Merge pull request #1033 from lammps/doc-reorg-commands

"Previous Section"_Run.html - "LAMMPS WWW Site"_lws -

"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next

Section"_Packages.html :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Commands_all.html#comm)

:line

Commands :h2

These pages describe how a LAMMPS input script is formatted and the

commands in it are used to define a LAMMPS simulation.

<!-- RST

.. toctree::

   Commands_input

   Commands_parse

   Commands_structure

   Commands_category

.. toctree::

   Commands_all

   Commands_fix

   Commands_compute

   Commands_pair

   Commands_bond

   Commands_kspace

END_RST -->

<!-- HTML_ONLY -->

"LAMMPS input scripts"_Commands_input.html

"Parsing rules for input scripts"_Commands_parse.html

"Input script structure"_Commands_structure.html

"Commands by category"_Commands_category.html :all(b)

"All commands"_Commands_all.html 

"Fix commands"_Commands_fix.html 

"Compute commands"_Commands_compute.html 

"Pair commands"_Commands_pair.html 

"Bond, angle, dihedral, improper commands"_Commands_bond.html

"KSpace solvers"_Commands_kspace.html  :all(b)

<!-- END_HTML_ONLY -->

"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS

Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Commands_all.html)

:line

"All commands"_Commands_all.html,

"Fix styles"_Commands_fix.html,

"Compute styles"_Commands_compute.html,

"Pair styles"_Commands_pair.html,

"Bond styles"_Commands_bond.html,

"Angle styles"_Commands_bond.html#angle,

"Dihedral styles"_Commands_bond.html#dihedral,

"Improper styles"_Commands_bond.html#improper,

"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)

All commands :h3

An alphabetic list of all LAMMPS commmands.

"angle_coeff"_angle_coeff.html,

"angle_style"_angle_style.html,

"atom_modify"_atom_modify.html,

"atom_style"_atom_style.html,

"balance"_balance.html,

"bond_coeff"_bond_coeff.html,

"bond_style"_bond_style.html,

"bond_write"_bond_write.html,

"boundary"_boundary.html,

"box"_box.html,

"change_box"_change_box.html,

"clear"_clear.html,

"comm_modify"_comm_modify.html,

"comm_style"_comm_style.html,

"compute"_compute.html,

"compute_modify"_compute_modify.html,

"create_atoms"_create_atoms.html,

"create_bonds"_create_bonds.html,

"create_box"_create_box.html,

"delete_atoms"_delete_atoms.html,

"delete_bonds"_delete_bonds.html,

"dielectric"_dielectric.html,

"dihedral_coeff"_dihedral_coeff.html,

"dihedral_style"_dihedral_style.html,

"dimension"_dimension.html,

"displace_atoms"_displace_atoms.html,

"dump"_dump.html,

"dump image"_dump_image.html,

"dump_modify"_dump_modify.html,

"dump movie"_dump_image.html,

"dump netcdf"_dump_netcdf.html,

"dump netcdf/mpiio"_dump_netcdf.html,

"dump vtk"_dump_vtk.html,

"echo"_echo.html,

"fix"_fix.html,

"fix_modify"_fix_modify.html,

"group"_group.html,

"group2ndx"_group2ndx.html,

"if"_if.html,

"info"_info.html,

"improper_coeff"_improper_coeff.html,

"improper_style"_improper_style.html,

"include"_include.html,

"jump"_jump.html,

"kspace_modify"_kspace_modify.html,

"kspace_style"_kspace_style.html,

"label"_label.html,

"lattice"_lattice.html,

"log"_log.html,

"mass"_mass.html,

"minimize"_minimize.html,

"min_modify"_min_modify.html,

"min_style"_min_style.html,

"molecule"_molecule.html,

"ndx2group"_group2ndx.html,

"neb"_neb.html,

"neigh_modify"_neigh_modify.html,

"neighbor"_neighbor.html,

"newton"_newton.html,

"next"_next.html,

"package"_package.html,

"pair_coeff"_pair_coeff.html,

"pair_modify"_pair_modify.html,

"pair_style"_pair_style.html,

"pair_write"_pair_write.html,

"partition"_partition.html,

"prd"_prd.html,

"print"_print.html,

"processors"_processors.html,

"python"_python.html,

"quit"_quit.html,

"read_data"_read_data.html,

"read_dump"_read_dump.html,

"read_restart"_read_restart.html,

"region"_region.html,

"replicate"_replicate.html,

"rerun"_rerun.html,

"reset_ids"_reset_ids.html,

"reset_timestep"_reset_timestep.html,

"restart"_restart.html,

"run"_run.html,

"run_style"_run_style.html,

"set"_set.html,

"shell"_shell.html,

"special_bonds"_special_bonds.html,

"suffix"_suffix.html,

"tad"_tad.html,

"temper"_temper.html,

"temper/grem"_temper_grem.html,

"temper/npt"_temper_npt.html,

"thermo"_thermo.html,

"thermo_modify"_thermo_modify.html,

"thermo_style"_thermo_style.html,

"timer"_timer.html,

"timestep"_timestep.html,

"uncompute"_uncompute.html,

"undump"_undump.html,

"unfix"_unfix.html,

"units"_units.html,

"variable"_variable.html,

"velocity"_velocity.html,

"write_coeff"_write_coeff.html,

"write_data"_write_data.html,

"write_dump"_write_dump.html,

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

"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS

Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Commands_all.html)

"All commands"_Commands_all.html,

"Fix styles"_Commands_fix.html,

"Compute styles"_Commands_compute.html,

"Pair styles"_Commands_pair.html,

"Bond styles"_Commands_bond.html,

"Angle styles"_Commands_bond.html#angle,

"Dihedral styles"_Commands_bond.html#dihedral,

"Improper styles"_Commands_bond.html#improper,

"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)

Bond, angle, dihedral, and improper commands :h3

:line

Bond_style potentials :h3,link(bond)

All LAMMPS "bond_style"_bond_style.html commands.  Some styles have

accelerated versions.  This is indicated by additional letters in

parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =

OPT.

"none"_bond_none.html,

"zero"_bond_zero.html,

"hybrid"_bond_hybrid.html :tb(c=3,ea=c)

"class2 (ko)"_bond_class2.html,

"fene (iko)"_bond_fene.html,

"fene/expand (o)"_bond_fene_expand.html,

"gromos (o)"_bond_gromos.html,

"harmonic (ko)"_bond_harmonic.html,

"harmonic/shift (o)"_bond_harmonic_shift.html,

"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,

"morse (o)"_bond_morse.html,

"nonlinear (o)"_bond_nonlinear.html,

"oxdna/fene"_bond_oxdna.html,

"oxdna2/fene"_bond_oxdna.html,

"quartic (o)"_bond_quartic.html,

"table (o)"_bond_table.html :tb(c=4,ea=c)

:line

Angle_style potentials :h3,link(angle)

All LAMMPS "angle_style"_angle_style.html commands.  Some styles have

accelerated versions.  This is indicated by additional letters in

parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =

OPT.

"none"_angle_none.html,

"zero"_angle_zero.html,

"hybrid"_angle_hybrid.html :tb(c=3,ea=c)

"charmm (ko)"_angle_charmm.html,

"class2 (ko)"_angle_class2.html,

"cosine (o)"_angle_cosine.html,

"cosine/delta (o)"_angle_cosine_delta.html,

"cosine/periodic (o)"_angle_cosine_periodic.html,

"cosine/shift (o)"_angle_cosine_shift.html,

"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,

"cosine/squared (o)"_angle_cosine_squared.html,

"dipole (o)"_angle_dipole.html,

"fourier (o)"_angle_fourier.html,

"fourier/simple (o)"_angle_fourier_simple.html,

"harmonic (iko)"_angle_harmonic.html,

"quartic (o)"_angle_quartic.html,

"sdk"_angle_sdk.html,

"table (o)"_angle_table.html :tb(c=4,ea=c)

:line

Dihedral_style potentials :h3,link(dihedral)

All LAMMPS "dihedral_style"_dihedral_style.html commands.  Some styles

have accelerated versions.  This is indicated by additional letters in

parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =

OPT.

"none"_dihedral_none.html,

"zero"_dihedral_zero.html,

"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c)

"charmm (iko)"_dihedral_charmm.html,

"charmmfsw"_dihedral_charmm.html,

"class2 (ko)"_dihedral_class2.html,

"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,

"fourier (io)"_dihedral_fourier.html,

"harmonic (io)"_dihedral_harmonic.html,

"helix (o)"_dihedral_helix.html,

"multi/harmonic (o)"_dihedral_multi_harmonic.html,

"nharmonic (o)"_dihedral_nharmonic.html,

"opls (iko)"_dihedral_opls.htm;,

"quadratic (o)"_dihedral_quadratic.html,

"spherical (o)"_dihedral_spherical.html,

"table (o)"_dihedral_table.html,

"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)

:line

Improper_style potentials :h3,link(improper)

All LAMMPS "improper_style"_improper_style.html commands.  Some styles

have accelerated versions.  This is indicated by additional letters in

parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =

OPT.

"none"_improper_none.html,

"zero"_improper_zero.html,

"hybrid"_improper_hybrid.html  :tb(c=3,ea=c)

"class2 (ko)"_improper_class2.html,

"cossq (o)"_improper_cossq.html,

"cvff (io)"_improper_cvff.html,

"distance"_improper_distance.html,

"fourier (o)"_improper_fourier.html,

"harmonic (iko)"_improper_harmonic.html,

"ring (o)"_improper_ring.html,

"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS

Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Commands_all.html)

:line

Commands by category :h3

This page lists most of the LAMMPS commands, grouped by category.  The

"Commands all"_Commands_all.html doc page lists all commands

alphabetically.  It also includes long lists of style options for

entries that appear in the following categories as a single command

(fix, compute, pair, etc).

Initialization:

"newton"_newton.html,

"package"_package.html,

"processors"_processors.html,

"suffix"_suffix.html,

"units"_units.html :ul

Setup simulation box:

"boundary"_boundary.html,

"box"_box.html,

"change_box"_change_box.html,

"create_box"_create_box.html,

"dimension"_dimension.html,

"lattice"_lattice.html,

"region"_region.html :ul

Setup atoms:

"atom_modify"_atom_modify.html,

"atom_style"_atom_style.html,

"balance"_balance.html,

"create_atoms"_create_atoms.html,

"create_bonds"_create_bonds.html,

"delete_atoms"_delete_atoms.html,

"delete_bonds"_delete_bonds.html,

"displace_atoms"_displace_atoms.html,

"group"_group.html,

"mass"_mass.html,

"molecule"_molecule.html,

"read_data"_read_data.html,

"read_dump"_read_dump.html,

"read_restart"_read_restart.html,

"replicate"_replicate.html,

"set"_set.html,

"velocity"_velocity.html :ul

Force fields:

"angle_coeff"_angle_coeff.html,

"angle_style"_angle_style.html,

"bond_coeff"_bond_coeff.html,

"bond_style"_bond_style.html,

"bond_write"_bond_write.html,

"dielectric"_dielectric.html,

"dihedral_coeff"_dihedral_coeff.html,

"dihedral_style"_dihedral_style.html,

"improper_coeff"_improper_coeff.html,

"improper_style"_improper_style.html,

"kspace_modify"_kspace_modify.html,

"kspace_style"_kspace_style.html,

"pair_coeff"_pair_coeff.html,

"pair_modify"_pair_modify.html,

"pair_style"_pair_style.html,

"pair_write"_pair_write.html,

"special_bonds"_special_bonds.html :ul

Settings:

"comm_modify"_comm_modify.html,

"comm_style"_comm_style.html,

"info"_info.html,

"min_modify"_min_modify.html,

"min_style"_min_style.html,

"neigh_modify"_neigh_modify.html,

"neighbor"_neighbor.html,

"partition"_partition.html,

"reset_timestep"_reset_timestep.html,

"run_style"_run_style.html,

"timer"_timer.html,

"timestep"_timestep.html :ul

Operations within timestepping (fixes) and diagnostics (computes):

"compute"_compute.html,

"compute_modify"_compute_modify.html,

"fix"_fix.html,

"fix_modify"_fix_modify.html,

"uncompute"_uncompute.html,

"unfix"_unfix.html :ul

Output:

"dump image"_dump_image.html,

"dump movie"_dump_image.html,

"dump"_dump.html,

"dump_modify"_dump_modify.html,

"restart"_restart.html,

"thermo"_thermo.html,

"thermo_modify"_thermo_modify.html,

"thermo_style"_thermo_style.html,

"undump"_undump.html,

"write_coeff"_write_coeff.html,

"write_data"_write_data.html,

"write_dump"_write_dump.html,

"write_restart"_write_restart.html :ul

Actions:

"minimize"_minimize.html,

"neb"_neb.html,

"prd"_prd.html,

"rerun"_rerun.html,

"run"_run.html,

"tad"_tad.html,

"temper"_temper.html :ul

Input script control:

"clear"_clear.html,

"echo"_echo.html,

"if"_if.html,

"include"_include.html,

"jump"_jump.html,

"label"_label.html,

"log"_log.html,

"next"_next.html,

"print"_print.html,

"python"_python.html,

"quit"_quit.html,

"shell"_shell.html,

"variable"_variable.html :ul

"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS

Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Commands_all.html)

:line

"All commands"_Commands_all.html,

"Fix styles"_Commands_fix.html,

"Compute styles"_Commands_compute.html,

"Pair styles"_Commands_pair.html,

"Bond styles"_Commands_bond.html,

"Angle styles"_Commands_bond.html#angle,

"Dihedral styles"_Commands_bond.html#dihedral,

"Improper styles"_Commands_bond.html#improper,

"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)

Compute commands :h3

An alphabetic list of all LAMMPS "compute"_compute.html commands.

Some styles have accelerated versions.  This is indicated by

additional letters in parenthesis: g = GPU, i = USER-INTEL, k =

KOKKOS, o = USER-OMP, t = OPT.

"ackland/atom"_compute_ackland_atom.html,

"aggregate/atom"_compute_cluster_atom.html,

"angle"_compute_angle.html,

"angle/local"_compute_angle_local.html,

"angmom/chunk"_compute_angmom_chunk.html,

"basal/atom"_compute_basal_atom.html,

"body/local"_compute_body_local.html,

"bond"_compute_bond.html,

"bond/local"_compute_bond_local.html,

"centro/atom"_compute_centro_atom.html,

"chunk/atom"_compute_chunk_atom.html,

"cluster/atom"_compute_cluster_atom.html,

"cna/atom"_compute_cna_atom.html,

"cnp/atom"_compute_cnp_atom.html,

"com"_compute_com.html,

"com/chunk"_compute_com_chunk.html,

"contact/atom"_compute_contact_atom.html,

"coord/atom"_compute_coord_atom.html,

"damage/atom"_compute_damage_atom.html,

"dihedral"_compute_dihedral.html,

"dihedral/local"_compute_dihedral_local.html,

"dilatation/atom"_compute_dilatation_atom.html,

"dipole/chunk"_compute_dipole_chunk.html,

"displace/atom"_compute_displace_atom.html,

"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,

"erotate/rigid"_compute_erotate_rigid.html,

"erotate/sphere"_compute_erotate_sphere.html,

"erotate/sphere/atom"_compute_erotate_sphere_atom.html,

"event/displace"_compute_event_displace.html,

"fep"_compute_fep.html,

"force/tally"_compute_tally.html,

"fragment/atom"_compute_cluster_atom.html,

"global/atom"_compute_global_atom.html,

"group/group"_compute_group_group.html,

"gyration"_compute_gyration.html,

"gyration/chunk"_compute_gyration_chunk.html,

"heat/flux"_compute_heat_flux.html,

"heat/flux/tally"_compute_tally.html,

"hexorder/atom"_compute_hexorder_atom.html,

"improper"_compute_improper.html,

"improper/local"_compute_improper_local.html,

"inertia/chunk"_compute_inertia_chunk.html,

"ke"_compute_ke.html,

"ke/atom"_compute_ke_atom.html,

"ke/atom/eff"_compute_ke_atom_eff.html,

"ke/eff"_compute_ke_eff.html,

"ke/rigid"_compute_ke_rigid.html,

"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,

"msd/chunk"_compute_msd_chunk.html,

"msd/nongauss"_compute_msd_nongauss.html,

"omega/chunk"_compute_omega_chunk.html,

"orientorder/atom"_compute_orientorder_atom.html,

"pair"_compute_pair.html,

"pair/local"_compute_pair_local.html,

"pe"_compute_pe.html,

"pe/atom"_compute_pe_atom.html,

"pe/mol/tally"_compute_tally.html,

"pe/tally"_compute_tally.html,

"plasticity/atom"_compute_plasticity_atom.html,

"pressure"_compute_pressure.html,

"pressure/uef"_compute_pressure_uef.html,

"property/atom"_compute_property_atom.html,

"property/chunk"_compute_property_chunk.html,

"property/local"_compute_property_local.html,

"rdf"_compute_rdf.html,

"reduce"_compute_reduce.html,

"reduce/region"_compute_reduce.html,

"rigid/local"_compute_rigid_local.html,

"saed"_compute_saed.html,

"slice"_compute_slice.html,

"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/mesh/vertices"_compute_smd_triangle_mesh_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,

"snad/atom"_compute_sna_atom.html,

"snav/atom"_compute_sna_atom.html,

"spin"_compute_spin.html,

"stress/atom"_compute_stress_atom.html,

"stress/tally"_compute_tally.html,

"tdpd/cc/atom"_compute_tdpd_cc_atom.html,

"temp (k)"_compute_temp.html,

"temp/asphere"_compute_temp_asphere.html,

"temp/body"_compute_temp_body.html,

"temp/chunk"_compute_temp_chunk.html,

"temp/com"_compute_temp_com.html,

"temp/deform"_compute_temp_deform.html,

"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,

"temp/profile"_compute_temp_profile.html,

"temp/ramp"_compute_temp_ramp.html,

"temp/region"_compute_temp_region.html,

"temp/region/eff"_compute_temp_region_eff.html,

"temp/rotate"_compute_temp_rotate.html,

"temp/sphere"_compute_temp_sphere.html,

"temp/uef"_compute_temp_uef.html,

"ti"_compute_ti.html,

"torque/chunk"_compute_torque_chunk.html,

"vacf"_compute_vacf.html,

"vcm/chunk"_compute_vcm_chunk.html,

"voronoi/atom"_compute_voronoi_atom.html,

"xrd"_compute_xrd.html :tb(c=6,ea=c)