J.~Chem.~Phys.},\n"
" title = {Efficient on the Fly Calculation of Time Correlation Functions in Computer Simulations},"
" journal = {J.~Chem.\\ Phys.},\n"
" year = 2010,\n"
" volume = 133,\n"
" number = 15,\n"
" pages = {154103}\n"
"}\n\n";

16
src/EXTRA-FIX/fix_electron_stopping_fit.cpp
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@ -35,15 +35,15 @@ using namespace FixConst;
// ---------------------------------------------------------------------
static const char cite_fix_electron_stopping_fit_c[] =
"fix electron/stopping/fit command:\n\n"
"fix electron/stopping/fit command: doi:10.1063/1.5022471\n\n"
"@Article{Stewart2018,\n"
" author = { J.A. Stewart and G. Brookman and P. Price and M. Franco and W. Ji and K. Hattar and R. Dingreville },\n"
" title = { Characterizing single isolated radiation-damage events from molecular dynamics via virtual diffraction methods },\n"
" journal = { Journal of Applied Physics },\n"
" year = { 2018 },\n"
" volume = { 123 },\n"
" number = { 16 },\n"
" pages = { 165902 }\n"
" author = { J. A. Stewart and G. Brookman and P. Price and M. Franco and W. Ji and K. Hattar and R. Dingreville },\n"
" title = { Characterizing Single Isolated Radiation-Damage Events from Molecular Dynamics via Virtual Diffraction Methods },\n"
" journal = {Journal of Applied Physics},\n"
" year = {2018},\n"
" volume = {123},\n"
" number = {16},\n"
" pages = {165902}\n"
"}\n\n"
"@Article{Lee2020,\n"
" author = { C.W. Lee and J.A. Stewart and S.M. Foiles and R. Dingreville and A. Schleife },\n"

8
src/EXTRA-FIX/fix_filter_corotate.cpp
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@ -46,14 +46,14 @@ using namespace FixConst;
#define MASSDELTA 0.1
static const char cite_filter_corotate[] =
"Mollified Impulse Method with Corotational Filter:\n\n"
"Mollified Impulse Method with Corotational Filter: doi:10.1016/j.jcp.2016.12.024\n\n"
"@Article{Fath2017,\n"
" Title ="
"{A fast mollified impulse method for biomolecular atomistic simulations},\n"
" Author = {L. Fath and M. Hochbruck and C.V. Singh},\n"
"{A Fast Mollified Impulse Method for Biomolecular Atomistic Simulations},\n"
" Author = {L. Fath and M. Hochbruck and C. V. Singh},\n"
" Journal = {Journal of Computational Physics},\n"
" Year = {2017},\n"
" Pages = {180 - 198},\n"
" Pages = {180--198},\n"
" Volume = {333},\n\n"
" Doi = {https://doi.org/10.1016/j.jcp.2016.12.024},\n"
" ISSN = {0021-9991},\n"

4
src/EXTRA-FIX/fix_flow_gauss.cpp
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@ -33,7 +33,7 @@ using namespace LAMMPS_NS;
using namespace FixConst;
static const char cite_flow_gauss[] =
"Gaussian dynamics package:\n\n"
"Gaussian dynamics package: doi:10.1021/acs.jpcb.6b09387\n\n"
"@Article{strong_water_2017,\n"
"title = {The Dynamics of Water in Porous Two-Dimensional Crystals},\n"
"volume = {121},\n"
@ -41,7 +41,7 @@ static const char cite_flow_gauss[] =
"url = {https://doi.org/10.1021/acs.jpcb.6b09387},\n"
"doi = {10.1021/acs.jpcb.6b09387},\n"
"urldate = {2016-12-07},\n"
"journal = {J. Phys. Chem. B},\n"
"journal = {J.~Phys.\\ Chem.~B},\n"
"author = {Strong, Steven E. and Eaves, Joel D.},\n"
"year = {2017},\n"
"pages = {189--207}\n"

6
src/EXTRA-FIX/fix_pafi.cpp
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@ -40,11 +40,11 @@
using namespace LAMMPS_NS;
static const char cite_fix_pafi_package[] =
"citation for fix pafi:\n\n"
"citation for fix pafi: doi:10.1103/PhysRevLett.120.135503\n\n"
"@article{SwinburneMarinica2018,\n"
"author={T. D. Swinburne and M. C. Marinica},\n"
"title={Unsupervised calculation of free energy barriers in large "
"crystalline systems},\n"
"title={Unsupervised Calculation of Free Energy Barriers in Large "
"Crystalline Systems},\n"
"journal={Physical Review Letters},\n"
"volume={120},\n"
"number={13},\n"

6
src/EXTRA-FIX/fix_rhok.cpp
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@ -31,15 +31,15 @@ using namespace FixConst;
using namespace MathConst;
static const char cite_fix_rhok[] =
"Bias on the collective density field (fix rhok):\n\n"
"Bias on the collective density field (fix rhok): doi:10.1063/1.4818747\n\n"
"@Article{pedersen_jcp139_104102_2013,\n"
"title = {Direct calculation of the solid-liquid Gibbs free energy difference in a single equilibrium simulation},\n"
"title = {Direct Calculation of the Solid-Liquid {G}ibbs Free Energy Difference in a Single Equilibrium Simulation},\n"
"volume = {139},\n"
"number = {10},\n"
"url = {https://aip.scitation.org/doi/10.1063/1.4818747},\n"
"doi = {10.1063/1.4818747},\n"
"urldate = {2017-10-03},\n"
"journal = {J. Chem. Phys.},\n"
"journal = {J.~Chem.\\ Phys.},\n"
"author = {Pedersen, Ulf R.},\n"
"year = {2013},\n"
"pages = {104102}\n"

2
src/EXTRA-FIX/fix_ti_spring.cpp
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@ -38,7 +38,7 @@ static const char cite_fix_ti_spring[] =
"ti/spring command:\n\n"
"@article{freitas2016,\n"
" author={Freitas, Rodrigo and Asta, Mark and de Koning, Maurice},\n"
" title={Nonequilibrium free-energy calculation of solids using LAMMPS},\n"
" title={Nonequilibrium Free-Energy Calculation of Solids Using {LAMMPS}},\n"
" journal={Computational Materials Science},\n"
" volume={112},\n"
" pages={333--341},\n"

8
src/EXTRA-FIX/fix_ttm_mod.cpp
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@ -48,11 +48,11 @@ using namespace MathConst;
// to spatially average consistent with the TTM grid
static const char cite_fix_ttm_mod[] =
"fix ttm/mod command:\n\n"
"fix ttm/mod command: doi:10.1088/0953-8984/26/47/475401, doi:10.1002/ctpp.201310025\n\n"
"@article{Pisarev2014,\n"
"author = {Pisarev, V. V. and Starikov, S. V.},\n"
"title = {{Atomistic simulation of ion track formation in UO2.}},\n"
"journal = {J.~Phys.:~Condens.~Matter},\n"
"title = {{Atomistic Simulation of Ion Track Formation in {UO$_2$}.}},\n"
"journal = {J.~Phys.\\ Condens.\\ Matter},\n"
"volume = {26},\n"
"number = {47},\n"
"pages = {475401},\n"
@ -60,7 +60,7 @@ static const char cite_fix_ttm_mod[] =
"}\n\n"
"@article{Norman2013,\n"
"author = {Norman, G. E. and Starikov, S. V. and Stegailov, V. V. and Saitov, I. M. and Zhilyaev, P. A.},\n"
"title = {{Atomistic Modeling of Warm Dense Matter in the Two-Temperature State}},\n"
"title = {Atomistic Modeling of Warm Dense Matter in the Two-Temperature State},\n"
"journal = {Contrib.~Plasm.~Phys.},\n"
"number = {2},\n"
"volume = {53},\n"

6
src/EXTRA-MOLECULE/dihedral_table_cut.cpp
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@ -36,13 +36,13 @@ using namespace LAMMPS_NS;
using namespace MathConst;
static const char cite_dihedral_tablecut[] =
"dihedral_style table/cut command:\n\n"
"dihedral_style table/cut command: doi:10.1021/acs.jctc.7b01229\n\n"
"@Article{Salerno17,\n"
" author = {K. M. Salerno and N. Bernstein},\n"
" title = {Persistence Length, End-to-End Distance, and Structure of Coarse-Grained Polymers},\n"
" journal = {J.~Chem.~Theory Comput.},\n"
" journal = {J.~Chem.\\ Theory Comput.},\n"
" year = 2018,\n"
" DOI = 10.1021/acs.jctc.7b01229"
" DOI = \"10.1021/acs.jctc.7b01229\"\n"
"}\n\n";
/* ---------------------------------------------------------------------- */

16
src/EXTRA-PAIR/pair_e3b.cpp
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@ -468,40 +468,40 @@ void PairE3B::init_style()
}
static const char cite_E3B1[] =
"Explicit Three-Body (E3B) potential for water:\n\n"
"Explicit Three-Body (E3B) potential for water: doi:10.1021/jp8009468\n\n"
"@article{kumar_water_2008,\n"
"title = {Water Simulation Model with Explicit Three-Molecule Interactions},\n"
"volume = {112},\n"
"doi = {10.1021/jp8009468},\n"
"number = {28},\n"
"journal = {J Phys. Chem. B},\n"
"doi = {10.1021/jp8009468},\n"
"journal = {J.~Phys.\\ Chem.~B},\n"
"author = {Kumar, R. and Skinner, J. L.},\n"
"year = {2008},\n"
"pages = {8311--8318}\n"
"}\n\n";
static const char cite_E3B2[] =
"Explicit Three-Body (E3B) potential for water:\n\n"
"Explicit Three-Body (E3B) potential for water: doi:10.1063/1.3587053\n\n"
"@article{tainter_robust_2011,\n"
"title = {Robust three-body water simulation model},\n"
"title = {Robust Three-Body Water Simulation Model},\n"
"volume = {134},\n"
"doi = {10.1063/1.3587053},\n"
"number = {18},\n"
"journal = {J. Chem. Phys},\n"
"journal = {J.~Chem.\\ Phys},\n"
"author = {Tainter, C. J. and Pieniazek, P. A. and Lin, Y.-S. and Skinner, J. L.},\n"
"year = {2011},\n"
"pages = {184501}\n"
"}\n\n";
static const char cite_E3B3[] =
"Explicit Three-Body (E3B) potential for water:\n\n"
"Explicit Three-Body (E3B) potential for water: doi:10.1021/acs.jctc.5b00117\n\n"
"@article{tainter_reparametrized_2015,\n"
"title = {Reparametrized {E3B} (Explicit Three-Body) Water Model Using the {TIP4P/2005} Model "
"as a Reference},\n"
"volume = {11},\n"
"doi = {10.1021/acs.jctc.5b00117},\n"
"number = {5},\n"
"journal = {J. Chem. Theory Comput.},\n"
"journal = {J.~Chem.\\ Theory Comput.},\n"
"author = {Tainter, Craig J. and Shi, Liang and Skinner, James L.},\n"
"year = {2015},\n"
"pages = {2268--2277}\n"

10
src/EXTRA-PAIR/pair_lj_relres.cpp
View File

@ -31,18 +31,18 @@
using namespace LAMMPS_NS;
static const char cite_relres[] =
"Pair style lj/relres: doi:10.1021/acs.jctc.0c01003\n\n"
"Pair style lj/relres: doi:10.1021/acs.jctc.0c01003, doi:10.1021/acs.jctc.0c01003\n\n"
"@Article{Chaimovich1,\n"
" author = {A. Chaimovich, C. Peter, K. Kremer},\n"
" title = {Relative resolution: A hybrid formalism for fluid mixtures},\n"
" journal = {J.~Chem.~Phys.},\n"
" title = {Relative Resolution: {A} Hybrid Formalism for Fluid Mixtures},\n"
" journal = {J.~Chem.\\ Phys.},\n"
" year = 2015,\n"
" volume = 143,\n"
" pages = {243107}\n"
"@Article{Chaimovich2,\n"
" author = {M. Chaimovich, A. Chaimovich},\n"
" author = {M. Chaimovich and A. Chaimovich},\n"
" title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS},\n"
" journal = {J.~Chem.~Theory~Comput.},\n"
" journal = {J.~Chem.\\ Theory Comput.},\n"
" year = 2021,\n"
" volume = 17,\n"
" pages = {1045--1059}\n"

10
src/EXTRA-PAIR/pair_momb.cpp
View File

@ -32,16 +32,16 @@
using namespace LAMMPS_NS;
static const char cite_momb[] =
"Pair style momb:\n\n"
"Pair style momb: doi:10.1021/jp412098n\n\n"
"@Article{pair_momb_2015,\n"
"title = {A force field for describing the polyvinylpyrrolidone-mediated"
" solution-phase synthesis of shape-selective Ag nanoparticles.},\n"
"title = {A Force Field for Describing the Polyvinylpyrrolidone-Mediated"
" Solution-Phase Synthesis of Shape-Selective {Ag} Nanoparticles.},\n"
"volume = {118},\n"
"number = {6},\n"
"url = {https://doi.org/10.1021/jp412098n},\n"
"doi = {10.1021/jp412098n},\n"
"journal = {J. Phys. Chem. C},\n"
"author = {Zhou, Ya, Wissam A. Saidi, and Kristen A. Fichthorn},\n"
"journal = {J.~Phys.\ Chem.~C},\n"
"author = {Zhou, Ya and Wissam A. Saidi and Kristen A. Fichthorn},\n"
"year = {2014},\n"
"pages = {3366--3374}\n"
"}\n\n";

38
src/GPU/fix_gpu.cpp
View File

@ -53,51 +53,57 @@ extern double lmp_gpu_update_bin_size(const double subx, const double suby, cons
const int nlocal, const double cut);
static const char cite_gpu_package[] =
"GPU package (short-range, long-range and three-body potentials): doi:10.1016/j.cpc.2010.12.021\n\n"
"GPU package (short-range, long-range and three-body potentials): doi:10.1016/j.cpc.2010.12.021, doi:10.1016/j.cpc.2011.10.012, doi:10.1016/j.cpc.2013.08.002, doi:10.1016/j.commatsci.2014.10.068, doi:10.1016/j.cpc.2016.10.020, doi:10.3233/APC200086\n\n"
"@Article{Brown11,\n"
" author = {W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington},\n"
" title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" author = {W. M. Brown and P. Wang and S. J. Plimpton and A. N. Tharrington},\n"
" title = {Implementing Molecular Dynamics on Hybrid High Performance Computers---Short Range Forces},\n"
" journal = {Comput.\\ Phys.\\ Commun.},\n"
" year = 2011,\n"
" volume = 182,\n"
" pages = {898--911}\n"
" pages = {898--911},\n"
" doi = {10.1016/j.cpc.2010.12.021}\n"
"}\n\n"
"@Article{Brown12,\n"
" author = {W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington},\n"
" title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" journal = {Comput.\\ Phys.\\ Commun.},\n"
" year = 2012,\n"
" volume = 183,\n"
" doi = {10.1016/j.cpc.2011.10.012},\n"
" pages = {449--459}\n"
"}\n\n"
"@Article{Brown13,\n"
" author = {W. M. Brown, Y. Masako},\n"
" title = {Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" title = {Implementing Molecular Dynamics on Hybrid High Performance Computers---Three-Body Potentials},\n"
" journal = {Comput.\\ Phys.\\ Commun.},\n"
" year = 2013,\n"
" volume = 184,\n"
" pages = {2785--2793}\n"
" pages = {2785--2793},\n"
" doi = {10.1016/j.cpc.2013.08.002},\n"
"}\n\n"
"@Article{Trung15,\n"
" author = {T. D. Nguyen, S. J. Plimpton},\n"
" title = {Accelerating dissipative particle dynamics simulations for soft matter systems},\n"
" journal = {Comput.~Mater.~Sci.},\n"
" title = {Accelerating Dissipative Particle Dynamics Simulations for Soft Matter Systems},\n"
" journal = {Comput.\\ Mater.\\ Sci.},\n"
" year = 2015,\n"
" doi = {10.1016/j.commatsci.2014.10.068},\n"
" volume = 100,\n"
" pages = {173--180}\n"
"}\n\n"
"@Article{Trung17,\n"
" author = {T. D. Nguyen},\n"
" title = {GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" title = {{GPU}-Accelerated {T}ersoff Potentials for Massively Parallel Molecular Dynamics Simulations},\n"
" journal = {Comput.\ Phys.\ Commun.},\n"
" year = 2017,\n"
" doi = {10.1016/j.cpc.2016.10.020},\n"
" volume = 212,\n"
" pages = {113--122}\n"
"}\n\n"
"@Article{Nikolskiy19,\n"
"@inproceedings{Nikolskiy19,\n"
" author = {V. Nikolskiy, V. Stegailov},\n"
" title = {GPU acceleration of four-site water models in LAMMPS},\n"
" journal = {Proceeding of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic},\n"
" title = {{GPU} Acceleration of Four-Site Water Models in {LAMMPS}},\n"
" booktitle = {Proceedings of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic},\n"
" doi = {10.3233/APC200086}\n"
" year = 2019\n"
"}\n\n";

4
src/INTERLAYER/pair_ilp_graphene_hbn.cpp
View File

@ -47,11 +47,11 @@ using namespace InterLayer;
static const char cite_ilp[] =
"ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848\n"
"@Article{Ouyang2018\n"
" author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},\n"
" author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},\n"
" title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},\n"
" journal = {Nano Letters},\n"
" volume = 18,\n"
" pages = {6009}\n"
" pages = 6009\n"
" year = 2018,\n"
"}\n\n";

23
src/INTERLAYER/pair_ilp_tmd.cpp
View File

@ -42,17 +42,18 @@ using namespace InterLayer;
#define DELTA 4
#define PGDELTA 1
static const char cite_ilp_tmd[] = "ilp/tmd potential doi/10.1021/acs.jctc.1c00782\n"
"@Article{Ouyang2021\n"
" author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. "
"Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},\n"
" title = {Anisotropic Interlayer Force Field for Transition "
"Metal Dichalcogenides: The Case of Molybdenum Disulfide},\n"
" journal = {J. Chem. Theory Comput.},\n"
" volume = 17,\n"
" pages = {7237–7245}\n"
" year = 2021,\n"
"}\n\n";
static const char cite_ilp_tmd[] =
"ilp/tmd potential doi:10.1021/acs.jctc.1c00782\n"
"@Article{Ouyang2021\n"
" author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and\n"
" A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},\n"
" title = {Anisotropic Interlayer Force Field for Transition "
" Metal Dichalcogenides: The Case of Molybdenum Disulfide},\n"
" journal = {J.~Chem.\\ Theory Comput.},\n"
" volume = 17,\n"
" pages = {7237--7245}\n"
" year = 2021,\n"
"}\n\n";
/* ---------------------------------------------------------------------- */

2
src/INTERLAYER/pair_kolmogorov_crespi_full.cpp
View File

@ -47,7 +47,7 @@ using namespace InterLayer;
static const char cite_kc[] =
"kolmogorov/crespi/full potential doi:10.1021/acs.nanolett.8b02848\n"
"@Article{Ouyang2018\n"
" author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},\n"
" author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},\n"
" title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},\n"
" journal = {Nano Letters},\n"
" volume = 18,\n"

8
src/INTERLAYER/pair_saip_metal.cpp
View File

@ -40,13 +40,13 @@ using namespace InterLayer;
#define PGDELTA 1
static const char cite_saip[] =
"saip/metal potential doi.org/10.1021/acs.jctc.1c00622\n"
"saip/metal potential: doi:10.1021/acs.jctc.1c00622\n\n"
"@Article{Ouyang2021\n"
" author = {W. Ouyang, O. Hod, and R. Guerra},\n"
" author = {W. Ouyang and O. Hod and R. Guerra},\n"
" title = {Registry-Dependent Potential for Interfaces of Gold with Graphitic Systems},\n"
" journal = {J. Chem. Theory Comput.},\n"
" journal = {J.~Chem.\\ Theory Comput.},\n"
" volume = 17,\n"
" pages = {7215-7223}\n"
" pages = {7215--7223}\n"
" year = 2021,\n"
"}\n\n";

10
src/LATBOLTZ/fix_lb_fluid.cpp
View File

@ -45,11 +45,11 @@ using namespace FixConst;
static const char cite_fix_lbfluid[] =
"fix lb/fluid command: doi:10.1016/j.cpc.2022.108318\n\n"
"@Article{Denniston et al.,\n"
" author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,"
"F.E. Mackay, S.T.T. Ollila, T. Whitehead},\n"
" title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic "
"Forces Implemented into LAMMPS through a lattice-Boltzmann fluid},"
" journal = {Comp.~Phys.~Comm.},\n"
" author = {C. Denniston and N. Afrasiabian and M. G. Cole-Andre,"
" F. E. Mackay and S. T. T. Ollila and T. Whitehead},\n"
" title = {{LAMMPS} lb/fluid fix version 2: Improved Hydrodynamic "
" Forces Implemented into {LAMMPS} Through a Lattice-{B}oltzmann Fluid},"
" journal = {Comput.\\ Phys.\\ Commun.},\n"
" year = 2022,\n"
" volume = 275,\n"
" pages = {108318}\n"

4
src/MANYBODY/pair_atm.cpp
View File

@ -35,8 +35,8 @@ static const char cite_atm_package[] =
"ATM package: doi:10.1063/1.4704930\n\n"
"@Article{Lishchuk:2012:164501,\n"
" author = {S. V. Lishchuk},\n"
" title = {Role of three-body interactions in formation of bulk viscosity in liquid argon},\n"
" journal = {J.~Chem.~Phys.},\n"
" title = {Role of Three-Body Interactions in Formation of Bulk Viscosity in Liquid Argon},\n"
" journal = {J.~Chem.\\ Phys.},\n"
" year = 2012,\n"
" volume = 136,\n"
" number = 16,\n"

8
src/MANYBODY/pair_edip_multi.cpp
View File

@ -42,18 +42,20 @@ using namespace MathExtra;
#define DELTA 4
static const char cite_pair_edip[] =
"pair edip/multi: doi:10.1103/PhysRevB.86.144118, doi:10.1088/0953-8984/22/3/035802\n\n"
"@article{cjiang2012\n"
" author = {Jian, Chao and Morgan, Dane, and Szlufarska, Izabella},\n"
" title = {Carbon tri-interstitial defect: A model for DII center},\n"
" journal = {Physical Review B},\n"
" title = {Carbon Tri-Interstitial Defect: {A} Model for {D$_{\mathrm{II}}$} Center},\n"
" journal = {Phys.\ Rev.~B},\n"
" volume = {86},\n"
" pages = {144118},\n"
" year = {2012},\n"
"}\n\n"
"@article{lpizzagalli2010,\n"
" author = {G. Lucas, M. Bertolus, and L. Pizzagalli},\n"
" journal = {J. Phys. : Condens. Matter 22},\n"
" journal = {J.~Phys.\ Condens.\ Matter},\n"
" volume = {22},\n"
" number = 3,\n"
" pages = {035802},\n"
" year = {2010},\n"
"}\n\n";

18
src/MANYBODY/pair_local_density.cpp
View File

@ -37,20 +37,20 @@ using namespace LAMMPS_NS;
#define MAXLINE 1024
static const char cite_pair_local_density[] =
"pair_style local/density command:\n\n"
"pair_style local/density command: doi:10.1063/1.4958629, doi:10.1021/acs.jpcb.7b12446\n\n"
"@Article{Sanyal16,\n"
" author = {T.Sanyal and M.Scott Shell},\n"
" title = {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},\n"
" journal = {J.~Chem.~Phys.},\n"
" author = {T. Sanyal and M. Scott Shell},\n"
" title = {Coarse-Grained Models Using Local-Density Potentials Optimized With the Relative Entropy: {A}pplication to Implicit Solvation},\n"
" journal = {J.~Chem.\\ Phys.},\n"
" year = 2016,\n"
" DOI = doi.org/10.1063/1.4958629"
" DOI = {10.1063/1.4958629}"
"}\n\n"
"@Article{Sanyal18,\n"
" author = {T.Sanyal and M.Scott Shell},\n"
" title = {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},\n"
" journal = {J.~Phys.~Chem. B},\n"
" author = {T. Sanyal and M. Scott Shell},\n"
" title = {Transferable Coarse-Grained Models of Liquid-Liquid Equilibrium Using Local Density Potentials Optimized with the Relative Entropy},\n"
" journal = {J.~Phys.\\ Chem.~B},\n"
" year = 2018,\n"
" DOI = doi.org/10.1021/acs.jpcb.7b12446"
" DOI = {10.1021/acs.jpcb.7b12446}"
"}\n\n";
/* ---------------------------------------------------------------------- */

9
src/MC/fix_bond_swap.cpp
View File

@ -39,13 +39,14 @@ using namespace LAMMPS_NS;
using namespace FixConst;
static const char cite_fix_bond_swap[] =
"fix bond/swap command:\n\n"
"fix bond/swap command: doi:10.1063/1.1628670\n\n"
"@Article{Auhl03,\n"
" author = {R. Auhl, R. Everaers, G. S. Grest, K. Kremer, S. J. Plimpton},\n"
" title = {Equilibration of long chain polymer melts in computer simulations},\n"
" journal = {J.~Chem.~Phys.},\n"
" author = {R. Auhl and R. Everaers and G. S. Grest and K. Kremer and S. J. Plimpton},\n"
" title = {Equilibration of Long Chain Polymer Melts in Computer Simulations},\n"
" journal = {J.~Chem.\\ Phys.},\n"
" year = 2003,\n"
" volume = 119,\n"
" number = 12,\n"
" pages = {12718--12728}\n"
"}\n\n";

8
src/MC/fix_charge_regulation.cpp
View File

@ -54,11 +54,11 @@ using namespace MathConst;
using namespace MathSpecial;
static const char cite_fix_charge_regulation[] =
"fix charge/regulation: \n\n"
"fix charge/regulation: doi:10.1063/5.0066432\n\n"
"@Article{Curk22,\n"
" author = {T. Curk, J. Yuan, E. Luijten},\n"
" title = {Accelerated simulation method for charge regulation effects},\n"
" journal = {The Journal of Chemical Physics},\n"
" author = {T. Curk and J. Yuan and E. Luijten},\n"
" title = {Accelerated Simulation Method for Charge Regulation Effects},\n"
" journal = {Journal of Chemical Physics},\n"
" year = 2022,\n"
" volume = 156\n"
"}\n\n";

8
src/MISC/pair_agni.cpp
View File

@ -37,13 +37,13 @@ using namespace LAMMPS_NS;
using namespace MathSpecial;
static const char cite_pair_agni[] =
"pair agni command:\n\n"
"pair agni command: doi:10.1021/acs.jpcc.9b04207\n\n"
"@article{huan2019jpc,\n"
" author = {Huan, T. and Batra, R. and Chapman, J. and Kim, C. and Chandrasekaran, A. and Ramprasad, Rampi},\n"
" journal = {J. Phys. Chem. C},\n"
" volume = {121},\n"
" journal = {J.~Phys.\\ Chem.~C},\n"
" volume = {123},\n"
" number = {34},\n"
" pages = {20715},\n"
" pages = {20715--20722},\n"
" year = {2019},\n"
"}\n\n";

7
src/MISC/pair_srp.cpp
View File

@ -52,10 +52,11 @@ using namespace LAMMPS_NS;
#define ONETWOBIT 0x40000000
static const char cite_srp[] =
"pair srp command: doi:10.1063/1.3698476\n\n"
"@Article{Sirk2012\n"
" author = {T. Sirk and Y. Sliozberg and J. Brennan and M. Lisal and J. Andzelm},\n"
" title = {An enhanced entangled polymer model for dissipative particle dynamics},\n"
" journal = {J.~Chem.~Phys.},\n"
" author = {T. W. Sirk and Y. R. Sliozberg and J. K. Brennan and M. Lisal and J. W. Andzelm},\n"
" title = {An Enhanced Entangled Polymer Model for Dissipative Particle Dynamics},\n"
" journal = {J.~Chem.\\ Phys.},\n"
" year = 2012,\n"
" volume = 136,\n"
" pages = {134903}\n"

10
src/MISC/pair_srp_react.cpp
View File

@ -47,13 +47,15 @@ There is an example script for this package in examples/PACKAGES/srp_react/.
using namespace LAMMPS_NS;
static const char cite_srpreact[] =
"pair srp/react style: doi:10.1021/acs.jpcb.1c09570\n\n"
"@Article{palkar2022\n"
" author = {Palkar, Vaibhav and Kuksenok, Olga},\n"
" title = {Controlling Degradation and Erosion of Polymer Networks: Insights from Mesoscale Modeling},\n"
" journal = {J. Phys. Chem. B},\n"
" year = {2022},\n"
" volume = {126},\n"
" pages = {336-346}\n"
" journal = {J.~Phys.\\ Chem.~B},\n"
" year = 2022,\n"
" volume = 126,\n"
" number = 1,\n"
" pages = {336--346}\n"
"}\n\n";
static int srp_instance = 0;

8
src/ML-HDNNP/pair_hdnnp.cpp
View File

@ -36,17 +36,17 @@
using namespace LAMMPS_NS;
static const char cite_user_hdnnp_package[] =
"ML-HDNNP package: 10.1021/acs.jctc.8b00770\n\n"
"ML-HDNNP package: doi:10.1021/acs.jctc.8b00770\n\n"
"@Article{Singraber19,\n"
" author = {Singraber, Andreas and Behler, J{\"o}rg and Dellago, Christoph},\n"
" title = {Library-{{Based LAMMPS Implementation}} of {{High}}-{{Dimensional Neural Network "
"Potentials}}},\n"
" title = {Library-Based {LAMMPS} Implementation of High-Dimensional\n"
" Neural Network Potentials},\n"
" year = {2019},\n"
" month = mar,\n"
" volume = {15},\n"
" pages = {1827--1840},\n"
" doi = {10.1021/acs.jctc.8b00770},\n"
" journal = {J.~Chem.~Theory~Comput.},\n"
" journal = {J.~Chem.\\ Theory Comput.},\n"
" number = {3}\n"
"}\n\n";

6
src/ML-RANN/pair_rann.cpp
View File

@ -60,14 +60,14 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
using namespace LAMMPS_NS;
static const char cite_ml_rann_package[] =
"ML-RANN package:\n\n"
"ML-RANN package: doi:10.1016/j.commatsci.2020.110207\n\n"
"@Article{Nitol2021,\n"
" author = {Nitol, Mashroor S and Dickel, Doyl E and Barrett, Christopher D},\n"
" title = {Artificial neural network potential for pure zinc},\n"
" title = {Artificial Neural Network Potential for Pure Zinc},\n"
" journal = {Computational Materials Science},\n"
" year = 2021,\n"
" volume = 188,\n"
" pages = {110207}\n"
" pages = 110207\n"
"}\n\n";

10
src/OPENMP/pair_reaxff_omp.cpp
View File

@ -63,12 +63,14 @@ using namespace LAMMPS_NS;
using namespace ReaxFF;
static const char cite_pair_reaxff_omp[] =
"pair reaxff/omp and fix qeq/reaxff/omp command:\n\n"
"pair reaxff/omp and fix qeq/reaxff/omp command: doi:10.1177/1094342017746221\n\n"
"@Article{Aktulga17,\n"
" author = {H. M. Aktulga, C. Knight, P. Coffman, K. A. OHearn, T. R. Shan, W. Jiang},\n"
" title = {Optimizing the performance of reactive molecular dynamics simulations for multi-core architectures},\n"
" author = {H. M. Aktulga and C. Knight and P. Coffman and\n"
" K. A. O'Hearn and T. R. Shan and W. Jiang},\n"
" title = {Optimizing the Performance of Reactive Molecular Dynamics\n"
" Simulations for Multi-Core Architectures},\n"
" journal = {International Journal of High Performance Computing Applications},\n"
" year = to appear\n"
" year = 2018\n"
"}\n\n";
/* ---------------------------------------------------------------------- */

4
src/OPT/pair_ilp_graphene_hbn_opt.cpp
View File

@ -42,7 +42,7 @@ static const char cite_ilp_cur[] =
"ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137\n"
"@inproceedings{gao2021lmff\n"
" author = {Gao, Ping and Duan, Xiaohui and Others},\n"
" title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous "
" title = {{LMFF}: Efficient and Scalable Layered Materials Force Field on Heterogeneous "
"Many-Core Processors},\n"
" year = {2021},\n"
" isbn = {9781450384421},\n"
@ -54,7 +54,7 @@ static const char cite_ilp_cur[] =
"Networking, Storage and Analysis},\n"
" articleno = {42},\n"
" numpages = {14},\n"
" location = {St. Louis, Missouri},\n"
" location = {St.\\ Louis, Missouri},\n"
" series = {SC'21},\n"
"}\n\n";

15
src/ORIENT/fix_orient_bcc.cpp
View File

@ -41,14 +41,15 @@ using namespace MathConst;
#define BIG 1000000000
static const char cite_fix_orient_bcc[] =
"fix orient/bcc command:\n\n"
"fix orient/bcc command: doi:10.1016/j.commatsci.2016.02.016\n\n"
"@Article{Wicaksono16,\n"
" author = {A. T. Wicaksono, C. W. Sinclair, M. Militzer},\n"
" title = {An atomistic study of the correlation between the migration of planar and curved grain boundaries},\n"
" journal = {Computational Materials Science},\n"
" year = 2016,\n"
" volume = 117,\n"
" pages = {397--405}\n"
" author = {A. T. Wicaksono and C. W. Sinclair and M. Militzer},\n"
" title = {An Atomistic Study of the Correlation Between the Migration\n"
" of Planar and Curved Grain Boundaries},\n"
" journal = {Computational Materials Science},\n"
" year = 2016,\n"
" volume = 117,\n"
" pages = {397--405}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */

6
src/ORIENT/fix_orient_eco.cpp
View File

@ -38,10 +38,10 @@ using namespace FixConst;
using namespace MathConst;
static const char cite_fix_orient_eco[] =
"fix orient/eco command:\n\n"
"fix orient/eco command: doi:j.commatsci.2020.109774\n\n"
"@Article{Schratt20,\n"
" author = {A. A. Schratt, V. Mohles},\n"
" title = {Efficient calculation of the ECO driving force for atomistic simulations of grain boundary motion},\n"
" author = {A. A. Schratt and V. Mohles},\n"
" title = {Efficient Calculation of the {ECO} Driving Force for Atomistic Simulations of Grain Boundary Motion},\n"
" journal = {Computational Materials Science},\n"
" volume = {182},\n"
" year = {2020},\n"

2
src/ORIENT/fix_orient_fcc.cpp
View File

@ -38,7 +38,7 @@ using namespace MathConst;
#define BIG 1000000000
static const char cite_fix_orient_fcc[] =
"fix orient/fcc command:\n\n"
"fix orient/fcc command: doi:10.1038/nmat1559\n\n"
"@Article{Janssens06,\n"
" author = {K. G. F. Janssens, D. Olmsted, E.A. Holm, S. M. Foiles, S. J. Plimpton, and P. M. Derlet},\n"
" title = {Computing the Mobility of Grain Boundaries},\n"

9
src/PERI/atom_vec_peri.cpp
View File

@ -26,13 +26,14 @@
using namespace LAMMPS_NS;
static const char cite_peri_package[] =
"PERI package for Peridynamics:\n\n"
"PERI package for Peridynamics: doi:10.1016/j.cpc.2008.06.011\n\n"
"@Article{Parks08,\n"
" author = {M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling},\n"
" title = {Implementing peridynamics within a molecular dynamics code},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" author = {M. L. Parks and R. B. Lehoucq and S. J. Plimpton and S. A. Silling},\n"
" title = {Implementing Peridynamics Within a Molecular Dynamics Code},\n"
" journal = {Comput.\\ Phys.\\ Commun.},\n"
" year = 2008,\n"
" volume = 179,\n"
" number = 11,\n"
" pages = {777--783}\n"
"}\n\n";

6
src/PHONON/fix_phonon.cpp
View File

@ -50,11 +50,11 @@ using namespace FixConst;
enum{FORWARD=-1,BACKWARD=1};
static const char cite_fix_phonon[] =
"fix phonon command:\n\n"
"fix phonon command: doi:10.1016/j.cpc.2011.04.019\n\n"
"@Article{Kong11,\n"
" author = {L. T. Kong},\n"
" title = {Phonon dispersion measured directly from molecular dynamics simulations},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" title = {Phonon Dispersion Measured Directly from Molecular Dynamics Simulations},\n"
" journal = {Comput.\\ Phys.\\ Commun.},\n"
" year = 2011,\n"
" volume = 182,\n"
" pages = {2201--2207}\n"

11
src/POEMS/fix_poems.cpp
View File

@ -47,14 +47,15 @@ using namespace FixConst;
#define EPSILON 1.0e-7
static const char cite_fix_poems[] =
"fix poems command:\n\n"
"fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003\n\n"
"@Article{Mukherjee08,\n"
" author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},\n"
" title = {Substructured molecular dynamics using multibody dynamics algorithms},\n"
" journal = {Intl.~J.~Non-linear Mechanics},\n"
" author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson},\n"
" title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms},\n"
" journal = {Intl.\\ J.\\ Non-Linear Mechanics},\n"
" year = 2008,\n"
" volume = 43,\n"
" pages = {1045--1055}\n"
" number = 10,\n"
" pages = {1040--1055}\n"
"}\n\n";
/* ----------------------------------------------------------------------

6
src/PTM/compute_ptm_atom.cpp
View File

@ -47,13 +47,13 @@ under
using namespace LAMMPS_NS;
static const char cite_user_ptm_package[] =
"PTM package:\n\n"
"PTM package: doi:10.1088/0965-0393/24/5/055007\n\n"
"@Article{larsen2016ptm,\n"
" author={Larsen, Peter Mahler and Schmidt, S{\\o}ren and Schi{\\o}tz, "
"Jakob},\n"
" title={Robust structural identification via polyhedral template "
" title={Robust Structural Identification via Polyhedral Template "
"matching},\n"
" journal={Modelling~Simul.~Mater.~Sci.~Eng.},\n"
" journal={Model.\\ Simulat.\\ Mater.\\ Sci.\\ Eng.},\n"
" year={2016},\n"
" number={5},\n"
" volume={24},\n"

9
src/REACTION/fix_bond_react.cpp
View File

@ -57,10 +57,10 @@ using namespace FixConst;
using namespace MathConst;
static const char cite_fix_bond_react[] =
"fix bond/react: reacter.org\n\n"
"fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038 doi:10.1021/acs.macromol.0c02012\n\n"
"@Article{Gissinger17,\n"
" author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n"
" title = {Modeling chemical reactions in classical molecular dynamics simulations},\n"
" author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},\n"
" title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},\n"
" journal = {Polymer},\n"
" year = 2017,\n"
" volume = 128,\n"
@ -68,10 +68,11 @@ static const char cite_fix_bond_react[] =
"}\n\n"
"@Article{Gissinger20,\n"
" author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n"
" title = {REACTER: A Heuristic Method for Reactive Molecular Dynamics},\n"
" title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},\n"
" journal = {Macromolecules},\n"
" year = 2020,\n"
" volume = 53,\n"
" number = 22,\n"
" pages = {9953--9961}\n"
"}\n\n";

7
src/REAXFF/fix_acks2_reaxff.cpp
View File

@ -38,13 +38,14 @@ using namespace LAMMPS_NS;
using namespace FixConst;
static const char cite_fix_acks2_reax[] =
"fix acks2/reaxff command:\n\n"
"fix acks2/reaxff command: doi:10.1137/18M1224684\n\n"
"@Article{O'Hearn2020,\n"
" author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},\n"
" author = {K. A. {O'Hearn} and A. Alperen and H. M. Aktulga},\n"
" title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},\n"
" journal = {SIAM J. Sci. Comput.},\n"
" journal = {SIAM J.\\ Sci.\\ Comput.},\n"
" year = 2020,\n"
" volume = 42,\n"
" number = 1,\n"
" pages = {1--22}\n"
"}\n\n";

6
src/REAXFF/fix_qeq_reaxff.cpp
View File

@ -54,10 +54,10 @@ static constexpr double SMALL = 1.0e-14;
static constexpr double QSUMSMALL = 0.00001;
static const char cite_fix_qeq_reaxff[] =
"fix qeq/reaxff command:\n\n"
"fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005\n\n"
"@Article{Aktulga12,\n"
" author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},\n"
" title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},\n"
" author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},\n"
" title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},\n"
" journal = {Parallel Computing},\n"
" year = 2012,\n"
" volume = 38,\n"

7
src/REAXFF/pair_reaxff.cpp
View File

@ -46,13 +46,14 @@ using namespace LAMMPS_NS;
using namespace ReaxFF;
static const char cite_pair_reax_c[] =
"pair reaxff command:\n\n"
"pair reaxff command: doi:10.1016/j.parco.2011.08.005\n\n"
"@Article{Aktulga12,\n"
" author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},\n"
" title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},\n"
" author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},\n"
" title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},\n"
" journal = {Parallel Computing},\n"
" year = 2012,\n"
" volume = 38,\n"
" number = {4--5}\n"
" pages = {245--259}\n"
"}\n\n";

10
src/SPIN/fix_nve_spin.cpp
View File

@ -45,14 +45,14 @@ using namespace LAMMPS_NS;
using namespace FixConst;
static const char cite_fix_nve_spin[] =
"fix nve/spin command:\n\n"
"fix nve/spin command: doi:10.1016/j.jcp.2018.06.042\n\n"
"@article{tranchida2018massively,\n"
"title={Massively parallel symplectic algorithm for coupled magnetic spin "
"dynamics and molecular dynamics},\n"
"author={Tranchida, J and Plimpton, SJ and Thibaudeau, P and Thompson, AP},\n"
"title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin "
" Dynamics and Molecular Dynamics},\n"
"author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},\n"
"journal={Journal of Computational Physics},\n"
"volume={372},\n"
"pages={406-425},\n"
"pages={406--425},\n"
"year={2018},\n"
"publisher={Elsevier}\n"
"doi={10.1016/j.jcp.2018.06.042}\n"

2
src/SPIN/min_spin_cg.cpp
View File

@ -43,7 +43,7 @@ using namespace LAMMPS_NS;
using namespace MathConst;
static const char cite_minstyle_spin_cg[] =
"min_style spin/cg command:\n\n"
"min_style spin/cg command: doi:10.48550/arXiv.1904.02669\n\n"
"@article{ivanov2019fast,\n"
"title={Fast and Robust Algorithm for the Minimisation of the Energy of "
"Spin Systems},\n"

2
src/SPIN/min_spin_lbfgs.cpp
View File

@ -46,7 +46,7 @@ static const char cite_minstyle_spin_lbfgs[] =
"min_style spin/lbfgs command:\n\n"
"@article{ivanov2019fast,\n"
"title={Fast and Robust Algorithm for the Minimisation of the Energy of "
"Spin Systems},\n"
" Spin Systems},\n"
"author={Ivanov, A. V and Uzdin, V. M. and J{\'o}nsson, H.},\n"
"journal={arXiv preprint arXiv:1904.02669},\n"
"year={2019}\n"

8
src/SPIN/neb_spin.cpp
View File

@ -48,12 +48,12 @@
using namespace LAMMPS_NS;
static const char cite_neb_spin[] =
"neb/spin command:\n\n"
"neb/spin command: doi:10.1016/j.cpc.2015.07.001\n\n"
"@article{bessarab2015method,\n"
"title={Method for finding mechanism and activation energy of "
"magnetic transitions, applied to skyrmion and antivortex "
"annihilation},\n"
"author={Bessarab, P.F. and Uzdin, V.M. and J{\'o}nsson, H.},\n"
" magnetic transitions, applied to skyrmion and antivortex "
" annihilation},\n"
"author={Bessarab, P. F. and Uzdin, V. M. and J{\'o}nsson, H.},\n"
"journal={Computer Physics Communications},\n"
"volume={196},\n"
"pages={335--347},\n"

23
src/SRD/fix_srd.cpp
View File

@ -60,17 +60,18 @@ enum { SHIFT_NO, SHIFT_YES, SHIFT_POSSIBLE };
#define TOLERANCE 0.00001
#define MAXITER 20
static const char cite_fix_srd[] = "fix srd command:\n\n"
"@Article{Petersen10,\n"
" author = {M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. "
"S. Grest, P. J. in 't Veld, P. R. Schunk},\n"
" title = {Mesoscale Hydrodynamics via Stochastic Rotation "
"Dynamics: Comparison with Lennard-Jones Fluid},"
" journal = {J.~Chem.~Phys.},\n"
" year = 2010,\n"
" volume = 132,\n"
" pages = {174106}\n"
"}\n\n";
static const char cite_fix_srd[] =
"fix srd command: doi:10.1063/1.3419070\n\n"
"@Article{Petersen10,\n"
" author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and\n"
" G. S. Grest and in 't Veld, P. J. and P. R. Schunk},\n"
" title = {Mesoscale Hydrodynamics via Stochastic Rotation\n"
" Dynamics: Comparison with Lennard-Jones Fluid},\n"
" journal = {J.~Chem.\\ Phys.},\n"
" year = 2010,\n"
" volume = 132,\n"
" pages = 174106\n"
"}\n\n";
//#define SRD_DEBUG 1
//#define SRD_DEBUG_ATOMID 58

6
src/UEF/fix_nh_uef.cpp
View File

@ -44,14 +44,16 @@ enum{ISO,ANISO,TRICLINIC};
// citation info
static const char cite_user_uef_package[] =
"UEF package:\n\n"
"UEF package: src:10.1063/1.4972894\n\n"
"@Article{NicholsonRutledge16,\n"
"author = {David A. Nicholson and Gregory C. Rutledge},\n"
"title = {Molecular simulation of flow-enhanced nucleation in n-eicosane melts under steady shear and uniaxial extension},\n"
"title = {Molecular Simulation of Flow-Enhanced Nucleation in\n",
" {$n$}-Eicosane Melts Under Steady Shear and Uniaxial Extension},\n"
"journal = {The Journal of Chemical Physics},\n"
"volume = {145},\n"
"number = {24},\n"
"pages = {244903},\n"
"doi = {10.1063/1.4972894},\n",
"year = {2016}\n"
"}\n\n";

6
src/compute_centroid_stress_atom.cpp
View File

@ -38,10 +38,10 @@ enum { NOBIAS, BIAS };
static const char cite_centroid_angle_improper_dihedral[] =
"compute centroid/stress/atom for angles, impropers and dihedrals:\n\n"
"@article{PhysRevE.99.051301,\n"
" title = {Application of atomic stress to compute heat flux via molecular dynamics for "
"systems with many-body interactions},\n"
" title = {Application of Atomic Stress to Compute Heat Flux via Molecular Dynamics for "
"Systems With Many-Body Interactions},\n"
" author = {Surblys, Donatas and Matsubara, Hiroki and Kikugawa, Gota and Ohara, Taku},\n"
" journal = {Physical Review E},\n"
" journal = {Physical Review~E},\n"
" volume = {99},\n"
" issue = {5},\n"
" pages = {051301},\n"

15
src/neighbor.cpp
View File

@ -68,24 +68,23 @@ enum{NONE,ALL,PARTIAL,TEMPLATE};
static const char cite_neigh_multi_old[] =
"neighbor multi/old command: doi:10.1016/j.cpc.2008.03.005\n\n"
"@Article{Intveld08,\n"
" author = {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton"
" and G.{\\,}S.~Grest},\n"
" author = {in 't Veld, P. J. and S. J. Plimpton and G. S. Grest},\n"
" title = {Accurate and Efficient Methods for Modeling Colloidal\n"
" Mixtures in an Explicit Solvent using Molecular Dynamics},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" journal = {Comput.\\ Phys.\\ Commun.},\n"
" year = 2008,\n"
" volume = 179,\n"
" number = 5,\n"
" pages = {320--329}\n"
"}\n\n";
static const char cite_neigh_multi[] =
"neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2\n\n"
"@Article{Intveld08,\n"
" author = {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton"
" and G.{\\,}S.~Grest},\n"
" author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},\n"
" title = {Accurate and Efficient Methods for Modeling Colloidal\n"
" Mixtures in an Explicit Solvent using Molecular Dynamics},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" journal = {Comput.\\ Phys.\\ Commut.},\n"
" year = 2008,\n"
" volume = 179,\n"
" pages = {320--329}\n"
@ -97,8 +96,8 @@ static const char cite_neigh_multi[] =
"}\n\n"
"@article{Shire2020,\n"
" author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},\n"
" title = {DEM simulations of polydisperse media: efficient contact\n"
" detection applied to investigate the quasi-static limit},\n"
" title = {{DEM} Simulations of Polydisperse Media: Efficient Contact\n"
" Detection Applied to Investigate the Quasi-Static Limit},\n"
" journal = {Computational Particle Mechanics},\n"
" year = {2020}\n"
"}\n\n";