<BR>

  2.2 <A HREF = "Section_start.html#2_2">Making LAMMPS</A> 

<BR>

  2.3 <A HREF = "Section_start.html#2_3">Running LAMMPS</A> 

  2.3 <A HREF = "#2_3">Making LAMMPS with optional packages</A> 

<BR>

  2.4 <A HREF = "Section_start.html#2_4">Command-line options</A> 

  2.4 <A HREF = "#2_4">Building LAMMPS as a library</A> 

<BR>

  2.5 <A HREF = "Section_start.html#2_5">Screen output</A> 

  2.5 <A HREF = "Section_start.html#2_5">Running LAMMPS</A> 

<BR>

  2.6 <A HREF = "Section_start.html#2_6">Tips for users of previous versions</A> 

  2.6 <A HREF = "Section_start.html#2_6">Command-line options</A> 

<BR>

  2.7 <A HREF = "Section_start.html#2_7">Screen output</A> 

<BR>

  2.8 <A HREF = "Section_start.html#2_8">Tips for users of previous versions</A> 

<BR></UL>

<LI><A HREF = "Section_commands.html">Commands</A> 

"Getting started"_Section_start.html :l

  2.1 "What's in the LAMMPS distribution"_2_1 :ulb,b

  2.2 "Making LAMMPS"_2_2 :b

  2.3 "Running LAMMPS"_2_3 :b

  2.4 "Command-line options"_2_4 :b

  2.5 "Screen output"_2_5 :b

  2.6 "Tips for users of previous versions"_2_6 :ule,b

  2.3 "Making LAMMPS with optional packages"_#2_3 :b

  2.4 "Building LAMMPS as a library"_#2_4 :b

  2.5 "Running LAMMPS"_2_5 :b

  2.6 "Command-line options"_2_6 :b

  2.7 "Screen output"_2_7 :b

  2.8 "Tips for users of previous versions"_2_8 :ule,b

"Commands"_Section_commands.html :l

  3.1 "LAMMPS input script"_3_1 :ulb,b

  3.2 "Parsing rules"_3_2 :b

:link(2_4,Section_start.html#2_4)

:link(2_5,Section_start.html#2_5)

:link(2_6,Section_start.html#2_6)

:link(2_7,Section_start.html#2_7)

:link(2_8,Section_start.html#2_8)

:link(3_1,Section_commands.html#3_1)

:link(3_2,Section_commands.html#3_2)

"special_bonds"_special_bonds.html.

Various simulation parameters are set by these commands:

"temperature"_temperature.html, "temp_modify"_temp_modify.html,

"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,

"group"_group.html, "timestep"_timestep.html,

"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,

Fixes impose a variety of boundary conditions, time integration, and

diagnostic options.  The "fix"_fix.html command comes in many flavors.

Output options are set by these commands: "thermo"_thermo.html,

"dump"_dump.html, "restart"_restart.html.

Various computations can be specified for execution during a

simulation using the "compute"_compute.html,

"compute_modify"_compute_modify.html, and "variable"_variable.html

commands.

Output options are set by the "thermo"_thermo.html, "dump"_dump.html,

and "restart"_restart.html commands.

(4) Run a simulation

"min_modify"_min_modify.html, "min_style"_min_style.html,

"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html,

"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,

"set"_set.html, "temp_modify"_temp_modify.html,

"temperature"_temperature.html, "timestep"_timestep.html,

"velocity"_velocity.html

"set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html

Fixes:

"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html

Computes:

"compute"_compute.html, "compute_modify"_compute_modify.html,

"uncompute"_uncompute.html

Output:

"dump"_dump.html, "dump_modify"_dump_modify.html,

"bond_style"_bond_style.html,

"boundary"_boundary.html,

"clear"_clear.html,

"compute"_compute.html,

"compute_modify"_compute_modify.html,

"create_atoms"_create_atoms.html,

"create_box"_create_box.html,

"delete_atoms"_delete_atoms.html,

"set"_set.html,

"shell"_shell.html,

"special_bonds"_special_bonds.html,

"temp_modify"_temp_modify.html,

"temper"_temper.html,

"temperature"_temperature.html,

"thermo"_thermo.html,

"thermo_modify"_thermo_modify.html,

"thermo_style"_thermo_style.html,

"timestep"_timestep.html,

"uncompute"_uncompute.html,

"undump"_undump.html,

"unfix"_unfix.html,

"units"_units.html,

"velocity"_velocity.html,

"write_restart"_write_restart.html :tb(c=6,ea=c)

Fix styles.  See the "fix"_fix.html command for one-line descriptions

or click on the command itself for a full description:

"fix addforce"_fix_addforce.html,

"fix aveforce"_fix_aveforce.html,

"fix com"_fix_com.html,

"fix deposit"_fix_deposit.html,

"fix drag"_fix_drag.html,

"fix efield"_fix_efield.html,

"fix enforce2d"_fix_enforce2d.html,

"fix freeze"_fix_freeze.html,

"fix gran/diag"_fix_gran_diag.html,

"fix gravity"_fix_gravity.html,

"fix gyration"_fix_gyration.html,

"fix indent"_fix_indent.html,

"fix langevin"_fix_langevin.html,

"fix lineforce"_fix_lineforce.html,

"fix msd"_fix_msd.html,

"fix momentum"_fix_momentum.html,

"fix nph"_fix_nph.html,

"fix npt"_fix_npt.html,

"fix nve"_fix_nve.html,

"fix nve/gran"_fix_nve_gran.html,

"fix nvt"_fix_nvt.html,

"fix orient/fcc"_fix_orient_fcc.html,

"fix planeforce"_fix_planeforce.html,

"fix poems"_fix_poems.html,

"fix pour"_fix_pour.html,

"fix print"_fix_print.html,

"fix rdf"_fix_rdf.html,

"fix recenter"_fix_recenter.html,

"fix rigid"_fix_rigid.html,

"fix setforce"_fix_setforce.html,

"fix shake"_fix_shake.html,

"fix spring"_fix_spring.html,

"fix spring/rg"_fix_spring_rg.html,

"fix spring/self"_fix_spring_self.html,

"fix temp/rescale"_fix_temp_rescale.html,

"fix tmd"_fix_tmd.html,

"fix uniaxial"_fix_uniaxial.html,

"fix vcm"_fix_vcm.html,

"fix viscous"_fix_viscous.html,

"fix volume/rescale"_fix_volume_rescale.html,

"fix wall/gran"_fix_wall_gran.html,

"fix wall/lj93"_fix_wall_lj93.html,

"fix wall/lj126"_fix_wall_lj126.html,

"fix wall/reflect"_fix_wall_reflect.html,

"fix wiggle"_fix_wiggle.html :tb(c=6,ea=c)

Pair styles.  See the "pair_style"_pair_style.html command for an

overview of pair potentials.  Click on the style itself for a full

:line

Fix commands.  See the "fix"_fix.html command for one-line

descriptions of each style or click on the style itself for a full

description:

"none"_pair_style_none.html,

"hybrid"_pair_style_hybrid.html,

"buck"_pair_style_buck.html,

"buck/coul/cut"_pair_style_buck.html,

"buck/coul/long"_pair_style_buck.html,

"dpd"_pair_style_dpd.html,

"eam"_pair_style_eam.html,

"eam/alloy"_pair_style_eam.html,

"eam/fs"_pair_style_eam.html,

"gran/hertzian"_pair_style_gran.html,

"gran/history"_pair_style_gran.html,

"gran/no_history"_pair_style_gran.html,

"lj/charmm/coul/charmm"_pair_style_charmm.html,

"lj/charmm/coul/charmm/implicit"_pair_style_charmm.html,

"lj/charmm/coul/long"_pair_style_charmm.html,

"lj/class2"_pair_style_class2.html,

"lj/class2/coul/cut"_pair_style_class2.html,

"lj/class2/coul/long"_pair_style_class2.html,

"lj/cut"_pair_style_lj.html,

"lj/cut/coul/cut"_pair_style_lj.html,

"lj/cut/coul/debye"_pair_style_lj.html,

"lj/cut/coul/long"_pair_style_lj.html,

"lj/cut/coul/long/tip4p"_pair_style_lj.html,

"lj/expand"_pair_style_lj_expand.html,

"lj/smooth"_pair_style_lj_smooth.html,

"meam"_pair_style_meam.html,

"morse"_pair_style_morse.html,

"soft"_pair_style_soft.html,

"sw"_pair_style_sw.html,

"table"_pair_style_table.html,

"tersoff"_pair_style_tersoff.html,

"yukawa"_pair_style_yukawa.html :tb(c=4,ea=c)

Bond styles.  See the "bond_style"_bond_style.html command for an

overview of bond potentials.  Click on the style itself for a full

"addforce"_fix_addforce.html,

"aveforce"_fix_aveforce.html,

"com"_fix_com.html,

"deposit"_fix_deposit.html,

"drag"_fix_drag.html,

"efield"_fix_efield.html,

"enforce2d"_fix_enforce2d.html,

"freeze"_fix_freeze.html,

"gran/diag"_fix_gran_diag.html,

"gravity"_fix_gravity.html,

"gyration"_fix_gyration.html,

"indent"_fix_indent.html,

"langevin"_fix_langevin.html,

"lineforce"_fix_lineforce.html,

"msd"_fix_msd.html,

"momentum"_fix_momentum.html,

"nph"_fix_nph.html,

"npt"_fix_npt.html,

"nve"_fix_nve.html,

"nve/gran"_fix_nve_gran.html,

"nvt"_fix_nvt.html,

"orient/fcc"_fix_orient_fcc.html,

"planeforce"_fix_planeforce.html,

"poems"_fix_poems.html,

"pour"_fix_pour.html,

"print"_fix_print.html,

"rdf"_fix_rdf.html,

"recenter"_fix_recenter.html,

"rigid"_fix_rigid.html,

"setforce"_fix_setforce.html,

"shake"_fix_shake.html,

"spring"_fix_spring.html,

"spring/rg"_fix_spring_rg.html,

"spring/self"_fix_spring_self.html,

"temp/rescale"_fix_temp_rescale.html,

"tmd"_fix_tmd.html,

"uniaxial"_fix_uniaxial.html,

"vcm"_fix_vcm.html,

"viscous"_fix_viscous.html,

"volume/rescale"_fix_volume_rescale.html,

"wall/gran"_fix_wall_gran.html,

"wall/lj93"_fix_wall_lj93.html,

"wall/lj126"_fix_wall_lj126.html,

"wall/reflect"_fix_wall_reflect.html,

"wiggle"_fix_wiggle.html :tb(c=8,ea=c)

:line

Compute commands.  See the "compute"_compute.html command for one-line

descriptions of each style or click on the style itself for a full

description:

"none"_bond_style_none.html,

"hybrid"_bond_style_hybrid.html,

"class2"_bond_style_class2.html,

"fene"_bond_style_fene.html,

"fene/expand"_bond_style_fene_expand.html,

"harmonic"_bond_style_harmonic.html,

"morse"_bond_style_morse.html,

"nonlinear"_bond_style_nonlinear.html,

"quartic"_bond_style_quartic.html :tb(c=4,ea=c,w=100)

Angle styles.  See the "angle_style"_angle_style.html command for an

overview of angle potentials.  Click on the style itself for a full

"centro/atom"_compute_centro_atom.html,

"epair/atom"_compute_epair_atom.html,

"etotal/atom"_compute_etotal_atom.html,

"ke/atom"_compute_ke_atom.html,

"pressure"_compute_pressure.html,

"rotate/dipole"_compute_rotate_dipole.html,

"rotate/gran"_compute_rotate_gran.html,

"stress/atom"_compute_stress_atom.html,

"temp"_compute_temp.html,

"temp/partial"_compute_temp_partial.html,

"temp/ramp"_compute_temp_ramp.html,

"temp/region"_compute_temp_region.html :tb(c=6,ea=c)

:line

Pair_style potentials.  See the "pair_style"_pair_style.html command

for an overview of pair potentials.  Click on the style itself for a

full description:

"none"_pair_none.html,

"hybrid"_pair_hybrid.html,

"buck"_pair_buck.html,

"buck/coul/cut"_pair_buck.html,

"buck/coul/long"_pair_buck.html,

"dpd"_pair_dpd.html,

"eam"_pair_eam.html,

"eam/opt"_pair_eam.html,

"eam/alloy"_pair_eam.html,

"eam/alloy/opt"_pair_eam.html,

"eam/fs"_pair_eam.html,

"eam/fs/opt"_pair_eam.html,

"gran/hertzian"_pair_gran.html,

"gran/history"_pair_gran.html,

"gran/no_history"_pair_gran.html,

"lj/charmm/coul/charmm"_pair_charmm.html,

"lj/charmm/coul/charmm/implicit"_pair_charmm.html,

"lj/charmm/coul/long"_pair_charmm.html,

"lj/charmm/coul/long/opt"_pair_charmm.html,

"lj/class2"_pair_class2.html,

"lj/class2/coul/cut"_pair_class2.html,

"lj/class2/coul/long"_pair_class2.html,

"lj/cut"_pair_lj.html,

"lj/cut/opt"_pair_lj.html,

"lj/cut/coul/cut"_pair_lj.html,

"lj/cut/coul/debye"_pair_lj.html,

"lj/cut/coul/long"_pair_lj.html,

"lj/cut/coul/long/tip4p"_pair_lj.html,

"lj/expand"_pair_lj_expand.html,

"lj/smooth"_pair_lj_smooth.html,

"meam"_pair_meam.html,

"morse"_pair_morse.html,

"morse/opt"_pair_morse.html,

"soft"_pair_soft.html,

"sw"_pair_sw.html,

"table"_pair_table.html,

"tersoff"_pair_tersoff.html,

"yukawa"_pair_yukawa.html :tb(c=4,ea=c)

:line

Bond_style potentials.  See the "bond_style"_bond_style.html command

for an overview of bond potentials.  Click on the style itself for a

full description:

"none"_bond_none.html,

"hybrid"_bond_hybrid.html,

"class2"_bond_class2.html,

"fene"_bond_fene.html,

"fene/expand"_bond_fene_expand.html,

"harmonic"_bond_harmonic.html,

"morse"_bond_morse.html,

"nonlinear"_bond_nonlinear.html,

"quartic"_bond_quartic.html :tb(c=4,ea=c,w=100)

:line

Angle_style potentials.  See the "angle_style"_angle_style.html

command for an overview of angle potentials.  Click on the style

itself for a full description:

"none"_angle_none.html,

"hybrid"_angle_hybrid.html,

"charmm"_angle_charmm.html,

"class2"_angle_class2.html,

"cosine"_angle_cosine.html,

"cosine/squared"_angle_cosine_squared.html,

"harmonic"_angle_harmonic.html :tb(c=4,ea=c,w=100)

:line

Dihedral_style potentials.  See the

"dihedral_style"_dihedral_style.html command for an overview of

dihedral potentials.  Click on the style itself for a full

description:

"none"_angle_style_none.html,

"hybrid"_angle_style_hybrid.html,

"charmm"_angle_style_charmm.html,

"class2"_angle_style_class2.html,

"cosine"_angle_style_cosine.html,

"cosine/squared"_angle_style_cosine_squared.html,

"harmonic"_angle_style_harmonic.html :tb(c=6,ea=c,w=100)

Dihedral styles.  See the "dihedral_style"_dihedral_style.html command

for an overview of dihedral potentials.  Click on the style itself for

a full description:

"none"_dihedral_style_none.html,

"hybrid"_dihedral_style_hybrid.html,

"charmm"_dihedral_style_charmm.html,

"class2"_dihedral_style_class2.html,

"harmonic"_dihedral_style_harmonic.html,

"helix"_dihedral_style_helix.html,

"multi/harmonic"_dihedral_style_multi_harmonic.html,

"opls"_dihedral_style_opls.html :tb(c=7,ea=c,w=100)

Improper styles.  See the "improper_style"_improper_style.html command for an

overview of improper potentials.  Click on the style itself for a full

"none"_dihedral_none.html,

"hybrid"_dihedral_hybrid.html,

"charmm"_dihedral_charmm.html,

"class2"_dihedral_class2.html,

"harmonic"_dihedral_harmonic.html,

"helix"_dihedral_helix.html,

"multi/harmonic"_dihedral_multi_harmonic.html,

"opls"_dihedral_opls.html :tb(c=4,ea=c,w=100)

:line

Improper_style potentials.  See the

"improper_style"_improper_style.html command for an overview of

improper potentials.  Click on the style itself for a full

description:

"none"_improper_style_none.html,

"hybrid"_improper_style_hybrid.html,

"class2"_improper_style_class2.html,

"cvff"_improper_style_cvff.html,

"harmonic"_improper_style_harmonic.html :tb(c=4,ea=c,w=100)

"none"_improper_none.html,

"hybrid"_improper_hybrid.html,

"class2"_improper_class2.html,

"cvff"_improper_cvff.html,

"harmonic"_improper_harmonic.html :tb(c=4,ea=c,w=100)

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