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fixed merge conflict

This commit is contained in:
Rene Halver 2018-08-08 09:53:27 -06:00
parent 48fd8b46ee e88311235f
commit 74633ce28f
690 changed files with 8233 additions and 7669 deletions
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16
cmake/CMakeLists.txt
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@ -166,8 +166,11 @@ set_property(CACHE LAMMPS_SIZE_LIMIT PROPERTY STRINGS LAMMPS_SMALLBIG LAMMPS_BIG
add_definitions(-D${LAMMPS_SIZE_LIMIT})
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${LAMMPS_SIZE_LIMIT}")
set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
# posix_memalign is not available on Windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
endif()
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
if(LAMMPS_EXCEPTIONS)
@ -519,6 +522,11 @@ if(PKG_COMPRESS)
list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
endif()
# the windows version of LAMMPS requires a couple extra libraries
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
list(APPEND LAMMPS_LINK_LIBS -lwsock32 -lpsapi)
endif()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
@ -678,6 +686,10 @@ if(PKG_USER-OMP)
# manually add package dependent source files from USER-OMP that do not provide styles
if(PKG_ASPHERE)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
endif()
if(PKG_RIGID)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
endif()

51
doc/src/Commands.txt Normal file
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@ -0,0 +1,51 @@
"Previous Section"_Run.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Packages.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html#comm)
:line
Commands :h2
These pages describe how a LAMMPS input script is formatted and the
commands in it are used to define a LAMMPS simulation.
<!-- RST
.. toctree::
Commands_input
Commands_parse
Commands_structure
Commands_category
.. toctree::
Commands_all
Commands_fix
Commands_compute
Commands_pair
Commands_bond
Commands_kspace
END_RST -->
<!-- HTML_ONLY -->
"LAMMPS input scripts"_Commands_input.html
"Parsing rules for input scripts"_Commands_parse.html
"Input script structure"_Commands_structure.html
"Commands by category"_Commands_category.html :all(b)
"All commands"_Commands_all.html
"Fix commands"_Commands_fix.html
"Compute commands"_Commands_compute.html
"Pair commands"_Commands_pair.html
"Bond, angle, dihedral, improper commands"_Commands_bond.html
"KSpace solvers"_Commands_kspace.html :all(b)
<!-- END_HTML_ONLY -->

128
doc/src/Commands_all.txt Normal file
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@ -0,0 +1,128 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
"All commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
"Bond styles"_Commands_bond.html,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
All commands :h3
An alphabetic list of all LAMMPS commmands.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,
"atom_modify"_atom_modify.html,
"atom_style"_atom_style.html,
"balance"_balance.html,
"bond_coeff"_bond_coeff.html,
"bond_style"_bond_style.html,
"bond_write"_bond_write.html,
"boundary"_boundary.html,
"box"_box.html,
"change_box"_change_box.html,
"clear"_clear.html,
"comm_modify"_comm_modify.html,
"comm_style"_comm_style.html,
"compute"_compute.html,
"compute_modify"_compute_modify.html,
"create_atoms"_create_atoms.html,
"create_bonds"_create_bonds.html,
"create_box"_create_box.html,
"delete_atoms"_delete_atoms.html,
"delete_bonds"_delete_bonds.html,
"dielectric"_dielectric.html,
"dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"dimension"_dimension.html,
"displace_atoms"_displace_atoms.html,
"dump"_dump.html,
"dump image"_dump_image.html,
"dump_modify"_dump_modify.html,
"dump movie"_dump_image.html,
"dump netcdf"_dump_netcdf.html,
"dump netcdf/mpiio"_dump_netcdf.html,
"dump vtk"_dump_vtk.html,
"echo"_echo.html,
"fix"_fix.html,
"fix_modify"_fix_modify.html,
"group"_group.html,
"group2ndx"_group2ndx.html,
"if"_if.html,
"info"_info.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"include"_include.html,
"jump"_jump.html,
"kspace_modify"_kspace_modify.html,
"kspace_style"_kspace_style.html,
"label"_label.html,
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
"molecule"_molecule.html,
"ndx2group"_group2ndx.html,
"neb"_neb.html,
"neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html,
"newton"_newton.html,
"next"_next.html,
"package"_package.html,
"pair_coeff"_pair_coeff.html,
"pair_modify"_pair_modify.html,
"pair_style"_pair_style.html,
"pair_write"_pair_write.html,
"partition"_partition.html,
"prd"_prd.html,
"print"_print.html,
"processors"_processors.html,
"python"_python.html,
"quit"_quit.html,
"read_data"_read_data.html,
"read_dump"_read_dump.html,
"read_restart"_read_restart.html,
"region"_region.html,
"replicate"_replicate.html,
"rerun"_rerun.html,
"reset_ids"_reset_ids.html,
"reset_timestep"_reset_timestep.html,
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
"suffix"_suffix.html,
"tad"_tad.html,
"temper"_temper.html,
"temper/grem"_temper_grem.html,
"temper/npt"_temper_npt.html,
"thermo"_thermo.html,
"thermo_modify"_thermo_modify.html,
"thermo_style"_thermo_style.html,
"timer"_timer.html,
"timestep"_timestep.html,
"uncompute"_uncompute.html,
"undump"_undump.html,
"unfix"_unfix.html,
"units"_units.html,
"variable"_variable.html,
"velocity"_velocity.html,
"write_coeff"_write_coeff.html,
"write_data"_write_data.html,
"write_dump"_write_dump.html,
"write_restart"_write_restart.html :tb(c=6,ea=c)

124
doc/src/Commands_bond.txt Normal file
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@ -0,0 +1,124 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
"All commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
"Bond styles"_Commands_bond.html,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
Bond, angle, dihedral, and improper commands :h3
:line
Bond_style potentials :h3,link(bond)
All LAMMPS "bond_style"_bond_style.html commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_bond_none.html,
"zero"_bond_zero.html,
"hybrid"_bond_hybrid.html :tb(c=3,ea=c)
"class2 (ko)"_bond_class2.html,
"fene (iko)"_bond_fene.html,
"fene/expand (o)"_bond_fene_expand.html,
"gromos (o)"_bond_gromos.html,
"harmonic (ko)"_bond_harmonic.html,
"harmonic/shift (o)"_bond_harmonic_shift.html,
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
"morse (o)"_bond_morse.html,
"nonlinear (o)"_bond_nonlinear.html,
"oxdna/fene"_bond_oxdna.html,
"oxdna2/fene"_bond_oxdna.html,
"quartic (o)"_bond_quartic.html,
"table (o)"_bond_table.html :tb(c=4,ea=c)
:line
Angle_style potentials :h3,link(angle)
All LAMMPS "angle_style"_angle_style.html commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_angle_none.html,
"zero"_angle_zero.html,
"hybrid"_angle_hybrid.html :tb(c=3,ea=c)
"charmm (ko)"_angle_charmm.html,
"class2 (ko)"_angle_class2.html,
"cosine (o)"_angle_cosine.html,
"cosine/delta (o)"_angle_cosine_delta.html,
"cosine/periodic (o)"_angle_cosine_periodic.html,
"cosine/shift (o)"_angle_cosine_shift.html,
"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
"cosine/squared (o)"_angle_cosine_squared.html,
"dipole (o)"_angle_dipole.html,
"fourier (o)"_angle_fourier.html,
"fourier/simple (o)"_angle_fourier_simple.html,
"harmonic (iko)"_angle_harmonic.html,
"quartic (o)"_angle_quartic.html,
"sdk"_angle_sdk.html,
"table (o)"_angle_table.html :tb(c=4,ea=c)
:line
Dihedral_style potentials :h3,link(dihedral)
All LAMMPS "dihedral_style"_dihedral_style.html commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_dihedral_none.html,
"zero"_dihedral_zero.html,
"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c)
"charmm (iko)"_dihedral_charmm.html,
"charmmfsw"_dihedral_charmm.html,
"class2 (ko)"_dihedral_class2.html,
"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
"fourier (io)"_dihedral_fourier.html,
"harmonic (io)"_dihedral_harmonic.html,
"helix (o)"_dihedral_helix.html,
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
"nharmonic (o)"_dihedral_nharmonic.html,
"opls (iko)"_dihedral_opls.htm;,
"quadratic (o)"_dihedral_quadratic.html,
"spherical (o)"_dihedral_spherical.html,
"table (o)"_dihedral_table.html,
"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
:line
Improper_style potentials :h3,link(improper)
All LAMMPS "improper_style"_improper_style.html commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_improper_none.html,
"zero"_improper_zero.html,
"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
"class2 (ko)"_improper_class2.html,
"cossq (o)"_improper_cossq.html,
"cvff (io)"_improper_cvff.html,
"distance"_improper_distance.html,
"fourier (o)"_improper_fourier.html,
"harmonic (iko)"_improper_harmonic.html,
"ring (o)"_improper_ring.html,
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

141
doc/src/Commands_category.txt Normal file
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@ -0,0 +1,141 @@
"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
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@ -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)

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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
"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)

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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
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.

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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.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)

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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
"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)

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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
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.

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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
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.

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@ -1,10 +1,10 @@
"Previous Section"_Python.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_history.html :c
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

2
doc/src/Errors_bugs.txt
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@ -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
doc/src/Errors_common.txt
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@ -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
doc/src/Errors_messages.txt
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@ -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
doc/src/Errors_warnings.txt
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@ -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

8
doc/src/Examples.txt
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@ -1,10 +1,10 @@
"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_perf.html :c
"Previous Section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc - "Next
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

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"Previous Section"_Performance.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Examples.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands.html#comm)
:line
How to discussions :h2
These doc pages describe how to perform various tasks with LAMMPS,
both for users and developers. The
"glossary"_http://lammps.sandia.gov website page also lists MD
terminology with links to corresponding LAMMPS manual pages.
The example input scripts included in the examples dir of the LAMMPS
distribution and highlighted on the "Examples"_Examples.html doc page
also show how to setup and run various kinds of simulations.
<!-- RST
.. toctree::
Howto_github
Howto_pylammps
Howto_bash
.. toctree::
Howto_restart
Howto_viz
Howto_multiple
Howto_replica
Howto_library
Howto_couple
.. toctree::
Howto_output
Howto_chunk
.. toctree::
Howto_2d
Howto_triclinic
Howto_walls
Howto_nemd
Howto_granular
Howto_spherical
Howto_dispersion
.. toctree::
Howto_temperature
Howto_thermostat
Howto_barostat
Howto_elastic
Howto_kappa
Howto_viscosity
Howto_diffusion
.. toctree::
Howto_bioFF
Howto_tip3p
Howto_tip4p
Howto_spc
.. toctree::
Howto_body
Howto_polarizable
Howto_coreshell
Howto_drude
Howto_drude2
Howto_manifold
Howto_spins
END_RST -->
<!-- HTML_ONLY -->
"Using GitHub with LAMMPS"_Howto_github.html
"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
"Using LAMMPS with bash on Windows"_Howto_bash.html
"Restart a simulation"_Howto_restart.html
"Visualize LAMMPS snapshots"_Howto_viz.html
"Run multiple simulations from one input script"_Howto_multiple.html
"Multi-replica simulations"_Howto_replica.html
"Library interface to LAMMPS"_Howto_library.html
"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
"2d simulations"_Howto_2d.html
"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
"Walls"_Howto_walls.html
"NEMD simulations"_Howto_nemd.html
"Granular models"_Howto_granular.html
"Finite-size spherical and aspherical particles"_Howto_spherical.html
"Long-range dispersion settings"_Howto_dispersion.html :all(b)
"Calculate temperature"_Howto_temperature.html
"Thermostats"_Howto_thermostat.html
"Barostats"_Howto_barostat.html
"Calculate elastic constants"_Howto_elastic.html
"Calculate thermal conductivity"_Howto_kappa.html
"Calculate viscosity"_Howto_viscosity.html
"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
"TIP3P water model"_Howto_tip3p.html
"TIP4P water model"_Howto_tip4p.html
"SPC water model"_Howto_spc.html :all(b)
"Body style particles"_Howto_body.html
"Polarizable models"_Howto_polarizable.html
"Adiabatic core/shell model"_Howto_coreshell.html
"Drude induced dipoles"_Howto_drude.html
"Drude induced dipoles (extended)"_Howto_drude2.html :all(b)
"Manifolds (surfaces)"_Howto_manifold.html
"Magnetic spins"_Howto_spins.html
<!-- END_HTML_ONLY -->

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"Higher level section"_Howto.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
2d simulations :h3
Use the "dimension"_dimension.html command to specify a 2d simulation.
Make the simulation box periodic in z via the "boundary"_boundary.html
command. This is the default.
If using the "create box"_create_box.html command to define a
simulation box, set the z dimensions narrow, but finite, so that the
create_atoms command will tile the 3d simulation box with a single z
plane of atoms - e.g.
"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre
If using the "read data"_read_data.html command to read in a file of
atom coordinates, set the "zlo zhi" values to be finite but narrow,
similar to the create_box command settings just described. For each
atom in the file, assign a z coordinate so it falls inside the
z-boundaries of the box - e.g. 0.0.
Use the "fix enforce2d"_fix_enforce2d.html command as the last
defined fix to insure that the z-components of velocities and forces
are zeroed out every timestep. The reason to make it the last fix is
so that any forces induced by other fixes will be zeroed out.
Many of the example input scripts included in the LAMMPS distribution
are for 2d models.
NOTE: Some models in LAMMPS treat particles as finite-size spheres, as
opposed to point particles. See the "atom_style
sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html
commands for details. By default, for 2d simulations, such particles
will still be modeled as 3d spheres, not 2d discs (circles), meaning
their moment of inertia will be that of a sphere. If you wish to
model them as 2d discs, see the "set density/disc"_set.html command
and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html,
"fix nvt/sphere"_fix_nvt_sphere.html, "fix
nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html
commands.

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"Higher level section"_Howto.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
Barostats :h3
Barostatting means controlling the pressure in an MD simulation.
"Thermostatting"_Howto_thermostat.html means controlling the
temperature of the particles. Since the pressure includes a kinetic
component due to particle velocities, both these operations require
calculation of the temperature. Typically a target temperature (T)
and/or pressure (P) is specified by the user, and the thermostat or
barostat attempts to equilibrate the system to the requested T and/or
P.
Barostatting in LAMMPS is performed by "fixes"_fix.html. Two
barosttating methods are currently available: Nose-Hoover (npt and
nph) and Berendsen:
"fix npt"_fix_nh.html
"fix npt/sphere"_fix_npt_sphere.html
"fix npt/asphere"_fix_npt_asphere.html
"fix nph"_fix_nh.html
"fix press/berendsen"_fix_press_berendsen.html :ul
The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat
and barostat. "Fix nph"_fix_nh.html is just a Nose/Hoover barostat;
it does no thermostatting. Both "fix nph"_fix_nh.html and "fix
press/berendsen"_fix_press_berendsen.html can be used in conjunction
with any of the thermostatting fixes.
As with the "thermostats"_Howto_thermostat.html, "fix npt"_fix_nh.html
and "fix nph"_fix_nh.html only use translational motion of the
particles in computing T and P and performing thermo/barostatting.
"Fix npt/sphere"_fix_npt_sphere.html and "fix
npt/asphere"_fix_npt_asphere.html thermo/barostat using not only
translation velocities but also rotational velocities for spherical
and aspherical particles.
All of the barostatting fixes use the "compute
pressure"_compute_pressure.html compute to calculate a current
pressure. By default, this compute is created with a simple "compute
temp"_compute_temp.html (see the last argument of the "compute
pressure"_compute_pressure.html command), which is used to calculated
the kinetic component of the pressure. The barostatting fixes can
also use temperature computes that remove bias for the purpose of
computing the kinetic component which contributes to the current
pressure. See the doc pages for the individual fixes and for the
"fix_modify"_fix_modify.html command for instructions on how to assign
a temperature or pressure compute to a barostatting fix.
NOTE: As with the thermostats, the Nose/Hoover methods ("fix
npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration.
"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should
be used with one of the constant NVE fixes or with one of the NVT
fixes.
Thermodynamic output, which can be setup via the
"thermo_style"_thermo_style.html command, often includes pressure
values. As explained on the doc page for the
"thermo_style"_thermo_style.html command, the default pressure is
setup by the thermo command itself. It is NOT the presure associated
with any barostatting fix you have defined or with any compute you
have defined that calculates a presure. The doc pages for the
barostatting fixes explain the ID of the pressure compute they create.
Thus if you want to view these pressurse, you need to specify them
explicitly via the "thermo_style custom"_thermo_style.html command.
Or you can use the "thermo_modify"_thermo_modify.html command to
re-define what pressure compute is used for default thermodynamic
output.

3
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@ -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
@ -10,6 +10,7 @@ Using LAMMPS with Bash on Windows :h3
[written by Richard Berger]
:line
Starting with Windows 10 you can install Linux tools directly in Windows. This
allows you to compile LAMMPS following the same procedure as on a real Ubuntu
Linux installation. Software can be easily installed using the package manager

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"Higher level section"_Howto.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
CHARMM, AMBER, and DREIDING force fields :h3
A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly
used in the CHARMM, AMBER, and DREIDING force fields. Setting
coefficients is done in the input data file via the
"read_data"_read_data.html command or in the input script with
commands like "pair_coeff"_pair_coeff.html or
"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for
additional tools that can use CHARMM or AMBER to assign force field
coefficients and convert their output into LAMMPS input.
See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force
field.
:link(charmm,http://www.scripps.edu/brooks)
:link(amber,http://amber.scripps.edu)
These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command's
documentation for the formula it computes.
"bond_style"_bond_harmonic.html harmonic
"angle_style"_angle_charmm.html charmm
"dihedral_style"_dihedral_charmm.html charmmfsh
"dihedral_style"_dihedral_charmm.html charmm
"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh
"pair_style"_pair_charmm.html lj/charmmfsw/coul/long
"pair_style"_pair_charmm.html lj/charmm/coul/charmm
"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
"pair_style"_pair_charmm.html lj/charmm/coul/long :ul
"special_bonds"_special_bonds.html charmm
"special_bonds"_special_bonds.html amber :ul
NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
released in March 2017. We recommend they be used instead of the
older {charmm} styles. See discussion of the differences on the "pair
charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
doc pages.
DREIDING is a generic force field developed by the "Goddard
group"_http://www.wag.caltech.edu at Caltech and is useful for
predicting structures and dynamics of organic, biological and
main-group inorganic molecules. The philosophy in DREIDING is to use
general force constants and geometry parameters based on simple
hybridization considerations, rather than individual force constants
and geometric parameters that depend on the particular combinations of
atoms involved in the bond, angle, or torsion terms. DREIDING has an
"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
interactions involving a hydrogen atom on very electronegative atoms
(N, O, F).
See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field
These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command's
documentation for the formula it computes.
"bond_style"_bond_harmonic.html harmonic
"bond_style"_bond_morse.html morse :ul
"angle_style"_angle_harmonic.html harmonic
"angle_style"_angle_cosine.html cosine
"angle_style"_angle_cosine_periodic.html cosine/periodic :ul
"dihedral_style"_dihedral_charmm.html charmm
"improper_style"_improper_umbrella.html umbrella :ul
"pair_style"_pair_buck.html buck
"pair_style"_pair_buck.html buck/coul/cut
"pair_style"_pair_buck.html buck/coul/long
"pair_style"_pair_lj.html lj/cut
"pair_style"_pair_lj.html lj/cut/coul/cut
"pair_style"_pair_lj.html lj/cut/coul/long :ul
"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj
"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul
"special_bonds"_special_bonds.html dreiding :ul
:line
:link(howto-MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
:link(howto-Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
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
Body particles :h2
Body particles :h3
[Overview:]
This doc page is not about a LAMMPS input script command, but about
body particles, which are generalized finite-size particles.
In LAMMPS, body particles are generalized finite-size particles.
Individual body particles can represent complex entities, such as
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
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
@ -151,8 +151,8 @@ center-of-mass position of the particle is specified by the x,y,z
values in the {Atoms} section of the data file, as is the total mass
of the body particle.
The "pair_style body"_pair_body.html command can be used with this
body style to compute body/body and body/non-body interactions.
The "pair_style body/nparticle"_pair_body_nparticle.html command can be used
with this body style to compute body/body and body/non-body interactions.
For output purposes via the "compute
body/local"_compute_body_local.html and "dump local"_dump.html

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"Higher level section"_Howto.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
Use chunks to calculate system properties :h3
In LAMMS, "chunks" are collections of atoms, as defined by the
"compute chunk/atom"_compute_chunk_atom.html command, which assigns
each atom to a chunk ID (or to no chunk at all). The number of chunks
and the assignment of chunk IDs to atoms can be static or change over
time. Examples of "chunks" are molecules or spatial bins or atoms
with similar values (e.g. coordination number or potential energy).
The per-atom chunk IDs can be used as input to two other kinds of
commands, to calculate various properties of a system:
"fix ave/chunk"_fix_ave_chunk.html
any of the "compute */chunk"_compute.html commands :ul
Here, each of the 3 kinds of chunk-related commands is briefly
overviewed. Then some examples are given of how to compute different
properties with chunk commands.
Compute chunk/atom command: :h4
This compute can assign atoms to chunks of various styles. Only atoms
in the specified group and optional specified region are assigned to a
chunk. Here are some possible chunk definitions:
atoms in same molecule | chunk ID = molecule ID |
atoms of same atom type | chunk ID = atom type |
all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom |
atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command |
atoms in same spatial bin | chunk ID = bin ID |
atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies |
atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html |
atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2)
Note that chunk IDs are integer values, so for atom properties or
computes that produce a floating point value, they will be truncated
to an integer. You could also use the compute in a variable that
scales the floating point value to spread it across multiple integers.
Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
pencils, 3d bins = boxes, spherical bins, cylindrical bins.
This compute also calculates the number of chunks {Nchunk}, which is
used by other commands to tally per-chunk data. {Nchunk} can be a
static value or change over time (e.g. the number of clusters). The
chunk ID for an individual atom can also be static (e.g. a molecule
ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
Note that this compute allows the per-atom output of other
"computes"_compute.html, "fixes"_fix.html, and
"variables"_variable.html to be used to define chunk IDs for each
atom. This means you can write your own compute or fix to output a
per-atom quantity to use as chunk ID. See the "Modify"_Modify.html
doc pages for info on how to do this. You can also define a "per-atom
variable"_variable.html in the input script that uses a formula to
generate a chunk ID for each atom.
Fix ave/chunk command: :h4
This fix takes the ID of a "compute
chunk/atom"_compute_chunk_atom.html command as input. For each chunk,
it then sums one or more specified per-atom values over the atoms in
each chunk. The per-atom values can be any atom property, such as
velocity, force, charge, potential energy, kinetic energy, stress,
etc. Additional keywords are defined for per-chunk properties like
density and temperature. More generally any per-atom value generated
by other "computes"_compute.html, "fixes"_fix.html, and "per-atom
variables"_variable.html, can be summed over atoms in each chunk.
Similar to other averaging fixes, this fix allows the summed per-chunk
values to be time-averaged in various ways, and output to a file. The
fix produces a global array as output with one row of values per
chunk.
Compute */chunk commands: :h4
Currently the following computes operate on chunks of atoms to produce
per-chunk values.
"compute com/chunk"_compute_com_chunk.html
"compute gyration/chunk"_compute_gyration_chunk.html
"compute inertia/chunk"_compute_inertia_chunk.html
"compute msd/chunk"_compute_msd_chunk.html
"compute property/chunk"_compute_property_chunk.html
"compute temp/chunk"_compute_temp_chunk.html
"compute torque/chunk"_compute_vcm_chunk.html
"compute vcm/chunk"_compute_vcm_chunk.html :ul
They each take the ID of a "compute
chunk/atom"_compute_chunk_atom.html command as input. As their names
indicate, they calculate the center-of-mass, radius of gyration,
moments of inertia, mean-squared displacement, temperature, torque,
and velocity of center-of-mass for each chunk of atoms. The "compute
property/chunk"_compute_property_chunk.html command can tally the
count of atoms in each chunk and extract other per-chunk properties.
The reason these various calculations are not part of the "fix
ave/chunk command"_fix_ave_chunk.html, is that each requires a more
complicated operation than simply summing and averaging over per-atom
values in each chunk. For example, many of them require calculation
of a center of mass, which requires summing mass*position over the
atoms and then dividing by summed mass.
All of these computes produce a global vector or global array as
output, wih one or more values per chunk. They can be used
in various ways:
As input to the "fix ave/time"_fix_ave_time.html command, which can
write the values to a file and optionally time average them. :ulb,l
As input to the "fix ave/histo"_fix_ave_histo.html command to
histogram values across chunks. E.g. a histogram of cluster sizes or
molecule diffusion rates. :l
As input to special functions of "equal-style
variables"_variable.html, like sum() and max(). E.g. to find the
largest cluster or fastest diffusing molecule. :l
:ule
Example calculations with chunks :h4
Here are examples using chunk commands to calculate various
properties:
(1) Average velocity in each of 1000 2d spatial bins:
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre
(2) Temperature in each spatial bin, after subtracting a flow
velocity:
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
compute vbias all temp/profile 1 0 0 y 10
fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre
(3) Center of mass of each molecule:
compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre
(4) Total force on each molecule and ave/max across all molecules:
compute cc1 all chunk/atom molecule
fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
variable xave equal ave(f_1\[2\])
variable xmax equal max(f_1\[2\])
thermo 1000
thermo_style custom step temp v_xave v_xmax :pre
(5) Histogram of cluster sizes:
compute cluster all cluster/atom 1.0
compute cc1 all chunk/atom c_cluster compress yes
compute size all property/chunk cc1 count
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre

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"Higher level section"_Howto.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
Adiabatic core/shell model :h3
The adiabatic core-shell model by "Mitchell and
Fincham"_#MitchellFincham is a simple method for adding polarizability
to a system. In order to mimic the electron shell of an ion, a
satellite particle is attached to it. This way the ions are split into
a core and a shell where the latter is meant to react to the
electrostatic environment inducing polarizability. See the "Howto
polarizable"_Howto_polarizable.html doc page for a discussion of all
the polarizable models available in LAMMPS.
Technically, shells are attached to the cores by a spring force f =
k*r where k is a parametrized spring constant and r is the distance
between the core and the shell. The charges of the core and the shell
add up to the ion charge, thus q(ion) = q(core) + q(shell). This
setup introduces the ion polarizability (alpha) given by
alpha = q(shell)^2 / k. In a
similar fashion the mass of the ion is distributed on the core and the
shell with the core having the larger mass.
To run this model in LAMMPS, "atom_style"_atom_style.html {full} can
be used since atom charge and bonds are needed. Each kind of
core/shell pair requires two atom types and a bond type. The core and
shell of a core/shell pair should be bonded to each other with a
harmonic bond that provides the spring force. For example, a data file
for NaCl, as found in examples/coreshell, has this format:
432 atoms # core and shell atoms
216 bonds # number of core/shell springs :pre
4 atom types # 2 cores and 2 shells for Na and Cl
2 bond types :pre
0.0 24.09597 xlo xhi
0.0 24.09597 ylo yhi
0.0 24.09597 zlo zhi :pre
Masses # core/shell mass ratio = 0.1 :pre
1 20.690784 # Na core
2 31.90500 # Cl core
3 2.298976 # Na shell
4 3.54500 # Cl shell :pre
Atoms :pre
1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
(...) :pre
Bonds # Bond topology for spring forces :pre
1 2 1 2 # spring for core/shell pair 1
2 2 3 4 # spring for core/shell pair 2
(...) :pre
Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
defined between the shells. Coulombic interactions are defined
between all cores and shells. If desired, additional bonds can be
specified between cores.
The "special_bonds"_special_bonds.html command should be used to
turn-off the Coulombic interaction within core/shell pairs, since that
interaction is set by the bond spring. This is done using the
"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0,
which is the default value. It needs to be considered whether one has
to adjust the "special_bonds"_special_bonds.html weighting according
to the molecular topology since the interactions of the shells are
bypassed over an extra bond.
Note that this core/shell implementation does not require all ions to
be polarized. One can mix core/shell pairs and ions without a
satellite particle if desired.
Since the core/shell model permits distances of r = 0.0 between the
core and shell, a pair style with a "cs" suffix needs to be used to
implement a valid long-range Coulombic correction. Several such pair
styles are provided in the CORESHELL package. See "this doc
page"_pair_cs.html for details. All of the core/shell enabled pair
styles require the use of a long-range Coulombic solver, as specified
by the "kspace_style"_kspace_style.html command. Either the PPPM or
Ewald solvers can be used.
For the NaCL example problem, these pair style and bond style settings
are used:
pair_style born/coul/long/cs 20.0 20.0
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0 :pre
When running dynamics with the adiabatic core/shell model, the
following issues should be considered. The relative motion of
the core and shell particles corresponds to the polarization,
hereby an instantaneous relaxation of the shells is approximated
and a fast core/shell spring frequency ensures a nearly constant
internal kinetic energy during the simulation.
Thermostats can alter this polarization behaviour, by scaling the
internal kinetic energy, meaning the shell will not react freely to
its electrostatic environment.
Therefore it is typically desirable to decouple the relative motion of
the core/shell pair, which is an imaginary degree of freedom, from the
real physical system. To do that, the "compute
temp/cs"_compute_temp_cs.html command can be used, in conjunction with
any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin. This compute uses the center-of-mass velocity
of the core/shell pairs to calculate a temperature, and insures that
velocity is what is rescaled for thermostatting purposes. This
compute also works for a system with both core/shell pairs and
non-polarized ions (ions without an attached satellite particle). The
"compute temp/cs"_compute_temp_cs.html command requires input of two
groups, one for the core atoms, another for the shell atoms.
Non-polarized ions which might also be included in the treated system
should not be included into either of these groups, they are taken
into account by the {group-ID} (2nd argument) of the compute. The
groups can be defined using the "group {type}"_group.html command.
Note that to perform thermostatting using this definition of
temperature, the "fix modify temp"_fix_modify.html command should be
used to assign the compute to the thermostat fix. Likewise the
"thermo_modify temp"_thermo_modify.html command can be used to make
this temperature be output for the overall system.
For the NaCl example, this can be done as follows:
group cores type 1 2
group shells type 3 4
compute CSequ all temp/cs cores shells
fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
fix thermostatequ all nve # integrator as needed for the berendsen thermostat
fix_modify thermoberendsen temp CSequ
thermo_modify temp CSequ # output of center-of-mass derived temperature :pre
The pressure for the core/shell system is computed via the regular
LAMMPS convention by "treating the cores and shells as individual
particles"_#MitchellFincham2. For the thermo output of the pressure
as well as for the application of a barostat, it is necessary to
use an additional "pressure"_compute_pressure compute based on the
default "temperature"_compute_temp and specifying it as a second
argument in "fix modify"_fix_modify.html and
"thermo_modify"_thermo_modify.html resulting in:
(...)
compute CSequ all temp/cs cores shells
compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles
thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure
fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre
If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
relative motion of the core and the shell should in theory be
stable. However numerical fluctuation can introduce a small
momentum to the system, which is noticable over long trajectories.
Therefore it is recommendable to use the "fix
momentum"_fix_momentum.html command in combination with "compute
temp/cs"_compute_temp_cs.html when equilibrating the system to
prevent any drift.
When initializing the velocities of a system with core/shell pairs, it
is also desirable to not introduce energy into the relative motion of
the core/shell particles, but only assign a center-of-mass velocity to
the pairs. This can be done by using the {bias} keyword of the
"velocity create"_velocity.html command and assigning the "compute
temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
"velocity"_velocity.html command, e.g.
velocity all create 1427 134 bias yes temp CSequ
velocity all scale 1427 temp CSequ :pre
To maintain the correct polarizability of the core/shell pairs, the
kinetic energy of the internal motion shall remain nearly constant.
Therefore the choice of spring force and mass ratio need to ensure
much faster relative motion of the 2 atoms within the core/shell pair
than their center-of-mass velocity. This allows the shells to
effectively react instantaneously to the electrostatic environment and
limits energy transfer to or from the core/shell oscillators.
This fast movement also dictates the timestep that can be used.
The primary literature of the adiabatic core/shell model suggests that
the fast relative motion of the core/shell pairs only allows negligible
energy transfer to the environment.
The mentioned energy transfer will typically lead to a small drift
in total energy over time. This internal energy can be monitored
using the "compute chunk/atom"_compute_chunk_atom.html and "compute
temp/chunk"_compute_temp_chunk.html commands. The internal kinetic
energies of each core/shell pair can then be summed using the sum()
special function of the "variable"_variable.html command. Or they can
be time/averaged and output using the "fix ave/time"_fix_ave_time.html
command. To use these commands, each core/shell pair must be defined
as a "chunk". If each core/shell pair is defined as its own molecule,
the molecule ID can be used to define the chunks. If cores are bonded
to each other to form larger molecules, the chunks can be identified
by the "fix property/atom"_fix_property_atom.html via assigning a
core/shell ID to each atom using a special field in the data file read
by the "read_data"_read_data.html command. This field can then be
accessed by the "compute property/atom"_compute_property_atom.html
command, to use as input to the "compute
chunk/atom"_compute_chunk_atom.html command to define the core/shell
pairs as chunks.
For example if core/shell pairs are the only molecules:
read_data NaCl_CS_x0.1_prop.data
compute prop all property/atom molecule
compute cs_chunk all chunk/atom c_prop
compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
For example if core/shell pairs and other molecules are present:
fix csinfo all property/atom i_CSID # property/atom command
read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
compute prop all property/atom i_CSID
(...) :pre
The additional section in the date file would be formatted like this:
CS-Info # header of additional section :pre
1 1 # column 1 = atom ID, column 2 = core/shell ID
2 1
3 2
4 2
5 3
6 3
7 4
8 4
(...) :pre
:line
:link(MitchellFincham)
[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter,
5, 1031-1038 (1993).
:link(MitchellFincham2)
[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
6, 393-404 (1994).

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"Higher level section"_Howto.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
Coupling LAMMPS to other codes :h3
LAMMPS is designed to allow it to be coupled to other codes. For
example, a quantum mechanics code might compute forces on a subset of
atoms and pass those forces to LAMMPS. Or a continuum finite element
(FE) simulation might use atom positions as boundary conditions on FE
nodal points, compute a FE solution, and return interpolated forces on
MD atoms.
LAMMPS can be coupled to other codes in at least 3 ways. Each has
advantages and disadvantages, which you'll have to think about in the
context of your application.
(1) Define a new "fix"_fix.html command that calls the other code. In
this scenario, LAMMPS is the driver code. During its timestepping,
the fix is invoked, and can make library calls to the other code,
which has been linked to LAMMPS as a library. This is the way the
"POEMS"_poems package that performs constrained rigid-body motion on
groups of atoms is hooked to LAMMPS. See the "fix
poems"_fix_poems.html command for more details. See the
"Modify"_Modify.html doc pages for info on how to add a new fix to
LAMMPS.
:link(poems,http://www.rpi.edu/~anderk5/lab)
(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the
other code are on a more equal footing. Note that now the other code
is not called during the timestepping of a LAMMPS run, but between
runs. The LAMMPS input script can be used to alternate LAMMPS runs
with calls to the other code, invoked via the new command. The
"run"_run.html command facilitates this with its {every} option, which
makes it easy to run a few steps, invoke the command, run a few steps,
invoke the command, etc.
In this scenario, the other code can be called as a library, as in
(1), or it could be a stand-alone code, invoked by a system() call
made by the command (assuming your parallel machine allows one or more
processors to start up another program). In the latter case the
stand-alone code could communicate with LAMMPS thru files that the
command writes and reads.
See the "Modify command"_Modify_command.html doc page for info on how
to add a new command to LAMMPS.
(3) Use LAMMPS as a library called by another code. In this case the
other code is the driver and calls LAMMPS as needed. Or a wrapper
code could link and call both LAMMPS and another code as libraries.
Again, the "run"_run.html command has options that allow it to be
invoked with minimal overhead (no setup or clean-up) if you wish to do
multiple short runs, driven by another program.
Examples of driver codes that call LAMMPS as a library are included in
the examples/COUPLE directory of the LAMMPS distribution; see
examples/COUPLE/README for more details:
simple: simple driver programs in C++ and C which invoke LAMMPS as a
library :ulb,l
lammps_quest: coupling of LAMMPS and "Quest"_quest, to run classical
MD with quantum forces calculated by a density functional code :l
lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple
a kinetic Monte Carlo model for grain growth using MD to calculate
strain induced across grain boundaries :l
:ule
:link(quest,http://dft.sandia.gov/Quest)
:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
"This section"_Section_start.html#start_5 of the documentation
describes how to build LAMMPS as a library. Once this is done, you
can interface with LAMMPS either via C++, C, Fortran, or Python (or
any other language that supports a vanilla C-like interface). For
example, from C++ you could create one (or more) "instances" of
LAMMPS, pass it an input script to process, or execute individual
commands, all by invoking the correct class methods in LAMMPS. From C
or Fortran you can make function calls to do the same things. See the
"Python"_Python.html doc pages for a description of the Python wrapper
provided with LAMMPS that operates through the LAMMPS library
interface.
The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See the "Howto library"_Howto_library.html doc page for a
description of the interface and how to extend it for your needs.
Note that the lammps_open() function that creates an instance of
LAMMPS takes an MPI communicator as an argument. This means that
instance of LAMMPS will run on the set of processors in the
communicator. Thus the calling code can run LAMMPS on all or a subset
of processors. For example, a wrapper script might decide to
alternate between LAMMPS and another code, allowing them both to run
on all the processors. Or it might allocate half the processors to
LAMMPS and half to the other code and run both codes simultaneously
before syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.

31
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@ -0,0 +1,31 @@
"Higher level section"_Howto.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
Calculate a diffusion coefficient :h3
The diffusion coefficient D of a material can be measured in at least
2 ways using various options in LAMMPS. See the examples/DIFFUSE
directory for scripts that implement the 2 methods discussed here for
a simple Lennard-Jones fluid model.
The first method is to measure the mean-squared displacement (MSD) of
the system, via the "compute msd"_compute_msd.html command. The slope
of the MSD versus time is proportional to the diffusion coefficient.
The instantaneous MSD values can be accumulated in a vector via the
"fix vector"_fix_vector.html command, and a line fit to the vector to
compute its slope via the "variable slope"_variable.html function, and
thus extract D.
The second method is to measure the velocity auto-correlation function
(VACF) of the system, via the "compute vacf"_compute_vacf.html
command. The time-integral of the VACF is proportional to the
diffusion coefficient. The instantaneous VACF values can be
accumulated in a vector via the "fix vector"_fix_vector.html command,
and time integrated via the "variable trap"_variable.html function,
and thus extract D.

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@ -0,0 +1,108 @@
"Higher level section"_Howto.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
Long-raage dispersion settings :h3
The PPPM method computes interactions by splitting the pair potential
into two parts, one of which is computed in a normal pairwise fashion,
the so-called real-space part, and one of which is computed using the
Fourier transform, the so called reciprocal-space or kspace part. For
both parts, the potential is not computed exactly but is approximated.
Thus, there is an error in both parts of the computation, the
real-space and the kspace error. The just mentioned facts are true
both for the PPPM for Coulomb as well as dispersion interactions. The
deciding difference - and also the reason why the parameters for
pppm/disp have to be selected with more care - is the impact of the
errors on the results: The kspace error of the PPPM for Coulomb and
dispersion interaction and the real-space error of the PPPM for
Coulomb interaction have the character of noise. In contrast, the
real-space error of the PPPM for dispersion has a clear physical
interpretation: the underprediction of cohesion. As a consequence, the
real-space error has a much stronger effect than the kspace error on
simulation results for pppm/disp. Parameters must thus be chosen in a
way that this error is much smaller than the kspace error.
When using pppm/disp and not making any specifications on the PPPM
parameters via the kspace modify command, parameters will be tuned
such that the real-space error and the kspace error are equal. This
will result in simulations that are either inaccurate or slow, both of
which is not desirable. For selecting parameters for the pppm/disp
that provide fast and accurate simulations, there are two approaches,
which both have their up- and downsides.
The first approach is to set desired real-space an kspace accuracies
via the {kspace_modify force/disp/real} and {kspace_modify
force/disp/kspace} commands. Note that the accuracies have to be
specified in force units and are thus dependent on the chosen unit
settings. For real units, 0.0001 and 0.002 seem to provide reasonable
accurate and efficient computations for the real-space and kspace
accuracies. 0.002 and 0.05 work well for most systems using lj
units. PPPM parameters will be generated based on the desired
accuracies. The upside of this approach is that it usually provides a
good set of parameters and will work for both the {kspace_modify diff
ad} and {kspace_modify diff ik} options. The downside of the method
is that setting the PPPM parameters will take some time during the
initialization of the simulation.
The second approach is to set the parameters for the pppm/disp
explicitly using the {kspace_modify mesh/disp}, {kspace_modify
order/disp}, and {kspace_modify gewald/disp} commands. This approach
requires a more experienced user who understands well the impact of
the choice of parameters on the simulation accuracy and
performance. This approach provides a fast initialization of the
simulation. However, it is sensitive to errors: A combination of
parameters that will perform well for one system might result in
far-from-optimal conditions for other simulations. For example,
parameters that provide accurate and fast computations for
all-atomistic force fields can provide insufficient accuracy or
united-atomistic force fields (which is related to that the latter
typically have larger dispersion coefficients).
To avoid inaccurate or inefficient simulations, the pppm/disp stops
simulations with an error message if no action is taken to control the
PPPM parameters. If the automatic parameter generation is desired and
real-space and kspace accuracies are desired to be equal, this error
message can be suppressed using the {kspace_modify disp/auto yes}
command.
A reasonable approach that combines the upsides of both methods is to
make the first run using the {kspace_modify force/disp/real} and
{kspace_modify force/disp/kspace} commands, write down the PPPM
parameters from the outut, and specify these parameters using the
second approach in subsequent runs (which have the same composition,
force field, and approximately the same volume).
Concerning the performance of the pppm/disp there are two more things
to consider. The first is that when using the pppm/disp, the cutoff
parameter does no longer affect the accuracy of the simulation
(subject to that gewald/disp is adjusted when changing the cutoff).
The performance can thus be increased by examining different values
for the cutoff parameter. A lower bound for the cutoff is only set by
the truncation error of the repulsive term of pair potentials.
The second is that the mixing rule of the pair style has an impact on
the computation time when using the pppm/disp. Fastest computations
are achieved when using the geometric mixing rule. Using the
arithmetic mixing rule substantially increases the computational cost.
The computational overhead can be reduced using the {kspace_modify
mix/disp geom} and {kspace_modify splittol} commands. The first
command simply enforces geometric mixing of the dispersion
coefficients in kspace computations. This introduces some error in
the computations but will also significantly speed-up the
simulations. The second keyword sets the accuracy with which the
dispersion coefficients are approximated using a matrix factorization
approach. This may result in better accuracy then using the first
command, but will usually also not provide an equally good increase of
efficiency.
Finally, pppm/disp can also be used when no mixing rules apply.
This can be achieved using the {kspace_modify mix/disp none} command.
Note that the code does not check automatically whether any mixing
rule is fulfilled. If mixing rules do not apply, the user will have
to specify this command explicitly.

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"Higher level section"_Howto.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
Drude induced dipoles :h3
The thermalized Drude model represents induced dipoles by a pair of
charges (the core atom and the Drude particle) connected by a harmonic
spring. See the "Howto polarizable"_Howto_polarizable.html doc page
for a discussion of all the polarizable models available in LAMMPS.
The Drude model has a number of features aimed at its use in
molecular systems ("Lamoureux and Roux"_#howto-Lamoureux):
Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced
coordinates of the Drude particles with respect to their cores. This
makes the trajectory close to that of relaxed induced dipoles. :ulb,l
Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
pair represents a single (polarizable) atom, so the special screening
factors in a covalent structure should be the same for the core and
the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4
special neighbor relations from their respective cores. :l
Stabilization of the interactions between induced dipoles. Drude
dipoles on covalently bonded atoms interact too strongly due to the
short distances, so an atom may capture the Drude particle of a
neighbor, or the induced dipoles within the same molecule may align
too much. To avoid this, damping at short range can be done by Thole
functions (for which there are physical grounds). This Thole damping
is applied to the point charges composing the induced dipole (the
charge of the Drude particle and the opposite charge on the core, not
to the total charge of the core atom). :l,ule
A detailed tutorial covering the usage of Drude induced dipoles in
LAMMPS is on the "Howto drude2e"_Howto_drude2.html doc page.
As with the core-shell model, the cores and Drude particles should
appear in the data file as standard atoms. The same holds for the
springs between them, which are described by standard harmonic bonds.
The nature of the atoms (core, Drude particle or non-polarizable) is
specified via the "fix drude"_fix_drude.html command. The special
list of neighbors is automatically refactored to account for the
equivalence of core and Drude particles as regards special 1-2 to 1-4
screening. It may be necessary to use the {extra/special/per/atom}
keyword of the "read_data"_read_data.html command. If using "fix
shake"_fix_shake.html, make sure no Drude particle is in this fix
group.
There are two ways to thermostat the Drude particles at a low
temperature: use either "fix langevin/drude"_fix_langevin_drude.html
for a Langevin thermostat, or "fix
drude/transform/*"_fix_drude_transform.html for a Nose-Hoover
thermostat. The former requires use of the command "comm_modify vel
yes"_comm_modify.html. The latter requires two separate integration
fixes like {nvt} or {npt}. The correct temperatures of the reduced
degrees of freedom can be calculated using the "compute
temp/drude"_compute_temp_drude.html. This requires also to use the
command {comm_modify vel yes}.
Short-range damping of the induced dipole interactions can be achieved
using Thole functions through the "pair style
thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
with a Coulomb pair style. It may be useful to use {coul/long/cs} or
similar from the CORESHELL package if the core and Drude particle come
too close, which can cause numerical issues.
:line
:link(howto-Lamoureux)
[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)

2
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@ -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

47
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@ -0,0 +1,47 @@
"Higher level section"_Howto.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
Calculate elastic constants :h3
Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
stress and strain tensors in the limit of infinitesimal deformation.
In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where
the repeated indices imply summation. s_ij are the elements of the
symmetric stress tensor. e_kl are the elements of the symmetric strain
tensor. C_ijkl are the elements of the fourth rank tensor of elastic
constants. In three dimensions, this tensor has 3^4=81 elements. Using
Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
most 7*6/2 = 21 distinct elements.
At zero temperature, it is easy to estimate these derivatives by
deforming the simulation box in one of the six directions using the
"change_box"_change_box.html command and measuring the change in the
stress tensor. A general-purpose script that does this is given in the
examples/elastic directory described on the "Examples"_Examples.html
doc page.
Calculating elastic constants at finite temperature is more
challenging, because it is necessary to run a simulation that perfoms
time averages of differential properties. One way to do this is to
measure the change in average stress tensor in an NVT simulations when
the cell volume undergoes a finite deformation. In order to balance
the systematic and statistical errors in this method, the magnitude of
the deformation must be chosen judiciously, and care must be taken to
fully equilibrate the deformed cell before sampling the stress
tensor. Another approach is to sample the triclinic cell fluctuations
that occur in an NPT simulation. This method can also be slow to
converge and requires careful post-processing "(Shinoda)"_#Shinoda1
:line
:link(Shinoda1)
[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).

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@ -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
@ -25,8 +25,8 @@ or improvements to LAMMPS, as it significantly reduces the amount of
work required by the LAMMPS developers. Consequently, creating a pull
request will increase your chances to have your contribution included
and will reduce the time until the integration is complete. For more
information on the requirements to have your code included in LAMMPS,
see the "Modify contribute"_Modify_contribute.html doc page.
information on the requirements to have your code included into LAMMPS
please see the "Modify contribute"_Modify_contribute.html doc page.
:line
@ -124,7 +124,7 @@ unrelated feature, you should switch branches!
After everything is done, add the files to the branch and commit them:
$ git add doc/src/tutorial_github.txt
$ git add doc/src/Howto_github.txt
$ git add doc/src/JPG/tutorial*.png :pre
IMPORTANT NOTE: Do not use {git commit -a} (or {git add -A}). The -a
@ -318,7 +318,7 @@ Because the changes are OK with us, we are going to merge by clicking on
Now, since in the meantime our local text for the tutorial also changed,
we need to pull Axel's change back into our branch, and merge them:
$ git add tutorial_github.txt
$ git add Howto_github.txt
$ git add JPG/tutorial_reverse_pull_request*.png
$ git commit -m "Updated text and images on reverse pull requests"
$ git pull :pre
@ -331,7 +331,7 @@ With Axel's changes merged in and some final text updates, our feature
branch is now perfect as far as we are concerned, so we are going to
commit and push again:
$ git add tutorial_github.txt
$ git add Howto_github.txt
$ git add JPG/tutorial_reverse_pull_request6.png
$ git commit -m "Merged Axel's suggestions and updated text"
$ git push git@github.com:Pakketeretet2/lammps :pre

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@ -0,0 +1,57 @@
"Higher level section"_Howto.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
Granular models :h3
Granular system are composed of spherical particles with a diameter,
as opposed to point particles. This means they have an angular
velocity and torque can be imparted to them to cause them to rotate.
To run a simulation of a granular model, you will want to use
the following commands:
"atom_style sphere"_atom_style.html
"fix nve/sphere"_fix_nve_sphere.html
"fix gravity"_fix_gravity.html :ul
This compute
"compute erotate/sphere"_compute_erotate_sphere.html :ul
calculates rotational kinetic energy which can be "output with
thermodynamic info"_Howto_output.html.
Use one of these 3 pair potentials, which compute forces and torques
between interacting pairs of particles:
"pair_style"_pair_style.html gran/history
"pair_style"_pair_style.html gran/no_history
"pair_style"_pair_style.html gran/hertzian :ul
These commands implement fix options specific to granular systems:
"fix freeze"_fix_freeze.html
"fix pour"_fix_pour.html
"fix viscous"_fix_viscous.html
"fix wall/gran"_fix_wall_gran.html :ul
The fix style {freeze} zeroes both the force and torque of frozen
atoms, and should be used for granular system instead of the fix style
{setforce}.
For computational efficiency, you can eliminate needless pairwise
computations between frozen atoms by using this command:
"neigh_modify"_neigh_modify.html exclude :ul
NOTE: By default, for 2d systems, granular particles are still modeled
as 3d spheres, not 2d discs (circles), meaning their moment of inertia
will be the same as in 3d. If you wish to model granular particles in
2d as 2d discs, see the note on this topic on the "Howto 2d"_Howto_2d
doc page, where 2d simulations are discussed.

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"Higher level section"_Howto.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
Calculate thermal conductivity :h3
The thermal conductivity kappa of a material can be measured in at
least 4 ways using various options in LAMMPS. See the examples/KAPPA
directory for scripts that implement the 4 methods discussed here for
a simple Lennard-Jones fluid model. Also, see the "Howto
viscosity"_Howto_viscosity.html doc page for an analogous discussion
for viscosity.
The thermal conductivity tensor kappa is a measure of the propensity
of a material to transmit heat energy in a diffusive manner as given
by Fourier's law
J = -kappa grad(T)
where J is the heat flux in units of energy per area per time and
grad(T) is the spatial gradient of temperature. The thermal
conductivity thus has units of energy per distance per time per degree
K and is often approximated as an isotropic quantity, i.e. as a
scalar.
The first method is to setup two thermostatted regions at opposite
ends of a simulation box, or one in the middle and one at the end of a
periodic box. By holding the two regions at different temperatures
with a "thermostatting fix"_Howto_thermostat.html, the energy added to
the hot region should equal the energy subtracted from the cold region
and be proportional to the heat flux moving between the regions. See
the papers by "Ikeshoji and Hafskjold"_#howto-Ikeshoji and
"Wirnsberger et al"_#howto-Wirnsberger for details of this idea. Note
that thermostatting fixes such as "fix nvt"_fix_nh.html, "fix
langevin"_fix_langevin.html, and "fix
temp/rescale"_fix_temp_rescale.html store the cumulative energy they
add/subtract.
Alternatively, as a second method, the "fix heat"_fix_heat.html or
"fix ehex"_fix_ehex.html commands can be used in place of thermostats
on each of two regions to add/subtract specified amounts of energy to
both regions. In both cases, the resulting temperatures of the two
regions can be monitored with the "compute temp/region" command and
the temperature profile of the intermediate region can be monitored
with the "fix ave/chunk"_fix_ave_chunk.html and "compute
ke/atom"_compute_ke_atom.html commands.
The third method is to perform a reverse non-equilibrium MD simulation
using the "fix thermal/conductivity"_fix_thermal_conductivity.html
command which implements the rNEMD algorithm of Muller-Plathe.
Kinetic energy is swapped between atoms in two different layers of the
simulation box. This induces a temperature gradient between the two
layers which can be monitored with the "fix
ave/chunk"_fix_ave_chunk.html and "compute
ke/atom"_compute_ke_atom.html commands. The fix tallies the
cumulative energy transfer that it performs. See the "fix
thermal/conductivity"_fix_thermal_conductivity.html command for
details.
The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the heat flux
to kappa. The heat flux can be calculated from the fluctuations of
per-atom potential and kinetic energies and per-atom stress tensor in
a steady-state equilibrated simulation. This is in contrast to the
two preceding non-equilibrium methods, where energy flows continuously
between hot and cold regions of the simulation box.
The "compute heat/flux"_compute_heat_flux.html command can calculate
the needed heat flux and describes how to implement the Green_Kubo
formalism using additional LAMMPS commands, such as the "fix
ave/correlate"_fix_ave_correlate.html command to calculate the needed
auto-correlation. See the doc page for the "compute
heat/flux"_compute_heat_flux.html command for an example input script
that calculates the thermal conductivity of solid Ar via the GK
formalism.
:line
:link(howto-Ikeshoji)
[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994).
:link(howto-Wirnsberger)
[(Wirnsberger)] Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104
(2015).

208
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@ -0,0 +1,208 @@
"Higher level section"_Howto.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
Library interface to LAMMPS :h3
As described in "Section 2.5"_Section_start.html#start_5, LAMMPS can
be built as a library, so that it can be called by another code, used
in a "coupled manner"_Howto_couple.html with other codes, or driven
through a "Python interface"_Python.html.
All of these methodologies use a C-style interface to LAMMPS that is
provided in the files src/library.cpp and src/library.h. The
functions therein have a C-style argument list, but contain C++ code
you could write yourself in a C++ application that was invoking LAMMPS
directly. The C++ code in the functions illustrates how to invoke
internal LAMMPS operations. Note that LAMMPS classes are defined
within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
application.
The examples/COUPLE and python/examples directories have example C++
and C and Python codes which show how a driver code can link to LAMMPS
as a library, run LAMMPS on a subset of processors, grab data from
LAMMPS, change it, and put it back into LAMMPS.
The file src/library.cpp contains the following functions for creating
and destroying an instance of LAMMPS and sending it commands to
execute. See the documentation in the src/library.cpp file for
details.
NOTE: You can write code for additional functions as needed to define
how your code talks to LAMMPS and add them to src/library.cpp and
src/library.h, as well as to the "Python interface"_Python.html. The
added functions can access or change any internal LAMMPS data you
wish.
void lammps_open(int, char **, MPI_Comm, void **)
void lammps_open_no_mpi(int, char **, void **)
void lammps_close(void *)
int lammps_version(void *)
void lammps_file(void *, char *)
char *lammps_command(void *, char *)
void lammps_commands_list(void *, int, char **)
void lammps_commands_string(void *, char *)
void lammps_free(void *) :pre
The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were "command-line
arguments"_Section_start.html#start_6 when LAMMPS is run in
stand-alone mode from the command line, and a MPI communicator for
LAMMPS to run under. It returns a ptr to the LAMMPS object that is
created, and which is used in subsequent library calls. The
lammps_open() function can be called multiple times, to create
multiple instances of LAMMPS.
LAMMPS will run on the set of processors in the communicator. This
means the calling code can run LAMMPS on all or a subset of
processors. For example, a wrapper script might decide to alternate
between LAMMPS and another code, allowing them both to run on all the
processors. Or it might allocate half the processors to LAMMPS and
half to the other code and run both codes simultaneously before
syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
The lammps_open_no_mpi() function is similar except that no MPI
communicator is passed from the caller. Instead, MPI_COMM_WORLD is
used to instantiate LAMMPS, and MPI is initialized if necessary.
The lammps_close() function is used to shut down an instance of LAMMPS
and free all its memory.
The lammps_version() function can be used to determined the specific
version of the underlying LAMMPS code. This is particularly useful
when loading LAMMPS as a shared library via dlopen(). The code using
the library interface can than use this information to adapt to
changes to the LAMMPS command syntax between versions. The returned
LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
20150902) that grows with every new LAMMPS version.
The lammps_file(), lammps_command(), lammps_commands_list(), and
lammps_commands_string() functions are used to pass one or more
commands to LAMMPS to execute, the same as if they were coming from an
input script.
Via these functions, the calling code can read or generate a series of
LAMMPS commands one or multiple at a time and pass it thru the library
interface to setup a problem and then run it in stages. The caller
can interleave the command function calls with operations it performs,
calls to extract information from or set information within LAMMPS, or
calls to another code's library.
The lammps_file() function passes the filename of an input script.
The lammps_command() function passes a single command as a string.
The lammps_commands_list() function passes multiple commands in a
char** list. In both lammps_command() and lammps_commands_list(),
individual commands may or may not have a trailing newline. The
lammps_commands_string() function passes multiple commands
concatenated into one long string, separated by newline characters.
In both lammps_commands_list() and lammps_commands_string(), a single
command can be spread across multiple lines, if the last printable
character of all but the last line is "&", the same as if the lines
appeared in an input script.
The lammps_free() function is a clean-up function to free memory that
the library allocated previously via other function calls. See
comments in src/library.cpp file for which other functions need this
clean-up.
The file src/library.cpp also contains these functions for extracting
information from LAMMPS and setting value within LAMMPS. Again, see
the documentation in the src/library.cpp file for details, including
which quantities can be queried by name:
int lammps_extract_setting(void *, char *)
void *lammps_extract_global(void *, char *)
void lammps_extract_box(void *, double *, double *,
double *, double *, double *, int *, int *)
void *lammps_extract_atom(void *, char *)
void *lammps_extract_compute(void *, char *, int, int)
void *lammps_extract_fix(void *, char *, int, int, int, int)
void *lammps_extract_variable(void *, char *, char *) :pre
The extract_setting() function returns info on the size
of data types (e.g. 32-bit or 64-bit atom IDs) used
by the LAMMPS executable (a compile-time choice).
The other extract functions return a pointer to various global or
per-atom quantities stored in LAMMPS or to values calculated by a
compute, fix, or variable. The pointer returned by the
extract_global() function can be used as a permanent reference to a
value which may change. For the extract_atom() method, see the
extract() method in the src/atom.cpp file for a list of valid per-atom
properties. New names could easily be added if the property you want
is not listed. For the other extract functions, the underlying
storage may be reallocated as LAMMPS runs, so you need to re-call the
function to assure a current pointer or returned value(s).
double lammps_get_thermo(void *, char *)
int lammps_get_natoms(void *) :pre
int lammps_set_variable(void *, char *, char *)
void lammps_reset_box(void *, double *, double *, double, double, double) :pre
The lammps_get_thermo() function returns the current value of a thermo
keyword as a double precision value.
The lammps_get_natoms() function returns the total number of atoms in
the system and can be used by the caller to allocate memory for the
lammps_gather_atoms() and lammps_scatter_atoms() functions.
The lammps_set_variable() function can set an existing string-style
variable to a new string value, so that subsequent LAMMPS commands can
access the variable.
The lammps_reset_box() function resets the size and shape of the
simulation box, e.g. as part of restoring a previously extracted and
saved state of a simulation.
void lammps_gather_atoms(void *, char *, int, int, void *)
void lammps_gather_atoms_concat(void *, char *, int, int, void *)
void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *)
void lammps_scatter_atoms(void *, char *, int, int, void *)
void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre
void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
imageint *, int) :pre
The gather functions collect peratom info of the requested type (atom
coords, atom types, forces, etc) from all processors, and returns the
same vector of values to each callling processor. The scatter
functions do the inverse. They distribute a vector of peratom values,
passed by all calling processors, to invididual atoms, which may be
owned by different processos.
The lammps_gather_atoms() function does this for all N atoms in the
system, ordered by atom ID, from 1 to N. The
lammps_gather_atoms_concat() function does it for all N atoms, but
simply concatenates the subset of atoms owned by each processor. The
resulting vector is not ordered by atom ID. Atom IDs can be requetsed
by the same function if the caller needs to know the ordering. The
lammps_gather_subset() function allows the caller to request values
for only a subset of atoms (identified by ID).
For all 3 gather function, per-atom image flags can be retrieved in 2 ways.
If the count is specified as 1, they are returned
in a packed format with all three image flags stored in a single integer.
If the count is specified as 3, the values are unpacked into xyz flags
by the library before returning them.
The lammps_scatter_atoms() function takes a list of values for all N
atoms in the system, ordered by atom ID, from 1 to N, and assigns
those values to each atom in the system. The
lammps_scatter_atoms_subset() function takes a subset of IDs as an
argument and only scatters those values to the owning atoms.
The lammps_create_atoms() function takes a list of N atoms as input
with atom types and coords (required), an optionally atom IDs and
velocities and image flags. It uses the coords of each atom to assign
it as a new atom to the processor that owns it. This function is
useful to add atoms to a simulation or (in tandem with
lammps_reset_box()) to restore a previously extracted and saved state
of a simulation. Additional properties for the new atoms can then be
assigned via the lammps_scatter_atoms() or lammps_extract_atom()
functions.

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@ -2,11 +2,11 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:link(lc,Commands_all.html)
:line
Manifolds (surfaces) :h2
Manifolds (surfaces) :h3
[Overview:]

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"Higher level section"_Howto.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
Run multiple simulations from one input script :h3
This can be done in several ways. See the documentation for
individual commands for more details on how these examples work.
If "multiple simulations" means continue a previous simulation for
more timesteps, then you simply use the "run"_run.html command
multiple times. For example, this script
units lj
atom_style atomic
read_data data.lj
run 10000
run 10000
run 10000
run 10000
run 10000 :pre
would run 5 successive simulations of the same system for a total of
50,000 timesteps.
If you wish to run totally different simulations, one after the other,
the "clear"_clear.html command can be used in between them to
re-initialize LAMMPS. For example, this script
units lj
atom_style atomic
read_data data.lj
run 10000
clear
units lj
atom_style atomic
read_data data.lj.new
run 10000 :pre
would run 2 independent simulations, one after the other.
For large numbers of independent simulations, you can use
"variables"_variable.html and the "next"_next.html and
"jump"_jump.html commands to loop over the same input script
multiple times with different settings. For example, this
script, named in.polymer
variable d index run1 run2 run3 run4 run5 run6 run7 run8
shell cd $d
read_data data.polymer
run 10000
shell cd ..
clear
next d
jump in.polymer :pre
would run 8 simulations in different directories, using a data.polymer
file in each directory. The same concept could be used to run the
same system at 8 different temperatures, using a temperature variable
and storing the output in different log and dump files, for example
variable a loop 8
variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
log log.$a
read data.polymer
velocity all create $t 352839
fix 1 all nvt $t $t 100.0
dump 1 all atom 1000 dump.$a
run 100000
clear
next t
next a
jump in.polymer :pre
All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
the "-partition" command-line switch as described in "this
section"_Section_start.html#start_6 of the manual.
In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were
replaced with {universe}-style variables, as described in the
"variable"_variable.html command. Also, the "next t" and "next a"
commands would need to be replaced with a single "next a t" command.
With these modifications, the 8 simulations of each script would run
on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each
partition. When one finished, that partition would then start
the 4th simulation, and so forth, until all 8 were completed.

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"Higher level section"_Howto.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
NEMD simulations :h3
Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceding Howto section).
A shear strain can be applied to the simulation box at a desired
strain rate by using the "fix deform"_fix_deform.html command. The
"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat
the sheared fluid and integrate the SLLOD equations of motion for the
system. Fix nvt/sllod uses "compute
temp/deform"_compute_temp_deform.html to compute a thermal temperature
by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the "fix ave/chunk"_fix_ave_chunk.html command.
As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computational efficiency to be 1/2 of the parallel box
length. However, "fix deform"_fix_deform.html can continuously strain
a box by an arbitrary amount. As discussed in the "fix
deform"_fix_deform.html command, when the tilt value reaches a limit,
the box is flipped to the opposite limit which is an equivalent tiling
of periodic space. The strain rate can then continue to change as
before. In a long NEMD simulation these box re-shaping events may
occur many times.
In a NEMD simulation, the "remap" option of "fix
deform"_fix_deform.html should be set to "remap v", since that is what
"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity
profile consistent with the applied shear strain rate.
An alternative method for calculating viscosities is provided via the
"fix viscosity"_fix_viscosity.html command.
NEMD simulations can also be used to measure transport properties of a fluid
through a pore or channel. Simulations of steady-state flow can be performed
using the "fix flow/gauss"_fix_flow_gauss.html command.

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"Higher level section"_Howto.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
Output from LAMMPS (thermo, dumps, computes, fixes, variables) :h3
There are four basic kinds of LAMMPS output:
"Thermodynamic output"_thermo_style.html, which is a list
of quantities printed every few timesteps to the screen and logfile. :ulb,l
"Dump files"_dump.html, which contain snapshots of atoms and various
per-atom values and are written at a specified frequency. :l
Certain fixes can output user-specified quantities to files: "fix
ave/time"_fix_ave_time.html for time averaging, "fix
ave/chunk"_fix_ave_chunk.html for spatial or other averaging, and "fix
print"_fix_print.html for single-line output of
"variables"_variable.html. Fix print can also output to the
screen. :l
"Restart files"_restart.html. :l
:ule
A simulation prints one set of thermodynamic output and (optionally)
restart files. It can generate any number of dump files and fix
output files, depending on what "dump"_dump.html and "fix"_fix.html
commands you specify.
As discussed below, LAMMPS gives you a variety of ways to determine
what quantities are computed and printed when the thermodynamics,
dump, or fix commands listed above perform output. Throughout this
discussion, note that users can also "add their own computes and fixes
to LAMMPS"_Modify.html which can then generate values that can then be
output with these commands.
The following sub-sections discuss different LAMMPS command related
to output and the kind of data they operate on and produce:
"Global/per-atom/local data"_#global
"Scalar/vector/array data"_#scalar
"Thermodynamic output"_#thermo
"Dump file output"_#dump
"Fixes that write output files"_#fixoutput
"Computes that process output quantities"_#computeoutput
"Fixes that process output quantities"_#fixprocoutput
"Computes that generate values to output"_#compute
"Fixes that generate values to output"_#fix
"Variables that generate values to output"_#variable
"Summary table of output options and data flow between commands"_#table :ul
Global/per-atom/local data :h4,link(global)
Various output-related commands work with three different styles of
data: global, per-atom, or local. A global datum is one or more
system-wide values, e.g. the temperature of the system. A per-atom
datum is one or more values per atom, e.g. the kinetic energy of each
atom. Local datums are calculated by each processor based on the
atoms it owns, but there may be zero or more per atom, e.g. a list of
bond distances.
Scalar/vector/array data :h4,link(scalar)
Global, per-atom, and local datums can each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
doc page for a "compute" or "fix" or "variable" that generates data
will specify both the style and kind of data it produces, e.g. a
per-atom vector.
When a quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket
notation, where ID in this case is the ID of a compute. The leading
"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
c_ID | entire scalar, vector, or array
c_ID\[I\] | one element of vector, one column of array
c_ID\[I\]\[J\] | one element of array :tb(s=|)
In other words, using one bracket reduces the dimension of the data
once (vector -> scalar, array -> vector). Using two brackets reduces
the dimension twice (array -> scalar). Thus a command that uses
scalar values as input can typically also process elements of a vector
or array.
Thermodynamic output :h4,link(thermo)
The frequency and format of thermodynamic output is set by the
"thermo"_thermo.html, "thermo_style"_thermo_style.html, and
"thermo_modify"_thermo_modify.html commands. The
"thermo_style"_thermo_style.html command also specifies what values
are calculated and written out. Pre-defined keywords can be specified
(e.g. press, etotal, etc). Three additional kinds of keywords can
also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html
or "fix"_fix.html or "variable"_variable.html provides the value to be
output. In each case, the compute, fix, or variable must generate
global values for input to the "thermo_style custom"_dump.html
command.
Note that thermodynamic output values can be "extensive" or
"intensive". The former scale with the number of atoms in the system
(e.g. total energy), the latter do not (e.g. temperature). The
setting for "thermo_modify norm"_thermo_modify.html determines whether
extensive quantities are normalized or not. Computes and fixes
produce either extensive or intensive values; see their individual doc
pages for details. "Equal-style variables"_variable.html produce only
intensive values; you can include a division by "natoms" in the
formula if desired, to make an extensive calculation produce an
intensive result.
Dump file output :h4,link(dump)
Dump file output is specified by the "dump"_dump.html and
"dump_modify"_dump_modify.html commands. There are several
pre-defined formats (dump atom, dump xtc, etc).
There is also a "dump custom"_dump.html format where the user
specifies what values are output with each atom. Pre-defined atom
attributes can be specified (id, x, fx, etc). Three additional kinds
of keywords can also be specified (c_ID, f_ID, v_name), where a
"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
provides the values to be output. In each case, the compute, fix, or
variable must generate per-atom values for input to the "dump
custom"_dump.html command.
There is also a "dump local"_dump.html format where the user specifies
what local values to output. A pre-defined index keyword can be
specified to enumerate the local values. Two additional kinds of
keywords can also be specified (c_ID, f_ID), where a
"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
provides the values to be output. In each case, the compute or fix
must generate local values for input to the "dump local"_dump.html
command.
Fixes that write output files :h4,link(fixoutput)
Several fixes take various quantities as input and can write output
files: "fix ave/time"_fix_ave_time.html, "fix
ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html,
"fix ave/correlate"_fix_ave_correlate.html, and "fix
print"_fix_print.html.
The "fix ave/time"_fix_ave_time.html command enables direct output to
a file and/or time-averaging of global scalars or vectors. The user
specifies one or more quantities as input. These can be global
"compute"_compute.html values, global "fix"_fix.html values, or
"variables"_variable.html of any style except the atom style which
produces per-atom values. Since a variable can refer to keywords used
by the "thermo_style custom"_thermo_style.html command (like temp or
press) and individual per-atom values, a wide variety of quantities
can be time averaged and/or output in this way. If the inputs are one
or more scalar values, then the fix generate a global scalar or vector
of output. If the inputs are one or more vector values, then the fix
generates a global vector or array of output. The time-averaged
output of this fix can also be used as input to other output commands.
The "fix ave/chunk"_fix_ave_chunk.html command enables direct output
to a file of chunk-averaged per-atom quantities like those output in
dump files. Chunks can represent spatial bins or other collections of
atoms, e.g. individual molecules. The per-atom quantities can be atom
density (mass or number) or atom attributes such as position,
velocity, force. They can also be per-atom quantities calculated by a
"compute"_compute.html, by a "fix"_fix.html, or by an atom-style
"variable"_variable.html. The chunk-averaged output of this fix can
also be used as input to other output commands.
The "fix ave/histo"_fix_ave_histo.html command enables direct output
to a file of histogrammed quantities, which can be global or per-atom
or local quantities. The histogram output of this fix can also be
used as input to other output commands.
The "fix ave/correlate"_fix_ave_correlate.html command enables direct
output to a file of time-correlated quantities, which can be global
values. The correlation matrix output of this fix can also be used as
input to other output commands.
The "fix print"_fix_print.html command can generate a line of output
written to the screen and log file or to a separate file, periodically
during a running simulation. The line can contain one or more
"variable"_variable.html values for any style variable except the
vector or atom styles). As explained above, variables themselves can
contain references to global values generated by "thermodynamic
keywords"_thermo_style.html, "computes"_compute.html,
"fixes"_fix.html, or other "variables"_variable.html, or to per-atom
values for a specific atom. Thus the "fix print"_fix_print.html
command is a means to output a wide variety of quantities separate
from normal thermodynamic or dump file output.
Computes that process output quantities :h4,link(computeoutput)
The "compute reduce"_compute_reduce.html and "compute
reduce/region"_compute_reduce.html commands take one or more per-atom
or local vector quantities as inputs and "reduce" them (sum, min, max,
ave) to scalar quantities. These are produced as output values which
can be used as input to other output commands.
The "compute slice"_compute_slice.html command take one or more global
vector or array quantities as inputs and extracts a subset of their
values to create a new vector or array. These are produced as output
values which can be used as input to other output commands.
The "compute property/atom"_compute_property_atom.html command takes a
list of one or more pre-defined atom attributes (id, x, fx, etc) and
stores the values in a per-atom vector or array. These are produced
as output values which can be used as input to other output commands.
The list of atom attributes is the same as for the "dump
custom"_dump.html command.
The "compute property/local"_compute_property_local.html command takes
a list of one or more pre-defined local attributes (bond info, angle
info, etc) and stores the values in a local vector or array. These
are produced as output values which can be used as input to other
output commands.
Fixes that process output quantities :h4,link(fixprocoutput)
The "fix vector"_fix_vector.html command can create global vectors as
output from global scalars as input, accumulating them one element at
a time.
The "fix ave/atom"_fix_ave_atom.html command performs time-averaging
of per-atom vectors. The per-atom quantities can be atom attributes
such as position, velocity, force. They can also be per-atom
quantities calculated by a "compute"_compute.html, by a
"fix"_fix.html, or by an atom-style "variable"_variable.html. The
time-averaged per-atom output of this fix can be used as input to
other output commands.
The "fix store/state"_fix_store_state.html command can archive one or
more per-atom attributes at a particular time, so that the old values
can be used in a future calculation or output. The list of atom
attributes is the same as for the "dump custom"_dump.html command,
including per-atom quantities calculated by a "compute"_compute.html,
by a "fix"_fix.html, or by an atom-style "variable"_variable.html.
The output of this fix can be used as input to other output commands.
Computes that generate values to output :h4,link(compute)
Every "compute"_compute.html in LAMMPS produces either global or
per-atom or local values. The values can be scalars or vectors or
arrays of data. These values can be output using the other commands
described in this section. The doc page for each compute command
describes what it produces. Computes that produce per-atom or local
values have the word "atom" or "local" in their style name. Computes
without the word "atom" or "local" produce global values.
Fixes that generate values to output :h4,link(fix)
Some "fixes"_fix.html in LAMMPS produces either global or per-atom or
local values which can be accessed by other commands. The values can
be scalars or vectors or arrays of data. These values can be output
using the other commands described in this section. The doc page for
each fix command tells whether it produces any output quantities and
describes them.
Variables that generate values to output :h4,link(variable)
"Variables"_variable.html defined in an input script can store one or
more strings. But equal-style, vector-style, and atom-style or
atomfile-style variables generate a global scalar value, global vector
or values, or a per-atom vector, respectively, when accessed. The
formulas used to define these variables can contain references to the
thermodynamic keywords and to global and per-atom data generated by
computes, fixes, and other variables. The values generated by
variables can be used as input to and thus output by the other
commands described in this section.
Summary table of output options and data flow between commands :h4,link(table)
This table summarizes the various commands that can be used for
generating output from LAMMPS. Each command produces output data of
some kind and/or writes data to a file. Most of the commands can take
data from other commands as input. Thus you can link many of these
commands together in pipeline form, where data produced by one command
is used as input to another command and eventually written to the
screen or to a file. Note that to hook two commands together the
output and input data types must match, e.g. global/per-atom/local
data and scalar/vector/array data.
Also note that, as described above, when a command takes a scalar as
input, that could be an element of a vector or array. Likewise a
vector input could be a column of an array.
Command: Input: Output:
"thermo_style custom"_thermo_style.html: global scalars: screen, log file:
"dump custom"_dump.html: per-atom vectors: dump file:
"dump local"_dump.html: local vectors: dump file:
"fix print"_fix_print.html: global scalar from variable: screen, file:
"print"_print.html: global scalar from variable: screen:
"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array:
"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array:
"variables"_variable.html: global scalars and vectors, per-atom vectors: global scalar and vector, per-atom vector:
"compute reduce"_compute_reduce.html: per-atom/local vectors: global scalar/vector:
"compute slice"_compute_slice.html: global vectors/arrays: global vector/array:
"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array:
"compute property/local"_compute_property_local.html: local vectors: local vector/array:
"fix vector"_fix_vector.html: global scalars: global vector:
"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array:
"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file:
"fix ave/chunk"_fix_ave_chunk.html: per-atom vectors: global array, file:
"fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file:
"fix ave/correlate"_fix_ave_correlate.html: global scalars: global array, file:
"fix store/state"_fix_store_state.html: per-atom vectors: per-atom vector/array :tb(c=3,s=:)

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"Higher level section"_Howto.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
Polarizable models :h3
In polarizable force fields the charge distributions in molecules and
materials respond to their electrostatic environments. Polarizable
systems can be simulated in LAMMPS using three methods:
the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html
package, :ulb,l
the adiabatic core-shell method, implemented in the
"CORESHELL"_Howto_coreshell.html package, :l
the thermalized Drude dipole method, implemented in the
"USER-DRUDE"_Howto_drude.html package. :l,ule
The fluctuating charge method calculates instantaneous charges on
interacting atoms based on the electronegativity equalization
principle. It is implemented in the "fix qeq"_fix_qeq.html which is
available in several variants. It is a relatively efficient technique
since no additional particles are introduced. This method allows for
charge transfer between molecules or atom groups. However, because the
charges are located at the interaction sites, off-plane components of
polarization cannot be represented in planar molecules or atom groups.
The two other methods share the same basic idea: polarizable atoms are
split into one core atom and one satellite particle (called shell or
Drude particle) attached to it by a harmonic spring. Both atoms bear
a charge and they represent collectively an induced electric dipole.
These techniques are computationally more expensive than the QEq
method because of additional particles and bonds. These two
charge-on-spring methods differ in certain features, with the
core-shell model being normally used for ionic/crystalline materials,
whereas the so-called Drude model is normally used for molecular
systems and fluid states.
The core-shell model is applicable to crystalline materials where the
high symmetry around each site leads to stable trajectories of the
core-shell pairs. However, bonded atoms in molecules can be so close
that a core would interact too strongly or even capture the Drude
particle of a neighbor. The Drude dipole model is relatively more
complex in order to remediate this and other issues. Specifically, the
Drude model includes specific thermostating of the core-Drude pairs
and short-range damping of the induced dipoles.
The three polarization methods can be implemented through a
self-consistent calculation of charges or induced dipoles at each
timestep. In the fluctuating charge scheme this is done by the matrix
inversion method in "fix qeq/point"_fix_qeq.html, but for core-shell
or Drude-dipoles the relaxed-dipoles technique would require an slow
iterative procedure. These self-consistent solutions yield accurate
trajectories since the additional degrees of freedom representing
polarization are massless. An alternative is to attribute a mass to
the additional degrees of freedom and perform time integration using
an extended Lagrangian technique. For the fluctuating charge scheme
this is done by "fix qeq/dynamic"_fix_qeq.html, and for the
charge-on-spring models by the methods outlined in the next two
sections. The assignment of masses to the additional degrees of
freedom can lead to unphysical trajectories if care is not exerted in
choosing the parameters of the polarizable models and the simulation
conditions.
In the core-shell model the vibration of the shells is kept faster
than the ionic vibrations to mimic the fast response of the
polarizable electrons. But in molecular systems thermalizing the
core-Drude pairs at temperatures comparable to the rest of the
simulation leads to several problems (kinetic energy transfer, too
short a timestep, etc.) In order to avoid these problems the relative
motion of the Drude particles with respect to their cores is kept
"cold" so the vibration of the core-Drude pairs is very slow,
approaching the self-consistent regime. In both models the
temperature is regulated using the velocities of the center of mass of
core+shell (or Drude) pairs, but in the Drude model the actual
relative core-Drude particle motion is thermostated separately as
well.

23
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@ -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
@ -15,13 +15,19 @@ END_RST -->
Overview :h4
PyLammps is a Python wrapper class which can be created on its own or use an
existing lammps Python object. It creates a simpler, Python-like interface to
common LAMMPS functionality. Unlike the original flat C-types interface, it
exposes a discoverable API. It no longer requires knowledge of the underlying
C++ code implementation. Finally, the IPyLammps wrapper builds on top of
PyLammps and adds some additional features for IPython integration into IPython
notebooks, e.g. for embedded visualization output from dump/image.
PyLammps is a Python wrapper class which can be created on its own or
use an existing lammps Python object. It creates a simpler,
Python-like interface to common LAMMPS functionality, in contrast to
the lammps.py wrapper on the C-style LAMMPS library interface which is
written using Python ctypes. The lammps.py wrapper is discussed on
the "Python library"_Python_library.html doc page.
Unlike the flat ctypes interface, PyLammps exposes a discoverable API.
It no longer requires knowledge of the underlying C++ code
implementation. Finally, the IPyLammps wrapper builds on top of
PyLammps and adds some additional features for IPython integration
into IPython notebooks, e.g. for embedded visualization output from
dump/image.
Comparison of lammps and PyLammps interfaces :h5
@ -40,7 +46,6 @@ communication with LAMMPS is hidden from API user
shorter, more concise Python
better IPython integration, designed for quick prototyping :ul
Quick Start :h4
System-wide Installation :h5

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"Higher level section"_Howto.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
Multi-replica simulations :h3
Several commands in LAMMPS run mutli-replica simulations, meaning
that multiple instances (replicas) of your simulation are run
simultaneously, with small amounts of data exchanged between replicas
periodically.
These are the relevant commands:
"neb"_neb.html for nudged elastic band calculations
"prd"_prd.html for parallel replica dynamics
"tad"_tad.html for temperature accelerated dynamics
"temper"_temper.html for parallel tempering
"fix pimd"_fix_pimd.html for path-integral molecular dynamics (PIMD) :ul
NEB is a method for finding transition states and barrier energies.
PRD and TAD are methods for performing accelerated dynamics to find
and perform infrequent events. Parallel tempering or replica exchange
runs different replicas at a series of temperature to facilitate
rare-event sampling.
These commands can only be used if LAMMPS was built with the REPLICA
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
PIMD runs different replicas whose individual particles are coupled
together by springs to model a system or ring-polymers.
This commands can only be used if LAMMPS was built with the USER-MISC
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the "-partition command-line
switch"_Section_start.html#start_6 to launch LAMMPS on multiple
partitions, which in this context are the same as replicas. E.g.
these commands:
mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
would each run 8 replicas, on either 16 or 8 processors. Note the use
of the "-in command-line switch"_Section_start.html#start_6 to specify
the input script which is required when running in multi-replica mode.
Also note that with MPI installed on a machine (e.g. your desktop),
you can run on more (virtual) processors than you have physical
processors. Thus the above commands could be run on a
single-processor (or few-processor) desktop so that you can run
a multi-replica simulation on more replicas than you have
physical processors.

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"Higher level section"_Howto.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
Restart a simulation :h3
There are 3 ways to continue a long LAMMPS simulation. Multiple
"run"_run.html commands can be used in the same input script. Each
run will continue from where the previous run left off. Or binary
restart files can be saved to disk using the "restart"_restart.html
command. At a later time, these binary files can be read via a
"read_restart"_read_restart.html command in a new script. Or they can
be converted to text data files using the "-r command-line
switch"_Section_start.html#start_6 and read by a
"read_data"_read_data.html command in a new script.
Here we give examples of 2 scripts that read either a binary restart
file or a converted data file and then issue a new run command to
continue where the previous run left off. They illustrate what
settings must be made in the new script. Details are discussed in the
documentation for the "read_restart"_read_restart.html and
"read_data"_read_data.html commands.
Look at the {in.chain} input script provided in the {bench} directory
of the LAMMPS distribution to see the original script that these 2
scripts are based on. If that script had the line
restart 50 tmp.restart :pre
added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran.
This script could be used to read the 1st restart file and re-run the
last 50 timesteps:
read_restart tmp.restart.50 :pre
neighbor 0.4 bin
neigh_modify every 1 delay 1 :pre
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
timestep 0.012 :pre
run 50 :pre
Note that the following commands do not need to be repeated because
their settings are included in the restart file: {units, atom_style,
special_bonds, pair_style, bond_style}. However these commands do
need to be used, since their settings are not in the restart file:
{neighbor, fix, timestep}.
If you actually use this script to perform a restarted run, you will
notice that the thermodynamic data match at step 50 (if you also put a
"thermo 50" command in the original script), but do not match at step
100. This is because the "fix langevin"_fix_langevin.html command
uses random numbers in a way that does not allow for perfect restarts.
As an alternate approach, the restart file could be converted to a data
file as follows:
lmp_g++ -r tmp.restart.50 tmp.restart.data :pre
Then, this script could be used to re-run the last 50 steps:
units lj
atom_style bond
pair_style lj/cut 1.12
pair_modify shift yes
bond_style fene
special_bonds 0.0 1.0 1.0 :pre
read_data tmp.restart.data :pre
neighbor 0.4 bin
neigh_modify every 1 delay 1 :pre
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
timestep 0.012 :pre
reset_timestep 50
run 50 :pre
Note that nearly all the settings specified in the original {in.chain}
script must be repeated, except the {pair_coeff} and {bond_coeff}
commands since the new data file lists the force field coefficients.
Also, the "reset_timestep"_reset_timestep.html command is used to tell
LAMMPS the current timestep. This value is stored in restart files,
but not in data files.

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"Higher level section"_Howto.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
SPC water model :h3
The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
{harmonic} and an angle style of {harmonic} or {charmm} should also be
used.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid SPC model.
O mass = 15.9994
H mass = 1.008
O charge = -0.820
H charge = 0.410
LJ epsilon of OO = 0.1553
LJ sigma of OO = 3.166
LJ epsilon, sigma of OH, HH = 0.0
r0 of OH bond = 1.0
theta of HOH angle = 109.47 :all(b),p
Note that as originally proposed, the SPC model was run with a 9
Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
any of the parameters above, though it becomes a different model in
that mode of usage.
The SPC/E (extended) water model is the same, except
the partial charge assignments change:
O charge = -0.8476
H charge = 0.4238 :all(b),p
See the "(Berendsen)"_#howto-Berendsen reference for more details on both
the SPC and SPC/E models.
Wikipedia also has a nice article on "water
models"_http://en.wikipedia.org/wiki/Water_model.
:line
:link(howto-Berendsen)
[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987).

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@ -0,0 +1,243 @@
"Higher level section"_Howto.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
Finite-size spherical and aspherical particles :h3
Typical MD models treat atoms or particles as point masses. Sometimes
it is desirable to have a model with finite-size particles such as
spheroids or ellipsoids or generalized aspherical bodies. The
difference is that such particles have a moment of inertia, rotational
energy, and angular momentum. Rotation is induced by torque coming
from interactions with other particles.
LAMMPS has several options for running simulations with these kinds of
particles. The following aspects are discussed in turn:
atom styles
pair potentials
time integration
computes, thermodynamics, and dump output
rigid bodies composed of finite-size particles :ul
Example input scripts for these kinds of models are in the body,
colloid, dipole, ellipse, line, peri, pour, and tri directories of the
"examples directory"_Examples.html in the LAMMPS distribution.
Atom styles :h4
There are several "atom styles"_atom_style.html that allow for
definition of finite-size particles: sphere, dipole, ellipsoid, line,
tri, peri, and body.
The sphere style defines particles that are spheriods and each
particle can have a unique diameter and mass (or density). These
particles store an angular velocity (omega) and can be acted upon by
torque. The "set" command can be used to modify the diameter and mass
of individual particles, after then are created.
The dipole style does not actually define finite-size particles, but
is often used in conjunction with spherical particles, via a command
like
atom_style hybrid sphere dipole :pre
This is because when dipoles interact with each other, they induce
torques, and a particle must be finite-size (i.e. have a moment of
inertia) in order to respond and rotate. See the "atom_style
dipole"_atom_style.html command for details. The "set" command can be
used to modify the orientation and length of the dipole moment of
individual particles, after then are created.
The ellipsoid style defines particles that are ellipsoids and thus can
be aspherical. Each particle has a shape, specified by 3 diameters,
and mass (or density). These particles store an angular momentum and
their orientation (quaternion), and can be acted upon by torque. They
do not store an angular velocity (omega), which can be in a different
direction than angular momentum, rather they compute it as needed.
The "set" command can be used to modify the diameter, orientation, and
mass of individual particles, after then are created. It also has a
brief explanation of what quaternions are.
The line style defines line segment particles with two end points and
a mass (or density). They can be used in 2d simulations, and they can
be joined together to form rigid bodies which represent arbitrary
polygons.
The tri style defines triangular particles with three corner points
and a mass (or density). They can be used in 3d simulations, and they
can be joined together to form rigid bodies which represent arbitrary
particles with a triangulated surface.
The peri style is used with "Peridynamic models"_pair_peri.html and
defines particles as having a volume, that is used internally in the
"pair_style peri"_pair_peri.html potentials.
The body style allows for definition of particles which can represent
complex entities, such as surface meshes of discrete points,
collections of sub-particles, deformable objects, etc. The body style
is discussed in more detail on the "Howto body"_Howto_body.html doc
page.
Note that if one of these atom styles is used (or multiple styles via
the "atom_style hybrid"_atom_style.html command), not all particles in
the system are required to be finite-size or aspherical.
For example, in the ellipsoid style, if the 3 shape parameters are set
to the same value, the particle will be a sphere rather than an
ellipsoid. If the 3 shape parameters are all set to 0.0 or if the
diameter is set to 0.0, it will be a point particle. In the line or
tri style, if the lineflag or triflag is specified as 0, then it
will be a point particle.
Some of the pair styles used to compute pairwise interactions between
finite-size particles also compute the correct interaction with point
particles as well, e.g. the interaction between a point particle and a
finite-size particle or between two point particles. If necessary,
"pair_style hybrid"_pair_hybrid.html can be used to insure the correct
interactions are computed for the appropriate style of interactions.
Likewise, using groups to partition particles (ellipsoids versus
spheres versus point particles) will allow you to use the appropriate
time integrators and temperature computations for each class of
particles. See the doc pages for various commands for details.
Also note that for "2d simulations"_dimension.html, atom styles sphere
and ellipsoid still use 3d particles, rather than as circular disks or
ellipses. This means they have the same moment of inertia as the 3d
object. When temperature is computed, the correct degrees of freedom
are used for rotation in a 2d versus 3d system.
Pair potentials :h4
When a system with finite-size particles is defined, the particles
will only rotate and experience torque if the force field computes
such interactions. These are the various "pair
styles"_pair_style.html that generate torque:
"pair_style gran/history"_pair_gran.html
"pair_style gran/hertzian"_pair_gran.html
"pair_style gran/no_history"_pair_gran.html
"pair_style dipole/cut"_pair_dipole.html
"pair_style gayberne"_pair_gayberne.html
"pair_style resquared"_pair_resquared.html
"pair_style brownian"_pair_brownian.html
"pair_style lubricate"_pair_lubricate.html
"pair_style line/lj"_pair_line_lj.html
"pair_style tri/lj"_pair_tri_lj.html
"pair_style body/nparticle"_pair_body_nparticle.html :ul
The granular pair styles are used with spherical particles. The
dipole pair style is used with the dipole atom style, which could be
applied to spherical or ellipsoidal particles. The GayBerne and
REsquared potentials require ellipsoidal particles, though they will
also work if the 3 shape parameters are the same (a sphere). The
Brownian and lubrication potentials are used with spherical particles.
The line, tri, and body potentials are used with line segment,
triangular, and body particles respectively.
Time integration :h4
There are several fixes that perform time integration on finite-size
spherical particles, meaning the integrators update the rotational
orientation and angular velocity or angular momentum of the particles:
"fix nve/sphere"_fix_nve_sphere.html
"fix nvt/sphere"_fix_nvt_sphere.html
"fix npt/sphere"_fix_npt_sphere.html :ul
Likewise, there are 3 fixes that perform time integration on
ellipsoidal particles:
"fix nve/asphere"_fix_nve_asphere.html
"fix nvt/asphere"_fix_nvt_asphere.html
"fix npt/asphere"_fix_npt_asphere.html :ul
The advantage of these fixes is that those which thermostat the
particles include the rotational degrees of freedom in the temperature
calculation and thermostatting. The "fix langevin"_fix_langevin
command can also be used with its {omgea} or {angmom} options to
thermostat the rotational degrees of freedom for spherical or
ellipsoidal particles. Other thermostatting fixes only operate on the
translational kinetic energy of finite-size particles.
These fixes perform constant NVE time integration on line segment,
triangular, and body particles:
"fix nve/line"_fix_nve_line.html
"fix nve/tri"_fix_nve_tri.html
"fix nve/body"_fix_nve_body.html :ul
Note that for mixtures of point and finite-size particles, these
integration fixes can only be used with "groups"_group.html which
contain finite-size particles.
Computes, thermodynamics, and dump output :h4
There are several computes that calculate the temperature or
rotational energy of spherical or ellipsoidal particles:
"compute temp/sphere"_compute_temp_sphere.html
"compute temp/asphere"_compute_temp_asphere.html
"compute erotate/sphere"_compute_erotate_sphere.html
"compute erotate/asphere"_compute_erotate_asphere.html :ul
These include rotational degrees of freedom in their computation. If
you wish the thermodynamic output of temperature or pressure to use
one of these computes (e.g. for a system entirely composed of
finite-size particles), then the compute can be defined and the
"thermo_modify"_thermo_modify.html command used. Note that by default
thermodynamic quantities will be calculated with a temperature that
only includes translational degrees of freedom. See the
"thermo_style"_thermo_style.html command for details.
These commands can be used to output various attributes of finite-size
particles:
"dump custom"_dump.html
"compute property/atom"_compute_property_atom.html
"dump local"_dump.html
"compute body/local"_compute_body_local.html :ul
Attributes include the dipole moment, the angular velocity, the
angular momentum, the quaternion, the torque, the end-point and
corner-point coordinates (for line and tri particles), and
sub-particle attributes of body particles.
Rigid bodies composed of finite-size particles :h4
The "fix rigid"_fix_rigid.html command treats a collection of
particles as a rigid body, computes its inertia tensor, sums the total
force and torque on the rigid body each timestep due to forces on its
constituent particles, and integrates the motion of the rigid body.
If any of the constituent particles of a rigid body are finite-size
particles (spheres or ellipsoids or line segments or triangles), then
their contribution to the inertia tensor of the body is different than
if they were point particles. This means the rotational dynamics of
the rigid body will be different. Thus a model of a dimer is
different if the dimer consists of two point masses versus two
spheroids, even if the two particles have the same mass. Finite-size
particles that experience torque due to their interaction with other
particles will also impart that torque to a rigid body they are part
of.
See the "fix rigid" command for example of complex rigid-body models
it is possible to define in LAMMPS.
Note that the "fix shake"_fix_shake.html command can also be used to
treat 2, 3, or 4 particles as a rigid body, but it always assumes the
particles are point masses.
Also note that body particles cannot be modeled with the "fix
rigid"_fix_rigid.html command. Body particles are treated by LAMMPS
as single particles, though they can store internal state, such as a
list of sub-particles. Individual body partices are typically treated
as rigid bodies, and their motion integrated with a command like "fix
nve/body"_fix_nve_body.html. Interactions between pairs of body
particles are computed via a command like "pair_style
body/nparticle"_pair_body_nparticle.html.

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"Higher level section"_Howto.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
Magnetic spins :h3
The magnetic spin simualtions are enabled by the SPIN package, whose
implementation is detailed in "Tranchida"_#Tranchida7.
The model representents the simulation of atomic magnetic spins coupled
to lattice vibrations. The dynamics of those magnetic spins can be used
to simulate a broad range a phenomena related to magneto-elasticity, or
or to study the influence of defects on the magnetic properties of
materials.
The magnetic spins are interacting with each others and with the
lattice via pair interactions. Typically, the magnetic exchange
interaction can be defined using the
"pair/spin/exchange"_pair_spin_exchange.html command. This exchange
applies a magnetic torque to a given spin, considering the orientation
of its neighboring spins and their relative distances.
It also applies a force on the atoms as a function of the spin
orientations and their associated inter-atomic distances.
The command "fix precession/spin"_fix_precession_spin.html allows to
apply a constant magnetic torque on all the spins in the system. This
torque can be an external magnetic field (Zeeman interaction), or an
uniaxial magnetic anisotropy.
A Langevin thermostat can be applied to those magnetic spins using
"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
can be coupled to another Langevin thermostat applied to the atoms
using "fix langevin"_fix_langevin.html in order to simulate
thermostated spin-lattice system.
The magnetic Gilbert damping can also be applied using "fix
langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
the thermal energy of the Langevin thermostat, or to perform a
relaxation of the magnetic configuration toward an equilibrium state.
All the computed magnetic properties can be outputed by two main
commands. The first one is "compute spin"_compute_spin.html, that
enables to evaluate magnetic averaged quantities, such as the total
magnetization of the system along x, y, or z, the spin temperature, or
the magnetic energy. The second command is "compute
property/atom"_compute_property_atom.html. It enables to output all the
per atom magnetic quantities. Typically, the orientation of a given
magnetic spin, or the magnetic force acting on this spin.
:line
:link(Tranchida7)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
arXiv preprint arXiv:1801.10233, (2018).

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"Higher level section"_Howto.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
Calcalate temperature :h3
Temperature is computed as kinetic energy divided by some number of
degrees of freedom (and the Boltzmann constant). Since kinetic energy
is a function of particle velocity, there is often a need to
distinguish between a particle's advection velocity (due to some
aggregate motion of particles) and its thermal velocity. The sum of
the two is the particle's total velocity, but the latter is often what
is wanted to compute a temperature.
LAMMPS has several options for computing temperatures, any of which can be used in "thermostatting"_Howto_thermostat.html and "barostatting"_Howto_barostat.html. These "compute commands"_compute.html calculate temperature:
"compute temp"_compute_temp.html
"compute temp/sphere"_compute_temp_sphere.html
"compute temp/asphere"_compute_temp_asphere.html
"compute temp/com"_compute_temp_com.html
"compute temp/deform"_compute_temp_deform.html
"compute temp/partial"_compute_temp_partial.html
"compute temp/profile"_compute_temp_profile.html
"compute temp/ramp"_compute_temp_ramp.html
"compute temp/region"_compute_temp_region.html :ul
All but the first 3 calculate velocity biases directly (e.g. advection
velocities) that are removed when computing the thermal temperature.
"Compute temp/sphere"_compute_temp_sphere.html and "compute
temp/asphere"_compute_temp_asphere.html compute kinetic energy for
finite-size particles that includes rotational degrees of freedom.
They both allow for velocity biases indirectly, via an optional extra
argument which is another temperature compute that subtracts a velocity bias.
This allows the translational velocity of spherical or aspherical
particles to be adjusted in prescribed ways.

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"Higher level section"_Howto.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
Thermostats :h3
Thermostatting means controlling the temperature of particles in an MD
simulation. "Barostatting"_Howto_barostat.html means controlling the
pressure. Since the pressure includes a kinetic component due to
particle velocities, both these operations require calculation of the
temperature. Typically a target temperature (T) and/or pressure (P)
is specified by the user, and the thermostat or barostat attempts to
equilibrate the system to the requested T and/or P.
Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one
case by a pair style. Several thermostatting fixes are available:
Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
(temp/rescale). Dissipative particle dynamics (DPD) thermostatting
can be invoked via the {dpd/tstat} pair style:
"fix nvt"_fix_nh.html
"fix nvt/sphere"_fix_nvt_sphere.html
"fix nvt/asphere"_fix_nvt_asphere.html
"fix nvt/sllod"_fix_nvt_sllod.html
"fix temp/berendsen"_fix_temp_berendsen.html
"fix temp/csvr"_fix_temp_csvr.html
"fix langevin"_fix_langevin.html
"fix temp/rescale"_fix_temp_rescale.html
"pair_style dpd/tstat"_pair_dpd.html :ul
"Fix nvt"_fix_nh.html only thermostats the translational velocity of
particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the "Howto
nemd"_Howto_nemd.html doc page for further details. "Fix
nvt/sphere"_fix_nvt_sphere.html and "fix
nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
DPD thermostatting alters pairwise interactions in a manner analogous
to the per-particle thermostatting of "fix
langevin"_fix_langevin.html.
Any of the thermostatting fixes can use "temperature
computes"_Howto_thermostat.html that remove bias which has two
effects. First, the current calculated temperature, which is compared
to the requested target temperature, is calculated with the velocity
bias removed. Second, the thermostat adjusts only the thermal
temperature component of the particle's velocities, which are the
velocities with the bias removed. The removed bias is then added back
to the adjusted velocities. See the doc pages for the individual
fixes and for the "fix_modify"_fix_modify.html command for
instructions on how to assign a temperature compute to a
thermostatting fix. For example, you can apply a thermostat to only
the x and z components of velocity by using it in conjunction with
"compute temp/partial"_compute_temp_partial.html. Of you could
thermostat only the thermal temperature of a streaming flow of
particles without affecting the streaming velocity, by using "compute
temp/profile"_compute_temp_profile.html.
NOTE: Only the nvt fixes perform time integration, meaning they update
the velocities and positions of particles due to forces and velocities
respectively. The other thermostat fixes only adjust velocities; they
do NOT perform time integration updates. Thus they should be used in
conjunction with a constant NVE integration fix such as these:
"fix nve"_fix_nve.html
"fix nve/sphere"_fix_nve_sphere.html
"fix nve/asphere"_fix_nve_asphere.html :ul
Thermodynamic output, which can be setup via the
"thermo_style"_thermo_style.html command, often includes temperature
values. As explained on the doc page for the
"thermo_style"_thermo_style.html command, the default temperature is
setup by the thermo command itself. It is NOT the temperature
associated with any thermostatting fix you have defined or with any
compute you have defined that calculates a temperature. The doc pages
for the thermostatting fixes explain the ID of the temperature compute
they create. Thus if you want to view these temperatures, you need to
specify them explicitly via the "thermo_style
custom"_thermo_style.html command. Or you can use the
"thermo_modify"_thermo_modify.html command to re-define what
temperature compute is used for default thermodynamic output.

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"Higher level section"_Howto.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
TIP3P water model :h3
The TIP3P water model as implemented in CHARMM
"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
{harmonic} and an angle style of {harmonic} or {charmm} should also be
used.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
cutoff. The K values can be used if a flexible TIP3P model (without
fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
set to 0.0, it corresponds to the original 1983 TIP3P model
"(Jorgensen)"_#Jorgensen1.
O mass = 15.9994
H mass = 1.008
O charge = -0.834
H charge = 0.417
LJ epsilon of OO = 0.1521
LJ sigma of OO = 3.1507
LJ epsilon of HH = 0.0460
LJ sigma of HH = 0.4000
LJ epsilon of OH = 0.0836
LJ sigma of OH = 1.7753
K of OH bond = 450
r0 of OH bond = 0.9572
K of HOH angle = 55
theta of HOH angle = 104.52 :all(b),p
These are the parameters to use for TIP3P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for
details:
O mass = 15.9994
H mass = 1.008
O charge = -0.830
H charge = 0.415
LJ epsilon of OO = 0.102
LJ sigma of OO = 3.188
LJ epsilon, sigma of OH, HH = 0.0
K of OH bond = 450
r0 of OH bond = 0.9572
K of HOH angle = 55
theta of HOH angle = 104.52 :all(b),p
Wikipedia also has a nice article on "water
models"_http://en.wikipedia.org/wiki/Water_model.
:line
:link(Jorgensen1)
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
:link(Price1)
[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004).

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"Higher level section"_Howto.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
TIP4P water model :h3
The four-point TIP4P rigid water model extends the traditional
three-point TIP3P model by adding an additional site, usually
massless, where the charge associated with the oxygen atom is placed.
This site M is located at a fixed distance away from the oxygen along
the bisector of the HOH bond angle. A bond style of {harmonic} and an
angle style of {harmonic} or {charmm} should also be used.
A TIP4P model is run with LAMMPS using either this command
for a cutoff model:
"pair_style lj/cut/tip4p/cut"_pair_lj.html
or these two commands for a long-range model:
"pair_style lj/cut/tip4p/long"_pair_lj.html
"kspace_style pppm/tip4p"_kspace_style.html :ul
For both models, the bond lengths and bond angles should be held fixed
using the "fix shake"_fix_shake.html command.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
"(Jorgensen)"_#Jorgensen1. Note that the OM distance is specified in
the "pair_style"_pair_style.html command, not as part of the pair
coefficients.
O mass = 15.9994
H mass = 1.008
O charge = -1.040
H charge = 0.520
r0 of OH bond = 0.9572
theta of HOH angle = 104.52
OM distance = 0.15
LJ epsilon of O-O = 0.1550
LJ sigma of O-O = 3.1536
LJ epsilon, sigma of OH, HH = 0.0
Coulombic cutoff = 8.5 :all(b),p
For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
http://dx.doi.org/10.1063/1.1931662) these values can be used:
O mass = 15.9994
H mass = 1.008
O charge = -1.1794
H charge = 0.5897
r0 of OH bond = 0.9572
theta of HOH angle = 104.52
OM distance = 0.1577
LJ epsilon of O-O = 0.21084
LJ sigma of O-O = 3.1668
LJ epsilon, sigma of OH, HH = 0.0
Coulombic cutoff = 8.5 :all(b),p
For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
http://dx.doi.org/10.1063/1.2121687), these values can be used:
O mass = 15.9994
H mass = 1.008
O charge = -1.1128
H charge = 0.5564
r0 of OH bond = 0.9572
theta of HOH angle = 104.52
OM distance = 0.1546
LJ epsilon of O-O = 0.1852
LJ sigma of O-O = 3.1589
LJ epsilon, sigma of OH, HH = 0.0
Coulombic cutoff = 8.5 :all(b),p
These are the parameters to use for TIP4P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS):
O mass = 15.9994
H mass = 1.008
O charge = -1.0484
H charge = 0.5242
r0 of OH bond = 0.9572
theta of HOH angle = 104.52
OM distance = 0.1250
LJ epsilon of O-O = 0.16275
LJ sigma of O-O = 3.16435
LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
Note that the when using the TIP4P pair style, the neighbor list
cutoff for Coulomb interactions is effectively extended by a distance
2 * (OM distance), to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
typically best in an efficiency sense to use a LJ cutoff >= Coulomb
cutoff + 2*(OM distance), to shrink the size of the neighbor list.
This leads to slightly larger cost for the long-range calculation, so
you can test the trade-off for your model. The OM distance and the LJ
and Coulombic cutoffs are set in the "pair_style
lj/cut/tip4p/long"_pair_lj.html command.
Wikipedia also has a nice article on "water
models"_http://en.wikipedia.org/wiki/Water_model.
:line
:link(Jorgensen1)
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).

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"Higher level section"_Howto.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)
Triclinic (non-orthogonal) simulation boxes :h3
By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The "boundary"_boundary.html command sets the boundary
conditions of the box (periodic, non-periodic, etc). The orthogonal
box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
starting from the origin given by [a] = (xhi-xlo,0,0); [b] =
(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters
(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
is created, e.g. by the "create_box"_create_box.html or
"read_data"_read_data.html or "read_restart"_read_restart.html
commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
parameters, as well as lx,ly,lz, can be output via the "thermo_style
custom"_thermo_style.html command.
LAMMPS also allows simulations to be performed in triclinic
(non-orthogonal) simulation boxes shaped as a parallelepiped with
triclinic symmetry. The parallelepiped has its "origin" at
(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
origin given by [a] = (xhi-xlo,0,0); [b] = (xy,yhi-ylo,0); [c] =
(xz,yz,zhi-zlo). {xy,xz,yz} can be 0.0 or positive or negative values
and are called "tilt factors" because they are the amount of
displacement applied to faces of an originally orthogonal box to
transform it into the parallelepiped. In LAMMPS the triclinic
simulation box edge vectors [a], [b], and [c] cannot be arbitrary
vectors. As indicated, [a] must lie on the positive x axis. [b] must
lie in the xy plane, with strictly positive y component. [c] may have
any orientation with strictly positive z component. The requirement
that [a], [b], and [c] have strictly positive x, y, and z components,
respectively, ensures that [a], [b], and [c] form a complete
right-handed basis. These restrictions impose no loss of generality,
since it is possible to rotate/invert any set of 3 crystal basis
vectors so that they conform to the restrictions.
For example, assume that the 3 vectors [A],[B],[C] are the edge
vectors of a general parallelepiped, where there is no restriction on
[A],[B],[C] other than they form a complete right-handed basis i.e.
[A] x [B] . [C] > 0. The equivalent LAMMPS [a],[b],[c] are a linear
rotation of [A], [B], and [C] and can be computed as follows:
:c,image(Eqs/transform.jpg)
where A = | [A] | indicates the scalar length of [A]. The hat symbol (^)
indicates the corresponding unit vector. {beta} and {gamma} are angles
between the vectors described below. Note that by construction,
[a], [b], and [c] have strictly positive x, y, and z components, respectively.
If it should happen that
[A], [B], and [C] form a left-handed basis, then the above equations
are not valid for [c]. In this case, it is necessary
to first apply an inversion. This can be achieved
by interchanging two basis vectors or by changing the sign of one of them.
For consistency, the same rotation/inversion applied to the basis vectors
must also be applied to atom positions, velocities,
and any other vector quantities.
This can be conveniently achieved by first converting to
fractional coordinates in the
old basis and then converting to distance coordinates in the new basis.
The transformation is given by the following equation:
:c,image(Eqs/rotate.jpg)
where {V} is the volume of the box, [X] is the original vector quantity and
[x] is the vector in the LAMMPS basis.
There is no requirement that a triclinic box be periodic in any
dimension, though it typically should be in at least the 2nd dimension
of the tilt (y in xy) if you want to enforce a shift in periodic
boundary conditions across that boundary. Some commands that work
with triclinic boxes, e.g. the "fix deform"_fix_deform.html and "fix
npt"_fix_nh.html commands, require periodicity or non-shrink-wrap
boundary conditions in specific dimensions. See the command doc pages
for details.
The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
time the simulation box is created. This happens in one of 3 ways.
If the "create_box"_create_box.html command is used with a region of
style {prism}, then a triclinic box is setup. See the
"region"_region.html command for details. If the
"read_data"_read_data.html command is used to define the simulation
box, and the header of the data file contains a line with the "xy xz
yz" keyword, then a triclinic box is setup. See the
"read_data"_read_data.html command for details. Finally, if the
"read_restart"_read_restart.html command reads a restart file which
was written from a simulation using a triclinic box, then a triclinic
box will be setup for the restarted simulation.
Note that you can define a triclinic box with all 3 tilt factors =
0.0, so that it is initially orthogonal. This is necessary if the box
will become non-orthogonal, e.g. due to the "fix npt"_fix_nh.html or
"fix deform"_fix_deform.html commands. Alternatively, you can use the
"change_box"_change_box.html command to convert a simulation box from
orthogonal to triclinic and vice versa.
As with orthogonal boxes, LAMMPS defines triclinic box size parameters
lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
The 9 parameters, as well as lx,ly,lz, can be output via the
"thermo_style custom"_thermo_style.html command.
To avoid extremely tilted boxes (which would be computationally
inefficient), LAMMPS normally requires that no tilt factor can skew
the box more than half the distance of the parallel box length, which
is the 1st dimension in the tilt factor (x for xz). This is required
both when the simulation box is created, e.g. via the
"create_box"_create_box.html or "read_data"_read_data.html commands,
as well as when the box shape changes dynamically during a simulation,
e.g. via the "fix deform"_fix_deform.html or "fix npt"_fix_nh.html
commands.
For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
the xy tilt factor must be between -5 and 5. Similarly, both xz and
yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
not a limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are geometrically all equivalent. If the box tilt exceeds this
limit during a dynamics run (e.g. via the "fix deform"_fix_deform.html
command), then the box is "flipped" to an equivalent shape with a tilt
factor within the bounds, so the run can continue. See the "fix
deform"_fix_deform.html doc page for further details.
One exception to this rule is if the 1st dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.
The limitation on not creating a simulation box with a tilt factor
skewing the box more than half the distance of the parallel box length
can be overridden via the "box"_box.html command. Setting the {tilt}
keyword to {large} allows any tilt factors to be specified.
Box flips that may occur using the "fix deform"_fix_deform.html or
"fix npt"_fix_nh.html commands can be turned off using the {flip no}
option with either of the commands.
Note that if a simulation box has a large tilt factor, LAMMPS will run
less efficiently, due to the large volume of communication needed to
acquire ghost atoms around a processor's irregular-shaped sub-domain.
For extreme values of tilt, LAMMPS may also lose atoms and generate an
error.
Triclinic crystal structures are often defined using three lattice
constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and
{gamma}. Note that in this nomenclature, the a, b, and c lattice
constants are the scalar lengths of the edge vectors [a], [b], and [c]
defined above. The relationship between these 6 quantities
(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
:c,image(Eqs/box.jpg)
The inverse relationship can be written as follows:
:c,image(Eqs/box_inverse.jpg)
The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed
out or accessed by computes using the
"thermo_style custom"_thermo_style.html keywords
{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma},
respectively.
As discussed on the "dump"_dump.html command doc page, when the BOX
BOUNDS for a snapshot is written to a dump file for a triclinic box,
an orthogonal bounding box which encloses the triclinic simulation box
is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
box, formatted as follows:
ITEM: BOX BOUNDS xy xz yz
xlo_bound xhi_bound xy
ylo_bound yhi_bound xz
zlo_bound zhi_bound yz :pre
This bounding box is convenient for many visualization programs and is
calculated from the 9 triclinic box parameters
(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
ylo_bound = ylo + MIN(0.0,yz)
yhi_bound = yhi + MAX(0.0,yz)
zlo_bound = zlo
zhi_bound = zhi :pre
These formulas can be inverted if you need to convert the bounding box
back into the triclinic box parameters, e.g. xlo = xlo_bound -
MIN(0.0,xy,xz,xy+xz).
One use of triclinic simulation boxes is to model solid-state crystals
with triclinic symmetry. The "lattice"_lattice.html command can be
used with non-orthogonal basis vectors to define a lattice that will
tile a triclinic simulation box via the
"create_atoms"_create_atoms.html command.
A second use is to run Parinello-Rahman dynamics via the "fix
npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt
factors to compensate for off-diagonal components of the pressure
tensor. The analog for an "energy minimization"_minimize.html is
the "fix box/relax"_fix_box_relax.html command.
A third use is to shear a bulk solid to study the response of the
material. The "fix deform"_fix_deform.html command can be used for
this purpose. It allows dynamic control of the xy, xz, yz tilt
factors as a simulation runs. This is discussed in the next section
on non-equilibrium MD (NEMD) simulations.

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"Higher level section"_Howto.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
Calculate viscosity :h3
The shear viscosity eta of a fluid can be measured in at least 5 ways
using various options in LAMMPS. See the examples/VISCOSITY directory
for scripts that implement the 5 methods discussed here for a simple
Lennard-Jones fluid model. Also, see the "Howto
kappa"_Howto_kappa.html doc page for an analogous discussion for
thermal conductivity.
Eta is a measure of the propensity of a fluid to transmit momentum in
a direction perpendicular to the direction of velocity or momentum
flow. Alternatively it is the resistance the fluid has to being
sheared. It is given by
J = -eta grad(Vstream)
where J is the momentum flux in units of momentum per area per time.
and grad(Vstream) is the spatial gradient of the velocity of the fluid
moving in another direction, normal to the area through which the
momentum flows. Viscosity thus has units of pressure-time.
The first method is to perform a non-equilibrium MD (NEMD) simulation
by shearing the simulation box via the "fix deform"_fix_deform.html
command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to
thermostat the fluid via the SLLOD equations of motion.
Alternatively, as a second method, one or more moving walls can be
used to shear the fluid in between them, again with some kind of
thermostat that modifies only the thermal (non-shearing) components of
velocity to prevent the fluid from heating up.
In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html
command, which determines grad(Vstream) in the equation above.
E.g. the derivative in the y-direction of the Vx component of fluid
motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of
the pressure or stress tensor, as calculated by the "compute
pressure"_compute_pressure.html command, can also be monitored, which
is the J term in the equation above. See the "Howto
nemd"_Howto_nemd.html doc page for details on NEMD simulations.
The third method is to perform a reverse non-equilibrium MD simulation
using the "fix viscosity"_fix_viscosity.html command which implements
the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
swapped between atoms in two different layers of the simulation box in
a different dimension. This induces a velocity gradient which can be
monitored with the "fix ave/chunk"_fix_ave_chunk.html command.
The fix tallies the cumulative momentum transfer that it performs.
See the "fix viscosity"_fix_viscosity.html command for details.
The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the
stress/pressure tensor to eta. This can be done in a fully
equilibrated simulation which is in contrast to the two preceding
non-equilibrium methods, where momentum flows continuously through the
simulation box.
Here is an example input script that calculates the viscosity of
liquid Ar via the GK formalism:
# Sample LAMMPS input script for viscosity of liquid Ar :pre
units real
variable T equal 86.4956
variable V equal vol
variable dt equal 4.0
variable p equal 400 # correlation length
variable s equal 5 # sample interval
variable d equal $p*$s # dump interval :pre
# convert from LAMMPS real units to SI :pre
variable kB equal 1.3806504e-23 # \[J/K/] Boltzmann
variable atm2Pa equal 101325.0
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal $\{atm2Pa\}*$\{atm2Pa\}*$\{fs2s\}*$\{A2m\}*$\{A2m\}*$\{A2m\} :pre
# setup problem :pre
dimension 3
boundary p p p
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 39.948
pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405
timestep $\{dt\}
thermo $d :pre
# equilibration and thermalization :pre
velocity all create $T 102486 mom yes rot yes dist gaussian
fix NVT all nvt temp $T $T 10 drag 0.2
run 8000 :pre
# viscosity calculation, switch to NVE if desired :pre
#unfix NVT
#fix NVE all nve :pre
reset_timestep 0
variable pxy equal pxy
variable pxz equal pxz
variable pyz equal pyz
fix SS all ave/correlate $s $p $d &
v_pxy v_pxz v_pyz type auto file S0St.dat ave running
variable scale equal $\{convert\}/($\{kB\}*$T)*$V*$s*$\{dt\}
variable v11 equal trap(f_SS\[3\])*$\{scale\}
variable v22 equal trap(f_SS\[4\])*$\{scale\}
variable v33 equal trap(f_SS\[5\])*$\{scale\}
thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
run 100000
variable v equal (v_v11+v_v22+v_v33)/3.0
variable ndens equal count(all)/vol
print "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre
The fifth method is related to the above Green-Kubo method,
but uses the Einstein formulation, analogous to the Einstein
mean-square-displacement formulation for self-diffusivity. The
time-integrated momentum fluxes play the role of Cartesian
coordinates, whose mean-square displacement increases linearly
with time at sufficiently long times.

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"Higher level section"_Howto.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
Visualize LAMMPS snapshots :h3
LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.
Mention dump image and dump movie.
LAMMPS snapshots are created by the "dump"_dump.html command which can
create files in several formats. The native LAMMPS dump format is a
text file (see "dump atom" or "dump custom") which can be visualized
by several popular visualization tools. The "dump
image"_dump_image.html and "dump movie"_dump_image.html styles can
output internally rendered images and convert a sequence of them to a
movie during the MD run. Several programs included with LAMMPS as
auxiliary tools can convert between LAMMPS format files and other
formats. See the "Tools"_Tools.html doc page for details.
A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of
user-specified atom information, and convert them to various formats
or pipe them into visualization software directly. See the "Pizza.py
WWW site"_pizza for details. Specifically, Pizza.py can convert
LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats.
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
RasMol visualization programs. Pizza.py has tools that do interactive
3d OpenGL visualization and one that creates SVG images of dump file
snapshots.
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(ensight,http://www.ensight.com)
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)

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"Higher level section"_Howto.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
Walls :h3
Walls in an MD simulation are typically used to bound particle motion,
i.e. to serve as a boundary condition.
Walls in LAMMPS can be of rough (made of particles) or idealized
surfaces. Ideal walls can be smooth, generating forces only in the
normal direction, or frictional, generating forces also in the
tangential direction.
Rough walls, built of particles, can be created in various ways. The
particles themselves can be generated like any other particle, via the
"lattice"_lattice.html and "create_atoms"_create_atoms.html commands,
or read in via the "read_data"_read_data.html command.
Their motion can be constrained by many different commands, so that
they do not move at all, move together as a group at constant velocity
or in response to a net force acting on them, move in a prescribed
fashion (e.g. rotate around a point), etc. Note that if a time
integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html
is not used with the group that contains wall particles, their
positions and velocities will not be updated.
"fix aveforce"_fix_aveforce.html - set force on particles to average value, so they move together
"fix setforce"_fix_setforce.html - set force on particles to a value, e.g. 0.0
"fix freeze"_fix_freeze.html - freeze particles for use as granular walls
"fix nve/noforce"_fix_nve_noforce.html - advect particles by their velocity, but without force
"fix move"_fix_move.html - prescribe motion of particles by a linear velocity, oscillation, rotation, variable :ul
The "fix move"_fix_move.html command offers the most generality, since
the motion of individual particles can be specified with
"variable"_variable.html formula which depends on time and/or the
particle position.
For rough walls, it may be useful to turn off pairwise interactions
between wall particles via the "neigh_modify
exclude"_neigh_modify.html command.
Rough walls can also be created by specifying frozen particles that do
not move and do not interact with mobile particles, and then tethering
other particles to the fixed particles, via a "bond"_bond_style.html.
The bonded particles do interact with other mobile particles.
Idealized walls can be specified via several fix commands. "Fix
wall/gran"_fix_wall_gran.html creates frictional walls for use with
granular particles; all the other commands create smooth walls.
"fix wall/reflect"_fix_wall_reflect.html - reflective flat walls
"fix wall/lj93"_fix_wall.html - flat walls, with Lennard-Jones 9/3 potential
"fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential
"fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential
"fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential
"fix wall/region"_fix_wall_region.html - use region surface as wall
"fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul
The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the
flat walls to move with a constant velocity, or oscillate in time.
The "fix wall/region"_fix_wall_region.html command offers the most
generality, since the region surface is treated as a wall, and the
geometry of the region can be a simple primitive volume (e.g. a
sphere, or cube, or plane), or a complex volume made from the union
and intersection of primitive volumes. "Regions"_region.html can also
specify a volume "interior" or "exterior" to the specified primitive
shape or {union} or {intersection}. "Regions"_region.html can also be
"dynamic" meaning they move with constant velocity, oscillate, or
rotate.
The only frictional idealized walls currently in LAMMPS are flat or
curved surfaces specified by the "fix wall/gran"_fix_wall_gran.html
command. At some point we plan to allow regoin surfaces to be used as
frictional walls, as well as triangulated surfaces.

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"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Install.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands.html#comm)
:line
Introduction :h2
These pages provide a brief introduction to LAMMPS.
<!-- RST
.. toctree::
Intro_overview
Intro_features
Intro_nonfeatures
Intro_opensource
Intro_authors
Intro_website
END_RST -->
<!-- HTML_ONLY -->
"Overview of LAMMPS"_Intro_overview.html
"LAMMPS features"_Intro_features.html
"LAMMPS non-features"_Intro_nonfeatures.html
"LAMMPS open-source license"_Intro_license.html
"LAMMPS authors"_Intro_authors.html
"Additional website links"_Intro_website.html :all(b)
<!-- END_HTML_ONLY -->

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"Higher level section"_Intro.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 authors :h3
The primary LAMMPS developers are at Sandia National Labs and Temple
University:
"Steve Plimpton"_sjp, sjplimp at sandia.gov
Aidan Thompson, athomps at sandia.gov
Stan Moore, stamoor at sandia.gov
Axel Kohlmeyer, akohlmey at gmail.com :ul
:link(sjp,http://www.cs.sandia.gov/~sjplimp)
Past developers include Paul Crozier and Mark Stevens, both at Sandia,
and Ray Shan, now at Materials Design.
:line
The following folks are responsible for significant contributions to
the code, or other aspects of the LAMMPS development effort. Many of
the packages they have written are somewhat unique to LAMMPS and the
code would not be as general-purpose as it is without their expertise
and efforts.
Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM packages
Roy Pollock (LLNL), Ewald and PPPM solvers
Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages
Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
Georg Gunzenmueller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul
:line
As discussed on the "History
page"_http://lammps.sandia.gov/history.html of the website, LAMMPS
originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:
John Carpenter (Mayo Clinic, formerly at Cray Research)
Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
Steve Lustig (Dupont)
Jim Belak and Roy Pollock (LLNL) :ul
:line
:line
Here is a timeline for when various individuals contributed to a new
feature or command or tool added to LAMMPS:
Jul18 : DEM polygonal and polyhedron particles : Trung Nguyen (Northwestern U)
Jun18 : SPIN package : Julien Tranchida (Sandia and CEA)
Jun18 : compute entropy/atom : Pablo Piaggi (EPLF, Switzerland)
May18 : fix bond/react : Jake Gissinger (CU Boulder)
Apr18 : USER-BOCS package : Nicholas Dunn and Michael DeLyser (Penn State U)
Mar18: pair coul/shield, kolmogorov/crespi/full, ilp/graphene/hbn : Wengen Ouyang (Tel Aviv U)
Feb18 : pair lj/cut/coul/wolf : Vishal Boddu (U of Erlangen-Nuremberg)
Feb18 : USER-MOFFF package : Hendrik Heenen (Technical U of Munich) and Rochus Schmid (Ruhr-University Bochum)
Feb18 : pair ufm : Rodolfo Paula Leite and Maurice de Koning (Unicamp/Brazil)
Dec17 : fix python/move : Richard Berger (Temple U)
Nov17 : pair extep : Jaap Kroes (Radboud U)
Oct17 : USER-UEF package : David Nicholson (MIT)
Oct17 : fix rhok : Ulf Pederson (Roskilde U)
Oct17 : bond gromos : Axel Kohlmeyer (Temple U)
Oct17 : pair born/coul/wolf/cs and coul/wolf/cs : Vishal Boddu
Sep17 : fix latte : Christian Negre (LANL)
Sep17 : temper_npt : Amulya Pervaje and Cody Addington (NCSU)
Aug17 : USER-MESO package : Zhen Li (Brown University)
Aug17 : compute aggregate/atom & fragment/atom : Axel Kohlmeyer (Temple U)
Jul17 : pair meam/c : Sebastian Hutter (Otto-von-Guericke University)
Jun17 : pair reaxc/omp : Metin Aktulga (MSU) and Axel Kohlmeyer (Temple U)
Jun17 : pair vashishita/gpu : Anders Hafreager (UiO)
Jun17 : kspace pppm/disp/intel and pair lj/long/coul/long/intel : Mike Brown (Intel) and William McDoniel (RWTH Aachen U)
Jun17 : compute cnp/atom : Paulo Branicio (USC)
May17 : fix python and pair python : Richard Berger (Temple U)
May17 : pair edip/multi : Chao Jiang (U Wisconsin)
May17 : pair gw and gw/zbl : German Samolyuk (ORNL)
Mar17 : pair charmm fsw and fsh : Robert Meissner & Lucio Colombi Ciacchi (Bremen U), Robert Latour (Clemson U)
Mar17 : pair momb : Ya Zhou, Kristen Fichthorn, and Tonnam Balankura (PSU)
Mar17 : fix filter/corotate : Lukas Fath (KIT)
Mar17 : pair kolmogorov/crespi/z : Jaap Kroes (Radboud Universiteit)
Feb17 : Kokkos versions of the class2 bond/angle/dihedral/improper : Ray Shan (Materials Design)
Jan17 : USER-CGDNA package : Oliver Henrich (U Edinburgh)
Jan17 : fix mscg : Lauren Abbott (Sandia)
Nov16 : temper/grem and fix grem : David Stelter (BU), Edyta Malolepsza (Broad Institute), Tom Keyes (BU)
Nov16 : pair agni : Axel Kohlmeyer (Temple U) and Venkatesh Botu
Nov16 : pair tersoff/mod.c : Ganga P Purja Pun (George Mason University)
Nov16 : pair born/coul/dsf and pair born/coul/dsf/cs : Ariel Lozano
Nov16 : fix reaxc/species/kk & fix reaxc/bonds/kk : Stan Moore (Sandia)
Oct16 : fix wall/gran/region : Dan Bolintineanu (Sandia)
Sep16 : weight options for balance & fix balance : Axel Kohlmeyer (Temple U) & Iain Bethune (EPCC)
Sep16 : fix cmap : Xiaohu Hu (ORNL), David Hyde-Volpe & Tigran Abramyan & Robert Latour (Clemson U), Chris Lorenz (Kings College, London)
Sep16 : pair vashishta/table : Anders Hafreager (U Oslo)
Sep16 : kspace pppm/kk : Stan Moore (Sandia)
Aug16 : fix flow/gauss : Steve Strong and Joel Eaves (U Colorado)
Aug16 : fix controller : Aidan Thompson (Sandia)
Jul16 : dipole integration by DLM method : Iain Bethune (EPCC)
Jul16 : dihedral spherical : Andrew Jewett
Jun16 : pair reax/c/kk : Ray Shan (Materials Design), Stan Moore (Sandia)
Jun16 : fix orient/bcc : Tegar Wicaksono (UBC)
Jun16 : fix ehex : Peter Wirnsberger (University of Cambridge)
Jun16 : reactive DPD extensions to USER-DPD : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL), Christopher Stone (Computational Science & Engineering, LLC)
May16 : USER-MANIFOLD package : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
Apr16 : write_coeff : Axel Kohlmeyer (Temple U)
Apr16 : pair morse/soft : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
Apr16 : compute dipole/chunk : Axel Kohlmeyer (Temple U)
Apr16 : bond write : Axel Kohlmeyer (Temple U)
Mar16 : pair morse/smooth/linear : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
Feb16 : pair/bond/angle/dihedral/improper zero : Carsten Svaneborg (SDU)
Feb16 : dump custom/vtk : Richard Berger (JKU) and Daniel Queteschiner (DCS Computing)
Feb16 : fix (nvt/npt/nph)/body and compute temp/body : Trung Nguyen
Feb16 : USER-DPD package : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL)
Dec15 : fix qeq/fire : Ray Shan (Sandia)
Dec15 : pair lj/mdf, pair lennard/mdf, pair buck/mdf, improper distance : Paolo Raiteri (Curtin University)
Nov15 : compute orientorder/atom : Aidan Thompson (Sandia) and Axel Kohlmeyer (U Temple)
Nov15 : compute hexorder/atom : Aidan Thompson (Sandia)
Oct15 : displace_atoms variable option : Reese Jones (Sandia)
Oct15 : pair mgpt & USER-MGPT package : Tomas Oppelstrup and John Moriarty (LLNL)
Oct15 : pair smtbq & USER-SMTBQ package : Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS)
Oct15 : fix ave/correlate/long command : Jorge Ramirez (UPM) and Alexei Likhtman (U Reading)
Oct15 : pair vashishta command : Aidan Thompson (Sandia) and Yongnan Xiong (HNU)
Aug15 : USER-TALLY package : Axel Kohlmeyer (Temple U)
Aug15 : timer command : Axel Kohlmeyer (Temple U)
Aug15 : USER-H5MD package : Pierre de Buyl (KU Leuven)
Aug15 : COMPRESS package : Axel Kohlmeyer (Temple U)
Aug15 : USER-SMD package : Georg Gunzenmueller (EMI)
Jul15 : new HTML format for "doc pages"_Manual.html with search option : Richard Berger (JKU)
Jul15 : rRESPA with pair hybrid : Sam Genheden (U of Southampton)
Jul15 : pair_modify special : Axel Kohlmeyer (Temple U)
Jul15 : pair polymorphic : Xiaowang Zhou and Reese Jones (Sandia)
Jul15 : USER-DRUDE package : Alain Dequidt and Agilio Padua (U Blaise Pascal Clermont-Ferrand) and Julien Devemy (CNRS)
Jul15 : USER-QTB package : Yuan Shen, Tingting Qi, and Evan Reed (Stanford U)
Jul15 : USER-DIFFRACTION package : Shawn Coleman (ARL)
Mar15 : fix temp/csld : Axel Kohlmeyer (Temple U)
Mar15 : CORESHELL package : Hendrik Heenen (Technical University of Munich)
Feb15 : pair quip for GAP and other potentials : Albert Bartok-Partay (U Cambridge)
Feb15 : pair coul/streitz for Streitz-Mintmire potential : Ray Shan (Sandia)
Feb15 : fix tfmc : Kristof Bal (U of Antwerp)
Feb15 : fix ttm/mod : Sergey Starikov and Vasily Pisarev (JIHT of RAS)
Jan15 : fix atom/swap for MC swaps of atom types/charge : Paul Crozier (Sandia)
Nov14 : fix pimd for path-integral MD : Chris Knight and Yuxing Peng (U Chicago)
Nov14 : fix gle and fix ipi for path-integral MD : Michele Ceriotti (EPFL)
Nov14 : pair style srp : Tim Sirk (ARL) and Pieter in 't Veld (BASF)
Nov14 : fix ave/spatial/sphere : Niall Jackson (Imperial College)
Sep14 : QEQ package and several fix qeq/variant styles : Ray Shan (Sandia)
Sep14 : SNAP package and pair style : Aidan Thompson (Sandia) and collaborators
Aug14 : USER-INTEL package : Mike Brown (Intel)
May14 : KOKKOS pacakge : Christian Trott and Carter Edwards (Sandia)
May14 : USER-FEP pacakge : Agilio Padua (U Blaise Pascal Clermont-Ferrand)
Apr14 : fix rigid/small NVE/NVT/NPH/NPT : Trung Nguyen (ORNL)
Apr14 : fix qmmm for QM/MM coupling : Axel Kohlmeyer (Temple U)
Mar14 : kspace_modify collective for faster FFTs on BG/Q : Paul Coffman (IBM)
Mar14 : fix temp/csvr and fix oneway : Axel Kohlmeyer (Temple U)
Feb14 : pair peri/eps, compute dilatation/atom, compute plasticity/atom : Rezwanur Rahman and John Foster (UTSA)
Jan14 : MPI-IO options for dump and restart files : Paul Coffman (IBM)
Nov13 : USER-LB package for Lattice Boltzmann : Francis Mackay and Colin Denniston (U Western Ontario)
Nov13 : fix ti/rs and ti/spring : Rodrigo Freitas (UC Berkeley)
Nov13 : pair comb3 : Ray Shan (Sandia), Tao Liang and Dundar Yilmaz (U Florida)
Nov13 : write_dump and dump movie : Axel Kohlmeyer (Temple U)
Sep13 : xmgrace tool : Vikas Varshney
Sep13 : pair zbl : Aidan Thompson and Stephen Foiles (Sandia)
Aug13 : pair nm and variants : Julien Devemy (ICCF)
Aug13 : fix wall/lj1043 : Jonathan Lee (Sandia)
Jul13 : pair peri/ves : Rezwan Rahman, JT Foster (U Texas San Antonio)
Jul13 : pair tersoff/mod : Vitaly Dozhdikov (JIHT of RAS)
Jul13 : compute basal/atom : Christopher Barrett,(Mississippi State)
Jul13 : polybond tool : Zachary Kraus (Georgia Tech)
Jul13 : fix gld : Stephen Bond and Andrew Baczewski (Sandia)
Jun13 : pair nb3b/harmonic : Todd Zeitler (Sandia)
Jun13 : kspace_style pppm/stagger : Stan Moore (Sandia)
Jun13 : fix tune/kspace : Paul Crozier (Sandia)
Jun13 : long-range point dipoles : Stan Moore (Sandia) and Pieter in 't Veld (BASF)
May13 : compute msd/nongauss : Rob Hoy
May13 : pair list : Axel Kohlmeyer (Temple U)
May13 : triclinic support for long-range solvers : Stan Moore (Sandia)
Apr13 : dump_modify nfile and fileper : Christopher Knight
Mar13 : fix phonon : Ling-Ti Kong (Shanghai Jiao Tong University)
Mar13 : pair_style lj/cut/tip4p/cut : Pavel Elkind (Gothenburg University)
Feb13 : immediate variables in input script : Daniel Moller (Autonomous University of Barcelona)
Feb13 : fix species : Ray Shan (Sandia)
Jan13 : compute voronoi/atom : Daniel Schwen
Nov12 : pair_style mie/cut : Cassiano Aimoli Petrobras (U Notre Dame)
Oct12 : pair_style meam/sw/spline : Robert Rudd (LLNL)
Oct12 : angle_style fourier and fourier/simple and quartic : Loukas Peristeras (Scienomics)
Oct12 : dihedral_style fourier and nharmonic and quadratic : Loukas Peristeras (Scienomics)
Oct12 : improper_style fourier : Loukas Peristeras (Scienomics)
Oct12 : kspace_style pppm/disp for 1/r^6 : Rolf Isele-Holder (Aachen University)
Oct12 : moltemplate molecular builder tool : Andrew Jewett (UCSB)
Sep12 : pair_style lj/cut/coul/dsf and coul/dsf : Trung Nguyen (ORNL)
Sep12 : multi-level summation long-range solver : Stan Moore, Stephen Bond, and Paul Crozier (Sandia)
Aug12 : fix rigid/npt and fix rigid/nph : Trung Nguyen (ORNL)
Aug12 : Fortran wrapper on lib interface : Karl Hammond (UT, Knoxville)
Aug12 : kspace_modify diff for 2-FFT PPPM : Rolf Isele-Holder (Aachen University), Stan Moore (BYU), Paul Crozier (Sandia)
Jun12 : pair_style bop : Don Ward and Xiaowang Zhou (Sandia)
Jun12 : USER-MOLFILE package : Axel Kohlmeyer (U Temple)
Jun12 : USER-COLVARS package : Axel Kohlmeyer (U Temple)
May12 : read_dump : Tim Sirk (ARL)
May12 : improper_style cossq and ring : Georgios Vogiatzis (CoMSE, NTU Athens)
May12 : pair_style lcbop : Dominik Wojt (Wroclaw University of Technology)
Feb12 : PPPM per-atom energy/virial : Stan Moore (BYU)
Feb12 : Ewald per-atom energy/virial : German Samolyuk (ORNL), Stan Moore (BYU)
Feb12 : minimize forcezero linesearch : Asad Hasan (CMU)
Feb12 : pair_style beck : Jon Zimmerman (Sandia)
Feb12 : pair_style meam/spline : Alex Stukowski (LLNL)
Jan12 : pair_style kim : Valeriu Smirichinski, Ryan Elliott, Ellad Tadmor (U Minn)
Jan12 : dihedral_style table : Andrew Jewett (UCSB)
Jan12 : angle_style dipole : Mario Orsi
Jan12 : pair_style lj/smooth/linear : Jon Zimmerman (Sandia)
Jan12 : fix reax/c/bond : Tzu-Ray Shan (Sandia)
Dec11 : pair_style coul/wolf : Yongfeng Zhang (INL)
Dec11 : run_style verlet/split : Yuxing Peng and Chris Knight (U Chicago)
Dec11 : pair_style tersoff/table : Luca Ferraro (CASPUR)
Nov11 : per-atom energy/stress for reax/c : Tzu-Ray Shan (Sandia)
Oct11 : Fast Lubrication Dynamics (FLD) package: Amit Kumar, Michael Bybee, Jonathan Higdon (UIUC)
Oct11 : USER-OMP package : Axel Kohlmeyer (Temple U)
Sep11 : pair_style edip : Luca Ferraro (CASPUR)
Aug11 : USER-SPH package : Georg Ganzenmuller (FIHSD, EMI, Germany)
Aug11 : fix restrain : Craig Tenney (Sandia)
Aug11 : USER-CUDA package : Christian Trott (U Tech Ilmenau)
Aug11 : pair_style lj/sf : Laurent Joly (U Lyon)
Aug11 : bond_style harmonic/shift and harmonic/shift/cut : Carsten Svaneborg
Aug11 : angle_style cosine/shift and cosine/shift/exp : Carsten Svaneborg
Aug11 : dihedral_style cosine/shift/exp : Carsten Svaneborg
Aug11 : pair_style dipole/sf : Mario Orsi
Aug11 : fix addtorque and compute temp/rotate : Laurent Joly (U Lyon)
Aug11 : FFT support via FFTW3, MKL, ACML, KISSFFT libraries : \
Axel Kohlmeyer (Temple U)
Jun11 : pair_style adp : Chris Weinberger (Sandia), Stephen Foiles (Sandia), \
Chandra Veer Singh (Cornell)
Jun11 : Windows build option via Microsoft Visual Studio : \
Ilya Valuev (JIHT, Moscow, Russia)
Jun11 : antisymmetrized wave packet MD : Ilya Valuev (JIHT, Moscow, Russia)
Jun11 : dump image : Nathan Fabian (Sandia)
May11 : pppm GPU single and double : Mike Brown (ORNL)
May11 : pair_style lj/expand/gpu : Inderaj Bains (NVIDIA)
2010 : pair_style reax/c and fix qeq/reax : Metin Aktulga (Purdue, now LBNL)
- : DREIDING force field, pair_style hbond/dreiding, etc : Tod Pascal (Caltech)
- : fix adapt and compute ti for thermodynamic integration for \
free energies : Sai Jayaraman (Sandia)
- : pair_style born and gauss : Sai Jayaraman (Sandia)
- : stochastic rotation dynamics (SRD) via fix srd : \
Jeremy Lechman (Sandia) and Pieter in 't Veld (BASF)
- : ipp Perl script tool : Reese Jones (Sandia)
- : eam_database and createatoms tools : Xiaowang Zhou (Sandia)
- : electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech)
- : embedded ion method (EIM) potential : Xiaowang Zhou (Sandia)
- : COMB potential with charge equilibration : Tzu-Ray Shan (U Florida)
- : fix ave/correlate : Benoit Leblanc, Dave Rigby, \
Paul Saxe (Materials Design) and Reese Jones (Sandia)
- : pair_style peri/lps : Mike Parks (Sandia)
- : fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)
- : thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U)
- : fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan)
- : public SVN & Git repositories for LAMMPS : \
Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)
- : compute heat/flux : German Samolyuk (ORNL) and \
Mario Pinto (Computational Research Lab, Pune, India)
- : pair_style yukawa/colloid : Randy Schunk (Sandia)
- : fix wall/colloid : Jeremy Lechman (Sandia)
2009 : fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ)
- : concentration-dependent EAM potential : \
Alexander Stukowski (Technical University of Darmstadt)
- : parallel replica dymamics (PRD) : Mike Brown (Sandia)
- : min_style hftn : Todd Plantenga (Sandia)
- : fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)
- : dump cfg : Liang Wan (Chinese Academy of Sciences)
- : fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland)
- : pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia)
- : pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo
- : fix langevin tally : Carolyn Phillips (U Michigan)
- : compute heat/flux for Green-Kubo : Reese Jones (Sandia), \
Philip Howell (Siemens), Vikas Varsney (AFRL)
- : region cone : Pim Schravendijk
- : pair_style born/coul/long : Ahmed Ismail (Sandia)
- : fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
- : fix box/relax : Aidan Thompson and David Olmsted (Sandia)
- : ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT)
- : compute cna/atom : Liang Wan (Chinese Academy of Sciences)
2008 : Tersoff/ZBL potential : Dave Farrell (Northwestern U)
- : peridynamics : Mike Parks (Sandia)
- : fix smd for steered MD : Axel Kohlmeyer (U Penn)
- : GROMACS pair potentials : Mark Stevens (Sandia)
- : lmp2vmd tool : Axel Kohlmeyer (U Penn)
- : compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U)
- : USER-CG-CMM package for coarse-graining : Axel Kohlmeyer (U Penn)
- : cosine/delta angle potential : Axel Kohlmeyer (U Penn)
- : VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain
- : pair_style lubricate : Randy Schunk (Sandia)
- : compute ackland/atom : Gerolf Ziegenhain
- : kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \
Pieter in 't Veld (Sandia)
- : AI-REBO bond-order potential : Ase Henry (MIT)
- : making LAMMPS a true "object" that can be instantiated \
multiple times, e.g. as a library : Ben FrantzDale (RPI)
- : pymol_asphere viz tool : Mike Brown (Sandia)
2007 : NEMD SLLOD integration : Pieter in 't Veld (Sandia)
- : tensile and shear deformations : Pieter in 't Veld (Sandia)
- : GayBerne potential : Mike Brown (Sandia)
- : ellipsoidal particles : Mike Brown (Sandia)
- : colloid potentials : Pieter in 't Veld (Sandia)
- : fix heat : Paul Crozier and Ed Webb (Sandia)
- : neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
- : MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
- : triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
- : thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
- : fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
- : MEAM potential : Greg Wagner (Sandia)
- : optimized pair potentials for lj/cut, charmm/long, eam, morse : \
James Fischer (High Performance Technologies), \
David Richie and Vincent Natoli (Stone Ridge Technologies)
2006 : fix wall/lj126 : Mark Stevens (Sandia)
- : Stillinger-Weber and Tersoff potentials : \
Aidan Thompson and Xiaowang Zhou (Sandia)
- : region prism : Pieter in 't Veld (Sandia)
- : fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U)
- : multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U)
- : OPLS dihedral potential: Mark Stevens (Sandia)
- : POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI)
- : faster pair hybrid potential: James Fischer \
(High Performance Technologies, Inc), Vincent Natoli and \
David Richie (Stone Ridge Technology)
- : breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia)
- : DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U)
- : grain boundary orientation fix : Koenraad Janssens and \
David Olmsted (Sandia)
- : pair_style lj/smooth potential : Craig Maloney (UCSB)
- : radius-of-gyration spring fix : Naveen Michaud-Agrawal \
(Johns Hopkins U) and Paul Crozier (Sandia)
- : self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U)
- : EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea)
- : cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U)
- : helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \
Mark Stevens (Sandia)
- : Finnis/Sinclair EAM: Tim Lau (MIT)
- : dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \
Frank van Swol (Sandia)
- : TIP4P potential (4-site water): Ahmed Ismail and \
Amalie Frischknecht (Sandia)
2005 : uniaxial strain fix: Carsten Svaneborg (Max Planck Institute)
- : compressed dump files: Erik Luijten (U Illinois)
- : cylindrical indenter fix: Ravi Agrawal (Northwestern U)
- : electric field fix: Christina Payne (Vanderbilt U)
- : AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \
Vikas Varshney (U Akron)
- : CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia)
- : Morse bond potential: Jeff Greathouse (Sandia)
- : radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
- : force tables for long-range Coulombics: Paul Crozier (Sandia)
2004 : targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \
Christian Burisch (Bochum University, Germany)
- : FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech)
- : lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \
Andrey Kalinichev (Sandia)
- : parallel tempering: Mark Sears (Sandia)
earlier : granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
- : multi-harmonic dihedral potential: Mathias Putz (Sandia)
- : embedded atom method (EAM) potential: Stephen Foiles (Sandia)
- : msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)
- : HTFN energy minimizer: Todd Plantenga (Sandia)
- : class 2 force fields: Eric Simon (Cray)
- : NVT/NPT integrators: Mark Stevens (Sandia)
- : rRESPA: Mark Stevens & Paul Crozier (Sandia)
- : Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:,ca1=c)

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"Higher level section"_Intro.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 features :h3
LAMMPS is a classical molecular dynamics (MD) code with these general
classes of functionality:
"General features"_#general
"Particle and model types"_#particle
"Interatomic potentials (force fields)"_#ff
"Atom creation"_#create
"Ensembles, constraints, and boundary conditions"_#ensemble
"Integrators"_#integrate
"Diagnostics"_#diag
"Output"_#output
"Multi-replica models"_#replica
"Pre- and post-processing"_#prepost
"Specialized features (beyond MD itself)"_#special :ul
:line
General features :h4,link(general)
runs on a single processor or in parallel
distributed-memory message-passing parallelism (MPI)
spatial-decomposition of simulation domain for parallelism
open-source distribution
highly portable C++
optional libraries used: MPI and single-processor FFT
GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features
easy to extend with new features and functionality
runs from an input script
syntax for defining and using variables and formulas
syntax for looping over runs and breaking out of loops
run one or multiple simulations simultaneously (in parallel) from one script
build as library, invoke LAMMPS thru library interface or provided Python wrapper
couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
Particle and model types :h4,link(particle)
("atom style"_atom_style.html command)
atoms
coarse-grained particles (e.g. bead-spring polymers)
united-atom polymers or organic molecules
all-atom polymers, organic molecules, proteins, DNA
metals
granular materials
coarse-grained mesoscale models
finite-size spherical and ellipsoidal particles
finite-size line segment (2d) and triangle (3d) particles
point dipole particles
rigid collections of particles
hybrid combinations of these :ul
Interatomic potentials (force fields) :h4,link(ff)
("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, "kspace style"_kspace_style.html
commands)
pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
charged pairwise potentials: Coulombic, point-dipole
manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \
REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
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"_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
electron force field (eFF, AWPMD)
bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
quartic (breakable)
angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \
class 2 (COMPASS)
dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
class 2 (COMPASS), OPLS
improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
polymer potentials: all-atom, united-atom, bead-spring, breakable
water potentials: TIP3P, TIP4P, SPC
implicit solvent potentials: hydrodynamic lubrication, Debye
force-field compatibility with common CHARMM, AMBER, DREIDING, \
OPLS, GROMACS, COMPASS options
access to "KIM archive"_http://openkim.org of potentials via \
"pair kim"_pair_kim.html
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
potentials can be used in one simulation
overlaid potentials: superposition of multiple pair potentials :ul
Atom creation :h4,link(create)
("read_data"_read_data.html, "lattice"_lattice.html,
"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
read in atom coords from files
create atoms on one or more lattices (e.g. grain boundaries)
delete geometric or logical groups of atoms (e.g. voids)
replicate existing atoms multiple times
displace atoms :ul
Ensembles, constraints, and boundary conditions :h4,link(ensemble)
("fix"_fix.html command)
2d or 3d systems
orthogonal or non-orthogonal (triclinic symmetry) simulation domains
constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
thermostatting options for groups and geometric regions of atoms
pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
simulation box deformation (tensile and shear)
harmonic (umbrella) constraint forces
rigid body constraints
SHAKE bond and angle constraints
Monte Carlo bond breaking, formation, swapping
atom/molecule insertion and deletion
walls of various kinds
non-equilibrium molecular dynamics (NEMD)
variety of additional boundary conditions and constraints :ul
Integrators :h4,link(integrate)
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
velocity-Verlet integrator
Brownian dynamics
rigid body integration
energy minimization via conjugate gradient or steepest descent relaxation
rRESPA hierarchical timestepping
rerun command for post-processing of dump files :ul
Diagnostics :h4,link(diag)
see various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
Output :h4,link(output)
("dump"_dump.html, "restart"_restart.html commands)
log file of thermodynamic info
text dump files of atom coords, velocities, other per-atom quantities
binary restart files
parallel I/O of dump and restart files
per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
user-defined system-wide (log file) or per-atom (dump file) calculations
spatial and time averaging of per-atom quantities
time averaging of system-wide quantities
atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
Multi-replica models :h4,link(replica)
"nudged elastic band"_neb.html
"parallel replica dynamics"_prd.html
"temperature accelerated dynamics"_tad.html
"parallel tempering"_temper.html :ul
Pre- and post-processing :h4,link(prepost)
A handful of pre- and post-processing tools are packaged with LAMMPS,
some of which can convert input and output files to/from formats used
by other codes; see the "Toos"_Tools.html doc page. :ulb,l
Our group has also written and released a separate toolkit called
"Pizza.py"_pizza which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in "Python"_python and is available for download from "the
Pizza.py WWW site"_pizza. :l,ule
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(python,http://www.python.org)
Specialized features :h4,link(special)
LAMMPS can be built with optional packages which implement a variety
of additional capabilities. See the "Packages"_Packages.html doc
page for details.
These are LAMMPS capabilities which you may not think of as typical
classical MD options:
"static"_balance.html and "dynamic load-balancing"_fix_balance.html
"generalized aspherical particles"_Howto_body.html
"stochastic rotation dynamics (SRD)"_fix_srd.html
"real-time visualization and interactive MD"_fix_imd.html
calculate "virtual diffraction patterns"_compute_xrd.html
"atom-to-continuum coupling"_fix_atc.html with finite elements
coupled rigid body integration via the "POEMS"_fix_poems.html library
"QM/MM coupling"_fix_qmmm.html
Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_atom_swap.html
"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html
"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
"Peridynamics mesoscale modeling"_pair_peri.html
"Lattice Boltzmann fluid"_fix_lb_fluid.html
"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
"two-temperature electron model"_fix_ttm.html :ul

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"Higher level section"_Intro.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 non-features :h3
LAMMPS is designed to be a fast, parallel engine for molecular
dynamics (MD) simulations. It provides only a modest amount of
functionality for setting up simulations and analyzing their output.
Specifically, LAMMPS does not:
run thru a GUI
build molecular systems
assign force-field coefficients automagically
perform sophisticated analyses of your MD simulation
visualize your MD simulation interactively
plot your output data :ul
Here are suggestions on how to perform these tasks:
GUI: LAMMPS can be built as a library and a Python wrapper that wraps
the library interface is provided. Thus, GUI interfaces can be
written in Python (or C or C++ if desired) that run LAMMPS and
visualize or plot its output. Examples of this are provided in the
python directory and described on the "Python"_Python.html doc
page. :ulb,l
Builder: Several pre-processing tools are packaged with LAMMPS. Some
of them convert input files in formats produced by other MD codes such
as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of them
are simple programs that will build simple molecular systems, such as
linear bead-spring polymer chains. The moltemplate program is a true
molecular builder that will generate complex molecular models. See
the "Tools"_Tools.html doc page for details on tools packaged with
LAMMPS. The "Pre/post processing
page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
describes a variety of 3rd party tools for this task. :l
Force-field assignment: The conversion tools described in the previous
bullet for CHARMM, AMBER, and Insight will also assign force field
coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
or Accelerys force field files. :l
Simulation analyses: If you want to perform analyses on-the-fly as
your simulation runs, see the "compute"_compute.html and
"fix"_fix.html doc pages, which list commands that can be used in a
LAMMPS input script. Also see the "Modify"_Modify.html doc page for
info on how to add your own analysis code or algorithms to LAMMPS.
For post-processing, LAMMPS output such as "dump file
snapshots"_dump.html can be converted into formats used by other MD or
post-processing codes. Some post-processing tools packaged with
LAMMPS will do these conversions. Scripts provided with the {python}
tool in the tools directory can extract and massage data in dump files
to make it easier to import into other programs. See the
"Tools"_Tools.html doc page for details on these various options. :l
Visualization: LAMMPS can produce JPG or PNG snapshot images
on-the-fly via its "dump image"_dump_image.html command. For
high-quality, interactive visualization there are many excellent and
free tools available. See the "Other Codes
page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for
visualization packages that can use LAMMPS output data. :l
Plotting: See the next bullet about Pizza.py as well as the
"Python"_Python.html doc page for examples of plotting LAMMPS output.
Scripts provided with the {python} tool in the tools directory will
extract and massage data in log and dump files to make it easier to
analyze and plot. See the "Tools"_Tools.html doc page for more
discussion of the various tools. :l
Pizza.py: Our group has also written a separate toolkit called
"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
simulations. It thus provides some functionality for several of the
above bullets. Pizza.py is written in "Python"_http://www.python.org
and is available for download from "this
page"_http://www.cs.sandia.gov/~sjplimp/download.html. :l,ule

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"Higher level section"_Intro.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 open-source license :h3
LAMMPS is a freely-available open-source code, distributed under the
terms of the "GNU Public License"_gnu, which means you can use or
modify the code however you wish.
LAMMPS comes with no warranty of any kind. As each source file states
in its header, it is a copyrighted code that is distributed free-of-
charge, under the terms of the "GNU Public License"_gnu (GPL). This
is often referred to as open-source distribution - see
"www.gnu.org"_gnuorg or "www.opensource.org"_opensource. The legal
text of the GPL is in the LICENSE file included in the LAMMPS
distribution.
:link(gnu,http://www.gnu.org/copyleft/gpl.html)
:link(gnuorg,http://www.gnu.org)
:link(opensource,http://www.opensource.org)
Here is a summary of what the GPL means for LAMMPS users:
(1) Anyone is free to use, modify, or extend LAMMPS in any way they
choose, including for commercial purposes.
(2) If you distribute a modified version of LAMMPS, it must remain
open-source, meaning you distribute it under the terms of the GPL.
You should clearly annotate such a code as a derivative version of
LAMMPS.
(3) If you release any code that includes LAMMPS source code, then it
must also be open-sourced, meaning you distribute it under the terms
of the GPL.
(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
source file headers (including the copyright and GPL notices) should
remain part of the code.

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"Higher level section"_Intro.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
Overview of LAMMPS :h3
LAMMPS is a classical molecular dynamics (MD) code that models
ensembles of particles in a liquid, solid, or gaseous state. It can
model atomic, polymeric, biological, solid-state (metals, ceramics,
oxides), granular, coarse-grained, or macroscopic systems using a
variety of interatomic potentials (force fields) and boundary
conditions. It can model 2d or 3d systems with only a few particles
up to millions or billions.
LAMMPS can be built and run on a laptop or destop machine, but is
designed for parallel computers. It will run on any parallel machine
that supports the "MPI"_mpi message-passing library. This includes
shared-memory boxes and distributed-memory clusters and
supercomputers.
:link(mpi,http://www-unix.mcs.anl.gov/mpi)
LAMMPS is written in C++. Earlier versions were written in F77 and
F90. See the "History page"_http://lammps.sandia.gov/history.html of
the website for details. All versions can be downloaded from the
"LAMMPS website"_lws.
LAMMPS is designed to be easy to modify or extend with new
capabilities, such as new force fields, atom types, boundary
conditions, or diagnostics. See the "Modify"_Modify.html doc page for
more details.
In the most general sense, LAMMPS integrates Newton's equations of
motion for a collection of interacting particles. A single particle
can be an atom or molecule or electron, a coarse-grained cluster of
atoms, or a mesoscopic or macroscopic clump of material. The
interaction models that LAMMPS includes are mostly short-range in
nature; some long-range models are included as well.
LAMMPS uses neighbor lists to keep track of nearby particles. The
lists are optimized for systems with particles that are repulsive at
short distances, so that the local density of particles never becomes
too large. This is in contrast to methods used for modeling plasmas
or gravitational bodies (e.g. galaxy formation).
On parallel machines, LAMMPS uses spatial-decomposition techniques to
partition the simulation domain into small sub-domains of equal
computational cost, one of which is assigned to each processor.
Processors communicate and store "ghost" atom information for atoms
that border their sub-domain.

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"Higher level section"_Intro.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
Additional website links :h3
The "LAMMPS website"_lws has a variety of additional info about
LAMMPS, beyond what is in this manual. Some of the other pages in
this Intr are included in this list.
"Brief intro and recently added significant features"_lws
"List of features"_http://lammps.sandia.gov/features.html
"List of non-features"_http://lammps.sandia.gov/non_features.html
"Recent bug fixes and new features"_http://lammps.sandia.gov/bug.html :ul
"Download info"_http://lammps.sandia.gov/download.html
"GitHub site"_https://github.com/lammps/lammps
"SourceForge site"_https://sourceforge.net/projects/lammps
"LAMMPS open-source license"_http://lammps.sandia.gov/open_source.html :ul
"Glossary of MD terms relevant to LAMMPS"_http://lammps.sandia.gov/glossary.html
"LAMMPS highlights with images"_http://lammps.sandia.gov/pictures.html
"LAMMPS highlights with movies"_http://lammps.sandia.gov/movies.html
"Mail list"_http://lammps.sandia.gov/mail.html
"Workshops"_http://lammps.sandia.gov/workshops.html
"Tutorials"_http://lammps.sandia.gov/tutorials.html
"Developer guide"_http://lammps.sandia.gov/Developer.pdf :ul
"Pre- and post-processing tools for LAMMPS"_http://lammps.sandia.gov/prepost.html
"Other software usable with LAMMPS"_http://lammps.sandia.gov/offsite.html
"Viz tools usable with LAMMPS"_http://lammps.sandia.gov/viz.html :ul
"Benchmark performance"_http://lammps.sandia.gov/bench.html
"Publications that have cited LAMMPS"_http://lammps.sandia.gov/papers.html
"Authors of LAMMPS"_http://lammps.sandia.gov/authors.html
"History of LAMMPS development"_http://lammps.sandia.gov/history.html
"Funding for LAMMPS"_http://lammps.sandia.gov/funding.html :ul

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@ -1,5 +1,5 @@
<!-- HTML_ONLY -->
<
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="2 Aug 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
@ -14,91 +14,54 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:link(lc,Commands_all.html#comm)
:line
<H1></H1>
LAMMPS Documentation :c,h1
2 Aug 2018 version :c,h2
Version info: :h3
The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on "this page of
the WWW site"_bug. Every 2-4 months one of the incremental releases
is subjected to more thorough testing and labeled as a {stable} version.
Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).
If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current [development] version of LAMMPS. :ulb,l
If you browse the HTML doc pages included in your tarball, they
describe the version you have. :l
The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch. :l
There is also a "Developer.pdf"_Developer.pdf file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS. :l
:ule
"What is a LAMMPS version?"_Manual_version.html
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
LAMMPS is a classical molecular dynamics simulation code with a focus
on materials modeling. It was designed to run efficiently on parallel
computers. It was developed originally at Sandia National
Laboratories, a US Department of Energy facility. The majority of
funding for LAMMPS has come from the US Department of Energy (DOE).
LAMMPS is an open-source code, distributed freely under the terms of
the GNU Public License (GPL).
The current core group of LAMMPS developers is at Sandia National
Labs and Temple University:
"Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l
Aidan Thompson, athomps at sandia.gov :l
Stan Moore, stamoor at sandia.gov :l
"Axel Kohlmeyer"_ako, akohlmey at gmail.com :l
:ule
Past core developers include Paul Crozier, Ray Shan and Mark Stevens,
all at Sandia. The [LAMMPS home page] at
"http://lammps.sandia.gov"_http://lammps.sandia.gov has more information
about the code and its uses. Interaction with external LAMMPS developers,
bug reports and feature requests are mainly coordinated through the
"LAMMPS project on GitHub."_https://github.com/lammps/lammps
The lammps.org domain, currently hosting "public continuous integration
testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux
RPM and Windows installer packages"_http://packages.lammps.org is located
at Temple University and managed by Richard Berger,
richard.berger at temple.edu.
:link(bug,http://lammps.sandia.gov/bug.html)
:link(sjp,http://www.sandia.gov/~sjplimp)
:link(ako,http://goo.gl/1wk0)
The "LAMMPS website"_lws has a variety of information about the code.
It includes links to an on-line version of this manual, a "mail
list"_http://lammps.sandia.gov/mail.html where users can post
questions, and a "GitHub site"https://github.com/lammps/lammps where
all LAMMPS development is coordinated.
:line
The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
Once you are familiar with LAMMPS, you may want to bookmark "this
page"_Section_commands.html#comm at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
"PDF file"_Manual.pdf of the entire manual, generated by
"htmldoc"_http://freecode.com/projects/htmldoc
The content for this manual is part of the LAMMPS distribution.
You can build a local copy of the Manual as HTML pages or a PDF file,
by following the steps on the "this page"_Build_manual.html.
There is also a "Developer.pdf"_Developer.pdf document which gives
a brief description of the basic code structure of LAMMPS.
:line
This manual is organized into the following sections.
Once you are familiar with LAMMPS, you may want to bookmark "this
page"_Commands.html since it gives quick access to a doc page for
every LAMMPS command.
<!-- RST
.. toctree::
@ -108,25 +71,23 @@ it gives quick access to documentation for all LAMMPS commands.
:name: userdoc
:includehidden:
Section_intro
Intro
Section_start
Section_commands
Commands
Packages
Speed
Section_howto
Howto
Examples
Tools
Modify
Python
Errors
Section_history
.. toctree::
:caption: Index
:name: index
:hidden:
tutorials
commands
fixes
computes
@ -145,12 +106,7 @@ Indices and tables
END_RST -->
<!-- HTML_ONLY -->
"Introduction"_Section_intro.html :olb,l
1.1 "What is LAMMPS"_intro_1 :ulb,b
1.2 "LAMMPS features"_intro_2 :b
1.3 "LAMMPS non-features"_intro_3 :b
1.4 "Open source distribution"_intro_4 :b
1.5 "Acknowledgments and citations"_intro_5 :ule,b
"Introduction"_Intro.html :olb,l
"Getting started"_Section_start.html :l
2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
2.2 "Making LAMMPS"_start_2 :b
@ -160,58 +116,17 @@ 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"_Section_howto.html :l
6.1 "Restarting a simulation"_howto_1 :ulb,b
6.2 "2d simulations"_howto_2 :b
6.3 "CHARMM and AMBER force fields"_howto_3 :b
6.4 "Running multiple simulations from one input script"_howto_4 :b
6.5 "Multi-replica simulations"_howto_5 :b
6.6 "Granular models"_howto_6 :b
6.7 "TIP3P water model"_howto_7 :b
6.8 "TIP4P water model"_howto_8 :b
6.9 "SPC water model"_howto_9 :b
6.10 "Coupling LAMMPS to other codes"_howto_10 :b
6.11 "Visualizing LAMMPS snapshots"_howto_11 :b
6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b
6.13 "NEMD simulations"_howto_13 :b
6.14 "Finite-size spherical and aspherical particles"_howto_14 :b
6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b
6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b
6.17 "Walls"_howto_17 :b
6.18 "Elastic constants"_howto_18 :b
6.19 "Library interface to LAMMPS"_howto_19 :b
6.20 "Calculating thermal conductivity"_howto_20 :b
6.21 "Calculating viscosity"_howto_21 :b
6.22 "Calculating a diffusion coefficient"_howto_22 :b
6.23 "Using chunks to calculate system properties"_howto_23 :b
6.24 "Setting parameters for pppm/disp"_howto_24 :b
6.25 "Polarizable models"_howto_25 :b
6.26 "Adiabatic core/shell model"_howto_26 :b
6.27 "Drude induced dipoles"_howto_27 :ule,b
"How-to discussions"_Howto.html :l
"Example scripts"_Examples.html :l
"Auxiliary tools"_Tools.html :l
"Modify & extend LAMMPS"_Modify.html :l
"Use Python with LAMMPS"_Python.html :l
"Errors"_Errors.html :l
"Future and history"_Section_history.html :l
13.1 "Coming attractions"_hist_1 :ulb,b
13.2 "Past versions"_hist_2 :ule,b
:ole
:link(intro_1,Section_intro.html#intro_1)
:link(intro_2,Section_intro.html#intro_2)
:link(intro_3,Section_intro.html#intro_3)
:link(intro_4,Section_intro.html#intro_4)
:link(intro_5,Section_intro.html#intro_5)
:link(start_1,Section_start.html#start_1)
:link(start_2,Section_start.html#start_2)
:link(start_3,Section_start.html#start_3)
@ -221,42 +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)
:link(howto_1,Section_howto.html#howto_1)
:link(howto_2,Section_howto.html#howto_2)
:link(howto_3,Section_howto.html#howto_3)
:link(howto_4,Section_howto.html#howto_4)
:link(howto_5,Section_howto.html#howto_5)
:link(howto_6,Section_howto.html#howto_6)
:link(howto_7,Section_howto.html#howto_7)
:link(howto_8,Section_howto.html#howto_8)
:link(howto_9,Section_howto.html#howto_9)
:link(howto_10,Section_howto.html#howto_10)
:link(howto_11,Section_howto.html#howto_11)
:link(howto_12,Section_howto.html#howto_12)
:link(howto_13,Section_howto.html#howto_13)
:link(howto_14,Section_howto.html#howto_14)
:link(howto_15,Section_howto.html#howto_15)
:link(howto_16,Section_howto.html#howto_16)
:link(howto_17,Section_howto.html#howto_17)
:link(howto_18,Section_howto.html#howto_18)
:link(howto_19,Section_howto.html#howto_19)
:link(howto_20,Section_howto.html#howto_20)
:link(howto_21,Section_howto.html#howto_21)
:link(howto_22,Section_howto.html#howto_22)
:link(howto_23,Section_howto.html#howto_23)
:link(howto_24,Section_howto.html#howto_24)
:link(howto_25,Section_howto.html#howto_25)
:link(howto_26,Section_howto.html#howto_26)
:link(howto_27,Section_howto.html#howto_27)
:link(hist_1,Section_history.html#hist_1)
:link(hist_2,Section_history.html#hist_2)
<!-- END_HTML_ONLY -->
</BODY>

33
doc/src/Manual_version.txt Normal file
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@ -0,0 +1,33 @@
"Higher level section"_Manual.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
What does a LAMMPS version mean: :h3
The LAMMPS "version" is the date when it was released, such as 1 May
2014. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it in the next {patch} release, which are
typically made every couple of weeks. Info on patch releases are on
"this website page"_http://lammps.sandia.gov/bug.html. Every few
months, the latest patch release is subjected to more thorough testing
and labeled as a {stable} version.
Each version of LAMMPS contains all the features and bug-fixes up to
and including its version date.
The version date is printed to the screen and logfile every time you
run LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball. And it is on the
first page of the "manual"_Manual.html.
If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current patch release of LAMMPS. :ulb,l
If you browse the HTML doc pages included in your tarball, they
describe the version you have, which may be older. :l,ule

2
doc/src/Modify.txt
View File

@ -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

2
doc/src/Modify_atom.txt
View File

@ -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
doc/src/Modify_body.txt
View File

@ -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
@ -14,10 +14,9 @@ Body particles can represent complex entities, such as surface meshes
of discrete points, collections of sub-particles, deformable objects,
etc.
See "Section 6.14"_Section_howto.html#howto_14 of the manual for
an overview of using body particles and the "body"_body.html doc page
for details on the various body styles LAMMPS supports. New styles
can be created to add new kinds of body particles to LAMMPS.
See the "Howto body"_Howto_body.html doc page for an overview of using
body particles and the various body styles LAMMPS supports. New
styles can be created to add new kinds of body particles to LAMMPS.
Body_nparticle.cpp is an example of a body particle that is treated as
a rigid body containing N sub-particles.

2
doc/src/Modify_bond.txt
View File

@ -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
doc/src/Modify_command.txt
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@ -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
doc/src/Modify_compute.txt
View File

@ -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

23
doc/src/Modify_contribute.txt
View File

@ -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
@ -32,14 +32,14 @@ How quickly your contribution will be integrated depends largely on
how much effort it will cause to integrate and test it, how much it
requires changes to the core codebase, and of how much interest it is
to the larger LAMMPS community. Please see below for a checklist of
typical requirements. Once you have prepared everything, see "this
tutorial"_tutorial_github.html for instructions on how to submit your
changes or new files through a GitHub pull request. If you prefer to
submit patches or full files, you should first make certain, that your
code works correctly with the latest patch-level version of LAMMPS and
contains all bugfixes from it. Then create a gzipped tar file of all
changed or added files or a corresponding patch file using 'diff -u'
or 'diff -c' and compress it with gzip. Please only use gzip
typical requirements. Once you have prepared everything, see the
"Howto github"_Howto_github.html doc page for instructions on how to
submit your changes or new files through a GitHub pull request. If you
prefer to submit patches or full files, you should first make certain,
that your code works correctly with the latest patch-level version of
LAMMPS and contains all bugfixes from it. Then create a gzipped tar
file of all changed or added files or a corresponding patch file using
'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip
compression, as this works well on all platforms.
If the new features/files are broadly useful we may add them as core
@ -54,8 +54,9 @@ packages by typing "make package" in the LAMMPS src directory.
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
used as a license for the rest of LAMMPS. See "Section
1.4"_Section_intro.html#intro_4 for details.
used as a license for the rest of LAMMPS. See the "Open
source"_http://lammps.sandia.gov/open_source.html page on the LAMMPS
website for details.
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source

2
doc/src/Modify_dump.txt
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@ -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
doc/src/Modify_fix.txt
View File

@ -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
doc/src/Modify_kspace.txt
View File

@ -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
doc/src/Modify_min.txt
View File

@ -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
doc/src/Modify_overview.txt
View File

@ -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
doc/src/Modify_pair.txt
View File

@ -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
doc/src/Modify_region.txt
View File

@ -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
doc/src/Modify_thermo.txt
View File

@ -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
doc/src/Modify_variable.txt
View File

@ -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
doc/src/Packages.txt
View File

@ -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

113
doc/src/Packages_details.txt
View File

@ -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
@ -53,6 +53,7 @@ as contained in the file name.
"RIGID"_#RIGID,
"SHOCK"_#SHOCK,
"SNAP"_#SNAP,
"SPIN"_#SPIN,
"SRD"_#SRD,
"VORONOI"_#VORONOI :tb(c=6,ea=c)
@ -113,7 +114,7 @@ make machine :pre
[Supporting info:]
src/ASPHERE: filenames -> commands
"Section 6.14"_Section_howto.html#howto_14
"Howto spherical"_Howto_spherical.html
"pair_style gayberne"_pair_gayberne.html
"pair_style resquared"_pair_resquared.html
"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf
@ -131,7 +132,8 @@ BODY package :link(BODY),h4
Body-style particles with internal structure. Computes,
time-integration fixes, pair styles, as well as the body styles
themselves. See the "body"_body.html doc page for an overview.
themselves. See the "Howto body"_Howto_body.html doc page for an
overview.
[Install or un-install:]
@ -144,10 +146,10 @@ make machine :pre
[Supporting info:]
src/BODY filenames -> commands
"body"_body.html
"Howto_body"_Howto_body.html
"atom_style body"_atom_style.html
"fix nve/body"_fix_nve_body.html
"pair_style body"_pair_body.html
"pair_style body/nparticle"_pair_body_nparticle.html
examples/body :ul
:line
@ -259,9 +261,9 @@ Compute and pair styles that implement the adiabatic core/shell model
for polarizability. The pair styles augment Born, Buckingham, and
Lennard-Jones styles with core/shell capabilities. The "compute
temp/cs"_compute_temp_cs.html command calculates the temperature of a
system with core/shell particles. See "Section
6.26"_Section_howto.html#howto_26 for an overview of how to use this
package.
system with core/shell particles. See the "Howto
coreshell"_Howto_coreshell.html doc page for an overview of how to use
this package.
[Author:] Hendrik Heenen (Technical U of Munich).
@ -276,8 +278,8 @@ make machine :pre
[Supporting info:]
src/CORESHELL: filenames -> commands
"Section 6.26"_Section_howto.html#howto_26
"Section 6.25"_Section_howto.html#howto_25
"Howto coreshell"_Howto_coreshell.html
"Howto polarizable"_Howto_polarizable.html
"compute temp/cs"_compute_temp_cs.html
"pair_style born/coul/long/cs"_pair_cs.html
"pair_style buck/coul/long/cs"_pair_cs.html
@ -395,7 +397,7 @@ 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
@ -419,7 +421,7 @@ make machine :pre
[Supporting info:]
src/GRANULAR: filenames -> commands
"Section 6.6"_Section_howto.html#howto_6,
"Howto granular"_Howto_granular.html
"fix pour"_fix_pour.html
"fix wall/gran"_fix_wall_gran.html
"pair_style gran/hooke"_pair_gran.html
@ -486,8 +488,8 @@ 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:
@ -592,7 +594,7 @@ 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
@ -626,11 +628,11 @@ make machine :pre
src/KSPACE: filenames -> commands
"kspace_style"_kspace_style.html
"doc/PDF/kspace.pdf"_PDF/kspace.pdf
"Section 6.7"_Section_howto.html#howto_7
"Section 6.8"_Section_howto.html#howto_8
"Section 6.9"_Section_howto.html#howto_9
"Howto tip3p"_Howto_tip3p.html
"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
@ -714,7 +716,7 @@ 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
@ -877,7 +879,7 @@ src/MOLECULE: filenames -> commands
"improper_style"_improper_style.html
"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html
"pair_style lj/charmm/coul/charmm"_pair_charmm.html
"Section 6.3"_Section_howto.html#howto_3
"Howto bioFF"_Howto_bioFF.html
examples/cmap
examples/dreiding
examples/micelle,
@ -1016,7 +1018,7 @@ 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
@ -1115,10 +1117,10 @@ PYTHON package :link(PYTHON),h4
A "python"_python.html command which allow you to execute Python code
from a LAMMPS input script. The code can be in a separate file or
embedded in the input script itself. See "Section
11.2"_Section_python.html#py_2 for an overview of using Python from
LAMMPS in this manner and the entire section for other ways to use
LAMMPS and Python together.
embedded in the input script itself. See the "Python
call"_Python_call.html doc page for an overview of using Python from
LAMMPS in this manner and all the "Python"_Python.html doc pages for
other ways to use LAMMPS and Python together.
[Install or un-install:]
@ -1139,7 +1141,7 @@ to Makefile.lammps) if the LAMMPS build fails.
[Supporting info:]
src/PYTHON: filenames -> commands
"Section 11"_Section_python.html
"Python call"_Python.html
lib/python/README
examples/python :ul
@ -1229,8 +1231,8 @@ REPLICA package :link(REPLICA),h4
[Contents:]
A collection of multi-replica methods which can be used when running
multiple LAMMPS simulations (replicas). See "Section
6.5"_Section_howto.html#howto_5 for an overview of how to run
multiple LAMMPS simulations (replicas). See the "Howto
replica"_Howto_replica.html doc page for an overview of how to run
multi-replica simulations in LAMMPS. Methods in the package include
nudged elastic band (NEB), parallel replica dynamics (PRD),
temperature accelerated dynamics (TAD), parallel tempering, and a
@ -1249,7 +1251,7 @@ make machine :pre
[Supporting info:]
src/REPLICA: filenames -> commands
"Section 6.5"_Section_howto.html#howto_5
"Howto replica"_Howto_replica.html
"neb"_neb.html
"prd"_prd.html
"tad"_tad.html
@ -1352,6 +1354,38 @@ examples/snap :ul
:line
SPIN package :link(SPIN),h4
[Contents:]
Model atomic magnetic spins classically, coupled to atoms moving in
the usual manner via MD. Various pair, fix, and compute styles.
[Author:] Julian Tranchida (Sandia).
[Install or un-install:]
make yes-spin
make machine :pre
make no-spin
make machine :pre
[Supporting info:]
src/SPIN: filenames -> commands
"Howto spin"_Howto_spin.html
"pair_style spin/dmi"_pair_spin_dmi.html
"pair_style spin/exchange"_pair_spin_exchange.html
"pair_style spin/magelec"_pair_spin_magelec.html
"pair_style spin/neel"_pair_spin_neel.html
"fix nve/spin"_fix_nve_spin.html
"fix precession/spin"_fix_precession_spin.html
"compute spin"_compute_spin.html
examples/SPIN :ul
:line
SRD package :link(SRD),h4
[Contents:]
@ -1799,10 +1833,10 @@ USER-DRUDE package :link(USER-DRUDE),h4
[Contents:]
Fixes, pair styles, and a compute to simulate thermalized Drude
oscillators as a model of polarization. See "Section
6.27"_Section_howto.html#howto_27 for an overview of how to use the
package. There are auxiliary tools for using this package in
tools/drude.
oscillators as a model of polarization. See the "Howto
drude"_Howto_drude.html and "Howto drude2"_Howto_drude2.html doc pages
for an overview of how to use the package. There are auxiliary tools
for using this package in tools/drude.
[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
@ -1818,8 +1852,9 @@ make machine :pre
[Supporting info:]
src/USER-DRUDE: filenames -> commands
"Section 6.27"_Section_howto.html#howto_27
"Section 6.25"_Section_howto.html#howto_25
"Howto drude"_Howto_drude.html
"Howto drude2"_Howto_drude2.html
"Howto polarizable"_Howto_polarizable.html
src/USER-DRUDE/README
"fix drude"_fix_drude.html
"fix drude/transform/*"_fix_drude_transform.html
@ -2038,7 +2073,7 @@ 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
@ -2159,7 +2194,7 @@ make machine :pre
src/USER-MANIFOLD: filenames -> commands
src/USER-MANIFOLD/README
"doc/manifolds"_manifolds.html
"Howto manifold"_Howto_manifold.html
"fix manifoldforce"_fix_manifoldforce.html
"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
@ -2423,7 +2458,7 @@ 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

16
doc/src/Packages_standard.txt
View File

@ -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
@ -31,15 +31,15 @@ int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul
Package, Description, Doc page, Example, Library
"ASPHERE"_Packages_details.html#ASPHERE, aspherical particle models, "Section 6.6.14"_Section_howto.html#howto_14, ellipse, -
"BODY"_Packages_details.html#BODY, body-style particles, "body"_body.html, body, -
"ASPHERE"_Packages_details.html#ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, -
"BODY"_Packages_details.html#BODY, body-style particles, "Howto body"_Howto_body.html, body, -
"CLASS2"_Packages_details.html#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
"COLLOID"_Packages_details.html#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
"COMPRESS"_Packages_details.html#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
"CORESHELL"_Packages_details.html#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -
"CORESHELL"_Packages_details.html#CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, -
"DIPOLE"_Packages_details.html#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
"GPU"_Packages_details.html#GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
"GRANULAR"_Packages_details.html#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
"GRANULAR"_Packages_details.html#GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, -
"KIM"_Packages_details.html#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
"KOKKOS"_Packages_details.html#KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"KSPACE"_Packages_details.html#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
@ -48,7 +48,7 @@ Package, Description, Doc page, Example, Library
"MC"_Packages_details.html#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
"MEAM"_Packages_details.html#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
"MISC"_Packages_details.html#MISC, miscellanous single-file commands, -, -, -
"MOLECULE"_Packages_details.html#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
"MOLECULE"_Packages_details.html#MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, -
"MPIIO"_Packages_details.html#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
"MSCG"_Packages_details.html#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
"OPT"_Packages_details.html#OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
@ -57,9 +57,9 @@ Package, Description, Doc page, Example, Library
"PYTHON"_Packages_details.html#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
"QEQ"_Packages_details.html#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
"REAX"_Packages_details.html#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
"REPLICA"_Packages_details.html#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
"REPLICA"_Packages_details.html#REPLICA, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
"RIGID"_Packages_details.html#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
"SHOCK"_Packages_details.html#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
"SNAP"_Packages_details.html#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
"SRD"_Packages_details.html#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
"SPIN"_#SPIN, magnetic atomic spin dynamics, "Howto spin"_Howto_spin.html, SPIN, -"SRD"_Packages_details.html#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
"VORONOI"_Packages_details.html#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)

4
doc/src/Packages_user.txt
View File

@ -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
@ -46,7 +46,7 @@ Package, Description, Doc page, Example, Library
"USER-COLVARS"_Packages_details.html#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
"USER-DIFFRACTION"_Packages_details.html#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
"USER-DPD"_Packages_details.html#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
"USER-DRUDE"_Packages_details.html#USER-DRUDE, Drude oscillators, "tutorial"_tutorial_drude.html, USER/drude, -
"USER-DRUDE"_Packages_details.html#USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, -
"USER-EFF"_Packages_details.html#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
"USER-FEP"_Packages_details.html#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
"USER-H5MD"_Packages_details.html#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext

2
doc/src/Python.txt
View File

@ -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

2
doc/src/Python_call.txt
View File

@ -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
doc/src/Python_examples.txt
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@ -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
doc/src/Python_install.txt
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@ -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

16
doc/src/Python_library.txt
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@ -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
@ -21,8 +21,8 @@ from lammps import lammps :pre
These are the methods defined by the lammps module. If you look at
the files src/library.cpp and src/library.h you will see they
correspond one-to-one with calls you can make to the LAMMPS library
from a C++ or C or Fortran program, and which are described in
"Section 6.19"_Section_howto.html#howto_19 of the manual.
from a C++ or C or Fortran program, and which are described on the
"Howto library"_Howto_library.html doc page.
The python/examples directory has Python scripts which show how Python
can run LAMMPS, grab data, change it, and put it back into LAMMPS.
@ -165,11 +165,11 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
See "Section 6.15"_Section_howto.html#howto_15 of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
"computes"_compute.html and "fixes"_fix.html for a description of what
they calculate and store.
See the "Howto output"_Howto_output.html doc page for a discussion of
global, per-atom, and local data, and of scalar, vector, and array
data types. See the doc pages for individual "computes"_compute.html
and "fixes"_fix.html for a description of what they calculate and
store.
For extract_variable(), an "equal-style or atom-style
variable"_variable.html is evaluated and its result returned.

2
doc/src/Python_mpi.txt
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@ -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

6
doc/src/Python_pylammps.txt
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@ -3,12 +3,12 @@ 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
PyLammps interface :h3
PyLammps is a Python wrapper class which can be created on its own or
use an existing lammps Python object. It has its own "PyLammps
Tutorial"_tutorial_pylammps.html doc page.
use an existing lammps Python object. It has its own "Howto
pylammps"_Howto_pylammps.html doc page.

2
doc/src/Python_run.txt
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@ -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
doc/src/Python_shlib.txt
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@ -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
doc/src/Python_test.txt
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@ -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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@ -1,135 +0,0 @@
"Previous Section"_Errors.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Manual.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
13. Future and history :h2
This section lists features we plan to add to LAMMPS, features of
previous versions of LAMMPS, and features of other parallel molecular
dynamics codes our group has distributed.
13.1 "Coming attractions"_#hist_1
13.2 "Past versions"_#hist_2 :all(b)
:line
:line
13.1 Coming attractions :h3,link(hist_1)
As of summer 2016 we are using the "LAMMPS project issue tracker
on GitHub"_https://github.com/lammps/lammps/issues for keeping
track of suggested, planned or pending new features. This includes
discussions of how to best implement them, or why they would be
useful. Especially if a planned or proposed feature is non-trivial
to add, e.g. because it requires changes to some of the core
classes of LAMMPS, people planning to contribute a new feature to
LAMMS are encouraged to submit an issue about their planned
implementation this way in order to receive feedback from the
LAMMPS core developers. They will provide suggestions about
the validity of the proposed approach and possible improvements,
pitfalls or alternatives.
Please see some of the closed issues for examples of how to
suggest code enhancements, submit proposed changes, or report
possible bugs and how they are resolved.
As an alternative to using GitHub, you may e-mail the
"core developers"_http://lammps.sandia.gov/authors.html or send
an e-mail to the "LAMMPS Mail list"_http://lammps.sandia.gov/mail.html
if you want to have your suggestion added to the list.
:line
13.2 Past versions :h3,link(hist_2)
LAMMPS development began in the mid 1990s under a cooperative research
& development agreement (CRADA) between two DOE labs (Sandia and LLNL)
and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
to develop a large-scale parallel classical MD code; the coding effort
was led by Steve Plimpton at Sandia.
After the CRADA ended, a final F77 version, LAMMPS 99, was
released. As development of LAMMPS continued at Sandia, its memory
management was converted to F90; a final F90 version was released as
LAMMPS 2001.
The current LAMMPS is a rewrite in C++ and was first publicly released
as an open source code in 2004. It includes many new features beyond
those in LAMMPS 99 or 2001. It also includes features from older
parallel MD codes written at Sandia, namely ParaDyn, Warp, and
GranFlow (see below).
In late 2006 we began merging new capabilities into LAMMPS that were
developed by Aidan Thompson at Sandia for his MD code GRASP, which has
a parallel framework similar to LAMMPS. Most notably, these have
included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
and the associated charge-equilibration routines needed for ReaxFF.
The "History link"_http://lammps.sandia.gov/history.html on the
LAMMPS WWW page gives a timeline of features added to the
C++ open-source version of LAMMPS over the last several years.
These older codes are available for download from the "LAMMPS WWW
site"_lws, except for Warp & GranFlow which were primarily used
internally. A brief listing of their features is given here.
LAMMPS 2001
F90 + MPI
dynamic memory
spatial-decomposition parallelism
NVE, NVT, NPT, NPH, rRESPA integrators
LJ and Coulombic pairwise force fields
all-atom, united-atom, bead-spring polymer force fields
CHARMM-compatible force fields
class 2 force fields
3d/2d Ewald & PPPM
various force and temperature constraints
SHAKE
Hessian-free truncated-Newton minimizer
user-defined diagnostics :ul
LAMMPS 99
F77 + MPI
static memory allocation
spatial-decomposition parallelism
most of the LAMMPS 2001 features with a few exceptions
no 2d Ewald & PPPM
molecular force fields are missing a few CHARMM terms
no SHAKE :ul
Warp
F90 + MPI
spatial-decomposition parallelism
embedded atom method (EAM) metal potentials + LJ
lattice and grain-boundary atom creation
NVE, NVT integrators
boundary conditions for applying shear stresses
temperature controls for actively sheared systems
per-atom energy and centro-symmetry computation and output :ul
ParaDyn
F77 + MPI
atom- and force-decomposition parallelism
embedded atom method (EAM) metal potentials
lattice atom creation
NVE, NVT, NPT integrators
all serial DYNAMO features for controls and constraints :ul
GranFlow
F90 + MPI
spatial-decomposition parallelism
frictional granular potentials
NVE integrator
boundary conditions for granular flow and packing and walls
particle insertion :ul

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@ -1,550 +0,0 @@
"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_start.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
1. Introduction :h2
This section provides an overview of what LAMMPS can and can't do,
describes what it means for LAMMPS to be an open-source code, and
acknowledges the funding and people who have contributed to LAMMPS
over the years.
1.1 "What is LAMMPS"_#intro_1
1.2 "LAMMPS features"_#intro_2
1.3 "LAMMPS non-features"_#intro_3
1.4 "Open source distribution"_#intro_4
1.5 "Acknowledgments and citations"_#intro_5 :all(b)
:line
:line
1.1 What is LAMMPS :link(intro_1),h4
LAMMPS is a classical molecular dynamics code that models an ensemble
of particles in a liquid, solid, or gaseous state. It can model
atomic, polymeric, biological, metallic, granular, and coarse-grained
systems using a variety of force fields and boundary conditions.
For examples of LAMMPS simulations, see the Publications page of the
"LAMMPS WWW Site"_lws.
LAMMPS runs efficiently on single-processor desktop or laptop
machines, but is designed for parallel computers. It will run on any
parallel machine that compiles C++ and supports the "MPI"_mpi
message-passing library. This includes distributed- or shared-memory
parallel machines and Beowulf-style clusters.
:link(mpi,http://www-unix.mcs.anl.gov/mpi)
LAMMPS can model systems with only a few particles up to millions or
billions. See "Section 8"_Section_perf.html for information on
LAMMPS performance and scalability, or the Benchmarks section of the
"LAMMPS WWW Site"_lws.
LAMMPS is a freely-available open-source code, distributed under the
terms of the "GNU Public License"_gnu, which means you can use or
modify the code however you wish. See "this section"_#intro_4 for a
brief discussion of the open-source philosophy.
:link(gnu,http://www.gnu.org/copyleft/gpl.html)
LAMMPS is designed to be easy to modify or extend with new
capabilities, such as new force fields, atom types, boundary
conditions, or diagnostics. See the "Modify"_Modify.html doc page for
more details.
The current version of LAMMPS is written in C++. Earlier versions
were written in F77 and F90. See
"Section 13"_Section_history.html for more information on
different versions. All versions can be downloaded from the "LAMMPS
WWW Site"_lws.
LAMMPS was originally developed under a US Department of Energy CRADA
(Cooperative Research and Development Agreement) between two DOE labs
and 3 companies. It is distributed by "Sandia National Labs"_snl.
See "this section"_#intro_5 for more information on LAMMPS funding and
individuals who have contributed to LAMMPS.
:link(snl,http://www.sandia.gov)
In the most general sense, LAMMPS integrates Newton's equations of
motion for collections of atoms, molecules, or macroscopic particles
that interact via short- or long-range forces with a variety of
initial and/or boundary conditions. For computational efficiency
LAMMPS uses neighbor lists to keep track of nearby particles. The
lists are optimized for systems with particles that are repulsive at
short distances, so that the local density of particles never becomes
too large. On parallel machines, LAMMPS uses spatial-decomposition
techniques to partition the simulation domain into small 3d
sub-domains, one of which is assigned to each processor. Processors
communicate and store "ghost" atom information for atoms that border
their sub-domain. LAMMPS is most efficient (in a parallel sense) for
systems whose particles fill a 3d rectangular box with roughly uniform
density. Papers with technical details of the algorithms used in
LAMMPS are listed in "this section"_#intro_5.
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1.2 LAMMPS features :link(intro_2),h4
This section highlights LAMMPS features, with pointers to specific
commands which give more details. If LAMMPS doesn't have your
favorite interatomic potential, boundary condition, or atom type, see
the "Modify"_Modify.html doc page, which describes how you can add it
to LAMMPS.
General features :h4
runs on a single processor or in parallel
distributed-memory message-passing parallelism (MPI)
spatial-decomposition of simulation domain for parallelism
open-source distribution
highly portable C++
optional libraries used: MPI and single-processor FFT
GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features
easy to extend with new features and functionality
runs from an input script
syntax for defining and using variables and formulas
syntax for looping over runs and breaking out of loops
run one or multiple simulations simultaneously (in parallel) from one script
build as library, invoke LAMMPS thru library interface or provided Python wrapper
couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
Particle and model types :h4
("atom style"_atom_style.html command)
atoms
coarse-grained particles (e.g. bead-spring polymers)
united-atom polymers or organic molecules
all-atom polymers, organic molecules, proteins, DNA
metals
granular materials
coarse-grained mesoscale models
finite-size spherical and ellipsoidal particles
finite-size line segment (2d) and triangle (3d) particles
point dipole particles
rigid collections of particles
hybrid combinations of these :ul
Force fields :h4
("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, "kspace style"_kspace_style.html
commands)
pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
charged pairwise potentials: Coulombic, point-dipole
manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \
REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
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
charge equilibration (QEq via dynamic, point, shielded, Slater methods)
coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
mesoscopic potentials: granular, Peridynamics, SPH
electron force field (eFF, AWPMD)
bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
quartic (breakable)
angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \
class 2 (COMPASS)
dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
class 2 (COMPASS), OPLS
improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
polymer potentials: all-atom, united-atom, bead-spring, breakable
water potentials: TIP3P, TIP4P, SPC
implicit solvent potentials: hydrodynamic lubrication, Debye
force-field compatibility with common CHARMM, AMBER, DREIDING, \
OPLS, GROMACS, COMPASS options
access to "KIM archive"_http://openkim.org of potentials via \
"pair kim"_pair_kim.html
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
potentials can be used in one simulation
overlaid potentials: superposition of multiple pair potentials :ul
Atom creation :h4
("read_data"_read_data.html, "lattice"_lattice.html,
"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
read in atom coords from files
create atoms on one or more lattices (e.g. grain boundaries)
delete geometric or logical groups of atoms (e.g. voids)
replicate existing atoms multiple times
displace atoms :ul
Ensembles, constraints, and boundary conditions :h4
("fix"_fix.html command)
2d or 3d systems
orthogonal or non-orthogonal (triclinic symmetry) simulation domains
constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
thermostatting options for groups and geometric regions of atoms
pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
simulation box deformation (tensile and shear)
harmonic (umbrella) constraint forces
rigid body constraints
SHAKE bond and angle constraints
Monte Carlo bond breaking, formation, swapping
atom/molecule insertion and deletion
walls of various kinds
non-equilibrium molecular dynamics (NEMD)
variety of additional boundary conditions and constraints :ul
Integrators :h4
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
velocity-Verlet integrator
Brownian dynamics
rigid body integration
energy minimization via conjugate gradient or steepest descent relaxation
rRESPA hierarchical timestepping
rerun command for post-processing of dump files :ul
Diagnostics :h4
see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
Output :h4
("dump"_dump.html, "restart"_restart.html commands)
log file of thermodynamic info
text dump files of atom coords, velocities, other per-atom quantities
binary restart files
parallel I/O of dump and restart files
per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
user-defined system-wide (log file) or per-atom (dump file) calculations
spatial and time averaging of per-atom quantities
time averaging of system-wide quantities
atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
Multi-replica models :h4
"nudged elastic band"_neb.html
"parallel replica dynamics"_prd.html
"temperature accelerated dynamics"_tad.html
"parallel tempering"_temper.html
Pre- and post-processing :h4
Various pre- and post-processing serial tools are packaged with
LAMMPS; see the "Tools"_Tools.html doc page for details. :ulb,l
Our group has also written and released a separate toolkit called
"Pizza.py"_pizza which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in "Python"_python and is available for download from "the
Pizza.py WWW site"_pizza. :l
:ule
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(python,http://www.python.org)
Specialized features :h4
LAMMPS can be built with optional packages which implement a variety
of additional capabilities. An overview of all the packages is "given
here"_Packages.html.
These are some LAMMPS capabilities which you may not think of as
typical classical molecular dynamics options:
"static"_balance.html and "dynamic load-balancing"_fix_balance.html
"generalized aspherical particles"_body.html
"stochastic rotation dynamics (SRD)"_fix_srd.html
"real-time visualization and interactive MD"_fix_imd.html
calculate "virtual diffraction patterns"_compute_xrd.html
"atom-to-continuum coupling"_fix_atc.html with finite elements
coupled rigid body integration via the "POEMS"_fix_poems.html library
"QM/MM coupling"_fix_qmmm.html
"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html
Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html "atom swapping"_fix_atom_swap.html and "bond swapping"_fix_bond_swap.html
"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
"Peridynamics mesoscale modeling"_pair_peri.html
"Lattice Boltzmann fluid"_fix_lb_fluid.html
"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
"two-temperature electron model"_fix_ttm.html :ul
:line
1.3 LAMMPS non-features :link(intro_3),h4
LAMMPS is designed to efficiently compute Newton's equations of motion
for a system of interacting particles. Many of the tools needed to
pre- and post-process the data for such simulations are not included
in the LAMMPS kernel for several reasons:
the desire to keep LAMMPS simple
they are not parallel operations
other codes already do them
limited development resources :ul
Specifically, LAMMPS itself does not:
run thru a GUI
build molecular systems
assign force-field coefficients automagically
perform sophisticated analyses of your MD simulation
visualize your MD simulation
plot your output data :ul
A few tools for pre- and post-processing tasks are provided as part of
the LAMMPS package; they are described on the "Tools"_Tools.html doc
page. However, many people use other codes or write their own tools
for these tasks.
As noted above, our group has also written and released a separate
toolkit called "Pizza.py"_pizza which addresses some of the listed
bullets. It provides tools for doing setup, analysis, plotting, and
visualization for LAMMPS simulations. Pizza.py is written in
"Python"_python and is available for download from "the Pizza.py WWW
site"_pizza.
LAMMPS requires as input a list of initial atom coordinates and types,
molecular topology information, and force-field coefficients assigned
to all atoms and bonds. LAMMPS will not build molecular systems and
assign force-field parameters for you.
For atomic systems LAMMPS provides a "create_atoms"_create_atoms.html
command which places atoms on solid-state lattices (fcc, bcc,
user-defined, etc). Assigning small numbers of force field
coefficients can be done via the "pair coeff"_pair_coeff.html, "bond
coeff"_bond_coeff.html, "angle coeff"_angle_coeff.html, etc commands.
For molecular systems or more complicated simulation geometries, users
typically use another code as a builder and convert its output to
LAMMPS input format, or write their own code to generate atom
coordinate and molecular topology for LAMMPS to read in.
For complicated molecular systems (e.g. a protein), a multitude of
topology information and hundreds of force-field coefficients must
typically be specified. We suggest you use a program like
"CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup
such problems and dump its information to a file. You can then
reformat the file as LAMMPS input. Some of the tools described on the
"Tools"_Tools.html doc page can assist in this process.
Similarly, LAMMPS creates output files in a simple format. Most users
post-process these files with their own analysis tools or re-format
them for input into other programs, including visualization packages.
If you are convinced you need to compute something on-the-fly as
LAMMPS runs, see the "Modify"_Modify.html doc page for a discussion of
how you can use the "dump"_dump.html and "compute"_compute.html and
"fix"_fix.html commands to print out data of your choosing. Keep in
mind that complicated computations can slow down the molecular
dynamics timestepping, particularly if the computations are not
parallel, so it is often better to leave such analysis to
post-processing codes.
For high-quality visualization we recommend the
following packages:
"VMD"_http://www.ks.uiuc.edu/Research/vmd
"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
"OVITO"_http://www.ovito.org/
"ParaView"_http://www.paraview.org/
"PyMol"_http://www.pymol.org
"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
"RasMol"_http://www.openrasmol.org :ul
Other features that LAMMPS does not yet (and may never) support are
discussed in "Section 13"_Section_history.html.
Finally, these are freely-available molecular dynamics codes, most of
them parallel, which may be well-suited to the problems you want to
model. They can also be used in conjunction with LAMMPS to perform
complementary modeling tasks.
"CHARMM"_charmm
"AMBER"_amber
"NAMD"_namd
"NWCHEM"_nwchem
"DL_POLY"_dlpoly
"Tinker"_tinker :ul
:link(charmm,http://www.charmm.org)
:link(amber,http://ambermd.org)
:link(namd,http://www.ks.uiuc.edu/Research/namd/)
:link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
:link(dlpoly,http://www.ccp5.ac.uk/DL_POLY_CLASSIC)
:link(tinker,http://dasher.wustl.edu/tinker)
CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
modeling biological molecules. CHARMM and AMBER use
atom-decomposition (replicated-data) strategies for parallelism; NAMD
and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
Tinker is a serial code. DL_POLY includes potentials for a variety of
biological and non-biological materials; both a replicated-data and
spatial-decomposition version exist.
:line
1.4 Open source distribution :link(intro_4),h4
LAMMPS comes with no warranty of any kind. As each source file states
in its header, it is a copyrighted code that is distributed free-of-
charge, under the terms of the "GNU Public License"_gnu (GPL). This
is often referred to as open-source distribution - see
"www.gnu.org"_gnuorg or "www.opensource.org"_opensource for more
details. The legal text of the GPL is in the LICENSE file that is
included in the LAMMPS distribution.
:link(gnuorg,http://www.gnu.org)
:link(opensource,http://www.opensource.org)
Here is a summary of what the GPL means for LAMMPS users:
(1) Anyone is free to use, modify, or extend LAMMPS in any way they
choose, including for commercial purposes.
(2) If you distribute a modified version of LAMMPS, it must remain
open-source, meaning you distribute it under the terms of the GPL.
You should clearly annotate such a code as a derivative version of
LAMMPS.
(3) If you release any code that includes LAMMPS source code, then it
must also be open-sourced, meaning you distribute it under the terms
of the GPL.
(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
source file headers (including the copyright and GPL notices) should
remain part of the code.
In the spirit of an open-source code, these are various ways you can
contribute to making LAMMPS better. You can send email to the
"developers"_http://lammps.sandia.gov/authors.html on any of these
items.
Point prospective users to the "LAMMPS WWW Site"_lws. Mention it in
talks or link to it from your WWW site. :ulb,l
If you find an error or omission in this manual or on the "LAMMPS WWW
Site"_lws, or have a suggestion for something to clarify or include,
send an email to the
"developers"_http://lammps.sandia.gov/authors.html. :l
If you find a bug, the "Errors bugs"_Errors_bugs.html doc page
describes how to report it. :l
If you publish a paper using LAMMPS results, send the citation (and
any cool pictures or movies if you like) to add to the Publications,
Pictures, and Movies pages of the "LAMMPS WWW Site"_lws, with links
and attributions back to you. :l
Create a new Makefile.machine that can be added to the src/MAKE
directory. :l
The tools sub-directory of the LAMMPS distribution has various
stand-alone codes for pre- and post-processing of LAMMPS data. More
details are given on the "Tools"_Tools.html doc page. If you write a
new tool that users will find useful, it can be added to the LAMMPS
distribution. :l
LAMMPS is designed to be easy to extend with new code for features
like potentials, boundary conditions, diagnostic computations, etc.
The "Modify"_Modify.html doc page gives details. If you add a feature
of general interest, it can be added to the LAMMPS distribution. :l
The Benchmark page of the "LAMMPS WWW Site"_lws lists LAMMPS
performance on various platforms. The files needed to run the
benchmarks are part of the LAMMPS distribution. If your machine is
sufficiently different from those listed, your timing data can be
added to the page. :l
You can send feedback for the User Comments page of the "LAMMPS WWW
Site"_lws. It might be added to the page. No promises. :l
Cash. Small denominations, unmarked bills preferred. Paper sack OK.
Leave on desk. VISA also accepted. Chocolate chip cookies
encouraged. :l
:ule
:line
1.5 Acknowledgments and citations :h3,link(intro_5)
LAMMPS development has been funded by the "US Department of
Energy"_doe (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
programs and its "OASCR"_oascr and "OBER"_ober offices.
Specifically, work on the latest version was funded in part by the US
Department of Energy's Genomics:GTL program
("www.doegenomestolife.org"_gtl) under the "project"_ourgtl, "Carbon
Sequestration in Synechococcus Sp.: From Molecular Machines to
Hierarchical Modeling".
:link(doe,http://www.doe.gov)
:link(gtl,http://www.doegenomestolife.org)
:link(ourgtl,http://www.genomes2life.org)
:link(oascr,http://www.sc.doe.gov/ascr/home.html)
:link(ober,http://www.er.doe.gov/production/ober/ober_top.html)
The following paper describe the basic parallel algorithms used in
LAMMPS. If you use LAMMPS results in your published work, please cite
this paper and include a pointer to the "LAMMPS WWW Site"_lws
(http://lammps.sandia.gov):
S. Plimpton, [Fast Parallel Algorithms for Short-Range Molecular
Dynamics], J Comp Phys, 117, 1-19 (1995).
Other papers describing specific algorithms used in LAMMPS are listed
under the "Citing LAMMPS link"_http://lammps.sandia.gov/cite.html of
the LAMMPS WWW page.
The "Publications link"_http://lammps.sandia.gov/papers.html on the
LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is
not listed there for some reason, feel free to send us the info. If
the simulations in your paper produced cool pictures or animations,
we'll be pleased to add them to the
"Pictures"_http://lammps.sandia.gov/pictures.html or
"Movies"_http://lammps.sandia.gov/movies.html pages of the LAMMPS WWW
site.
The primary LAMMPS developers are at Sandia National Labs and Temple University:
Steve Plimpton, sjplimp at sandia.gov
Aidan Thompson, athomps at sandia.gov
Stan Moore, stamoor at sandia.gov
Axel Kohlmeyer, akohlmey at gmail.com :ul
Past primary developers include Paul Crozier and Mark Stevens,
both at Sandia, and Ray Shan, now at Materials Design.
The following folks are responsible for significant contributions to
the code, or other aspects of the LAMMPS development effort. Many of
the packages they have written are somewhat unique to LAMMPS and the
code would not be as general-purpose as it is without their expertise
and efforts.
Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM, USER-TALLY, and COMPRESS packages
Roy Pollock (LLNL), Ewald and PPPM solvers
Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential (superseded by USER-MEAMC)
Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA (obsoleted by KOKKOS) and KOKKOS packages
Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
Christoph Kloss (JKU), Christoph.Kloss at jku.at, LIGGGHTS fork for granular models and granular/fluid coupling
Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul
As discussed in "Section 13"_Section_history.html, LAMMPS
originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:
John Carpenter (Mayo Clinic, formerly at Cray Research)
Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
Steve Lustig (Dupont)
Jim Belak (LLNL) :ul

64
doc/src/Section_start.txt
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@ -1,10 +1,10 @@
"Previous Section"_Section_intro.html - "LAMMPS WWW Site"_lws -
"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
@ -934,9 +934,9 @@ Makefile.opt :ul
LAMMPS can be built as either a static or shared library, which can
then be called from another application or a scripting language. See
"this section"_Section_howto.html#howto_10 for more info on coupling
LAMMPS to other codes. See the "Python"_Python.html doc page for more
info on wrapping and running LAMMPS from Python.
the "Howto couple"_Howto_couple.html doc page for more info on
coupling LAMMPS to other codes. See the "Python"_Python.html doc page
for more info on wrapping and running LAMMPS from Python.
Static library :h4
@ -1039,16 +1039,16 @@ src/library.cpp and src/library.h.
See the sample codes in examples/COUPLE/simple for examples of C++ and
C and Fortran codes that invoke LAMMPS thru its library interface.
There are other examples as well in the COUPLE directory which are
discussed in "Section 6.10"_Section_howto.html#howto_10 of the manual.
See the "Python"_Python.html doc page for a description of the Python
wrapper provided with LAMMPS that operates through the LAMMPS library
interface.
There are other examples as well in the COUPLE directory which use
coupling ideas discussed on the "Howto couple"_Howto_couple.html doc
page. See the "Python"_Python.html doc page for a description of the
Python wrapper provided with LAMMPS that operates through the LAMMPS
library interface.
The files src/library.cpp and library.h define the C-style API for
using LAMMPS as a library. See "Section
6.19"_Section_howto.html#howto_19 of the manual for a description of the
interface and how to extend it for your needs.
using LAMMPS as a library. See the "Howto library"_Howto_library.html
doc page for a description of the interface and how to extend it for
your needs.
: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
@ -1391,16 +1391,16 @@ processors in all partitions must equal P. Thus the command
"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
processors.
Running with multiple partitions can e useful for running
"multi-replica simulations"_Section_howto.html#howto_5, where each
replica runs on on one or a few processors. Note that with MPI
installed on a machine (e.g. your desktop), you can run on more
(virtual) processors than you have physical processors.
Running with multiple partitions can be useful for running
"multi-replica simulations"_Howto_replica.html, where each replica
runs on on one or a few processors. Note that with MPI installed on a
machine (e.g. your desktop), you can run on more (virtual) processors
than you have physical processors.
To run multiple independent simulations from one input script, using
multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
of the manual. World- and universe-style "variables"_variable.html
are useful in this context.
multiple partitions, see the "Howto multiple"_Howto_multiple.html doc
page. World- and universe-style "variables"_variable.html are useful
in this context.
-plog file :pre
@ -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
@ -1787,11 +1787,13 @@ communication, roughly 75% in the example above.
The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed
in "Section 13"_Section_history.html. The F90 and F77 versions
(2001 and 99) are also freely distributed as open-source codes; check
the "LAMMPS WWW Site"_lws for distribution information if you prefer
those versions. The 99 and 2001 versions are no longer under active
development; they do not have all the features of C++ LAMMPS.
on the "History page"_http://lammps.sandia.gov/history.html of the
LAMMPS website. The F90 and F77 versions (2001 and 99) are also
freely distributed as open-source codes; check the "History
page"_http://lammps.sandia.gov/history.html of the LAMMPS website for
info about those versions. The 99 and 2001 versions are no longer
under active development; they do not have all the features of C++
LAMMPS.
If you are a previous user of LAMMPS 2001, these are the most
significant changes you will notice in C++ LAMMPS:

4
doc/src/Speed.txt
View File

@ -1,10 +1,10 @@
"Previous Section"_Package.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_howto.html :c
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

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