diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 53cdecc8f1..71b8a82cc7 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -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" diff --git a/src/BOCS/fix_bocs.cpp b/src/BOCS/fix_bocs.cpp index 204994f21f..449deefd59 100644 --- a/src/BOCS/fix_bocs.cpp +++ b/src/BOCS/fix_bocs.cpp @@ -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" diff --git a/src/DIELECTRIC/atom_vec_dielectric.cpp b/src/DIELECTRIC/atom_vec_dielectric.cpp index 67bb9f7dc3..d43c9ec6eb 100644 --- a/src/DIELECTRIC/atom_vec_dielectric.cpp +++ b/src/DIELECTRIC/atom_vec_dielectric.cpp @@ -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" diff --git a/src/DIFFRACTION/compute_saed.cpp b/src/DIFFRACTION/compute_saed.cpp index e21570d76d..6688d7a010 100644 --- a/src/DIFFRACTION/compute_saed.cpp +++ b/src/DIFFRACTION/compute_saed.cpp @@ -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" diff --git a/src/DIFFRACTION/compute_xrd.cpp b/src/DIFFRACTION/compute_xrd.cpp index aef4d932a9..874fc614ce 100644 --- a/src/DIFFRACTION/compute_xrd.cpp +++ b/src/DIFFRACTION/compute_xrd.cpp @@ -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" diff --git a/src/DPD-MESO/pair_edpd.cpp b/src/DPD-MESO/pair_edpd.cpp index e9e379273b..9050ac9dd7 100644 --- a/src/DPD-MESO/pair_edpd.cpp +++ b/src/DPD-MESO/pair_edpd.cpp @@ -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" diff --git a/src/DPD-MESO/pair_mdpd.cpp b/src/DPD-MESO/pair_mdpd.cpp index b4878cd27c..c08ac2dde3 100644 --- a/src/DPD-MESO/pair_mdpd.cpp +++ b/src/DPD-MESO/pair_mdpd.cpp @@ -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" diff --git a/src/DPD-MESO/pair_tdpd.cpp b/src/DPD-MESO/pair_tdpd.cpp index 448cc41181..6efe3f4546 100644 --- a/src/DPD-MESO/pair_tdpd.cpp +++ b/src/DPD-MESO/pair_tdpd.cpp @@ -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" diff --git a/src/DPD-REACT/fix_shardlow.cpp b/src/DPD-REACT/fix_shardlow.cpp index 7ab8c6f857..41239c9058 100644 --- a/src/DPD-REACT/fix_shardlow.cpp +++ b/src/DPD-REACT/fix_shardlow.cpp @@ -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"; diff --git a/src/DPD-REACT/pair_multi_lucy.cpp b/src/DPD-REACT/pair_multi_lucy.cpp index 009ebfc21f..bb6792da74 100644 --- a/src/DPD-REACT/pair_multi_lucy.cpp +++ b/src/DPD-REACT/pair_multi_lucy.cpp @@ -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"; diff --git a/src/DPD-REACT/pair_multi_lucy_rx.cpp b/src/DPD-REACT/pair_multi_lucy_rx.cpp index bd508707dd..c2a3f1a55e 100644 --- a/src/DPD-REACT/pair_multi_lucy_rx.cpp +++ b/src/DPD-REACT/pair_multi_lucy_rx.cpp @@ -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" diff --git a/src/EFF/atom_vec_electron.cpp b/src/EFF/atom_vec_electron.cpp index 1f9d1f3e65..76d6a98bcd 100644 --- a/src/EFF/atom_vec_electron.cpp +++ b/src/EFF/atom_vec_electron.cpp @@ -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"; diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp index 2dde2397db..257dcb4f51 100644 --- a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp @@ -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" diff --git a/src/EXTRA-COMPUTE/compute_stress_cylinder.cpp b/src/EXTRA-COMPUTE/compute_stress_cylinder.cpp index e4c246b469..6304744ba1 100644 --- a/src/EXTRA-COMPUTE/compute_stress_cylinder.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_cylinder.cpp @@ -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"; diff --git a/src/EXTRA-COMPUTE/compute_stress_spherical.cpp b/src/EXTRA-COMPUTE/compute_stress_spherical.cpp index 18165513f9..c893d21f51 100644 --- a/src/EXTRA-COMPUTE/compute_stress_spherical.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_spherical.cpp @@ -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"; diff --git a/src/EXTRA-FIX/fix_ave_correlate_long.cpp b/src/EXTRA-FIX/fix_ave_correlate_long.cpp index c51ff7f3bd..9ed8a1e466 100644 --- a/src/EXTRA-FIX/fix_ave_correlate_long.cpp +++ b/src/EXTRA-FIX/fix_ave_correlate_long.cpp @@ -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"; diff --git a/src/EXTRA-FIX/fix_electron_stopping_fit.cpp b/src/EXTRA-FIX/fix_electron_stopping_fit.cpp index 0e0ccc0ebb..f35f4ce0dd 100644 --- a/src/EXTRA-FIX/fix_electron_stopping_fit.cpp +++ b/src/EXTRA-FIX/fix_electron_stopping_fit.cpp @@ -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" diff --git a/src/EXTRA-FIX/fix_filter_corotate.cpp b/src/EXTRA-FIX/fix_filter_corotate.cpp index e2bd982617..06eefd9ebd 100644 --- a/src/EXTRA-FIX/fix_filter_corotate.cpp +++ b/src/EXTRA-FIX/fix_filter_corotate.cpp @@ -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" diff --git a/src/EXTRA-FIX/fix_flow_gauss.cpp b/src/EXTRA-FIX/fix_flow_gauss.cpp index a1238ea748..8b9d9dca8f 100644 --- a/src/EXTRA-FIX/fix_flow_gauss.cpp +++ b/src/EXTRA-FIX/fix_flow_gauss.cpp @@ -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" diff --git a/src/EXTRA-FIX/fix_pafi.cpp b/src/EXTRA-FIX/fix_pafi.cpp index d6ee4627c9..f0932c94ff 100644 --- a/src/EXTRA-FIX/fix_pafi.cpp +++ b/src/EXTRA-FIX/fix_pafi.cpp @@ -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" diff --git a/src/EXTRA-FIX/fix_rhok.cpp b/src/EXTRA-FIX/fix_rhok.cpp index 9bdf940a7b..077dad7f25 100644 --- a/src/EXTRA-FIX/fix_rhok.cpp +++ b/src/EXTRA-FIX/fix_rhok.cpp @@ -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" diff --git a/src/EXTRA-FIX/fix_ti_spring.cpp b/src/EXTRA-FIX/fix_ti_spring.cpp index b332c18148..48babd57a2 100644 --- a/src/EXTRA-FIX/fix_ti_spring.cpp +++ b/src/EXTRA-FIX/fix_ti_spring.cpp @@ -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" diff --git a/src/EXTRA-FIX/fix_ttm_mod.cpp b/src/EXTRA-FIX/fix_ttm_mod.cpp index 8979a30bf4..d09dcf28b5 100644 --- a/src/EXTRA-FIX/fix_ttm_mod.cpp +++ b/src/EXTRA-FIX/fix_ttm_mod.cpp @@ -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" diff --git a/src/EXTRA-MOLECULE/dihedral_table_cut.cpp b/src/EXTRA-MOLECULE/dihedral_table_cut.cpp index 5ac3ab6ebb..986d9f1773 100644 --- a/src/EXTRA-MOLECULE/dihedral_table_cut.cpp +++ b/src/EXTRA-MOLECULE/dihedral_table_cut.cpp @@ -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"; /* ---------------------------------------------------------------------- */ diff --git a/src/EXTRA-PAIR/pair_e3b.cpp b/src/EXTRA-PAIR/pair_e3b.cpp index 5011cc01e0..ab68b5c729 100644 --- a/src/EXTRA-PAIR/pair_e3b.cpp +++ b/src/EXTRA-PAIR/pair_e3b.cpp @@ -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" diff --git a/src/EXTRA-PAIR/pair_lj_relres.cpp b/src/EXTRA-PAIR/pair_lj_relres.cpp index 5d1ed4fdf0..88621fe54a 100644 --- a/src/EXTRA-PAIR/pair_lj_relres.cpp +++ b/src/EXTRA-PAIR/pair_lj_relres.cpp @@ -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" diff --git a/src/EXTRA-PAIR/pair_momb.cpp b/src/EXTRA-PAIR/pair_momb.cpp index 2adb206308..5ace279621 100644 --- a/src/EXTRA-PAIR/pair_momb.cpp +++ b/src/EXTRA-PAIR/pair_momb.cpp @@ -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"; diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index e6f682a2a3..4a3b79ce51 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -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"; diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp index 49b2adbd33..fbcadbd94f 100644 --- a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp +++ b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp @@ -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"; diff --git a/src/INTERLAYER/pair_ilp_tmd.cpp b/src/INTERLAYER/pair_ilp_tmd.cpp index 52119cbf12..e15b93de0e 100644 --- a/src/INTERLAYER/pair_ilp_tmd.cpp +++ b/src/INTERLAYER/pair_ilp_tmd.cpp @@ -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"; /* ---------------------------------------------------------------------- */ diff --git a/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp b/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp index 116018f18a..0f9dd9ec47 100644 --- a/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp +++ b/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp @@ -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" diff --git a/src/INTERLAYER/pair_saip_metal.cpp b/src/INTERLAYER/pair_saip_metal.cpp index bb23cad840..4e768a9168 100644 --- a/src/INTERLAYER/pair_saip_metal.cpp +++ b/src/INTERLAYER/pair_saip_metal.cpp @@ -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"; diff --git a/src/LATBOLTZ/fix_lb_fluid.cpp b/src/LATBOLTZ/fix_lb_fluid.cpp index e3662b338b..049d9ce44e 100644 --- a/src/LATBOLTZ/fix_lb_fluid.cpp +++ b/src/LATBOLTZ/fix_lb_fluid.cpp @@ -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" diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index 1d1432c330..9e125c3403 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -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" diff --git a/src/MANYBODY/pair_edip_multi.cpp b/src/MANYBODY/pair_edip_multi.cpp index cb50426033..07b265ba48 100644 --- a/src/MANYBODY/pair_edip_multi.cpp +++ b/src/MANYBODY/pair_edip_multi.cpp @@ -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"; diff --git a/src/MANYBODY/pair_local_density.cpp b/src/MANYBODY/pair_local_density.cpp index d8bfd9d03a..c9fe782eb8 100644 --- a/src/MANYBODY/pair_local_density.cpp +++ b/src/MANYBODY/pair_local_density.cpp @@ -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"; /* ---------------------------------------------------------------------- */ diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index 59fabc8ffe..6a7ab6dbb7 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -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"; diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 81f722bb6c..795ccb75d1 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -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"; diff --git a/src/MISC/pair_agni.cpp b/src/MISC/pair_agni.cpp index ee744173fc..3c309d578b 100644 --- a/src/MISC/pair_agni.cpp +++ b/src/MISC/pair_agni.cpp @@ -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"; diff --git a/src/MISC/pair_srp.cpp b/src/MISC/pair_srp.cpp index bb731cdc32..1c95caadc2 100644 --- a/src/MISC/pair_srp.cpp +++ b/src/MISC/pair_srp.cpp @@ -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" diff --git a/src/MISC/pair_srp_react.cpp b/src/MISC/pair_srp_react.cpp index f486aa33b7..25975c7fb0 100644 --- a/src/MISC/pair_srp_react.cpp +++ b/src/MISC/pair_srp_react.cpp @@ -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; diff --git a/src/ML-HDNNP/pair_hdnnp.cpp b/src/ML-HDNNP/pair_hdnnp.cpp index eb79a396b2..6873f76779 100644 --- a/src/ML-HDNNP/pair_hdnnp.cpp +++ b/src/ML-HDNNP/pair_hdnnp.cpp @@ -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"; diff --git a/src/ML-RANN/pair_rann.cpp b/src/ML-RANN/pair_rann.cpp index d20a750ff8..8eb95f6dfb 100644 --- a/src/ML-RANN/pair_rann.cpp +++ b/src/ML-RANN/pair_rann.cpp @@ -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"; diff --git a/src/OPENMP/pair_reaxff_omp.cpp b/src/OPENMP/pair_reaxff_omp.cpp index f10f5885bd..7112681b06 100644 --- a/src/OPENMP/pair_reaxff_omp.cpp +++ b/src/OPENMP/pair_reaxff_omp.cpp @@ -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"; /* ---------------------------------------------------------------------- */ diff --git a/src/OPT/pair_ilp_graphene_hbn_opt.cpp b/src/OPT/pair_ilp_graphene_hbn_opt.cpp index 36fac54f52..d0ed0f917e 100644 --- a/src/OPT/pair_ilp_graphene_hbn_opt.cpp +++ b/src/OPT/pair_ilp_graphene_hbn_opt.cpp @@ -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"; diff --git a/src/ORIENT/fix_orient_bcc.cpp b/src/ORIENT/fix_orient_bcc.cpp index 919927ea07..c8979794e8 100644 --- a/src/ORIENT/fix_orient_bcc.cpp +++ b/src/ORIENT/fix_orient_bcc.cpp @@ -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"; /* ---------------------------------------------------------------------- */ diff --git a/src/ORIENT/fix_orient_eco.cpp b/src/ORIENT/fix_orient_eco.cpp index 7c8ff1f6aa..5f725a9e06 100644 --- a/src/ORIENT/fix_orient_eco.cpp +++ b/src/ORIENT/fix_orient_eco.cpp @@ -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" diff --git a/src/ORIENT/fix_orient_fcc.cpp b/src/ORIENT/fix_orient_fcc.cpp index f64889d141..069d4b58fc 100644 --- a/src/ORIENT/fix_orient_fcc.cpp +++ b/src/ORIENT/fix_orient_fcc.cpp @@ -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" diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index fd6b47990a..20eeef3042 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -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"; diff --git a/src/PHONON/fix_phonon.cpp b/src/PHONON/fix_phonon.cpp index b5774ad97c..3b4f182a16 100644 --- a/src/PHONON/fix_phonon.cpp +++ b/src/PHONON/fix_phonon.cpp @@ -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" diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 20e0b7cc6b..b2b0366b9e 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -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"; /* ---------------------------------------------------------------------- diff --git a/src/PTM/compute_ptm_atom.cpp b/src/PTM/compute_ptm_atom.cpp index 10341d3cd0..5ad2c6c043 100644 --- a/src/PTM/compute_ptm_atom.cpp +++ b/src/PTM/compute_ptm_atom.cpp @@ -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" diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index 0383449bbd..35cb239d62 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -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"; diff --git a/src/REAXFF/fix_acks2_reaxff.cpp b/src/REAXFF/fix_acks2_reaxff.cpp index be71bc761f..9d1775c272 100644 --- a/src/REAXFF/fix_acks2_reaxff.cpp +++ b/src/REAXFF/fix_acks2_reaxff.cpp @@ -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"; diff --git a/src/REAXFF/fix_qeq_reaxff.cpp b/src/REAXFF/fix_qeq_reaxff.cpp index 48e93f682a..6c03683518 100644 --- a/src/REAXFF/fix_qeq_reaxff.cpp +++ b/src/REAXFF/fix_qeq_reaxff.cpp @@ -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" diff --git a/src/REAXFF/pair_reaxff.cpp b/src/REAXFF/pair_reaxff.cpp index e78edea9a9..3af6ad77d0 100644 --- a/src/REAXFF/pair_reaxff.cpp +++ b/src/REAXFF/pair_reaxff.cpp @@ -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"; diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 062f3c1b00..b075c2f88b 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -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" diff --git a/src/SPIN/min_spin_cg.cpp b/src/SPIN/min_spin_cg.cpp index 9867f7aab5..84540a4a7f 100644 --- a/src/SPIN/min_spin_cg.cpp +++ b/src/SPIN/min_spin_cg.cpp @@ -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" diff --git a/src/SPIN/min_spin_lbfgs.cpp b/src/SPIN/min_spin_lbfgs.cpp index de3b70f01f..ad019efa56 100644 --- a/src/SPIN/min_spin_lbfgs.cpp +++ b/src/SPIN/min_spin_lbfgs.cpp @@ -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" diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 692883fc0a..eea9baecf8 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -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" diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index 76c5237f2d..cb6afaf082 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -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 diff --git a/src/UEF/fix_nh_uef.cpp b/src/UEF/fix_nh_uef.cpp index 720c960252..06cb611893 100644 --- a/src/UEF/fix_nh_uef.cpp +++ b/src/UEF/fix_nh_uef.cpp @@ -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"; diff --git a/src/compute_centroid_stress_atom.cpp b/src/compute_centroid_stress_atom.cpp index ee362927cf..1c8fee08c7 100644 --- a/src/compute_centroid_stress_atom.cpp +++ b/src/compute_centroid_stress_atom.cpp @@ -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" diff --git a/src/neighbor.cpp b/src/neighbor.cpp index b6b095ddf4..9ff7ce0df2 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -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";