Merge branch 'master' into reax_dup (bf2a942f) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+14 −2

Original line number	Diff line number	Diff line
		@@ -138,8 +138,11 @@ 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}")

		# 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)
		@@ -467,6 +470,11 @@ 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) #
		########################################################################
		@@ -626,6 +634,10 @@ 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()

doc/src/Commands.txt

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+51 −0

Original line number	Diff line number	Diff line
		"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 -->

doc/src/Commands_all.txt

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+128 −0

Original line number	Diff line number	Diff line
		"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)

doc/src/Commands_bond.txt

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+124 −0

Original line number	Diff line number	Diff line
		"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)

doc/src/Commands_category.txt

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Original line number	Diff line number	Diff line
		"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

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