Loading doc/src/angle_cosine_buck6d.txt +4 −4 Original line number Diff line number Diff line Loading @@ -40,8 +40,8 @@ internally. Additional to the cosine term the {cosine/buck6d} angle style computes the short range (vdW) interaction belonging to the "pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of the angle. For this reason this angle style only works in combination "pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of the angle. For this reason this angle style only works in combination with the "pair_buck6d"_pair_buck6d_coul_gauss.html styles and needs the "special_bonds"_special_bonds.html 1-3 interactions to be weighted 0.0 to prevent double counting. Loading doc/src/bond_oxdna.txt +41 −26 Original line number Diff line number Diff line Loading @@ -28,34 +28,44 @@ The {oxdna/fene} and {oxdna2/fene} bond styles use the potential :c,image(Eqs/bond_oxdna_fene.jpg) to define a modified finite extensible nonlinear elastic (FENE) potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone in the oxDNA force field for coarse-grained modelling of DNA. to define a modified finite extensible nonlinear elastic (FENE) potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone in the oxDNA force field for coarse-grained modelling of DNA. The following coefficients must be defined for the bond type via the "bond_coeff"_bond_coeff.html command as given in the above example, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html commands: "bond_coeff"_bond_coeff.html command as given in the above example, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html commands: epsilon (energy) Delta (distance) r0 (distance) :ul NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of "pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair style {oxdna2/dh} have to be defined. The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation. The article contains more information on the model, the structure of the input file, the setup tool and the performance of the LAMMPS-implementation of oxDNA. The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of "pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair style {oxdna2/dh} have to be defined. The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation. The article contains more information on the model, the structure of the input file, the setup tool and the performance of the LAMMPS-implementation of oxDNA. The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line Loading @@ -65,20 +75,25 @@ This bond style can only be used if LAMMPS was built with the USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Build package"_Build_package.html doc page for more info. [Related commands:] "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html [Default:] none :line :link(Henrich2) [(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). [(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). :link(oxdna_fene) [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). :link(oxdna2) [(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015). [(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015). doc/src/pair_style.txt +42 −45 Original line number Diff line number Diff line Loading @@ -101,89 +101,86 @@ pair"_Commands_pair.html doc page are followed by one or more of "zero"_pair_zero.html - neighbor list but no interactions :ul "adp"_pair_adp.html - angular dependent potential (ADP) of Mishin "agni"_pair_agni.html - "agni"_pair_agni.html - machine learned potential mapping atomic environment to forces "airebo"_pair_airebo.html - AIREBO potential of Stuart "airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ "atm"_pair_atm.html - Axilrod-Teller-Muto potential "awpmd/cut"_pair_awpmd.html - "awpmd/cut"_pair_awpmd.html - Antisymmetrized Wave Packet MD potential for atoms and electrons "beck"_pair_beck.html - Beck potential "body/nparticle"_pair_body_nparticle.html - interactions between body particles "body/rounded/polygon"_pair_body_rounded_polygon.html - "body/rounded/polyhedron"_pair_body_rounded_polyhedron.html - "body/rounded/polygon"_pair_body_rounded_polygon.html - granular-style 2d polygon potential "body/rounded/polyhedron"_pair_body_rounded_polyhedron.html - granular-style 3d polyhedron potential "bop"_pair_bop.html - BOP potential of Pettifor "born"_pair_born.html - Born-Mayer-Huggins potential "born/coul/dsf"_pair_born.html - "born/coul/dsf/cs"_pair_cs.html - "born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics "born/coul/long/cs"_pair_cs.html - "born/coul/long/cs"_pair_cs.html - Born-Mayer-Huggins with long-range Coulombics and core/shell "born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics "born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential "born/coul/wolf/cs"_pair_cs.html - "born/coul/dsf"_pair_born.html - Born with damped-shifted-force model "born/coul/dsf/cs"_pair_cs.html - Born with damped-shifted-force and core/shell model "born/coul/long"_pair_born.html - Born with long-range Coulombics "born/coul/long/cs"_pair_cs.html - Born with long-range Coulombics and core/shell "born/coul/msm"_pair_born.html - Born with long-range MSM Coulombics "born/coul/wolf"_pair_born.html - Born with Wolf potential for Coulombics "born/coul/wolf/cs"_pair_cs.html - Born with Wolf potential for Coulombics and core/shell model "brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics "brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity "buck"_pair_buck.html - Buckingham potential "buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb "buck/coul/long"_pair_buck.html - Buckingham with long-range Coulombics "buck/coul/long/cs"_pair_cs.html - Buckingham with long-range Coulombics and core/shell "buck/coul/msm"_pair_buck.html - Buckingham long-range MSM Coulombics "buck/coul/msm"_pair_buck.html - Buckingham with long-range MSM Coulombics "buck/long/coul/long"_pair_buck_long.html - long-range Buckingham with long-range Coulombics "buck/mdf"_pair_mdf.html - "buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - "buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - "buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - "buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - "buck/mdf"_pair_mdf.html - Buckingham with a taper function "buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with damped-shift-force model "buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with long-range Coulombics "colloid"_pair_colloid.html - integrated colloidal potential "comb"_pair_comb.html - charge-optimized many-body (COMB) potential "comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential "coul/cut"_pair_coul.html - cutoff Coulombic potential "coul/cut/soft"_pair_lj_soft.html - "coul/cut/soft"_pair_lj_soft.html - Coulombic potential with a soft core "coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening "coul/diel"_pair_coul_diel.html - "coul/dsf"_pair_coul.html - Coulombics via damped shifted forces "coul/diel"_pair_coul_diel.html - Coulomb potential with dielectric permittivity "coul/dsf"_pair_coul.html - Coulombics with damped-shifted-force model "coul/long"_pair_coul.html - long-range Coulombic potential "coul/long/cs"_pair_cs.html - long-range Coulombic potential and core/shell "coul/long/soft"_pair_lj_soft.html - "coul/long/soft"_pair_lj_soft.html - long-range Coulombic potential with a soft core "coul/msm"_pair_coul.html - long-range MSM Coulombics "coul/shield"_pair_coul_shield.html - "coul/shield"_pair_coul_shield.html - Coulombics for boron nitride for use with "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html potential "coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals "coul/wolf"_pair_coul.html - Coulombics via Wolf potential "coul/wolf/cs"_pair_cs.html - ditto with core/shell adjustments "dpd"_pair_dpd.html - dissipative particle dynamics (DPD) "dpd/fdt"_pair_dpd_fdt.html - "dpd/fdt/energy"_pair_dpd_fdt.html - "dpd/tstat"_pair_dpd.html - DPD thermostatting "dpd/fdt"_pair_dpd_fdt.html - DPD for constant temperature and pressure "dpd/fdt/energy"_pair_dpd_fdt.html - DPD for constant energy and enthalpy "dpd/tstat"_pair_dpd.html - pair-wise DPD thermostatting "dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC) "eam"_pair_eam.html - embedded atom method (EAM) "eam/alloy"_pair_eam.html - alloy EAM "eam/cd"_pair_eam.html - "eam/cd/old"_pair_eam.html - "eam/cd"_pair_eam.html - concentration-dependent EAM "eam/cd/old"_pair_eam.html - older two-site model for concentration-dependent EAM "eam/fs"_pair_eam.html - Finnis-Sinclair EAM "edip"_pair_edip.html - "edip/multi"_pair_edip.html - "edpd"_pair_meso.html - "eff/cut"_pair_eff.html - "edip"_pair_edip.html - three-body EDIP potential "edip/multi"_pair_edip.html - multi-element EDIP potential "edpd"_pair_meso.html - eDPD particle interactions "eff/cut"_pair_eff.html - electron force field with a cutoff "eim"_pair_eim.html - embedded ion method (EIM) "exp6/rx"_pair_exp6_rx.html - "extep"_pair_extep.html - "exp6/rx"_pair_exp6_rx.html - reactive DPD potential "extep"_pair_extep.html - extended Tersoff potential "gauss"_pair_gauss.html - Gaussian potential "gauss/cut"_pair_gauss.html - "gauss/cut"_pair_gauss.html - generalized Gaussian potential "gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential "gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions "gran/hooke"_pair_gran.html - granular potential with history effects "gran/hooke/history"_pair_gran.html - granular potential without history effects "gw"_pair_gw.html - "gw/zbl"_pair_gw.html - "gw"_pair_gw.html - Gao-Weber potential "gw/zbl"_pair_gw.html - Gao-Weber potential with a repulsive ZBL core "hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential "hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - registry-dependent interlayer potential (ILP) "kim"_pair_kim.html - interface to potentials provided by KIM project "kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - "kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis "lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP) "lennard/mdf"_pair_mdf.html - "lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function "line/lj"_pair_line_lj.html - LJ potential between line segments "list"_pair_list.html - "list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file "lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb "lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent "lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb Loading Loading @@ -219,7 +216,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics "lj/long/dipole/long"_pair_dipole.html - long-range LJ and long-range point dipoles "lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulomb for TIP4P water "lj/mdf"_pair_mdf.html - "lj/mdf"_pair_mdf.html - LJ potential with a taper function "lj/sdk"_pair_sdk.html - "lj/sdk/coul/long"_pair_sdk.html - "lj/sdk/coul/msm"_pair_sdk.html - Loading @@ -231,7 +228,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity "lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics "lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity "mdpd"_pair_meso.html - "mdpd"_pair_meso.html - mDPD particle interactions "mdpd/rhosum"_pair_meso.html - "meam"_pair_meam.html - modified embedded atom method (MEAM) "meam/c"_pair_meam.html - Loading Loading @@ -292,7 +289,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "sw"_pair_sw.html - Stillinger-Weber 3-body potential "table"_pair_table.html - tabulated pair potential "table/rx"_pair_table_rx.html - "tdpd"_pair_meso.html - "tdpd"_pair_meso.html - tDPD particle interactions "tersoff"_pair_tersoff.html - Tersoff 3-body potential "tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential "tersoff/mod/c"_pair_tersoff_mod.html - Loading Loading
doc/src/angle_cosine_buck6d.txt +4 −4 Original line number Diff line number Diff line Loading @@ -40,8 +40,8 @@ internally. Additional to the cosine term the {cosine/buck6d} angle style computes the short range (vdW) interaction belonging to the "pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of the angle. For this reason this angle style only works in combination "pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of the angle. For this reason this angle style only works in combination with the "pair_buck6d"_pair_buck6d_coul_gauss.html styles and needs the "special_bonds"_special_bonds.html 1-3 interactions to be weighted 0.0 to prevent double counting. Loading
doc/src/bond_oxdna.txt +41 −26 Original line number Diff line number Diff line Loading @@ -28,34 +28,44 @@ The {oxdna/fene} and {oxdna2/fene} bond styles use the potential :c,image(Eqs/bond_oxdna_fene.jpg) to define a modified finite extensible nonlinear elastic (FENE) potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone in the oxDNA force field for coarse-grained modelling of DNA. to define a modified finite extensible nonlinear elastic (FENE) potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone in the oxDNA force field for coarse-grained modelling of DNA. The following coefficients must be defined for the bond type via the "bond_coeff"_bond_coeff.html command as given in the above example, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html commands: "bond_coeff"_bond_coeff.html command as given in the above example, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html commands: epsilon (energy) Delta (distance) r0 (distance) :ul NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of "pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair style {oxdna2/dh} have to be defined. The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation. The article contains more information on the model, the structure of the input file, the setup tool and the performance of the LAMMPS-implementation of oxDNA. The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of "pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair style {oxdna2/dh} have to be defined. The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation. The article contains more information on the model, the structure of the input file, the setup tool and the performance of the LAMMPS-implementation of oxDNA. The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line Loading @@ -65,20 +75,25 @@ This bond style can only be used if LAMMPS was built with the USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Build package"_Build_package.html doc page for more info. [Related commands:] "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html [Default:] none :line :link(Henrich2) [(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). [(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). :link(oxdna_fene) [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). :link(oxdna2) [(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015). [(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
doc/src/pair_style.txt +42 −45 Original line number Diff line number Diff line Loading @@ -101,89 +101,86 @@ pair"_Commands_pair.html doc page are followed by one or more of "zero"_pair_zero.html - neighbor list but no interactions :ul "adp"_pair_adp.html - angular dependent potential (ADP) of Mishin "agni"_pair_agni.html - "agni"_pair_agni.html - machine learned potential mapping atomic environment to forces "airebo"_pair_airebo.html - AIREBO potential of Stuart "airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ "atm"_pair_atm.html - Axilrod-Teller-Muto potential "awpmd/cut"_pair_awpmd.html - "awpmd/cut"_pair_awpmd.html - Antisymmetrized Wave Packet MD potential for atoms and electrons "beck"_pair_beck.html - Beck potential "body/nparticle"_pair_body_nparticle.html - interactions between body particles "body/rounded/polygon"_pair_body_rounded_polygon.html - "body/rounded/polyhedron"_pair_body_rounded_polyhedron.html - "body/rounded/polygon"_pair_body_rounded_polygon.html - granular-style 2d polygon potential "body/rounded/polyhedron"_pair_body_rounded_polyhedron.html - granular-style 3d polyhedron potential "bop"_pair_bop.html - BOP potential of Pettifor "born"_pair_born.html - Born-Mayer-Huggins potential "born/coul/dsf"_pair_born.html - "born/coul/dsf/cs"_pair_cs.html - "born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics "born/coul/long/cs"_pair_cs.html - "born/coul/long/cs"_pair_cs.html - Born-Mayer-Huggins with long-range Coulombics and core/shell "born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics "born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential "born/coul/wolf/cs"_pair_cs.html - "born/coul/dsf"_pair_born.html - Born with damped-shifted-force model "born/coul/dsf/cs"_pair_cs.html - Born with damped-shifted-force and core/shell model "born/coul/long"_pair_born.html - Born with long-range Coulombics "born/coul/long/cs"_pair_cs.html - Born with long-range Coulombics and core/shell "born/coul/msm"_pair_born.html - Born with long-range MSM Coulombics "born/coul/wolf"_pair_born.html - Born with Wolf potential for Coulombics "born/coul/wolf/cs"_pair_cs.html - Born with Wolf potential for Coulombics and core/shell model "brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics "brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity "buck"_pair_buck.html - Buckingham potential "buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb "buck/coul/long"_pair_buck.html - Buckingham with long-range Coulombics "buck/coul/long/cs"_pair_cs.html - Buckingham with long-range Coulombics and core/shell "buck/coul/msm"_pair_buck.html - Buckingham long-range MSM Coulombics "buck/coul/msm"_pair_buck.html - Buckingham with long-range MSM Coulombics "buck/long/coul/long"_pair_buck_long.html - long-range Buckingham with long-range Coulombics "buck/mdf"_pair_mdf.html - "buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - "buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - "buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - "buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - "buck/mdf"_pair_mdf.html - Buckingham with a taper function "buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with damped-shift-force model "buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with long-range Coulombics "colloid"_pair_colloid.html - integrated colloidal potential "comb"_pair_comb.html - charge-optimized many-body (COMB) potential "comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential "coul/cut"_pair_coul.html - cutoff Coulombic potential "coul/cut/soft"_pair_lj_soft.html - "coul/cut/soft"_pair_lj_soft.html - Coulombic potential with a soft core "coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening "coul/diel"_pair_coul_diel.html - "coul/dsf"_pair_coul.html - Coulombics via damped shifted forces "coul/diel"_pair_coul_diel.html - Coulomb potential with dielectric permittivity "coul/dsf"_pair_coul.html - Coulombics with damped-shifted-force model "coul/long"_pair_coul.html - long-range Coulombic potential "coul/long/cs"_pair_cs.html - long-range Coulombic potential and core/shell "coul/long/soft"_pair_lj_soft.html - "coul/long/soft"_pair_lj_soft.html - long-range Coulombic potential with a soft core "coul/msm"_pair_coul.html - long-range MSM Coulombics "coul/shield"_pair_coul_shield.html - "coul/shield"_pair_coul_shield.html - Coulombics for boron nitride for use with "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html potential "coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals "coul/wolf"_pair_coul.html - Coulombics via Wolf potential "coul/wolf/cs"_pair_cs.html - ditto with core/shell adjustments "dpd"_pair_dpd.html - dissipative particle dynamics (DPD) "dpd/fdt"_pair_dpd_fdt.html - "dpd/fdt/energy"_pair_dpd_fdt.html - "dpd/tstat"_pair_dpd.html - DPD thermostatting "dpd/fdt"_pair_dpd_fdt.html - DPD for constant temperature and pressure "dpd/fdt/energy"_pair_dpd_fdt.html - DPD for constant energy and enthalpy "dpd/tstat"_pair_dpd.html - pair-wise DPD thermostatting "dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC) "eam"_pair_eam.html - embedded atom method (EAM) "eam/alloy"_pair_eam.html - alloy EAM "eam/cd"_pair_eam.html - "eam/cd/old"_pair_eam.html - "eam/cd"_pair_eam.html - concentration-dependent EAM "eam/cd/old"_pair_eam.html - older two-site model for concentration-dependent EAM "eam/fs"_pair_eam.html - Finnis-Sinclair EAM "edip"_pair_edip.html - "edip/multi"_pair_edip.html - "edpd"_pair_meso.html - "eff/cut"_pair_eff.html - "edip"_pair_edip.html - three-body EDIP potential "edip/multi"_pair_edip.html - multi-element EDIP potential "edpd"_pair_meso.html - eDPD particle interactions "eff/cut"_pair_eff.html - electron force field with a cutoff "eim"_pair_eim.html - embedded ion method (EIM) "exp6/rx"_pair_exp6_rx.html - "extep"_pair_extep.html - "exp6/rx"_pair_exp6_rx.html - reactive DPD potential "extep"_pair_extep.html - extended Tersoff potential "gauss"_pair_gauss.html - Gaussian potential "gauss/cut"_pair_gauss.html - "gauss/cut"_pair_gauss.html - generalized Gaussian potential "gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential "gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions "gran/hooke"_pair_gran.html - granular potential with history effects "gran/hooke/history"_pair_gran.html - granular potential without history effects "gw"_pair_gw.html - "gw/zbl"_pair_gw.html - "gw"_pair_gw.html - Gao-Weber potential "gw/zbl"_pair_gw.html - Gao-Weber potential with a repulsive ZBL core "hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential "hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - registry-dependent interlayer potential (ILP) "kim"_pair_kim.html - interface to potentials provided by KIM project "kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - "kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis "lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP) "lennard/mdf"_pair_mdf.html - "lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function "line/lj"_pair_line_lj.html - LJ potential between line segments "list"_pair_list.html - "list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file "lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb "lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent "lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb Loading Loading @@ -219,7 +216,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics "lj/long/dipole/long"_pair_dipole.html - long-range LJ and long-range point dipoles "lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulomb for TIP4P water "lj/mdf"_pair_mdf.html - "lj/mdf"_pair_mdf.html - LJ potential with a taper function "lj/sdk"_pair_sdk.html - "lj/sdk/coul/long"_pair_sdk.html - "lj/sdk/coul/msm"_pair_sdk.html - Loading @@ -231,7 +228,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity "lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics "lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity "mdpd"_pair_meso.html - "mdpd"_pair_meso.html - mDPD particle interactions "mdpd/rhosum"_pair_meso.html - "meam"_pair_meam.html - modified embedded atom method (MEAM) "meam/c"_pair_meam.html - Loading Loading @@ -292,7 +289,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "sw"_pair_sw.html - Stillinger-Weber 3-body potential "table"_pair_table.html - tabulated pair potential "table/rx"_pair_table_rx.html - "tdpd"_pair_meso.html - "tdpd"_pair_meso.html - tDPD particle interactions "tersoff"_pair_tersoff.html - Tersoff 3-body potential "tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential "tersoff/mod/c"_pair_tersoff_mod.html - Loading
