diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt index 85ebcdda10..a74574367c 100644 --- a/doc/src/Commands_pair.txt +++ b/doc/src/Commands_pair.txt @@ -68,13 +68,13 @@ OPT. "coul/diel (o)"_pair_coul_diel.html, "coul/dsf (gko)"_pair_coul.html, "coul/long (gko)"_pair_coul.html, -"coul/long/cs"_pair_coul.html, +"coul/long/cs (g)"_pair_cs.html, "coul/long/soft (o)"_pair_lj_soft.html, "coul/msm (o)"_pair_coul.html, "coul/shield"_pair_coul_shield.html, "coul/streitz"_pair_coul.html, "coul/wolf (ko)"_pair_coul.html, -"coul/wolf/cs"_pair_coul.html, +"coul/wolf/cs"_pair_cs.html, "dpd (gio)"_pair_dpd.html, "dpd/fdt"_pair_dpd_fdt.html, "dpd/fdt/energy (k)"_pair_dpd_fdt.html, @@ -127,7 +127,7 @@ OPT. "lj/cut/coul/debye (gko)"_pair_lj.html, "lj/cut/coul/dsf (gko)"_pair_lj.html, "lj/cut/coul/long (gikot)"_pair_lj.html, -"lj/cut/coul/long/cs"_pair_lj.html, +"lj/cut/coul/long/cs"_pair_cs.html, "lj/cut/coul/long/soft (o)"_pair_lj_soft.html, "lj/cut/coul/msm (go)"_pair_lj.html, "lj/cut/coul/wolf (o)"_pair_lj.html, diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt index 817179eacf..68d69d488d 100644 --- a/doc/src/angle_style.txt +++ b/doc/src/angle_style.txt @@ -68,11 +68,20 @@ doc page. "charmm"_angle_charmm.html - CHARMM angle "class2"_angle_class2.html - COMPASS (class 2) angle +"class2/p6"_angle_class2.html - "cosine"_angle_cosine.html - cosine angle potential +"cosine/buck6d"_angle_cosine_buck6d.html - "cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential "cosine/periodic"_angle_cosine_periodic.html - DREIDING angle +"cosine/shift"_angle_cosine_shift.html - +"cosine/shift/exp"_angle_cosine_shift_exp.html - "cosine/squared"_angle_cosine_squared.html - cosine squared angle potential +"dipole"_angle_dipole.html - +"fourier"_angle_fourier.html - +"fourier/simple"_angle_fourier_simple.html - "harmonic"_angle_harmonic.html - harmonic angle +"quartic"_angle_quartic.html - +"sdk"_angle_sdk.html - "table"_angle_table.html - tabulated by angle :ul :line diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt index dd406c7da0..c9252a8eb3 100644 --- a/doc/src/bond_style.txt +++ b/doc/src/bond_style.txt @@ -76,9 +76,14 @@ bond styles is on the "Commands bond"_Commands_bond.html doc page. "class2"_bond_class2.html - COMPASS (class 2) bond "fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond "fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles +"gromos"_bond_gromos.html - "harmonic"_bond_harmonic.html - harmonic bond +"harmonic/shift"_bond_harmonic_shift.html - +"harmonic/shift/cut"_bond_harmonic_shift_cut.html - "morse"_bond_morse.html - Morse bond "nonlinear"_bond_nonlinear.html - nonlinear bond +"oxdna/fene"_bond_oxdna.html - +"oxdna2/fene"_bond_oxdna.html - "quartic"_bond_quartic.html - breakable quartic bond "table"_bond_table.html - tabulated by bond length :ul diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 14ab84b436..857795ffe5 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -175,9 +175,13 @@ The individual style names on the "Commands compute"_Commands_compute.html doc page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. +"ackland/atom"_compute_ackland_atom.html - "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom +"angle"_compute_angle.html - +"angle/local"_compute_angle_local.html - "angle/local"_compute_bond_local.html - theta and energy of each angle "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk +"basal/atom"_compute_basal_atom.html - "body/local"_compute_body_local.html - attributes of body sub-particles "bond"_compute_bond.html - values computed by a bond style "bond/local"_compute_bond_local.html - distance and energy of each bond @@ -186,30 +190,48 @@ compute"_Commands_compute.html doc page are followed by one or more of "chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom +"cnp/atom"_compute_cnp_atom.html - "com"_compute_com.html - center-of-mass of group of atoms "com/chunk"_compute_com_chunk.html - center-of-mass for each chunk "contact/atom"_compute_contact_atom.html - contact count for each spherical particle "coord/atom"_compute_coord_atom.html - coordination number for each atom "damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom +"dihedral"_compute_dihedral.html - "dihedral/local"_compute_dihedral_local.html - angle of each dihedral "dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom +"dipole/chunk"_compute_dipole_chunk.html - "displace/atom"_compute_displace_atom.html - displacement of each atom +"dpd"_compute_dpd.html - +"dpd/atom"_compute_dpd_atom.html - +"edpd/temp/atom"_compute_edpd_temp_atom.html - +"entropy/atom"_compute_entropy_atom.html - "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles "erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles "erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle +"erotate/sphere/atom"_compute_erotate_sphere_atom.html - "event/displace"_compute_event_displace.html - detect event on atom displacement +"fep"_compute_fep.html - +"force/tally"_compute_tally.html - "fragment/atom"_compute_cluster_atom.html - fragment ID for each atom +"global/atom"_compute_global_atom.html - "group/group"_compute_group_group.html - energy/force between two groups of atoms "gyration"_compute_gyration.html - radius of gyration of group of atoms "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms +"heat/flux/tally"_compute_tally.html - "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6 +"improper"_compute_improper.html - "improper/local"_compute_improper_local.html - angle of each improper "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom +"ke/atom/eff"_compute_ke_atom_eff.html - +"ke/eff"_compute_ke_eff.html - "ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies +"meso/e/atom"_compute_meso_e_atom.html - +"meso/rho/atom"_compute_meso_rho_atom.html - +"meso/t/atom"_compute_meso_t_atom.html - "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms @@ -219,41 +241,77 @@ compute"_Commands_compute.html doc page are followed by one or more of "pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction "pe"_compute_pe.html - potential energy "pe/atom"_compute_pe_atom.html - potential energy for each atom +"pe/mol/tally"_compute_tally.html - +"pe/tally"_compute_tally.html - "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor +"pressure/cylinder"_compute_pressure_cylinder.html - +"pressure/uef"_compute_pressure_uef.html - "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays -"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes +"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays +"ptm/atom"_compute_ptm_atom.html - "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value "reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk "reduce/region"_compute_reduce.html - same as compute reduce, within a region "rigid/local"_compute_rigid_local.html - extract rigid body attributes +"saed"_compute_saed.html - "slice"_compute_slice.html - extract values from global vector or array +"smd/contact/radius"_compute_smd_contact_radius.html - +"smd/damage"_compute_smd_damage.html - +"smd/hourglass/error"_compute_smd_hourglass_error.html - +"smd/internal/energy"_compute_smd_internal_energy.html - +"smd/plastic/strain"_compute_smd_plastic_strain.html - +"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - +"smd/rho"_compute_smd_rho.html - +"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - +"smd/tlsph/dt"_compute_smd_tlsph_dt.html - +"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html - +"smd/tlsph/shape"_compute_smd_tlsph_shape.html - +"smd/tlsph/strain"_compute_smd_tlsph_strain.html - +"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html - +"smd/tlsph/stress"_compute_smd_tlsph_stress.html - "smd/triangle/vertices"_compute_smd_triangle_vertices.html - +"smd/triangle/vertices"_compute_smd_triangle_vertices.html - +"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html - +"smd/ulsph/strain"_compute_smd_ulsph_strain.html - +"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html - +"smd/ulsph/stress"_compute_smd_ulsph_stress.html - +"smd/vol"_compute_smd_vol.html - "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom "snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom +"spin"_compute_spin.html - "stress/atom"_compute_stress_atom.html - stress tensor for each atom -"stress/mop"_compute_stress_mop.html - -"stress/mop/profile"_compute_stress_mop.html - +"stress/mop"_compute_stress_mop.html - +"stress/mop/profile"_compute_stress_mop.html - +"stress/tally"_compute_tally.html - +"tdpd/cc/atom"_compute_tdpd_cc_atom.html - "temp"_compute_temp.html - temperature of group of atoms "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles "temp/body"_compute_temp_body.html - temperature of body particles "temp/chunk"_compute_temp_chunk.html - temperature of each chunk "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity -"temp/cs"_compute_temp_cs.html - +"temp/cs"_compute_temp_cs.html - "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity +"temp/deform/eff"_compute_temp_deform_eff.html - +"temp/drude"_compute_temp_drude.html - +"temp/eff"_compute_temp_eff.html - "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity "temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component "temp/region"_compute_temp_region.html - temperature of a region of atoms +"temp/region/eff"_compute_temp_region_eff.html - +"temp/rotate"_compute_temp_rotate.html - "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles +"temp/uef"_compute_temp_uef.html - "ti"_compute_ti.html - thermodynamic integration free energy values "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk "vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk -"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul +"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom +"xrd"_compute_xrd.html - :ul [Restrictions:] none diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt index 9744f1b71f..02634c6073 100644 --- a/doc/src/dihedral_style.txt +++ b/doc/src/dihedral_style.txt @@ -90,11 +90,19 @@ doc page. "hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul "charmm"_dihedral_charmm.html - CHARMM dihedral +"charmmfsw"_dihedral_charmm.html - "class2"_dihedral_class2.html - COMPASS (class 2) dihedral +"cosine/shift/exp"_dihedral_cosine_shift_exp.html - +"fourier"_dihedral_fourier.html - "harmonic"_dihedral_harmonic.html - harmonic dihedral "helix"_dihedral_helix.html - helix dihedral "multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral -"opls"_dihedral_opls.html - OPLS dihedral :ul +"nharmonic"_dihedral_nharmonic.html - +"opls"_dihedral_opls.html - OPLS dihedral +"quadratic"_dihedral_quadratic.html - +"spherical"_dihedral_spherical.html - +"table"_dihedral_table.html - +"table/cut"_dihedral_table_cut.html - :ul :line diff --git a/doc/src/fix.txt b/doc/src/fix.txt index ee0d006fe8..27cc0467e2 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -167,136 +167,211 @@ page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. "adapt"_fix_adapt.html - change a simulation parameter over time +"adapt/fep"_fix_adapt_fep.html - "addforce"_fix_addforce.html - add a force to each atom +"addtorque"_fix_addtorque.html - "append/atoms"_fix_append_atoms.html - append atoms to a running simulation +"atc"_fix_atc.html - "atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping -"aveforce"_fix_aveforce.html - add an averaged force to each atom "ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities "ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities "ave/correlate"_fix_ave_correlate.html - compute/output time correlations +"ave/correlate/long"_fix_ave_correlate_long.html - "ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms +"ave/histo/weight"_fix_ave_histo.html - "ave/time"_fix_ave_time.html - compute/output global time-averaged quantities +"aveforce"_fix_aveforce.html - add an averaged force to each atom "balance"_fix_balance.html - perform dynamic load-balancing +"bocs"_fix_bocs.html - "bond/break"_fix_bond_break.html - break bonds on the fly "bond/create"_fix_bond_create.html - create bonds on the fly +"bond/react"_fix_bond_react.html - "bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping "box/relax"_fix_box_relax.html - relax box size during energy minimization +"client/md"_fix_client_md.html - +"cmap"_fix_cmap.html - +"colvars"_fix_colvars.html - +"controller"_fix_controller.html - "deform"_fix_deform.html - change the simulation box size/shape "deposit"_fix_deposit.html - add new atoms above a surface +"dpd/energy"_fix_dpd_energy.html - "drag"_fix_drag.html - drag atoms towards a defined coordinate +"drude"_fix_drude.html - +"drude/transform/direct"_fix_drude_transform.html - +"drude/transform/inverse"_fix_drude_transform.html - "dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces +"edpd/source"_fix_dpd_source.html - "efield"_fix_efield.html - impose electric field on system "ehex"_fix_ehex.html - ehanced heat exchange algorithm "enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force +"eos/cv"_fix_eos_cv.html - +"eos/table"_fix_eos_table.html - +"eos/table/rx"_fix_eos_table_rx.html - "evaporate"_fix_evaporate.html - remove atoms from simulation periodically "external"_fix_external.html - callback to an external driver program +"ffl"_fix_ffl.html - +"filter/corotate"_fix_filter_corotate.html - +"flow/gauss"_fix_flow_gauss.html - "freeze"_fix_freeze.html - freeze atoms in a granular simulation "gcmc"_fix_gcmc.html - grand canonical insertions/deletions "gld"_fix_gcmc.html - generalized Langevin dynamics integrator +"gld"_fix_gld.html - +"gle"_fix_gle.html - "gravity"_fix_gravity.html - add gravity to atoms in a granular simulation +"grem"_fix_grem.html - "halt"_fix_halt.html - terminate a dynamics run or minimization "heat"_fix_heat.html - add/subtract momentum-conserving heat +"imd"_fix_imd.html - "indent"_fix_indent.html - impose force due to an indenter -"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code +"ipi"_fix_ipi.html - "langevin"_fix_langevin.html - Langevin temperature control +"langevin/drude"_fix_langevin_drude.html - +"langevin/eff"_fix_langevin_eff.html - +"langevin/spin"_fix_langevin_spin.html - +"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code +"lb/fluid"_fix_lb_fluid.html - +"lb/momentum"_fix_lb_momentum.html - +"lb/pc"_fix_lb_pc.html - +"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html - +"lb/viscous"_fix_lb_viscous.html - "lineforce"_fix_lineforce.html - constrain atoms to move in a line +"manifoldforce"_fix_manifoldforce.html - +"meso"_fix_meso.html - +"meso/stationary"_fix_meso_stationary.html - "momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms "move"_fix_move.html - move atoms in a prescribed fashion +"mscg"_fix_mscg.html - "msst"_fix_msst.html - multi-scale shock technique (MSST) integration +"mvv/dpd"_fix_mvv_dpd.html - +"mvv/edpd"_fix_mvv_dpd.html - +"mvv/tdpd"_fix_mvv_dpd.html - "neb"_fix_neb.html - nudged elastic band (NEB) spring forces "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover -"nphug"_fix_nphug.html - constant-stress Hugoniostat integration "nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles +"nph/body"_fix_nph_body.html - "nph/body"_fix_nve_body.html - NPH for body particles +"nph/eff"_fix_nh_eff.html - "nph/sphere"_fix_nph_sphere.html - NPH for spherical particles +"nphug"_fix_nphug.html - constant-stress Hugoniostat integration "npt"_fix_nh.html - constant NPT time integration via Nose/Hoover "npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles +"npt/body"_fix_npt_body.html - "npt/body"_fix_nve_body.html - NPT for body particles +"npt/eff"_fix_nh_eff.html - "npt/sphere"_fix_npt_sphere.html - NPT for spherical particles +"npt/uef"_fix_nh_uef.html - "nve"_fix_nve.html - constant NVE time integration "nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles "nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces" +"nve/awpmd"_fix_nve_awpmd.html - "nve/body"_fix_nve_body.html - NVE for body particles +"nve/dot"_fix_nve_dot.html - +"nve/dotc/langevin"_fix_nve_dotc_langevin.html - +"nve/eff"_fix_nve_eff.html - "nve/limit"_fix_nve_limit.html - NVE with limited step length "nve/line"_fix_nve_line.html - NVE for line segments +"nve/manifold/rattle"_fix_nve_manifold_rattle.html - "nve/noforce"_fix_nve_noforce.html - NVE without forces (v only) "nve/sphere"_fix_nve_sphere.html - NVE for spherical particles +"nve/spin"_fix_nve_spin.html - "nve/tri"_fix_nve_tri.html - NVE for triangles +"nvk"_fix_nvk.html - "nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover "nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles "nvt/body"_fix_nve_body.html - NVT for body particles +"nvt/body"_fix_nvt_body.html - +"nvt/eff"_fix_nh_eff.html - +"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html - "nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations +"nvt/sllod/eff"_fix_nvt_sllod_eff.html - "nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles +"nvt/uef"_fix_nh_uef.html - "oneway"_fix_oneway.html - constrain particles on move in one direction "orient/bcc"_fix_orient.html - add grain boundary migration force for BCC "orient/fcc"_fix_orient.html - add grain boundary migration force for FCC +"phonon"_fix_phonon.html - +"pimd"_fix_pimd.html - "planeforce"_fix_planeforce.html - constrain atoms to move in a plane -"poems"_fix_poems.html - constrain clusters of atoms to move \ - as coupled rigid bodies +"poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies "pour"_fix_pour.html - pour new atoms/molecules into a granular simulation domain -"press/berendsen"_fix_press_berendsen.html - pressure control by \ - Berendsen barostat +"precession/spin"_fix_precession_spin.html - +"press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat "print"_fix_print.html - print text and variables during a simulation "property/atom"_fix_property_atom.html - add customized per-atom values -"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential \ -"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method \ -"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer \ -"qeq/point"_fix_qeq.html - charge equilibration via point method \ -"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method \ -"qeq/slater"_fix_qeq.html - charge equilibration via Slater method \ +"python/invoke"_fix_python_invoke.html - +"python/move"_fix_python_move.html - +"qbmsst"_fix_qbmsst.html - +"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential +"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method +"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer +"qeq/point"_fix_qeq.html - charge equilibration via point method +"qeq/reax"_fix_qeq_reax.html - +"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method +"qeq/slater"_fix_qeq.html - charge equilibration via Slater method +"qmmm"_fix_qmmm.html - +"qtb"_fix_qtb.html - "rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles -"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \ -"recenter"_fix_recenter.html - constrain the center-of-mass position \ - of a group of atoms +"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information +"reax/c/bonds"_fix_reax_bonds.html - +"reax/c/species"_fix_reaxc_species.html - +"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms "restrain"_fix_restrain.html - constrain a bond, angle, dihedral -"rigid"_fix_rigid.html - constrain one or more clusters of atoms to \ - move as a rigid body with NVE integration -"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to \ - move as a rigid body with NPH integration -"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to \ - move as a rigid body with NPT integration -"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to \ - move as a rigid body with alternate NVE integration -"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to \ - move as a rigid body with NVT integration -"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to \ - move as a rigid body with NVE integration -"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to \ - move as a rigid body with NPH integration -"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to \ - move as a rigid body with NPT integration -"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to \ - move as a rigid body with alternate NVE integration -"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to \ - move as a rigid body with NVT integration +"rhok"_fix_rhok.html - +"rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration +"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration +"rigid/nph/small"_fix_rigid.html - +"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration +"rigid/npt/small"_fix_rigid.html - +"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration +"rigid/nve/small"_fix_rigid.html - +"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration +"rigid/nvt/small"_fix_rigid.html - +"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration +"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration +"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration +"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration +"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration +"rx"_fix_rx.html - +"saed/vtk"_fix_saed_vtk.html - "setforce"_fix_setforce.html - set the force on each atom "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles +"shardlow"_fix_shardlow.html - +"smd"_fix_smd.html - +"smd/adjust_dt"_fix_smd_adjust_dt.html - +"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html - +"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html - +"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html - +"smd/setvel"_fix_smd_setvel.html - +"smd/wall_surface"_fix_smd_wall_surface.html - "spring"_fix_spring.html - apply harmonic spring force to group of atoms "spring/chunk"_fix_spring_chunk.html - apply harmonic spring force to each chunk of atoms -"spring/rg"_fix_spring_rg.html - spring on radius of gyration of \ - group of atoms +"spring/rg"_fix_spring_rg.html - spring on radius of gyration of group of atoms "spring/self"_fix_spring_self.html - spring from each atom to its origin "srd"_fix_srd.html - stochastic rotation dynamics (SRD) "store/force"_fix_store_force.html - store force on each atom "store/state"_fix_store_state.html - store attributes for each atom -"temp/berendsen"_fix_temp_berendsen.html - temperature control by \ - Berendsen thermostat +"tdpd/source"_fix_dpd_source.html - +"temp/berendsen"_fix_temp_berendsen.html - temperature control by Berendsen thermostat "temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics "temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics -"temp/rescale"_fix_temp_rescale.html - temperature control by \ - velocity rescaling +"temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling +"temp/rescale/eff"_fix_temp_rescale_eff.html - "tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method -"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for \ - thermal conductivity calculation +"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation +"ti/spring"_fix_ti_spring.html - "tmd"_fix_tmd.html - guide a group of atoms to a new configuration "ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling +"ttm/mod"_fix_ttm.html - "tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters "vector"_fix_vector.html - accumulate a global vector every N timesteps -"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for \ - viscosity calculation +"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation "viscous"_fix_viscous.html - viscous damping for granular simulations +"wall/body/polygon"_fix_wall_body_polygon.html - +"wall/body/polyhedron"_fix_wall_body_polyhedron.html - "wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles +"wall/ees"_fix_wall_ees.html - "wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations +"wall/gran/region"_fix_wall_gran_region.html - "wall/harmonic"_fix_wall.html - harmonic spring wall "wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall "wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall @@ -304,6 +379,7 @@ accelerated styles exist. "wall/piston"_fix_wall_piston.html - moving reflective piston wall "wall/reflect"_fix_wall_reflect.html - reflecting wall(s) "wall/region"_fix_wall_region.html - use region surface as wall +"wall/region/ees"_fix_wall_ees.html - "wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul [Restrictions:] diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt index c9db7678a9..28b3b440b2 100644 --- a/doc/src/improper_style.txt +++ b/doc/src/improper_style.txt @@ -69,8 +69,13 @@ doc page. "hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul "class2"_improper_class2.html - COMPASS (class 2) improper +"cossq"_improper_cossq.html - "cvff"_improper_cvff.html - CVFF improper +"distance"_improper_distance.html - +"fourier"_improper_fourier.html - "harmonic"_improper_harmonic.html - harmonic improper +"inversion/harmonic"_improper_inversion_harmonic.html - +"ring"_improper_ring.html - "umbrella"_improper_umbrella.html - DREIDING improper :ul :line diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt index 80b971e393..830e0586d2 100644 --- a/doc/src/pair_cs.txt +++ b/doc/src/pair_cs.txt @@ -6,52 +6,69 @@ :line +pair_style born/coul/dsf/cs command :h3 pair_style born/coul/long/cs command :h3 pair_style born/coul/long/cs/gpu command :h3 -pair_style buck/coul/long/cs command :h3 -pair_style born/coul/dsf/cs command :h3 pair_style born/coul/wolf/cs command :h3 pair_style born/coul/wolf/cs/gpu command :h3 +pair_style buck/coul/long/cs command :h3 +pair_style coul/long/cs command :h3 +pair_style coul/long/cs/gpu command :h3 +pair_style coul/wolf/cs command :h3 pair_style lj/cut/coul/long/cs command :h3 [Syntax:] pair_style style args :pre -style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs} or {born/coul/wolf/cs} +style = {born/coul/dsf/cs} or {born/coul/long/cs} or {born/coul/wolf/cs} or {buck/coul/long/cs} or {coul/long/cs} or {coul/wolf/cs} or {lj/cut/coul/long/cs} args = list of arguments for a particular style :ul - {born/coul/long/cs} args = cutoff (cutoff2) - cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {buck/coul/long/cs} args = cutoff (cutoff2) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) {born/coul/dsf/cs} args = alpha cutoff (cutoff2) alpha = damping parameter (inverse distance units) cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (distance units) :pre + cutoff2 = global cutoff for Coulombic (distance units) + {born/coul/long/cs} args = cutoff (cutoff2) + cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) {born/coul/wolf/cs} args = alpha cutoff (cutoff2) alpha = damping parameter (inverse distance units) cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) + {buck/coul/long/cs} args = cutoff (cutoff2) + cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) + {coul/long} args = cutoff + cutoff = global cutoff for Coulombic (distance units) + {coul/wolf} args = alpha cutoff + alpha = damping parameter (inverse distance units) + cutoff = global cutoff for Coulombic (distance units) + {lj/cut/coul/long/cs} args = cutoff (cutoff2) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre [Examples:] +pair_style born/coul/dsf/cs 0.1 10.0 12.0 +pair_coeff * * 0.0 1.00 0.00 0.00 0.00 +pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre + pair_style born/coul/long/cs 10.0 8.0 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre +pair_style born/coul/wolf/cs 0.25 10.0 12.0 +pair_coeff * * 0.0 1.00 0.00 0.00 0.00 +pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre + pair_style buck/coul/long/cs 10.0 pair_style buck/coul/long/cs 10.0 8.0 pair_coeff * * 100.0 1.5 200.0 pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre -pair_style born/coul/dsf/cs 0.1 10.0 12.0 -pair_coeff * * 0.0 1.00 0.00 0.00 0.00 -pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre +pair_style coul/long/cs 10.0 +pair_coeff * * :pre -pair_style born/coul/wolf/cs 0.25 10.0 12.0 -pair_coeff * * 0.0 1.00 0.00 0.00 0.00 -pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre +pair_style coul/wolf/cs 0.2 9.0 +pair_coeff * * :pre pair_style lj/cut/coul/long/cs 10.0 pair_style lj/cut/coul/long/cs 10.0 8.0 @@ -65,16 +82,28 @@ core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham2. See the "Howto coreshell"_Howto_coreshell.html doc page for an overview of the model as implemented in LAMMPS. -The styles with a {coul/long} term are identical to the "pair_style -born/coul/long"_pair_born.html and "pair_style -buck/coul/long"_pair_buck.html styles, except they correctly treat the -special case where the distance between two charged core and shell -atoms in the same core/shell pair approach r = 0.0. This needs -special treatment when a long-range solver for Coulombic interactions -is also used, i.e. via the "kspace_style"_kspace_style.html command. +All the styles are identical to the corresponding pair style without +the "/cs" in the name: -More specifically, the short-range Coulomb interaction between a core -and its shell should be turned off using the +"pair_style born/coul/dsf"_pair_born.html +"pair_style born/coul/long"_pair_born.html +"pair_style born/coul/wolf"_pair_born.html +"pair_style buck/coul/long"_pair_buck.html +"pair_style coul/long"_pair_coul.html +"pair_style coul/wolf"_pair_coul.html +"pair_style lj/cut/coul/long"_pair_lj.html :ul + +except that they correctly treat the special case where the distance +between two charged core and shell atoms in the same core/shell pair +approach r = 0.0. + +Styles with a "/long" in the name are used with a long-range solver +for Coulombic interactions via the "kspace_style"_kspace_style.html +command. They require special treatment of the short-range Coulombic +interactions within the cor/shell model. + +Specifically, the short-range Coulomb interaction between a core and +its shell should be turned off using the "special_bonds"_special_bonds.html command by setting the 1-2 weight to 0.0, which works because the core and shell atoms are bonded to each other. This induces a long-range correction approximation which @@ -89,26 +118,10 @@ where C is an energy-conversion constant, Qi and Qj are the charges on the core and shell, epsilon is the dielectric constant and r_min is the minimal distance. -The pair style {born/coul/dsf/cs} is identical to the -"pair_style born/coul/dsf"_pair_born.html style, which uses -the damped shifted force model as in "coul/dsf"_pair_coul.html -to compute the Coulomb contribution. This approach does not require -a long-range solver, thus the only correction is the addition of a -minimal distance to avoid the possible r = 0.0 case for a -core/shell pair. - -The pair style {born/coul/wolf/cs} is identical to the -"pair_style born/coul/wolf"_pair_born.html style, which uses -the Wolf summation as in "coul/wolf"_pair_coul.html to compute -the Coulomb contribution. This approach does not require -a long-range solver, thus the only correction is the addition of a -minimal distance to avoid the possible r = 0.0 case for a -core/shell pair. - -Style {lj/cut/coul/long/cs} is identical to {lj/cut/coul/long} except -that a term is added for the "core/shell model"_Howto_coreshell.html -to allow charges on core and shell particles to be separated by r = -0.0. +For styles that are not used with a long-range solver, i.e. those with +"/dsf" or "/wolf" in the name, the only correction is the addition of +a minimal distance to avoid the possible r = 0.0 case for a core/shell +pair. :line diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index 86ac61c752..c728445952 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -101,17 +101,25 @@ 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 - "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 - "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 - "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 - "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 @@ -120,61 +128,102 @@ pair"_Commands_pair.html doc page are followed by one or more of "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/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 - "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/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/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/msm"_pair_coul.html - long-range MSM Coulombics +"coul/shield"_pair_coul_shield.html - "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 "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/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 - "eim"_pair_eim.html - embedded ion method (EIM) +"exp6/rx"_pair_exp6_rx.html - +"extep"_pair_extep.html - "gauss"_pair_gauss.html - Gaussian potential +"gauss/cut"_pair_gauss.html - "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 - "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 - "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 - "lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP) +"lennard/mdf"_pair_mdf.html - "line/lj"_pair_line_lj.html - LJ potential between line segments +"list"_pair_list.html - "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 +"lj/charmm/coul/long/soft"_pair_lj_soft.html - "lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics +"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html - +"lj/charmmfsw/coul/long"_pair_charmm.html - "lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb "lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb "lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb "lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point "lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb "lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb +"lj/cut/coul/cut/soft"_pair_lj_soft.html - "lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb "lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces "lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics -"lj/cut/coul/long/cs"_pair_lj.html - LJ with long-range Coulombics and core/shell +"lj/cut/coul/long/cs"_pair_cs.html - ditto with core/shell adjustments +"lj/cut/coul/long/soft"_pair_lj_soft.html - "lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics +"lj/cut/coul/wolf"_pair_lj.html - "lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff "lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald +"lj/cut/soft"_pair_lj_soft.html - +"lj/cut/thole/long"_pair_thole.html - "lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water "lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water +"lj/cut/tip4p/long/soft"_pair_lj_soft.html - "lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles +"lj/expand/coul/long"_pair_lj_expand.html - "lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential "lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential "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/sdk"_pair_sdk.html - +"lj/sdk/coul/long"_pair_sdk.html - +"lj/sdk/coul/msm"_pair_sdk.html - +"lj/sf/dipole/sf"_pair_dipole.html - "lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential "lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed Lennard-Jones potential "lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential @@ -182,32 +231,81 @@ 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/rhosum"_pair_meso.html - "meam"_pair_meam.html - modified embedded atom method (MEAM) +"meam/c"_pair_meam.html - +"meam/spline"_pair_meam_spline.html - +"meam/sw/spline"_pair_meam_sw_spline.html - +"mgpt"_pair_mgpt.html - "mie/cut"_pair_mie.html - Mie potential +"momb"_pair_momb.html - "morse"_pair_morse.html - Morse potential +"morse/smooth/linear"_pair_morse.html - +"morse/soft"_pair_morse.html - +"multi/lucy"_pair_multi_lucy.html - +"multi/lucy/rx"_pair_multi_lucy_rx.html - "nb3b/harmonic"_pair_nb3b_harmonic.html - nonbonded 3-body harmonic potential "nm/cut"_pair_nm.html - N-M potential "nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb "nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics +"oxdna/coaxstk"_pair_oxdna.html - +"oxdna/excv"_pair_oxdna.html - +"oxdna/hbond"_pair_oxdna.html - +"oxdna/stk"_pair_oxdna.html - +"oxdna/xstk"_pair_oxdna.html - +"oxdna2/coaxstk"_pair_oxdna2.html - +"oxdna2/dh"_pair_oxdna2.html - +"oxdna2/excv"_pair_oxdna2.html - +"oxdna2/hbond"_pair_oxdna2.html - +"oxdna2/stk"_pair_oxdna2.html - +"oxdna2/xstk"_pair_oxdna2.html - "peri/eps"_pair_peri.html - peridynamic EPS potential "peri/lps"_pair_peri.html - peridynamic LPS potential "peri/pmb"_pair_peri.html - peridynamic PMB potential "peri/ves"_pair_peri.html - peridynamic VES potential "polymorphic"_pair_polymorphic.html - polymorphic 3-body potential +"python"_pair_python.html - +"quip"_pair_quip.html - "reax"_pair_reax.html - ReaxFF potential +"reax/c"_pair_reaxc.html - "rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner "resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential +"smd/hertz"_pair_smd_hertz.html - +"smd/tlsph"_pair_smd_tlsph.html - +"smd/tri_surface"_pair_smd_triangulated_surface.html - +"smd/ulsph"_pair_smd_ulsph.html - +"smtbq"_pair_smtbq.html - "snap"_pair_snap.html - SNAP quantum-accurate potential "soft"_pair_soft.html - Soft (cosine) potential +"sph/heatconduction"_pair_sph_heatconduction.html - +"sph/idealgas"_pair_sph_idealgas.html - +"sph/lj"_pair_sph_lj.html - +"sph/rhosum"_pair_sph_rhosum.html - +"sph/taitwater"_pair_sph_taitwater.html - +"sph/taitwater/morris"_pair_sph_taitwater_morris.html - +"spin/dmi"_pair_spin_dmi.html - +"spin/exchange"_pair_spin_exchange.html - +"spin/magelec"_pair_spin_magelec.html - +"spin/neel"_pair_spin_neel.html - +"srp"_pair_srp.html - "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 - "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 - +"tersoff/table"_pair_tersoff.html - "tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential +"thole"_pair_thole.html - "tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ "tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ +"tip4p/long/soft"_pair_lj_soft.html - "tri/lj"_pair_tri_lj.html - LJ potential between triangles +"ufm"_pair_ufm.html - "vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential +"vashishta/table"_pair_vashishta.html - "yukawa"_pair_yukawa.html - Yukawa potential "yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles "zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul