replace Section_commands.txt file
This commit is contained in:
Steven J. Plimpton
51
doc/src/Commands.txt
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51
doc/src/Commands.txt
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"Previous Section"_Run.html - "LAMMPS WWW Site"_lws -
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"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
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Section"_Packages.html :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html#comm)
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:line
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Commands :h2
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These pages describe how a LAMMPS input script is formatted and the
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commands in it are used to define a LAMMPS simulation.
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<!-- RST
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.. toctree::
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Commands_input
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Commands_parse
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Commands_structure
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Commands_category
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.. toctree::
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Commands_all
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Commands_fix
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Commands_compute
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Commands_pair
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Commands_bond
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Commands_kspace
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END_RST -->
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<!-- HTML_ONLY -->
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"LAMMPS input scripts"_Commands_input.html
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"Parsing rules for input scripts"_Commands_parse.html
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"Input script structure"_Commands_structure.html
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"Commands by category"_Commands_category.html :all(b)
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"All commands"_Commands_all.html
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"Fix commands"_Commands_fix.html
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"Compute commands"_Commands_compute.html
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"Pair commands"_Commands_pair.html
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"Bond, angle, dihedral, improper commands"_Commands_bond.html
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"KSpace solvers"_Commands_kspace.html :all(b)
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<!-- END_HTML_ONLY -->
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128
doc/src/Commands_all.txt
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128
doc/src/Commands_all.txt
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"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
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Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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"All commands"_Commands_all.html,
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"Fix styles"_Commands_fix.html,
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"Compute styles"_Commands_compute.html,
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"Pair styles"_Commands_pair.html,
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"Bond styles"_Commands_bond.html,
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"Angle styles"_Commands_bond.html#angle,
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"Dihedral styles"_Commands_bond.html#dihedral,
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"Improper styles"_Commands_bond.html#improper,
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"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
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All commands :h3
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An alphabetic list of all LAMMPS commmands.
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"angle_coeff"_angle_coeff.html,
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"angle_style"_angle_style.html,
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"atom_modify"_atom_modify.html,
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"atom_style"_atom_style.html,
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"balance"_balance.html,
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"bond_coeff"_bond_coeff.html,
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"bond_style"_bond_style.html,
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"bond_write"_bond_write.html,
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"boundary"_boundary.html,
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"box"_box.html,
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"change_box"_change_box.html,
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"clear"_clear.html,
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"comm_modify"_comm_modify.html,
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"comm_style"_comm_style.html,
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"compute"_compute.html,
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"compute_modify"_compute_modify.html,
|
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"create_atoms"_create_atoms.html,
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"create_bonds"_create_bonds.html,
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"create_box"_create_box.html,
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"delete_atoms"_delete_atoms.html,
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"delete_bonds"_delete_bonds.html,
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"dielectric"_dielectric.html,
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"dihedral_coeff"_dihedral_coeff.html,
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"dihedral_style"_dihedral_style.html,
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"dimension"_dimension.html,
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"displace_atoms"_displace_atoms.html,
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"dump"_dump.html,
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"dump image"_dump_image.html,
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"dump_modify"_dump_modify.html,
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"dump movie"_dump_image.html,
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"dump netcdf"_dump_netcdf.html,
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"dump netcdf/mpiio"_dump_netcdf.html,
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"dump vtk"_dump_vtk.html,
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"echo"_echo.html,
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"fix"_fix.html,
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"fix_modify"_fix_modify.html,
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"group"_group.html,
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"group2ndx"_group2ndx.html,
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"if"_if.html,
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"info"_info.html,
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"improper_coeff"_improper_coeff.html,
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"improper_style"_improper_style.html,
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"include"_include.html,
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"jump"_jump.html,
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"kspace_modify"_kspace_modify.html,
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"kspace_style"_kspace_style.html,
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"label"_label.html,
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"lattice"_lattice.html,
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"log"_log.html,
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"mass"_mass.html,
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"minimize"_minimize.html,
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"min_modify"_min_modify.html,
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"min_style"_min_style.html,
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"molecule"_molecule.html,
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"ndx2group"_group2ndx.html,
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"neb"_neb.html,
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"neigh_modify"_neigh_modify.html,
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"neighbor"_neighbor.html,
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"newton"_newton.html,
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"next"_next.html,
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"package"_package.html,
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"pair_coeff"_pair_coeff.html,
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"pair_modify"_pair_modify.html,
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"pair_style"_pair_style.html,
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"pair_write"_pair_write.html,
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"partition"_partition.html,
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"prd"_prd.html,
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"print"_print.html,
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"processors"_processors.html,
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"python"_python.html,
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"quit"_quit.html,
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"read_data"_read_data.html,
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"read_dump"_read_dump.html,
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"read_restart"_read_restart.html,
|
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"region"_region.html,
|
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"replicate"_replicate.html,
|
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"rerun"_rerun.html,
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"reset_ids"_reset_ids.html,
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"reset_timestep"_reset_timestep.html,
|
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"restart"_restart.html,
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"run"_run.html,
|
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"run_style"_run_style.html,
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"set"_set.html,
|
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"shell"_shell.html,
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"special_bonds"_special_bonds.html,
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"suffix"_suffix.html,
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"tad"_tad.html,
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"temper"_temper.html,
|
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"temper/grem"_temper_grem.html,
|
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"temper/npt"_temper_npt.html,
|
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"thermo"_thermo.html,
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"thermo_modify"_thermo_modify.html,
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"thermo_style"_thermo_style.html,
|
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"timer"_timer.html,
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"timestep"_timestep.html,
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"uncompute"_uncompute.html,
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"undump"_undump.html,
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"unfix"_unfix.html,
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"units"_units.html,
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"variable"_variable.html,
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"velocity"_velocity.html,
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"write_coeff"_write_coeff.html,
|
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"write_data"_write_data.html,
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"write_dump"_write_dump.html,
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"write_restart"_write_restart.html :tb(c=6,ea=c)
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124
doc/src/Commands_bond.txt
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124
doc/src/Commands_bond.txt
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"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
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|
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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"All commands"_Commands_all.html,
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"Fix styles"_Commands_fix.html,
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"Compute styles"_Commands_compute.html,
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"Pair styles"_Commands_pair.html,
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"Bond styles"_Commands_bond.html,
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"Angle styles"_Commands_bond.html#angle,
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"Dihedral styles"_Commands_bond.html#dihedral,
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"Improper styles"_Commands_bond.html#improper,
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"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
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Bond, angle, dihedral, and improper commands :h3
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:line
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Bond_style potentials :h3,link(bond)
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All LAMMPS "bond_style"_bond_style.html commands. Some styles have
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accelerated versions. This is indicated by additional letters in
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parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
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OPT.
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"none"_bond_none.html,
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"zero"_bond_zero.html,
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"hybrid"_bond_hybrid.html :tb(c=3,ea=c)
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"class2 (ko)"_bond_class2.html,
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"fene (iko)"_bond_fene.html,
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"fene/expand (o)"_bond_fene_expand.html,
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"gromos (o)"_bond_gromos.html,
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"harmonic (ko)"_bond_harmonic.html,
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"harmonic/shift (o)"_bond_harmonic_shift.html,
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"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
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"morse (o)"_bond_morse.html,
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"nonlinear (o)"_bond_nonlinear.html,
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"oxdna/fene"_bond_oxdna.html,
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"oxdna2/fene"_bond_oxdna.html,
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"quartic (o)"_bond_quartic.html,
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"table (o)"_bond_table.html :tb(c=4,ea=c)
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|
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:line
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Angle_style potentials :h3,link(angle)
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All LAMMPS "angle_style"_angle_style.html commands. Some styles have
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accelerated versions. This is indicated by additional letters in
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parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
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OPT.
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"none"_angle_none.html,
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"zero"_angle_zero.html,
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"hybrid"_angle_hybrid.html :tb(c=3,ea=c)
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"charmm (ko)"_angle_charmm.html,
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"class2 (ko)"_angle_class2.html,
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"cosine (o)"_angle_cosine.html,
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"cosine/delta (o)"_angle_cosine_delta.html,
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"cosine/periodic (o)"_angle_cosine_periodic.html,
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"cosine/shift (o)"_angle_cosine_shift.html,
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"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
|
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"cosine/squared (o)"_angle_cosine_squared.html,
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"dipole (o)"_angle_dipole.html,
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"fourier (o)"_angle_fourier.html,
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"fourier/simple (o)"_angle_fourier_simple.html,
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"harmonic (iko)"_angle_harmonic.html,
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"quartic (o)"_angle_quartic.html,
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"sdk"_angle_sdk.html,
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"table (o)"_angle_table.html :tb(c=4,ea=c)
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:line
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|
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Dihedral_style potentials :h3,link(dihedral)
|
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|
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All LAMMPS "dihedral_style"_dihedral_style.html commands. Some styles
|
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have accelerated versions. This is indicated by additional letters in
|
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parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
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OPT.
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|
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"none"_dihedral_none.html,
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"zero"_dihedral_zero.html,
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"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c)
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||||
|
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"charmm (iko)"_dihedral_charmm.html,
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"charmmfsw"_dihedral_charmm.html,
|
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"class2 (ko)"_dihedral_class2.html,
|
||||
"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
|
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"fourier (io)"_dihedral_fourier.html,
|
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"harmonic (io)"_dihedral_harmonic.html,
|
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"helix (o)"_dihedral_helix.html,
|
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"multi/harmonic (o)"_dihedral_multi_harmonic.html,
|
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"nharmonic (o)"_dihedral_nharmonic.html,
|
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"opls (iko)"_dihedral_opls.htm;,
|
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"quadratic (o)"_dihedral_quadratic.html,
|
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"spherical (o)"_dihedral_spherical.html,
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"table (o)"_dihedral_table.html,
|
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"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
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|
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:line
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Improper_style potentials :h3,link(improper)
|
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All LAMMPS "improper_style"_improper_style.html commands. Some styles
|
||||
have accelerated versions. This is indicated by additional letters in
|
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parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
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OPT.
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||||
|
||||
"none"_improper_none.html,
|
||||
"zero"_improper_zero.html,
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||||
"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
|
||||
|
||||
"class2 (ko)"_improper_class2.html,
|
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"cossq (o)"_improper_cossq.html,
|
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"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)
|
||||
141
doc/src/Commands_category.txt
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141
doc/src/Commands_category.txt
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@ -0,0 +1,141 @@
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"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
|
||||
|
||||
153
doc/src/Commands_compute.txt
Normal file
153
doc/src/Commands_compute.txt
Normal file
@ -0,0 +1,153 @@
|
||||
"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)
|
||||
229
doc/src/Commands_fix.txt
Normal file
229
doc/src/Commands_fix.txt
Normal file
@ -0,0 +1,229 @@
|
||||
"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)
|
||||
|
||||
Fix commands :h3
|
||||
|
||||
An alphabetic list of all LAMMPS "fix"_fix.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.
|
||||
|
||||
"adapt"_fix_adapt.html,
|
||||
"adapt/fep"_fix_adapt_fep.html,
|
||||
"addforce"_fix_addforce.html,
|
||||
"addtorque"_fix_addtorque.html,
|
||||
"append/atoms"_fix_append_atoms.html,
|
||||
"atc"_fix_atc.html,
|
||||
"atom/swap"_fix_atom_swap.html,
|
||||
"ave/atom"_fix_ave_atom.html,
|
||||
"ave/chunk"_fix_ave_chunk.html,
|
||||
"ave/correlate"_fix_ave_correlate.html,
|
||||
"ave/correlate/long"_fix_ave_correlate_long.html,
|
||||
"ave/histo"_fix_ave_histo.html,
|
||||
"ave/histo/weight"_fix_ave_histo.html,
|
||||
"ave/time"_fix_ave_time.html,
|
||||
"aveforce"_fix_aveforce.html,
|
||||
"balance"_fix_balance.html,
|
||||
"bond/break"_fix_bond_break.html,
|
||||
"bond/create"_fix_bond_create.html,
|
||||
"bond/react"_fix_bond_react.html,
|
||||
"bond/swap"_fix_bond_swap.html,
|
||||
"box/relax"_fix_box_relax.html,
|
||||
"cmap"_fix_cmap.html,
|
||||
"colvars"_fix_colvars.html,
|
||||
"controller"_fix_controller.html,
|
||||
"deform (k)"_fix_deform.html,
|
||||
"deposit"_fix_deposit.html,
|
||||
"dpd/energy (k)"_fix_dpd_energy.html,
|
||||
"drag"_fix_drag.html,
|
||||
"drude"_fix_drude.html,
|
||||
"drude/transform/direct"_fix_drude_transform.html,
|
||||
"drude/transform/reverse"_fix_drude_transform.html,
|
||||
"dt/reset"_fix_dt_reset.html,
|
||||
"edpd/source"_fix_dpd_source.html,
|
||||
"efield"_fix_efield.html,
|
||||
"ehex"_fix_ehex.html,
|
||||
"enforce2d (k)"_fix_enforce2d.html,
|
||||
"eos/cv"_fix_eos_cv.html,
|
||||
"eos/table"_fix_eos_table.html,
|
||||
"eos/table/rx (k)"_fix_eos_table_rx.html,
|
||||
"evaporate"_fix_evaporate.html,
|
||||
"external"_fix_external.html,
|
||||
"filter/corotate"_fix_filter_corotate.html,
|
||||
"flow/gauss"_fix_flow_gauss.html,
|
||||
"freeze"_fix_freeze.html,
|
||||
"gcmc"_fix_gcmc.html,
|
||||
"gld"_fix_gld.html,
|
||||
"gle"_fix_gle.html,
|
||||
"gravity (o)"_fix_gravity.html,
|
||||
"grem"_fix_grem.html,
|
||||
"halt"_fix_halt.html,
|
||||
"heat"_fix_heat.html,
|
||||
"imd"_fix_imd.html,
|
||||
"indent"_fix_indent.html,
|
||||
"ipi"_fix_ipi.html,
|
||||
"langevin (k)"_fix_langevin.html,
|
||||
"langevin/drude"_fix_langevin_drude.html,
|
||||
"langevin/eff"_fix_langevin_eff.html,
|
||||
"langevin/spin"_fix_langevin_spin.html,
|
||||
"latte"_fix_latte.html,
|
||||
"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,
|
||||
"manifoldforce"_fix_manifoldforce.html,
|
||||
"meso"_fix_meso.html,
|
||||
"meso/stationary"_fix_meso_stationary.html,
|
||||
"momentum (k)"_fix_momentum.html,
|
||||
"move"_fix_move.html,
|
||||
"mscg"_fix_mscg.html,
|
||||
"msst"_fix_msst.html,
|
||||
"mvv/dpd"_fix_mvv_dpd.html,
|
||||
"mvv/edpd"_fix_mvv_dpd.html,
|
||||
"mvv/tdpd"_fix_mvv_dpd.html,
|
||||
"neb"_fix_neb.html,
|
||||
"nph (ko)"_fix_nh.html,
|
||||
"nph/asphere (o)"_fix_nph_asphere.html,
|
||||
"nph/body"_fix_nph_body.html,
|
||||
"nph/eff"_fix_nh_eff.html,
|
||||
"nph/sphere (o)"_fix_nph_sphere.html,
|
||||
"nphug (o)"_fix_nphug.html,
|
||||
"npt (kio)"_fix_nh.html,
|
||||
"npt/asphere (o)"_fix_npt_asphere.html,
|
||||
"npt/body"_fix_npt_body.html,
|
||||
"npt/eff"_fix_nh_eff.html,
|
||||
"npt/sphere (o)"_fix_npt_sphere.html,
|
||||
"npt/uef"_fix_nh_uef.html,
|
||||
"nve (kio)"_fix_nve.html,
|
||||
"nve/asphere (i)"_fix_nve_asphere.html,
|
||||
"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
|
||||
"nve/body"_fix_nve_body.html,
|
||||
"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/line"_fix_nve_line.html,
|
||||
"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
|
||||
"nve/noforce"_fix_nve_noforce.html,
|
||||
"nve/sphere (o)"_fix_nve_sphere.html,
|
||||
"nve/spin"_fix_nve_spin.html,
|
||||
"nve/tri"_fix_nve_tri.html,
|
||||
"nvk"_fix_nvk.html,
|
||||
"nvt (iko)"_fix_nh.html,
|
||||
"nvt/asphere (o)"_fix_nvt_asphere.html,
|
||||
"nvt/body"_fix_nvt_body.html,
|
||||
"nvt/eff"_fix_nh_eff.html,
|
||||
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
|
||||
"nvt/sllod (io)"_fix_nvt_sllod.html,
|
||||
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
|
||||
"nvt/sphere (o)"_fix_nvt_sphere.html,
|
||||
"nvt/uef"_fix_nh_uef.html,
|
||||
"oneway"_fix_oneway.html,
|
||||
"orient/bcc"_fix_orient.html,
|
||||
"orient/fcc"_fix_orient.html,
|
||||
"phonon"_fix_phonon.html,
|
||||
"pimd"_fix_pimd.html,
|
||||
"planeforce"_fix_planeforce.html,
|
||||
"poems"_fix_poems.html,
|
||||
"pour"_fix_pour.html,
|
||||
"precession/spin"_fix_precession_spin.html,
|
||||
"press/berendsen"_fix_press_berendsen.html,
|
||||
"print"_fix_print.html,
|
||||
"property/atom (k)"_fix_property_atom.html,
|
||||
"python/invoke"_fix_python_invoke.html,
|
||||
"python/move"_fix_python_move.html,
|
||||
"qbmsst"_fix_qbmsst.html,
|
||||
"qeq/comb (o)"_fix_qeq_comb.html,
|
||||
"qeq/dynamic"_fix_qeq.html,
|
||||
"qeq/fire"_fix_qeq.html,
|
||||
"qeq/point"_fix_qeq.html,
|
||||
"qeq/reax (ko)"_fix_qeq_reax.html,
|
||||
"qeq/shielded"_fix_qeq.html,
|
||||
"qeq/slater"_fix_qeq.html,
|
||||
"qmmm"_fix_qmmm.html,
|
||||
"qtb"_fix_qtb.html,
|
||||
"rattle"_fix_shake.html,
|
||||
"reax/bonds"_fix_reax_bonds.html,
|
||||
"reax/c/bonds (k)"_fix_reax_bonds.html,
|
||||
"reax/c/species (k)"_fix_reaxc_species.html,
|
||||
"recenter"_fix_recenter.html,
|
||||
"restrain"_fix_restrain.html,
|
||||
"rhok"_fix_rhok.html,
|
||||
"rigid (o)"_fix_rigid.html,
|
||||
"rigid/nph (o)"_fix_rigid.html,
|
||||
"rigid/npt (o)"_fix_rigid.html,
|
||||
"rigid/nve (o)"_fix_rigid.html,
|
||||
"rigid/nvt (o)"_fix_rigid.html,
|
||||
"rigid/small (o)"_fix_rigid.html,
|
||||
"rigid/small/nph"_fix_rigid.html,
|
||||
"rigid/small/npt"_fix_rigid.html,
|
||||
"rigid/small/nve"_fix_rigid.html,
|
||||
"rigid/small/nvt"_fix_rigid.html,
|
||||
"rx (k)"_fix_rx.html,
|
||||
"saed/vtk"_fix_saed_vtk.html,
|
||||
"setforce (k)"_fix_setforce.html,
|
||||
"shake"_fix_shake.html,
|
||||
"shardlow (k)"_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/triangulated/surface"_fix_smd_move_triangulated_surface.html,
|
||||
"smd/setvel"_fix_smd_setvel.html,
|
||||
"smd/wall/surface"_fix_smd_wall_surface.html,
|
||||
"spring"_fix_spring.html,
|
||||
"spring/chunk"_fix_spring_chunk.html,
|
||||
"spring/rg"_fix_spring_rg.html,
|
||||
"spring/self"_fix_spring_self.html,
|
||||
"srd"_fix_srd.html,
|
||||
"store/force"_fix_store_force.html,
|
||||
"store/state"_fix_store_state.html,
|
||||
"tdpd/source"_fix_dpd_source.html,
|
||||
"temp/berendsen"_fix_temp_berendsen.html,
|
||||
"temp/csld"_fix_temp_csvr.html,
|
||||
"temp/csvr"_fix_temp_csvr.html,
|
||||
"temp/rescale"_fix_temp_rescale.html,
|
||||
"temp/rescale/eff"_fix_temp_rescale_eff.html,
|
||||
"tfmc"_fix_tfmc.html,
|
||||
"thermal/conductivity"_fix_thermal_conductivity.html,
|
||||
"ti/spring"_fix_ti_spring.html,
|
||||
"tmd"_fix_tmd.html,
|
||||
"ttm"_fix_ttm.html,
|
||||
"ttm/mod"_fix_ttm.html,
|
||||
"tune/kspace"_fix_tune_kspace.html,
|
||||
"vector"_fix_vector.html,
|
||||
"viscosity"_fix_viscosity.html,
|
||||
"viscous"_fix_viscous.html,
|
||||
"wall/body/polygon"_fix_wall_body_polygon.html,
|
||||
"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
|
||||
"wall/colloid"_fix_wall.html,
|
||||
"wall/ees"_fix_wall_ees.html,
|
||||
"wall/gran"_fix_wall_gran.html,
|
||||
"wall/gran/region"_fix_wall_gran_region.html,
|
||||
"wall/harmonic"_fix_wall.html,
|
||||
"wall/lj1043"_fix_wall.html,
|
||||
"wall/lj126"_fix_wall.html,
|
||||
"wall/lj93 (k)"_fix_wall.html,
|
||||
"wall/piston"_fix_wall_piston.html,
|
||||
"wall/reflect (k)"_fix_wall_reflect.html,
|
||||
"wall/region"_fix_wall_region.html,
|
||||
"wall/region/ees"_fix_wall_ees.html,
|
||||
"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
|
||||
60
doc/src/Commands_input.txt
Normal file
60
doc/src/Commands_input.txt
Normal file
@ -0,0 +1,60 @@
|
||||
"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
|
||||
|
||||
LAMMPS input scripts :h3
|
||||
|
||||
LAMMPS executes by reading commands from a input script (text file),
|
||||
one line at a time. When the input script ends, LAMMPS exits. Each
|
||||
command causes LAMMPS to take some action. It may set an internal
|
||||
variable, read in a file, or run a simulation. Most commands have
|
||||
default settings, which means you only need to use the command if you
|
||||
wish to change the default.
|
||||
|
||||
In many cases, the ordering of commands in an input script is not
|
||||
important. However the following rules apply:
|
||||
|
||||
(1) LAMMPS does not read your entire input script and then perform a
|
||||
simulation with all the settings. Rather, the input script is read
|
||||
one line at a time and each command takes effect when it is read.
|
||||
Thus this sequence of commands:
|
||||
|
||||
timestep 0.5
|
||||
run 100
|
||||
run 100 :pre
|
||||
|
||||
does something different than this sequence:
|
||||
|
||||
run 100
|
||||
timestep 0.5
|
||||
run 100 :pre
|
||||
|
||||
In the first case, the specified timestep (0.5 fs) is used for two
|
||||
simulations of 100 timesteps each. In the 2nd case, the default
|
||||
timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
|
||||
timestep is used for the 2nd one.
|
||||
|
||||
(2) Some commands are only valid when they follow other commands. For
|
||||
example you cannot set the temperature of a group of atoms until atoms
|
||||
have been defined and a group command is used to define which atoms
|
||||
belong to the group.
|
||||
|
||||
(3) Sometimes command B will use values that can be set by command A.
|
||||
This means command A must precede command B in the input script if it
|
||||
is to have the desired effect. For example, the
|
||||
"read_data"_read_data.html command initializes the system by setting
|
||||
up the simulation box and assigning atoms to processors. If default
|
||||
values are not desired, the "processors"_processors.html and
|
||||
"boundary"_boundary.html commands need to be used before read_data to
|
||||
tell LAMMPS how to map processors to the simulation box.
|
||||
|
||||
Many input script errors are detected by LAMMPS and an ERROR or
|
||||
WARNING message is printed. The "Errors"_Errors.html doc page gives
|
||||
more information on what errors mean. The documentation for each
|
||||
command lists restrictions on how the command can be used.
|
||||
|
||||
36
doc/src/Commands_kspace.txt
Normal file
36
doc/src/Commands_kspace.txt
Normal file
@ -0,0 +1,36 @@
|
||||
"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.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)
|
||||
|
||||
KSpace solvers :h3
|
||||
|
||||
All LAMMPS "kspace_style"_kspace_style.html solvers. 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.
|
||||
|
||||
"ewald (o)"_kspace_style.html,
|
||||
"ewald/disp"_kspace_style.html,
|
||||
"msm (o)"_kspace_style.html,
|
||||
"msm/cg (o)"_kspace_style.html,
|
||||
"pppm (gok)"_kspace_style.html,
|
||||
"pppm/cg (o)"_kspace_style.html,
|
||||
"pppm/disp (i)"_kspace_style.html,
|
||||
"pppm/disp/tip4p"_kspace_style.html,
|
||||
"pppm/stagger"_kspace_style.html,
|
||||
"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
|
||||
231
doc/src/Commands_pair.txt
Normal file
231
doc/src/Commands_pair.txt
Normal file
@ -0,0 +1,231 @@
|
||||
"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)
|
||||
|
||||
Pair_style potentials :h3
|
||||
|
||||
All LAMMPS "pair_style"_pair_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"_pair_none.html,
|
||||
"zero"_pair_zero.html,
|
||||
"hybrid"_pair_hybrid.html,
|
||||
"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
|
||||
|
||||
"adp (o)"_pair_adp.html,
|
||||
"agni (o)"_pair_agni.html,
|
||||
"airebo (oi)"_pair_airebo.html,
|
||||
"airebo/morse (oi)"_pair_airebo.html,
|
||||
"awpmd/cut"_pair_awpmd.html,
|
||||
"beck (go)"_pair_beck.html,
|
||||
"body/nparticle"_pair_body_nparticle.html,
|
||||
"body/rounded/polygon"_pair_body_rounded/polygon.html,
|
||||
"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html,
|
||||
"bop"_pair_bop.html,
|
||||
"born (go)"_pair_born.html,
|
||||
"born/coul/dsf"_pair_born.html,
|
||||
"born/coul/dsf/cs"_pair_born.html,
|
||||
"born/coul/long (go)"_pair_born.html,
|
||||
"born/coul/long/cs"_pair_born.html,
|
||||
"born/coul/msm (o)"_pair_born.html,
|
||||
"born/coul/wolf (go)"_pair_born.html,
|
||||
"born/coul/wolf/cs"_pair_born.html,
|
||||
"brownian (o)"_pair_brownian.html,
|
||||
"brownian/poly (o)"_pair_brownian.html,
|
||||
"buck (giko)"_pair_buck.html,
|
||||
"buck/coul/cut (giko)"_pair_buck.html,
|
||||
"buck/coul/long (giko)"_pair_buck.html,
|
||||
"buck/coul/long/cs"_pair_buck.html,
|
||||
"buck/coul/msm (o)"_pair_buck.html,
|
||||
"buck/long/coul/long (o)"_pair_buck_long.html,
|
||||
"buck/mdf"_pair_mdf.html,
|
||||
"colloid (go)"_pair_colloid.html,
|
||||
"comb (o)"_pair_comb.html,
|
||||
"comb3"_pair_comb.html,
|
||||
"coul/cut (gko)"_pair_coul.html,
|
||||
"coul/cut/soft (o)"_pair_lj_soft.html,
|
||||
"coul/debye (gko)"_pair_coul.html,
|
||||
"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/soft (o)"_pair_lj_soft.html,
|
||||
"coul/msm"_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,
|
||||
"dpd (gio)"_pair_dpd.html,
|
||||
"dpd/fdt"_pair_dpd_fdt.html,
|
||||
"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
|
||||
"dpd/tstat (go)"_pair_dpd.html,
|
||||
"dsmc"_pair_dsmc.html,
|
||||
"eam (gikot)"_pair_eam.html,
|
||||
"eam/alloy (gikot)"_pair_eam.html,
|
||||
"eam/cd (o)"_pair_eam.html,
|
||||
"eam/fs (gikot)"_pair_eam.html,
|
||||
"edip (o)"_pair_edip.html,
|
||||
"edip/multi"_pair_edip.html,
|
||||
"edpd"_pair_meso.html,
|
||||
"eff/cut"_pair_eff.html,
|
||||
"eim (o)"_pair_eim.html,
|
||||
"exp6/rx (k)"_pair_exp6_rx.html,
|
||||
"extep"_pair_extep.html,
|
||||
"gauss (go)"_pair_gauss.html,
|
||||
"gauss/cut"_pair_gauss.html,
|
||||
"gayberne (gio)"_pair_gayberne.html,
|
||||
"gran/hertz/history (o)"_pair_gran.html,
|
||||
"gran/hooke (o)"_pair_gran.html,
|
||||
"gran/hooke/history (o)"_pair_gran.html,
|
||||
"gw"_pair_gw.html,
|
||||
"gw/zbl"_pair_gw.html,
|
||||
"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
|
||||
"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
|
||||
"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
|
||||
"kim"_pair_kim.html,
|
||||
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
|
||||
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
|
||||
"lcbop"_pair_lcbop.html,
|
||||
"lennard/mdf"_pair_mdf.html,
|
||||
"line/lj"_pair_line_lj.html,
|
||||
"list"_pair_list.html,
|
||||
"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
|
||||
"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
|
||||
"lj/charmm/coul/long (giko)"_pair_charmm.html,
|
||||
"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
|
||||
"lj/charmm/coul/msm"_pair_charmm.html,
|
||||
"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
|
||||
"lj/charmmfsw/coul/long"_pair_charmm.html,
|
||||
"lj/class2 (gko)"_pair_class2.html,
|
||||
"lj/class2/coul/cut (ko)"_pair_class2.html,
|
||||
"lj/class2/coul/long (gko)"_pair_class2.html,
|
||||
"lj/cubic (go)"_pair_lj_cubic.html,
|
||||
"lj/cut (gikot)"_pair_lj.html,
|
||||
"lj/cut/coul/cut (gko)"_pair_lj.html,
|
||||
"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
|
||||
"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/soft (o)"_pair_lj_soft.html,
|
||||
"lj/cut/coul/msm (go)"_pair_lj.html,
|
||||
"lj/cut/coul/wolf (o)"_pair_lj.html,
|
||||
"lj/cut/dipole/cut (go)"_pair_dipole.html,
|
||||
"lj/cut/dipole/long"_pair_dipole.html,
|
||||
"lj/cut/dipole/sf (go)"_pair_dipole.html,
|
||||
"lj/cut/soft (o)"_pair_lj_soft.html,
|
||||
"lj/cut/thole/long (o)"_pair_thole.html,
|
||||
"lj/cut/tip4p/cut (o)"_pair_lj.html,
|
||||
"lj/cut/tip4p/long (ot)"_pair_lj.html,
|
||||
"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
|
||||
"lj/expand (gko)"_pair_lj_expand.html,
|
||||
"lj/gromacs (gko)"_pair_gromacs.html,
|
||||
"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
|
||||
"lj/long/coul/long (io)"_pair_lj_long.html,
|
||||
"lj/long/dipole/long"_pair_dipole.html,
|
||||
"lj/long/tip4p/long"_pair_lj_long.html,
|
||||
"lj/mdf"_pair_mdf.html,
|
||||
"lj/sdk (gko)"_pair_sdk.html,
|
||||
"lj/sdk/coul/long (go)"_pair_sdk.html,
|
||||
"lj/sdk/coul/msm (o)"_pair_sdk.html,
|
||||
"lj/smooth (o)"_pair_lj_smooth.html,
|
||||
"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
|
||||
"lj96/cut (go)"_pair_lj96.html,
|
||||
"lubricate (o)"_pair_lubricate.html,
|
||||
"lubricate/poly (o)"_pair_lubricate.html,
|
||||
"lubricateU"_pair_lubricateU.html,
|
||||
"lubricateU/poly"_pair_lubricateU.html,
|
||||
"mdpd"_pair_meso.html,
|
||||
"mdpd/rhosum"_pair_meso.html,
|
||||
"meam"_pair_meam.html,
|
||||
"meam/c"_pair_meam.html,
|
||||
"meam/spline (o)"_pair_meam_spline.html,
|
||||
"meam/sw/spline"_pair_meam_sw_spline.html,
|
||||
"mgpt"_pair_mgpt.html,
|
||||
"mie/cut (o)"_pair_mie.html,
|
||||
"momb"_pair_momb.html,
|
||||
"morse (gkot)"_pair_morse.html,
|
||||
"morse/smooth/linear"_pair_morse.html,
|
||||
"morse/soft"_pair_morse.html,
|
||||
"multi/lucy"_pair_multi_lucy.html,
|
||||
"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
|
||||
"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
|
||||
"nm/cut (o)"_pair_nm.html,
|
||||
"nm/cut/coul/cut (o)"_pair_nm.html,
|
||||
"nm/cut/coul/long (o)"_pair_nm.html,
|
||||
"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/stk"_pair_oxdna2.html,
|
||||
"peri/eps"_pair_peri.html,
|
||||
"peri/lps (o)"_pair_peri.html,
|
||||
"peri/pmb (o)"_pair_peri.html,
|
||||
"peri/ves"_pair_peri.html,
|
||||
"polymorphic"_pair_polymorphic.html,
|
||||
"python"_pair_python.html,
|
||||
"quip"_pair_quip.html,
|
||||
"reax"_pair_reax.html,
|
||||
"reax/c (ko)"_pair_reaxc.html,
|
||||
"rebo (oi)"_pair_airebo.html,
|
||||
"resquared (go)"_pair_resquared.html,
|
||||
"smd/hertz"_pair_smd_hertz.html,
|
||||
"smd/tlsph"_pair_smd_tlsph.html,
|
||||
"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
|
||||
"smd/ulsph"_pair_smd_ulsph.html,
|
||||
"smtbq"_pair_smtbq.html,
|
||||
"snap (k)"_pair_snap.html,
|
||||
"snap (k)"_pair_snap.html,
|
||||
"soft (go)"_pair_soft.html,
|
||||
"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 (giko)"_pair_sw.html,
|
||||
"table (gko)"_pair_table.html,
|
||||
"table/rx (k)"_pair_table_rx.html,
|
||||
"tdpd"_pair_meso.html,
|
||||
"tersoff (giko)"_pair_tersoff.html,
|
||||
"tersoff/mod (gko)"_pair_tersoff_mod.html,
|
||||
"tersoff/mod/c (o)"_pair_tersoff_mod.html,
|
||||
"tersoff/table (o)"_pair_tersoff.html,
|
||||
"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
|
||||
"thole"_pair_thole.html,
|
||||
"tip4p/cut (o)"_pair_coul.html,
|
||||
"tip4p/long (o)"_pair_coul.html,
|
||||
"tip4p/long/soft (o)"_pair_lj_soft.html,
|
||||
"tri/lj"_pair_tri_lj.html,
|
||||
"ufm (got)"_pair_ufm.html,
|
||||
"vashishta (ko)"_pair_vashishta.html,
|
||||
"vashishta/table (o)"_pair_vashishta.html,
|
||||
"yukawa (gok)"_pair_yukawa.html,
|
||||
"yukawa/colloid (go)"_pair_yukawa_colloid.html,
|
||||
"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
|
||||
136
doc/src/Commands_parse.txt
Normal file
136
doc/src/Commands_parse.txt
Normal file
@ -0,0 +1,136 @@
|
||||
"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
|
||||
|
||||
Parsing rules for input scripts :h3
|
||||
|
||||
Each non-blank line in the input script is treated as a command.
|
||||
LAMMPS commands are case sensitive. Command names are lower-case, as
|
||||
are specified command arguments. Upper case letters may be used in
|
||||
file names or user-chosen ID strings.
|
||||
|
||||
Here are 6 rulse for how each line in the input script is parsed by
|
||||
LAMMPS:
|
||||
|
||||
(1) If the last printable character on the line is a "&" character,
|
||||
the command is assumed to continue on the next line. The next line is
|
||||
concatenated to the previous line by removing the "&" character and
|
||||
line break. This allows long commands to be continued across two or
|
||||
more lines. See the discussion of triple quotes in (6) for how to
|
||||
continue a command across multiple line without using "&" characters.
|
||||
|
||||
(2) All characters from the first "#" character onward are treated as
|
||||
comment and discarded. See an exception in (6). Note that a
|
||||
comment after a trailing "&" character will prevent the command from
|
||||
continuing on the next line. Also note that for multi-line commands a
|
||||
single leading "#" will comment out the entire command.
|
||||
|
||||
(3) The line is searched repeatedly for $ characters, which indicate
|
||||
variables that are replaced with a text string. See an exception in
|
||||
(6).
|
||||
|
||||
If the $ is followed by curly brackets, then the variable name is the
|
||||
text inside the curly brackets. If no curly brackets follow the $,
|
||||
then the variable name is the single character immediately following
|
||||
the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and
|
||||
"x".
|
||||
|
||||
How the variable is converted to a text string depends on what style
|
||||
of variable it is; see the "variable"_variable.html doc page for details.
|
||||
It can be a variable that stores multiple text strings, and return one
|
||||
of them. The returned text string can be multiple "words" (space
|
||||
separated) which will then be interpreted as multiple arguments in the
|
||||
input command. The variable can also store a numeric formula which
|
||||
will be evaluated and its numeric result returned as a string.
|
||||
|
||||
As a special case, if the $ is followed by parenthesis, then the text
|
||||
inside the parenthesis is treated as an "immediate" variable and
|
||||
evaluated as an "equal-style variable"_variable.html. This is a way
|
||||
to use numeric formulas in an input script without having to assign
|
||||
them to variable names. For example, these 3 input script lines:
|
||||
|
||||
variable X equal (xlo+xhi)/2+sqrt(v_area)
|
||||
region 1 block $X 2 INF INF EDGE EDGE
|
||||
variable X delete :pre
|
||||
|
||||
can be replaced by
|
||||
|
||||
region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
|
||||
|
||||
so that you do not have to define (or discard) a temporary variable X.
|
||||
|
||||
Additionally, the "immediate" variable expression may be followed by a
|
||||
colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
|
||||
The format string must be appropriate for a double-precision
|
||||
floating-point value. The format string is used to output the result
|
||||
of the variable expression evaluation. If a format string is not
|
||||
specified a high-precision "%.20g" is used as the default.
|
||||
|
||||
This can be useful for formatting print output to a desired precion:
|
||||
|
||||
print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
|
||||
|
||||
Note that neither the curly-bracket or immediate form of variables can
|
||||
contain nested $ characters for other variables to substitute for.
|
||||
Thus you cannot do this:
|
||||
|
||||
variable a equal 2
|
||||
variable b2 equal 4
|
||||
print "B2 = $\{b$a\}" :pre
|
||||
|
||||
Nor can you specify this $($x-1.0) for an immediate variable, but
|
||||
you could use $(v_x-1.0), since the latter is valid syntax for an
|
||||
"equal-style variable"_variable.html.
|
||||
|
||||
See the "variable"_variable.html command for more details of how
|
||||
strings are assigned to variables and evaluated, and how they can be
|
||||
used in input script commands.
|
||||
|
||||
(4) The line is broken into "words" separated by whitespace (tabs,
|
||||
spaces). Note that words can thus contain letters, digits,
|
||||
underscores, or punctuation characters.
|
||||
|
||||
(5) The first word is the command name. All successive words in the
|
||||
line are arguments.
|
||||
|
||||
(6) If you want text with spaces to be treated as a single argument,
|
||||
it can be enclosed in either single or double or triple quotes. A
|
||||
long single argument enclosed in single or double quotes can span
|
||||
multiple lines if the "&" character is used, as described above. When
|
||||
the lines are concatenated together (and the "&" characters and line
|
||||
breaks removed), the text will become a single line. If you want
|
||||
multiple lines of an argument to retain their line breaks, the text
|
||||
can be enclosed in triple quotes, in which case "&" characters are not
|
||||
needed. For example:
|
||||
|
||||
print "Volume = $v"
|
||||
print 'Volume = $v'
|
||||
if "$\{steps\} > 1000" then quit
|
||||
variable a string "red green blue &
|
||||
purple orange cyan"
|
||||
print """
|
||||
System volume = $v
|
||||
System temperature = $t
|
||||
""" :pre
|
||||
|
||||
In each case, the single, double, or triple quotes are removed when
|
||||
the single argument they enclose is stored internally.
|
||||
|
||||
See the "dump modify format"_dump_modify.html, "print"_print.html,
|
||||
"if"_if.html, and "python"_python.html commands for examples.
|
||||
|
||||
A "#" or "$" character that is between quotes will not be treated as a
|
||||
comment indicator in (2) or substituted for as a variable in (3).
|
||||
|
||||
NOTE: If the argument is itself a command that requires a quoted
|
||||
argument (e.g. using a "print"_print.html command as part of an
|
||||
"if"_if.html or "run every"_run.html command), then single, double, or
|
||||
triple quotes can be nested in the usual manner. See the doc pages
|
||||
for those commands for examples. Only one of level of nesting is
|
||||
allowed, but that should be sufficient for most use cases.
|
||||
|
||||
95
doc/src/Commands_structure.txt
Normal file
95
doc/src/Commands_structure.txt
Normal file
@ -0,0 +1,95 @@
|
||||
"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
|
||||
|
||||
Input script structure :h3
|
||||
|
||||
This page describes the structure of a typical LAMMPS input script.
|
||||
The examples directory in the LAMMPS distribution contains many sample
|
||||
input scripts; it is discussed on the "Examples"_Examples.html doc
|
||||
page.
|
||||
|
||||
A LAMMPS input script typically has 4 parts:
|
||||
|
||||
Initialization
|
||||
Atom definition
|
||||
Settings
|
||||
Run a simulation :ol
|
||||
|
||||
The last 2 parts can be repeated as many times as desired. I.e. run a
|
||||
simulation, change some settings, run some more, etc. Each of the 4
|
||||
parts is now described in more detail. Remember that almost all
|
||||
commands need only be used if a non-default value is desired.
|
||||
|
||||
(1) Initialization
|
||||
|
||||
Set parameters that need to be defined before atoms are created or
|
||||
read-in from a file.
|
||||
|
||||
The relevant commands are "units"_units.html,
|
||||
"dimension"_dimension.html, "newton"_newton.html,
|
||||
"processors"_processors.html, "boundary"_boundary.html,
|
||||
"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
|
||||
|
||||
If force-field parameters appear in the files that will be read, these
|
||||
commands tell LAMMPS what kinds of force fields are being used:
|
||||
"pair_style"_pair_style.html, "bond_style"_bond_style.html,
|
||||
"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
|
||||
"improper_style"_improper_style.html.
|
||||
|
||||
(2) Atom definition
|
||||
|
||||
There are 3 ways to define atoms in LAMMPS. Read them in from a data
|
||||
or restart file via the "read_data"_read_data.html or
|
||||
"read_restart"_read_restart.html commands. These files can contain
|
||||
molecular topology information. Or create atoms on a lattice (with no
|
||||
molecular topology), using these commands: "lattice"_lattice.html,
|
||||
"region"_region.html, "create_box"_create_box.html,
|
||||
"create_atoms"_create_atoms.html. The entire set of atoms can be
|
||||
duplicated to make a larger simulation using the
|
||||
"replicate"_replicate.html command.
|
||||
|
||||
(3) Settings
|
||||
|
||||
Once atoms and molecular topology are defined, a variety of settings
|
||||
can be specified: force field coefficients, simulation parameters,
|
||||
output options, etc.
|
||||
|
||||
Force field coefficients are set by these commands (they can also be
|
||||
set in the read-in files): "pair_coeff"_pair_coeff.html,
|
||||
"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
|
||||
"dihedral_coeff"_dihedral_coeff.html,
|
||||
"improper_coeff"_improper_coeff.html,
|
||||
"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
|
||||
"special_bonds"_special_bonds.html.
|
||||
|
||||
Various simulation parameters are set by these commands:
|
||||
"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
|
||||
"group"_group.html, "timestep"_timestep.html,
|
||||
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
|
||||
"min_style"_min_style.html, "min_modify"_min_modify.html.
|
||||
|
||||
Fixes impose a variety of boundary conditions, time integration, and
|
||||
diagnostic options. The "fix"_fix.html command comes in many flavors.
|
||||
|
||||
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
|
||||
|
||||
A molecular dynamics simulation is run using the "run"_run.html
|
||||
command. Energy minimization (molecular statics) is performed using
|
||||
the "minimize"_minimize.html command. A parallel tempering
|
||||
(replica-exchange) simulation can be run using the
|
||||
"temper"_temper.html command.
|
||||
|
||||
@ -4,7 +4,7 @@ Section"_Manual.html :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -4,7 +4,7 @@ Section"_Tools.html :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
@ -17,9 +17,9 @@ surface meshes of discrete points, collections of sub-particles,
|
||||
deformable objects, etc. Note that other kinds of finite-size
|
||||
spherical and aspherical particles are also supported by LAMMPS, such
|
||||
as spheres, ellipsoids, line segments, and triangles, but they are
|
||||
simpler entities that body particles. See "Section
|
||||
6.14"_Section_howto.html#howto_14 for a general overview of all these
|
||||
particle types.
|
||||
simpler entities that body particles. See the "Howto
|
||||
spherical"_Howto_spherical.html doc page for a general overview of all
|
||||
these particle types.
|
||||
|
||||
Body particles are used via the "atom_style body"_atom_style.html
|
||||
command. It takes a body style as an argument. The current body
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -9,7 +9,7 @@
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
Triclinic (non-orthogonal) simulation boxes :h3
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
@ -74,8 +74,8 @@ commands)
|
||||
long-range interactions for charge, point-dipoles, and LJ dispersion: \
|
||||
Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
|
||||
polarization models: "QEq"_fix_qeq.html, \
|
||||
"core/shell model"_Section_howto.html#howto_26, \
|
||||
"Drude dipole model"_Section_howto.html#howto_27
|
||||
"core/shell model"_Howto_coreshell.html, \
|
||||
"Drude dipole model"_Howto_drude.html
|
||||
charge equilibration (QEq via dynamic, point, shielded, Slater methods)
|
||||
coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
|
||||
mesoscopic potentials: granular, Peridynamics, SPH
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -14,7 +14,7 @@
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
@ -73,7 +73,7 @@ every LAMMPS command.
|
||||
|
||||
Intro
|
||||
Section_start
|
||||
Section_commands
|
||||
Commands
|
||||
Packages
|
||||
Speed
|
||||
Howto
|
||||
@ -116,12 +116,7 @@ END_RST -->
|
||||
2.6 "Command-line options"_start_6 :b
|
||||
2.7 "Screen output"_start_7 :b
|
||||
2.8 "Tips for users of previous versions"_start_8 :ule,b
|
||||
"Commands"_Section_commands.html :l
|
||||
3.1 "LAMMPS input script"_cmd_1 :ulb,b
|
||||
3.2 "Parsing rules"_cmd_2 :b
|
||||
3.3 "Input script structure"_cmd_3 :b
|
||||
3.4 "Commands listed by category"_cmd_4 :b
|
||||
3.5 "Commands listed alphabetically"_cmd_5 :ule,b
|
||||
"Commands"_Commands.html :l
|
||||
"Optional packages"_Packages.html :l
|
||||
"Accelerate performance"_Speed.html :l
|
||||
"How-to discussions"_Howto.html :l
|
||||
@ -141,12 +136,6 @@ END_RST -->
|
||||
:link(start_7,Section_start.html#start_7)
|
||||
:link(start_8,Section_start.html#start_8)
|
||||
|
||||
:link(cmd_1,Section_commands.html#cmd_1)
|
||||
:link(cmd_2,Section_commands.html#cmd_2)
|
||||
:link(cmd_3,Section_commands.html#cmd_3)
|
||||
:link(cmd_4,Section_commands.html#cmd_4)
|
||||
:link(cmd_5,Section_commands.html#cmd_5)
|
||||
|
||||
<!-- END_HTML_ONLY -->
|
||||
|
||||
</BODY>
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -4,7 +4,7 @@ Section"_Python.html :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -1,10 +1,10 @@
|
||||
"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws -
|
||||
"Previous Section"_Commands.html - "LAMMPS WWW Site"_lws -
|
||||
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
|
||||
Section"_Speed.html :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
@ -396,7 +396,7 @@ lib/gpu/README
|
||||
"Section 2.6 -sf gpu"_Section_start.html#start_6
|
||||
"Section 2.6 -pk gpu"_Section_start.html#start_6
|
||||
"package gpu"_package.html
|
||||
Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g)
|
||||
"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
|
||||
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
|
||||
|
||||
:line
|
||||
@ -487,8 +487,8 @@ See the list of all KIM models here:
|
||||
https://openkim.org/kim-items/models/by-model-drivers
|
||||
|
||||
See the list of example KIM models included by default here:
|
||||
https://openkim.org/kim-api in the "What is in the KIM API source
|
||||
package?" section
|
||||
https://openkim.org/kim-api on the "What is in the KIM API source
|
||||
package?" page.
|
||||
|
||||
You can then install/un-install the package and build LAMMPS in the
|
||||
usual manner:
|
||||
@ -593,7 +593,7 @@ lib/kokkos/README
|
||||
"Section 2.6 -sf kk"_Section_start.html#start_6
|
||||
"Section 2.6 -pk kokkos"_Section_start.html#start_6
|
||||
"package kokkos"_package.html
|
||||
Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k)
|
||||
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
|
||||
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
|
||||
|
||||
:line
|
||||
@ -631,7 +631,7 @@ src/KSPACE: filenames -> commands
|
||||
"Howto tip4p"_Howto_tip4p.html
|
||||
"Howto spc"_Howto_spc.html
|
||||
"pair_style coul"_pair_coul.html
|
||||
Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 with "long" or "msm" in pair style name
|
||||
"Commands pair"_Commands_pair.html page for styles with "long" or "msm" in name
|
||||
examples/peptide
|
||||
bench/in.rhodo :ul
|
||||
|
||||
@ -715,7 +715,7 @@ make machine :pre
|
||||
[Supporting info:]
|
||||
|
||||
src/MANYBODY: filenames -> commands
|
||||
Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
|
||||
"Commands pair"_Commands_pair.html page
|
||||
examples/comb
|
||||
examples/eim
|
||||
examples/nb3d
|
||||
@ -1017,7 +1017,7 @@ src/OPT: filenames -> commands
|
||||
"Speed packages"_Speed_packages.html
|
||||
"Speed opt"_Speed_opt.html
|
||||
"Section 2.6 -sf opt"_Section_start.html#start_6
|
||||
Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t)
|
||||
"Commands pair"_Commands_pair.html for styles followed by (t)
|
||||
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
|
||||
|
||||
:line
|
||||
@ -2072,7 +2072,7 @@ src/USER-INTEL/README
|
||||
"Section 2.6 -sf intel"_Section_start.html#start_6
|
||||
"Section 2.6 -pk intel"_Section_start.html#start_6
|
||||
"package intel"_package.html
|
||||
Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i)
|
||||
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
|
||||
src/USER-INTEL/TEST
|
||||
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
|
||||
|
||||
@ -2457,7 +2457,7 @@ src/USER-OMP/README
|
||||
"Section 2.6 -sf omp"_Section_start.html#start_6
|
||||
"Section 2.6 -pk omp"_Section_start.html#start_6
|
||||
"package omp"_package.html
|
||||
Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o)
|
||||
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
|
||||
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
|
||||
|
||||
:line
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -4,7 +4,7 @@ Section"_Errors.html :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,10 +1,10 @@
|
||||
"Previous Section"_Intro.html - "LAMMPS WWW Site"_lws -
|
||||
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
|
||||
Section"_Section_commands.html :c
|
||||
Section"_Commands.html :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
@ -1070,7 +1070,7 @@ the '-in' command-line switch, e.g.
|
||||
|
||||
lmp_linux -in in.file :pre
|
||||
|
||||
"This section"_Section_commands.html describes how input scripts are
|
||||
The "Commands"_Commands.html doc page describes how input scripts are
|
||||
structured and what commands they contain.
|
||||
|
||||
You can test LAMMPS on any of the sample inputs provided in the
|
||||
@ -1615,9 +1615,9 @@ value2 ..." at the beginning of the input script. Defining an index
|
||||
variable as a command-line argument overrides any setting for the same
|
||||
index variable in the input script, since index variables cannot be
|
||||
re-defined. See the "variable"_variable.html command for more info on
|
||||
defining index and other kinds of variables and "this
|
||||
section"_Section_commands.html#cmd_2 for more info on using variables
|
||||
in input scripts.
|
||||
defining index and other kinds of variables and the "Commands
|
||||
parse"_Commands_parse.html page for more info on using variables in
|
||||
input scripts.
|
||||
|
||||
NOTE: Currently, the command-line parser looks for arguments that
|
||||
start with "-" to indicate new switches. Thus you cannot specify
|
||||
|
||||
@ -4,7 +4,7 @@ Section"_Howto.html :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -3,34 +3,39 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
KOKKOS package :h3
|
||||
|
||||
Kokkos is a templated C++ library that provides abstractions to allow
|
||||
a single implementation of an application kernel (e.g. a pair style) to run efficiently on
|
||||
different kinds of hardware, such as GPUs, Intel Xeon Phis, or many-core
|
||||
CPUs. Kokkos maps the C++ kernel onto different backend languages such as CUDA, OpenMP, or Pthreads.
|
||||
The Kokkos library also provides data abstractions to adjust (at
|
||||
compile time) the memory layout of data structures like 2d and
|
||||
3d arrays to optimize performance on different hardware. For more information on Kokkos, see
|
||||
"Github"_https://github.com/kokkos/kokkos. Kokkos is part of
|
||||
"Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos library was written primarily by Carter Edwards,
|
||||
Christian Trott, and Dan Sunderland (all Sandia).
|
||||
a single implementation of an application kernel (e.g. a pair style)
|
||||
to run efficiently on different kinds of hardware, such as GPUs, Intel
|
||||
Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto
|
||||
different backend languages such as CUDA, OpenMP, or Pthreads. The
|
||||
Kokkos library also provides data abstractions to adjust (at compile
|
||||
time) the memory layout of data structures like 2d and 3d arrays to
|
||||
optimize performance on different hardware. For more information on
|
||||
Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part
|
||||
of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos
|
||||
library was written primarily by Carter Edwards, Christian Trott, and
|
||||
Dan Sunderland (all Sandia).
|
||||
|
||||
The LAMMPS KOKKOS package contains versions of pair, fix, and atom styles
|
||||
that use data structures and macros provided by the Kokkos library,
|
||||
which is included with LAMMPS in /lib/kokkos. The KOKKOS package was developed primarily by Christian Trott (Sandia)
|
||||
and Stan Moore (Sandia) with contributions of various styles by others, including Sikandar
|
||||
Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions
|
||||
The LAMMPS KOKKOS package contains versions of pair, fix, and atom
|
||||
styles that use data structures and macros provided by the Kokkos
|
||||
library, which is included with LAMMPS in /lib/kokkos. The KOKKOS
|
||||
package was developed primarily by Christian Trott (Sandia) and Stan
|
||||
Moore (Sandia) with contributions of various styles by others,
|
||||
including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
|
||||
(Sandia). For more information on developing using Kokkos abstractions
|
||||
see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf.
|
||||
|
||||
Kokkos currently provides support for 3 modes of execution (per MPI
|
||||
task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP (threading
|
||||
for many-core CPUs and Intel Phi), and CUDA (for NVIDIA GPUs). You choose the mode at build time to
|
||||
produce an executable compatible with specific hardware.
|
||||
task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
|
||||
(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA
|
||||
GPUs). You choose the mode at build time to produce an executable
|
||||
compatible with specific hardware.
|
||||
|
||||
[Building LAMMPS with the KOKKOS package:]
|
||||
|
||||
@ -38,16 +43,18 @@ NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible
|
||||
compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or
|
||||
Clang 3.5.2 or later is required.
|
||||
|
||||
The recommended method of building the KOKKOS package is to start with the provided Kokkos
|
||||
Makefiles in /src/MAKE/OPTIONS/. You may need to modify the KOKKOS_ARCH variable in the Makefile
|
||||
to match your specific hardware. For example:
|
||||
The recommended method of building the KOKKOS package is to start with
|
||||
the provided Kokkos Makefiles in /src/MAKE/OPTIONS/. You may need to
|
||||
modify the KOKKOS_ARCH variable in the Makefile to match your specific
|
||||
hardware. For example:
|
||||
|
||||
for Sandy Bridge CPUs, set KOKKOS_ARCH=SNB
|
||||
for Broadwell CPUs, set KOKKOS_ARCH=BWD
|
||||
for K80 GPUs, set KOKKOS_ARCH=Kepler37
|
||||
for P100 GPUs and Power8 CPUs, set KOKKOS_ARCH=Pascal60,Power8 :ul
|
||||
|
||||
See the [Advanced Kokkos Options] section below for a listing of all KOKKOS_ARCH options.
|
||||
See the [Advanced Kokkos Options] section below for a listing of all
|
||||
KOKKOS_ARCH options.
|
||||
|
||||
[Compile for CPU-only (MPI only, no threading):]
|
||||
|
||||
@ -61,11 +68,12 @@ make kokkos_mpi_only :pre
|
||||
|
||||
[Compile for CPU-only (MPI plus OpenMP threading):]
|
||||
|
||||
NOTE: To build with Kokkos support for OpenMP threading, your compiler must support the
|
||||
OpenMP interface. You should have one or more multi-core CPUs so that
|
||||
multiple threads can be launched by each MPI task running on a CPU.
|
||||
NOTE: To build with Kokkos support for OpenMP threading, your compiler
|
||||
must support the OpenMP interface. You should have one or more
|
||||
multi-core CPUs so that multiple threads can be launched by each MPI
|
||||
task running on a CPU.
|
||||
|
||||
use a C++11 compatible compiler and set KOKKOS_ARCH variable in
|
||||
Use a C++11 compatible compiler and set KOKKOS_ARCH variable in
|
||||
/src/MAKE/OPTIONS/Makefile.kokkos_omp as described above. Then do the
|
||||
following:
|
||||
|
||||
@ -88,9 +96,9 @@ software version 7.5 or later must be installed on your system. See
|
||||
the discussion for the "GPU package"_Speed_gpu.html for details of how
|
||||
to check and do this.
|
||||
|
||||
use a C++11 compatible compiler and set KOKKOS_ARCH variable in
|
||||
/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as described
|
||||
above. Then do the following:
|
||||
Use a C++11 compatible compiler and set KOKKOS_ARCH variable in
|
||||
/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as
|
||||
described above. Then do the following:
|
||||
|
||||
cd lammps/src
|
||||
make yes-kokkos
|
||||
@ -104,24 +112,24 @@ on the make command line. For example:
|
||||
make mpi KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=SNB # set the KOKKOS_DEVICES and KOKKOS_ARCH variable explicitly
|
||||
make kokkos_cuda_mpi KOKKOS_ARCH=Pascal60,Power8 # set the KOKKOS_ARCH variable explicitly :pre
|
||||
|
||||
Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the
|
||||
make command line requires a GNU-compatible make command. Try
|
||||
"gmake" if your system's standard make complains.
|
||||
Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the make
|
||||
command line requires a GNU-compatible make command. Try "gmake" if
|
||||
your system's standard make complains.
|
||||
|
||||
NOTE: If you build using make line variables and re-build LAMMPS twice
|
||||
with different KOKKOS options and the *same* target, then you *must* perform a "make clean-all"
|
||||
or "make clean-machine" before each build. This is to force all the
|
||||
KOKKOS-dependent files to be re-compiled with the new options.
|
||||
with different KOKKOS options and the *same* target, then you *must*
|
||||
perform a "make clean-all" or "make clean-machine" before each
|
||||
build. This is to force all the KOKKOS-dependent files to be
|
||||
re-compiled with the new options.
|
||||
|
||||
[Running LAMMPS with the KOKKOS package:]
|
||||
|
||||
All Kokkos operations occur within the
|
||||
context of an individual MPI task running on a single node of the
|
||||
machine. The total number of MPI tasks used by LAMMPS (one or
|
||||
multiple per compute node) is set in the usual manner via the mpirun
|
||||
or mpiexec commands, and is independent of Kokkos. E.g. the mpirun
|
||||
command in OpenMPI does this via its
|
||||
-np and -npernode switches. Ditto for MPICH via -np and -ppn.
|
||||
All Kokkos operations occur within the context of an individual MPI
|
||||
task running on a single node of the machine. The total number of MPI
|
||||
tasks used by LAMMPS (one or multiple per compute node) is set in the
|
||||
usual manner via the mpirun or mpiexec commands, and is independent of
|
||||
Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
|
||||
-npernode switches. Ditto for MPICH via -np and -ppn.
|
||||
|
||||
[Running on a multi-core CPU:]
|
||||
|
||||
@ -133,8 +141,9 @@ mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI
|
||||
mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task
|
||||
mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
|
||||
|
||||
To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk kokkos" "command-line switches"_Section_start.html#start_7 in your mpirun command.
|
||||
You must use the "-k on" "command-line
|
||||
To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk
|
||||
kokkos" "command-line switches"_Section_start.html#start_7 in your
|
||||
mpirun command. You must use the "-k on" "command-line
|
||||
switch"_Section_start.html#start_7 to enable the KOKKOS package. It
|
||||
takes additional arguments for hardware settings appropriate to your
|
||||
system. Those arguments are "documented
|
||||
@ -142,32 +151,33 @@ here"_Section_start.html#start_7. For OpenMP use:
|
||||
|
||||
-k on t Nt :pre
|
||||
|
||||
The "t Nt" option specifies how many OpenMP threads per MPI
|
||||
task to use with a node. The default is Nt = 1, which is MPI-only mode.
|
||||
Note that the product of MPI tasks * OpenMP
|
||||
threads/task should not exceed the physical number of cores (on a
|
||||
node), otherwise performance will suffer. If hyperthreading is enabled, then
|
||||
the product of MPI tasks * OpenMP threads/task should not exceed the
|
||||
physical number of cores * hardware threads.
|
||||
The "-k on" switch also issues a "package kokkos" command (with no
|
||||
additional arguments) which sets various KOKKOS options to default
|
||||
values, as discussed on the "package"_package.html command doc page.
|
||||
The "t Nt" option specifies how many OpenMP threads per MPI task to
|
||||
use with a node. The default is Nt = 1, which is MPI-only mode. Note
|
||||
that the product of MPI tasks * OpenMP threads/task should not exceed
|
||||
the physical number of cores (on a node), otherwise performance will
|
||||
suffer. If hyperthreading is enabled, then the product of MPI tasks *
|
||||
OpenMP threads/task should not exceed the physical number of cores *
|
||||
hardware threads. The "-k on" switch also issues a "package kokkos"
|
||||
command (with no additional arguments) which sets various KOKKOS
|
||||
options to default values, as discussed on the "package"_package.html
|
||||
command doc page.
|
||||
|
||||
The "-sf kk" "command-line switch"_Section_start.html#start_7
|
||||
will automatically append the "/kk" suffix to styles that support it.
|
||||
In this manner no modification to the input script is needed. Alternatively,
|
||||
one can run with the KOKKOS package by editing the input script as described below.
|
||||
The "-sf kk" "command-line switch"_Section_start.html#start_7 will
|
||||
automatically append the "/kk" suffix to styles that support it. In
|
||||
this manner no modification to the input script is
|
||||
needed. Alternatively, one can run with the KOKKOS package by editing
|
||||
the input script as described below.
|
||||
|
||||
NOTE: The default for the "package kokkos"_package.html command is
|
||||
to use "full" neighbor lists and set the Newton flag to "off" for both
|
||||
NOTE: The default for the "package kokkos"_package.html command is to
|
||||
use "full" neighbor lists and set the Newton flag to "off" for both
|
||||
pairwise and bonded interactions. However, when running on CPUs, it
|
||||
will typically be faster to use "half" neighbor lists and set the
|
||||
Newton flag to "on", just as is the case for non-accelerated pair
|
||||
styles. It can also be faster to use non-threaded communication.
|
||||
Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
|
||||
change the default "package kokkos"_package.html
|
||||
options. See its doc page for details and default settings. Experimenting with
|
||||
its options can provide a speed-up for specific calculations. For example:
|
||||
styles. It can also be faster to use non-threaded communication. Use
|
||||
the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
|
||||
change the default "package kokkos"_package.html options. See its doc
|
||||
page for details and default settings. Experimenting with its options
|
||||
can provide a speed-up for specific calculations. For example:
|
||||
|
||||
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre
|
||||
|
||||
@ -176,9 +186,9 @@ script, it can also override the Newton flag defaults.
|
||||
|
||||
[Core and Thread Affinity:]
|
||||
|
||||
When using multi-threading, it is important for
|
||||
performance to bind both MPI tasks to physical cores, and threads to
|
||||
physical cores, so they do not migrate during a simulation.
|
||||
When using multi-threading, it is important for performance to bind
|
||||
both MPI tasks to physical cores, and threads to physical cores, so
|
||||
they do not migrate during a simulation.
|
||||
|
||||
If you are not certain MPI tasks are being bound (check the defaults
|
||||
for your MPI installation), binding can be forced with these flags:
|
||||
@ -189,24 +199,24 @@ Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... :
|
||||
For binding threads with KOKKOS OpenMP, use thread affinity
|
||||
environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
|
||||
later, intel 12 or later) setting the environment variable
|
||||
OMP_PROC_BIND=true should be sufficient. In general, for best performance
|
||||
with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads.
|
||||
For binding threads with the
|
||||
KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option
|
||||
as described below.
|
||||
OMP_PROC_BIND=true should be sufficient. In general, for best
|
||||
performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and
|
||||
OMP_PLACES=threads. For binding threads with the KOKKOS pthreads
|
||||
option, compile LAMMPS the KOKKOS HWLOC=yes option as described below.
|
||||
|
||||
[Running on Knight's Landing (KNL) Intel Xeon Phi:]
|
||||
|
||||
Here is a quick overview of how to use the KOKKOS package
|
||||
for the Intel Knight's Landing (KNL) Xeon Phi:
|
||||
Here is a quick overview of how to use the KOKKOS package for the
|
||||
Intel Knight's Landing (KNL) Xeon Phi:
|
||||
|
||||
KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores
|
||||
are reserved for the OS, and only 64 or 66 cores are used. Each core
|
||||
has 4 hyperthreads,so there are effectively N = 256 (4*64) or
|
||||
N = 264 (4*66) cores to run on. The product of MPI tasks * OpenMP threads/task should not exceed this limit,
|
||||
otherwise performance will suffer. Note that with the KOKKOS package you do not need to
|
||||
specify how many KNLs there are per node; each
|
||||
KNL is simply treated as running some number of MPI tasks.
|
||||
KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are
|
||||
reserved for the OS, and only 64 or 66 cores are used. Each core has 4
|
||||
hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
|
||||
cores to run on. The product of MPI tasks * OpenMP threads/task should
|
||||
not exceed this limit, otherwise performance will suffer. Note that
|
||||
with the KOKKOS package you do not need to specify how many KNLs there
|
||||
are per node; each KNL is simply treated as running some number of MPI
|
||||
tasks.
|
||||
|
||||
Examples of mpirun commands that follow these rules are shown below.
|
||||
|
||||
@ -221,57 +231,60 @@ tasks/node. The "-k on t Nt" command-line switch sets the number of
|
||||
threads/task as Nt. The product of these two values should be N, i.e.
|
||||
256 or 264.
|
||||
|
||||
NOTE: The default for the "package kokkos"_package.html command is
|
||||
to use "full" neighbor lists and set the Newton flag to "off" for both
|
||||
pairwise and bonded interactions. When running on KNL, this
|
||||
will typically be best for pair-wise potentials. For manybody potentials,
|
||||
using "half" neighbor lists and setting the
|
||||
Newton flag to "on" may be faster. It can also be faster to use non-threaded communication.
|
||||
Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
|
||||
change the default "package kokkos"_package.html
|
||||
options. See its doc page for details and default settings. Experimenting with
|
||||
its options can provide a speed-up for specific calculations. For example:
|
||||
NOTE: The default for the "package kokkos"_package.html command is to
|
||||
use "full" neighbor lists and set the Newton flag to "off" for both
|
||||
pairwise and bonded interactions. When running on KNL, this will
|
||||
typically be best for pair-wise potentials. For manybody potentials,
|
||||
using "half" neighbor lists and setting the Newton flag to "on" may be
|
||||
faster. It can also be faster to use non-threaded communication. Use
|
||||
the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
|
||||
change the default "package kokkos"_package.html options. See its doc
|
||||
page for details and default settings. Experimenting with its options
|
||||
can provide a speed-up for specific calculations. For example:
|
||||
|
||||
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj # Newton off, full neighbor list, non-threaded comm
|
||||
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax # Newton on, half neighbor list, non-threaded comm :pre
|
||||
|
||||
NOTE: MPI tasks and threads should be bound to cores as described above for CPUs.
|
||||
NOTE: MPI tasks and threads should be bound to cores as described
|
||||
above for CPUs.
|
||||
|
||||
NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors such as Knight's Corner (KNC), your
|
||||
system must be configured to use them in "native" mode, not "offload"
|
||||
mode like the USER-INTEL package supports.
|
||||
NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors
|
||||
such as Knight's Corner (KNC), your system must be configured to use
|
||||
them in "native" mode, not "offload" mode like the USER-INTEL package
|
||||
supports.
|
||||
|
||||
[Running on GPUs:]
|
||||
|
||||
Use the "-k" "command-line switch"_Section_commands.html#start_7 to
|
||||
specify the number of GPUs per node. Typically the -np setting
|
||||
of the mpirun command should set the number of MPI
|
||||
tasks/node to be equal to the # of physical GPUs on the node.
|
||||
You can assign multiple MPI tasks to the same GPU with the
|
||||
KOKKOS package, but this is usually only faster if significant portions
|
||||
of the input script have not been ported to use Kokkos. Using CUDA MPS
|
||||
is recommended in this scenario. As above for multi-core CPUs (and no GPU), if N is the number
|
||||
of physical cores/node, then the number of MPI tasks/node should not exceed N.
|
||||
Use the "-k" "command-line switch"_Section_start.html#start_7 to
|
||||
specify the number of GPUs per node. Typically the -np setting of the
|
||||
mpirun command should set the number of MPI tasks/node to be equal to
|
||||
the # of physical GPUs on the node. You can assign multiple MPI tasks
|
||||
to the same GPU with the KOKKOS package, but this is usually only
|
||||
faster if significant portions of the input script have not been
|
||||
ported to use Kokkos. Using CUDA MPS is recommended in this
|
||||
scenario. As above for multi-core CPUs (and no GPU), if N is the
|
||||
number of physical cores/node, then the number of MPI tasks/node
|
||||
should not exceed N.
|
||||
|
||||
-k on g Ng :pre
|
||||
|
||||
Here are examples of how to use the KOKKOS package for GPUs,
|
||||
assuming one or more nodes, each with two GPUs:
|
||||
Here are examples of how to use the KOKKOS package for GPUs, assuming
|
||||
one or more nodes, each with two GPUs:
|
||||
|
||||
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node
|
||||
mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre
|
||||
|
||||
NOTE: The default for the "package kokkos"_package.html command is
|
||||
to use "full" neighbor lists and set the Newton flag to "off" for both
|
||||
NOTE: The default for the "package kokkos"_package.html command is to
|
||||
use "full" neighbor lists and set the Newton flag to "off" for both
|
||||
pairwise and bonded interactions, along with threaded communication.
|
||||
When running on Maxwell or Kepler GPUs, this will typically be best. For Pascal GPUs,
|
||||
using "half" neighbor lists and setting the
|
||||
Newton flag to "on" may be faster. For many pair styles, setting the neighbor binsize
|
||||
equal to the ghost atom cutoff will give speedup.
|
||||
Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
|
||||
change the default "package kokkos"_package.html
|
||||
options. See its doc page for details and default settings. Experimenting with
|
||||
its options can provide a speed-up for specific calculations. For example:
|
||||
When running on Maxwell or Kepler GPUs, this will typically be
|
||||
best. For Pascal GPUs, using "half" neighbor lists and setting the
|
||||
Newton flag to "on" may be faster. For many pair styles, setting the
|
||||
neighbor binsize equal to the ghost atom cutoff will give speedup.
|
||||
Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7
|
||||
to change the default "package kokkos"_package.html options. See its
|
||||
doc page for details and default settings. Experimenting with its
|
||||
options can provide a speed-up for specific calculations. For example:
|
||||
|
||||
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff
|
||||
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
|
||||
@ -299,8 +312,8 @@ Alternatively the effect of the "-sf" or "-pk" switches can be
|
||||
duplicated by adding the "package kokkos"_package.html or "suffix
|
||||
kk"_suffix.html commands to your input script.
|
||||
|
||||
The discussion above for building LAMMPS with the KOKKOS package, the mpirun/mpiexec command, and setting
|
||||
appropriate thread are the same.
|
||||
The discussion above for building LAMMPS with the KOKKOS package, the
|
||||
mpirun/mpiexec command, and setting appropriate thread are the same.
|
||||
|
||||
You must still use the "-k on" "command-line
|
||||
switch"_Section_start.html#start_7 to enable the KOKKOS package, and
|
||||
@ -318,17 +331,19 @@ wish to change any of its option defaults, as set by the "-k on"
|
||||
|
||||
[Using OpenMP threading and CUDA together (experimental):]
|
||||
|
||||
With the KOKKOS package, both OpenMP multi-threading and GPUs can be used
|
||||
together in a few special cases. In the Makefile, the KOKKOS_DEVICES variable must
|
||||
include both "Cuda" and "OpenMP", as is the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
|
||||
With the KOKKOS package, both OpenMP multi-threading and GPUs can be
|
||||
used together in a few special cases. In the Makefile, the
|
||||
KOKKOS_DEVICES variable must include both "Cuda" and "OpenMP", as is
|
||||
the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
|
||||
|
||||
KOKKOS_DEVICES=Cuda,OpenMP :pre
|
||||
|
||||
The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,
|
||||
using the "-sf kk" in the command line gives the default CUDA version everywhere.
|
||||
However, if the "/kk/host" suffix is added to a specific style in the input
|
||||
script, the Kokkos OpenMP (CPU) version of that specific style will be used instead.
|
||||
Set the number of OpenMP threads as "t Nt" and the number of GPUs as "g Ng"
|
||||
using the "-sf kk" in the command line gives the default CUDA version
|
||||
everywhere. However, if the "/kk/host" suffix is added to a specific
|
||||
style in the input script, the Kokkos OpenMP (CPU) version of that
|
||||
specific style will be used instead. Set the number of OpenMP threads
|
||||
as "t Nt" and the number of GPUs as "g Ng"
|
||||
|
||||
-k on t Nt g Ng :pre
|
||||
|
||||
@ -336,18 +351,20 @@ For example, the command to run with 1 GPU and 8 OpenMP threads is then:
|
||||
|
||||
mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre
|
||||
|
||||
Conversely, if the "-sf kk/host" is used in the command line and then the
|
||||
"/kk" or "/kk/device" suffix is added to a specific style in your input script,
|
||||
then only that specific style will run on the GPU while everything else will
|
||||
run on the CPU in OpenMP mode. Note that the execution of the CPU and GPU
|
||||
styles will NOT overlap, except for a special case:
|
||||
Conversely, if the "-sf kk/host" is used in the command line and then
|
||||
the "/kk" or "/kk/device" suffix is added to a specific style in your
|
||||
input script, then only that specific style will run on the GPU while
|
||||
everything else will run on the CPU in OpenMP mode. Note that the
|
||||
execution of the CPU and GPU styles will NOT overlap, except for a
|
||||
special case:
|
||||
|
||||
A kspace style and/or molecular topology (bonds, angles, etc.) running on
|
||||
the host CPU can overlap with a pair style running on the GPU. First compile
|
||||
with "--default-stream per-thread" added to CCFLAGS in the Kokkos CUDA Makefile.
|
||||
Then explicitly use the "/kk/host" suffix for kspace and bonds, angles, etc.
|
||||
in the input file and the "kk" suffix (equal to "kk/device") on the command line.
|
||||
Also make sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
|
||||
A kspace style and/or molecular topology (bonds, angles, etc.) running
|
||||
on the host CPU can overlap with a pair style running on the
|
||||
GPU. First compile with "--default-stream per-thread" added to CCFLAGS
|
||||
in the Kokkos CUDA Makefile. Then explicitly use the "/kk/host"
|
||||
suffix for kspace and bonds, angles, etc. in the input file and the
|
||||
"kk" suffix (equal to "kk/device") on the command line. Also make
|
||||
sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
|
||||
so CPU/GPU overlap can occur.
|
||||
|
||||
[Speed-ups to expect:]
|
||||
@ -384,9 +401,8 @@ hardware.
|
||||
There are other allowed options when building with the KOKKOS package.
|
||||
As above, they can be set either as variables on the make command line
|
||||
or in Makefile.machine. This is the full list of options, including
|
||||
those discussed above. Each takes a value shown below. The
|
||||
default value is listed, which is set in the
|
||||
/lib/kokkos/Makefile.kokkos file.
|
||||
those discussed above. Each takes a value shown below. The default
|
||||
value is listed, which is set in the /lib/kokkos/Makefile.kokkos file.
|
||||
|
||||
KOKKOS_DEVICES, values = {Serial}, {OpenMP}, {Pthreads}, {Cuda}, default = {OpenMP}
|
||||
KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {Pascal60}, {Pascal61}, {ARMv80}, {ARMv81}, {ARMv81}, {ARMv8-ThunderX}, {BGQ}, {Power7}, {Power8}, {Power9}, {KNL}, {BDW}, {SKX}, default = {none}
|
||||
@ -444,13 +460,14 @@ within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
|
||||
debugging information that can be useful. It also enables runtime
|
||||
bounds checking on Kokkos data structures.
|
||||
|
||||
KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when building LAMMPS.
|
||||
KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when
|
||||
building LAMMPS.
|
||||
|
||||
KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS package must be compiled
|
||||
with the {enable_lambda} option when using GPUs.
|
||||
KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS
|
||||
package must be compiled with the {enable_lambda} option when using
|
||||
GPUs.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Currently, there are no precision options with the KOKKOS
|
||||
package. All compilation and computation is performed in double
|
||||
precision.
|
||||
Currently, there are no precision options with the KOKKOS package. All
|
||||
compilation and computation is performed in double precision.
|
||||
|
||||
@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
|
||||
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Reference in New Issue
Block a user